using scratch to enhance students' 21st century...
TRANSCRIPT
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1030X9MkSgt0PJTBS7)B89=C9BCC9gt88
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=B$1))$)I)(9)$BIMQQ0(cUP0
$$amp()+-- 4
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88ABC9ltS
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6U0ONk7
$$amp()+-- I
Photo courtesy httpsyntheticbiologyorg
Table of Contents
How are scientists thinking mechanistically in the 21st centuryhelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip1
Lesson 1 Introduction to Scratchhelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip5
Scratch Resources (not provided)helliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellipX
Lesson 2 Case Study of Jay Keaslinghelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip6
Case Study of Jay Keaslinghelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip8
Lesson 3 Mechanistic Thinkinghelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip10
Designing a New Microbehelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip12
Organism Cardshelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip13
copy 2009 Yu-Tzu Debbie Liu
Photo courtesy httpsyntheticbiologyorg
How are scientists thinkingmechanistically in the 21st century
Understanding Goals The rapid advancement of technology and the accumulation of information are changing
the patterns of scientific thinking and research in the 21st century Designing and creating novel organisms by combining various biological components
from different cells is one way scientists think mechanistically in the 21st century Designing and creating Scratch projects using graphical programming blocks is one way
students can display mechanistic thinking Identifying characteristics of successful scientist and their thinking patterns help us
become better (science) students by applying these skills to our own learning
Background Information Beyond the Scientific Method The scientific method has been commonly taught in science classrooms and textbooks as the only correct way to conduct scientific investigations This leaves students with the impression that all of science proceeds in much the same way Unfortunately this view is not entirely accurate Perhaps some scientists might conduct their work in this manner but rarely do they use it in the stereotyped step-by-step way that schools tend to teach itmdashdespite the fact that scientists report their work in this way in journals In fact scientists throughout history conduct their research in a variety of ways The exact approach a scientist uses depends on the individual doing the investigation as well as the particular question or problem being studied Furthermore scientists often engage in thinking patterns that are specific to its particular socio-cultural context 21st Century Scientific Thinking Skills With the explosion of advancements in scientific knowledge and technology at the turn of the century scientists at the cutting edge of research must adapt to new ways of interacting with their work Five prominent scientific thinking patterns of the 21st century are systems thinking mechanistic thinking interdisciplinary thinking quantitative thinking and distributed thinking1 In this lesson students will explore what mechanistic thinking Mechanistic Thinking It is a way of thinking that has a mechanical or engineering undertone This is shown through scientistsrsquo modular synthetic and purpose-driven approach towards their research problems Due to recent developments in new technologies and knowledge scientists are able to manipulate biology more directly allowing them to engineer and create novel biological systems for practical applications
1 Liu Y-T D amp Grotzer T A (2009) Looking forward Teaching the nature of the science of today and tomorrow In I M Saleh amp M S Khine (Eds) Fostering scientific habits of mind Pedagogical knowledge and best practices in science education (pp 9-36) Rotterdam Sense Publishers
copy 2009 Yu-Tzu Debbie Liu 1
What is Synthetic Biology The thinking involved in the field of synthetic biology is the best examples of mechanistic thinking With the rapidly emerging field of synthetic biology blurring the lines of biology and engineering scientists are no longer limited to working with organisms that naturally exist in the world Scientists often think synthetically by re-designing and constructing new organisms for practical and novel applications
Synthetic biology is an extension of genetic engineering Some even describe it as a more sophisticated version of genetic engineering taking into account a broader rational design perspective2 The engineering influence seeks out the simplicity in biological systems and brings standardization and modular design principles to biology
Synthetic biologists can use interchangeable parts from natural biology to assemble systems that function in new ways never existing before in living systems hence synthetic Modular circuit components (eg metabolic enzymes or fluorescent output genes) that are well characterized and can act independently of other cellular processes are used to build synthetic biological circuits Much like the ease of using LEGO bricksmdashstandardized bricks that can attach to any other partmdashsynthetic biology starts from the use of standardized biological building blocks The goal of synthetic biology is to both better understand how organisms function at the DNA protein and cell level by creating artificial biological systems and to solve important real-world problems the latter having caught the attention of scientists politicians and entrepreneurs Promising fields of application include energy environmental monitoring and remediation biotech and pharmaceuticals and materials fabrication
As pointed out in the detailed case study of Jay Keasling (one of the pioneers of synthetic biology) another key difference between synthetic biology and genetic engineering is the complexity of products or task the engineered organism can produce and accomplish Genetic engineering is typically limited to having microbes produce small proteins (eg insulin growth hormones) by simply inserting a single gene from a different organism into a microbe However with synthetic biology a complex interaction of several genes can be produced in a specified sequence much like what goes on in a chemical plant petroleum goes in and after a whole chain of reactions plastic comes out Scratch Scratch (httpscratchmitedu) is a programming language for young people (ages 8 and up) that makes it easy to create interactive projects (eg stories animations games simulations music and art) that can be shared on the Scratch website It is highly conducive to learning and teaching 21st century scientific thinking skills The Scratch grammar is designed so that users are presented with a versatile collection of graphical programming blocks that they can be snapped together to create programs much like LEGO bricks (and synthetic biology) Connectors on the blocks suggest how they should be put together so that over the process of tinkering with these blocks the emerging structure can give rise to new ideas and direction to the project Not only does snapping together complimentary blocks provide an easy way into learning programming but the idea of modularization as a problem-solving and design strategy is directly relevant to mechanistic thinking
2 Salisbury MW (2006) Get Ready for Synthetic Biology Genome Technology Magazine Retrieved from httpwwwgenome-technologycom
copy 2009 Yu-Tzu Debbie Liu 2
In this lesson Scratch is used to have students experience thinking mechanistically in their own work And since programming involves the creation of external representations of the problem-solving process Scratch provides students with opportunities of reflecting on their own thinking Lesson Layout These three lessons (one lesson per day) are designed to help students 1) understand how modern scientists think mechanistically 2) practice thinking mechanistically by simulating how synthetic biologists think in the field and 3) recognize mechanistic thinking even when it is not in the context of science as in their own work via Scratch Lesson 1 Designed to familiarize students with the Scratch programming language so that they can create projects on it At this point Scratch is presented simply as a medium for expressing what they have learned much like posters Powerpoint presentations and paper write-ups Lesson 2 Designed to expose students to the creative field of synthetic biology as a means to illustrate how scientists think mechanistically in the field This is done by a case study of Jay Keasling one of the pioneers of synthetic biology By analyzing how a modern scientist work and think students are provided with a broader view of scientific inquiry and the nature of scientific thinking Students will be asked to demonstrate their understanding of what they have learned so far by creating a Scratch project This allows students to work more closely and creatively with Scratch It also acts as a quick formative assessment for teachers of studentsrsquo learning thus far However the real goal of this exercise is to have students engage in mechanistic thinking in their own work which they may not recognize as it is not in the direct context of science This will be revealed in lesson 3 Lesson 3 Designed to have students practice thinking mechanistically by simulating how synthetic biologists think in the field via the Designing a New Microbe activity adapted from an actual experiment conducted in 20073 This activity presents students with a problem (need for hydrogen gas as alternative fuel) and asks students to design a microbe that can use starch and water to make hydrogen gas Students are given a set of organism cards to work with each card symbolizing a different type of organism (bacteria rabbit yeast archea spinach and mouse) Proteins (molecules that can convert one molecule into another) that are unique to each organism are listed on the card Studentsrsquo engineered microbe will essentially have different proteins from different organisms placed in a certain sequence to end up with a final product of hydrogen gas Students are given the Designing a New Microbe worksheet to help them visualize the problem better and reduce their cognitive loads (ie amount of information they need to carry in their heads) The activity allows students to discover that synthetic biology is a very mind-blowing field accomplishing things that some people never thought was possible Students will come to appreciate how seemingly impossible feats can be possible especially when scientists are thinking creatively By thinking and working mechanistically scientists have more freedom then before in designing and creating novel organisms for real-world applications
3 Zhang YH Evans BR Mielenz JR Hopkins RC Adams MW (2007) High-yield hydrogen production from starch and water by a synthetic enzymatic pathway PLoS ONE 5 e456
copy 2009 Yu-Tzu Debbie Liu 3
After the activity when students have grasped a much deeper understanding of what mechanistic thinking looks like in practice students are asked to reflect on their experience with Scratch The goal is to have students make the connection that they themselves have been engaging in mechanistic thinking while working on their own Scratch projects This reflective exercise encourages students to transfer their understanding of mechanistic thinking across different domains Students will also gain an appreciation of how studying trends in scientistsrsquo way of thinking can help them in their own thinking Lesson Placement These lessons can be used at the beginning of the school year when the scientific method is usually being presented Alternatively this lesson can be infused during the school year as students learn more about genetic engineering or creative thinking These lessons follow a constructivist approach to learning encouraging students to discover the meaning of mechanistic thinking through their exploration of a case study simulating how synthetic biologists think and making connections to their own work in Scratch Students are always encouraged to formulate their own ideas and connections before being presented with any information
copy 2009 Yu-Tzu Debbie Liu 4
Lesson Plan Day 1 Materials
Computers with Scratch installed Scratch Resources
Prep Step Review lesson plan background information and understanding goals Obtain computers with Scratch installed for students to work on Make copies of Scratch Resources (not provided)
Explore Step 1 Introduction to lesson Introduce the lesson by giving students a sense of what they will be doing and where they are headed by telling students ldquoThis will be a three-day lesson where we will be exploring how scientists think and more specifically what mechanistic thinking looks like in practice In this process we will also be learning Scratch We will tie everything together at the end of the third dayrdquo Step 2 Playing with Scratch Depending on the level of your students and any future goals you wish to achieve with Scratch structure the class so that students are comfortable navigating around the Scratch environment and are able to get started on their own Scratch project by the end of the class Please provide students with any Scratch resources you see fit Check out the ScratchEds resource search (httpscratchedmediamiteduresourcessearch) for more info Some good examples found in ScratchEd of Scratch lesson plans (video tutorials PowerPoints and worksheets) include
bull Having Fun with Computer Programming and Games (httpwwwleroieeducationoutreachsecondlevelscratchlessonplans)
bull A TeachNetUK Project 6 Lessons on Getting Started with Scratch (httpwwwteachnet-ukorguk200720ProjectsICT-ScratchScratchpages8_schemeofworkhtml)
bull Scratch Lessons Shall We Learn Scratch Programming for Tweens (httpwwwshallwelearncomscratchprogrammingforkidscategory)
bull Designing Animations and GamesmdashA Creative Introduction to Programming (httpwwwcsuni-potsdamde~romeikeUEWettbewerbindex-englishhtm)
Make sure to also introduce students to the Scratch online community and let them know that they can download the source code of any project to help them see how others are using the Scratch programming language to create projects
Review Extend and Apply Step 3 Scratch Assignment End the day by informing students that they will apply what they have learned today to create a mini-Scratch project for an assignment after the next dayrsquos lesson Emphasize to students that the goal is not to create a complex programming project but to use Scratch creatively as a medium for creative expressing not matter how simple the project is Encourage students to play with Scratch on their own time and make it clear that you highly encourage them to borrow adapt and build upon the ideas and projects of others (this is not considered cheating)
copy 2009 Yu-Tzu Debbie Liu 5
Lesson Plan Day 2 Materials
21st century scientist case study of Jay Keasling Student notebooks or journals
Prep Step Review lesson plan background information and understanding goals Make copies of 21st century scientist case study of Jay Keasling (p 8)
Explore Step 1 What is scientific thinking Ask students to describe what they think is scientific thinking Collect a representative list of studentsrsquo thoughts on the board Ask students to explain or expound on the meaning behind what they are saying After reviewing the list ask them ldquo Do you think all scientists come to their discoveries in the same wayrdquo ldquoDo scientists display all these characteristics at all timesrdquo It is important to point out to students that scientists have various methods going about their experimentation and work and depending on the type of work they are doing scientists donrsquot always share the same methods Furthermore scientists engage in thinking patterns that are specific to its particular socio-cultural context and one of which is mechanistic thinking Engage in a discussion with students on how might the explosion of advancements in scientific knowledge and technology at the turn of the century change the way scientists at the cutting edge of research interact with their work
Step 2 Analyze case study of a 21st century scientist Let students know that they will be learning about the field of synthetic biology as a means to illustrate how modern scientists work and think Specifically they will be studying Jay Keasling one of the pioneers of synthetic biology Hand out the case study on Jay Keasling Have students work in groups of 3-4 students to identify any patterns of thinking that the scientist displays Make sure to ask students to specifically identify what part of the case study justifies their claims Have students write the class findings in their journalsnotebooks
Possible findings from case analysis Jay Keasling
Keasling is a pioneer of synthetic biologymdasha field that designs and constructs new organisms for useful purposes He is most known for creating a microbe that produces a drug to treat malaria (making drugs from bugs) Some of his characteristics as a scientist include
bull Creative and imaginative wanted to invent new tools that can turn cells into chemical plants take in something very simple and spits out something complicated and valuable coming up with other applications of synthetic biology (use microbes to break down pesticides make biodegradable plastics create fuels from plants)
bull Critical thinking thought about how to design and create microbes to produce artemisinin much quicker and cheaper how to integrate genes from different species into a microbe to fabricate the drug
copy 2009 Yu-Tzu Debbie Liu 6
bull Seek and integrate information integrated methods and concepts from engineering and biology leading to synthetic biology
bull Supported with significant resources did research at universities and received grant money
bull Practical-minded microbes will churn out anti-malarial drug for a fraction of its current cost making it accessible to much more of the world these microbes could save millions of lives
bull Strong disciplinary understanding studied biology and chemical engineering extensively leading to his PhD and professor position at UC Berkeley
Step 3 What is mechanistic thinking Introduce students to the idea of mechanistic thinking as a prominent thinking pattern in the 21st
century
Mechanistic Thinking
Mechanistic thinking is a way of thinking that has a mechanical or engineering undertone This is shown through scientistsrsquo regular use of mechanical analogies to conceptualize their work and their modular synthetic and purpose-driven approach towards their research problems The display of mechanistic thinking by scientists appears to be a result of the merging of biology and engineering practices that is increasingly observed in 21st century biology as compared to a time when most of biologymdashtraditionally known for its pure basic researchmdashremain clearly demarcated from engineeringmdasha purely applied research field A mechanistic way of thinking has come to the forefront of 21st century science because of recent developments in new technologies and knowledge that enable scientists to manipulate the object or organism they are working with more directly allowing them to engineer and create novel biological systems for practical applications
Let students know that the work synthetic biologists do often require them to think mechanistically Now that students are given a definition of mechanistic thinking have students revisit their case study analysis and explore how synthetic biologists might think mechanistically
Review Extend and Apply
Step 4 Scratch Assignment Ask students to create a mini-Scratch project to demonstrate what they have learned so far (the project does not have to be all inclusive students can choose to focus on just one thing they learned either about scientific thinking mechanistic thinking or synthetic biology) Emphasize to students that the goal is not to create a complex programming project but to use Scratch creatively as a medium for creative expressing not matter how simple the project is Encourage students to work with partners and collaborate by borrowing adapting or building upon the ideas and projects of others (this is not considered cheating)
copy 2009 Yu-Tzu Debbie Liu 7
Detailed Case Study Jay Keasling
(1964 ndash present)
Best known for pioneering the new field of synthetic biology which designs and constructs new organisms for useful purposes He is also most known for creating a microbe that produces a drug to treat malaria (making drugs from bugs)
Jay Keasling was raised on a farm and spent his childhood exploring the practical side of biology chemistry and engineering This background eventually led him to work in the rapidly growing field that uses living organisms like bacteria for various practical purposes such as food processing agriculture and medicine
In the early 1980s genetic engineering became popular because you can ldquoconvincerdquo microbes to produce insulin growth hormones and other valuable proteins by simply inserting a single gene from a different organism into bacteria However Keasling believed that genetic engineering isnrsquot harnessing the full power of these cells The production of molecules isnt always so simple it requires a complex interaction of several genes (not just one) being produced in a certain sequence So Keasling wanted to invent the tools that would allow him to create these kinds of genetic assembly lines Thus what goes on in a cell is a lot like what goes on in a chemical plant petroleum goes in and after a whole chain of reactions plastic comes out
Keasling went to college studying biology and chemical engineering extensively and got his PhD in 1991 He is now a professor at the University of California at Berkeley He spent his first 10 years at UC Berkeley building the new tools he would need to turn cells into chemical plants He also invented powerful chemical switches (like a light switch) that allowed him to control when he wanted to ldquoturn onrdquo and ldquoturn offrdquo protein production in cells This way of borrowing techniques from engineering and figuring out how to manipulate microbes came to be call synthetic biology
After years of perfecting his biological tool kit Keasling wanted to find a real-world use for it In 2002 he learned of the dire need for artemisinin a compound derived from the sweet wormwood plant which is 90 percent effective against the parasite that causes malaria and has few side effects (malaria kills some 3 million people a year) However extracting the drug from sweet wormwood is a slow and expensive process Keasling figured he could design and create microbes to produce artemisinin much quicker and cheaper Rather than wait months for sweet wormwood to grow on farms Keasling wanted to create it simply by pouring sugar in a tank full of microbes that can use the sugar to make the drug via a chemical pathway he has designedmdashhe wanted to integrate genes from different species into a microbe to fabricate the drug for malaria
copy 2009 Yu-Tzu Debbie Liu 8
In 2006 Keaslings team (comprised of graduate students post-docs and research assistants) published their success of the production of artemisinin It is expected to lower the cost of artemisinin production from a dollar per gram to just 10 cents He was awarded a $43 million grant from the Bill and Melinda Gates Foundation and awarded DISCOVER magazinersquos first ever Scientist of the Year Award
Fighting malaria is just one part of Keaslings larger agenda to explore the potential of synthetic biology In his laboratory students are engineering microbes to break down pesticides make biodegradable plastics and create ethanol and other fuels from plants
Excerpts of i interview w Jay Keasling
1 You arrived at UC Berkeley in 1992 with training as both a chemical engineer and a biologist What did you hope to do
2 Why hadnt anybody tried to engineer cells that way before
3 How did you get involved in your antimalaria project
Jay Keisling biography adapted fromZimmer C (2006) Scientist of the Year Jay Keasling Discovermagazinecom Retrieved from
httpdiscovermagazinecom2006deccover
copy 2009 Yu-Tzu Debbie Liu 9
See responses to these questions atZimmer C (2006) Scientist of the Year Jay Keasling Discovermagazinecom Retrieved from
httpdiscovermagazinecom2006deccover
Interview content removed due to copyright restrictions
Interview content removed due to copyright restrictions
Interview content removed due to copyright restrictions
Lesson Plan Day 3 Materials
Designing a New Microbe worksheet Organism cards Student notebooks or journals
Prep Step Review lesson plan background information and understanding goals Photocopy Designing a New Microbe worksheet (p 28) Cut out organism cards (each group of 3-4 students will have a set of cards) (p29)
Explore Step 1 Designing a New Microbe Introduce todayrsquos activity by saying ldquoYou will be simulating how synthetic biologists think mechanistically by doing an the activity that is actually modeled after a real experiment done by scientists in 2007rdquo Divide students into groups of 3 or 4 Each group receives a set of organism cards Each student receives a Designing a New Microbe worksheet Remind students that proteins (or enzymes) are molecules inside cells that convert one molecule into another (eg the make-believe molecule How is converted to the molecule Home by Protein T in bacteria) Following the directions of the handout have students create a kind of assembly line that integrate proteins from different organisms into a microbe that uses water and starch (inputs) to ultimately produce hydrogen (output)
Possible answers to Designing a New Microbe
There are two possible pathways that can lead to hydrogen production
1 Starch amp water Protein G Protein P Protein D Protein R Protein T Protein F Protein H Hydrogen
2 Starch amp water Protein G Protein P Protein D Protein H Hydrogen
Guide students along by encouraging students who have already figured out how to attempt the problem to reveal and share with the class how they are thinking through the problem Stop students periodically to ask ldquoHow are you thinking through this problem What is your goal and how is your thinking helping you reach that goalrdquo Students may find either working sequentially forward or backward to fill in the worksheet to be easier
Note to teachers The hydrogen production pathway from starch and water is a shorten version of the actual 2007 experiment for learning purposes The organism types and molecule names are true to the experiment Protein names are made up for simplicity
copy 2009 Yu-Tzu Debbie Liu 10
Step 2 Discuss studentsrsquo findings Have students tell you what they found as you write their findings on the board Students may have discovered by now that there are two paths that lead to hydrogen production Students might recall that Jay Keasling have done something similar by making an antimalarial drug from sugar using synthetic biology Students may have also discovered that no proteins from the mouse organism were used for the design of their new microbe Ask students ldquowhat do you think is the purpose of having a mouse organism when we didnrsquot need itrdquo Help students understand how in reality scientists have hundreds of organisms to choose from some of which are irrelevant to their work In fact a common skill that scientists share is being about to identify and pull together important and relevant information The activity allows students to discover that synthetic biology is a very mind-blowing field accomplishing things that some people never thought was possible Students will come to appreciate how seemingly impossible feats can be possible especially when scientists are thinking creatively By thinking and working mechanistically scientists have more freedom then before in designing and creating novel organisms for real-world applications
Review Extend and Apply Step 3 How do you think mechanistically Ask students to reflect on their experience with Scratch and how they might have engaged in mechanistic thinking in their own work Helps students make the connection that they themselves have been engaging in mechanistic thinking while working on their own Scratch projects The Scratch grammar is designed so that users are presented with a versatile collection of graphical programming blocks that they can be snapped together to create programs much like synthetic biology Connectors on the blocks suggest how they should be put together so that over the process of tinkering with these blocks the emerging structure can give rise to new ideas and direction to the project Not only does snapping together complimentary blocks provide an easy way into learning programming but the idea of modularization as a problem-solving and design strategy is directly relevant to mechanistic thinking Go on to discuss how they can apply scientistsrsquo patterns of thinking to our own thinking in science class and daily life
copy 2009 Yu-Tzu Debbie Liu 11
Name___________________________ Date ____________
Designing a New Microbe
Task Gas prices have reached its all time high Thus scientists are trying to think of ways to produce alternative fuels such as hydrogen gas in a much cheaper and quicker way You are a scientist and you are familiar with six different organisms Based on what you know can you come up with a way to generate hydrogen from starch and water by designing a microbe that borrows different mechanismsproteins from different cells Fill in the blanks with protein names and the organism that the protein was taken from
Materials Each team has a set of cards each card symbolizing a different organism On the card you will see the name of the organism a picture of the organism and proteins that is unique to them Proteins (or enzymes) convert one molecule into another
Starch amp Water Protein borrowed Protein borrowed
Input Organism Organism
Protein borrowed $ Protein borrowed $ Protein borrowed Organism Organism Organism
Protein borrowed Protein borrowed Protein borrowed Hydrogen Organism Organism Organism Output
Experiment adapted from Zhang YH Evans BR Mielenz JR Hopkins RC Adams MW (2007) High-yield hydrogen production from
starch and water by a synthetic enzymatic pathway PLoS ONE 5 e456
copy 2009 Yu-Tzu Debbie Liu 12
Organism Cards (one set)
Teachers Please make as many copies as the number of groups of students Cut the cards out and shuffle before handing to students
Source NIH
Bacteria
Rabbitbull Protein T uses [X5P] to make [S7P]
Photo US Fish and Wildlife Service bull Protein F uses [S7P] to make [NADPH] bull Protein G uses starch and water to make [G-1-P] bull Protein P uses [G-1-P] to make [G-6-P]
Yeast
Public domain image (Source Wikimedia Commons)
bull Protein D uses [G-6-P] to make [NADPH] and [R5P]
Public domain image (Source Wikimedia Commons) Spinach
bull Protein R uses [R5P] to make [X5P]
Experiment adapted from
Archea Courtesy of Angels Tapias (License CC BY)
bull Protein H uses [NADPH] to make Hydrogen
Source NIH Mouse
bull Protein X uses [T8P] to make Hydrogen
Zhang YH Evans BR Mielenz JR Hopkins RC Adams MW (2007) High-yield hydrogen production from starch and water by a synthetic enzymatic pathway PLoS ONE 5 e456
copy 2009 Yu-Tzu Debbie Liu 13
MIT OpenCourseWarehttpocwmitedu
MAS714J STS445J Technologies for Creative Learning Fall 2009
For information about citing these materials or our Terms of Use visit httpocwmiteduterms
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88ABC9ltS
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6U0ONk7
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Photo courtesy httpsyntheticbiologyorg
Table of Contents
How are scientists thinking mechanistically in the 21st centuryhelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip1
Lesson 1 Introduction to Scratchhelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip5
Scratch Resources (not provided)helliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellipX
Lesson 2 Case Study of Jay Keaslinghelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip6
Case Study of Jay Keaslinghelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip8
Lesson 3 Mechanistic Thinkinghelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip10
Designing a New Microbehelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip12
Organism Cardshelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip13
copy 2009 Yu-Tzu Debbie Liu
Photo courtesy httpsyntheticbiologyorg
How are scientists thinkingmechanistically in the 21st century
Understanding Goals The rapid advancement of technology and the accumulation of information are changing
the patterns of scientific thinking and research in the 21st century Designing and creating novel organisms by combining various biological components
from different cells is one way scientists think mechanistically in the 21st century Designing and creating Scratch projects using graphical programming blocks is one way
students can display mechanistic thinking Identifying characteristics of successful scientist and their thinking patterns help us
become better (science) students by applying these skills to our own learning
Background Information Beyond the Scientific Method The scientific method has been commonly taught in science classrooms and textbooks as the only correct way to conduct scientific investigations This leaves students with the impression that all of science proceeds in much the same way Unfortunately this view is not entirely accurate Perhaps some scientists might conduct their work in this manner but rarely do they use it in the stereotyped step-by-step way that schools tend to teach itmdashdespite the fact that scientists report their work in this way in journals In fact scientists throughout history conduct their research in a variety of ways The exact approach a scientist uses depends on the individual doing the investigation as well as the particular question or problem being studied Furthermore scientists often engage in thinking patterns that are specific to its particular socio-cultural context 21st Century Scientific Thinking Skills With the explosion of advancements in scientific knowledge and technology at the turn of the century scientists at the cutting edge of research must adapt to new ways of interacting with their work Five prominent scientific thinking patterns of the 21st century are systems thinking mechanistic thinking interdisciplinary thinking quantitative thinking and distributed thinking1 In this lesson students will explore what mechanistic thinking Mechanistic Thinking It is a way of thinking that has a mechanical or engineering undertone This is shown through scientistsrsquo modular synthetic and purpose-driven approach towards their research problems Due to recent developments in new technologies and knowledge scientists are able to manipulate biology more directly allowing them to engineer and create novel biological systems for practical applications
1 Liu Y-T D amp Grotzer T A (2009) Looking forward Teaching the nature of the science of today and tomorrow In I M Saleh amp M S Khine (Eds) Fostering scientific habits of mind Pedagogical knowledge and best practices in science education (pp 9-36) Rotterdam Sense Publishers
copy 2009 Yu-Tzu Debbie Liu 1
What is Synthetic Biology The thinking involved in the field of synthetic biology is the best examples of mechanistic thinking With the rapidly emerging field of synthetic biology blurring the lines of biology and engineering scientists are no longer limited to working with organisms that naturally exist in the world Scientists often think synthetically by re-designing and constructing new organisms for practical and novel applications
Synthetic biology is an extension of genetic engineering Some even describe it as a more sophisticated version of genetic engineering taking into account a broader rational design perspective2 The engineering influence seeks out the simplicity in biological systems and brings standardization and modular design principles to biology
Synthetic biologists can use interchangeable parts from natural biology to assemble systems that function in new ways never existing before in living systems hence synthetic Modular circuit components (eg metabolic enzymes or fluorescent output genes) that are well characterized and can act independently of other cellular processes are used to build synthetic biological circuits Much like the ease of using LEGO bricksmdashstandardized bricks that can attach to any other partmdashsynthetic biology starts from the use of standardized biological building blocks The goal of synthetic biology is to both better understand how organisms function at the DNA protein and cell level by creating artificial biological systems and to solve important real-world problems the latter having caught the attention of scientists politicians and entrepreneurs Promising fields of application include energy environmental monitoring and remediation biotech and pharmaceuticals and materials fabrication
As pointed out in the detailed case study of Jay Keasling (one of the pioneers of synthetic biology) another key difference between synthetic biology and genetic engineering is the complexity of products or task the engineered organism can produce and accomplish Genetic engineering is typically limited to having microbes produce small proteins (eg insulin growth hormones) by simply inserting a single gene from a different organism into a microbe However with synthetic biology a complex interaction of several genes can be produced in a specified sequence much like what goes on in a chemical plant petroleum goes in and after a whole chain of reactions plastic comes out Scratch Scratch (httpscratchmitedu) is a programming language for young people (ages 8 and up) that makes it easy to create interactive projects (eg stories animations games simulations music and art) that can be shared on the Scratch website It is highly conducive to learning and teaching 21st century scientific thinking skills The Scratch grammar is designed so that users are presented with a versatile collection of graphical programming blocks that they can be snapped together to create programs much like LEGO bricks (and synthetic biology) Connectors on the blocks suggest how they should be put together so that over the process of tinkering with these blocks the emerging structure can give rise to new ideas and direction to the project Not only does snapping together complimentary blocks provide an easy way into learning programming but the idea of modularization as a problem-solving and design strategy is directly relevant to mechanistic thinking
2 Salisbury MW (2006) Get Ready for Synthetic Biology Genome Technology Magazine Retrieved from httpwwwgenome-technologycom
copy 2009 Yu-Tzu Debbie Liu 2
In this lesson Scratch is used to have students experience thinking mechanistically in their own work And since programming involves the creation of external representations of the problem-solving process Scratch provides students with opportunities of reflecting on their own thinking Lesson Layout These three lessons (one lesson per day) are designed to help students 1) understand how modern scientists think mechanistically 2) practice thinking mechanistically by simulating how synthetic biologists think in the field and 3) recognize mechanistic thinking even when it is not in the context of science as in their own work via Scratch Lesson 1 Designed to familiarize students with the Scratch programming language so that they can create projects on it At this point Scratch is presented simply as a medium for expressing what they have learned much like posters Powerpoint presentations and paper write-ups Lesson 2 Designed to expose students to the creative field of synthetic biology as a means to illustrate how scientists think mechanistically in the field This is done by a case study of Jay Keasling one of the pioneers of synthetic biology By analyzing how a modern scientist work and think students are provided with a broader view of scientific inquiry and the nature of scientific thinking Students will be asked to demonstrate their understanding of what they have learned so far by creating a Scratch project This allows students to work more closely and creatively with Scratch It also acts as a quick formative assessment for teachers of studentsrsquo learning thus far However the real goal of this exercise is to have students engage in mechanistic thinking in their own work which they may not recognize as it is not in the direct context of science This will be revealed in lesson 3 Lesson 3 Designed to have students practice thinking mechanistically by simulating how synthetic biologists think in the field via the Designing a New Microbe activity adapted from an actual experiment conducted in 20073 This activity presents students with a problem (need for hydrogen gas as alternative fuel) and asks students to design a microbe that can use starch and water to make hydrogen gas Students are given a set of organism cards to work with each card symbolizing a different type of organism (bacteria rabbit yeast archea spinach and mouse) Proteins (molecules that can convert one molecule into another) that are unique to each organism are listed on the card Studentsrsquo engineered microbe will essentially have different proteins from different organisms placed in a certain sequence to end up with a final product of hydrogen gas Students are given the Designing a New Microbe worksheet to help them visualize the problem better and reduce their cognitive loads (ie amount of information they need to carry in their heads) The activity allows students to discover that synthetic biology is a very mind-blowing field accomplishing things that some people never thought was possible Students will come to appreciate how seemingly impossible feats can be possible especially when scientists are thinking creatively By thinking and working mechanistically scientists have more freedom then before in designing and creating novel organisms for real-world applications
3 Zhang YH Evans BR Mielenz JR Hopkins RC Adams MW (2007) High-yield hydrogen production from starch and water by a synthetic enzymatic pathway PLoS ONE 5 e456
copy 2009 Yu-Tzu Debbie Liu 3
After the activity when students have grasped a much deeper understanding of what mechanistic thinking looks like in practice students are asked to reflect on their experience with Scratch The goal is to have students make the connection that they themselves have been engaging in mechanistic thinking while working on their own Scratch projects This reflective exercise encourages students to transfer their understanding of mechanistic thinking across different domains Students will also gain an appreciation of how studying trends in scientistsrsquo way of thinking can help them in their own thinking Lesson Placement These lessons can be used at the beginning of the school year when the scientific method is usually being presented Alternatively this lesson can be infused during the school year as students learn more about genetic engineering or creative thinking These lessons follow a constructivist approach to learning encouraging students to discover the meaning of mechanistic thinking through their exploration of a case study simulating how synthetic biologists think and making connections to their own work in Scratch Students are always encouraged to formulate their own ideas and connections before being presented with any information
copy 2009 Yu-Tzu Debbie Liu 4
Lesson Plan Day 1 Materials
Computers with Scratch installed Scratch Resources
Prep Step Review lesson plan background information and understanding goals Obtain computers with Scratch installed for students to work on Make copies of Scratch Resources (not provided)
Explore Step 1 Introduction to lesson Introduce the lesson by giving students a sense of what they will be doing and where they are headed by telling students ldquoThis will be a three-day lesson where we will be exploring how scientists think and more specifically what mechanistic thinking looks like in practice In this process we will also be learning Scratch We will tie everything together at the end of the third dayrdquo Step 2 Playing with Scratch Depending on the level of your students and any future goals you wish to achieve with Scratch structure the class so that students are comfortable navigating around the Scratch environment and are able to get started on their own Scratch project by the end of the class Please provide students with any Scratch resources you see fit Check out the ScratchEds resource search (httpscratchedmediamiteduresourcessearch) for more info Some good examples found in ScratchEd of Scratch lesson plans (video tutorials PowerPoints and worksheets) include
bull Having Fun with Computer Programming and Games (httpwwwleroieeducationoutreachsecondlevelscratchlessonplans)
bull A TeachNetUK Project 6 Lessons on Getting Started with Scratch (httpwwwteachnet-ukorguk200720ProjectsICT-ScratchScratchpages8_schemeofworkhtml)
bull Scratch Lessons Shall We Learn Scratch Programming for Tweens (httpwwwshallwelearncomscratchprogrammingforkidscategory)
bull Designing Animations and GamesmdashA Creative Introduction to Programming (httpwwwcsuni-potsdamde~romeikeUEWettbewerbindex-englishhtm)
Make sure to also introduce students to the Scratch online community and let them know that they can download the source code of any project to help them see how others are using the Scratch programming language to create projects
Review Extend and Apply Step 3 Scratch Assignment End the day by informing students that they will apply what they have learned today to create a mini-Scratch project for an assignment after the next dayrsquos lesson Emphasize to students that the goal is not to create a complex programming project but to use Scratch creatively as a medium for creative expressing not matter how simple the project is Encourage students to play with Scratch on their own time and make it clear that you highly encourage them to borrow adapt and build upon the ideas and projects of others (this is not considered cheating)
copy 2009 Yu-Tzu Debbie Liu 5
Lesson Plan Day 2 Materials
21st century scientist case study of Jay Keasling Student notebooks or journals
Prep Step Review lesson plan background information and understanding goals Make copies of 21st century scientist case study of Jay Keasling (p 8)
Explore Step 1 What is scientific thinking Ask students to describe what they think is scientific thinking Collect a representative list of studentsrsquo thoughts on the board Ask students to explain or expound on the meaning behind what they are saying After reviewing the list ask them ldquo Do you think all scientists come to their discoveries in the same wayrdquo ldquoDo scientists display all these characteristics at all timesrdquo It is important to point out to students that scientists have various methods going about their experimentation and work and depending on the type of work they are doing scientists donrsquot always share the same methods Furthermore scientists engage in thinking patterns that are specific to its particular socio-cultural context and one of which is mechanistic thinking Engage in a discussion with students on how might the explosion of advancements in scientific knowledge and technology at the turn of the century change the way scientists at the cutting edge of research interact with their work
Step 2 Analyze case study of a 21st century scientist Let students know that they will be learning about the field of synthetic biology as a means to illustrate how modern scientists work and think Specifically they will be studying Jay Keasling one of the pioneers of synthetic biology Hand out the case study on Jay Keasling Have students work in groups of 3-4 students to identify any patterns of thinking that the scientist displays Make sure to ask students to specifically identify what part of the case study justifies their claims Have students write the class findings in their journalsnotebooks
Possible findings from case analysis Jay Keasling
Keasling is a pioneer of synthetic biologymdasha field that designs and constructs new organisms for useful purposes He is most known for creating a microbe that produces a drug to treat malaria (making drugs from bugs) Some of his characteristics as a scientist include
bull Creative and imaginative wanted to invent new tools that can turn cells into chemical plants take in something very simple and spits out something complicated and valuable coming up with other applications of synthetic biology (use microbes to break down pesticides make biodegradable plastics create fuels from plants)
bull Critical thinking thought about how to design and create microbes to produce artemisinin much quicker and cheaper how to integrate genes from different species into a microbe to fabricate the drug
copy 2009 Yu-Tzu Debbie Liu 6
bull Seek and integrate information integrated methods and concepts from engineering and biology leading to synthetic biology
bull Supported with significant resources did research at universities and received grant money
bull Practical-minded microbes will churn out anti-malarial drug for a fraction of its current cost making it accessible to much more of the world these microbes could save millions of lives
bull Strong disciplinary understanding studied biology and chemical engineering extensively leading to his PhD and professor position at UC Berkeley
Step 3 What is mechanistic thinking Introduce students to the idea of mechanistic thinking as a prominent thinking pattern in the 21st
century
Mechanistic Thinking
Mechanistic thinking is a way of thinking that has a mechanical or engineering undertone This is shown through scientistsrsquo regular use of mechanical analogies to conceptualize their work and their modular synthetic and purpose-driven approach towards their research problems The display of mechanistic thinking by scientists appears to be a result of the merging of biology and engineering practices that is increasingly observed in 21st century biology as compared to a time when most of biologymdashtraditionally known for its pure basic researchmdashremain clearly demarcated from engineeringmdasha purely applied research field A mechanistic way of thinking has come to the forefront of 21st century science because of recent developments in new technologies and knowledge that enable scientists to manipulate the object or organism they are working with more directly allowing them to engineer and create novel biological systems for practical applications
Let students know that the work synthetic biologists do often require them to think mechanistically Now that students are given a definition of mechanistic thinking have students revisit their case study analysis and explore how synthetic biologists might think mechanistically
Review Extend and Apply
Step 4 Scratch Assignment Ask students to create a mini-Scratch project to demonstrate what they have learned so far (the project does not have to be all inclusive students can choose to focus on just one thing they learned either about scientific thinking mechanistic thinking or synthetic biology) Emphasize to students that the goal is not to create a complex programming project but to use Scratch creatively as a medium for creative expressing not matter how simple the project is Encourage students to work with partners and collaborate by borrowing adapting or building upon the ideas and projects of others (this is not considered cheating)
copy 2009 Yu-Tzu Debbie Liu 7
Detailed Case Study Jay Keasling
(1964 ndash present)
Best known for pioneering the new field of synthetic biology which designs and constructs new organisms for useful purposes He is also most known for creating a microbe that produces a drug to treat malaria (making drugs from bugs)
Jay Keasling was raised on a farm and spent his childhood exploring the practical side of biology chemistry and engineering This background eventually led him to work in the rapidly growing field that uses living organisms like bacteria for various practical purposes such as food processing agriculture and medicine
In the early 1980s genetic engineering became popular because you can ldquoconvincerdquo microbes to produce insulin growth hormones and other valuable proteins by simply inserting a single gene from a different organism into bacteria However Keasling believed that genetic engineering isnrsquot harnessing the full power of these cells The production of molecules isnt always so simple it requires a complex interaction of several genes (not just one) being produced in a certain sequence So Keasling wanted to invent the tools that would allow him to create these kinds of genetic assembly lines Thus what goes on in a cell is a lot like what goes on in a chemical plant petroleum goes in and after a whole chain of reactions plastic comes out
Keasling went to college studying biology and chemical engineering extensively and got his PhD in 1991 He is now a professor at the University of California at Berkeley He spent his first 10 years at UC Berkeley building the new tools he would need to turn cells into chemical plants He also invented powerful chemical switches (like a light switch) that allowed him to control when he wanted to ldquoturn onrdquo and ldquoturn offrdquo protein production in cells This way of borrowing techniques from engineering and figuring out how to manipulate microbes came to be call synthetic biology
After years of perfecting his biological tool kit Keasling wanted to find a real-world use for it In 2002 he learned of the dire need for artemisinin a compound derived from the sweet wormwood plant which is 90 percent effective against the parasite that causes malaria and has few side effects (malaria kills some 3 million people a year) However extracting the drug from sweet wormwood is a slow and expensive process Keasling figured he could design and create microbes to produce artemisinin much quicker and cheaper Rather than wait months for sweet wormwood to grow on farms Keasling wanted to create it simply by pouring sugar in a tank full of microbes that can use the sugar to make the drug via a chemical pathway he has designedmdashhe wanted to integrate genes from different species into a microbe to fabricate the drug for malaria
copy 2009 Yu-Tzu Debbie Liu 8
In 2006 Keaslings team (comprised of graduate students post-docs and research assistants) published their success of the production of artemisinin It is expected to lower the cost of artemisinin production from a dollar per gram to just 10 cents He was awarded a $43 million grant from the Bill and Melinda Gates Foundation and awarded DISCOVER magazinersquos first ever Scientist of the Year Award
Fighting malaria is just one part of Keaslings larger agenda to explore the potential of synthetic biology In his laboratory students are engineering microbes to break down pesticides make biodegradable plastics and create ethanol and other fuels from plants
Excerpts of i interview w Jay Keasling
1 You arrived at UC Berkeley in 1992 with training as both a chemical engineer and a biologist What did you hope to do
2 Why hadnt anybody tried to engineer cells that way before
3 How did you get involved in your antimalaria project
Jay Keisling biography adapted fromZimmer C (2006) Scientist of the Year Jay Keasling Discovermagazinecom Retrieved from
httpdiscovermagazinecom2006deccover
copy 2009 Yu-Tzu Debbie Liu 9
See responses to these questions atZimmer C (2006) Scientist of the Year Jay Keasling Discovermagazinecom Retrieved from
httpdiscovermagazinecom2006deccover
Interview content removed due to copyright restrictions
Interview content removed due to copyright restrictions
Interview content removed due to copyright restrictions
Lesson Plan Day 3 Materials
Designing a New Microbe worksheet Organism cards Student notebooks or journals
Prep Step Review lesson plan background information and understanding goals Photocopy Designing a New Microbe worksheet (p 28) Cut out organism cards (each group of 3-4 students will have a set of cards) (p29)
Explore Step 1 Designing a New Microbe Introduce todayrsquos activity by saying ldquoYou will be simulating how synthetic biologists think mechanistically by doing an the activity that is actually modeled after a real experiment done by scientists in 2007rdquo Divide students into groups of 3 or 4 Each group receives a set of organism cards Each student receives a Designing a New Microbe worksheet Remind students that proteins (or enzymes) are molecules inside cells that convert one molecule into another (eg the make-believe molecule How is converted to the molecule Home by Protein T in bacteria) Following the directions of the handout have students create a kind of assembly line that integrate proteins from different organisms into a microbe that uses water and starch (inputs) to ultimately produce hydrogen (output)
Possible answers to Designing a New Microbe
There are two possible pathways that can lead to hydrogen production
1 Starch amp water Protein G Protein P Protein D Protein R Protein T Protein F Protein H Hydrogen
2 Starch amp water Protein G Protein P Protein D Protein H Hydrogen
Guide students along by encouraging students who have already figured out how to attempt the problem to reveal and share with the class how they are thinking through the problem Stop students periodically to ask ldquoHow are you thinking through this problem What is your goal and how is your thinking helping you reach that goalrdquo Students may find either working sequentially forward or backward to fill in the worksheet to be easier
Note to teachers The hydrogen production pathway from starch and water is a shorten version of the actual 2007 experiment for learning purposes The organism types and molecule names are true to the experiment Protein names are made up for simplicity
copy 2009 Yu-Tzu Debbie Liu 10
Step 2 Discuss studentsrsquo findings Have students tell you what they found as you write their findings on the board Students may have discovered by now that there are two paths that lead to hydrogen production Students might recall that Jay Keasling have done something similar by making an antimalarial drug from sugar using synthetic biology Students may have also discovered that no proteins from the mouse organism were used for the design of their new microbe Ask students ldquowhat do you think is the purpose of having a mouse organism when we didnrsquot need itrdquo Help students understand how in reality scientists have hundreds of organisms to choose from some of which are irrelevant to their work In fact a common skill that scientists share is being about to identify and pull together important and relevant information The activity allows students to discover that synthetic biology is a very mind-blowing field accomplishing things that some people never thought was possible Students will come to appreciate how seemingly impossible feats can be possible especially when scientists are thinking creatively By thinking and working mechanistically scientists have more freedom then before in designing and creating novel organisms for real-world applications
Review Extend and Apply Step 3 How do you think mechanistically Ask students to reflect on their experience with Scratch and how they might have engaged in mechanistic thinking in their own work Helps students make the connection that they themselves have been engaging in mechanistic thinking while working on their own Scratch projects The Scratch grammar is designed so that users are presented with a versatile collection of graphical programming blocks that they can be snapped together to create programs much like synthetic biology Connectors on the blocks suggest how they should be put together so that over the process of tinkering with these blocks the emerging structure can give rise to new ideas and direction to the project Not only does snapping together complimentary blocks provide an easy way into learning programming but the idea of modularization as a problem-solving and design strategy is directly relevant to mechanistic thinking Go on to discuss how they can apply scientistsrsquo patterns of thinking to our own thinking in science class and daily life
copy 2009 Yu-Tzu Debbie Liu 11
Name___________________________ Date ____________
Designing a New Microbe
Task Gas prices have reached its all time high Thus scientists are trying to think of ways to produce alternative fuels such as hydrogen gas in a much cheaper and quicker way You are a scientist and you are familiar with six different organisms Based on what you know can you come up with a way to generate hydrogen from starch and water by designing a microbe that borrows different mechanismsproteins from different cells Fill in the blanks with protein names and the organism that the protein was taken from
Materials Each team has a set of cards each card symbolizing a different organism On the card you will see the name of the organism a picture of the organism and proteins that is unique to them Proteins (or enzymes) convert one molecule into another
Starch amp Water Protein borrowed Protein borrowed
Input Organism Organism
Protein borrowed $ Protein borrowed $ Protein borrowed Organism Organism Organism
Protein borrowed Protein borrowed Protein borrowed Hydrogen Organism Organism Organism Output
Experiment adapted from Zhang YH Evans BR Mielenz JR Hopkins RC Adams MW (2007) High-yield hydrogen production from
starch and water by a synthetic enzymatic pathway PLoS ONE 5 e456
copy 2009 Yu-Tzu Debbie Liu 12
Organism Cards (one set)
Teachers Please make as many copies as the number of groups of students Cut the cards out and shuffle before handing to students
Source NIH
Bacteria
Rabbitbull Protein T uses [X5P] to make [S7P]
Photo US Fish and Wildlife Service bull Protein F uses [S7P] to make [NADPH] bull Protein G uses starch and water to make [G-1-P] bull Protein P uses [G-1-P] to make [G-6-P]
Yeast
Public domain image (Source Wikimedia Commons)
bull Protein D uses [G-6-P] to make [NADPH] and [R5P]
Public domain image (Source Wikimedia Commons) Spinach
bull Protein R uses [R5P] to make [X5P]
Experiment adapted from
Archea Courtesy of Angels Tapias (License CC BY)
bull Protein H uses [NADPH] to make Hydrogen
Source NIH Mouse
bull Protein X uses [T8P] to make Hydrogen
Zhang YH Evans BR Mielenz JR Hopkins RC Adams MW (2007) High-yield hydrogen production from starch and water by a synthetic enzymatic pathway PLoS ONE 5 e456
copy 2009 Yu-Tzu Debbie Liu 13
MIT OpenCourseWarehttpocwmitedu
MAS714J STS445J Technologies for Creative Learning Fall 2009
For information about citing these materials or our Terms of Use visit httpocwmiteduterms
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6U0ONk7
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Photo courtesy httpsyntheticbiologyorg
Table of Contents
How are scientists thinking mechanistically in the 21st centuryhelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip1
Lesson 1 Introduction to Scratchhelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip5
Scratch Resources (not provided)helliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellipX
Lesson 2 Case Study of Jay Keaslinghelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip6
Case Study of Jay Keaslinghelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip8
Lesson 3 Mechanistic Thinkinghelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip10
Designing a New Microbehelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip12
Organism Cardshelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip13
copy 2009 Yu-Tzu Debbie Liu
Photo courtesy httpsyntheticbiologyorg
How are scientists thinkingmechanistically in the 21st century
Understanding Goals The rapid advancement of technology and the accumulation of information are changing
the patterns of scientific thinking and research in the 21st century Designing and creating novel organisms by combining various biological components
from different cells is one way scientists think mechanistically in the 21st century Designing and creating Scratch projects using graphical programming blocks is one way
students can display mechanistic thinking Identifying characteristics of successful scientist and their thinking patterns help us
become better (science) students by applying these skills to our own learning
Background Information Beyond the Scientific Method The scientific method has been commonly taught in science classrooms and textbooks as the only correct way to conduct scientific investigations This leaves students with the impression that all of science proceeds in much the same way Unfortunately this view is not entirely accurate Perhaps some scientists might conduct their work in this manner but rarely do they use it in the stereotyped step-by-step way that schools tend to teach itmdashdespite the fact that scientists report their work in this way in journals In fact scientists throughout history conduct their research in a variety of ways The exact approach a scientist uses depends on the individual doing the investigation as well as the particular question or problem being studied Furthermore scientists often engage in thinking patterns that are specific to its particular socio-cultural context 21st Century Scientific Thinking Skills With the explosion of advancements in scientific knowledge and technology at the turn of the century scientists at the cutting edge of research must adapt to new ways of interacting with their work Five prominent scientific thinking patterns of the 21st century are systems thinking mechanistic thinking interdisciplinary thinking quantitative thinking and distributed thinking1 In this lesson students will explore what mechanistic thinking Mechanistic Thinking It is a way of thinking that has a mechanical or engineering undertone This is shown through scientistsrsquo modular synthetic and purpose-driven approach towards their research problems Due to recent developments in new technologies and knowledge scientists are able to manipulate biology more directly allowing them to engineer and create novel biological systems for practical applications
1 Liu Y-T D amp Grotzer T A (2009) Looking forward Teaching the nature of the science of today and tomorrow In I M Saleh amp M S Khine (Eds) Fostering scientific habits of mind Pedagogical knowledge and best practices in science education (pp 9-36) Rotterdam Sense Publishers
copy 2009 Yu-Tzu Debbie Liu 1
What is Synthetic Biology The thinking involved in the field of synthetic biology is the best examples of mechanistic thinking With the rapidly emerging field of synthetic biology blurring the lines of biology and engineering scientists are no longer limited to working with organisms that naturally exist in the world Scientists often think synthetically by re-designing and constructing new organisms for practical and novel applications
Synthetic biology is an extension of genetic engineering Some even describe it as a more sophisticated version of genetic engineering taking into account a broader rational design perspective2 The engineering influence seeks out the simplicity in biological systems and brings standardization and modular design principles to biology
Synthetic biologists can use interchangeable parts from natural biology to assemble systems that function in new ways never existing before in living systems hence synthetic Modular circuit components (eg metabolic enzymes or fluorescent output genes) that are well characterized and can act independently of other cellular processes are used to build synthetic biological circuits Much like the ease of using LEGO bricksmdashstandardized bricks that can attach to any other partmdashsynthetic biology starts from the use of standardized biological building blocks The goal of synthetic biology is to both better understand how organisms function at the DNA protein and cell level by creating artificial biological systems and to solve important real-world problems the latter having caught the attention of scientists politicians and entrepreneurs Promising fields of application include energy environmental monitoring and remediation biotech and pharmaceuticals and materials fabrication
As pointed out in the detailed case study of Jay Keasling (one of the pioneers of synthetic biology) another key difference between synthetic biology and genetic engineering is the complexity of products or task the engineered organism can produce and accomplish Genetic engineering is typically limited to having microbes produce small proteins (eg insulin growth hormones) by simply inserting a single gene from a different organism into a microbe However with synthetic biology a complex interaction of several genes can be produced in a specified sequence much like what goes on in a chemical plant petroleum goes in and after a whole chain of reactions plastic comes out Scratch Scratch (httpscratchmitedu) is a programming language for young people (ages 8 and up) that makes it easy to create interactive projects (eg stories animations games simulations music and art) that can be shared on the Scratch website It is highly conducive to learning and teaching 21st century scientific thinking skills The Scratch grammar is designed so that users are presented with a versatile collection of graphical programming blocks that they can be snapped together to create programs much like LEGO bricks (and synthetic biology) Connectors on the blocks suggest how they should be put together so that over the process of tinkering with these blocks the emerging structure can give rise to new ideas and direction to the project Not only does snapping together complimentary blocks provide an easy way into learning programming but the idea of modularization as a problem-solving and design strategy is directly relevant to mechanistic thinking
2 Salisbury MW (2006) Get Ready for Synthetic Biology Genome Technology Magazine Retrieved from httpwwwgenome-technologycom
copy 2009 Yu-Tzu Debbie Liu 2
In this lesson Scratch is used to have students experience thinking mechanistically in their own work And since programming involves the creation of external representations of the problem-solving process Scratch provides students with opportunities of reflecting on their own thinking Lesson Layout These three lessons (one lesson per day) are designed to help students 1) understand how modern scientists think mechanistically 2) practice thinking mechanistically by simulating how synthetic biologists think in the field and 3) recognize mechanistic thinking even when it is not in the context of science as in their own work via Scratch Lesson 1 Designed to familiarize students with the Scratch programming language so that they can create projects on it At this point Scratch is presented simply as a medium for expressing what they have learned much like posters Powerpoint presentations and paper write-ups Lesson 2 Designed to expose students to the creative field of synthetic biology as a means to illustrate how scientists think mechanistically in the field This is done by a case study of Jay Keasling one of the pioneers of synthetic biology By analyzing how a modern scientist work and think students are provided with a broader view of scientific inquiry and the nature of scientific thinking Students will be asked to demonstrate their understanding of what they have learned so far by creating a Scratch project This allows students to work more closely and creatively with Scratch It also acts as a quick formative assessment for teachers of studentsrsquo learning thus far However the real goal of this exercise is to have students engage in mechanistic thinking in their own work which they may not recognize as it is not in the direct context of science This will be revealed in lesson 3 Lesson 3 Designed to have students practice thinking mechanistically by simulating how synthetic biologists think in the field via the Designing a New Microbe activity adapted from an actual experiment conducted in 20073 This activity presents students with a problem (need for hydrogen gas as alternative fuel) and asks students to design a microbe that can use starch and water to make hydrogen gas Students are given a set of organism cards to work with each card symbolizing a different type of organism (bacteria rabbit yeast archea spinach and mouse) Proteins (molecules that can convert one molecule into another) that are unique to each organism are listed on the card Studentsrsquo engineered microbe will essentially have different proteins from different organisms placed in a certain sequence to end up with a final product of hydrogen gas Students are given the Designing a New Microbe worksheet to help them visualize the problem better and reduce their cognitive loads (ie amount of information they need to carry in their heads) The activity allows students to discover that synthetic biology is a very mind-blowing field accomplishing things that some people never thought was possible Students will come to appreciate how seemingly impossible feats can be possible especially when scientists are thinking creatively By thinking and working mechanistically scientists have more freedom then before in designing and creating novel organisms for real-world applications
3 Zhang YH Evans BR Mielenz JR Hopkins RC Adams MW (2007) High-yield hydrogen production from starch and water by a synthetic enzymatic pathway PLoS ONE 5 e456
copy 2009 Yu-Tzu Debbie Liu 3
After the activity when students have grasped a much deeper understanding of what mechanistic thinking looks like in practice students are asked to reflect on their experience with Scratch The goal is to have students make the connection that they themselves have been engaging in mechanistic thinking while working on their own Scratch projects This reflective exercise encourages students to transfer their understanding of mechanistic thinking across different domains Students will also gain an appreciation of how studying trends in scientistsrsquo way of thinking can help them in their own thinking Lesson Placement These lessons can be used at the beginning of the school year when the scientific method is usually being presented Alternatively this lesson can be infused during the school year as students learn more about genetic engineering or creative thinking These lessons follow a constructivist approach to learning encouraging students to discover the meaning of mechanistic thinking through their exploration of a case study simulating how synthetic biologists think and making connections to their own work in Scratch Students are always encouraged to formulate their own ideas and connections before being presented with any information
copy 2009 Yu-Tzu Debbie Liu 4
Lesson Plan Day 1 Materials
Computers with Scratch installed Scratch Resources
Prep Step Review lesson plan background information and understanding goals Obtain computers with Scratch installed for students to work on Make copies of Scratch Resources (not provided)
Explore Step 1 Introduction to lesson Introduce the lesson by giving students a sense of what they will be doing and where they are headed by telling students ldquoThis will be a three-day lesson where we will be exploring how scientists think and more specifically what mechanistic thinking looks like in practice In this process we will also be learning Scratch We will tie everything together at the end of the third dayrdquo Step 2 Playing with Scratch Depending on the level of your students and any future goals you wish to achieve with Scratch structure the class so that students are comfortable navigating around the Scratch environment and are able to get started on their own Scratch project by the end of the class Please provide students with any Scratch resources you see fit Check out the ScratchEds resource search (httpscratchedmediamiteduresourcessearch) for more info Some good examples found in ScratchEd of Scratch lesson plans (video tutorials PowerPoints and worksheets) include
bull Having Fun with Computer Programming and Games (httpwwwleroieeducationoutreachsecondlevelscratchlessonplans)
bull A TeachNetUK Project 6 Lessons on Getting Started with Scratch (httpwwwteachnet-ukorguk200720ProjectsICT-ScratchScratchpages8_schemeofworkhtml)
bull Scratch Lessons Shall We Learn Scratch Programming for Tweens (httpwwwshallwelearncomscratchprogrammingforkidscategory)
bull Designing Animations and GamesmdashA Creative Introduction to Programming (httpwwwcsuni-potsdamde~romeikeUEWettbewerbindex-englishhtm)
Make sure to also introduce students to the Scratch online community and let them know that they can download the source code of any project to help them see how others are using the Scratch programming language to create projects
Review Extend and Apply Step 3 Scratch Assignment End the day by informing students that they will apply what they have learned today to create a mini-Scratch project for an assignment after the next dayrsquos lesson Emphasize to students that the goal is not to create a complex programming project but to use Scratch creatively as a medium for creative expressing not matter how simple the project is Encourage students to play with Scratch on their own time and make it clear that you highly encourage them to borrow adapt and build upon the ideas and projects of others (this is not considered cheating)
copy 2009 Yu-Tzu Debbie Liu 5
Lesson Plan Day 2 Materials
21st century scientist case study of Jay Keasling Student notebooks or journals
Prep Step Review lesson plan background information and understanding goals Make copies of 21st century scientist case study of Jay Keasling (p 8)
Explore Step 1 What is scientific thinking Ask students to describe what they think is scientific thinking Collect a representative list of studentsrsquo thoughts on the board Ask students to explain or expound on the meaning behind what they are saying After reviewing the list ask them ldquo Do you think all scientists come to their discoveries in the same wayrdquo ldquoDo scientists display all these characteristics at all timesrdquo It is important to point out to students that scientists have various methods going about their experimentation and work and depending on the type of work they are doing scientists donrsquot always share the same methods Furthermore scientists engage in thinking patterns that are specific to its particular socio-cultural context and one of which is mechanistic thinking Engage in a discussion with students on how might the explosion of advancements in scientific knowledge and technology at the turn of the century change the way scientists at the cutting edge of research interact with their work
Step 2 Analyze case study of a 21st century scientist Let students know that they will be learning about the field of synthetic biology as a means to illustrate how modern scientists work and think Specifically they will be studying Jay Keasling one of the pioneers of synthetic biology Hand out the case study on Jay Keasling Have students work in groups of 3-4 students to identify any patterns of thinking that the scientist displays Make sure to ask students to specifically identify what part of the case study justifies their claims Have students write the class findings in their journalsnotebooks
Possible findings from case analysis Jay Keasling
Keasling is a pioneer of synthetic biologymdasha field that designs and constructs new organisms for useful purposes He is most known for creating a microbe that produces a drug to treat malaria (making drugs from bugs) Some of his characteristics as a scientist include
bull Creative and imaginative wanted to invent new tools that can turn cells into chemical plants take in something very simple and spits out something complicated and valuable coming up with other applications of synthetic biology (use microbes to break down pesticides make biodegradable plastics create fuels from plants)
bull Critical thinking thought about how to design and create microbes to produce artemisinin much quicker and cheaper how to integrate genes from different species into a microbe to fabricate the drug
copy 2009 Yu-Tzu Debbie Liu 6
bull Seek and integrate information integrated methods and concepts from engineering and biology leading to synthetic biology
bull Supported with significant resources did research at universities and received grant money
bull Practical-minded microbes will churn out anti-malarial drug for a fraction of its current cost making it accessible to much more of the world these microbes could save millions of lives
bull Strong disciplinary understanding studied biology and chemical engineering extensively leading to his PhD and professor position at UC Berkeley
Step 3 What is mechanistic thinking Introduce students to the idea of mechanistic thinking as a prominent thinking pattern in the 21st
century
Mechanistic Thinking
Mechanistic thinking is a way of thinking that has a mechanical or engineering undertone This is shown through scientistsrsquo regular use of mechanical analogies to conceptualize their work and their modular synthetic and purpose-driven approach towards their research problems The display of mechanistic thinking by scientists appears to be a result of the merging of biology and engineering practices that is increasingly observed in 21st century biology as compared to a time when most of biologymdashtraditionally known for its pure basic researchmdashremain clearly demarcated from engineeringmdasha purely applied research field A mechanistic way of thinking has come to the forefront of 21st century science because of recent developments in new technologies and knowledge that enable scientists to manipulate the object or organism they are working with more directly allowing them to engineer and create novel biological systems for practical applications
Let students know that the work synthetic biologists do often require them to think mechanistically Now that students are given a definition of mechanistic thinking have students revisit their case study analysis and explore how synthetic biologists might think mechanistically
Review Extend and Apply
Step 4 Scratch Assignment Ask students to create a mini-Scratch project to demonstrate what they have learned so far (the project does not have to be all inclusive students can choose to focus on just one thing they learned either about scientific thinking mechanistic thinking or synthetic biology) Emphasize to students that the goal is not to create a complex programming project but to use Scratch creatively as a medium for creative expressing not matter how simple the project is Encourage students to work with partners and collaborate by borrowing adapting or building upon the ideas and projects of others (this is not considered cheating)
copy 2009 Yu-Tzu Debbie Liu 7
Detailed Case Study Jay Keasling
(1964 ndash present)
Best known for pioneering the new field of synthetic biology which designs and constructs new organisms for useful purposes He is also most known for creating a microbe that produces a drug to treat malaria (making drugs from bugs)
Jay Keasling was raised on a farm and spent his childhood exploring the practical side of biology chemistry and engineering This background eventually led him to work in the rapidly growing field that uses living organisms like bacteria for various practical purposes such as food processing agriculture and medicine
In the early 1980s genetic engineering became popular because you can ldquoconvincerdquo microbes to produce insulin growth hormones and other valuable proteins by simply inserting a single gene from a different organism into bacteria However Keasling believed that genetic engineering isnrsquot harnessing the full power of these cells The production of molecules isnt always so simple it requires a complex interaction of several genes (not just one) being produced in a certain sequence So Keasling wanted to invent the tools that would allow him to create these kinds of genetic assembly lines Thus what goes on in a cell is a lot like what goes on in a chemical plant petroleum goes in and after a whole chain of reactions plastic comes out
Keasling went to college studying biology and chemical engineering extensively and got his PhD in 1991 He is now a professor at the University of California at Berkeley He spent his first 10 years at UC Berkeley building the new tools he would need to turn cells into chemical plants He also invented powerful chemical switches (like a light switch) that allowed him to control when he wanted to ldquoturn onrdquo and ldquoturn offrdquo protein production in cells This way of borrowing techniques from engineering and figuring out how to manipulate microbes came to be call synthetic biology
After years of perfecting his biological tool kit Keasling wanted to find a real-world use for it In 2002 he learned of the dire need for artemisinin a compound derived from the sweet wormwood plant which is 90 percent effective against the parasite that causes malaria and has few side effects (malaria kills some 3 million people a year) However extracting the drug from sweet wormwood is a slow and expensive process Keasling figured he could design and create microbes to produce artemisinin much quicker and cheaper Rather than wait months for sweet wormwood to grow on farms Keasling wanted to create it simply by pouring sugar in a tank full of microbes that can use the sugar to make the drug via a chemical pathway he has designedmdashhe wanted to integrate genes from different species into a microbe to fabricate the drug for malaria
copy 2009 Yu-Tzu Debbie Liu 8
In 2006 Keaslings team (comprised of graduate students post-docs and research assistants) published their success of the production of artemisinin It is expected to lower the cost of artemisinin production from a dollar per gram to just 10 cents He was awarded a $43 million grant from the Bill and Melinda Gates Foundation and awarded DISCOVER magazinersquos first ever Scientist of the Year Award
Fighting malaria is just one part of Keaslings larger agenda to explore the potential of synthetic biology In his laboratory students are engineering microbes to break down pesticides make biodegradable plastics and create ethanol and other fuels from plants
Excerpts of i interview w Jay Keasling
1 You arrived at UC Berkeley in 1992 with training as both a chemical engineer and a biologist What did you hope to do
2 Why hadnt anybody tried to engineer cells that way before
3 How did you get involved in your antimalaria project
Jay Keisling biography adapted fromZimmer C (2006) Scientist of the Year Jay Keasling Discovermagazinecom Retrieved from
httpdiscovermagazinecom2006deccover
copy 2009 Yu-Tzu Debbie Liu 9
See responses to these questions atZimmer C (2006) Scientist of the Year Jay Keasling Discovermagazinecom Retrieved from
httpdiscovermagazinecom2006deccover
Interview content removed due to copyright restrictions
Interview content removed due to copyright restrictions
Interview content removed due to copyright restrictions
Lesson Plan Day 3 Materials
Designing a New Microbe worksheet Organism cards Student notebooks or journals
Prep Step Review lesson plan background information and understanding goals Photocopy Designing a New Microbe worksheet (p 28) Cut out organism cards (each group of 3-4 students will have a set of cards) (p29)
Explore Step 1 Designing a New Microbe Introduce todayrsquos activity by saying ldquoYou will be simulating how synthetic biologists think mechanistically by doing an the activity that is actually modeled after a real experiment done by scientists in 2007rdquo Divide students into groups of 3 or 4 Each group receives a set of organism cards Each student receives a Designing a New Microbe worksheet Remind students that proteins (or enzymes) are molecules inside cells that convert one molecule into another (eg the make-believe molecule How is converted to the molecule Home by Protein T in bacteria) Following the directions of the handout have students create a kind of assembly line that integrate proteins from different organisms into a microbe that uses water and starch (inputs) to ultimately produce hydrogen (output)
Possible answers to Designing a New Microbe
There are two possible pathways that can lead to hydrogen production
1 Starch amp water Protein G Protein P Protein D Protein R Protein T Protein F Protein H Hydrogen
2 Starch amp water Protein G Protein P Protein D Protein H Hydrogen
Guide students along by encouraging students who have already figured out how to attempt the problem to reveal and share with the class how they are thinking through the problem Stop students periodically to ask ldquoHow are you thinking through this problem What is your goal and how is your thinking helping you reach that goalrdquo Students may find either working sequentially forward or backward to fill in the worksheet to be easier
Note to teachers The hydrogen production pathway from starch and water is a shorten version of the actual 2007 experiment for learning purposes The organism types and molecule names are true to the experiment Protein names are made up for simplicity
copy 2009 Yu-Tzu Debbie Liu 10
Step 2 Discuss studentsrsquo findings Have students tell you what they found as you write their findings on the board Students may have discovered by now that there are two paths that lead to hydrogen production Students might recall that Jay Keasling have done something similar by making an antimalarial drug from sugar using synthetic biology Students may have also discovered that no proteins from the mouse organism were used for the design of their new microbe Ask students ldquowhat do you think is the purpose of having a mouse organism when we didnrsquot need itrdquo Help students understand how in reality scientists have hundreds of organisms to choose from some of which are irrelevant to their work In fact a common skill that scientists share is being about to identify and pull together important and relevant information The activity allows students to discover that synthetic biology is a very mind-blowing field accomplishing things that some people never thought was possible Students will come to appreciate how seemingly impossible feats can be possible especially when scientists are thinking creatively By thinking and working mechanistically scientists have more freedom then before in designing and creating novel organisms for real-world applications
Review Extend and Apply Step 3 How do you think mechanistically Ask students to reflect on their experience with Scratch and how they might have engaged in mechanistic thinking in their own work Helps students make the connection that they themselves have been engaging in mechanistic thinking while working on their own Scratch projects The Scratch grammar is designed so that users are presented with a versatile collection of graphical programming blocks that they can be snapped together to create programs much like synthetic biology Connectors on the blocks suggest how they should be put together so that over the process of tinkering with these blocks the emerging structure can give rise to new ideas and direction to the project Not only does snapping together complimentary blocks provide an easy way into learning programming but the idea of modularization as a problem-solving and design strategy is directly relevant to mechanistic thinking Go on to discuss how they can apply scientistsrsquo patterns of thinking to our own thinking in science class and daily life
copy 2009 Yu-Tzu Debbie Liu 11
Name___________________________ Date ____________
Designing a New Microbe
Task Gas prices have reached its all time high Thus scientists are trying to think of ways to produce alternative fuels such as hydrogen gas in a much cheaper and quicker way You are a scientist and you are familiar with six different organisms Based on what you know can you come up with a way to generate hydrogen from starch and water by designing a microbe that borrows different mechanismsproteins from different cells Fill in the blanks with protein names and the organism that the protein was taken from
Materials Each team has a set of cards each card symbolizing a different organism On the card you will see the name of the organism a picture of the organism and proteins that is unique to them Proteins (or enzymes) convert one molecule into another
Starch amp Water Protein borrowed Protein borrowed
Input Organism Organism
Protein borrowed $ Protein borrowed $ Protein borrowed Organism Organism Organism
Protein borrowed Protein borrowed Protein borrowed Hydrogen Organism Organism Organism Output
Experiment adapted from Zhang YH Evans BR Mielenz JR Hopkins RC Adams MW (2007) High-yield hydrogen production from
starch and water by a synthetic enzymatic pathway PLoS ONE 5 e456
copy 2009 Yu-Tzu Debbie Liu 12
Organism Cards (one set)
Teachers Please make as many copies as the number of groups of students Cut the cards out and shuffle before handing to students
Source NIH
Bacteria
Rabbitbull Protein T uses [X5P] to make [S7P]
Photo US Fish and Wildlife Service bull Protein F uses [S7P] to make [NADPH] bull Protein G uses starch and water to make [G-1-P] bull Protein P uses [G-1-P] to make [G-6-P]
Yeast
Public domain image (Source Wikimedia Commons)
bull Protein D uses [G-6-P] to make [NADPH] and [R5P]
Public domain image (Source Wikimedia Commons) Spinach
bull Protein R uses [R5P] to make [X5P]
Experiment adapted from
Archea Courtesy of Angels Tapias (License CC BY)
bull Protein H uses [NADPH] to make Hydrogen
Source NIH Mouse
bull Protein X uses [T8P] to make Hydrogen
Zhang YH Evans BR Mielenz JR Hopkins RC Adams MW (2007) High-yield hydrogen production from starch and water by a synthetic enzymatic pathway PLoS ONE 5 e456
copy 2009 Yu-Tzu Debbie Liu 13
MIT OpenCourseWarehttpocwmitedu
MAS714J STS445J Technologies for Creative Learning Fall 2009
For information about citing these materials or our Terms of Use visit httpocwmiteduterms
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$$amp()+-- I
Photo courtesy httpsyntheticbiologyorg
Table of Contents
How are scientists thinking mechanistically in the 21st centuryhelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip1
Lesson 1 Introduction to Scratchhelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip5
Scratch Resources (not provided)helliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellipX
Lesson 2 Case Study of Jay Keaslinghelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip6
Case Study of Jay Keaslinghelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip8
Lesson 3 Mechanistic Thinkinghelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip10
Designing a New Microbehelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip12
Organism Cardshelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip13
copy 2009 Yu-Tzu Debbie Liu
Photo courtesy httpsyntheticbiologyorg
How are scientists thinkingmechanistically in the 21st century
Understanding Goals The rapid advancement of technology and the accumulation of information are changing
the patterns of scientific thinking and research in the 21st century Designing and creating novel organisms by combining various biological components
from different cells is one way scientists think mechanistically in the 21st century Designing and creating Scratch projects using graphical programming blocks is one way
students can display mechanistic thinking Identifying characteristics of successful scientist and their thinking patterns help us
become better (science) students by applying these skills to our own learning
Background Information Beyond the Scientific Method The scientific method has been commonly taught in science classrooms and textbooks as the only correct way to conduct scientific investigations This leaves students with the impression that all of science proceeds in much the same way Unfortunately this view is not entirely accurate Perhaps some scientists might conduct their work in this manner but rarely do they use it in the stereotyped step-by-step way that schools tend to teach itmdashdespite the fact that scientists report their work in this way in journals In fact scientists throughout history conduct their research in a variety of ways The exact approach a scientist uses depends on the individual doing the investigation as well as the particular question or problem being studied Furthermore scientists often engage in thinking patterns that are specific to its particular socio-cultural context 21st Century Scientific Thinking Skills With the explosion of advancements in scientific knowledge and technology at the turn of the century scientists at the cutting edge of research must adapt to new ways of interacting with their work Five prominent scientific thinking patterns of the 21st century are systems thinking mechanistic thinking interdisciplinary thinking quantitative thinking and distributed thinking1 In this lesson students will explore what mechanistic thinking Mechanistic Thinking It is a way of thinking that has a mechanical or engineering undertone This is shown through scientistsrsquo modular synthetic and purpose-driven approach towards their research problems Due to recent developments in new technologies and knowledge scientists are able to manipulate biology more directly allowing them to engineer and create novel biological systems for practical applications
1 Liu Y-T D amp Grotzer T A (2009) Looking forward Teaching the nature of the science of today and tomorrow In I M Saleh amp M S Khine (Eds) Fostering scientific habits of mind Pedagogical knowledge and best practices in science education (pp 9-36) Rotterdam Sense Publishers
copy 2009 Yu-Tzu Debbie Liu 1
What is Synthetic Biology The thinking involved in the field of synthetic biology is the best examples of mechanistic thinking With the rapidly emerging field of synthetic biology blurring the lines of biology and engineering scientists are no longer limited to working with organisms that naturally exist in the world Scientists often think synthetically by re-designing and constructing new organisms for practical and novel applications
Synthetic biology is an extension of genetic engineering Some even describe it as a more sophisticated version of genetic engineering taking into account a broader rational design perspective2 The engineering influence seeks out the simplicity in biological systems and brings standardization and modular design principles to biology
Synthetic biologists can use interchangeable parts from natural biology to assemble systems that function in new ways never existing before in living systems hence synthetic Modular circuit components (eg metabolic enzymes or fluorescent output genes) that are well characterized and can act independently of other cellular processes are used to build synthetic biological circuits Much like the ease of using LEGO bricksmdashstandardized bricks that can attach to any other partmdashsynthetic biology starts from the use of standardized biological building blocks The goal of synthetic biology is to both better understand how organisms function at the DNA protein and cell level by creating artificial biological systems and to solve important real-world problems the latter having caught the attention of scientists politicians and entrepreneurs Promising fields of application include energy environmental monitoring and remediation biotech and pharmaceuticals and materials fabrication
As pointed out in the detailed case study of Jay Keasling (one of the pioneers of synthetic biology) another key difference between synthetic biology and genetic engineering is the complexity of products or task the engineered organism can produce and accomplish Genetic engineering is typically limited to having microbes produce small proteins (eg insulin growth hormones) by simply inserting a single gene from a different organism into a microbe However with synthetic biology a complex interaction of several genes can be produced in a specified sequence much like what goes on in a chemical plant petroleum goes in and after a whole chain of reactions plastic comes out Scratch Scratch (httpscratchmitedu) is a programming language for young people (ages 8 and up) that makes it easy to create interactive projects (eg stories animations games simulations music and art) that can be shared on the Scratch website It is highly conducive to learning and teaching 21st century scientific thinking skills The Scratch grammar is designed so that users are presented with a versatile collection of graphical programming blocks that they can be snapped together to create programs much like LEGO bricks (and synthetic biology) Connectors on the blocks suggest how they should be put together so that over the process of tinkering with these blocks the emerging structure can give rise to new ideas and direction to the project Not only does snapping together complimentary blocks provide an easy way into learning programming but the idea of modularization as a problem-solving and design strategy is directly relevant to mechanistic thinking
2 Salisbury MW (2006) Get Ready for Synthetic Biology Genome Technology Magazine Retrieved from httpwwwgenome-technologycom
copy 2009 Yu-Tzu Debbie Liu 2
In this lesson Scratch is used to have students experience thinking mechanistically in their own work And since programming involves the creation of external representations of the problem-solving process Scratch provides students with opportunities of reflecting on their own thinking Lesson Layout These three lessons (one lesson per day) are designed to help students 1) understand how modern scientists think mechanistically 2) practice thinking mechanistically by simulating how synthetic biologists think in the field and 3) recognize mechanistic thinking even when it is not in the context of science as in their own work via Scratch Lesson 1 Designed to familiarize students with the Scratch programming language so that they can create projects on it At this point Scratch is presented simply as a medium for expressing what they have learned much like posters Powerpoint presentations and paper write-ups Lesson 2 Designed to expose students to the creative field of synthetic biology as a means to illustrate how scientists think mechanistically in the field This is done by a case study of Jay Keasling one of the pioneers of synthetic biology By analyzing how a modern scientist work and think students are provided with a broader view of scientific inquiry and the nature of scientific thinking Students will be asked to demonstrate their understanding of what they have learned so far by creating a Scratch project This allows students to work more closely and creatively with Scratch It also acts as a quick formative assessment for teachers of studentsrsquo learning thus far However the real goal of this exercise is to have students engage in mechanistic thinking in their own work which they may not recognize as it is not in the direct context of science This will be revealed in lesson 3 Lesson 3 Designed to have students practice thinking mechanistically by simulating how synthetic biologists think in the field via the Designing a New Microbe activity adapted from an actual experiment conducted in 20073 This activity presents students with a problem (need for hydrogen gas as alternative fuel) and asks students to design a microbe that can use starch and water to make hydrogen gas Students are given a set of organism cards to work with each card symbolizing a different type of organism (bacteria rabbit yeast archea spinach and mouse) Proteins (molecules that can convert one molecule into another) that are unique to each organism are listed on the card Studentsrsquo engineered microbe will essentially have different proteins from different organisms placed in a certain sequence to end up with a final product of hydrogen gas Students are given the Designing a New Microbe worksheet to help them visualize the problem better and reduce their cognitive loads (ie amount of information they need to carry in their heads) The activity allows students to discover that synthetic biology is a very mind-blowing field accomplishing things that some people never thought was possible Students will come to appreciate how seemingly impossible feats can be possible especially when scientists are thinking creatively By thinking and working mechanistically scientists have more freedom then before in designing and creating novel organisms for real-world applications
3 Zhang YH Evans BR Mielenz JR Hopkins RC Adams MW (2007) High-yield hydrogen production from starch and water by a synthetic enzymatic pathway PLoS ONE 5 e456
copy 2009 Yu-Tzu Debbie Liu 3
After the activity when students have grasped a much deeper understanding of what mechanistic thinking looks like in practice students are asked to reflect on their experience with Scratch The goal is to have students make the connection that they themselves have been engaging in mechanistic thinking while working on their own Scratch projects This reflective exercise encourages students to transfer their understanding of mechanistic thinking across different domains Students will also gain an appreciation of how studying trends in scientistsrsquo way of thinking can help them in their own thinking Lesson Placement These lessons can be used at the beginning of the school year when the scientific method is usually being presented Alternatively this lesson can be infused during the school year as students learn more about genetic engineering or creative thinking These lessons follow a constructivist approach to learning encouraging students to discover the meaning of mechanistic thinking through their exploration of a case study simulating how synthetic biologists think and making connections to their own work in Scratch Students are always encouraged to formulate their own ideas and connections before being presented with any information
copy 2009 Yu-Tzu Debbie Liu 4
Lesson Plan Day 1 Materials
Computers with Scratch installed Scratch Resources
Prep Step Review lesson plan background information and understanding goals Obtain computers with Scratch installed for students to work on Make copies of Scratch Resources (not provided)
Explore Step 1 Introduction to lesson Introduce the lesson by giving students a sense of what they will be doing and where they are headed by telling students ldquoThis will be a three-day lesson where we will be exploring how scientists think and more specifically what mechanistic thinking looks like in practice In this process we will also be learning Scratch We will tie everything together at the end of the third dayrdquo Step 2 Playing with Scratch Depending on the level of your students and any future goals you wish to achieve with Scratch structure the class so that students are comfortable navigating around the Scratch environment and are able to get started on their own Scratch project by the end of the class Please provide students with any Scratch resources you see fit Check out the ScratchEds resource search (httpscratchedmediamiteduresourcessearch) for more info Some good examples found in ScratchEd of Scratch lesson plans (video tutorials PowerPoints and worksheets) include
bull Having Fun with Computer Programming and Games (httpwwwleroieeducationoutreachsecondlevelscratchlessonplans)
bull A TeachNetUK Project 6 Lessons on Getting Started with Scratch (httpwwwteachnet-ukorguk200720ProjectsICT-ScratchScratchpages8_schemeofworkhtml)
bull Scratch Lessons Shall We Learn Scratch Programming for Tweens (httpwwwshallwelearncomscratchprogrammingforkidscategory)
bull Designing Animations and GamesmdashA Creative Introduction to Programming (httpwwwcsuni-potsdamde~romeikeUEWettbewerbindex-englishhtm)
Make sure to also introduce students to the Scratch online community and let them know that they can download the source code of any project to help them see how others are using the Scratch programming language to create projects
Review Extend and Apply Step 3 Scratch Assignment End the day by informing students that they will apply what they have learned today to create a mini-Scratch project for an assignment after the next dayrsquos lesson Emphasize to students that the goal is not to create a complex programming project but to use Scratch creatively as a medium for creative expressing not matter how simple the project is Encourage students to play with Scratch on their own time and make it clear that you highly encourage them to borrow adapt and build upon the ideas and projects of others (this is not considered cheating)
copy 2009 Yu-Tzu Debbie Liu 5
Lesson Plan Day 2 Materials
21st century scientist case study of Jay Keasling Student notebooks or journals
Prep Step Review lesson plan background information and understanding goals Make copies of 21st century scientist case study of Jay Keasling (p 8)
Explore Step 1 What is scientific thinking Ask students to describe what they think is scientific thinking Collect a representative list of studentsrsquo thoughts on the board Ask students to explain or expound on the meaning behind what they are saying After reviewing the list ask them ldquo Do you think all scientists come to their discoveries in the same wayrdquo ldquoDo scientists display all these characteristics at all timesrdquo It is important to point out to students that scientists have various methods going about their experimentation and work and depending on the type of work they are doing scientists donrsquot always share the same methods Furthermore scientists engage in thinking patterns that are specific to its particular socio-cultural context and one of which is mechanistic thinking Engage in a discussion with students on how might the explosion of advancements in scientific knowledge and technology at the turn of the century change the way scientists at the cutting edge of research interact with their work
Step 2 Analyze case study of a 21st century scientist Let students know that they will be learning about the field of synthetic biology as a means to illustrate how modern scientists work and think Specifically they will be studying Jay Keasling one of the pioneers of synthetic biology Hand out the case study on Jay Keasling Have students work in groups of 3-4 students to identify any patterns of thinking that the scientist displays Make sure to ask students to specifically identify what part of the case study justifies their claims Have students write the class findings in their journalsnotebooks
Possible findings from case analysis Jay Keasling
Keasling is a pioneer of synthetic biologymdasha field that designs and constructs new organisms for useful purposes He is most known for creating a microbe that produces a drug to treat malaria (making drugs from bugs) Some of his characteristics as a scientist include
bull Creative and imaginative wanted to invent new tools that can turn cells into chemical plants take in something very simple and spits out something complicated and valuable coming up with other applications of synthetic biology (use microbes to break down pesticides make biodegradable plastics create fuels from plants)
bull Critical thinking thought about how to design and create microbes to produce artemisinin much quicker and cheaper how to integrate genes from different species into a microbe to fabricate the drug
copy 2009 Yu-Tzu Debbie Liu 6
bull Seek and integrate information integrated methods and concepts from engineering and biology leading to synthetic biology
bull Supported with significant resources did research at universities and received grant money
bull Practical-minded microbes will churn out anti-malarial drug for a fraction of its current cost making it accessible to much more of the world these microbes could save millions of lives
bull Strong disciplinary understanding studied biology and chemical engineering extensively leading to his PhD and professor position at UC Berkeley
Step 3 What is mechanistic thinking Introduce students to the idea of mechanistic thinking as a prominent thinking pattern in the 21st
century
Mechanistic Thinking
Mechanistic thinking is a way of thinking that has a mechanical or engineering undertone This is shown through scientistsrsquo regular use of mechanical analogies to conceptualize their work and their modular synthetic and purpose-driven approach towards their research problems The display of mechanistic thinking by scientists appears to be a result of the merging of biology and engineering practices that is increasingly observed in 21st century biology as compared to a time when most of biologymdashtraditionally known for its pure basic researchmdashremain clearly demarcated from engineeringmdasha purely applied research field A mechanistic way of thinking has come to the forefront of 21st century science because of recent developments in new technologies and knowledge that enable scientists to manipulate the object or organism they are working with more directly allowing them to engineer and create novel biological systems for practical applications
Let students know that the work synthetic biologists do often require them to think mechanistically Now that students are given a definition of mechanistic thinking have students revisit their case study analysis and explore how synthetic biologists might think mechanistically
Review Extend and Apply
Step 4 Scratch Assignment Ask students to create a mini-Scratch project to demonstrate what they have learned so far (the project does not have to be all inclusive students can choose to focus on just one thing they learned either about scientific thinking mechanistic thinking or synthetic biology) Emphasize to students that the goal is not to create a complex programming project but to use Scratch creatively as a medium for creative expressing not matter how simple the project is Encourage students to work with partners and collaborate by borrowing adapting or building upon the ideas and projects of others (this is not considered cheating)
copy 2009 Yu-Tzu Debbie Liu 7
Detailed Case Study Jay Keasling
(1964 ndash present)
Best known for pioneering the new field of synthetic biology which designs and constructs new organisms for useful purposes He is also most known for creating a microbe that produces a drug to treat malaria (making drugs from bugs)
Jay Keasling was raised on a farm and spent his childhood exploring the practical side of biology chemistry and engineering This background eventually led him to work in the rapidly growing field that uses living organisms like bacteria for various practical purposes such as food processing agriculture and medicine
In the early 1980s genetic engineering became popular because you can ldquoconvincerdquo microbes to produce insulin growth hormones and other valuable proteins by simply inserting a single gene from a different organism into bacteria However Keasling believed that genetic engineering isnrsquot harnessing the full power of these cells The production of molecules isnt always so simple it requires a complex interaction of several genes (not just one) being produced in a certain sequence So Keasling wanted to invent the tools that would allow him to create these kinds of genetic assembly lines Thus what goes on in a cell is a lot like what goes on in a chemical plant petroleum goes in and after a whole chain of reactions plastic comes out
Keasling went to college studying biology and chemical engineering extensively and got his PhD in 1991 He is now a professor at the University of California at Berkeley He spent his first 10 years at UC Berkeley building the new tools he would need to turn cells into chemical plants He also invented powerful chemical switches (like a light switch) that allowed him to control when he wanted to ldquoturn onrdquo and ldquoturn offrdquo protein production in cells This way of borrowing techniques from engineering and figuring out how to manipulate microbes came to be call synthetic biology
After years of perfecting his biological tool kit Keasling wanted to find a real-world use for it In 2002 he learned of the dire need for artemisinin a compound derived from the sweet wormwood plant which is 90 percent effective against the parasite that causes malaria and has few side effects (malaria kills some 3 million people a year) However extracting the drug from sweet wormwood is a slow and expensive process Keasling figured he could design and create microbes to produce artemisinin much quicker and cheaper Rather than wait months for sweet wormwood to grow on farms Keasling wanted to create it simply by pouring sugar in a tank full of microbes that can use the sugar to make the drug via a chemical pathway he has designedmdashhe wanted to integrate genes from different species into a microbe to fabricate the drug for malaria
copy 2009 Yu-Tzu Debbie Liu 8
In 2006 Keaslings team (comprised of graduate students post-docs and research assistants) published their success of the production of artemisinin It is expected to lower the cost of artemisinin production from a dollar per gram to just 10 cents He was awarded a $43 million grant from the Bill and Melinda Gates Foundation and awarded DISCOVER magazinersquos first ever Scientist of the Year Award
Fighting malaria is just one part of Keaslings larger agenda to explore the potential of synthetic biology In his laboratory students are engineering microbes to break down pesticides make biodegradable plastics and create ethanol and other fuels from plants
Excerpts of i interview w Jay Keasling
1 You arrived at UC Berkeley in 1992 with training as both a chemical engineer and a biologist What did you hope to do
2 Why hadnt anybody tried to engineer cells that way before
3 How did you get involved in your antimalaria project
Jay Keisling biography adapted fromZimmer C (2006) Scientist of the Year Jay Keasling Discovermagazinecom Retrieved from
httpdiscovermagazinecom2006deccover
copy 2009 Yu-Tzu Debbie Liu 9
See responses to these questions atZimmer C (2006) Scientist of the Year Jay Keasling Discovermagazinecom Retrieved from
httpdiscovermagazinecom2006deccover
Interview content removed due to copyright restrictions
Interview content removed due to copyright restrictions
Interview content removed due to copyright restrictions
Lesson Plan Day 3 Materials
Designing a New Microbe worksheet Organism cards Student notebooks or journals
Prep Step Review lesson plan background information and understanding goals Photocopy Designing a New Microbe worksheet (p 28) Cut out organism cards (each group of 3-4 students will have a set of cards) (p29)
Explore Step 1 Designing a New Microbe Introduce todayrsquos activity by saying ldquoYou will be simulating how synthetic biologists think mechanistically by doing an the activity that is actually modeled after a real experiment done by scientists in 2007rdquo Divide students into groups of 3 or 4 Each group receives a set of organism cards Each student receives a Designing a New Microbe worksheet Remind students that proteins (or enzymes) are molecules inside cells that convert one molecule into another (eg the make-believe molecule How is converted to the molecule Home by Protein T in bacteria) Following the directions of the handout have students create a kind of assembly line that integrate proteins from different organisms into a microbe that uses water and starch (inputs) to ultimately produce hydrogen (output)
Possible answers to Designing a New Microbe
There are two possible pathways that can lead to hydrogen production
1 Starch amp water Protein G Protein P Protein D Protein R Protein T Protein F Protein H Hydrogen
2 Starch amp water Protein G Protein P Protein D Protein H Hydrogen
Guide students along by encouraging students who have already figured out how to attempt the problem to reveal and share with the class how they are thinking through the problem Stop students periodically to ask ldquoHow are you thinking through this problem What is your goal and how is your thinking helping you reach that goalrdquo Students may find either working sequentially forward or backward to fill in the worksheet to be easier
Note to teachers The hydrogen production pathway from starch and water is a shorten version of the actual 2007 experiment for learning purposes The organism types and molecule names are true to the experiment Protein names are made up for simplicity
copy 2009 Yu-Tzu Debbie Liu 10
Step 2 Discuss studentsrsquo findings Have students tell you what they found as you write their findings on the board Students may have discovered by now that there are two paths that lead to hydrogen production Students might recall that Jay Keasling have done something similar by making an antimalarial drug from sugar using synthetic biology Students may have also discovered that no proteins from the mouse organism were used for the design of their new microbe Ask students ldquowhat do you think is the purpose of having a mouse organism when we didnrsquot need itrdquo Help students understand how in reality scientists have hundreds of organisms to choose from some of which are irrelevant to their work In fact a common skill that scientists share is being about to identify and pull together important and relevant information The activity allows students to discover that synthetic biology is a very mind-blowing field accomplishing things that some people never thought was possible Students will come to appreciate how seemingly impossible feats can be possible especially when scientists are thinking creatively By thinking and working mechanistically scientists have more freedom then before in designing and creating novel organisms for real-world applications
Review Extend and Apply Step 3 How do you think mechanistically Ask students to reflect on their experience with Scratch and how they might have engaged in mechanistic thinking in their own work Helps students make the connection that they themselves have been engaging in mechanistic thinking while working on their own Scratch projects The Scratch grammar is designed so that users are presented with a versatile collection of graphical programming blocks that they can be snapped together to create programs much like synthetic biology Connectors on the blocks suggest how they should be put together so that over the process of tinkering with these blocks the emerging structure can give rise to new ideas and direction to the project Not only does snapping together complimentary blocks provide an easy way into learning programming but the idea of modularization as a problem-solving and design strategy is directly relevant to mechanistic thinking Go on to discuss how they can apply scientistsrsquo patterns of thinking to our own thinking in science class and daily life
copy 2009 Yu-Tzu Debbie Liu 11
Name___________________________ Date ____________
Designing a New Microbe
Task Gas prices have reached its all time high Thus scientists are trying to think of ways to produce alternative fuels such as hydrogen gas in a much cheaper and quicker way You are a scientist and you are familiar with six different organisms Based on what you know can you come up with a way to generate hydrogen from starch and water by designing a microbe that borrows different mechanismsproteins from different cells Fill in the blanks with protein names and the organism that the protein was taken from
Materials Each team has a set of cards each card symbolizing a different organism On the card you will see the name of the organism a picture of the organism and proteins that is unique to them Proteins (or enzymes) convert one molecule into another
Starch amp Water Protein borrowed Protein borrowed
Input Organism Organism
Protein borrowed $ Protein borrowed $ Protein borrowed Organism Organism Organism
Protein borrowed Protein borrowed Protein borrowed Hydrogen Organism Organism Organism Output
Experiment adapted from Zhang YH Evans BR Mielenz JR Hopkins RC Adams MW (2007) High-yield hydrogen production from
starch and water by a synthetic enzymatic pathway PLoS ONE 5 e456
copy 2009 Yu-Tzu Debbie Liu 12
Organism Cards (one set)
Teachers Please make as many copies as the number of groups of students Cut the cards out and shuffle before handing to students
Source NIH
Bacteria
Rabbitbull Protein T uses [X5P] to make [S7P]
Photo US Fish and Wildlife Service bull Protein F uses [S7P] to make [NADPH] bull Protein G uses starch and water to make [G-1-P] bull Protein P uses [G-1-P] to make [G-6-P]
Yeast
Public domain image (Source Wikimedia Commons)
bull Protein D uses [G-6-P] to make [NADPH] and [R5P]
Public domain image (Source Wikimedia Commons) Spinach
bull Protein R uses [R5P] to make [X5P]
Experiment adapted from
Archea Courtesy of Angels Tapias (License CC BY)
bull Protein H uses [NADPH] to make Hydrogen
Source NIH Mouse
bull Protein X uses [T8P] to make Hydrogen
Zhang YH Evans BR Mielenz JR Hopkins RC Adams MW (2007) High-yield hydrogen production from starch and water by a synthetic enzymatic pathway PLoS ONE 5 e456
copy 2009 Yu-Tzu Debbie Liu 13
MIT OpenCourseWarehttpocwmitedu
MAS714J STS445J Technologies for Creative Learning Fall 2009
For information about citing these materials or our Terms of Use visit httpocwmiteduterms
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Photo courtesy httpsyntheticbiologyorg
Table of Contents
How are scientists thinking mechanistically in the 21st centuryhelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip1
Lesson 1 Introduction to Scratchhelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip5
Scratch Resources (not provided)helliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellipX
Lesson 2 Case Study of Jay Keaslinghelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip6
Case Study of Jay Keaslinghelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip8
Lesson 3 Mechanistic Thinkinghelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip10
Designing a New Microbehelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip12
Organism Cardshelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip13
copy 2009 Yu-Tzu Debbie Liu
Photo courtesy httpsyntheticbiologyorg
How are scientists thinkingmechanistically in the 21st century
Understanding Goals The rapid advancement of technology and the accumulation of information are changing
the patterns of scientific thinking and research in the 21st century Designing and creating novel organisms by combining various biological components
from different cells is one way scientists think mechanistically in the 21st century Designing and creating Scratch projects using graphical programming blocks is one way
students can display mechanistic thinking Identifying characteristics of successful scientist and their thinking patterns help us
become better (science) students by applying these skills to our own learning
Background Information Beyond the Scientific Method The scientific method has been commonly taught in science classrooms and textbooks as the only correct way to conduct scientific investigations This leaves students with the impression that all of science proceeds in much the same way Unfortunately this view is not entirely accurate Perhaps some scientists might conduct their work in this manner but rarely do they use it in the stereotyped step-by-step way that schools tend to teach itmdashdespite the fact that scientists report their work in this way in journals In fact scientists throughout history conduct their research in a variety of ways The exact approach a scientist uses depends on the individual doing the investigation as well as the particular question or problem being studied Furthermore scientists often engage in thinking patterns that are specific to its particular socio-cultural context 21st Century Scientific Thinking Skills With the explosion of advancements in scientific knowledge and technology at the turn of the century scientists at the cutting edge of research must adapt to new ways of interacting with their work Five prominent scientific thinking patterns of the 21st century are systems thinking mechanistic thinking interdisciplinary thinking quantitative thinking and distributed thinking1 In this lesson students will explore what mechanistic thinking Mechanistic Thinking It is a way of thinking that has a mechanical or engineering undertone This is shown through scientistsrsquo modular synthetic and purpose-driven approach towards their research problems Due to recent developments in new technologies and knowledge scientists are able to manipulate biology more directly allowing them to engineer and create novel biological systems for practical applications
1 Liu Y-T D amp Grotzer T A (2009) Looking forward Teaching the nature of the science of today and tomorrow In I M Saleh amp M S Khine (Eds) Fostering scientific habits of mind Pedagogical knowledge and best practices in science education (pp 9-36) Rotterdam Sense Publishers
copy 2009 Yu-Tzu Debbie Liu 1
What is Synthetic Biology The thinking involved in the field of synthetic biology is the best examples of mechanistic thinking With the rapidly emerging field of synthetic biology blurring the lines of biology and engineering scientists are no longer limited to working with organisms that naturally exist in the world Scientists often think synthetically by re-designing and constructing new organisms for practical and novel applications
Synthetic biology is an extension of genetic engineering Some even describe it as a more sophisticated version of genetic engineering taking into account a broader rational design perspective2 The engineering influence seeks out the simplicity in biological systems and brings standardization and modular design principles to biology
Synthetic biologists can use interchangeable parts from natural biology to assemble systems that function in new ways never existing before in living systems hence synthetic Modular circuit components (eg metabolic enzymes or fluorescent output genes) that are well characterized and can act independently of other cellular processes are used to build synthetic biological circuits Much like the ease of using LEGO bricksmdashstandardized bricks that can attach to any other partmdashsynthetic biology starts from the use of standardized biological building blocks The goal of synthetic biology is to both better understand how organisms function at the DNA protein and cell level by creating artificial biological systems and to solve important real-world problems the latter having caught the attention of scientists politicians and entrepreneurs Promising fields of application include energy environmental monitoring and remediation biotech and pharmaceuticals and materials fabrication
As pointed out in the detailed case study of Jay Keasling (one of the pioneers of synthetic biology) another key difference between synthetic biology and genetic engineering is the complexity of products or task the engineered organism can produce and accomplish Genetic engineering is typically limited to having microbes produce small proteins (eg insulin growth hormones) by simply inserting a single gene from a different organism into a microbe However with synthetic biology a complex interaction of several genes can be produced in a specified sequence much like what goes on in a chemical plant petroleum goes in and after a whole chain of reactions plastic comes out Scratch Scratch (httpscratchmitedu) is a programming language for young people (ages 8 and up) that makes it easy to create interactive projects (eg stories animations games simulations music and art) that can be shared on the Scratch website It is highly conducive to learning and teaching 21st century scientific thinking skills The Scratch grammar is designed so that users are presented with a versatile collection of graphical programming blocks that they can be snapped together to create programs much like LEGO bricks (and synthetic biology) Connectors on the blocks suggest how they should be put together so that over the process of tinkering with these blocks the emerging structure can give rise to new ideas and direction to the project Not only does snapping together complimentary blocks provide an easy way into learning programming but the idea of modularization as a problem-solving and design strategy is directly relevant to mechanistic thinking
2 Salisbury MW (2006) Get Ready for Synthetic Biology Genome Technology Magazine Retrieved from httpwwwgenome-technologycom
copy 2009 Yu-Tzu Debbie Liu 2
In this lesson Scratch is used to have students experience thinking mechanistically in their own work And since programming involves the creation of external representations of the problem-solving process Scratch provides students with opportunities of reflecting on their own thinking Lesson Layout These three lessons (one lesson per day) are designed to help students 1) understand how modern scientists think mechanistically 2) practice thinking mechanistically by simulating how synthetic biologists think in the field and 3) recognize mechanistic thinking even when it is not in the context of science as in their own work via Scratch Lesson 1 Designed to familiarize students with the Scratch programming language so that they can create projects on it At this point Scratch is presented simply as a medium for expressing what they have learned much like posters Powerpoint presentations and paper write-ups Lesson 2 Designed to expose students to the creative field of synthetic biology as a means to illustrate how scientists think mechanistically in the field This is done by a case study of Jay Keasling one of the pioneers of synthetic biology By analyzing how a modern scientist work and think students are provided with a broader view of scientific inquiry and the nature of scientific thinking Students will be asked to demonstrate their understanding of what they have learned so far by creating a Scratch project This allows students to work more closely and creatively with Scratch It also acts as a quick formative assessment for teachers of studentsrsquo learning thus far However the real goal of this exercise is to have students engage in mechanistic thinking in their own work which they may not recognize as it is not in the direct context of science This will be revealed in lesson 3 Lesson 3 Designed to have students practice thinking mechanistically by simulating how synthetic biologists think in the field via the Designing a New Microbe activity adapted from an actual experiment conducted in 20073 This activity presents students with a problem (need for hydrogen gas as alternative fuel) and asks students to design a microbe that can use starch and water to make hydrogen gas Students are given a set of organism cards to work with each card symbolizing a different type of organism (bacteria rabbit yeast archea spinach and mouse) Proteins (molecules that can convert one molecule into another) that are unique to each organism are listed on the card Studentsrsquo engineered microbe will essentially have different proteins from different organisms placed in a certain sequence to end up with a final product of hydrogen gas Students are given the Designing a New Microbe worksheet to help them visualize the problem better and reduce their cognitive loads (ie amount of information they need to carry in their heads) The activity allows students to discover that synthetic biology is a very mind-blowing field accomplishing things that some people never thought was possible Students will come to appreciate how seemingly impossible feats can be possible especially when scientists are thinking creatively By thinking and working mechanistically scientists have more freedom then before in designing and creating novel organisms for real-world applications
3 Zhang YH Evans BR Mielenz JR Hopkins RC Adams MW (2007) High-yield hydrogen production from starch and water by a synthetic enzymatic pathway PLoS ONE 5 e456
copy 2009 Yu-Tzu Debbie Liu 3
After the activity when students have grasped a much deeper understanding of what mechanistic thinking looks like in practice students are asked to reflect on their experience with Scratch The goal is to have students make the connection that they themselves have been engaging in mechanistic thinking while working on their own Scratch projects This reflective exercise encourages students to transfer their understanding of mechanistic thinking across different domains Students will also gain an appreciation of how studying trends in scientistsrsquo way of thinking can help them in their own thinking Lesson Placement These lessons can be used at the beginning of the school year when the scientific method is usually being presented Alternatively this lesson can be infused during the school year as students learn more about genetic engineering or creative thinking These lessons follow a constructivist approach to learning encouraging students to discover the meaning of mechanistic thinking through their exploration of a case study simulating how synthetic biologists think and making connections to their own work in Scratch Students are always encouraged to formulate their own ideas and connections before being presented with any information
copy 2009 Yu-Tzu Debbie Liu 4
Lesson Plan Day 1 Materials
Computers with Scratch installed Scratch Resources
Prep Step Review lesson plan background information and understanding goals Obtain computers with Scratch installed for students to work on Make copies of Scratch Resources (not provided)
Explore Step 1 Introduction to lesson Introduce the lesson by giving students a sense of what they will be doing and where they are headed by telling students ldquoThis will be a three-day lesson where we will be exploring how scientists think and more specifically what mechanistic thinking looks like in practice In this process we will also be learning Scratch We will tie everything together at the end of the third dayrdquo Step 2 Playing with Scratch Depending on the level of your students and any future goals you wish to achieve with Scratch structure the class so that students are comfortable navigating around the Scratch environment and are able to get started on their own Scratch project by the end of the class Please provide students with any Scratch resources you see fit Check out the ScratchEds resource search (httpscratchedmediamiteduresourcessearch) for more info Some good examples found in ScratchEd of Scratch lesson plans (video tutorials PowerPoints and worksheets) include
bull Having Fun with Computer Programming and Games (httpwwwleroieeducationoutreachsecondlevelscratchlessonplans)
bull A TeachNetUK Project 6 Lessons on Getting Started with Scratch (httpwwwteachnet-ukorguk200720ProjectsICT-ScratchScratchpages8_schemeofworkhtml)
bull Scratch Lessons Shall We Learn Scratch Programming for Tweens (httpwwwshallwelearncomscratchprogrammingforkidscategory)
bull Designing Animations and GamesmdashA Creative Introduction to Programming (httpwwwcsuni-potsdamde~romeikeUEWettbewerbindex-englishhtm)
Make sure to also introduce students to the Scratch online community and let them know that they can download the source code of any project to help them see how others are using the Scratch programming language to create projects
Review Extend and Apply Step 3 Scratch Assignment End the day by informing students that they will apply what they have learned today to create a mini-Scratch project for an assignment after the next dayrsquos lesson Emphasize to students that the goal is not to create a complex programming project but to use Scratch creatively as a medium for creative expressing not matter how simple the project is Encourage students to play with Scratch on their own time and make it clear that you highly encourage them to borrow adapt and build upon the ideas and projects of others (this is not considered cheating)
copy 2009 Yu-Tzu Debbie Liu 5
Lesson Plan Day 2 Materials
21st century scientist case study of Jay Keasling Student notebooks or journals
Prep Step Review lesson plan background information and understanding goals Make copies of 21st century scientist case study of Jay Keasling (p 8)
Explore Step 1 What is scientific thinking Ask students to describe what they think is scientific thinking Collect a representative list of studentsrsquo thoughts on the board Ask students to explain or expound on the meaning behind what they are saying After reviewing the list ask them ldquo Do you think all scientists come to their discoveries in the same wayrdquo ldquoDo scientists display all these characteristics at all timesrdquo It is important to point out to students that scientists have various methods going about their experimentation and work and depending on the type of work they are doing scientists donrsquot always share the same methods Furthermore scientists engage in thinking patterns that are specific to its particular socio-cultural context and one of which is mechanistic thinking Engage in a discussion with students on how might the explosion of advancements in scientific knowledge and technology at the turn of the century change the way scientists at the cutting edge of research interact with their work
Step 2 Analyze case study of a 21st century scientist Let students know that they will be learning about the field of synthetic biology as a means to illustrate how modern scientists work and think Specifically they will be studying Jay Keasling one of the pioneers of synthetic biology Hand out the case study on Jay Keasling Have students work in groups of 3-4 students to identify any patterns of thinking that the scientist displays Make sure to ask students to specifically identify what part of the case study justifies their claims Have students write the class findings in their journalsnotebooks
Possible findings from case analysis Jay Keasling
Keasling is a pioneer of synthetic biologymdasha field that designs and constructs new organisms for useful purposes He is most known for creating a microbe that produces a drug to treat malaria (making drugs from bugs) Some of his characteristics as a scientist include
bull Creative and imaginative wanted to invent new tools that can turn cells into chemical plants take in something very simple and spits out something complicated and valuable coming up with other applications of synthetic biology (use microbes to break down pesticides make biodegradable plastics create fuels from plants)
bull Critical thinking thought about how to design and create microbes to produce artemisinin much quicker and cheaper how to integrate genes from different species into a microbe to fabricate the drug
copy 2009 Yu-Tzu Debbie Liu 6
bull Seek and integrate information integrated methods and concepts from engineering and biology leading to synthetic biology
bull Supported with significant resources did research at universities and received grant money
bull Practical-minded microbes will churn out anti-malarial drug for a fraction of its current cost making it accessible to much more of the world these microbes could save millions of lives
bull Strong disciplinary understanding studied biology and chemical engineering extensively leading to his PhD and professor position at UC Berkeley
Step 3 What is mechanistic thinking Introduce students to the idea of mechanistic thinking as a prominent thinking pattern in the 21st
century
Mechanistic Thinking
Mechanistic thinking is a way of thinking that has a mechanical or engineering undertone This is shown through scientistsrsquo regular use of mechanical analogies to conceptualize their work and their modular synthetic and purpose-driven approach towards their research problems The display of mechanistic thinking by scientists appears to be a result of the merging of biology and engineering practices that is increasingly observed in 21st century biology as compared to a time when most of biologymdashtraditionally known for its pure basic researchmdashremain clearly demarcated from engineeringmdasha purely applied research field A mechanistic way of thinking has come to the forefront of 21st century science because of recent developments in new technologies and knowledge that enable scientists to manipulate the object or organism they are working with more directly allowing them to engineer and create novel biological systems for practical applications
Let students know that the work synthetic biologists do often require them to think mechanistically Now that students are given a definition of mechanistic thinking have students revisit their case study analysis and explore how synthetic biologists might think mechanistically
Review Extend and Apply
Step 4 Scratch Assignment Ask students to create a mini-Scratch project to demonstrate what they have learned so far (the project does not have to be all inclusive students can choose to focus on just one thing they learned either about scientific thinking mechanistic thinking or synthetic biology) Emphasize to students that the goal is not to create a complex programming project but to use Scratch creatively as a medium for creative expressing not matter how simple the project is Encourage students to work with partners and collaborate by borrowing adapting or building upon the ideas and projects of others (this is not considered cheating)
copy 2009 Yu-Tzu Debbie Liu 7
Detailed Case Study Jay Keasling
(1964 ndash present)
Best known for pioneering the new field of synthetic biology which designs and constructs new organisms for useful purposes He is also most known for creating a microbe that produces a drug to treat malaria (making drugs from bugs)
Jay Keasling was raised on a farm and spent his childhood exploring the practical side of biology chemistry and engineering This background eventually led him to work in the rapidly growing field that uses living organisms like bacteria for various practical purposes such as food processing agriculture and medicine
In the early 1980s genetic engineering became popular because you can ldquoconvincerdquo microbes to produce insulin growth hormones and other valuable proteins by simply inserting a single gene from a different organism into bacteria However Keasling believed that genetic engineering isnrsquot harnessing the full power of these cells The production of molecules isnt always so simple it requires a complex interaction of several genes (not just one) being produced in a certain sequence So Keasling wanted to invent the tools that would allow him to create these kinds of genetic assembly lines Thus what goes on in a cell is a lot like what goes on in a chemical plant petroleum goes in and after a whole chain of reactions plastic comes out
Keasling went to college studying biology and chemical engineering extensively and got his PhD in 1991 He is now a professor at the University of California at Berkeley He spent his first 10 years at UC Berkeley building the new tools he would need to turn cells into chemical plants He also invented powerful chemical switches (like a light switch) that allowed him to control when he wanted to ldquoturn onrdquo and ldquoturn offrdquo protein production in cells This way of borrowing techniques from engineering and figuring out how to manipulate microbes came to be call synthetic biology
After years of perfecting his biological tool kit Keasling wanted to find a real-world use for it In 2002 he learned of the dire need for artemisinin a compound derived from the sweet wormwood plant which is 90 percent effective against the parasite that causes malaria and has few side effects (malaria kills some 3 million people a year) However extracting the drug from sweet wormwood is a slow and expensive process Keasling figured he could design and create microbes to produce artemisinin much quicker and cheaper Rather than wait months for sweet wormwood to grow on farms Keasling wanted to create it simply by pouring sugar in a tank full of microbes that can use the sugar to make the drug via a chemical pathway he has designedmdashhe wanted to integrate genes from different species into a microbe to fabricate the drug for malaria
copy 2009 Yu-Tzu Debbie Liu 8
In 2006 Keaslings team (comprised of graduate students post-docs and research assistants) published their success of the production of artemisinin It is expected to lower the cost of artemisinin production from a dollar per gram to just 10 cents He was awarded a $43 million grant from the Bill and Melinda Gates Foundation and awarded DISCOVER magazinersquos first ever Scientist of the Year Award
Fighting malaria is just one part of Keaslings larger agenda to explore the potential of synthetic biology In his laboratory students are engineering microbes to break down pesticides make biodegradable plastics and create ethanol and other fuels from plants
Excerpts of i interview w Jay Keasling
1 You arrived at UC Berkeley in 1992 with training as both a chemical engineer and a biologist What did you hope to do
2 Why hadnt anybody tried to engineer cells that way before
3 How did you get involved in your antimalaria project
Jay Keisling biography adapted fromZimmer C (2006) Scientist of the Year Jay Keasling Discovermagazinecom Retrieved from
httpdiscovermagazinecom2006deccover
copy 2009 Yu-Tzu Debbie Liu 9
See responses to these questions atZimmer C (2006) Scientist of the Year Jay Keasling Discovermagazinecom Retrieved from
httpdiscovermagazinecom2006deccover
Interview content removed due to copyright restrictions
Interview content removed due to copyright restrictions
Interview content removed due to copyright restrictions
Lesson Plan Day 3 Materials
Designing a New Microbe worksheet Organism cards Student notebooks or journals
Prep Step Review lesson plan background information and understanding goals Photocopy Designing a New Microbe worksheet (p 28) Cut out organism cards (each group of 3-4 students will have a set of cards) (p29)
Explore Step 1 Designing a New Microbe Introduce todayrsquos activity by saying ldquoYou will be simulating how synthetic biologists think mechanistically by doing an the activity that is actually modeled after a real experiment done by scientists in 2007rdquo Divide students into groups of 3 or 4 Each group receives a set of organism cards Each student receives a Designing a New Microbe worksheet Remind students that proteins (or enzymes) are molecules inside cells that convert one molecule into another (eg the make-believe molecule How is converted to the molecule Home by Protein T in bacteria) Following the directions of the handout have students create a kind of assembly line that integrate proteins from different organisms into a microbe that uses water and starch (inputs) to ultimately produce hydrogen (output)
Possible answers to Designing a New Microbe
There are two possible pathways that can lead to hydrogen production
1 Starch amp water Protein G Protein P Protein D Protein R Protein T Protein F Protein H Hydrogen
2 Starch amp water Protein G Protein P Protein D Protein H Hydrogen
Guide students along by encouraging students who have already figured out how to attempt the problem to reveal and share with the class how they are thinking through the problem Stop students periodically to ask ldquoHow are you thinking through this problem What is your goal and how is your thinking helping you reach that goalrdquo Students may find either working sequentially forward or backward to fill in the worksheet to be easier
Note to teachers The hydrogen production pathway from starch and water is a shorten version of the actual 2007 experiment for learning purposes The organism types and molecule names are true to the experiment Protein names are made up for simplicity
copy 2009 Yu-Tzu Debbie Liu 10
Step 2 Discuss studentsrsquo findings Have students tell you what they found as you write their findings on the board Students may have discovered by now that there are two paths that lead to hydrogen production Students might recall that Jay Keasling have done something similar by making an antimalarial drug from sugar using synthetic biology Students may have also discovered that no proteins from the mouse organism were used for the design of their new microbe Ask students ldquowhat do you think is the purpose of having a mouse organism when we didnrsquot need itrdquo Help students understand how in reality scientists have hundreds of organisms to choose from some of which are irrelevant to their work In fact a common skill that scientists share is being about to identify and pull together important and relevant information The activity allows students to discover that synthetic biology is a very mind-blowing field accomplishing things that some people never thought was possible Students will come to appreciate how seemingly impossible feats can be possible especially when scientists are thinking creatively By thinking and working mechanistically scientists have more freedom then before in designing and creating novel organisms for real-world applications
Review Extend and Apply Step 3 How do you think mechanistically Ask students to reflect on their experience with Scratch and how they might have engaged in mechanistic thinking in their own work Helps students make the connection that they themselves have been engaging in mechanistic thinking while working on their own Scratch projects The Scratch grammar is designed so that users are presented with a versatile collection of graphical programming blocks that they can be snapped together to create programs much like synthetic biology Connectors on the blocks suggest how they should be put together so that over the process of tinkering with these blocks the emerging structure can give rise to new ideas and direction to the project Not only does snapping together complimentary blocks provide an easy way into learning programming but the idea of modularization as a problem-solving and design strategy is directly relevant to mechanistic thinking Go on to discuss how they can apply scientistsrsquo patterns of thinking to our own thinking in science class and daily life
copy 2009 Yu-Tzu Debbie Liu 11
Name___________________________ Date ____________
Designing a New Microbe
Task Gas prices have reached its all time high Thus scientists are trying to think of ways to produce alternative fuels such as hydrogen gas in a much cheaper and quicker way You are a scientist and you are familiar with six different organisms Based on what you know can you come up with a way to generate hydrogen from starch and water by designing a microbe that borrows different mechanismsproteins from different cells Fill in the blanks with protein names and the organism that the protein was taken from
Materials Each team has a set of cards each card symbolizing a different organism On the card you will see the name of the organism a picture of the organism and proteins that is unique to them Proteins (or enzymes) convert one molecule into another
Starch amp Water Protein borrowed Protein borrowed
Input Organism Organism
Protein borrowed $ Protein borrowed $ Protein borrowed Organism Organism Organism
Protein borrowed Protein borrowed Protein borrowed Hydrogen Organism Organism Organism Output
Experiment adapted from Zhang YH Evans BR Mielenz JR Hopkins RC Adams MW (2007) High-yield hydrogen production from
starch and water by a synthetic enzymatic pathway PLoS ONE 5 e456
copy 2009 Yu-Tzu Debbie Liu 12
Organism Cards (one set)
Teachers Please make as many copies as the number of groups of students Cut the cards out and shuffle before handing to students
Source NIH
Bacteria
Rabbitbull Protein T uses [X5P] to make [S7P]
Photo US Fish and Wildlife Service bull Protein F uses [S7P] to make [NADPH] bull Protein G uses starch and water to make [G-1-P] bull Protein P uses [G-1-P] to make [G-6-P]
Yeast
Public domain image (Source Wikimedia Commons)
bull Protein D uses [G-6-P] to make [NADPH] and [R5P]
Public domain image (Source Wikimedia Commons) Spinach
bull Protein R uses [R5P] to make [X5P]
Experiment adapted from
Archea Courtesy of Angels Tapias (License CC BY)
bull Protein H uses [NADPH] to make Hydrogen
Source NIH Mouse
bull Protein X uses [T8P] to make Hydrogen
Zhang YH Evans BR Mielenz JR Hopkins RC Adams MW (2007) High-yield hydrogen production from starch and water by a synthetic enzymatic pathway PLoS ONE 5 e456
copy 2009 Yu-Tzu Debbie Liu 13
MIT OpenCourseWarehttpocwmitedu
MAS714J STS445J Technologies for Creative Learning Fall 2009
For information about citing these materials or our Terms of Use visit httpocwmiteduterms
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$$amp()+-- I
Photo courtesy httpsyntheticbiologyorg
Table of Contents
How are scientists thinking mechanistically in the 21st centuryhelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip1
Lesson 1 Introduction to Scratchhelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip5
Scratch Resources (not provided)helliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellipX
Lesson 2 Case Study of Jay Keaslinghelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip6
Case Study of Jay Keaslinghelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip8
Lesson 3 Mechanistic Thinkinghelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip10
Designing a New Microbehelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip12
Organism Cardshelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip13
copy 2009 Yu-Tzu Debbie Liu
Photo courtesy httpsyntheticbiologyorg
How are scientists thinkingmechanistically in the 21st century
Understanding Goals The rapid advancement of technology and the accumulation of information are changing
the patterns of scientific thinking and research in the 21st century Designing and creating novel organisms by combining various biological components
from different cells is one way scientists think mechanistically in the 21st century Designing and creating Scratch projects using graphical programming blocks is one way
students can display mechanistic thinking Identifying characteristics of successful scientist and their thinking patterns help us
become better (science) students by applying these skills to our own learning
Background Information Beyond the Scientific Method The scientific method has been commonly taught in science classrooms and textbooks as the only correct way to conduct scientific investigations This leaves students with the impression that all of science proceeds in much the same way Unfortunately this view is not entirely accurate Perhaps some scientists might conduct their work in this manner but rarely do they use it in the stereotyped step-by-step way that schools tend to teach itmdashdespite the fact that scientists report their work in this way in journals In fact scientists throughout history conduct their research in a variety of ways The exact approach a scientist uses depends on the individual doing the investigation as well as the particular question or problem being studied Furthermore scientists often engage in thinking patterns that are specific to its particular socio-cultural context 21st Century Scientific Thinking Skills With the explosion of advancements in scientific knowledge and technology at the turn of the century scientists at the cutting edge of research must adapt to new ways of interacting with their work Five prominent scientific thinking patterns of the 21st century are systems thinking mechanistic thinking interdisciplinary thinking quantitative thinking and distributed thinking1 In this lesson students will explore what mechanistic thinking Mechanistic Thinking It is a way of thinking that has a mechanical or engineering undertone This is shown through scientistsrsquo modular synthetic and purpose-driven approach towards their research problems Due to recent developments in new technologies and knowledge scientists are able to manipulate biology more directly allowing them to engineer and create novel biological systems for practical applications
1 Liu Y-T D amp Grotzer T A (2009) Looking forward Teaching the nature of the science of today and tomorrow In I M Saleh amp M S Khine (Eds) Fostering scientific habits of mind Pedagogical knowledge and best practices in science education (pp 9-36) Rotterdam Sense Publishers
copy 2009 Yu-Tzu Debbie Liu 1
What is Synthetic Biology The thinking involved in the field of synthetic biology is the best examples of mechanistic thinking With the rapidly emerging field of synthetic biology blurring the lines of biology and engineering scientists are no longer limited to working with organisms that naturally exist in the world Scientists often think synthetically by re-designing and constructing new organisms for practical and novel applications
Synthetic biology is an extension of genetic engineering Some even describe it as a more sophisticated version of genetic engineering taking into account a broader rational design perspective2 The engineering influence seeks out the simplicity in biological systems and brings standardization and modular design principles to biology
Synthetic biologists can use interchangeable parts from natural biology to assemble systems that function in new ways never existing before in living systems hence synthetic Modular circuit components (eg metabolic enzymes or fluorescent output genes) that are well characterized and can act independently of other cellular processes are used to build synthetic biological circuits Much like the ease of using LEGO bricksmdashstandardized bricks that can attach to any other partmdashsynthetic biology starts from the use of standardized biological building blocks The goal of synthetic biology is to both better understand how organisms function at the DNA protein and cell level by creating artificial biological systems and to solve important real-world problems the latter having caught the attention of scientists politicians and entrepreneurs Promising fields of application include energy environmental monitoring and remediation biotech and pharmaceuticals and materials fabrication
As pointed out in the detailed case study of Jay Keasling (one of the pioneers of synthetic biology) another key difference between synthetic biology and genetic engineering is the complexity of products or task the engineered organism can produce and accomplish Genetic engineering is typically limited to having microbes produce small proteins (eg insulin growth hormones) by simply inserting a single gene from a different organism into a microbe However with synthetic biology a complex interaction of several genes can be produced in a specified sequence much like what goes on in a chemical plant petroleum goes in and after a whole chain of reactions plastic comes out Scratch Scratch (httpscratchmitedu) is a programming language for young people (ages 8 and up) that makes it easy to create interactive projects (eg stories animations games simulations music and art) that can be shared on the Scratch website It is highly conducive to learning and teaching 21st century scientific thinking skills The Scratch grammar is designed so that users are presented with a versatile collection of graphical programming blocks that they can be snapped together to create programs much like LEGO bricks (and synthetic biology) Connectors on the blocks suggest how they should be put together so that over the process of tinkering with these blocks the emerging structure can give rise to new ideas and direction to the project Not only does snapping together complimentary blocks provide an easy way into learning programming but the idea of modularization as a problem-solving and design strategy is directly relevant to mechanistic thinking
2 Salisbury MW (2006) Get Ready for Synthetic Biology Genome Technology Magazine Retrieved from httpwwwgenome-technologycom
copy 2009 Yu-Tzu Debbie Liu 2
In this lesson Scratch is used to have students experience thinking mechanistically in their own work And since programming involves the creation of external representations of the problem-solving process Scratch provides students with opportunities of reflecting on their own thinking Lesson Layout These three lessons (one lesson per day) are designed to help students 1) understand how modern scientists think mechanistically 2) practice thinking mechanistically by simulating how synthetic biologists think in the field and 3) recognize mechanistic thinking even when it is not in the context of science as in their own work via Scratch Lesson 1 Designed to familiarize students with the Scratch programming language so that they can create projects on it At this point Scratch is presented simply as a medium for expressing what they have learned much like posters Powerpoint presentations and paper write-ups Lesson 2 Designed to expose students to the creative field of synthetic biology as a means to illustrate how scientists think mechanistically in the field This is done by a case study of Jay Keasling one of the pioneers of synthetic biology By analyzing how a modern scientist work and think students are provided with a broader view of scientific inquiry and the nature of scientific thinking Students will be asked to demonstrate their understanding of what they have learned so far by creating a Scratch project This allows students to work more closely and creatively with Scratch It also acts as a quick formative assessment for teachers of studentsrsquo learning thus far However the real goal of this exercise is to have students engage in mechanistic thinking in their own work which they may not recognize as it is not in the direct context of science This will be revealed in lesson 3 Lesson 3 Designed to have students practice thinking mechanistically by simulating how synthetic biologists think in the field via the Designing a New Microbe activity adapted from an actual experiment conducted in 20073 This activity presents students with a problem (need for hydrogen gas as alternative fuel) and asks students to design a microbe that can use starch and water to make hydrogen gas Students are given a set of organism cards to work with each card symbolizing a different type of organism (bacteria rabbit yeast archea spinach and mouse) Proteins (molecules that can convert one molecule into another) that are unique to each organism are listed on the card Studentsrsquo engineered microbe will essentially have different proteins from different organisms placed in a certain sequence to end up with a final product of hydrogen gas Students are given the Designing a New Microbe worksheet to help them visualize the problem better and reduce their cognitive loads (ie amount of information they need to carry in their heads) The activity allows students to discover that synthetic biology is a very mind-blowing field accomplishing things that some people never thought was possible Students will come to appreciate how seemingly impossible feats can be possible especially when scientists are thinking creatively By thinking and working mechanistically scientists have more freedom then before in designing and creating novel organisms for real-world applications
3 Zhang YH Evans BR Mielenz JR Hopkins RC Adams MW (2007) High-yield hydrogen production from starch and water by a synthetic enzymatic pathway PLoS ONE 5 e456
copy 2009 Yu-Tzu Debbie Liu 3
After the activity when students have grasped a much deeper understanding of what mechanistic thinking looks like in practice students are asked to reflect on their experience with Scratch The goal is to have students make the connection that they themselves have been engaging in mechanistic thinking while working on their own Scratch projects This reflective exercise encourages students to transfer their understanding of mechanistic thinking across different domains Students will also gain an appreciation of how studying trends in scientistsrsquo way of thinking can help them in their own thinking Lesson Placement These lessons can be used at the beginning of the school year when the scientific method is usually being presented Alternatively this lesson can be infused during the school year as students learn more about genetic engineering or creative thinking These lessons follow a constructivist approach to learning encouraging students to discover the meaning of mechanistic thinking through their exploration of a case study simulating how synthetic biologists think and making connections to their own work in Scratch Students are always encouraged to formulate their own ideas and connections before being presented with any information
copy 2009 Yu-Tzu Debbie Liu 4
Lesson Plan Day 1 Materials
Computers with Scratch installed Scratch Resources
Prep Step Review lesson plan background information and understanding goals Obtain computers with Scratch installed for students to work on Make copies of Scratch Resources (not provided)
Explore Step 1 Introduction to lesson Introduce the lesson by giving students a sense of what they will be doing and where they are headed by telling students ldquoThis will be a three-day lesson where we will be exploring how scientists think and more specifically what mechanistic thinking looks like in practice In this process we will also be learning Scratch We will tie everything together at the end of the third dayrdquo Step 2 Playing with Scratch Depending on the level of your students and any future goals you wish to achieve with Scratch structure the class so that students are comfortable navigating around the Scratch environment and are able to get started on their own Scratch project by the end of the class Please provide students with any Scratch resources you see fit Check out the ScratchEds resource search (httpscratchedmediamiteduresourcessearch) for more info Some good examples found in ScratchEd of Scratch lesson plans (video tutorials PowerPoints and worksheets) include
bull Having Fun with Computer Programming and Games (httpwwwleroieeducationoutreachsecondlevelscratchlessonplans)
bull A TeachNetUK Project 6 Lessons on Getting Started with Scratch (httpwwwteachnet-ukorguk200720ProjectsICT-ScratchScratchpages8_schemeofworkhtml)
bull Scratch Lessons Shall We Learn Scratch Programming for Tweens (httpwwwshallwelearncomscratchprogrammingforkidscategory)
bull Designing Animations and GamesmdashA Creative Introduction to Programming (httpwwwcsuni-potsdamde~romeikeUEWettbewerbindex-englishhtm)
Make sure to also introduce students to the Scratch online community and let them know that they can download the source code of any project to help them see how others are using the Scratch programming language to create projects
Review Extend and Apply Step 3 Scratch Assignment End the day by informing students that they will apply what they have learned today to create a mini-Scratch project for an assignment after the next dayrsquos lesson Emphasize to students that the goal is not to create a complex programming project but to use Scratch creatively as a medium for creative expressing not matter how simple the project is Encourage students to play with Scratch on their own time and make it clear that you highly encourage them to borrow adapt and build upon the ideas and projects of others (this is not considered cheating)
copy 2009 Yu-Tzu Debbie Liu 5
Lesson Plan Day 2 Materials
21st century scientist case study of Jay Keasling Student notebooks or journals
Prep Step Review lesson plan background information and understanding goals Make copies of 21st century scientist case study of Jay Keasling (p 8)
Explore Step 1 What is scientific thinking Ask students to describe what they think is scientific thinking Collect a representative list of studentsrsquo thoughts on the board Ask students to explain or expound on the meaning behind what they are saying After reviewing the list ask them ldquo Do you think all scientists come to their discoveries in the same wayrdquo ldquoDo scientists display all these characteristics at all timesrdquo It is important to point out to students that scientists have various methods going about their experimentation and work and depending on the type of work they are doing scientists donrsquot always share the same methods Furthermore scientists engage in thinking patterns that are specific to its particular socio-cultural context and one of which is mechanistic thinking Engage in a discussion with students on how might the explosion of advancements in scientific knowledge and technology at the turn of the century change the way scientists at the cutting edge of research interact with their work
Step 2 Analyze case study of a 21st century scientist Let students know that they will be learning about the field of synthetic biology as a means to illustrate how modern scientists work and think Specifically they will be studying Jay Keasling one of the pioneers of synthetic biology Hand out the case study on Jay Keasling Have students work in groups of 3-4 students to identify any patterns of thinking that the scientist displays Make sure to ask students to specifically identify what part of the case study justifies their claims Have students write the class findings in their journalsnotebooks
Possible findings from case analysis Jay Keasling
Keasling is a pioneer of synthetic biologymdasha field that designs and constructs new organisms for useful purposes He is most known for creating a microbe that produces a drug to treat malaria (making drugs from bugs) Some of his characteristics as a scientist include
bull Creative and imaginative wanted to invent new tools that can turn cells into chemical plants take in something very simple and spits out something complicated and valuable coming up with other applications of synthetic biology (use microbes to break down pesticides make biodegradable plastics create fuels from plants)
bull Critical thinking thought about how to design and create microbes to produce artemisinin much quicker and cheaper how to integrate genes from different species into a microbe to fabricate the drug
copy 2009 Yu-Tzu Debbie Liu 6
bull Seek and integrate information integrated methods and concepts from engineering and biology leading to synthetic biology
bull Supported with significant resources did research at universities and received grant money
bull Practical-minded microbes will churn out anti-malarial drug for a fraction of its current cost making it accessible to much more of the world these microbes could save millions of lives
bull Strong disciplinary understanding studied biology and chemical engineering extensively leading to his PhD and professor position at UC Berkeley
Step 3 What is mechanistic thinking Introduce students to the idea of mechanistic thinking as a prominent thinking pattern in the 21st
century
Mechanistic Thinking
Mechanistic thinking is a way of thinking that has a mechanical or engineering undertone This is shown through scientistsrsquo regular use of mechanical analogies to conceptualize their work and their modular synthetic and purpose-driven approach towards their research problems The display of mechanistic thinking by scientists appears to be a result of the merging of biology and engineering practices that is increasingly observed in 21st century biology as compared to a time when most of biologymdashtraditionally known for its pure basic researchmdashremain clearly demarcated from engineeringmdasha purely applied research field A mechanistic way of thinking has come to the forefront of 21st century science because of recent developments in new technologies and knowledge that enable scientists to manipulate the object or organism they are working with more directly allowing them to engineer and create novel biological systems for practical applications
Let students know that the work synthetic biologists do often require them to think mechanistically Now that students are given a definition of mechanistic thinking have students revisit their case study analysis and explore how synthetic biologists might think mechanistically
Review Extend and Apply
Step 4 Scratch Assignment Ask students to create a mini-Scratch project to demonstrate what they have learned so far (the project does not have to be all inclusive students can choose to focus on just one thing they learned either about scientific thinking mechanistic thinking or synthetic biology) Emphasize to students that the goal is not to create a complex programming project but to use Scratch creatively as a medium for creative expressing not matter how simple the project is Encourage students to work with partners and collaborate by borrowing adapting or building upon the ideas and projects of others (this is not considered cheating)
copy 2009 Yu-Tzu Debbie Liu 7
Detailed Case Study Jay Keasling
(1964 ndash present)
Best known for pioneering the new field of synthetic biology which designs and constructs new organisms for useful purposes He is also most known for creating a microbe that produces a drug to treat malaria (making drugs from bugs)
Jay Keasling was raised on a farm and spent his childhood exploring the practical side of biology chemistry and engineering This background eventually led him to work in the rapidly growing field that uses living organisms like bacteria for various practical purposes such as food processing agriculture and medicine
In the early 1980s genetic engineering became popular because you can ldquoconvincerdquo microbes to produce insulin growth hormones and other valuable proteins by simply inserting a single gene from a different organism into bacteria However Keasling believed that genetic engineering isnrsquot harnessing the full power of these cells The production of molecules isnt always so simple it requires a complex interaction of several genes (not just one) being produced in a certain sequence So Keasling wanted to invent the tools that would allow him to create these kinds of genetic assembly lines Thus what goes on in a cell is a lot like what goes on in a chemical plant petroleum goes in and after a whole chain of reactions plastic comes out
Keasling went to college studying biology and chemical engineering extensively and got his PhD in 1991 He is now a professor at the University of California at Berkeley He spent his first 10 years at UC Berkeley building the new tools he would need to turn cells into chemical plants He also invented powerful chemical switches (like a light switch) that allowed him to control when he wanted to ldquoturn onrdquo and ldquoturn offrdquo protein production in cells This way of borrowing techniques from engineering and figuring out how to manipulate microbes came to be call synthetic biology
After years of perfecting his biological tool kit Keasling wanted to find a real-world use for it In 2002 he learned of the dire need for artemisinin a compound derived from the sweet wormwood plant which is 90 percent effective against the parasite that causes malaria and has few side effects (malaria kills some 3 million people a year) However extracting the drug from sweet wormwood is a slow and expensive process Keasling figured he could design and create microbes to produce artemisinin much quicker and cheaper Rather than wait months for sweet wormwood to grow on farms Keasling wanted to create it simply by pouring sugar in a tank full of microbes that can use the sugar to make the drug via a chemical pathway he has designedmdashhe wanted to integrate genes from different species into a microbe to fabricate the drug for malaria
copy 2009 Yu-Tzu Debbie Liu 8
In 2006 Keaslings team (comprised of graduate students post-docs and research assistants) published their success of the production of artemisinin It is expected to lower the cost of artemisinin production from a dollar per gram to just 10 cents He was awarded a $43 million grant from the Bill and Melinda Gates Foundation and awarded DISCOVER magazinersquos first ever Scientist of the Year Award
Fighting malaria is just one part of Keaslings larger agenda to explore the potential of synthetic biology In his laboratory students are engineering microbes to break down pesticides make biodegradable plastics and create ethanol and other fuels from plants
Excerpts of i interview w Jay Keasling
1 You arrived at UC Berkeley in 1992 with training as both a chemical engineer and a biologist What did you hope to do
2 Why hadnt anybody tried to engineer cells that way before
3 How did you get involved in your antimalaria project
Jay Keisling biography adapted fromZimmer C (2006) Scientist of the Year Jay Keasling Discovermagazinecom Retrieved from
httpdiscovermagazinecom2006deccover
copy 2009 Yu-Tzu Debbie Liu 9
See responses to these questions atZimmer C (2006) Scientist of the Year Jay Keasling Discovermagazinecom Retrieved from
httpdiscovermagazinecom2006deccover
Interview content removed due to copyright restrictions
Interview content removed due to copyright restrictions
Interview content removed due to copyright restrictions
Lesson Plan Day 3 Materials
Designing a New Microbe worksheet Organism cards Student notebooks or journals
Prep Step Review lesson plan background information and understanding goals Photocopy Designing a New Microbe worksheet (p 28) Cut out organism cards (each group of 3-4 students will have a set of cards) (p29)
Explore Step 1 Designing a New Microbe Introduce todayrsquos activity by saying ldquoYou will be simulating how synthetic biologists think mechanistically by doing an the activity that is actually modeled after a real experiment done by scientists in 2007rdquo Divide students into groups of 3 or 4 Each group receives a set of organism cards Each student receives a Designing a New Microbe worksheet Remind students that proteins (or enzymes) are molecules inside cells that convert one molecule into another (eg the make-believe molecule How is converted to the molecule Home by Protein T in bacteria) Following the directions of the handout have students create a kind of assembly line that integrate proteins from different organisms into a microbe that uses water and starch (inputs) to ultimately produce hydrogen (output)
Possible answers to Designing a New Microbe
There are two possible pathways that can lead to hydrogen production
1 Starch amp water Protein G Protein P Protein D Protein R Protein T Protein F Protein H Hydrogen
2 Starch amp water Protein G Protein P Protein D Protein H Hydrogen
Guide students along by encouraging students who have already figured out how to attempt the problem to reveal and share with the class how they are thinking through the problem Stop students periodically to ask ldquoHow are you thinking through this problem What is your goal and how is your thinking helping you reach that goalrdquo Students may find either working sequentially forward or backward to fill in the worksheet to be easier
Note to teachers The hydrogen production pathway from starch and water is a shorten version of the actual 2007 experiment for learning purposes The organism types and molecule names are true to the experiment Protein names are made up for simplicity
copy 2009 Yu-Tzu Debbie Liu 10
Step 2 Discuss studentsrsquo findings Have students tell you what they found as you write their findings on the board Students may have discovered by now that there are two paths that lead to hydrogen production Students might recall that Jay Keasling have done something similar by making an antimalarial drug from sugar using synthetic biology Students may have also discovered that no proteins from the mouse organism were used for the design of their new microbe Ask students ldquowhat do you think is the purpose of having a mouse organism when we didnrsquot need itrdquo Help students understand how in reality scientists have hundreds of organisms to choose from some of which are irrelevant to their work In fact a common skill that scientists share is being about to identify and pull together important and relevant information The activity allows students to discover that synthetic biology is a very mind-blowing field accomplishing things that some people never thought was possible Students will come to appreciate how seemingly impossible feats can be possible especially when scientists are thinking creatively By thinking and working mechanistically scientists have more freedom then before in designing and creating novel organisms for real-world applications
Review Extend and Apply Step 3 How do you think mechanistically Ask students to reflect on their experience with Scratch and how they might have engaged in mechanistic thinking in their own work Helps students make the connection that they themselves have been engaging in mechanistic thinking while working on their own Scratch projects The Scratch grammar is designed so that users are presented with a versatile collection of graphical programming blocks that they can be snapped together to create programs much like synthetic biology Connectors on the blocks suggest how they should be put together so that over the process of tinkering with these blocks the emerging structure can give rise to new ideas and direction to the project Not only does snapping together complimentary blocks provide an easy way into learning programming but the idea of modularization as a problem-solving and design strategy is directly relevant to mechanistic thinking Go on to discuss how they can apply scientistsrsquo patterns of thinking to our own thinking in science class and daily life
copy 2009 Yu-Tzu Debbie Liu 11
Name___________________________ Date ____________
Designing a New Microbe
Task Gas prices have reached its all time high Thus scientists are trying to think of ways to produce alternative fuels such as hydrogen gas in a much cheaper and quicker way You are a scientist and you are familiar with six different organisms Based on what you know can you come up with a way to generate hydrogen from starch and water by designing a microbe that borrows different mechanismsproteins from different cells Fill in the blanks with protein names and the organism that the protein was taken from
Materials Each team has a set of cards each card symbolizing a different organism On the card you will see the name of the organism a picture of the organism and proteins that is unique to them Proteins (or enzymes) convert one molecule into another
Starch amp Water Protein borrowed Protein borrowed
Input Organism Organism
Protein borrowed $ Protein borrowed $ Protein borrowed Organism Organism Organism
Protein borrowed Protein borrowed Protein borrowed Hydrogen Organism Organism Organism Output
Experiment adapted from Zhang YH Evans BR Mielenz JR Hopkins RC Adams MW (2007) High-yield hydrogen production from
starch and water by a synthetic enzymatic pathway PLoS ONE 5 e456
copy 2009 Yu-Tzu Debbie Liu 12
Organism Cards (one set)
Teachers Please make as many copies as the number of groups of students Cut the cards out and shuffle before handing to students
Source NIH
Bacteria
Rabbitbull Protein T uses [X5P] to make [S7P]
Photo US Fish and Wildlife Service bull Protein F uses [S7P] to make [NADPH] bull Protein G uses starch and water to make [G-1-P] bull Protein P uses [G-1-P] to make [G-6-P]
Yeast
Public domain image (Source Wikimedia Commons)
bull Protein D uses [G-6-P] to make [NADPH] and [R5P]
Public domain image (Source Wikimedia Commons) Spinach
bull Protein R uses [R5P] to make [X5P]
Experiment adapted from
Archea Courtesy of Angels Tapias (License CC BY)
bull Protein H uses [NADPH] to make Hydrogen
Source NIH Mouse
bull Protein X uses [T8P] to make Hydrogen
Zhang YH Evans BR Mielenz JR Hopkins RC Adams MW (2007) High-yield hydrogen production from starch and water by a synthetic enzymatic pathway PLoS ONE 5 e456
copy 2009 Yu-Tzu Debbie Liu 13
MIT OpenCourseWarehttpocwmitedu
MAS714J STS445J Technologies for Creative Learning Fall 2009
For information about citing these materials or our Terms of Use visit httpocwmiteduterms
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1030X9MkSgt0PJTBS7)B89=C9BCC9gt88
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6U0ONk7
$$amp()+-- I
Photo courtesy httpsyntheticbiologyorg
Table of Contents
How are scientists thinking mechanistically in the 21st centuryhelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip1
Lesson 1 Introduction to Scratchhelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip5
Scratch Resources (not provided)helliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellipX
Lesson 2 Case Study of Jay Keaslinghelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip6
Case Study of Jay Keaslinghelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip8
Lesson 3 Mechanistic Thinkinghelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip10
Designing a New Microbehelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip12
Organism Cardshelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip13
copy 2009 Yu-Tzu Debbie Liu
Photo courtesy httpsyntheticbiologyorg
How are scientists thinkingmechanistically in the 21st century
Understanding Goals The rapid advancement of technology and the accumulation of information are changing
the patterns of scientific thinking and research in the 21st century Designing and creating novel organisms by combining various biological components
from different cells is one way scientists think mechanistically in the 21st century Designing and creating Scratch projects using graphical programming blocks is one way
students can display mechanistic thinking Identifying characteristics of successful scientist and their thinking patterns help us
become better (science) students by applying these skills to our own learning
Background Information Beyond the Scientific Method The scientific method has been commonly taught in science classrooms and textbooks as the only correct way to conduct scientific investigations This leaves students with the impression that all of science proceeds in much the same way Unfortunately this view is not entirely accurate Perhaps some scientists might conduct their work in this manner but rarely do they use it in the stereotyped step-by-step way that schools tend to teach itmdashdespite the fact that scientists report their work in this way in journals In fact scientists throughout history conduct their research in a variety of ways The exact approach a scientist uses depends on the individual doing the investigation as well as the particular question or problem being studied Furthermore scientists often engage in thinking patterns that are specific to its particular socio-cultural context 21st Century Scientific Thinking Skills With the explosion of advancements in scientific knowledge and technology at the turn of the century scientists at the cutting edge of research must adapt to new ways of interacting with their work Five prominent scientific thinking patterns of the 21st century are systems thinking mechanistic thinking interdisciplinary thinking quantitative thinking and distributed thinking1 In this lesson students will explore what mechanistic thinking Mechanistic Thinking It is a way of thinking that has a mechanical or engineering undertone This is shown through scientistsrsquo modular synthetic and purpose-driven approach towards their research problems Due to recent developments in new technologies and knowledge scientists are able to manipulate biology more directly allowing them to engineer and create novel biological systems for practical applications
1 Liu Y-T D amp Grotzer T A (2009) Looking forward Teaching the nature of the science of today and tomorrow In I M Saleh amp M S Khine (Eds) Fostering scientific habits of mind Pedagogical knowledge and best practices in science education (pp 9-36) Rotterdam Sense Publishers
copy 2009 Yu-Tzu Debbie Liu 1
What is Synthetic Biology The thinking involved in the field of synthetic biology is the best examples of mechanistic thinking With the rapidly emerging field of synthetic biology blurring the lines of biology and engineering scientists are no longer limited to working with organisms that naturally exist in the world Scientists often think synthetically by re-designing and constructing new organisms for practical and novel applications
Synthetic biology is an extension of genetic engineering Some even describe it as a more sophisticated version of genetic engineering taking into account a broader rational design perspective2 The engineering influence seeks out the simplicity in biological systems and brings standardization and modular design principles to biology
Synthetic biologists can use interchangeable parts from natural biology to assemble systems that function in new ways never existing before in living systems hence synthetic Modular circuit components (eg metabolic enzymes or fluorescent output genes) that are well characterized and can act independently of other cellular processes are used to build synthetic biological circuits Much like the ease of using LEGO bricksmdashstandardized bricks that can attach to any other partmdashsynthetic biology starts from the use of standardized biological building blocks The goal of synthetic biology is to both better understand how organisms function at the DNA protein and cell level by creating artificial biological systems and to solve important real-world problems the latter having caught the attention of scientists politicians and entrepreneurs Promising fields of application include energy environmental monitoring and remediation biotech and pharmaceuticals and materials fabrication
As pointed out in the detailed case study of Jay Keasling (one of the pioneers of synthetic biology) another key difference between synthetic biology and genetic engineering is the complexity of products or task the engineered organism can produce and accomplish Genetic engineering is typically limited to having microbes produce small proteins (eg insulin growth hormones) by simply inserting a single gene from a different organism into a microbe However with synthetic biology a complex interaction of several genes can be produced in a specified sequence much like what goes on in a chemical plant petroleum goes in and after a whole chain of reactions plastic comes out Scratch Scratch (httpscratchmitedu) is a programming language for young people (ages 8 and up) that makes it easy to create interactive projects (eg stories animations games simulations music and art) that can be shared on the Scratch website It is highly conducive to learning and teaching 21st century scientific thinking skills The Scratch grammar is designed so that users are presented with a versatile collection of graphical programming blocks that they can be snapped together to create programs much like LEGO bricks (and synthetic biology) Connectors on the blocks suggest how they should be put together so that over the process of tinkering with these blocks the emerging structure can give rise to new ideas and direction to the project Not only does snapping together complimentary blocks provide an easy way into learning programming but the idea of modularization as a problem-solving and design strategy is directly relevant to mechanistic thinking
2 Salisbury MW (2006) Get Ready for Synthetic Biology Genome Technology Magazine Retrieved from httpwwwgenome-technologycom
copy 2009 Yu-Tzu Debbie Liu 2
In this lesson Scratch is used to have students experience thinking mechanistically in their own work And since programming involves the creation of external representations of the problem-solving process Scratch provides students with opportunities of reflecting on their own thinking Lesson Layout These three lessons (one lesson per day) are designed to help students 1) understand how modern scientists think mechanistically 2) practice thinking mechanistically by simulating how synthetic biologists think in the field and 3) recognize mechanistic thinking even when it is not in the context of science as in their own work via Scratch Lesson 1 Designed to familiarize students with the Scratch programming language so that they can create projects on it At this point Scratch is presented simply as a medium for expressing what they have learned much like posters Powerpoint presentations and paper write-ups Lesson 2 Designed to expose students to the creative field of synthetic biology as a means to illustrate how scientists think mechanistically in the field This is done by a case study of Jay Keasling one of the pioneers of synthetic biology By analyzing how a modern scientist work and think students are provided with a broader view of scientific inquiry and the nature of scientific thinking Students will be asked to demonstrate their understanding of what they have learned so far by creating a Scratch project This allows students to work more closely and creatively with Scratch It also acts as a quick formative assessment for teachers of studentsrsquo learning thus far However the real goal of this exercise is to have students engage in mechanistic thinking in their own work which they may not recognize as it is not in the direct context of science This will be revealed in lesson 3 Lesson 3 Designed to have students practice thinking mechanistically by simulating how synthetic biologists think in the field via the Designing a New Microbe activity adapted from an actual experiment conducted in 20073 This activity presents students with a problem (need for hydrogen gas as alternative fuel) and asks students to design a microbe that can use starch and water to make hydrogen gas Students are given a set of organism cards to work with each card symbolizing a different type of organism (bacteria rabbit yeast archea spinach and mouse) Proteins (molecules that can convert one molecule into another) that are unique to each organism are listed on the card Studentsrsquo engineered microbe will essentially have different proteins from different organisms placed in a certain sequence to end up with a final product of hydrogen gas Students are given the Designing a New Microbe worksheet to help them visualize the problem better and reduce their cognitive loads (ie amount of information they need to carry in their heads) The activity allows students to discover that synthetic biology is a very mind-blowing field accomplishing things that some people never thought was possible Students will come to appreciate how seemingly impossible feats can be possible especially when scientists are thinking creatively By thinking and working mechanistically scientists have more freedom then before in designing and creating novel organisms for real-world applications
3 Zhang YH Evans BR Mielenz JR Hopkins RC Adams MW (2007) High-yield hydrogen production from starch and water by a synthetic enzymatic pathway PLoS ONE 5 e456
copy 2009 Yu-Tzu Debbie Liu 3
After the activity when students have grasped a much deeper understanding of what mechanistic thinking looks like in practice students are asked to reflect on their experience with Scratch The goal is to have students make the connection that they themselves have been engaging in mechanistic thinking while working on their own Scratch projects This reflective exercise encourages students to transfer their understanding of mechanistic thinking across different domains Students will also gain an appreciation of how studying trends in scientistsrsquo way of thinking can help them in their own thinking Lesson Placement These lessons can be used at the beginning of the school year when the scientific method is usually being presented Alternatively this lesson can be infused during the school year as students learn more about genetic engineering or creative thinking These lessons follow a constructivist approach to learning encouraging students to discover the meaning of mechanistic thinking through their exploration of a case study simulating how synthetic biologists think and making connections to their own work in Scratch Students are always encouraged to formulate their own ideas and connections before being presented with any information
copy 2009 Yu-Tzu Debbie Liu 4
Lesson Plan Day 1 Materials
Computers with Scratch installed Scratch Resources
Prep Step Review lesson plan background information and understanding goals Obtain computers with Scratch installed for students to work on Make copies of Scratch Resources (not provided)
Explore Step 1 Introduction to lesson Introduce the lesson by giving students a sense of what they will be doing and where they are headed by telling students ldquoThis will be a three-day lesson where we will be exploring how scientists think and more specifically what mechanistic thinking looks like in practice In this process we will also be learning Scratch We will tie everything together at the end of the third dayrdquo Step 2 Playing with Scratch Depending on the level of your students and any future goals you wish to achieve with Scratch structure the class so that students are comfortable navigating around the Scratch environment and are able to get started on their own Scratch project by the end of the class Please provide students with any Scratch resources you see fit Check out the ScratchEds resource search (httpscratchedmediamiteduresourcessearch) for more info Some good examples found in ScratchEd of Scratch lesson plans (video tutorials PowerPoints and worksheets) include
bull Having Fun with Computer Programming and Games (httpwwwleroieeducationoutreachsecondlevelscratchlessonplans)
bull A TeachNetUK Project 6 Lessons on Getting Started with Scratch (httpwwwteachnet-ukorguk200720ProjectsICT-ScratchScratchpages8_schemeofworkhtml)
bull Scratch Lessons Shall We Learn Scratch Programming for Tweens (httpwwwshallwelearncomscratchprogrammingforkidscategory)
bull Designing Animations and GamesmdashA Creative Introduction to Programming (httpwwwcsuni-potsdamde~romeikeUEWettbewerbindex-englishhtm)
Make sure to also introduce students to the Scratch online community and let them know that they can download the source code of any project to help them see how others are using the Scratch programming language to create projects
Review Extend and Apply Step 3 Scratch Assignment End the day by informing students that they will apply what they have learned today to create a mini-Scratch project for an assignment after the next dayrsquos lesson Emphasize to students that the goal is not to create a complex programming project but to use Scratch creatively as a medium for creative expressing not matter how simple the project is Encourage students to play with Scratch on their own time and make it clear that you highly encourage them to borrow adapt and build upon the ideas and projects of others (this is not considered cheating)
copy 2009 Yu-Tzu Debbie Liu 5
Lesson Plan Day 2 Materials
21st century scientist case study of Jay Keasling Student notebooks or journals
Prep Step Review lesson plan background information and understanding goals Make copies of 21st century scientist case study of Jay Keasling (p 8)
Explore Step 1 What is scientific thinking Ask students to describe what they think is scientific thinking Collect a representative list of studentsrsquo thoughts on the board Ask students to explain or expound on the meaning behind what they are saying After reviewing the list ask them ldquo Do you think all scientists come to their discoveries in the same wayrdquo ldquoDo scientists display all these characteristics at all timesrdquo It is important to point out to students that scientists have various methods going about their experimentation and work and depending on the type of work they are doing scientists donrsquot always share the same methods Furthermore scientists engage in thinking patterns that are specific to its particular socio-cultural context and one of which is mechanistic thinking Engage in a discussion with students on how might the explosion of advancements in scientific knowledge and technology at the turn of the century change the way scientists at the cutting edge of research interact with their work
Step 2 Analyze case study of a 21st century scientist Let students know that they will be learning about the field of synthetic biology as a means to illustrate how modern scientists work and think Specifically they will be studying Jay Keasling one of the pioneers of synthetic biology Hand out the case study on Jay Keasling Have students work in groups of 3-4 students to identify any patterns of thinking that the scientist displays Make sure to ask students to specifically identify what part of the case study justifies their claims Have students write the class findings in their journalsnotebooks
Possible findings from case analysis Jay Keasling
Keasling is a pioneer of synthetic biologymdasha field that designs and constructs new organisms for useful purposes He is most known for creating a microbe that produces a drug to treat malaria (making drugs from bugs) Some of his characteristics as a scientist include
bull Creative and imaginative wanted to invent new tools that can turn cells into chemical plants take in something very simple and spits out something complicated and valuable coming up with other applications of synthetic biology (use microbes to break down pesticides make biodegradable plastics create fuels from plants)
bull Critical thinking thought about how to design and create microbes to produce artemisinin much quicker and cheaper how to integrate genes from different species into a microbe to fabricate the drug
copy 2009 Yu-Tzu Debbie Liu 6
bull Seek and integrate information integrated methods and concepts from engineering and biology leading to synthetic biology
bull Supported with significant resources did research at universities and received grant money
bull Practical-minded microbes will churn out anti-malarial drug for a fraction of its current cost making it accessible to much more of the world these microbes could save millions of lives
bull Strong disciplinary understanding studied biology and chemical engineering extensively leading to his PhD and professor position at UC Berkeley
Step 3 What is mechanistic thinking Introduce students to the idea of mechanistic thinking as a prominent thinking pattern in the 21st
century
Mechanistic Thinking
Mechanistic thinking is a way of thinking that has a mechanical or engineering undertone This is shown through scientistsrsquo regular use of mechanical analogies to conceptualize their work and their modular synthetic and purpose-driven approach towards their research problems The display of mechanistic thinking by scientists appears to be a result of the merging of biology and engineering practices that is increasingly observed in 21st century biology as compared to a time when most of biologymdashtraditionally known for its pure basic researchmdashremain clearly demarcated from engineeringmdasha purely applied research field A mechanistic way of thinking has come to the forefront of 21st century science because of recent developments in new technologies and knowledge that enable scientists to manipulate the object or organism they are working with more directly allowing them to engineer and create novel biological systems for practical applications
Let students know that the work synthetic biologists do often require them to think mechanistically Now that students are given a definition of mechanistic thinking have students revisit their case study analysis and explore how synthetic biologists might think mechanistically
Review Extend and Apply
Step 4 Scratch Assignment Ask students to create a mini-Scratch project to demonstrate what they have learned so far (the project does not have to be all inclusive students can choose to focus on just one thing they learned either about scientific thinking mechanistic thinking or synthetic biology) Emphasize to students that the goal is not to create a complex programming project but to use Scratch creatively as a medium for creative expressing not matter how simple the project is Encourage students to work with partners and collaborate by borrowing adapting or building upon the ideas and projects of others (this is not considered cheating)
copy 2009 Yu-Tzu Debbie Liu 7
Detailed Case Study Jay Keasling
(1964 ndash present)
Best known for pioneering the new field of synthetic biology which designs and constructs new organisms for useful purposes He is also most known for creating a microbe that produces a drug to treat malaria (making drugs from bugs)
Jay Keasling was raised on a farm and spent his childhood exploring the practical side of biology chemistry and engineering This background eventually led him to work in the rapidly growing field that uses living organisms like bacteria for various practical purposes such as food processing agriculture and medicine
In the early 1980s genetic engineering became popular because you can ldquoconvincerdquo microbes to produce insulin growth hormones and other valuable proteins by simply inserting a single gene from a different organism into bacteria However Keasling believed that genetic engineering isnrsquot harnessing the full power of these cells The production of molecules isnt always so simple it requires a complex interaction of several genes (not just one) being produced in a certain sequence So Keasling wanted to invent the tools that would allow him to create these kinds of genetic assembly lines Thus what goes on in a cell is a lot like what goes on in a chemical plant petroleum goes in and after a whole chain of reactions plastic comes out
Keasling went to college studying biology and chemical engineering extensively and got his PhD in 1991 He is now a professor at the University of California at Berkeley He spent his first 10 years at UC Berkeley building the new tools he would need to turn cells into chemical plants He also invented powerful chemical switches (like a light switch) that allowed him to control when he wanted to ldquoturn onrdquo and ldquoturn offrdquo protein production in cells This way of borrowing techniques from engineering and figuring out how to manipulate microbes came to be call synthetic biology
After years of perfecting his biological tool kit Keasling wanted to find a real-world use for it In 2002 he learned of the dire need for artemisinin a compound derived from the sweet wormwood plant which is 90 percent effective against the parasite that causes malaria and has few side effects (malaria kills some 3 million people a year) However extracting the drug from sweet wormwood is a slow and expensive process Keasling figured he could design and create microbes to produce artemisinin much quicker and cheaper Rather than wait months for sweet wormwood to grow on farms Keasling wanted to create it simply by pouring sugar in a tank full of microbes that can use the sugar to make the drug via a chemical pathway he has designedmdashhe wanted to integrate genes from different species into a microbe to fabricate the drug for malaria
copy 2009 Yu-Tzu Debbie Liu 8
In 2006 Keaslings team (comprised of graduate students post-docs and research assistants) published their success of the production of artemisinin It is expected to lower the cost of artemisinin production from a dollar per gram to just 10 cents He was awarded a $43 million grant from the Bill and Melinda Gates Foundation and awarded DISCOVER magazinersquos first ever Scientist of the Year Award
Fighting malaria is just one part of Keaslings larger agenda to explore the potential of synthetic biology In his laboratory students are engineering microbes to break down pesticides make biodegradable plastics and create ethanol and other fuels from plants
Excerpts of i interview w Jay Keasling
1 You arrived at UC Berkeley in 1992 with training as both a chemical engineer and a biologist What did you hope to do
2 Why hadnt anybody tried to engineer cells that way before
3 How did you get involved in your antimalaria project
Jay Keisling biography adapted fromZimmer C (2006) Scientist of the Year Jay Keasling Discovermagazinecom Retrieved from
httpdiscovermagazinecom2006deccover
copy 2009 Yu-Tzu Debbie Liu 9
See responses to these questions atZimmer C (2006) Scientist of the Year Jay Keasling Discovermagazinecom Retrieved from
httpdiscovermagazinecom2006deccover
Interview content removed due to copyright restrictions
Interview content removed due to copyright restrictions
Interview content removed due to copyright restrictions
Lesson Plan Day 3 Materials
Designing a New Microbe worksheet Organism cards Student notebooks or journals
Prep Step Review lesson plan background information and understanding goals Photocopy Designing a New Microbe worksheet (p 28) Cut out organism cards (each group of 3-4 students will have a set of cards) (p29)
Explore Step 1 Designing a New Microbe Introduce todayrsquos activity by saying ldquoYou will be simulating how synthetic biologists think mechanistically by doing an the activity that is actually modeled after a real experiment done by scientists in 2007rdquo Divide students into groups of 3 or 4 Each group receives a set of organism cards Each student receives a Designing a New Microbe worksheet Remind students that proteins (or enzymes) are molecules inside cells that convert one molecule into another (eg the make-believe molecule How is converted to the molecule Home by Protein T in bacteria) Following the directions of the handout have students create a kind of assembly line that integrate proteins from different organisms into a microbe that uses water and starch (inputs) to ultimately produce hydrogen (output)
Possible answers to Designing a New Microbe
There are two possible pathways that can lead to hydrogen production
1 Starch amp water Protein G Protein P Protein D Protein R Protein T Protein F Protein H Hydrogen
2 Starch amp water Protein G Protein P Protein D Protein H Hydrogen
Guide students along by encouraging students who have already figured out how to attempt the problem to reveal and share with the class how they are thinking through the problem Stop students periodically to ask ldquoHow are you thinking through this problem What is your goal and how is your thinking helping you reach that goalrdquo Students may find either working sequentially forward or backward to fill in the worksheet to be easier
Note to teachers The hydrogen production pathway from starch and water is a shorten version of the actual 2007 experiment for learning purposes The organism types and molecule names are true to the experiment Protein names are made up for simplicity
copy 2009 Yu-Tzu Debbie Liu 10
Step 2 Discuss studentsrsquo findings Have students tell you what they found as you write their findings on the board Students may have discovered by now that there are two paths that lead to hydrogen production Students might recall that Jay Keasling have done something similar by making an antimalarial drug from sugar using synthetic biology Students may have also discovered that no proteins from the mouse organism were used for the design of their new microbe Ask students ldquowhat do you think is the purpose of having a mouse organism when we didnrsquot need itrdquo Help students understand how in reality scientists have hundreds of organisms to choose from some of which are irrelevant to their work In fact a common skill that scientists share is being about to identify and pull together important and relevant information The activity allows students to discover that synthetic biology is a very mind-blowing field accomplishing things that some people never thought was possible Students will come to appreciate how seemingly impossible feats can be possible especially when scientists are thinking creatively By thinking and working mechanistically scientists have more freedom then before in designing and creating novel organisms for real-world applications
Review Extend and Apply Step 3 How do you think mechanistically Ask students to reflect on their experience with Scratch and how they might have engaged in mechanistic thinking in their own work Helps students make the connection that they themselves have been engaging in mechanistic thinking while working on their own Scratch projects The Scratch grammar is designed so that users are presented with a versatile collection of graphical programming blocks that they can be snapped together to create programs much like synthetic biology Connectors on the blocks suggest how they should be put together so that over the process of tinkering with these blocks the emerging structure can give rise to new ideas and direction to the project Not only does snapping together complimentary blocks provide an easy way into learning programming but the idea of modularization as a problem-solving and design strategy is directly relevant to mechanistic thinking Go on to discuss how they can apply scientistsrsquo patterns of thinking to our own thinking in science class and daily life
copy 2009 Yu-Tzu Debbie Liu 11
Name___________________________ Date ____________
Designing a New Microbe
Task Gas prices have reached its all time high Thus scientists are trying to think of ways to produce alternative fuels such as hydrogen gas in a much cheaper and quicker way You are a scientist and you are familiar with six different organisms Based on what you know can you come up with a way to generate hydrogen from starch and water by designing a microbe that borrows different mechanismsproteins from different cells Fill in the blanks with protein names and the organism that the protein was taken from
Materials Each team has a set of cards each card symbolizing a different organism On the card you will see the name of the organism a picture of the organism and proteins that is unique to them Proteins (or enzymes) convert one molecule into another
Starch amp Water Protein borrowed Protein borrowed
Input Organism Organism
Protein borrowed $ Protein borrowed $ Protein borrowed Organism Organism Organism
Protein borrowed Protein borrowed Protein borrowed Hydrogen Organism Organism Organism Output
Experiment adapted from Zhang YH Evans BR Mielenz JR Hopkins RC Adams MW (2007) High-yield hydrogen production from
starch and water by a synthetic enzymatic pathway PLoS ONE 5 e456
copy 2009 Yu-Tzu Debbie Liu 12
Organism Cards (one set)
Teachers Please make as many copies as the number of groups of students Cut the cards out and shuffle before handing to students
Source NIH
Bacteria
Rabbitbull Protein T uses [X5P] to make [S7P]
Photo US Fish and Wildlife Service bull Protein F uses [S7P] to make [NADPH] bull Protein G uses starch and water to make [G-1-P] bull Protein P uses [G-1-P] to make [G-6-P]
Yeast
Public domain image (Source Wikimedia Commons)
bull Protein D uses [G-6-P] to make [NADPH] and [R5P]
Public domain image (Source Wikimedia Commons) Spinach
bull Protein R uses [R5P] to make [X5P]
Experiment adapted from
Archea Courtesy of Angels Tapias (License CC BY)
bull Protein H uses [NADPH] to make Hydrogen
Source NIH Mouse
bull Protein X uses [T8P] to make Hydrogen
Zhang YH Evans BR Mielenz JR Hopkins RC Adams MW (2007) High-yield hydrogen production from starch and water by a synthetic enzymatic pathway PLoS ONE 5 e456
copy 2009 Yu-Tzu Debbie Liu 13
MIT OpenCourseWarehttpocwmitedu
MAS714J STS445J Technologies for Creative Learning Fall 2009
For information about citing these materials or our Terms of Use visit httpocwmiteduterms
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J5JE0M5IM5PJc
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[SJ0M$$cP03RgtCHgt-lt=R7VC=BC=C89lt=RJ-lt=RJBS8HQCBC0
i-()ampBIJ)2874B3amp$ACDK
ABH-S=J1271V)Egtgt0
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SHBJN0`0J2-SNC9ltBSgt73Q
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)0+0J_`CJ)020M$$P0G=
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0J_389TBCJF030M$$P0dTgtBC
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1030X9MkSgt0PJTBS7)B89=C9BCC9gt88
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=B$1))$)I)(9)$BIMQQ0(cUP0
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8)$1)96$2B)$)BMG(B4B)4226$)B4B)21$)BQltgt72SgtC-CSDTC9G=BSltB=0V`0
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3CSR=[TABCD)9G=PVBSMhR
0
88ABC9ltS
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0M5IIP0)9gt88QBCC
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agtJA
aBGJ10M(5IU0
-)1B9)B4B2-B4641H)B4BO7)
S8CgtH00F0M$$6P02T-lt=RBT8CR0
MPJ54c
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cc0$$AWRIP0VC=BCD-lt=R7
M55PJ5$5U(5$$0
388C95gtC8CR0H)B)AVRM6PJc6(
l9B=amp0[QS8CHgtCB89BSTBC-RBgtRC9C8RHBC8QBC9TBR0E30JkDBgth0F0J1lti0F0J[QGgtF0A0J2SBHgt10a0M$$4P0[=9(RltS9RS=
6U0ONk7
$$amp()+-- I
Photo courtesy httpsyntheticbiologyorg
Table of Contents
How are scientists thinking mechanistically in the 21st centuryhelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip1
Lesson 1 Introduction to Scratchhelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip5
Scratch Resources (not provided)helliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellipX
Lesson 2 Case Study of Jay Keaslinghelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip6
Case Study of Jay Keaslinghelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip8
Lesson 3 Mechanistic Thinkinghelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip10
Designing a New Microbehelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip12
Organism Cardshelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip13
copy 2009 Yu-Tzu Debbie Liu
Photo courtesy httpsyntheticbiologyorg
How are scientists thinkingmechanistically in the 21st century
Understanding Goals The rapid advancement of technology and the accumulation of information are changing
the patterns of scientific thinking and research in the 21st century Designing and creating novel organisms by combining various biological components
from different cells is one way scientists think mechanistically in the 21st century Designing and creating Scratch projects using graphical programming blocks is one way
students can display mechanistic thinking Identifying characteristics of successful scientist and their thinking patterns help us
become better (science) students by applying these skills to our own learning
Background Information Beyond the Scientific Method The scientific method has been commonly taught in science classrooms and textbooks as the only correct way to conduct scientific investigations This leaves students with the impression that all of science proceeds in much the same way Unfortunately this view is not entirely accurate Perhaps some scientists might conduct their work in this manner but rarely do they use it in the stereotyped step-by-step way that schools tend to teach itmdashdespite the fact that scientists report their work in this way in journals In fact scientists throughout history conduct their research in a variety of ways The exact approach a scientist uses depends on the individual doing the investigation as well as the particular question or problem being studied Furthermore scientists often engage in thinking patterns that are specific to its particular socio-cultural context 21st Century Scientific Thinking Skills With the explosion of advancements in scientific knowledge and technology at the turn of the century scientists at the cutting edge of research must adapt to new ways of interacting with their work Five prominent scientific thinking patterns of the 21st century are systems thinking mechanistic thinking interdisciplinary thinking quantitative thinking and distributed thinking1 In this lesson students will explore what mechanistic thinking Mechanistic Thinking It is a way of thinking that has a mechanical or engineering undertone This is shown through scientistsrsquo modular synthetic and purpose-driven approach towards their research problems Due to recent developments in new technologies and knowledge scientists are able to manipulate biology more directly allowing them to engineer and create novel biological systems for practical applications
1 Liu Y-T D amp Grotzer T A (2009) Looking forward Teaching the nature of the science of today and tomorrow In I M Saleh amp M S Khine (Eds) Fostering scientific habits of mind Pedagogical knowledge and best practices in science education (pp 9-36) Rotterdam Sense Publishers
copy 2009 Yu-Tzu Debbie Liu 1
What is Synthetic Biology The thinking involved in the field of synthetic biology is the best examples of mechanistic thinking With the rapidly emerging field of synthetic biology blurring the lines of biology and engineering scientists are no longer limited to working with organisms that naturally exist in the world Scientists often think synthetically by re-designing and constructing new organisms for practical and novel applications
Synthetic biology is an extension of genetic engineering Some even describe it as a more sophisticated version of genetic engineering taking into account a broader rational design perspective2 The engineering influence seeks out the simplicity in biological systems and brings standardization and modular design principles to biology
Synthetic biologists can use interchangeable parts from natural biology to assemble systems that function in new ways never existing before in living systems hence synthetic Modular circuit components (eg metabolic enzymes or fluorescent output genes) that are well characterized and can act independently of other cellular processes are used to build synthetic biological circuits Much like the ease of using LEGO bricksmdashstandardized bricks that can attach to any other partmdashsynthetic biology starts from the use of standardized biological building blocks The goal of synthetic biology is to both better understand how organisms function at the DNA protein and cell level by creating artificial biological systems and to solve important real-world problems the latter having caught the attention of scientists politicians and entrepreneurs Promising fields of application include energy environmental monitoring and remediation biotech and pharmaceuticals and materials fabrication
As pointed out in the detailed case study of Jay Keasling (one of the pioneers of synthetic biology) another key difference between synthetic biology and genetic engineering is the complexity of products or task the engineered organism can produce and accomplish Genetic engineering is typically limited to having microbes produce small proteins (eg insulin growth hormones) by simply inserting a single gene from a different organism into a microbe However with synthetic biology a complex interaction of several genes can be produced in a specified sequence much like what goes on in a chemical plant petroleum goes in and after a whole chain of reactions plastic comes out Scratch Scratch (httpscratchmitedu) is a programming language for young people (ages 8 and up) that makes it easy to create interactive projects (eg stories animations games simulations music and art) that can be shared on the Scratch website It is highly conducive to learning and teaching 21st century scientific thinking skills The Scratch grammar is designed so that users are presented with a versatile collection of graphical programming blocks that they can be snapped together to create programs much like LEGO bricks (and synthetic biology) Connectors on the blocks suggest how they should be put together so that over the process of tinkering with these blocks the emerging structure can give rise to new ideas and direction to the project Not only does snapping together complimentary blocks provide an easy way into learning programming but the idea of modularization as a problem-solving and design strategy is directly relevant to mechanistic thinking
2 Salisbury MW (2006) Get Ready for Synthetic Biology Genome Technology Magazine Retrieved from httpwwwgenome-technologycom
copy 2009 Yu-Tzu Debbie Liu 2
In this lesson Scratch is used to have students experience thinking mechanistically in their own work And since programming involves the creation of external representations of the problem-solving process Scratch provides students with opportunities of reflecting on their own thinking Lesson Layout These three lessons (one lesson per day) are designed to help students 1) understand how modern scientists think mechanistically 2) practice thinking mechanistically by simulating how synthetic biologists think in the field and 3) recognize mechanistic thinking even when it is not in the context of science as in their own work via Scratch Lesson 1 Designed to familiarize students with the Scratch programming language so that they can create projects on it At this point Scratch is presented simply as a medium for expressing what they have learned much like posters Powerpoint presentations and paper write-ups Lesson 2 Designed to expose students to the creative field of synthetic biology as a means to illustrate how scientists think mechanistically in the field This is done by a case study of Jay Keasling one of the pioneers of synthetic biology By analyzing how a modern scientist work and think students are provided with a broader view of scientific inquiry and the nature of scientific thinking Students will be asked to demonstrate their understanding of what they have learned so far by creating a Scratch project This allows students to work more closely and creatively with Scratch It also acts as a quick formative assessment for teachers of studentsrsquo learning thus far However the real goal of this exercise is to have students engage in mechanistic thinking in their own work which they may not recognize as it is not in the direct context of science This will be revealed in lesson 3 Lesson 3 Designed to have students practice thinking mechanistically by simulating how synthetic biologists think in the field via the Designing a New Microbe activity adapted from an actual experiment conducted in 20073 This activity presents students with a problem (need for hydrogen gas as alternative fuel) and asks students to design a microbe that can use starch and water to make hydrogen gas Students are given a set of organism cards to work with each card symbolizing a different type of organism (bacteria rabbit yeast archea spinach and mouse) Proteins (molecules that can convert one molecule into another) that are unique to each organism are listed on the card Studentsrsquo engineered microbe will essentially have different proteins from different organisms placed in a certain sequence to end up with a final product of hydrogen gas Students are given the Designing a New Microbe worksheet to help them visualize the problem better and reduce their cognitive loads (ie amount of information they need to carry in their heads) The activity allows students to discover that synthetic biology is a very mind-blowing field accomplishing things that some people never thought was possible Students will come to appreciate how seemingly impossible feats can be possible especially when scientists are thinking creatively By thinking and working mechanistically scientists have more freedom then before in designing and creating novel organisms for real-world applications
3 Zhang YH Evans BR Mielenz JR Hopkins RC Adams MW (2007) High-yield hydrogen production from starch and water by a synthetic enzymatic pathway PLoS ONE 5 e456
copy 2009 Yu-Tzu Debbie Liu 3
After the activity when students have grasped a much deeper understanding of what mechanistic thinking looks like in practice students are asked to reflect on their experience with Scratch The goal is to have students make the connection that they themselves have been engaging in mechanistic thinking while working on their own Scratch projects This reflective exercise encourages students to transfer their understanding of mechanistic thinking across different domains Students will also gain an appreciation of how studying trends in scientistsrsquo way of thinking can help them in their own thinking Lesson Placement These lessons can be used at the beginning of the school year when the scientific method is usually being presented Alternatively this lesson can be infused during the school year as students learn more about genetic engineering or creative thinking These lessons follow a constructivist approach to learning encouraging students to discover the meaning of mechanistic thinking through their exploration of a case study simulating how synthetic biologists think and making connections to their own work in Scratch Students are always encouraged to formulate their own ideas and connections before being presented with any information
copy 2009 Yu-Tzu Debbie Liu 4
Lesson Plan Day 1 Materials
Computers with Scratch installed Scratch Resources
Prep Step Review lesson plan background information and understanding goals Obtain computers with Scratch installed for students to work on Make copies of Scratch Resources (not provided)
Explore Step 1 Introduction to lesson Introduce the lesson by giving students a sense of what they will be doing and where they are headed by telling students ldquoThis will be a three-day lesson where we will be exploring how scientists think and more specifically what mechanistic thinking looks like in practice In this process we will also be learning Scratch We will tie everything together at the end of the third dayrdquo Step 2 Playing with Scratch Depending on the level of your students and any future goals you wish to achieve with Scratch structure the class so that students are comfortable navigating around the Scratch environment and are able to get started on their own Scratch project by the end of the class Please provide students with any Scratch resources you see fit Check out the ScratchEds resource search (httpscratchedmediamiteduresourcessearch) for more info Some good examples found in ScratchEd of Scratch lesson plans (video tutorials PowerPoints and worksheets) include
bull Having Fun with Computer Programming and Games (httpwwwleroieeducationoutreachsecondlevelscratchlessonplans)
bull A TeachNetUK Project 6 Lessons on Getting Started with Scratch (httpwwwteachnet-ukorguk200720ProjectsICT-ScratchScratchpages8_schemeofworkhtml)
bull Scratch Lessons Shall We Learn Scratch Programming for Tweens (httpwwwshallwelearncomscratchprogrammingforkidscategory)
bull Designing Animations and GamesmdashA Creative Introduction to Programming (httpwwwcsuni-potsdamde~romeikeUEWettbewerbindex-englishhtm)
Make sure to also introduce students to the Scratch online community and let them know that they can download the source code of any project to help them see how others are using the Scratch programming language to create projects
Review Extend and Apply Step 3 Scratch Assignment End the day by informing students that they will apply what they have learned today to create a mini-Scratch project for an assignment after the next dayrsquos lesson Emphasize to students that the goal is not to create a complex programming project but to use Scratch creatively as a medium for creative expressing not matter how simple the project is Encourage students to play with Scratch on their own time and make it clear that you highly encourage them to borrow adapt and build upon the ideas and projects of others (this is not considered cheating)
copy 2009 Yu-Tzu Debbie Liu 5
Lesson Plan Day 2 Materials
21st century scientist case study of Jay Keasling Student notebooks or journals
Prep Step Review lesson plan background information and understanding goals Make copies of 21st century scientist case study of Jay Keasling (p 8)
Explore Step 1 What is scientific thinking Ask students to describe what they think is scientific thinking Collect a representative list of studentsrsquo thoughts on the board Ask students to explain or expound on the meaning behind what they are saying After reviewing the list ask them ldquo Do you think all scientists come to their discoveries in the same wayrdquo ldquoDo scientists display all these characteristics at all timesrdquo It is important to point out to students that scientists have various methods going about their experimentation and work and depending on the type of work they are doing scientists donrsquot always share the same methods Furthermore scientists engage in thinking patterns that are specific to its particular socio-cultural context and one of which is mechanistic thinking Engage in a discussion with students on how might the explosion of advancements in scientific knowledge and technology at the turn of the century change the way scientists at the cutting edge of research interact with their work
Step 2 Analyze case study of a 21st century scientist Let students know that they will be learning about the field of synthetic biology as a means to illustrate how modern scientists work and think Specifically they will be studying Jay Keasling one of the pioneers of synthetic biology Hand out the case study on Jay Keasling Have students work in groups of 3-4 students to identify any patterns of thinking that the scientist displays Make sure to ask students to specifically identify what part of the case study justifies their claims Have students write the class findings in their journalsnotebooks
Possible findings from case analysis Jay Keasling
Keasling is a pioneer of synthetic biologymdasha field that designs and constructs new organisms for useful purposes He is most known for creating a microbe that produces a drug to treat malaria (making drugs from bugs) Some of his characteristics as a scientist include
bull Creative and imaginative wanted to invent new tools that can turn cells into chemical plants take in something very simple and spits out something complicated and valuable coming up with other applications of synthetic biology (use microbes to break down pesticides make biodegradable plastics create fuels from plants)
bull Critical thinking thought about how to design and create microbes to produce artemisinin much quicker and cheaper how to integrate genes from different species into a microbe to fabricate the drug
copy 2009 Yu-Tzu Debbie Liu 6
bull Seek and integrate information integrated methods and concepts from engineering and biology leading to synthetic biology
bull Supported with significant resources did research at universities and received grant money
bull Practical-minded microbes will churn out anti-malarial drug for a fraction of its current cost making it accessible to much more of the world these microbes could save millions of lives
bull Strong disciplinary understanding studied biology and chemical engineering extensively leading to his PhD and professor position at UC Berkeley
Step 3 What is mechanistic thinking Introduce students to the idea of mechanistic thinking as a prominent thinking pattern in the 21st
century
Mechanistic Thinking
Mechanistic thinking is a way of thinking that has a mechanical or engineering undertone This is shown through scientistsrsquo regular use of mechanical analogies to conceptualize their work and their modular synthetic and purpose-driven approach towards their research problems The display of mechanistic thinking by scientists appears to be a result of the merging of biology and engineering practices that is increasingly observed in 21st century biology as compared to a time when most of biologymdashtraditionally known for its pure basic researchmdashremain clearly demarcated from engineeringmdasha purely applied research field A mechanistic way of thinking has come to the forefront of 21st century science because of recent developments in new technologies and knowledge that enable scientists to manipulate the object or organism they are working with more directly allowing them to engineer and create novel biological systems for practical applications
Let students know that the work synthetic biologists do often require them to think mechanistically Now that students are given a definition of mechanistic thinking have students revisit their case study analysis and explore how synthetic biologists might think mechanistically
Review Extend and Apply
Step 4 Scratch Assignment Ask students to create a mini-Scratch project to demonstrate what they have learned so far (the project does not have to be all inclusive students can choose to focus on just one thing they learned either about scientific thinking mechanistic thinking or synthetic biology) Emphasize to students that the goal is not to create a complex programming project but to use Scratch creatively as a medium for creative expressing not matter how simple the project is Encourage students to work with partners and collaborate by borrowing adapting or building upon the ideas and projects of others (this is not considered cheating)
copy 2009 Yu-Tzu Debbie Liu 7
Detailed Case Study Jay Keasling
(1964 ndash present)
Best known for pioneering the new field of synthetic biology which designs and constructs new organisms for useful purposes He is also most known for creating a microbe that produces a drug to treat malaria (making drugs from bugs)
Jay Keasling was raised on a farm and spent his childhood exploring the practical side of biology chemistry and engineering This background eventually led him to work in the rapidly growing field that uses living organisms like bacteria for various practical purposes such as food processing agriculture and medicine
In the early 1980s genetic engineering became popular because you can ldquoconvincerdquo microbes to produce insulin growth hormones and other valuable proteins by simply inserting a single gene from a different organism into bacteria However Keasling believed that genetic engineering isnrsquot harnessing the full power of these cells The production of molecules isnt always so simple it requires a complex interaction of several genes (not just one) being produced in a certain sequence So Keasling wanted to invent the tools that would allow him to create these kinds of genetic assembly lines Thus what goes on in a cell is a lot like what goes on in a chemical plant petroleum goes in and after a whole chain of reactions plastic comes out
Keasling went to college studying biology and chemical engineering extensively and got his PhD in 1991 He is now a professor at the University of California at Berkeley He spent his first 10 years at UC Berkeley building the new tools he would need to turn cells into chemical plants He also invented powerful chemical switches (like a light switch) that allowed him to control when he wanted to ldquoturn onrdquo and ldquoturn offrdquo protein production in cells This way of borrowing techniques from engineering and figuring out how to manipulate microbes came to be call synthetic biology
After years of perfecting his biological tool kit Keasling wanted to find a real-world use for it In 2002 he learned of the dire need for artemisinin a compound derived from the sweet wormwood plant which is 90 percent effective against the parasite that causes malaria and has few side effects (malaria kills some 3 million people a year) However extracting the drug from sweet wormwood is a slow and expensive process Keasling figured he could design and create microbes to produce artemisinin much quicker and cheaper Rather than wait months for sweet wormwood to grow on farms Keasling wanted to create it simply by pouring sugar in a tank full of microbes that can use the sugar to make the drug via a chemical pathway he has designedmdashhe wanted to integrate genes from different species into a microbe to fabricate the drug for malaria
copy 2009 Yu-Tzu Debbie Liu 8
In 2006 Keaslings team (comprised of graduate students post-docs and research assistants) published their success of the production of artemisinin It is expected to lower the cost of artemisinin production from a dollar per gram to just 10 cents He was awarded a $43 million grant from the Bill and Melinda Gates Foundation and awarded DISCOVER magazinersquos first ever Scientist of the Year Award
Fighting malaria is just one part of Keaslings larger agenda to explore the potential of synthetic biology In his laboratory students are engineering microbes to break down pesticides make biodegradable plastics and create ethanol and other fuels from plants
Excerpts of i interview w Jay Keasling
1 You arrived at UC Berkeley in 1992 with training as both a chemical engineer and a biologist What did you hope to do
2 Why hadnt anybody tried to engineer cells that way before
3 How did you get involved in your antimalaria project
Jay Keisling biography adapted fromZimmer C (2006) Scientist of the Year Jay Keasling Discovermagazinecom Retrieved from
httpdiscovermagazinecom2006deccover
copy 2009 Yu-Tzu Debbie Liu 9
See responses to these questions atZimmer C (2006) Scientist of the Year Jay Keasling Discovermagazinecom Retrieved from
httpdiscovermagazinecom2006deccover
Interview content removed due to copyright restrictions
Interview content removed due to copyright restrictions
Interview content removed due to copyright restrictions
Lesson Plan Day 3 Materials
Designing a New Microbe worksheet Organism cards Student notebooks or journals
Prep Step Review lesson plan background information and understanding goals Photocopy Designing a New Microbe worksheet (p 28) Cut out organism cards (each group of 3-4 students will have a set of cards) (p29)
Explore Step 1 Designing a New Microbe Introduce todayrsquos activity by saying ldquoYou will be simulating how synthetic biologists think mechanistically by doing an the activity that is actually modeled after a real experiment done by scientists in 2007rdquo Divide students into groups of 3 or 4 Each group receives a set of organism cards Each student receives a Designing a New Microbe worksheet Remind students that proteins (or enzymes) are molecules inside cells that convert one molecule into another (eg the make-believe molecule How is converted to the molecule Home by Protein T in bacteria) Following the directions of the handout have students create a kind of assembly line that integrate proteins from different organisms into a microbe that uses water and starch (inputs) to ultimately produce hydrogen (output)
Possible answers to Designing a New Microbe
There are two possible pathways that can lead to hydrogen production
1 Starch amp water Protein G Protein P Protein D Protein R Protein T Protein F Protein H Hydrogen
2 Starch amp water Protein G Protein P Protein D Protein H Hydrogen
Guide students along by encouraging students who have already figured out how to attempt the problem to reveal and share with the class how they are thinking through the problem Stop students periodically to ask ldquoHow are you thinking through this problem What is your goal and how is your thinking helping you reach that goalrdquo Students may find either working sequentially forward or backward to fill in the worksheet to be easier
Note to teachers The hydrogen production pathway from starch and water is a shorten version of the actual 2007 experiment for learning purposes The organism types and molecule names are true to the experiment Protein names are made up for simplicity
copy 2009 Yu-Tzu Debbie Liu 10
Step 2 Discuss studentsrsquo findings Have students tell you what they found as you write their findings on the board Students may have discovered by now that there are two paths that lead to hydrogen production Students might recall that Jay Keasling have done something similar by making an antimalarial drug from sugar using synthetic biology Students may have also discovered that no proteins from the mouse organism were used for the design of their new microbe Ask students ldquowhat do you think is the purpose of having a mouse organism when we didnrsquot need itrdquo Help students understand how in reality scientists have hundreds of organisms to choose from some of which are irrelevant to their work In fact a common skill that scientists share is being about to identify and pull together important and relevant information The activity allows students to discover that synthetic biology is a very mind-blowing field accomplishing things that some people never thought was possible Students will come to appreciate how seemingly impossible feats can be possible especially when scientists are thinking creatively By thinking and working mechanistically scientists have more freedom then before in designing and creating novel organisms for real-world applications
Review Extend and Apply Step 3 How do you think mechanistically Ask students to reflect on their experience with Scratch and how they might have engaged in mechanistic thinking in their own work Helps students make the connection that they themselves have been engaging in mechanistic thinking while working on their own Scratch projects The Scratch grammar is designed so that users are presented with a versatile collection of graphical programming blocks that they can be snapped together to create programs much like synthetic biology Connectors on the blocks suggest how they should be put together so that over the process of tinkering with these blocks the emerging structure can give rise to new ideas and direction to the project Not only does snapping together complimentary blocks provide an easy way into learning programming but the idea of modularization as a problem-solving and design strategy is directly relevant to mechanistic thinking Go on to discuss how they can apply scientistsrsquo patterns of thinking to our own thinking in science class and daily life
copy 2009 Yu-Tzu Debbie Liu 11
Name___________________________ Date ____________
Designing a New Microbe
Task Gas prices have reached its all time high Thus scientists are trying to think of ways to produce alternative fuels such as hydrogen gas in a much cheaper and quicker way You are a scientist and you are familiar with six different organisms Based on what you know can you come up with a way to generate hydrogen from starch and water by designing a microbe that borrows different mechanismsproteins from different cells Fill in the blanks with protein names and the organism that the protein was taken from
Materials Each team has a set of cards each card symbolizing a different organism On the card you will see the name of the organism a picture of the organism and proteins that is unique to them Proteins (or enzymes) convert one molecule into another
Starch amp Water Protein borrowed Protein borrowed
Input Organism Organism
Protein borrowed $ Protein borrowed $ Protein borrowed Organism Organism Organism
Protein borrowed Protein borrowed Protein borrowed Hydrogen Organism Organism Organism Output
Experiment adapted from Zhang YH Evans BR Mielenz JR Hopkins RC Adams MW (2007) High-yield hydrogen production from
starch and water by a synthetic enzymatic pathway PLoS ONE 5 e456
copy 2009 Yu-Tzu Debbie Liu 12
Organism Cards (one set)
Teachers Please make as many copies as the number of groups of students Cut the cards out and shuffle before handing to students
Source NIH
Bacteria
Rabbitbull Protein T uses [X5P] to make [S7P]
Photo US Fish and Wildlife Service bull Protein F uses [S7P] to make [NADPH] bull Protein G uses starch and water to make [G-1-P] bull Protein P uses [G-1-P] to make [G-6-P]
Yeast
Public domain image (Source Wikimedia Commons)
bull Protein D uses [G-6-P] to make [NADPH] and [R5P]
Public domain image (Source Wikimedia Commons) Spinach
bull Protein R uses [R5P] to make [X5P]
Experiment adapted from
Archea Courtesy of Angels Tapias (License CC BY)
bull Protein H uses [NADPH] to make Hydrogen
Source NIH Mouse
bull Protein X uses [T8P] to make Hydrogen
Zhang YH Evans BR Mielenz JR Hopkins RC Adams MW (2007) High-yield hydrogen production from starch and water by a synthetic enzymatic pathway PLoS ONE 5 e456
copy 2009 Yu-Tzu Debbie Liu 13
MIT OpenCourseWarehttpocwmitedu
MAS714J STS445J Technologies for Creative Learning Fall 2009
For information about citing these materials or our Terms of Use visit httpocwmiteduterms
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BC
EGgtJ+0N0M54P0Egt(B-BCR0
3BltHMkS0PJMQQ0II(
8)$1)96$2B)$)BMG(B4B)4226$)B4B)21$)BQltgt72SgtC-CSDTC9G=BSltB=0V`0
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0
88ABC9ltS
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20JFgt-BHJk0J3ltDJi0J3ltDHBJh0J
kDR0Bampamp6)$)BBI$(J-0_XBBJamp0M$$P038BC897E=BHH=
3BSDBltJa020_BSQgtCH8gt8BltSgtgt8C8WR0
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)ADKF
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0M5IIP0)9gt88QBCC
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5U0
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lt(S$I)I$1M
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0M$$6P0FS8CgtHBS8HQltZCRHlt8ltB-lt=R0
agtJA
aBGJ10M(5IU0
-)1B9)B4B2-B4641H)B4BO7)
S8CgtH00F0M$$6P02T-lt=RBT8CR0
MPJ54c
Q-HUO3B1$AV
cc0$$AWRIP0VC=BCD-lt=R7
M55PJ5$5U(5$$0
388C95gtC8CR0H)B)AVRM6PJc6(
l9B=amp0[QS8CHgtCB89BSTBC-RBgtRC9C8RHBC8QBC9TBR0E30JkDBgth0F0J1lti0F0J[QGgtF0A0J2SBHgt10a0M$$4P0[=9(RltS9RS=
6U0ONk7
$$amp()+-- I
Photo courtesy httpsyntheticbiologyorg
Table of Contents
How are scientists thinking mechanistically in the 21st centuryhelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip1
Lesson 1 Introduction to Scratchhelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip5
Scratch Resources (not provided)helliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellipX
Lesson 2 Case Study of Jay Keaslinghelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip6
Case Study of Jay Keaslinghelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip8
Lesson 3 Mechanistic Thinkinghelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip10
Designing a New Microbehelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip12
Organism Cardshelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip13
copy 2009 Yu-Tzu Debbie Liu
Photo courtesy httpsyntheticbiologyorg
How are scientists thinkingmechanistically in the 21st century
Understanding Goals The rapid advancement of technology and the accumulation of information are changing
the patterns of scientific thinking and research in the 21st century Designing and creating novel organisms by combining various biological components
from different cells is one way scientists think mechanistically in the 21st century Designing and creating Scratch projects using graphical programming blocks is one way
students can display mechanistic thinking Identifying characteristics of successful scientist and their thinking patterns help us
become better (science) students by applying these skills to our own learning
Background Information Beyond the Scientific Method The scientific method has been commonly taught in science classrooms and textbooks as the only correct way to conduct scientific investigations This leaves students with the impression that all of science proceeds in much the same way Unfortunately this view is not entirely accurate Perhaps some scientists might conduct their work in this manner but rarely do they use it in the stereotyped step-by-step way that schools tend to teach itmdashdespite the fact that scientists report their work in this way in journals In fact scientists throughout history conduct their research in a variety of ways The exact approach a scientist uses depends on the individual doing the investigation as well as the particular question or problem being studied Furthermore scientists often engage in thinking patterns that are specific to its particular socio-cultural context 21st Century Scientific Thinking Skills With the explosion of advancements in scientific knowledge and technology at the turn of the century scientists at the cutting edge of research must adapt to new ways of interacting with their work Five prominent scientific thinking patterns of the 21st century are systems thinking mechanistic thinking interdisciplinary thinking quantitative thinking and distributed thinking1 In this lesson students will explore what mechanistic thinking Mechanistic Thinking It is a way of thinking that has a mechanical or engineering undertone This is shown through scientistsrsquo modular synthetic and purpose-driven approach towards their research problems Due to recent developments in new technologies and knowledge scientists are able to manipulate biology more directly allowing them to engineer and create novel biological systems for practical applications
1 Liu Y-T D amp Grotzer T A (2009) Looking forward Teaching the nature of the science of today and tomorrow In I M Saleh amp M S Khine (Eds) Fostering scientific habits of mind Pedagogical knowledge and best practices in science education (pp 9-36) Rotterdam Sense Publishers
copy 2009 Yu-Tzu Debbie Liu 1
What is Synthetic Biology The thinking involved in the field of synthetic biology is the best examples of mechanistic thinking With the rapidly emerging field of synthetic biology blurring the lines of biology and engineering scientists are no longer limited to working with organisms that naturally exist in the world Scientists often think synthetically by re-designing and constructing new organisms for practical and novel applications
Synthetic biology is an extension of genetic engineering Some even describe it as a more sophisticated version of genetic engineering taking into account a broader rational design perspective2 The engineering influence seeks out the simplicity in biological systems and brings standardization and modular design principles to biology
Synthetic biologists can use interchangeable parts from natural biology to assemble systems that function in new ways never existing before in living systems hence synthetic Modular circuit components (eg metabolic enzymes or fluorescent output genes) that are well characterized and can act independently of other cellular processes are used to build synthetic biological circuits Much like the ease of using LEGO bricksmdashstandardized bricks that can attach to any other partmdashsynthetic biology starts from the use of standardized biological building blocks The goal of synthetic biology is to both better understand how organisms function at the DNA protein and cell level by creating artificial biological systems and to solve important real-world problems the latter having caught the attention of scientists politicians and entrepreneurs Promising fields of application include energy environmental monitoring and remediation biotech and pharmaceuticals and materials fabrication
As pointed out in the detailed case study of Jay Keasling (one of the pioneers of synthetic biology) another key difference between synthetic biology and genetic engineering is the complexity of products or task the engineered organism can produce and accomplish Genetic engineering is typically limited to having microbes produce small proteins (eg insulin growth hormones) by simply inserting a single gene from a different organism into a microbe However with synthetic biology a complex interaction of several genes can be produced in a specified sequence much like what goes on in a chemical plant petroleum goes in and after a whole chain of reactions plastic comes out Scratch Scratch (httpscratchmitedu) is a programming language for young people (ages 8 and up) that makes it easy to create interactive projects (eg stories animations games simulations music and art) that can be shared on the Scratch website It is highly conducive to learning and teaching 21st century scientific thinking skills The Scratch grammar is designed so that users are presented with a versatile collection of graphical programming blocks that they can be snapped together to create programs much like LEGO bricks (and synthetic biology) Connectors on the blocks suggest how they should be put together so that over the process of tinkering with these blocks the emerging structure can give rise to new ideas and direction to the project Not only does snapping together complimentary blocks provide an easy way into learning programming but the idea of modularization as a problem-solving and design strategy is directly relevant to mechanistic thinking
2 Salisbury MW (2006) Get Ready for Synthetic Biology Genome Technology Magazine Retrieved from httpwwwgenome-technologycom
copy 2009 Yu-Tzu Debbie Liu 2
In this lesson Scratch is used to have students experience thinking mechanistically in their own work And since programming involves the creation of external representations of the problem-solving process Scratch provides students with opportunities of reflecting on their own thinking Lesson Layout These three lessons (one lesson per day) are designed to help students 1) understand how modern scientists think mechanistically 2) practice thinking mechanistically by simulating how synthetic biologists think in the field and 3) recognize mechanistic thinking even when it is not in the context of science as in their own work via Scratch Lesson 1 Designed to familiarize students with the Scratch programming language so that they can create projects on it At this point Scratch is presented simply as a medium for expressing what they have learned much like posters Powerpoint presentations and paper write-ups Lesson 2 Designed to expose students to the creative field of synthetic biology as a means to illustrate how scientists think mechanistically in the field This is done by a case study of Jay Keasling one of the pioneers of synthetic biology By analyzing how a modern scientist work and think students are provided with a broader view of scientific inquiry and the nature of scientific thinking Students will be asked to demonstrate their understanding of what they have learned so far by creating a Scratch project This allows students to work more closely and creatively with Scratch It also acts as a quick formative assessment for teachers of studentsrsquo learning thus far However the real goal of this exercise is to have students engage in mechanistic thinking in their own work which they may not recognize as it is not in the direct context of science This will be revealed in lesson 3 Lesson 3 Designed to have students practice thinking mechanistically by simulating how synthetic biologists think in the field via the Designing a New Microbe activity adapted from an actual experiment conducted in 20073 This activity presents students with a problem (need for hydrogen gas as alternative fuel) and asks students to design a microbe that can use starch and water to make hydrogen gas Students are given a set of organism cards to work with each card symbolizing a different type of organism (bacteria rabbit yeast archea spinach and mouse) Proteins (molecules that can convert one molecule into another) that are unique to each organism are listed on the card Studentsrsquo engineered microbe will essentially have different proteins from different organisms placed in a certain sequence to end up with a final product of hydrogen gas Students are given the Designing a New Microbe worksheet to help them visualize the problem better and reduce their cognitive loads (ie amount of information they need to carry in their heads) The activity allows students to discover that synthetic biology is a very mind-blowing field accomplishing things that some people never thought was possible Students will come to appreciate how seemingly impossible feats can be possible especially when scientists are thinking creatively By thinking and working mechanistically scientists have more freedom then before in designing and creating novel organisms for real-world applications
3 Zhang YH Evans BR Mielenz JR Hopkins RC Adams MW (2007) High-yield hydrogen production from starch and water by a synthetic enzymatic pathway PLoS ONE 5 e456
copy 2009 Yu-Tzu Debbie Liu 3
After the activity when students have grasped a much deeper understanding of what mechanistic thinking looks like in practice students are asked to reflect on their experience with Scratch The goal is to have students make the connection that they themselves have been engaging in mechanistic thinking while working on their own Scratch projects This reflective exercise encourages students to transfer their understanding of mechanistic thinking across different domains Students will also gain an appreciation of how studying trends in scientistsrsquo way of thinking can help them in their own thinking Lesson Placement These lessons can be used at the beginning of the school year when the scientific method is usually being presented Alternatively this lesson can be infused during the school year as students learn more about genetic engineering or creative thinking These lessons follow a constructivist approach to learning encouraging students to discover the meaning of mechanistic thinking through their exploration of a case study simulating how synthetic biologists think and making connections to their own work in Scratch Students are always encouraged to formulate their own ideas and connections before being presented with any information
copy 2009 Yu-Tzu Debbie Liu 4
Lesson Plan Day 1 Materials
Computers with Scratch installed Scratch Resources
Prep Step Review lesson plan background information and understanding goals Obtain computers with Scratch installed for students to work on Make copies of Scratch Resources (not provided)
Explore Step 1 Introduction to lesson Introduce the lesson by giving students a sense of what they will be doing and where they are headed by telling students ldquoThis will be a three-day lesson where we will be exploring how scientists think and more specifically what mechanistic thinking looks like in practice In this process we will also be learning Scratch We will tie everything together at the end of the third dayrdquo Step 2 Playing with Scratch Depending on the level of your students and any future goals you wish to achieve with Scratch structure the class so that students are comfortable navigating around the Scratch environment and are able to get started on their own Scratch project by the end of the class Please provide students with any Scratch resources you see fit Check out the ScratchEds resource search (httpscratchedmediamiteduresourcessearch) for more info Some good examples found in ScratchEd of Scratch lesson plans (video tutorials PowerPoints and worksheets) include
bull Having Fun with Computer Programming and Games (httpwwwleroieeducationoutreachsecondlevelscratchlessonplans)
bull A TeachNetUK Project 6 Lessons on Getting Started with Scratch (httpwwwteachnet-ukorguk200720ProjectsICT-ScratchScratchpages8_schemeofworkhtml)
bull Scratch Lessons Shall We Learn Scratch Programming for Tweens (httpwwwshallwelearncomscratchprogrammingforkidscategory)
bull Designing Animations and GamesmdashA Creative Introduction to Programming (httpwwwcsuni-potsdamde~romeikeUEWettbewerbindex-englishhtm)
Make sure to also introduce students to the Scratch online community and let them know that they can download the source code of any project to help them see how others are using the Scratch programming language to create projects
Review Extend and Apply Step 3 Scratch Assignment End the day by informing students that they will apply what they have learned today to create a mini-Scratch project for an assignment after the next dayrsquos lesson Emphasize to students that the goal is not to create a complex programming project but to use Scratch creatively as a medium for creative expressing not matter how simple the project is Encourage students to play with Scratch on their own time and make it clear that you highly encourage them to borrow adapt and build upon the ideas and projects of others (this is not considered cheating)
copy 2009 Yu-Tzu Debbie Liu 5
Lesson Plan Day 2 Materials
21st century scientist case study of Jay Keasling Student notebooks or journals
Prep Step Review lesson plan background information and understanding goals Make copies of 21st century scientist case study of Jay Keasling (p 8)
Explore Step 1 What is scientific thinking Ask students to describe what they think is scientific thinking Collect a representative list of studentsrsquo thoughts on the board Ask students to explain or expound on the meaning behind what they are saying After reviewing the list ask them ldquo Do you think all scientists come to their discoveries in the same wayrdquo ldquoDo scientists display all these characteristics at all timesrdquo It is important to point out to students that scientists have various methods going about their experimentation and work and depending on the type of work they are doing scientists donrsquot always share the same methods Furthermore scientists engage in thinking patterns that are specific to its particular socio-cultural context and one of which is mechanistic thinking Engage in a discussion with students on how might the explosion of advancements in scientific knowledge and technology at the turn of the century change the way scientists at the cutting edge of research interact with their work
Step 2 Analyze case study of a 21st century scientist Let students know that they will be learning about the field of synthetic biology as a means to illustrate how modern scientists work and think Specifically they will be studying Jay Keasling one of the pioneers of synthetic biology Hand out the case study on Jay Keasling Have students work in groups of 3-4 students to identify any patterns of thinking that the scientist displays Make sure to ask students to specifically identify what part of the case study justifies their claims Have students write the class findings in their journalsnotebooks
Possible findings from case analysis Jay Keasling
Keasling is a pioneer of synthetic biologymdasha field that designs and constructs new organisms for useful purposes He is most known for creating a microbe that produces a drug to treat malaria (making drugs from bugs) Some of his characteristics as a scientist include
bull Creative and imaginative wanted to invent new tools that can turn cells into chemical plants take in something very simple and spits out something complicated and valuable coming up with other applications of synthetic biology (use microbes to break down pesticides make biodegradable plastics create fuels from plants)
bull Critical thinking thought about how to design and create microbes to produce artemisinin much quicker and cheaper how to integrate genes from different species into a microbe to fabricate the drug
copy 2009 Yu-Tzu Debbie Liu 6
bull Seek and integrate information integrated methods and concepts from engineering and biology leading to synthetic biology
bull Supported with significant resources did research at universities and received grant money
bull Practical-minded microbes will churn out anti-malarial drug for a fraction of its current cost making it accessible to much more of the world these microbes could save millions of lives
bull Strong disciplinary understanding studied biology and chemical engineering extensively leading to his PhD and professor position at UC Berkeley
Step 3 What is mechanistic thinking Introduce students to the idea of mechanistic thinking as a prominent thinking pattern in the 21st
century
Mechanistic Thinking
Mechanistic thinking is a way of thinking that has a mechanical or engineering undertone This is shown through scientistsrsquo regular use of mechanical analogies to conceptualize their work and their modular synthetic and purpose-driven approach towards their research problems The display of mechanistic thinking by scientists appears to be a result of the merging of biology and engineering practices that is increasingly observed in 21st century biology as compared to a time when most of biologymdashtraditionally known for its pure basic researchmdashremain clearly demarcated from engineeringmdasha purely applied research field A mechanistic way of thinking has come to the forefront of 21st century science because of recent developments in new technologies and knowledge that enable scientists to manipulate the object or organism they are working with more directly allowing them to engineer and create novel biological systems for practical applications
Let students know that the work synthetic biologists do often require them to think mechanistically Now that students are given a definition of mechanistic thinking have students revisit their case study analysis and explore how synthetic biologists might think mechanistically
Review Extend and Apply
Step 4 Scratch Assignment Ask students to create a mini-Scratch project to demonstrate what they have learned so far (the project does not have to be all inclusive students can choose to focus on just one thing they learned either about scientific thinking mechanistic thinking or synthetic biology) Emphasize to students that the goal is not to create a complex programming project but to use Scratch creatively as a medium for creative expressing not matter how simple the project is Encourage students to work with partners and collaborate by borrowing adapting or building upon the ideas and projects of others (this is not considered cheating)
copy 2009 Yu-Tzu Debbie Liu 7
Detailed Case Study Jay Keasling
(1964 ndash present)
Best known for pioneering the new field of synthetic biology which designs and constructs new organisms for useful purposes He is also most known for creating a microbe that produces a drug to treat malaria (making drugs from bugs)
Jay Keasling was raised on a farm and spent his childhood exploring the practical side of biology chemistry and engineering This background eventually led him to work in the rapidly growing field that uses living organisms like bacteria for various practical purposes such as food processing agriculture and medicine
In the early 1980s genetic engineering became popular because you can ldquoconvincerdquo microbes to produce insulin growth hormones and other valuable proteins by simply inserting a single gene from a different organism into bacteria However Keasling believed that genetic engineering isnrsquot harnessing the full power of these cells The production of molecules isnt always so simple it requires a complex interaction of several genes (not just one) being produced in a certain sequence So Keasling wanted to invent the tools that would allow him to create these kinds of genetic assembly lines Thus what goes on in a cell is a lot like what goes on in a chemical plant petroleum goes in and after a whole chain of reactions plastic comes out
Keasling went to college studying biology and chemical engineering extensively and got his PhD in 1991 He is now a professor at the University of California at Berkeley He spent his first 10 years at UC Berkeley building the new tools he would need to turn cells into chemical plants He also invented powerful chemical switches (like a light switch) that allowed him to control when he wanted to ldquoturn onrdquo and ldquoturn offrdquo protein production in cells This way of borrowing techniques from engineering and figuring out how to manipulate microbes came to be call synthetic biology
After years of perfecting his biological tool kit Keasling wanted to find a real-world use for it In 2002 he learned of the dire need for artemisinin a compound derived from the sweet wormwood plant which is 90 percent effective against the parasite that causes malaria and has few side effects (malaria kills some 3 million people a year) However extracting the drug from sweet wormwood is a slow and expensive process Keasling figured he could design and create microbes to produce artemisinin much quicker and cheaper Rather than wait months for sweet wormwood to grow on farms Keasling wanted to create it simply by pouring sugar in a tank full of microbes that can use the sugar to make the drug via a chemical pathway he has designedmdashhe wanted to integrate genes from different species into a microbe to fabricate the drug for malaria
copy 2009 Yu-Tzu Debbie Liu 8
In 2006 Keaslings team (comprised of graduate students post-docs and research assistants) published their success of the production of artemisinin It is expected to lower the cost of artemisinin production from a dollar per gram to just 10 cents He was awarded a $43 million grant from the Bill and Melinda Gates Foundation and awarded DISCOVER magazinersquos first ever Scientist of the Year Award
Fighting malaria is just one part of Keaslings larger agenda to explore the potential of synthetic biology In his laboratory students are engineering microbes to break down pesticides make biodegradable plastics and create ethanol and other fuels from plants
Excerpts of i interview w Jay Keasling
1 You arrived at UC Berkeley in 1992 with training as both a chemical engineer and a biologist What did you hope to do
2 Why hadnt anybody tried to engineer cells that way before
3 How did you get involved in your antimalaria project
Jay Keisling biography adapted fromZimmer C (2006) Scientist of the Year Jay Keasling Discovermagazinecom Retrieved from
httpdiscovermagazinecom2006deccover
copy 2009 Yu-Tzu Debbie Liu 9
See responses to these questions atZimmer C (2006) Scientist of the Year Jay Keasling Discovermagazinecom Retrieved from
httpdiscovermagazinecom2006deccover
Interview content removed due to copyright restrictions
Interview content removed due to copyright restrictions
Interview content removed due to copyright restrictions
Lesson Plan Day 3 Materials
Designing a New Microbe worksheet Organism cards Student notebooks or journals
Prep Step Review lesson plan background information and understanding goals Photocopy Designing a New Microbe worksheet (p 28) Cut out organism cards (each group of 3-4 students will have a set of cards) (p29)
Explore Step 1 Designing a New Microbe Introduce todayrsquos activity by saying ldquoYou will be simulating how synthetic biologists think mechanistically by doing an the activity that is actually modeled after a real experiment done by scientists in 2007rdquo Divide students into groups of 3 or 4 Each group receives a set of organism cards Each student receives a Designing a New Microbe worksheet Remind students that proteins (or enzymes) are molecules inside cells that convert one molecule into another (eg the make-believe molecule How is converted to the molecule Home by Protein T in bacteria) Following the directions of the handout have students create a kind of assembly line that integrate proteins from different organisms into a microbe that uses water and starch (inputs) to ultimately produce hydrogen (output)
Possible answers to Designing a New Microbe
There are two possible pathways that can lead to hydrogen production
1 Starch amp water Protein G Protein P Protein D Protein R Protein T Protein F Protein H Hydrogen
2 Starch amp water Protein G Protein P Protein D Protein H Hydrogen
Guide students along by encouraging students who have already figured out how to attempt the problem to reveal and share with the class how they are thinking through the problem Stop students periodically to ask ldquoHow are you thinking through this problem What is your goal and how is your thinking helping you reach that goalrdquo Students may find either working sequentially forward or backward to fill in the worksheet to be easier
Note to teachers The hydrogen production pathway from starch and water is a shorten version of the actual 2007 experiment for learning purposes The organism types and molecule names are true to the experiment Protein names are made up for simplicity
copy 2009 Yu-Tzu Debbie Liu 10
Step 2 Discuss studentsrsquo findings Have students tell you what they found as you write their findings on the board Students may have discovered by now that there are two paths that lead to hydrogen production Students might recall that Jay Keasling have done something similar by making an antimalarial drug from sugar using synthetic biology Students may have also discovered that no proteins from the mouse organism were used for the design of their new microbe Ask students ldquowhat do you think is the purpose of having a mouse organism when we didnrsquot need itrdquo Help students understand how in reality scientists have hundreds of organisms to choose from some of which are irrelevant to their work In fact a common skill that scientists share is being about to identify and pull together important and relevant information The activity allows students to discover that synthetic biology is a very mind-blowing field accomplishing things that some people never thought was possible Students will come to appreciate how seemingly impossible feats can be possible especially when scientists are thinking creatively By thinking and working mechanistically scientists have more freedom then before in designing and creating novel organisms for real-world applications
Review Extend and Apply Step 3 How do you think mechanistically Ask students to reflect on their experience with Scratch and how they might have engaged in mechanistic thinking in their own work Helps students make the connection that they themselves have been engaging in mechanistic thinking while working on their own Scratch projects The Scratch grammar is designed so that users are presented with a versatile collection of graphical programming blocks that they can be snapped together to create programs much like synthetic biology Connectors on the blocks suggest how they should be put together so that over the process of tinkering with these blocks the emerging structure can give rise to new ideas and direction to the project Not only does snapping together complimentary blocks provide an easy way into learning programming but the idea of modularization as a problem-solving and design strategy is directly relevant to mechanistic thinking Go on to discuss how they can apply scientistsrsquo patterns of thinking to our own thinking in science class and daily life
copy 2009 Yu-Tzu Debbie Liu 11
Name___________________________ Date ____________
Designing a New Microbe
Task Gas prices have reached its all time high Thus scientists are trying to think of ways to produce alternative fuels such as hydrogen gas in a much cheaper and quicker way You are a scientist and you are familiar with six different organisms Based on what you know can you come up with a way to generate hydrogen from starch and water by designing a microbe that borrows different mechanismsproteins from different cells Fill in the blanks with protein names and the organism that the protein was taken from
Materials Each team has a set of cards each card symbolizing a different organism On the card you will see the name of the organism a picture of the organism and proteins that is unique to them Proteins (or enzymes) convert one molecule into another
Starch amp Water Protein borrowed Protein borrowed
Input Organism Organism
Protein borrowed $ Protein borrowed $ Protein borrowed Organism Organism Organism
Protein borrowed Protein borrowed Protein borrowed Hydrogen Organism Organism Organism Output
Experiment adapted from Zhang YH Evans BR Mielenz JR Hopkins RC Adams MW (2007) High-yield hydrogen production from
starch and water by a synthetic enzymatic pathway PLoS ONE 5 e456
copy 2009 Yu-Tzu Debbie Liu 12
Organism Cards (one set)
Teachers Please make as many copies as the number of groups of students Cut the cards out and shuffle before handing to students
Source NIH
Bacteria
Rabbitbull Protein T uses [X5P] to make [S7P]
Photo US Fish and Wildlife Service bull Protein F uses [S7P] to make [NADPH] bull Protein G uses starch and water to make [G-1-P] bull Protein P uses [G-1-P] to make [G-6-P]
Yeast
Public domain image (Source Wikimedia Commons)
bull Protein D uses [G-6-P] to make [NADPH] and [R5P]
Public domain image (Source Wikimedia Commons) Spinach
bull Protein R uses [R5P] to make [X5P]
Experiment adapted from
Archea Courtesy of Angels Tapias (License CC BY)
bull Protein H uses [NADPH] to make Hydrogen
Source NIH Mouse
bull Protein X uses [T8P] to make Hydrogen
Zhang YH Evans BR Mielenz JR Hopkins RC Adams MW (2007) High-yield hydrogen production from starch and water by a synthetic enzymatic pathway PLoS ONE 5 e456
copy 2009 Yu-Tzu Debbie Liu 13
MIT OpenCourseWarehttpocwmitedu
MAS714J STS445J Technologies for Creative Learning Fall 2009
For information about citing these materials or our Terms of Use visit httpocwmiteduterms
Photo courtesy httpsyntheticbiologyorg
Table of Contents
How are scientists thinking mechanistically in the 21st centuryhelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip1
Lesson 1 Introduction to Scratchhelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip5
Scratch Resources (not provided)helliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellipX
Lesson 2 Case Study of Jay Keaslinghelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip6
Case Study of Jay Keaslinghelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip8
Lesson 3 Mechanistic Thinkinghelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip10
Designing a New Microbehelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip12
Organism Cardshelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphelliphellip13
copy 2009 Yu-Tzu Debbie Liu
Photo courtesy httpsyntheticbiologyorg
How are scientists thinkingmechanistically in the 21st century
Understanding Goals The rapid advancement of technology and the accumulation of information are changing
the patterns of scientific thinking and research in the 21st century Designing and creating novel organisms by combining various biological components
from different cells is one way scientists think mechanistically in the 21st century Designing and creating Scratch projects using graphical programming blocks is one way
students can display mechanistic thinking Identifying characteristics of successful scientist and their thinking patterns help us
become better (science) students by applying these skills to our own learning
Background Information Beyond the Scientific Method The scientific method has been commonly taught in science classrooms and textbooks as the only correct way to conduct scientific investigations This leaves students with the impression that all of science proceeds in much the same way Unfortunately this view is not entirely accurate Perhaps some scientists might conduct their work in this manner but rarely do they use it in the stereotyped step-by-step way that schools tend to teach itmdashdespite the fact that scientists report their work in this way in journals In fact scientists throughout history conduct their research in a variety of ways The exact approach a scientist uses depends on the individual doing the investigation as well as the particular question or problem being studied Furthermore scientists often engage in thinking patterns that are specific to its particular socio-cultural context 21st Century Scientific Thinking Skills With the explosion of advancements in scientific knowledge and technology at the turn of the century scientists at the cutting edge of research must adapt to new ways of interacting with their work Five prominent scientific thinking patterns of the 21st century are systems thinking mechanistic thinking interdisciplinary thinking quantitative thinking and distributed thinking1 In this lesson students will explore what mechanistic thinking Mechanistic Thinking It is a way of thinking that has a mechanical or engineering undertone This is shown through scientistsrsquo modular synthetic and purpose-driven approach towards their research problems Due to recent developments in new technologies and knowledge scientists are able to manipulate biology more directly allowing them to engineer and create novel biological systems for practical applications
1 Liu Y-T D amp Grotzer T A (2009) Looking forward Teaching the nature of the science of today and tomorrow In I M Saleh amp M S Khine (Eds) Fostering scientific habits of mind Pedagogical knowledge and best practices in science education (pp 9-36) Rotterdam Sense Publishers
copy 2009 Yu-Tzu Debbie Liu 1
What is Synthetic Biology The thinking involved in the field of synthetic biology is the best examples of mechanistic thinking With the rapidly emerging field of synthetic biology blurring the lines of biology and engineering scientists are no longer limited to working with organisms that naturally exist in the world Scientists often think synthetically by re-designing and constructing new organisms for practical and novel applications
Synthetic biology is an extension of genetic engineering Some even describe it as a more sophisticated version of genetic engineering taking into account a broader rational design perspective2 The engineering influence seeks out the simplicity in biological systems and brings standardization and modular design principles to biology
Synthetic biologists can use interchangeable parts from natural biology to assemble systems that function in new ways never existing before in living systems hence synthetic Modular circuit components (eg metabolic enzymes or fluorescent output genes) that are well characterized and can act independently of other cellular processes are used to build synthetic biological circuits Much like the ease of using LEGO bricksmdashstandardized bricks that can attach to any other partmdashsynthetic biology starts from the use of standardized biological building blocks The goal of synthetic biology is to both better understand how organisms function at the DNA protein and cell level by creating artificial biological systems and to solve important real-world problems the latter having caught the attention of scientists politicians and entrepreneurs Promising fields of application include energy environmental monitoring and remediation biotech and pharmaceuticals and materials fabrication
As pointed out in the detailed case study of Jay Keasling (one of the pioneers of synthetic biology) another key difference between synthetic biology and genetic engineering is the complexity of products or task the engineered organism can produce and accomplish Genetic engineering is typically limited to having microbes produce small proteins (eg insulin growth hormones) by simply inserting a single gene from a different organism into a microbe However with synthetic biology a complex interaction of several genes can be produced in a specified sequence much like what goes on in a chemical plant petroleum goes in and after a whole chain of reactions plastic comes out Scratch Scratch (httpscratchmitedu) is a programming language for young people (ages 8 and up) that makes it easy to create interactive projects (eg stories animations games simulations music and art) that can be shared on the Scratch website It is highly conducive to learning and teaching 21st century scientific thinking skills The Scratch grammar is designed so that users are presented with a versatile collection of graphical programming blocks that they can be snapped together to create programs much like LEGO bricks (and synthetic biology) Connectors on the blocks suggest how they should be put together so that over the process of tinkering with these blocks the emerging structure can give rise to new ideas and direction to the project Not only does snapping together complimentary blocks provide an easy way into learning programming but the idea of modularization as a problem-solving and design strategy is directly relevant to mechanistic thinking
2 Salisbury MW (2006) Get Ready for Synthetic Biology Genome Technology Magazine Retrieved from httpwwwgenome-technologycom
copy 2009 Yu-Tzu Debbie Liu 2
In this lesson Scratch is used to have students experience thinking mechanistically in their own work And since programming involves the creation of external representations of the problem-solving process Scratch provides students with opportunities of reflecting on their own thinking Lesson Layout These three lessons (one lesson per day) are designed to help students 1) understand how modern scientists think mechanistically 2) practice thinking mechanistically by simulating how synthetic biologists think in the field and 3) recognize mechanistic thinking even when it is not in the context of science as in their own work via Scratch Lesson 1 Designed to familiarize students with the Scratch programming language so that they can create projects on it At this point Scratch is presented simply as a medium for expressing what they have learned much like posters Powerpoint presentations and paper write-ups Lesson 2 Designed to expose students to the creative field of synthetic biology as a means to illustrate how scientists think mechanistically in the field This is done by a case study of Jay Keasling one of the pioneers of synthetic biology By analyzing how a modern scientist work and think students are provided with a broader view of scientific inquiry and the nature of scientific thinking Students will be asked to demonstrate their understanding of what they have learned so far by creating a Scratch project This allows students to work more closely and creatively with Scratch It also acts as a quick formative assessment for teachers of studentsrsquo learning thus far However the real goal of this exercise is to have students engage in mechanistic thinking in their own work which they may not recognize as it is not in the direct context of science This will be revealed in lesson 3 Lesson 3 Designed to have students practice thinking mechanistically by simulating how synthetic biologists think in the field via the Designing a New Microbe activity adapted from an actual experiment conducted in 20073 This activity presents students with a problem (need for hydrogen gas as alternative fuel) and asks students to design a microbe that can use starch and water to make hydrogen gas Students are given a set of organism cards to work with each card symbolizing a different type of organism (bacteria rabbit yeast archea spinach and mouse) Proteins (molecules that can convert one molecule into another) that are unique to each organism are listed on the card Studentsrsquo engineered microbe will essentially have different proteins from different organisms placed in a certain sequence to end up with a final product of hydrogen gas Students are given the Designing a New Microbe worksheet to help them visualize the problem better and reduce their cognitive loads (ie amount of information they need to carry in their heads) The activity allows students to discover that synthetic biology is a very mind-blowing field accomplishing things that some people never thought was possible Students will come to appreciate how seemingly impossible feats can be possible especially when scientists are thinking creatively By thinking and working mechanistically scientists have more freedom then before in designing and creating novel organisms for real-world applications
3 Zhang YH Evans BR Mielenz JR Hopkins RC Adams MW (2007) High-yield hydrogen production from starch and water by a synthetic enzymatic pathway PLoS ONE 5 e456
copy 2009 Yu-Tzu Debbie Liu 3
After the activity when students have grasped a much deeper understanding of what mechanistic thinking looks like in practice students are asked to reflect on their experience with Scratch The goal is to have students make the connection that they themselves have been engaging in mechanistic thinking while working on their own Scratch projects This reflective exercise encourages students to transfer their understanding of mechanistic thinking across different domains Students will also gain an appreciation of how studying trends in scientistsrsquo way of thinking can help them in their own thinking Lesson Placement These lessons can be used at the beginning of the school year when the scientific method is usually being presented Alternatively this lesson can be infused during the school year as students learn more about genetic engineering or creative thinking These lessons follow a constructivist approach to learning encouraging students to discover the meaning of mechanistic thinking through their exploration of a case study simulating how synthetic biologists think and making connections to their own work in Scratch Students are always encouraged to formulate their own ideas and connections before being presented with any information
copy 2009 Yu-Tzu Debbie Liu 4
Lesson Plan Day 1 Materials
Computers with Scratch installed Scratch Resources
Prep Step Review lesson plan background information and understanding goals Obtain computers with Scratch installed for students to work on Make copies of Scratch Resources (not provided)
Explore Step 1 Introduction to lesson Introduce the lesson by giving students a sense of what they will be doing and where they are headed by telling students ldquoThis will be a three-day lesson where we will be exploring how scientists think and more specifically what mechanistic thinking looks like in practice In this process we will also be learning Scratch We will tie everything together at the end of the third dayrdquo Step 2 Playing with Scratch Depending on the level of your students and any future goals you wish to achieve with Scratch structure the class so that students are comfortable navigating around the Scratch environment and are able to get started on their own Scratch project by the end of the class Please provide students with any Scratch resources you see fit Check out the ScratchEds resource search (httpscratchedmediamiteduresourcessearch) for more info Some good examples found in ScratchEd of Scratch lesson plans (video tutorials PowerPoints and worksheets) include
bull Having Fun with Computer Programming and Games (httpwwwleroieeducationoutreachsecondlevelscratchlessonplans)
bull A TeachNetUK Project 6 Lessons on Getting Started with Scratch (httpwwwteachnet-ukorguk200720ProjectsICT-ScratchScratchpages8_schemeofworkhtml)
bull Scratch Lessons Shall We Learn Scratch Programming for Tweens (httpwwwshallwelearncomscratchprogrammingforkidscategory)
bull Designing Animations and GamesmdashA Creative Introduction to Programming (httpwwwcsuni-potsdamde~romeikeUEWettbewerbindex-englishhtm)
Make sure to also introduce students to the Scratch online community and let them know that they can download the source code of any project to help them see how others are using the Scratch programming language to create projects
Review Extend and Apply Step 3 Scratch Assignment End the day by informing students that they will apply what they have learned today to create a mini-Scratch project for an assignment after the next dayrsquos lesson Emphasize to students that the goal is not to create a complex programming project but to use Scratch creatively as a medium for creative expressing not matter how simple the project is Encourage students to play with Scratch on their own time and make it clear that you highly encourage them to borrow adapt and build upon the ideas and projects of others (this is not considered cheating)
copy 2009 Yu-Tzu Debbie Liu 5
Lesson Plan Day 2 Materials
21st century scientist case study of Jay Keasling Student notebooks or journals
Prep Step Review lesson plan background information and understanding goals Make copies of 21st century scientist case study of Jay Keasling (p 8)
Explore Step 1 What is scientific thinking Ask students to describe what they think is scientific thinking Collect a representative list of studentsrsquo thoughts on the board Ask students to explain or expound on the meaning behind what they are saying After reviewing the list ask them ldquo Do you think all scientists come to their discoveries in the same wayrdquo ldquoDo scientists display all these characteristics at all timesrdquo It is important to point out to students that scientists have various methods going about their experimentation and work and depending on the type of work they are doing scientists donrsquot always share the same methods Furthermore scientists engage in thinking patterns that are specific to its particular socio-cultural context and one of which is mechanistic thinking Engage in a discussion with students on how might the explosion of advancements in scientific knowledge and technology at the turn of the century change the way scientists at the cutting edge of research interact with their work
Step 2 Analyze case study of a 21st century scientist Let students know that they will be learning about the field of synthetic biology as a means to illustrate how modern scientists work and think Specifically they will be studying Jay Keasling one of the pioneers of synthetic biology Hand out the case study on Jay Keasling Have students work in groups of 3-4 students to identify any patterns of thinking that the scientist displays Make sure to ask students to specifically identify what part of the case study justifies their claims Have students write the class findings in their journalsnotebooks
Possible findings from case analysis Jay Keasling
Keasling is a pioneer of synthetic biologymdasha field that designs and constructs new organisms for useful purposes He is most known for creating a microbe that produces a drug to treat malaria (making drugs from bugs) Some of his characteristics as a scientist include
bull Creative and imaginative wanted to invent new tools that can turn cells into chemical plants take in something very simple and spits out something complicated and valuable coming up with other applications of synthetic biology (use microbes to break down pesticides make biodegradable plastics create fuels from plants)
bull Critical thinking thought about how to design and create microbes to produce artemisinin much quicker and cheaper how to integrate genes from different species into a microbe to fabricate the drug
copy 2009 Yu-Tzu Debbie Liu 6
bull Seek and integrate information integrated methods and concepts from engineering and biology leading to synthetic biology
bull Supported with significant resources did research at universities and received grant money
bull Practical-minded microbes will churn out anti-malarial drug for a fraction of its current cost making it accessible to much more of the world these microbes could save millions of lives
bull Strong disciplinary understanding studied biology and chemical engineering extensively leading to his PhD and professor position at UC Berkeley
Step 3 What is mechanistic thinking Introduce students to the idea of mechanistic thinking as a prominent thinking pattern in the 21st
century
Mechanistic Thinking
Mechanistic thinking is a way of thinking that has a mechanical or engineering undertone This is shown through scientistsrsquo regular use of mechanical analogies to conceptualize their work and their modular synthetic and purpose-driven approach towards their research problems The display of mechanistic thinking by scientists appears to be a result of the merging of biology and engineering practices that is increasingly observed in 21st century biology as compared to a time when most of biologymdashtraditionally known for its pure basic researchmdashremain clearly demarcated from engineeringmdasha purely applied research field A mechanistic way of thinking has come to the forefront of 21st century science because of recent developments in new technologies and knowledge that enable scientists to manipulate the object or organism they are working with more directly allowing them to engineer and create novel biological systems for practical applications
Let students know that the work synthetic biologists do often require them to think mechanistically Now that students are given a definition of mechanistic thinking have students revisit their case study analysis and explore how synthetic biologists might think mechanistically
Review Extend and Apply
Step 4 Scratch Assignment Ask students to create a mini-Scratch project to demonstrate what they have learned so far (the project does not have to be all inclusive students can choose to focus on just one thing they learned either about scientific thinking mechanistic thinking or synthetic biology) Emphasize to students that the goal is not to create a complex programming project but to use Scratch creatively as a medium for creative expressing not matter how simple the project is Encourage students to work with partners and collaborate by borrowing adapting or building upon the ideas and projects of others (this is not considered cheating)
copy 2009 Yu-Tzu Debbie Liu 7
Detailed Case Study Jay Keasling
(1964 ndash present)
Best known for pioneering the new field of synthetic biology which designs and constructs new organisms for useful purposes He is also most known for creating a microbe that produces a drug to treat malaria (making drugs from bugs)
Jay Keasling was raised on a farm and spent his childhood exploring the practical side of biology chemistry and engineering This background eventually led him to work in the rapidly growing field that uses living organisms like bacteria for various practical purposes such as food processing agriculture and medicine
In the early 1980s genetic engineering became popular because you can ldquoconvincerdquo microbes to produce insulin growth hormones and other valuable proteins by simply inserting a single gene from a different organism into bacteria However Keasling believed that genetic engineering isnrsquot harnessing the full power of these cells The production of molecules isnt always so simple it requires a complex interaction of several genes (not just one) being produced in a certain sequence So Keasling wanted to invent the tools that would allow him to create these kinds of genetic assembly lines Thus what goes on in a cell is a lot like what goes on in a chemical plant petroleum goes in and after a whole chain of reactions plastic comes out
Keasling went to college studying biology and chemical engineering extensively and got his PhD in 1991 He is now a professor at the University of California at Berkeley He spent his first 10 years at UC Berkeley building the new tools he would need to turn cells into chemical plants He also invented powerful chemical switches (like a light switch) that allowed him to control when he wanted to ldquoturn onrdquo and ldquoturn offrdquo protein production in cells This way of borrowing techniques from engineering and figuring out how to manipulate microbes came to be call synthetic biology
After years of perfecting his biological tool kit Keasling wanted to find a real-world use for it In 2002 he learned of the dire need for artemisinin a compound derived from the sweet wormwood plant which is 90 percent effective against the parasite that causes malaria and has few side effects (malaria kills some 3 million people a year) However extracting the drug from sweet wormwood is a slow and expensive process Keasling figured he could design and create microbes to produce artemisinin much quicker and cheaper Rather than wait months for sweet wormwood to grow on farms Keasling wanted to create it simply by pouring sugar in a tank full of microbes that can use the sugar to make the drug via a chemical pathway he has designedmdashhe wanted to integrate genes from different species into a microbe to fabricate the drug for malaria
copy 2009 Yu-Tzu Debbie Liu 8
In 2006 Keaslings team (comprised of graduate students post-docs and research assistants) published their success of the production of artemisinin It is expected to lower the cost of artemisinin production from a dollar per gram to just 10 cents He was awarded a $43 million grant from the Bill and Melinda Gates Foundation and awarded DISCOVER magazinersquos first ever Scientist of the Year Award
Fighting malaria is just one part of Keaslings larger agenda to explore the potential of synthetic biology In his laboratory students are engineering microbes to break down pesticides make biodegradable plastics and create ethanol and other fuels from plants
Excerpts of i interview w Jay Keasling
1 You arrived at UC Berkeley in 1992 with training as both a chemical engineer and a biologist What did you hope to do
2 Why hadnt anybody tried to engineer cells that way before
3 How did you get involved in your antimalaria project
Jay Keisling biography adapted fromZimmer C (2006) Scientist of the Year Jay Keasling Discovermagazinecom Retrieved from
httpdiscovermagazinecom2006deccover
copy 2009 Yu-Tzu Debbie Liu 9
See responses to these questions atZimmer C (2006) Scientist of the Year Jay Keasling Discovermagazinecom Retrieved from
httpdiscovermagazinecom2006deccover
Interview content removed due to copyright restrictions
Interview content removed due to copyright restrictions
Interview content removed due to copyright restrictions
Lesson Plan Day 3 Materials
Designing a New Microbe worksheet Organism cards Student notebooks or journals
Prep Step Review lesson plan background information and understanding goals Photocopy Designing a New Microbe worksheet (p 28) Cut out organism cards (each group of 3-4 students will have a set of cards) (p29)
Explore Step 1 Designing a New Microbe Introduce todayrsquos activity by saying ldquoYou will be simulating how synthetic biologists think mechanistically by doing an the activity that is actually modeled after a real experiment done by scientists in 2007rdquo Divide students into groups of 3 or 4 Each group receives a set of organism cards Each student receives a Designing a New Microbe worksheet Remind students that proteins (or enzymes) are molecules inside cells that convert one molecule into another (eg the make-believe molecule How is converted to the molecule Home by Protein T in bacteria) Following the directions of the handout have students create a kind of assembly line that integrate proteins from different organisms into a microbe that uses water and starch (inputs) to ultimately produce hydrogen (output)
Possible answers to Designing a New Microbe
There are two possible pathways that can lead to hydrogen production
1 Starch amp water Protein G Protein P Protein D Protein R Protein T Protein F Protein H Hydrogen
2 Starch amp water Protein G Protein P Protein D Protein H Hydrogen
Guide students along by encouraging students who have already figured out how to attempt the problem to reveal and share with the class how they are thinking through the problem Stop students periodically to ask ldquoHow are you thinking through this problem What is your goal and how is your thinking helping you reach that goalrdquo Students may find either working sequentially forward or backward to fill in the worksheet to be easier
Note to teachers The hydrogen production pathway from starch and water is a shorten version of the actual 2007 experiment for learning purposes The organism types and molecule names are true to the experiment Protein names are made up for simplicity
copy 2009 Yu-Tzu Debbie Liu 10
Step 2 Discuss studentsrsquo findings Have students tell you what they found as you write their findings on the board Students may have discovered by now that there are two paths that lead to hydrogen production Students might recall that Jay Keasling have done something similar by making an antimalarial drug from sugar using synthetic biology Students may have also discovered that no proteins from the mouse organism were used for the design of their new microbe Ask students ldquowhat do you think is the purpose of having a mouse organism when we didnrsquot need itrdquo Help students understand how in reality scientists have hundreds of organisms to choose from some of which are irrelevant to their work In fact a common skill that scientists share is being about to identify and pull together important and relevant information The activity allows students to discover that synthetic biology is a very mind-blowing field accomplishing things that some people never thought was possible Students will come to appreciate how seemingly impossible feats can be possible especially when scientists are thinking creatively By thinking and working mechanistically scientists have more freedom then before in designing and creating novel organisms for real-world applications
Review Extend and Apply Step 3 How do you think mechanistically Ask students to reflect on their experience with Scratch and how they might have engaged in mechanistic thinking in their own work Helps students make the connection that they themselves have been engaging in mechanistic thinking while working on their own Scratch projects The Scratch grammar is designed so that users are presented with a versatile collection of graphical programming blocks that they can be snapped together to create programs much like synthetic biology Connectors on the blocks suggest how they should be put together so that over the process of tinkering with these blocks the emerging structure can give rise to new ideas and direction to the project Not only does snapping together complimentary blocks provide an easy way into learning programming but the idea of modularization as a problem-solving and design strategy is directly relevant to mechanistic thinking Go on to discuss how they can apply scientistsrsquo patterns of thinking to our own thinking in science class and daily life
copy 2009 Yu-Tzu Debbie Liu 11
Name___________________________ Date ____________
Designing a New Microbe
Task Gas prices have reached its all time high Thus scientists are trying to think of ways to produce alternative fuels such as hydrogen gas in a much cheaper and quicker way You are a scientist and you are familiar with six different organisms Based on what you know can you come up with a way to generate hydrogen from starch and water by designing a microbe that borrows different mechanismsproteins from different cells Fill in the blanks with protein names and the organism that the protein was taken from
Materials Each team has a set of cards each card symbolizing a different organism On the card you will see the name of the organism a picture of the organism and proteins that is unique to them Proteins (or enzymes) convert one molecule into another
Starch amp Water Protein borrowed Protein borrowed
Input Organism Organism
Protein borrowed $ Protein borrowed $ Protein borrowed Organism Organism Organism
Protein borrowed Protein borrowed Protein borrowed Hydrogen Organism Organism Organism Output
Experiment adapted from Zhang YH Evans BR Mielenz JR Hopkins RC Adams MW (2007) High-yield hydrogen production from
starch and water by a synthetic enzymatic pathway PLoS ONE 5 e456
copy 2009 Yu-Tzu Debbie Liu 12
Organism Cards (one set)
Teachers Please make as many copies as the number of groups of students Cut the cards out and shuffle before handing to students
Source NIH
Bacteria
Rabbitbull Protein T uses [X5P] to make [S7P]
Photo US Fish and Wildlife Service bull Protein F uses [S7P] to make [NADPH] bull Protein G uses starch and water to make [G-1-P] bull Protein P uses [G-1-P] to make [G-6-P]
Yeast
Public domain image (Source Wikimedia Commons)
bull Protein D uses [G-6-P] to make [NADPH] and [R5P]
Public domain image (Source Wikimedia Commons) Spinach
bull Protein R uses [R5P] to make [X5P]
Experiment adapted from
Archea Courtesy of Angels Tapias (License CC BY)
bull Protein H uses [NADPH] to make Hydrogen
Source NIH Mouse
bull Protein X uses [T8P] to make Hydrogen
Zhang YH Evans BR Mielenz JR Hopkins RC Adams MW (2007) High-yield hydrogen production from starch and water by a synthetic enzymatic pathway PLoS ONE 5 e456
copy 2009 Yu-Tzu Debbie Liu 13
MIT OpenCourseWarehttpocwmitedu
MAS714J STS445J Technologies for Creative Learning Fall 2009
For information about citing these materials or our Terms of Use visit httpocwmiteduterms
Photo courtesy httpsyntheticbiologyorg
How are scientists thinkingmechanistically in the 21st century
Understanding Goals The rapid advancement of technology and the accumulation of information are changing
the patterns of scientific thinking and research in the 21st century Designing and creating novel organisms by combining various biological components
from different cells is one way scientists think mechanistically in the 21st century Designing and creating Scratch projects using graphical programming blocks is one way
students can display mechanistic thinking Identifying characteristics of successful scientist and their thinking patterns help us
become better (science) students by applying these skills to our own learning
Background Information Beyond the Scientific Method The scientific method has been commonly taught in science classrooms and textbooks as the only correct way to conduct scientific investigations This leaves students with the impression that all of science proceeds in much the same way Unfortunately this view is not entirely accurate Perhaps some scientists might conduct their work in this manner but rarely do they use it in the stereotyped step-by-step way that schools tend to teach itmdashdespite the fact that scientists report their work in this way in journals In fact scientists throughout history conduct their research in a variety of ways The exact approach a scientist uses depends on the individual doing the investigation as well as the particular question or problem being studied Furthermore scientists often engage in thinking patterns that are specific to its particular socio-cultural context 21st Century Scientific Thinking Skills With the explosion of advancements in scientific knowledge and technology at the turn of the century scientists at the cutting edge of research must adapt to new ways of interacting with their work Five prominent scientific thinking patterns of the 21st century are systems thinking mechanistic thinking interdisciplinary thinking quantitative thinking and distributed thinking1 In this lesson students will explore what mechanistic thinking Mechanistic Thinking It is a way of thinking that has a mechanical or engineering undertone This is shown through scientistsrsquo modular synthetic and purpose-driven approach towards their research problems Due to recent developments in new technologies and knowledge scientists are able to manipulate biology more directly allowing them to engineer and create novel biological systems for practical applications
1 Liu Y-T D amp Grotzer T A (2009) Looking forward Teaching the nature of the science of today and tomorrow In I M Saleh amp M S Khine (Eds) Fostering scientific habits of mind Pedagogical knowledge and best practices in science education (pp 9-36) Rotterdam Sense Publishers
copy 2009 Yu-Tzu Debbie Liu 1
What is Synthetic Biology The thinking involved in the field of synthetic biology is the best examples of mechanistic thinking With the rapidly emerging field of synthetic biology blurring the lines of biology and engineering scientists are no longer limited to working with organisms that naturally exist in the world Scientists often think synthetically by re-designing and constructing new organisms for practical and novel applications
Synthetic biology is an extension of genetic engineering Some even describe it as a more sophisticated version of genetic engineering taking into account a broader rational design perspective2 The engineering influence seeks out the simplicity in biological systems and brings standardization and modular design principles to biology
Synthetic biologists can use interchangeable parts from natural biology to assemble systems that function in new ways never existing before in living systems hence synthetic Modular circuit components (eg metabolic enzymes or fluorescent output genes) that are well characterized and can act independently of other cellular processes are used to build synthetic biological circuits Much like the ease of using LEGO bricksmdashstandardized bricks that can attach to any other partmdashsynthetic biology starts from the use of standardized biological building blocks The goal of synthetic biology is to both better understand how organisms function at the DNA protein and cell level by creating artificial biological systems and to solve important real-world problems the latter having caught the attention of scientists politicians and entrepreneurs Promising fields of application include energy environmental monitoring and remediation biotech and pharmaceuticals and materials fabrication
As pointed out in the detailed case study of Jay Keasling (one of the pioneers of synthetic biology) another key difference between synthetic biology and genetic engineering is the complexity of products or task the engineered organism can produce and accomplish Genetic engineering is typically limited to having microbes produce small proteins (eg insulin growth hormones) by simply inserting a single gene from a different organism into a microbe However with synthetic biology a complex interaction of several genes can be produced in a specified sequence much like what goes on in a chemical plant petroleum goes in and after a whole chain of reactions plastic comes out Scratch Scratch (httpscratchmitedu) is a programming language for young people (ages 8 and up) that makes it easy to create interactive projects (eg stories animations games simulations music and art) that can be shared on the Scratch website It is highly conducive to learning and teaching 21st century scientific thinking skills The Scratch grammar is designed so that users are presented with a versatile collection of graphical programming blocks that they can be snapped together to create programs much like LEGO bricks (and synthetic biology) Connectors on the blocks suggest how they should be put together so that over the process of tinkering with these blocks the emerging structure can give rise to new ideas and direction to the project Not only does snapping together complimentary blocks provide an easy way into learning programming but the idea of modularization as a problem-solving and design strategy is directly relevant to mechanistic thinking
2 Salisbury MW (2006) Get Ready for Synthetic Biology Genome Technology Magazine Retrieved from httpwwwgenome-technologycom
copy 2009 Yu-Tzu Debbie Liu 2
In this lesson Scratch is used to have students experience thinking mechanistically in their own work And since programming involves the creation of external representations of the problem-solving process Scratch provides students with opportunities of reflecting on their own thinking Lesson Layout These three lessons (one lesson per day) are designed to help students 1) understand how modern scientists think mechanistically 2) practice thinking mechanistically by simulating how synthetic biologists think in the field and 3) recognize mechanistic thinking even when it is not in the context of science as in their own work via Scratch Lesson 1 Designed to familiarize students with the Scratch programming language so that they can create projects on it At this point Scratch is presented simply as a medium for expressing what they have learned much like posters Powerpoint presentations and paper write-ups Lesson 2 Designed to expose students to the creative field of synthetic biology as a means to illustrate how scientists think mechanistically in the field This is done by a case study of Jay Keasling one of the pioneers of synthetic biology By analyzing how a modern scientist work and think students are provided with a broader view of scientific inquiry and the nature of scientific thinking Students will be asked to demonstrate their understanding of what they have learned so far by creating a Scratch project This allows students to work more closely and creatively with Scratch It also acts as a quick formative assessment for teachers of studentsrsquo learning thus far However the real goal of this exercise is to have students engage in mechanistic thinking in their own work which they may not recognize as it is not in the direct context of science This will be revealed in lesson 3 Lesson 3 Designed to have students practice thinking mechanistically by simulating how synthetic biologists think in the field via the Designing a New Microbe activity adapted from an actual experiment conducted in 20073 This activity presents students with a problem (need for hydrogen gas as alternative fuel) and asks students to design a microbe that can use starch and water to make hydrogen gas Students are given a set of organism cards to work with each card symbolizing a different type of organism (bacteria rabbit yeast archea spinach and mouse) Proteins (molecules that can convert one molecule into another) that are unique to each organism are listed on the card Studentsrsquo engineered microbe will essentially have different proteins from different organisms placed in a certain sequence to end up with a final product of hydrogen gas Students are given the Designing a New Microbe worksheet to help them visualize the problem better and reduce their cognitive loads (ie amount of information they need to carry in their heads) The activity allows students to discover that synthetic biology is a very mind-blowing field accomplishing things that some people never thought was possible Students will come to appreciate how seemingly impossible feats can be possible especially when scientists are thinking creatively By thinking and working mechanistically scientists have more freedom then before in designing and creating novel organisms for real-world applications
3 Zhang YH Evans BR Mielenz JR Hopkins RC Adams MW (2007) High-yield hydrogen production from starch and water by a synthetic enzymatic pathway PLoS ONE 5 e456
copy 2009 Yu-Tzu Debbie Liu 3
After the activity when students have grasped a much deeper understanding of what mechanistic thinking looks like in practice students are asked to reflect on their experience with Scratch The goal is to have students make the connection that they themselves have been engaging in mechanistic thinking while working on their own Scratch projects This reflective exercise encourages students to transfer their understanding of mechanistic thinking across different domains Students will also gain an appreciation of how studying trends in scientistsrsquo way of thinking can help them in their own thinking Lesson Placement These lessons can be used at the beginning of the school year when the scientific method is usually being presented Alternatively this lesson can be infused during the school year as students learn more about genetic engineering or creative thinking These lessons follow a constructivist approach to learning encouraging students to discover the meaning of mechanistic thinking through their exploration of a case study simulating how synthetic biologists think and making connections to their own work in Scratch Students are always encouraged to formulate their own ideas and connections before being presented with any information
copy 2009 Yu-Tzu Debbie Liu 4
Lesson Plan Day 1 Materials
Computers with Scratch installed Scratch Resources
Prep Step Review lesson plan background information and understanding goals Obtain computers with Scratch installed for students to work on Make copies of Scratch Resources (not provided)
Explore Step 1 Introduction to lesson Introduce the lesson by giving students a sense of what they will be doing and where they are headed by telling students ldquoThis will be a three-day lesson where we will be exploring how scientists think and more specifically what mechanistic thinking looks like in practice In this process we will also be learning Scratch We will tie everything together at the end of the third dayrdquo Step 2 Playing with Scratch Depending on the level of your students and any future goals you wish to achieve with Scratch structure the class so that students are comfortable navigating around the Scratch environment and are able to get started on their own Scratch project by the end of the class Please provide students with any Scratch resources you see fit Check out the ScratchEds resource search (httpscratchedmediamiteduresourcessearch) for more info Some good examples found in ScratchEd of Scratch lesson plans (video tutorials PowerPoints and worksheets) include
bull Having Fun with Computer Programming and Games (httpwwwleroieeducationoutreachsecondlevelscratchlessonplans)
bull A TeachNetUK Project 6 Lessons on Getting Started with Scratch (httpwwwteachnet-ukorguk200720ProjectsICT-ScratchScratchpages8_schemeofworkhtml)
bull Scratch Lessons Shall We Learn Scratch Programming for Tweens (httpwwwshallwelearncomscratchprogrammingforkidscategory)
bull Designing Animations and GamesmdashA Creative Introduction to Programming (httpwwwcsuni-potsdamde~romeikeUEWettbewerbindex-englishhtm)
Make sure to also introduce students to the Scratch online community and let them know that they can download the source code of any project to help them see how others are using the Scratch programming language to create projects
Review Extend and Apply Step 3 Scratch Assignment End the day by informing students that they will apply what they have learned today to create a mini-Scratch project for an assignment after the next dayrsquos lesson Emphasize to students that the goal is not to create a complex programming project but to use Scratch creatively as a medium for creative expressing not matter how simple the project is Encourage students to play with Scratch on their own time and make it clear that you highly encourage them to borrow adapt and build upon the ideas and projects of others (this is not considered cheating)
copy 2009 Yu-Tzu Debbie Liu 5
Lesson Plan Day 2 Materials
21st century scientist case study of Jay Keasling Student notebooks or journals
Prep Step Review lesson plan background information and understanding goals Make copies of 21st century scientist case study of Jay Keasling (p 8)
Explore Step 1 What is scientific thinking Ask students to describe what they think is scientific thinking Collect a representative list of studentsrsquo thoughts on the board Ask students to explain or expound on the meaning behind what they are saying After reviewing the list ask them ldquo Do you think all scientists come to their discoveries in the same wayrdquo ldquoDo scientists display all these characteristics at all timesrdquo It is important to point out to students that scientists have various methods going about their experimentation and work and depending on the type of work they are doing scientists donrsquot always share the same methods Furthermore scientists engage in thinking patterns that are specific to its particular socio-cultural context and one of which is mechanistic thinking Engage in a discussion with students on how might the explosion of advancements in scientific knowledge and technology at the turn of the century change the way scientists at the cutting edge of research interact with their work
Step 2 Analyze case study of a 21st century scientist Let students know that they will be learning about the field of synthetic biology as a means to illustrate how modern scientists work and think Specifically they will be studying Jay Keasling one of the pioneers of synthetic biology Hand out the case study on Jay Keasling Have students work in groups of 3-4 students to identify any patterns of thinking that the scientist displays Make sure to ask students to specifically identify what part of the case study justifies their claims Have students write the class findings in their journalsnotebooks
Possible findings from case analysis Jay Keasling
Keasling is a pioneer of synthetic biologymdasha field that designs and constructs new organisms for useful purposes He is most known for creating a microbe that produces a drug to treat malaria (making drugs from bugs) Some of his characteristics as a scientist include
bull Creative and imaginative wanted to invent new tools that can turn cells into chemical plants take in something very simple and spits out something complicated and valuable coming up with other applications of synthetic biology (use microbes to break down pesticides make biodegradable plastics create fuels from plants)
bull Critical thinking thought about how to design and create microbes to produce artemisinin much quicker and cheaper how to integrate genes from different species into a microbe to fabricate the drug
copy 2009 Yu-Tzu Debbie Liu 6
bull Seek and integrate information integrated methods and concepts from engineering and biology leading to synthetic biology
bull Supported with significant resources did research at universities and received grant money
bull Practical-minded microbes will churn out anti-malarial drug for a fraction of its current cost making it accessible to much more of the world these microbes could save millions of lives
bull Strong disciplinary understanding studied biology and chemical engineering extensively leading to his PhD and professor position at UC Berkeley
Step 3 What is mechanistic thinking Introduce students to the idea of mechanistic thinking as a prominent thinking pattern in the 21st
century
Mechanistic Thinking
Mechanistic thinking is a way of thinking that has a mechanical or engineering undertone This is shown through scientistsrsquo regular use of mechanical analogies to conceptualize their work and their modular synthetic and purpose-driven approach towards their research problems The display of mechanistic thinking by scientists appears to be a result of the merging of biology and engineering practices that is increasingly observed in 21st century biology as compared to a time when most of biologymdashtraditionally known for its pure basic researchmdashremain clearly demarcated from engineeringmdasha purely applied research field A mechanistic way of thinking has come to the forefront of 21st century science because of recent developments in new technologies and knowledge that enable scientists to manipulate the object or organism they are working with more directly allowing them to engineer and create novel biological systems for practical applications
Let students know that the work synthetic biologists do often require them to think mechanistically Now that students are given a definition of mechanistic thinking have students revisit their case study analysis and explore how synthetic biologists might think mechanistically
Review Extend and Apply
Step 4 Scratch Assignment Ask students to create a mini-Scratch project to demonstrate what they have learned so far (the project does not have to be all inclusive students can choose to focus on just one thing they learned either about scientific thinking mechanistic thinking or synthetic biology) Emphasize to students that the goal is not to create a complex programming project but to use Scratch creatively as a medium for creative expressing not matter how simple the project is Encourage students to work with partners and collaborate by borrowing adapting or building upon the ideas and projects of others (this is not considered cheating)
copy 2009 Yu-Tzu Debbie Liu 7
Detailed Case Study Jay Keasling
(1964 ndash present)
Best known for pioneering the new field of synthetic biology which designs and constructs new organisms for useful purposes He is also most known for creating a microbe that produces a drug to treat malaria (making drugs from bugs)
Jay Keasling was raised on a farm and spent his childhood exploring the practical side of biology chemistry and engineering This background eventually led him to work in the rapidly growing field that uses living organisms like bacteria for various practical purposes such as food processing agriculture and medicine
In the early 1980s genetic engineering became popular because you can ldquoconvincerdquo microbes to produce insulin growth hormones and other valuable proteins by simply inserting a single gene from a different organism into bacteria However Keasling believed that genetic engineering isnrsquot harnessing the full power of these cells The production of molecules isnt always so simple it requires a complex interaction of several genes (not just one) being produced in a certain sequence So Keasling wanted to invent the tools that would allow him to create these kinds of genetic assembly lines Thus what goes on in a cell is a lot like what goes on in a chemical plant petroleum goes in and after a whole chain of reactions plastic comes out
Keasling went to college studying biology and chemical engineering extensively and got his PhD in 1991 He is now a professor at the University of California at Berkeley He spent his first 10 years at UC Berkeley building the new tools he would need to turn cells into chemical plants He also invented powerful chemical switches (like a light switch) that allowed him to control when he wanted to ldquoturn onrdquo and ldquoturn offrdquo protein production in cells This way of borrowing techniques from engineering and figuring out how to manipulate microbes came to be call synthetic biology
After years of perfecting his biological tool kit Keasling wanted to find a real-world use for it In 2002 he learned of the dire need for artemisinin a compound derived from the sweet wormwood plant which is 90 percent effective against the parasite that causes malaria and has few side effects (malaria kills some 3 million people a year) However extracting the drug from sweet wormwood is a slow and expensive process Keasling figured he could design and create microbes to produce artemisinin much quicker and cheaper Rather than wait months for sweet wormwood to grow on farms Keasling wanted to create it simply by pouring sugar in a tank full of microbes that can use the sugar to make the drug via a chemical pathway he has designedmdashhe wanted to integrate genes from different species into a microbe to fabricate the drug for malaria
copy 2009 Yu-Tzu Debbie Liu 8
In 2006 Keaslings team (comprised of graduate students post-docs and research assistants) published their success of the production of artemisinin It is expected to lower the cost of artemisinin production from a dollar per gram to just 10 cents He was awarded a $43 million grant from the Bill and Melinda Gates Foundation and awarded DISCOVER magazinersquos first ever Scientist of the Year Award
Fighting malaria is just one part of Keaslings larger agenda to explore the potential of synthetic biology In his laboratory students are engineering microbes to break down pesticides make biodegradable plastics and create ethanol and other fuels from plants
Excerpts of i interview w Jay Keasling
1 You arrived at UC Berkeley in 1992 with training as both a chemical engineer and a biologist What did you hope to do
2 Why hadnt anybody tried to engineer cells that way before
3 How did you get involved in your antimalaria project
Jay Keisling biography adapted fromZimmer C (2006) Scientist of the Year Jay Keasling Discovermagazinecom Retrieved from
httpdiscovermagazinecom2006deccover
copy 2009 Yu-Tzu Debbie Liu 9
See responses to these questions atZimmer C (2006) Scientist of the Year Jay Keasling Discovermagazinecom Retrieved from
httpdiscovermagazinecom2006deccover
Interview content removed due to copyright restrictions
Interview content removed due to copyright restrictions
Interview content removed due to copyright restrictions
Lesson Plan Day 3 Materials
Designing a New Microbe worksheet Organism cards Student notebooks or journals
Prep Step Review lesson plan background information and understanding goals Photocopy Designing a New Microbe worksheet (p 28) Cut out organism cards (each group of 3-4 students will have a set of cards) (p29)
Explore Step 1 Designing a New Microbe Introduce todayrsquos activity by saying ldquoYou will be simulating how synthetic biologists think mechanistically by doing an the activity that is actually modeled after a real experiment done by scientists in 2007rdquo Divide students into groups of 3 or 4 Each group receives a set of organism cards Each student receives a Designing a New Microbe worksheet Remind students that proteins (or enzymes) are molecules inside cells that convert one molecule into another (eg the make-believe molecule How is converted to the molecule Home by Protein T in bacteria) Following the directions of the handout have students create a kind of assembly line that integrate proteins from different organisms into a microbe that uses water and starch (inputs) to ultimately produce hydrogen (output)
Possible answers to Designing a New Microbe
There are two possible pathways that can lead to hydrogen production
1 Starch amp water Protein G Protein P Protein D Protein R Protein T Protein F Protein H Hydrogen
2 Starch amp water Protein G Protein P Protein D Protein H Hydrogen
Guide students along by encouraging students who have already figured out how to attempt the problem to reveal and share with the class how they are thinking through the problem Stop students periodically to ask ldquoHow are you thinking through this problem What is your goal and how is your thinking helping you reach that goalrdquo Students may find either working sequentially forward or backward to fill in the worksheet to be easier
Note to teachers The hydrogen production pathway from starch and water is a shorten version of the actual 2007 experiment for learning purposes The organism types and molecule names are true to the experiment Protein names are made up for simplicity
copy 2009 Yu-Tzu Debbie Liu 10
Step 2 Discuss studentsrsquo findings Have students tell you what they found as you write their findings on the board Students may have discovered by now that there are two paths that lead to hydrogen production Students might recall that Jay Keasling have done something similar by making an antimalarial drug from sugar using synthetic biology Students may have also discovered that no proteins from the mouse organism were used for the design of their new microbe Ask students ldquowhat do you think is the purpose of having a mouse organism when we didnrsquot need itrdquo Help students understand how in reality scientists have hundreds of organisms to choose from some of which are irrelevant to their work In fact a common skill that scientists share is being about to identify and pull together important and relevant information The activity allows students to discover that synthetic biology is a very mind-blowing field accomplishing things that some people never thought was possible Students will come to appreciate how seemingly impossible feats can be possible especially when scientists are thinking creatively By thinking and working mechanistically scientists have more freedom then before in designing and creating novel organisms for real-world applications
Review Extend and Apply Step 3 How do you think mechanistically Ask students to reflect on their experience with Scratch and how they might have engaged in mechanistic thinking in their own work Helps students make the connection that they themselves have been engaging in mechanistic thinking while working on their own Scratch projects The Scratch grammar is designed so that users are presented with a versatile collection of graphical programming blocks that they can be snapped together to create programs much like synthetic biology Connectors on the blocks suggest how they should be put together so that over the process of tinkering with these blocks the emerging structure can give rise to new ideas and direction to the project Not only does snapping together complimentary blocks provide an easy way into learning programming but the idea of modularization as a problem-solving and design strategy is directly relevant to mechanistic thinking Go on to discuss how they can apply scientistsrsquo patterns of thinking to our own thinking in science class and daily life
copy 2009 Yu-Tzu Debbie Liu 11
Name___________________________ Date ____________
Designing a New Microbe
Task Gas prices have reached its all time high Thus scientists are trying to think of ways to produce alternative fuels such as hydrogen gas in a much cheaper and quicker way You are a scientist and you are familiar with six different organisms Based on what you know can you come up with a way to generate hydrogen from starch and water by designing a microbe that borrows different mechanismsproteins from different cells Fill in the blanks with protein names and the organism that the protein was taken from
Materials Each team has a set of cards each card symbolizing a different organism On the card you will see the name of the organism a picture of the organism and proteins that is unique to them Proteins (or enzymes) convert one molecule into another
Starch amp Water Protein borrowed Protein borrowed
Input Organism Organism
Protein borrowed $ Protein borrowed $ Protein borrowed Organism Organism Organism
Protein borrowed Protein borrowed Protein borrowed Hydrogen Organism Organism Organism Output
Experiment adapted from Zhang YH Evans BR Mielenz JR Hopkins RC Adams MW (2007) High-yield hydrogen production from
starch and water by a synthetic enzymatic pathway PLoS ONE 5 e456
copy 2009 Yu-Tzu Debbie Liu 12
Organism Cards (one set)
Teachers Please make as many copies as the number of groups of students Cut the cards out and shuffle before handing to students
Source NIH
Bacteria
Rabbitbull Protein T uses [X5P] to make [S7P]
Photo US Fish and Wildlife Service bull Protein F uses [S7P] to make [NADPH] bull Protein G uses starch and water to make [G-1-P] bull Protein P uses [G-1-P] to make [G-6-P]
Yeast
Public domain image (Source Wikimedia Commons)
bull Protein D uses [G-6-P] to make [NADPH] and [R5P]
Public domain image (Source Wikimedia Commons) Spinach
bull Protein R uses [R5P] to make [X5P]
Experiment adapted from
Archea Courtesy of Angels Tapias (License CC BY)
bull Protein H uses [NADPH] to make Hydrogen
Source NIH Mouse
bull Protein X uses [T8P] to make Hydrogen
Zhang YH Evans BR Mielenz JR Hopkins RC Adams MW (2007) High-yield hydrogen production from starch and water by a synthetic enzymatic pathway PLoS ONE 5 e456
copy 2009 Yu-Tzu Debbie Liu 13
MIT OpenCourseWarehttpocwmitedu
MAS714J STS445J Technologies for Creative Learning Fall 2009
For information about citing these materials or our Terms of Use visit httpocwmiteduterms
What is Synthetic Biology The thinking involved in the field of synthetic biology is the best examples of mechanistic thinking With the rapidly emerging field of synthetic biology blurring the lines of biology and engineering scientists are no longer limited to working with organisms that naturally exist in the world Scientists often think synthetically by re-designing and constructing new organisms for practical and novel applications
Synthetic biology is an extension of genetic engineering Some even describe it as a more sophisticated version of genetic engineering taking into account a broader rational design perspective2 The engineering influence seeks out the simplicity in biological systems and brings standardization and modular design principles to biology
Synthetic biologists can use interchangeable parts from natural biology to assemble systems that function in new ways never existing before in living systems hence synthetic Modular circuit components (eg metabolic enzymes or fluorescent output genes) that are well characterized and can act independently of other cellular processes are used to build synthetic biological circuits Much like the ease of using LEGO bricksmdashstandardized bricks that can attach to any other partmdashsynthetic biology starts from the use of standardized biological building blocks The goal of synthetic biology is to both better understand how organisms function at the DNA protein and cell level by creating artificial biological systems and to solve important real-world problems the latter having caught the attention of scientists politicians and entrepreneurs Promising fields of application include energy environmental monitoring and remediation biotech and pharmaceuticals and materials fabrication
As pointed out in the detailed case study of Jay Keasling (one of the pioneers of synthetic biology) another key difference between synthetic biology and genetic engineering is the complexity of products or task the engineered organism can produce and accomplish Genetic engineering is typically limited to having microbes produce small proteins (eg insulin growth hormones) by simply inserting a single gene from a different organism into a microbe However with synthetic biology a complex interaction of several genes can be produced in a specified sequence much like what goes on in a chemical plant petroleum goes in and after a whole chain of reactions plastic comes out Scratch Scratch (httpscratchmitedu) is a programming language for young people (ages 8 and up) that makes it easy to create interactive projects (eg stories animations games simulations music and art) that can be shared on the Scratch website It is highly conducive to learning and teaching 21st century scientific thinking skills The Scratch grammar is designed so that users are presented with a versatile collection of graphical programming blocks that they can be snapped together to create programs much like LEGO bricks (and synthetic biology) Connectors on the blocks suggest how they should be put together so that over the process of tinkering with these blocks the emerging structure can give rise to new ideas and direction to the project Not only does snapping together complimentary blocks provide an easy way into learning programming but the idea of modularization as a problem-solving and design strategy is directly relevant to mechanistic thinking
2 Salisbury MW (2006) Get Ready for Synthetic Biology Genome Technology Magazine Retrieved from httpwwwgenome-technologycom
copy 2009 Yu-Tzu Debbie Liu 2
In this lesson Scratch is used to have students experience thinking mechanistically in their own work And since programming involves the creation of external representations of the problem-solving process Scratch provides students with opportunities of reflecting on their own thinking Lesson Layout These three lessons (one lesson per day) are designed to help students 1) understand how modern scientists think mechanistically 2) practice thinking mechanistically by simulating how synthetic biologists think in the field and 3) recognize mechanistic thinking even when it is not in the context of science as in their own work via Scratch Lesson 1 Designed to familiarize students with the Scratch programming language so that they can create projects on it At this point Scratch is presented simply as a medium for expressing what they have learned much like posters Powerpoint presentations and paper write-ups Lesson 2 Designed to expose students to the creative field of synthetic biology as a means to illustrate how scientists think mechanistically in the field This is done by a case study of Jay Keasling one of the pioneers of synthetic biology By analyzing how a modern scientist work and think students are provided with a broader view of scientific inquiry and the nature of scientific thinking Students will be asked to demonstrate their understanding of what they have learned so far by creating a Scratch project This allows students to work more closely and creatively with Scratch It also acts as a quick formative assessment for teachers of studentsrsquo learning thus far However the real goal of this exercise is to have students engage in mechanistic thinking in their own work which they may not recognize as it is not in the direct context of science This will be revealed in lesson 3 Lesson 3 Designed to have students practice thinking mechanistically by simulating how synthetic biologists think in the field via the Designing a New Microbe activity adapted from an actual experiment conducted in 20073 This activity presents students with a problem (need for hydrogen gas as alternative fuel) and asks students to design a microbe that can use starch and water to make hydrogen gas Students are given a set of organism cards to work with each card symbolizing a different type of organism (bacteria rabbit yeast archea spinach and mouse) Proteins (molecules that can convert one molecule into another) that are unique to each organism are listed on the card Studentsrsquo engineered microbe will essentially have different proteins from different organisms placed in a certain sequence to end up with a final product of hydrogen gas Students are given the Designing a New Microbe worksheet to help them visualize the problem better and reduce their cognitive loads (ie amount of information they need to carry in their heads) The activity allows students to discover that synthetic biology is a very mind-blowing field accomplishing things that some people never thought was possible Students will come to appreciate how seemingly impossible feats can be possible especially when scientists are thinking creatively By thinking and working mechanistically scientists have more freedom then before in designing and creating novel organisms for real-world applications
3 Zhang YH Evans BR Mielenz JR Hopkins RC Adams MW (2007) High-yield hydrogen production from starch and water by a synthetic enzymatic pathway PLoS ONE 5 e456
copy 2009 Yu-Tzu Debbie Liu 3
After the activity when students have grasped a much deeper understanding of what mechanistic thinking looks like in practice students are asked to reflect on their experience with Scratch The goal is to have students make the connection that they themselves have been engaging in mechanistic thinking while working on their own Scratch projects This reflective exercise encourages students to transfer their understanding of mechanistic thinking across different domains Students will also gain an appreciation of how studying trends in scientistsrsquo way of thinking can help them in their own thinking Lesson Placement These lessons can be used at the beginning of the school year when the scientific method is usually being presented Alternatively this lesson can be infused during the school year as students learn more about genetic engineering or creative thinking These lessons follow a constructivist approach to learning encouraging students to discover the meaning of mechanistic thinking through their exploration of a case study simulating how synthetic biologists think and making connections to their own work in Scratch Students are always encouraged to formulate their own ideas and connections before being presented with any information
copy 2009 Yu-Tzu Debbie Liu 4
Lesson Plan Day 1 Materials
Computers with Scratch installed Scratch Resources
Prep Step Review lesson plan background information and understanding goals Obtain computers with Scratch installed for students to work on Make copies of Scratch Resources (not provided)
Explore Step 1 Introduction to lesson Introduce the lesson by giving students a sense of what they will be doing and where they are headed by telling students ldquoThis will be a three-day lesson where we will be exploring how scientists think and more specifically what mechanistic thinking looks like in practice In this process we will also be learning Scratch We will tie everything together at the end of the third dayrdquo Step 2 Playing with Scratch Depending on the level of your students and any future goals you wish to achieve with Scratch structure the class so that students are comfortable navigating around the Scratch environment and are able to get started on their own Scratch project by the end of the class Please provide students with any Scratch resources you see fit Check out the ScratchEds resource search (httpscratchedmediamiteduresourcessearch) for more info Some good examples found in ScratchEd of Scratch lesson plans (video tutorials PowerPoints and worksheets) include
bull Having Fun with Computer Programming and Games (httpwwwleroieeducationoutreachsecondlevelscratchlessonplans)
bull A TeachNetUK Project 6 Lessons on Getting Started with Scratch (httpwwwteachnet-ukorguk200720ProjectsICT-ScratchScratchpages8_schemeofworkhtml)
bull Scratch Lessons Shall We Learn Scratch Programming for Tweens (httpwwwshallwelearncomscratchprogrammingforkidscategory)
bull Designing Animations and GamesmdashA Creative Introduction to Programming (httpwwwcsuni-potsdamde~romeikeUEWettbewerbindex-englishhtm)
Make sure to also introduce students to the Scratch online community and let them know that they can download the source code of any project to help them see how others are using the Scratch programming language to create projects
Review Extend and Apply Step 3 Scratch Assignment End the day by informing students that they will apply what they have learned today to create a mini-Scratch project for an assignment after the next dayrsquos lesson Emphasize to students that the goal is not to create a complex programming project but to use Scratch creatively as a medium for creative expressing not matter how simple the project is Encourage students to play with Scratch on their own time and make it clear that you highly encourage them to borrow adapt and build upon the ideas and projects of others (this is not considered cheating)
copy 2009 Yu-Tzu Debbie Liu 5
Lesson Plan Day 2 Materials
21st century scientist case study of Jay Keasling Student notebooks or journals
Prep Step Review lesson plan background information and understanding goals Make copies of 21st century scientist case study of Jay Keasling (p 8)
Explore Step 1 What is scientific thinking Ask students to describe what they think is scientific thinking Collect a representative list of studentsrsquo thoughts on the board Ask students to explain or expound on the meaning behind what they are saying After reviewing the list ask them ldquo Do you think all scientists come to their discoveries in the same wayrdquo ldquoDo scientists display all these characteristics at all timesrdquo It is important to point out to students that scientists have various methods going about their experimentation and work and depending on the type of work they are doing scientists donrsquot always share the same methods Furthermore scientists engage in thinking patterns that are specific to its particular socio-cultural context and one of which is mechanistic thinking Engage in a discussion with students on how might the explosion of advancements in scientific knowledge and technology at the turn of the century change the way scientists at the cutting edge of research interact with their work
Step 2 Analyze case study of a 21st century scientist Let students know that they will be learning about the field of synthetic biology as a means to illustrate how modern scientists work and think Specifically they will be studying Jay Keasling one of the pioneers of synthetic biology Hand out the case study on Jay Keasling Have students work in groups of 3-4 students to identify any patterns of thinking that the scientist displays Make sure to ask students to specifically identify what part of the case study justifies their claims Have students write the class findings in their journalsnotebooks
Possible findings from case analysis Jay Keasling
Keasling is a pioneer of synthetic biologymdasha field that designs and constructs new organisms for useful purposes He is most known for creating a microbe that produces a drug to treat malaria (making drugs from bugs) Some of his characteristics as a scientist include
bull Creative and imaginative wanted to invent new tools that can turn cells into chemical plants take in something very simple and spits out something complicated and valuable coming up with other applications of synthetic biology (use microbes to break down pesticides make biodegradable plastics create fuels from plants)
bull Critical thinking thought about how to design and create microbes to produce artemisinin much quicker and cheaper how to integrate genes from different species into a microbe to fabricate the drug
copy 2009 Yu-Tzu Debbie Liu 6
bull Seek and integrate information integrated methods and concepts from engineering and biology leading to synthetic biology
bull Supported with significant resources did research at universities and received grant money
bull Practical-minded microbes will churn out anti-malarial drug for a fraction of its current cost making it accessible to much more of the world these microbes could save millions of lives
bull Strong disciplinary understanding studied biology and chemical engineering extensively leading to his PhD and professor position at UC Berkeley
Step 3 What is mechanistic thinking Introduce students to the idea of mechanistic thinking as a prominent thinking pattern in the 21st
century
Mechanistic Thinking
Mechanistic thinking is a way of thinking that has a mechanical or engineering undertone This is shown through scientistsrsquo regular use of mechanical analogies to conceptualize their work and their modular synthetic and purpose-driven approach towards their research problems The display of mechanistic thinking by scientists appears to be a result of the merging of biology and engineering practices that is increasingly observed in 21st century biology as compared to a time when most of biologymdashtraditionally known for its pure basic researchmdashremain clearly demarcated from engineeringmdasha purely applied research field A mechanistic way of thinking has come to the forefront of 21st century science because of recent developments in new technologies and knowledge that enable scientists to manipulate the object or organism they are working with more directly allowing them to engineer and create novel biological systems for practical applications
Let students know that the work synthetic biologists do often require them to think mechanistically Now that students are given a definition of mechanistic thinking have students revisit their case study analysis and explore how synthetic biologists might think mechanistically
Review Extend and Apply
Step 4 Scratch Assignment Ask students to create a mini-Scratch project to demonstrate what they have learned so far (the project does not have to be all inclusive students can choose to focus on just one thing they learned either about scientific thinking mechanistic thinking or synthetic biology) Emphasize to students that the goal is not to create a complex programming project but to use Scratch creatively as a medium for creative expressing not matter how simple the project is Encourage students to work with partners and collaborate by borrowing adapting or building upon the ideas and projects of others (this is not considered cheating)
copy 2009 Yu-Tzu Debbie Liu 7
Detailed Case Study Jay Keasling
(1964 ndash present)
Best known for pioneering the new field of synthetic biology which designs and constructs new organisms for useful purposes He is also most known for creating a microbe that produces a drug to treat malaria (making drugs from bugs)
Jay Keasling was raised on a farm and spent his childhood exploring the practical side of biology chemistry and engineering This background eventually led him to work in the rapidly growing field that uses living organisms like bacteria for various practical purposes such as food processing agriculture and medicine
In the early 1980s genetic engineering became popular because you can ldquoconvincerdquo microbes to produce insulin growth hormones and other valuable proteins by simply inserting a single gene from a different organism into bacteria However Keasling believed that genetic engineering isnrsquot harnessing the full power of these cells The production of molecules isnt always so simple it requires a complex interaction of several genes (not just one) being produced in a certain sequence So Keasling wanted to invent the tools that would allow him to create these kinds of genetic assembly lines Thus what goes on in a cell is a lot like what goes on in a chemical plant petroleum goes in and after a whole chain of reactions plastic comes out
Keasling went to college studying biology and chemical engineering extensively and got his PhD in 1991 He is now a professor at the University of California at Berkeley He spent his first 10 years at UC Berkeley building the new tools he would need to turn cells into chemical plants He also invented powerful chemical switches (like a light switch) that allowed him to control when he wanted to ldquoturn onrdquo and ldquoturn offrdquo protein production in cells This way of borrowing techniques from engineering and figuring out how to manipulate microbes came to be call synthetic biology
After years of perfecting his biological tool kit Keasling wanted to find a real-world use for it In 2002 he learned of the dire need for artemisinin a compound derived from the sweet wormwood plant which is 90 percent effective against the parasite that causes malaria and has few side effects (malaria kills some 3 million people a year) However extracting the drug from sweet wormwood is a slow and expensive process Keasling figured he could design and create microbes to produce artemisinin much quicker and cheaper Rather than wait months for sweet wormwood to grow on farms Keasling wanted to create it simply by pouring sugar in a tank full of microbes that can use the sugar to make the drug via a chemical pathway he has designedmdashhe wanted to integrate genes from different species into a microbe to fabricate the drug for malaria
copy 2009 Yu-Tzu Debbie Liu 8
In 2006 Keaslings team (comprised of graduate students post-docs and research assistants) published their success of the production of artemisinin It is expected to lower the cost of artemisinin production from a dollar per gram to just 10 cents He was awarded a $43 million grant from the Bill and Melinda Gates Foundation and awarded DISCOVER magazinersquos first ever Scientist of the Year Award
Fighting malaria is just one part of Keaslings larger agenda to explore the potential of synthetic biology In his laboratory students are engineering microbes to break down pesticides make biodegradable plastics and create ethanol and other fuels from plants
Excerpts of i interview w Jay Keasling
1 You arrived at UC Berkeley in 1992 with training as both a chemical engineer and a biologist What did you hope to do
2 Why hadnt anybody tried to engineer cells that way before
3 How did you get involved in your antimalaria project
Jay Keisling biography adapted fromZimmer C (2006) Scientist of the Year Jay Keasling Discovermagazinecom Retrieved from
httpdiscovermagazinecom2006deccover
copy 2009 Yu-Tzu Debbie Liu 9
See responses to these questions atZimmer C (2006) Scientist of the Year Jay Keasling Discovermagazinecom Retrieved from
httpdiscovermagazinecom2006deccover
Interview content removed due to copyright restrictions
Interview content removed due to copyright restrictions
Interview content removed due to copyright restrictions
Lesson Plan Day 3 Materials
Designing a New Microbe worksheet Organism cards Student notebooks or journals
Prep Step Review lesson plan background information and understanding goals Photocopy Designing a New Microbe worksheet (p 28) Cut out organism cards (each group of 3-4 students will have a set of cards) (p29)
Explore Step 1 Designing a New Microbe Introduce todayrsquos activity by saying ldquoYou will be simulating how synthetic biologists think mechanistically by doing an the activity that is actually modeled after a real experiment done by scientists in 2007rdquo Divide students into groups of 3 or 4 Each group receives a set of organism cards Each student receives a Designing a New Microbe worksheet Remind students that proteins (or enzymes) are molecules inside cells that convert one molecule into another (eg the make-believe molecule How is converted to the molecule Home by Protein T in bacteria) Following the directions of the handout have students create a kind of assembly line that integrate proteins from different organisms into a microbe that uses water and starch (inputs) to ultimately produce hydrogen (output)
Possible answers to Designing a New Microbe
There are two possible pathways that can lead to hydrogen production
1 Starch amp water Protein G Protein P Protein D Protein R Protein T Protein F Protein H Hydrogen
2 Starch amp water Protein G Protein P Protein D Protein H Hydrogen
Guide students along by encouraging students who have already figured out how to attempt the problem to reveal and share with the class how they are thinking through the problem Stop students periodically to ask ldquoHow are you thinking through this problem What is your goal and how is your thinking helping you reach that goalrdquo Students may find either working sequentially forward or backward to fill in the worksheet to be easier
Note to teachers The hydrogen production pathway from starch and water is a shorten version of the actual 2007 experiment for learning purposes The organism types and molecule names are true to the experiment Protein names are made up for simplicity
copy 2009 Yu-Tzu Debbie Liu 10
Step 2 Discuss studentsrsquo findings Have students tell you what they found as you write their findings on the board Students may have discovered by now that there are two paths that lead to hydrogen production Students might recall that Jay Keasling have done something similar by making an antimalarial drug from sugar using synthetic biology Students may have also discovered that no proteins from the mouse organism were used for the design of their new microbe Ask students ldquowhat do you think is the purpose of having a mouse organism when we didnrsquot need itrdquo Help students understand how in reality scientists have hundreds of organisms to choose from some of which are irrelevant to their work In fact a common skill that scientists share is being about to identify and pull together important and relevant information The activity allows students to discover that synthetic biology is a very mind-blowing field accomplishing things that some people never thought was possible Students will come to appreciate how seemingly impossible feats can be possible especially when scientists are thinking creatively By thinking and working mechanistically scientists have more freedom then before in designing and creating novel organisms for real-world applications
Review Extend and Apply Step 3 How do you think mechanistically Ask students to reflect on their experience with Scratch and how they might have engaged in mechanistic thinking in their own work Helps students make the connection that they themselves have been engaging in mechanistic thinking while working on their own Scratch projects The Scratch grammar is designed so that users are presented with a versatile collection of graphical programming blocks that they can be snapped together to create programs much like synthetic biology Connectors on the blocks suggest how they should be put together so that over the process of tinkering with these blocks the emerging structure can give rise to new ideas and direction to the project Not only does snapping together complimentary blocks provide an easy way into learning programming but the idea of modularization as a problem-solving and design strategy is directly relevant to mechanistic thinking Go on to discuss how they can apply scientistsrsquo patterns of thinking to our own thinking in science class and daily life
copy 2009 Yu-Tzu Debbie Liu 11
Name___________________________ Date ____________
Designing a New Microbe
Task Gas prices have reached its all time high Thus scientists are trying to think of ways to produce alternative fuels such as hydrogen gas in a much cheaper and quicker way You are a scientist and you are familiar with six different organisms Based on what you know can you come up with a way to generate hydrogen from starch and water by designing a microbe that borrows different mechanismsproteins from different cells Fill in the blanks with protein names and the organism that the protein was taken from
Materials Each team has a set of cards each card symbolizing a different organism On the card you will see the name of the organism a picture of the organism and proteins that is unique to them Proteins (or enzymes) convert one molecule into another
Starch amp Water Protein borrowed Protein borrowed
Input Organism Organism
Protein borrowed $ Protein borrowed $ Protein borrowed Organism Organism Organism
Protein borrowed Protein borrowed Protein borrowed Hydrogen Organism Organism Organism Output
Experiment adapted from Zhang YH Evans BR Mielenz JR Hopkins RC Adams MW (2007) High-yield hydrogen production from
starch and water by a synthetic enzymatic pathway PLoS ONE 5 e456
copy 2009 Yu-Tzu Debbie Liu 12
Organism Cards (one set)
Teachers Please make as many copies as the number of groups of students Cut the cards out and shuffle before handing to students
Source NIH
Bacteria
Rabbitbull Protein T uses [X5P] to make [S7P]
Photo US Fish and Wildlife Service bull Protein F uses [S7P] to make [NADPH] bull Protein G uses starch and water to make [G-1-P] bull Protein P uses [G-1-P] to make [G-6-P]
Yeast
Public domain image (Source Wikimedia Commons)
bull Protein D uses [G-6-P] to make [NADPH] and [R5P]
Public domain image (Source Wikimedia Commons) Spinach
bull Protein R uses [R5P] to make [X5P]
Experiment adapted from
Archea Courtesy of Angels Tapias (License CC BY)
bull Protein H uses [NADPH] to make Hydrogen
Source NIH Mouse
bull Protein X uses [T8P] to make Hydrogen
Zhang YH Evans BR Mielenz JR Hopkins RC Adams MW (2007) High-yield hydrogen production from starch and water by a synthetic enzymatic pathway PLoS ONE 5 e456
copy 2009 Yu-Tzu Debbie Liu 13
MIT OpenCourseWarehttpocwmitedu
MAS714J STS445J Technologies for Creative Learning Fall 2009
For information about citing these materials or our Terms of Use visit httpocwmiteduterms
In this lesson Scratch is used to have students experience thinking mechanistically in their own work And since programming involves the creation of external representations of the problem-solving process Scratch provides students with opportunities of reflecting on their own thinking Lesson Layout These three lessons (one lesson per day) are designed to help students 1) understand how modern scientists think mechanistically 2) practice thinking mechanistically by simulating how synthetic biologists think in the field and 3) recognize mechanistic thinking even when it is not in the context of science as in their own work via Scratch Lesson 1 Designed to familiarize students with the Scratch programming language so that they can create projects on it At this point Scratch is presented simply as a medium for expressing what they have learned much like posters Powerpoint presentations and paper write-ups Lesson 2 Designed to expose students to the creative field of synthetic biology as a means to illustrate how scientists think mechanistically in the field This is done by a case study of Jay Keasling one of the pioneers of synthetic biology By analyzing how a modern scientist work and think students are provided with a broader view of scientific inquiry and the nature of scientific thinking Students will be asked to demonstrate their understanding of what they have learned so far by creating a Scratch project This allows students to work more closely and creatively with Scratch It also acts as a quick formative assessment for teachers of studentsrsquo learning thus far However the real goal of this exercise is to have students engage in mechanistic thinking in their own work which they may not recognize as it is not in the direct context of science This will be revealed in lesson 3 Lesson 3 Designed to have students practice thinking mechanistically by simulating how synthetic biologists think in the field via the Designing a New Microbe activity adapted from an actual experiment conducted in 20073 This activity presents students with a problem (need for hydrogen gas as alternative fuel) and asks students to design a microbe that can use starch and water to make hydrogen gas Students are given a set of organism cards to work with each card symbolizing a different type of organism (bacteria rabbit yeast archea spinach and mouse) Proteins (molecules that can convert one molecule into another) that are unique to each organism are listed on the card Studentsrsquo engineered microbe will essentially have different proteins from different organisms placed in a certain sequence to end up with a final product of hydrogen gas Students are given the Designing a New Microbe worksheet to help them visualize the problem better and reduce their cognitive loads (ie amount of information they need to carry in their heads) The activity allows students to discover that synthetic biology is a very mind-blowing field accomplishing things that some people never thought was possible Students will come to appreciate how seemingly impossible feats can be possible especially when scientists are thinking creatively By thinking and working mechanistically scientists have more freedom then before in designing and creating novel organisms for real-world applications
3 Zhang YH Evans BR Mielenz JR Hopkins RC Adams MW (2007) High-yield hydrogen production from starch and water by a synthetic enzymatic pathway PLoS ONE 5 e456
copy 2009 Yu-Tzu Debbie Liu 3
After the activity when students have grasped a much deeper understanding of what mechanistic thinking looks like in practice students are asked to reflect on their experience with Scratch The goal is to have students make the connection that they themselves have been engaging in mechanistic thinking while working on their own Scratch projects This reflective exercise encourages students to transfer their understanding of mechanistic thinking across different domains Students will also gain an appreciation of how studying trends in scientistsrsquo way of thinking can help them in their own thinking Lesson Placement These lessons can be used at the beginning of the school year when the scientific method is usually being presented Alternatively this lesson can be infused during the school year as students learn more about genetic engineering or creative thinking These lessons follow a constructivist approach to learning encouraging students to discover the meaning of mechanistic thinking through their exploration of a case study simulating how synthetic biologists think and making connections to their own work in Scratch Students are always encouraged to formulate their own ideas and connections before being presented with any information
copy 2009 Yu-Tzu Debbie Liu 4
Lesson Plan Day 1 Materials
Computers with Scratch installed Scratch Resources
Prep Step Review lesson plan background information and understanding goals Obtain computers with Scratch installed for students to work on Make copies of Scratch Resources (not provided)
Explore Step 1 Introduction to lesson Introduce the lesson by giving students a sense of what they will be doing and where they are headed by telling students ldquoThis will be a three-day lesson where we will be exploring how scientists think and more specifically what mechanistic thinking looks like in practice In this process we will also be learning Scratch We will tie everything together at the end of the third dayrdquo Step 2 Playing with Scratch Depending on the level of your students and any future goals you wish to achieve with Scratch structure the class so that students are comfortable navigating around the Scratch environment and are able to get started on their own Scratch project by the end of the class Please provide students with any Scratch resources you see fit Check out the ScratchEds resource search (httpscratchedmediamiteduresourcessearch) for more info Some good examples found in ScratchEd of Scratch lesson plans (video tutorials PowerPoints and worksheets) include
bull Having Fun with Computer Programming and Games (httpwwwleroieeducationoutreachsecondlevelscratchlessonplans)
bull A TeachNetUK Project 6 Lessons on Getting Started with Scratch (httpwwwteachnet-ukorguk200720ProjectsICT-ScratchScratchpages8_schemeofworkhtml)
bull Scratch Lessons Shall We Learn Scratch Programming for Tweens (httpwwwshallwelearncomscratchprogrammingforkidscategory)
bull Designing Animations and GamesmdashA Creative Introduction to Programming (httpwwwcsuni-potsdamde~romeikeUEWettbewerbindex-englishhtm)
Make sure to also introduce students to the Scratch online community and let them know that they can download the source code of any project to help them see how others are using the Scratch programming language to create projects
Review Extend and Apply Step 3 Scratch Assignment End the day by informing students that they will apply what they have learned today to create a mini-Scratch project for an assignment after the next dayrsquos lesson Emphasize to students that the goal is not to create a complex programming project but to use Scratch creatively as a medium for creative expressing not matter how simple the project is Encourage students to play with Scratch on their own time and make it clear that you highly encourage them to borrow adapt and build upon the ideas and projects of others (this is not considered cheating)
copy 2009 Yu-Tzu Debbie Liu 5
Lesson Plan Day 2 Materials
21st century scientist case study of Jay Keasling Student notebooks or journals
Prep Step Review lesson plan background information and understanding goals Make copies of 21st century scientist case study of Jay Keasling (p 8)
Explore Step 1 What is scientific thinking Ask students to describe what they think is scientific thinking Collect a representative list of studentsrsquo thoughts on the board Ask students to explain or expound on the meaning behind what they are saying After reviewing the list ask them ldquo Do you think all scientists come to their discoveries in the same wayrdquo ldquoDo scientists display all these characteristics at all timesrdquo It is important to point out to students that scientists have various methods going about their experimentation and work and depending on the type of work they are doing scientists donrsquot always share the same methods Furthermore scientists engage in thinking patterns that are specific to its particular socio-cultural context and one of which is mechanistic thinking Engage in a discussion with students on how might the explosion of advancements in scientific knowledge and technology at the turn of the century change the way scientists at the cutting edge of research interact with their work
Step 2 Analyze case study of a 21st century scientist Let students know that they will be learning about the field of synthetic biology as a means to illustrate how modern scientists work and think Specifically they will be studying Jay Keasling one of the pioneers of synthetic biology Hand out the case study on Jay Keasling Have students work in groups of 3-4 students to identify any patterns of thinking that the scientist displays Make sure to ask students to specifically identify what part of the case study justifies their claims Have students write the class findings in their journalsnotebooks
Possible findings from case analysis Jay Keasling
Keasling is a pioneer of synthetic biologymdasha field that designs and constructs new organisms for useful purposes He is most known for creating a microbe that produces a drug to treat malaria (making drugs from bugs) Some of his characteristics as a scientist include
bull Creative and imaginative wanted to invent new tools that can turn cells into chemical plants take in something very simple and spits out something complicated and valuable coming up with other applications of synthetic biology (use microbes to break down pesticides make biodegradable plastics create fuels from plants)
bull Critical thinking thought about how to design and create microbes to produce artemisinin much quicker and cheaper how to integrate genes from different species into a microbe to fabricate the drug
copy 2009 Yu-Tzu Debbie Liu 6
bull Seek and integrate information integrated methods and concepts from engineering and biology leading to synthetic biology
bull Supported with significant resources did research at universities and received grant money
bull Practical-minded microbes will churn out anti-malarial drug for a fraction of its current cost making it accessible to much more of the world these microbes could save millions of lives
bull Strong disciplinary understanding studied biology and chemical engineering extensively leading to his PhD and professor position at UC Berkeley
Step 3 What is mechanistic thinking Introduce students to the idea of mechanistic thinking as a prominent thinking pattern in the 21st
century
Mechanistic Thinking
Mechanistic thinking is a way of thinking that has a mechanical or engineering undertone This is shown through scientistsrsquo regular use of mechanical analogies to conceptualize their work and their modular synthetic and purpose-driven approach towards their research problems The display of mechanistic thinking by scientists appears to be a result of the merging of biology and engineering practices that is increasingly observed in 21st century biology as compared to a time when most of biologymdashtraditionally known for its pure basic researchmdashremain clearly demarcated from engineeringmdasha purely applied research field A mechanistic way of thinking has come to the forefront of 21st century science because of recent developments in new technologies and knowledge that enable scientists to manipulate the object or organism they are working with more directly allowing them to engineer and create novel biological systems for practical applications
Let students know that the work synthetic biologists do often require them to think mechanistically Now that students are given a definition of mechanistic thinking have students revisit their case study analysis and explore how synthetic biologists might think mechanistically
Review Extend and Apply
Step 4 Scratch Assignment Ask students to create a mini-Scratch project to demonstrate what they have learned so far (the project does not have to be all inclusive students can choose to focus on just one thing they learned either about scientific thinking mechanistic thinking or synthetic biology) Emphasize to students that the goal is not to create a complex programming project but to use Scratch creatively as a medium for creative expressing not matter how simple the project is Encourage students to work with partners and collaborate by borrowing adapting or building upon the ideas and projects of others (this is not considered cheating)
copy 2009 Yu-Tzu Debbie Liu 7
Detailed Case Study Jay Keasling
(1964 ndash present)
Best known for pioneering the new field of synthetic biology which designs and constructs new organisms for useful purposes He is also most known for creating a microbe that produces a drug to treat malaria (making drugs from bugs)
Jay Keasling was raised on a farm and spent his childhood exploring the practical side of biology chemistry and engineering This background eventually led him to work in the rapidly growing field that uses living organisms like bacteria for various practical purposes such as food processing agriculture and medicine
In the early 1980s genetic engineering became popular because you can ldquoconvincerdquo microbes to produce insulin growth hormones and other valuable proteins by simply inserting a single gene from a different organism into bacteria However Keasling believed that genetic engineering isnrsquot harnessing the full power of these cells The production of molecules isnt always so simple it requires a complex interaction of several genes (not just one) being produced in a certain sequence So Keasling wanted to invent the tools that would allow him to create these kinds of genetic assembly lines Thus what goes on in a cell is a lot like what goes on in a chemical plant petroleum goes in and after a whole chain of reactions plastic comes out
Keasling went to college studying biology and chemical engineering extensively and got his PhD in 1991 He is now a professor at the University of California at Berkeley He spent his first 10 years at UC Berkeley building the new tools he would need to turn cells into chemical plants He also invented powerful chemical switches (like a light switch) that allowed him to control when he wanted to ldquoturn onrdquo and ldquoturn offrdquo protein production in cells This way of borrowing techniques from engineering and figuring out how to manipulate microbes came to be call synthetic biology
After years of perfecting his biological tool kit Keasling wanted to find a real-world use for it In 2002 he learned of the dire need for artemisinin a compound derived from the sweet wormwood plant which is 90 percent effective against the parasite that causes malaria and has few side effects (malaria kills some 3 million people a year) However extracting the drug from sweet wormwood is a slow and expensive process Keasling figured he could design and create microbes to produce artemisinin much quicker and cheaper Rather than wait months for sweet wormwood to grow on farms Keasling wanted to create it simply by pouring sugar in a tank full of microbes that can use the sugar to make the drug via a chemical pathway he has designedmdashhe wanted to integrate genes from different species into a microbe to fabricate the drug for malaria
copy 2009 Yu-Tzu Debbie Liu 8
In 2006 Keaslings team (comprised of graduate students post-docs and research assistants) published their success of the production of artemisinin It is expected to lower the cost of artemisinin production from a dollar per gram to just 10 cents He was awarded a $43 million grant from the Bill and Melinda Gates Foundation and awarded DISCOVER magazinersquos first ever Scientist of the Year Award
Fighting malaria is just one part of Keaslings larger agenda to explore the potential of synthetic biology In his laboratory students are engineering microbes to break down pesticides make biodegradable plastics and create ethanol and other fuels from plants
Excerpts of i interview w Jay Keasling
1 You arrived at UC Berkeley in 1992 with training as both a chemical engineer and a biologist What did you hope to do
2 Why hadnt anybody tried to engineer cells that way before
3 How did you get involved in your antimalaria project
Jay Keisling biography adapted fromZimmer C (2006) Scientist of the Year Jay Keasling Discovermagazinecom Retrieved from
httpdiscovermagazinecom2006deccover
copy 2009 Yu-Tzu Debbie Liu 9
See responses to these questions atZimmer C (2006) Scientist of the Year Jay Keasling Discovermagazinecom Retrieved from
httpdiscovermagazinecom2006deccover
Interview content removed due to copyright restrictions
Interview content removed due to copyright restrictions
Interview content removed due to copyright restrictions
Lesson Plan Day 3 Materials
Designing a New Microbe worksheet Organism cards Student notebooks or journals
Prep Step Review lesson plan background information and understanding goals Photocopy Designing a New Microbe worksheet (p 28) Cut out organism cards (each group of 3-4 students will have a set of cards) (p29)
Explore Step 1 Designing a New Microbe Introduce todayrsquos activity by saying ldquoYou will be simulating how synthetic biologists think mechanistically by doing an the activity that is actually modeled after a real experiment done by scientists in 2007rdquo Divide students into groups of 3 or 4 Each group receives a set of organism cards Each student receives a Designing a New Microbe worksheet Remind students that proteins (or enzymes) are molecules inside cells that convert one molecule into another (eg the make-believe molecule How is converted to the molecule Home by Protein T in bacteria) Following the directions of the handout have students create a kind of assembly line that integrate proteins from different organisms into a microbe that uses water and starch (inputs) to ultimately produce hydrogen (output)
Possible answers to Designing a New Microbe
There are two possible pathways that can lead to hydrogen production
1 Starch amp water Protein G Protein P Protein D Protein R Protein T Protein F Protein H Hydrogen
2 Starch amp water Protein G Protein P Protein D Protein H Hydrogen
Guide students along by encouraging students who have already figured out how to attempt the problem to reveal and share with the class how they are thinking through the problem Stop students periodically to ask ldquoHow are you thinking through this problem What is your goal and how is your thinking helping you reach that goalrdquo Students may find either working sequentially forward or backward to fill in the worksheet to be easier
Note to teachers The hydrogen production pathway from starch and water is a shorten version of the actual 2007 experiment for learning purposes The organism types and molecule names are true to the experiment Protein names are made up for simplicity
copy 2009 Yu-Tzu Debbie Liu 10
Step 2 Discuss studentsrsquo findings Have students tell you what they found as you write their findings on the board Students may have discovered by now that there are two paths that lead to hydrogen production Students might recall that Jay Keasling have done something similar by making an antimalarial drug from sugar using synthetic biology Students may have also discovered that no proteins from the mouse organism were used for the design of their new microbe Ask students ldquowhat do you think is the purpose of having a mouse organism when we didnrsquot need itrdquo Help students understand how in reality scientists have hundreds of organisms to choose from some of which are irrelevant to their work In fact a common skill that scientists share is being about to identify and pull together important and relevant information The activity allows students to discover that synthetic biology is a very mind-blowing field accomplishing things that some people never thought was possible Students will come to appreciate how seemingly impossible feats can be possible especially when scientists are thinking creatively By thinking and working mechanistically scientists have more freedom then before in designing and creating novel organisms for real-world applications
Review Extend and Apply Step 3 How do you think mechanistically Ask students to reflect on their experience with Scratch and how they might have engaged in mechanistic thinking in their own work Helps students make the connection that they themselves have been engaging in mechanistic thinking while working on their own Scratch projects The Scratch grammar is designed so that users are presented with a versatile collection of graphical programming blocks that they can be snapped together to create programs much like synthetic biology Connectors on the blocks suggest how they should be put together so that over the process of tinkering with these blocks the emerging structure can give rise to new ideas and direction to the project Not only does snapping together complimentary blocks provide an easy way into learning programming but the idea of modularization as a problem-solving and design strategy is directly relevant to mechanistic thinking Go on to discuss how they can apply scientistsrsquo patterns of thinking to our own thinking in science class and daily life
copy 2009 Yu-Tzu Debbie Liu 11
Name___________________________ Date ____________
Designing a New Microbe
Task Gas prices have reached its all time high Thus scientists are trying to think of ways to produce alternative fuels such as hydrogen gas in a much cheaper and quicker way You are a scientist and you are familiar with six different organisms Based on what you know can you come up with a way to generate hydrogen from starch and water by designing a microbe that borrows different mechanismsproteins from different cells Fill in the blanks with protein names and the organism that the protein was taken from
Materials Each team has a set of cards each card symbolizing a different organism On the card you will see the name of the organism a picture of the organism and proteins that is unique to them Proteins (or enzymes) convert one molecule into another
Starch amp Water Protein borrowed Protein borrowed
Input Organism Organism
Protein borrowed $ Protein borrowed $ Protein borrowed Organism Organism Organism
Protein borrowed Protein borrowed Protein borrowed Hydrogen Organism Organism Organism Output
Experiment adapted from Zhang YH Evans BR Mielenz JR Hopkins RC Adams MW (2007) High-yield hydrogen production from
starch and water by a synthetic enzymatic pathway PLoS ONE 5 e456
copy 2009 Yu-Tzu Debbie Liu 12
Organism Cards (one set)
Teachers Please make as many copies as the number of groups of students Cut the cards out and shuffle before handing to students
Source NIH
Bacteria
Rabbitbull Protein T uses [X5P] to make [S7P]
Photo US Fish and Wildlife Service bull Protein F uses [S7P] to make [NADPH] bull Protein G uses starch and water to make [G-1-P] bull Protein P uses [G-1-P] to make [G-6-P]
Yeast
Public domain image (Source Wikimedia Commons)
bull Protein D uses [G-6-P] to make [NADPH] and [R5P]
Public domain image (Source Wikimedia Commons) Spinach
bull Protein R uses [R5P] to make [X5P]
Experiment adapted from
Archea Courtesy of Angels Tapias (License CC BY)
bull Protein H uses [NADPH] to make Hydrogen
Source NIH Mouse
bull Protein X uses [T8P] to make Hydrogen
Zhang YH Evans BR Mielenz JR Hopkins RC Adams MW (2007) High-yield hydrogen production from starch and water by a synthetic enzymatic pathway PLoS ONE 5 e456
copy 2009 Yu-Tzu Debbie Liu 13
MIT OpenCourseWarehttpocwmitedu
MAS714J STS445J Technologies for Creative Learning Fall 2009
For information about citing these materials or our Terms of Use visit httpocwmiteduterms
After the activity when students have grasped a much deeper understanding of what mechanistic thinking looks like in practice students are asked to reflect on their experience with Scratch The goal is to have students make the connection that they themselves have been engaging in mechanistic thinking while working on their own Scratch projects This reflective exercise encourages students to transfer their understanding of mechanistic thinking across different domains Students will also gain an appreciation of how studying trends in scientistsrsquo way of thinking can help them in their own thinking Lesson Placement These lessons can be used at the beginning of the school year when the scientific method is usually being presented Alternatively this lesson can be infused during the school year as students learn more about genetic engineering or creative thinking These lessons follow a constructivist approach to learning encouraging students to discover the meaning of mechanistic thinking through their exploration of a case study simulating how synthetic biologists think and making connections to their own work in Scratch Students are always encouraged to formulate their own ideas and connections before being presented with any information
copy 2009 Yu-Tzu Debbie Liu 4
Lesson Plan Day 1 Materials
Computers with Scratch installed Scratch Resources
Prep Step Review lesson plan background information and understanding goals Obtain computers with Scratch installed for students to work on Make copies of Scratch Resources (not provided)
Explore Step 1 Introduction to lesson Introduce the lesson by giving students a sense of what they will be doing and where they are headed by telling students ldquoThis will be a three-day lesson where we will be exploring how scientists think and more specifically what mechanistic thinking looks like in practice In this process we will also be learning Scratch We will tie everything together at the end of the third dayrdquo Step 2 Playing with Scratch Depending on the level of your students and any future goals you wish to achieve with Scratch structure the class so that students are comfortable navigating around the Scratch environment and are able to get started on their own Scratch project by the end of the class Please provide students with any Scratch resources you see fit Check out the ScratchEds resource search (httpscratchedmediamiteduresourcessearch) for more info Some good examples found in ScratchEd of Scratch lesson plans (video tutorials PowerPoints and worksheets) include
bull Having Fun with Computer Programming and Games (httpwwwleroieeducationoutreachsecondlevelscratchlessonplans)
bull A TeachNetUK Project 6 Lessons on Getting Started with Scratch (httpwwwteachnet-ukorguk200720ProjectsICT-ScratchScratchpages8_schemeofworkhtml)
bull Scratch Lessons Shall We Learn Scratch Programming for Tweens (httpwwwshallwelearncomscratchprogrammingforkidscategory)
bull Designing Animations and GamesmdashA Creative Introduction to Programming (httpwwwcsuni-potsdamde~romeikeUEWettbewerbindex-englishhtm)
Make sure to also introduce students to the Scratch online community and let them know that they can download the source code of any project to help them see how others are using the Scratch programming language to create projects
Review Extend and Apply Step 3 Scratch Assignment End the day by informing students that they will apply what they have learned today to create a mini-Scratch project for an assignment after the next dayrsquos lesson Emphasize to students that the goal is not to create a complex programming project but to use Scratch creatively as a medium for creative expressing not matter how simple the project is Encourage students to play with Scratch on their own time and make it clear that you highly encourage them to borrow adapt and build upon the ideas and projects of others (this is not considered cheating)
copy 2009 Yu-Tzu Debbie Liu 5
Lesson Plan Day 2 Materials
21st century scientist case study of Jay Keasling Student notebooks or journals
Prep Step Review lesson plan background information and understanding goals Make copies of 21st century scientist case study of Jay Keasling (p 8)
Explore Step 1 What is scientific thinking Ask students to describe what they think is scientific thinking Collect a representative list of studentsrsquo thoughts on the board Ask students to explain or expound on the meaning behind what they are saying After reviewing the list ask them ldquo Do you think all scientists come to their discoveries in the same wayrdquo ldquoDo scientists display all these characteristics at all timesrdquo It is important to point out to students that scientists have various methods going about their experimentation and work and depending on the type of work they are doing scientists donrsquot always share the same methods Furthermore scientists engage in thinking patterns that are specific to its particular socio-cultural context and one of which is mechanistic thinking Engage in a discussion with students on how might the explosion of advancements in scientific knowledge and technology at the turn of the century change the way scientists at the cutting edge of research interact with their work
Step 2 Analyze case study of a 21st century scientist Let students know that they will be learning about the field of synthetic biology as a means to illustrate how modern scientists work and think Specifically they will be studying Jay Keasling one of the pioneers of synthetic biology Hand out the case study on Jay Keasling Have students work in groups of 3-4 students to identify any patterns of thinking that the scientist displays Make sure to ask students to specifically identify what part of the case study justifies their claims Have students write the class findings in their journalsnotebooks
Possible findings from case analysis Jay Keasling
Keasling is a pioneer of synthetic biologymdasha field that designs and constructs new organisms for useful purposes He is most known for creating a microbe that produces a drug to treat malaria (making drugs from bugs) Some of his characteristics as a scientist include
bull Creative and imaginative wanted to invent new tools that can turn cells into chemical plants take in something very simple and spits out something complicated and valuable coming up with other applications of synthetic biology (use microbes to break down pesticides make biodegradable plastics create fuels from plants)
bull Critical thinking thought about how to design and create microbes to produce artemisinin much quicker and cheaper how to integrate genes from different species into a microbe to fabricate the drug
copy 2009 Yu-Tzu Debbie Liu 6
bull Seek and integrate information integrated methods and concepts from engineering and biology leading to synthetic biology
bull Supported with significant resources did research at universities and received grant money
bull Practical-minded microbes will churn out anti-malarial drug for a fraction of its current cost making it accessible to much more of the world these microbes could save millions of lives
bull Strong disciplinary understanding studied biology and chemical engineering extensively leading to his PhD and professor position at UC Berkeley
Step 3 What is mechanistic thinking Introduce students to the idea of mechanistic thinking as a prominent thinking pattern in the 21st
century
Mechanistic Thinking
Mechanistic thinking is a way of thinking that has a mechanical or engineering undertone This is shown through scientistsrsquo regular use of mechanical analogies to conceptualize their work and their modular synthetic and purpose-driven approach towards their research problems The display of mechanistic thinking by scientists appears to be a result of the merging of biology and engineering practices that is increasingly observed in 21st century biology as compared to a time when most of biologymdashtraditionally known for its pure basic researchmdashremain clearly demarcated from engineeringmdasha purely applied research field A mechanistic way of thinking has come to the forefront of 21st century science because of recent developments in new technologies and knowledge that enable scientists to manipulate the object or organism they are working with more directly allowing them to engineer and create novel biological systems for practical applications
Let students know that the work synthetic biologists do often require them to think mechanistically Now that students are given a definition of mechanistic thinking have students revisit their case study analysis and explore how synthetic biologists might think mechanistically
Review Extend and Apply
Step 4 Scratch Assignment Ask students to create a mini-Scratch project to demonstrate what they have learned so far (the project does not have to be all inclusive students can choose to focus on just one thing they learned either about scientific thinking mechanistic thinking or synthetic biology) Emphasize to students that the goal is not to create a complex programming project but to use Scratch creatively as a medium for creative expressing not matter how simple the project is Encourage students to work with partners and collaborate by borrowing adapting or building upon the ideas and projects of others (this is not considered cheating)
copy 2009 Yu-Tzu Debbie Liu 7
Detailed Case Study Jay Keasling
(1964 ndash present)
Best known for pioneering the new field of synthetic biology which designs and constructs new organisms for useful purposes He is also most known for creating a microbe that produces a drug to treat malaria (making drugs from bugs)
Jay Keasling was raised on a farm and spent his childhood exploring the practical side of biology chemistry and engineering This background eventually led him to work in the rapidly growing field that uses living organisms like bacteria for various practical purposes such as food processing agriculture and medicine
In the early 1980s genetic engineering became popular because you can ldquoconvincerdquo microbes to produce insulin growth hormones and other valuable proteins by simply inserting a single gene from a different organism into bacteria However Keasling believed that genetic engineering isnrsquot harnessing the full power of these cells The production of molecules isnt always so simple it requires a complex interaction of several genes (not just one) being produced in a certain sequence So Keasling wanted to invent the tools that would allow him to create these kinds of genetic assembly lines Thus what goes on in a cell is a lot like what goes on in a chemical plant petroleum goes in and after a whole chain of reactions plastic comes out
Keasling went to college studying biology and chemical engineering extensively and got his PhD in 1991 He is now a professor at the University of California at Berkeley He spent his first 10 years at UC Berkeley building the new tools he would need to turn cells into chemical plants He also invented powerful chemical switches (like a light switch) that allowed him to control when he wanted to ldquoturn onrdquo and ldquoturn offrdquo protein production in cells This way of borrowing techniques from engineering and figuring out how to manipulate microbes came to be call synthetic biology
After years of perfecting his biological tool kit Keasling wanted to find a real-world use for it In 2002 he learned of the dire need for artemisinin a compound derived from the sweet wormwood plant which is 90 percent effective against the parasite that causes malaria and has few side effects (malaria kills some 3 million people a year) However extracting the drug from sweet wormwood is a slow and expensive process Keasling figured he could design and create microbes to produce artemisinin much quicker and cheaper Rather than wait months for sweet wormwood to grow on farms Keasling wanted to create it simply by pouring sugar in a tank full of microbes that can use the sugar to make the drug via a chemical pathway he has designedmdashhe wanted to integrate genes from different species into a microbe to fabricate the drug for malaria
copy 2009 Yu-Tzu Debbie Liu 8
In 2006 Keaslings team (comprised of graduate students post-docs and research assistants) published their success of the production of artemisinin It is expected to lower the cost of artemisinin production from a dollar per gram to just 10 cents He was awarded a $43 million grant from the Bill and Melinda Gates Foundation and awarded DISCOVER magazinersquos first ever Scientist of the Year Award
Fighting malaria is just one part of Keaslings larger agenda to explore the potential of synthetic biology In his laboratory students are engineering microbes to break down pesticides make biodegradable plastics and create ethanol and other fuels from plants
Excerpts of i interview w Jay Keasling
1 You arrived at UC Berkeley in 1992 with training as both a chemical engineer and a biologist What did you hope to do
2 Why hadnt anybody tried to engineer cells that way before
3 How did you get involved in your antimalaria project
Jay Keisling biography adapted fromZimmer C (2006) Scientist of the Year Jay Keasling Discovermagazinecom Retrieved from
httpdiscovermagazinecom2006deccover
copy 2009 Yu-Tzu Debbie Liu 9
See responses to these questions atZimmer C (2006) Scientist of the Year Jay Keasling Discovermagazinecom Retrieved from
httpdiscovermagazinecom2006deccover
Interview content removed due to copyright restrictions
Interview content removed due to copyright restrictions
Interview content removed due to copyright restrictions
Lesson Plan Day 3 Materials
Designing a New Microbe worksheet Organism cards Student notebooks or journals
Prep Step Review lesson plan background information and understanding goals Photocopy Designing a New Microbe worksheet (p 28) Cut out organism cards (each group of 3-4 students will have a set of cards) (p29)
Explore Step 1 Designing a New Microbe Introduce todayrsquos activity by saying ldquoYou will be simulating how synthetic biologists think mechanistically by doing an the activity that is actually modeled after a real experiment done by scientists in 2007rdquo Divide students into groups of 3 or 4 Each group receives a set of organism cards Each student receives a Designing a New Microbe worksheet Remind students that proteins (or enzymes) are molecules inside cells that convert one molecule into another (eg the make-believe molecule How is converted to the molecule Home by Protein T in bacteria) Following the directions of the handout have students create a kind of assembly line that integrate proteins from different organisms into a microbe that uses water and starch (inputs) to ultimately produce hydrogen (output)
Possible answers to Designing a New Microbe
There are two possible pathways that can lead to hydrogen production
1 Starch amp water Protein G Protein P Protein D Protein R Protein T Protein F Protein H Hydrogen
2 Starch amp water Protein G Protein P Protein D Protein H Hydrogen
Guide students along by encouraging students who have already figured out how to attempt the problem to reveal and share with the class how they are thinking through the problem Stop students periodically to ask ldquoHow are you thinking through this problem What is your goal and how is your thinking helping you reach that goalrdquo Students may find either working sequentially forward or backward to fill in the worksheet to be easier
Note to teachers The hydrogen production pathway from starch and water is a shorten version of the actual 2007 experiment for learning purposes The organism types and molecule names are true to the experiment Protein names are made up for simplicity
copy 2009 Yu-Tzu Debbie Liu 10
Step 2 Discuss studentsrsquo findings Have students tell you what they found as you write their findings on the board Students may have discovered by now that there are two paths that lead to hydrogen production Students might recall that Jay Keasling have done something similar by making an antimalarial drug from sugar using synthetic biology Students may have also discovered that no proteins from the mouse organism were used for the design of their new microbe Ask students ldquowhat do you think is the purpose of having a mouse organism when we didnrsquot need itrdquo Help students understand how in reality scientists have hundreds of organisms to choose from some of which are irrelevant to their work In fact a common skill that scientists share is being about to identify and pull together important and relevant information The activity allows students to discover that synthetic biology is a very mind-blowing field accomplishing things that some people never thought was possible Students will come to appreciate how seemingly impossible feats can be possible especially when scientists are thinking creatively By thinking and working mechanistically scientists have more freedom then before in designing and creating novel organisms for real-world applications
Review Extend and Apply Step 3 How do you think mechanistically Ask students to reflect on their experience with Scratch and how they might have engaged in mechanistic thinking in their own work Helps students make the connection that they themselves have been engaging in mechanistic thinking while working on their own Scratch projects The Scratch grammar is designed so that users are presented with a versatile collection of graphical programming blocks that they can be snapped together to create programs much like synthetic biology Connectors on the blocks suggest how they should be put together so that over the process of tinkering with these blocks the emerging structure can give rise to new ideas and direction to the project Not only does snapping together complimentary blocks provide an easy way into learning programming but the idea of modularization as a problem-solving and design strategy is directly relevant to mechanistic thinking Go on to discuss how they can apply scientistsrsquo patterns of thinking to our own thinking in science class and daily life
copy 2009 Yu-Tzu Debbie Liu 11
Name___________________________ Date ____________
Designing a New Microbe
Task Gas prices have reached its all time high Thus scientists are trying to think of ways to produce alternative fuels such as hydrogen gas in a much cheaper and quicker way You are a scientist and you are familiar with six different organisms Based on what you know can you come up with a way to generate hydrogen from starch and water by designing a microbe that borrows different mechanismsproteins from different cells Fill in the blanks with protein names and the organism that the protein was taken from
Materials Each team has a set of cards each card symbolizing a different organism On the card you will see the name of the organism a picture of the organism and proteins that is unique to them Proteins (or enzymes) convert one molecule into another
Starch amp Water Protein borrowed Protein borrowed
Input Organism Organism
Protein borrowed $ Protein borrowed $ Protein borrowed Organism Organism Organism
Protein borrowed Protein borrowed Protein borrowed Hydrogen Organism Organism Organism Output
Experiment adapted from Zhang YH Evans BR Mielenz JR Hopkins RC Adams MW (2007) High-yield hydrogen production from
starch and water by a synthetic enzymatic pathway PLoS ONE 5 e456
copy 2009 Yu-Tzu Debbie Liu 12
Organism Cards (one set)
Teachers Please make as many copies as the number of groups of students Cut the cards out and shuffle before handing to students
Source NIH
Bacteria
Rabbitbull Protein T uses [X5P] to make [S7P]
Photo US Fish and Wildlife Service bull Protein F uses [S7P] to make [NADPH] bull Protein G uses starch and water to make [G-1-P] bull Protein P uses [G-1-P] to make [G-6-P]
Yeast
Public domain image (Source Wikimedia Commons)
bull Protein D uses [G-6-P] to make [NADPH] and [R5P]
Public domain image (Source Wikimedia Commons) Spinach
bull Protein R uses [R5P] to make [X5P]
Experiment adapted from
Archea Courtesy of Angels Tapias (License CC BY)
bull Protein H uses [NADPH] to make Hydrogen
Source NIH Mouse
bull Protein X uses [T8P] to make Hydrogen
Zhang YH Evans BR Mielenz JR Hopkins RC Adams MW (2007) High-yield hydrogen production from starch and water by a synthetic enzymatic pathway PLoS ONE 5 e456
copy 2009 Yu-Tzu Debbie Liu 13
MIT OpenCourseWarehttpocwmitedu
MAS714J STS445J Technologies for Creative Learning Fall 2009
For information about citing these materials or our Terms of Use visit httpocwmiteduterms
Lesson Plan Day 1 Materials
Computers with Scratch installed Scratch Resources
Prep Step Review lesson plan background information and understanding goals Obtain computers with Scratch installed for students to work on Make copies of Scratch Resources (not provided)
Explore Step 1 Introduction to lesson Introduce the lesson by giving students a sense of what they will be doing and where they are headed by telling students ldquoThis will be a three-day lesson where we will be exploring how scientists think and more specifically what mechanistic thinking looks like in practice In this process we will also be learning Scratch We will tie everything together at the end of the third dayrdquo Step 2 Playing with Scratch Depending on the level of your students and any future goals you wish to achieve with Scratch structure the class so that students are comfortable navigating around the Scratch environment and are able to get started on their own Scratch project by the end of the class Please provide students with any Scratch resources you see fit Check out the ScratchEds resource search (httpscratchedmediamiteduresourcessearch) for more info Some good examples found in ScratchEd of Scratch lesson plans (video tutorials PowerPoints and worksheets) include
bull Having Fun with Computer Programming and Games (httpwwwleroieeducationoutreachsecondlevelscratchlessonplans)
bull A TeachNetUK Project 6 Lessons on Getting Started with Scratch (httpwwwteachnet-ukorguk200720ProjectsICT-ScratchScratchpages8_schemeofworkhtml)
bull Scratch Lessons Shall We Learn Scratch Programming for Tweens (httpwwwshallwelearncomscratchprogrammingforkidscategory)
bull Designing Animations and GamesmdashA Creative Introduction to Programming (httpwwwcsuni-potsdamde~romeikeUEWettbewerbindex-englishhtm)
Make sure to also introduce students to the Scratch online community and let them know that they can download the source code of any project to help them see how others are using the Scratch programming language to create projects
Review Extend and Apply Step 3 Scratch Assignment End the day by informing students that they will apply what they have learned today to create a mini-Scratch project for an assignment after the next dayrsquos lesson Emphasize to students that the goal is not to create a complex programming project but to use Scratch creatively as a medium for creative expressing not matter how simple the project is Encourage students to play with Scratch on their own time and make it clear that you highly encourage them to borrow adapt and build upon the ideas and projects of others (this is not considered cheating)
copy 2009 Yu-Tzu Debbie Liu 5
Lesson Plan Day 2 Materials
21st century scientist case study of Jay Keasling Student notebooks or journals
Prep Step Review lesson plan background information and understanding goals Make copies of 21st century scientist case study of Jay Keasling (p 8)
Explore Step 1 What is scientific thinking Ask students to describe what they think is scientific thinking Collect a representative list of studentsrsquo thoughts on the board Ask students to explain or expound on the meaning behind what they are saying After reviewing the list ask them ldquo Do you think all scientists come to their discoveries in the same wayrdquo ldquoDo scientists display all these characteristics at all timesrdquo It is important to point out to students that scientists have various methods going about their experimentation and work and depending on the type of work they are doing scientists donrsquot always share the same methods Furthermore scientists engage in thinking patterns that are specific to its particular socio-cultural context and one of which is mechanistic thinking Engage in a discussion with students on how might the explosion of advancements in scientific knowledge and technology at the turn of the century change the way scientists at the cutting edge of research interact with their work
Step 2 Analyze case study of a 21st century scientist Let students know that they will be learning about the field of synthetic biology as a means to illustrate how modern scientists work and think Specifically they will be studying Jay Keasling one of the pioneers of synthetic biology Hand out the case study on Jay Keasling Have students work in groups of 3-4 students to identify any patterns of thinking that the scientist displays Make sure to ask students to specifically identify what part of the case study justifies their claims Have students write the class findings in their journalsnotebooks
Possible findings from case analysis Jay Keasling
Keasling is a pioneer of synthetic biologymdasha field that designs and constructs new organisms for useful purposes He is most known for creating a microbe that produces a drug to treat malaria (making drugs from bugs) Some of his characteristics as a scientist include
bull Creative and imaginative wanted to invent new tools that can turn cells into chemical plants take in something very simple and spits out something complicated and valuable coming up with other applications of synthetic biology (use microbes to break down pesticides make biodegradable plastics create fuels from plants)
bull Critical thinking thought about how to design and create microbes to produce artemisinin much quicker and cheaper how to integrate genes from different species into a microbe to fabricate the drug
copy 2009 Yu-Tzu Debbie Liu 6
bull Seek and integrate information integrated methods and concepts from engineering and biology leading to synthetic biology
bull Supported with significant resources did research at universities and received grant money
bull Practical-minded microbes will churn out anti-malarial drug for a fraction of its current cost making it accessible to much more of the world these microbes could save millions of lives
bull Strong disciplinary understanding studied biology and chemical engineering extensively leading to his PhD and professor position at UC Berkeley
Step 3 What is mechanistic thinking Introduce students to the idea of mechanistic thinking as a prominent thinking pattern in the 21st
century
Mechanistic Thinking
Mechanistic thinking is a way of thinking that has a mechanical or engineering undertone This is shown through scientistsrsquo regular use of mechanical analogies to conceptualize their work and their modular synthetic and purpose-driven approach towards their research problems The display of mechanistic thinking by scientists appears to be a result of the merging of biology and engineering practices that is increasingly observed in 21st century biology as compared to a time when most of biologymdashtraditionally known for its pure basic researchmdashremain clearly demarcated from engineeringmdasha purely applied research field A mechanistic way of thinking has come to the forefront of 21st century science because of recent developments in new technologies and knowledge that enable scientists to manipulate the object or organism they are working with more directly allowing them to engineer and create novel biological systems for practical applications
Let students know that the work synthetic biologists do often require them to think mechanistically Now that students are given a definition of mechanistic thinking have students revisit their case study analysis and explore how synthetic biologists might think mechanistically
Review Extend and Apply
Step 4 Scratch Assignment Ask students to create a mini-Scratch project to demonstrate what they have learned so far (the project does not have to be all inclusive students can choose to focus on just one thing they learned either about scientific thinking mechanistic thinking or synthetic biology) Emphasize to students that the goal is not to create a complex programming project but to use Scratch creatively as a medium for creative expressing not matter how simple the project is Encourage students to work with partners and collaborate by borrowing adapting or building upon the ideas and projects of others (this is not considered cheating)
copy 2009 Yu-Tzu Debbie Liu 7
Detailed Case Study Jay Keasling
(1964 ndash present)
Best known for pioneering the new field of synthetic biology which designs and constructs new organisms for useful purposes He is also most known for creating a microbe that produces a drug to treat malaria (making drugs from bugs)
Jay Keasling was raised on a farm and spent his childhood exploring the practical side of biology chemistry and engineering This background eventually led him to work in the rapidly growing field that uses living organisms like bacteria for various practical purposes such as food processing agriculture and medicine
In the early 1980s genetic engineering became popular because you can ldquoconvincerdquo microbes to produce insulin growth hormones and other valuable proteins by simply inserting a single gene from a different organism into bacteria However Keasling believed that genetic engineering isnrsquot harnessing the full power of these cells The production of molecules isnt always so simple it requires a complex interaction of several genes (not just one) being produced in a certain sequence So Keasling wanted to invent the tools that would allow him to create these kinds of genetic assembly lines Thus what goes on in a cell is a lot like what goes on in a chemical plant petroleum goes in and after a whole chain of reactions plastic comes out
Keasling went to college studying biology and chemical engineering extensively and got his PhD in 1991 He is now a professor at the University of California at Berkeley He spent his first 10 years at UC Berkeley building the new tools he would need to turn cells into chemical plants He also invented powerful chemical switches (like a light switch) that allowed him to control when he wanted to ldquoturn onrdquo and ldquoturn offrdquo protein production in cells This way of borrowing techniques from engineering and figuring out how to manipulate microbes came to be call synthetic biology
After years of perfecting his biological tool kit Keasling wanted to find a real-world use for it In 2002 he learned of the dire need for artemisinin a compound derived from the sweet wormwood plant which is 90 percent effective against the parasite that causes malaria and has few side effects (malaria kills some 3 million people a year) However extracting the drug from sweet wormwood is a slow and expensive process Keasling figured he could design and create microbes to produce artemisinin much quicker and cheaper Rather than wait months for sweet wormwood to grow on farms Keasling wanted to create it simply by pouring sugar in a tank full of microbes that can use the sugar to make the drug via a chemical pathway he has designedmdashhe wanted to integrate genes from different species into a microbe to fabricate the drug for malaria
copy 2009 Yu-Tzu Debbie Liu 8
In 2006 Keaslings team (comprised of graduate students post-docs and research assistants) published their success of the production of artemisinin It is expected to lower the cost of artemisinin production from a dollar per gram to just 10 cents He was awarded a $43 million grant from the Bill and Melinda Gates Foundation and awarded DISCOVER magazinersquos first ever Scientist of the Year Award
Fighting malaria is just one part of Keaslings larger agenda to explore the potential of synthetic biology In his laboratory students are engineering microbes to break down pesticides make biodegradable plastics and create ethanol and other fuels from plants
Excerpts of i interview w Jay Keasling
1 You arrived at UC Berkeley in 1992 with training as both a chemical engineer and a biologist What did you hope to do
2 Why hadnt anybody tried to engineer cells that way before
3 How did you get involved in your antimalaria project
Jay Keisling biography adapted fromZimmer C (2006) Scientist of the Year Jay Keasling Discovermagazinecom Retrieved from
httpdiscovermagazinecom2006deccover
copy 2009 Yu-Tzu Debbie Liu 9
See responses to these questions atZimmer C (2006) Scientist of the Year Jay Keasling Discovermagazinecom Retrieved from
httpdiscovermagazinecom2006deccover
Interview content removed due to copyright restrictions
Interview content removed due to copyright restrictions
Interview content removed due to copyright restrictions
Lesson Plan Day 3 Materials
Designing a New Microbe worksheet Organism cards Student notebooks or journals
Prep Step Review lesson plan background information and understanding goals Photocopy Designing a New Microbe worksheet (p 28) Cut out organism cards (each group of 3-4 students will have a set of cards) (p29)
Explore Step 1 Designing a New Microbe Introduce todayrsquos activity by saying ldquoYou will be simulating how synthetic biologists think mechanistically by doing an the activity that is actually modeled after a real experiment done by scientists in 2007rdquo Divide students into groups of 3 or 4 Each group receives a set of organism cards Each student receives a Designing a New Microbe worksheet Remind students that proteins (or enzymes) are molecules inside cells that convert one molecule into another (eg the make-believe molecule How is converted to the molecule Home by Protein T in bacteria) Following the directions of the handout have students create a kind of assembly line that integrate proteins from different organisms into a microbe that uses water and starch (inputs) to ultimately produce hydrogen (output)
Possible answers to Designing a New Microbe
There are two possible pathways that can lead to hydrogen production
1 Starch amp water Protein G Protein P Protein D Protein R Protein T Protein F Protein H Hydrogen
2 Starch amp water Protein G Protein P Protein D Protein H Hydrogen
Guide students along by encouraging students who have already figured out how to attempt the problem to reveal and share with the class how they are thinking through the problem Stop students periodically to ask ldquoHow are you thinking through this problem What is your goal and how is your thinking helping you reach that goalrdquo Students may find either working sequentially forward or backward to fill in the worksheet to be easier
Note to teachers The hydrogen production pathway from starch and water is a shorten version of the actual 2007 experiment for learning purposes The organism types and molecule names are true to the experiment Protein names are made up for simplicity
copy 2009 Yu-Tzu Debbie Liu 10
Step 2 Discuss studentsrsquo findings Have students tell you what they found as you write their findings on the board Students may have discovered by now that there are two paths that lead to hydrogen production Students might recall that Jay Keasling have done something similar by making an antimalarial drug from sugar using synthetic biology Students may have also discovered that no proteins from the mouse organism were used for the design of their new microbe Ask students ldquowhat do you think is the purpose of having a mouse organism when we didnrsquot need itrdquo Help students understand how in reality scientists have hundreds of organisms to choose from some of which are irrelevant to their work In fact a common skill that scientists share is being about to identify and pull together important and relevant information The activity allows students to discover that synthetic biology is a very mind-blowing field accomplishing things that some people never thought was possible Students will come to appreciate how seemingly impossible feats can be possible especially when scientists are thinking creatively By thinking and working mechanistically scientists have more freedom then before in designing and creating novel organisms for real-world applications
Review Extend and Apply Step 3 How do you think mechanistically Ask students to reflect on their experience with Scratch and how they might have engaged in mechanistic thinking in their own work Helps students make the connection that they themselves have been engaging in mechanistic thinking while working on their own Scratch projects The Scratch grammar is designed so that users are presented with a versatile collection of graphical programming blocks that they can be snapped together to create programs much like synthetic biology Connectors on the blocks suggest how they should be put together so that over the process of tinkering with these blocks the emerging structure can give rise to new ideas and direction to the project Not only does snapping together complimentary blocks provide an easy way into learning programming but the idea of modularization as a problem-solving and design strategy is directly relevant to mechanistic thinking Go on to discuss how they can apply scientistsrsquo patterns of thinking to our own thinking in science class and daily life
copy 2009 Yu-Tzu Debbie Liu 11
Name___________________________ Date ____________
Designing a New Microbe
Task Gas prices have reached its all time high Thus scientists are trying to think of ways to produce alternative fuels such as hydrogen gas in a much cheaper and quicker way You are a scientist and you are familiar with six different organisms Based on what you know can you come up with a way to generate hydrogen from starch and water by designing a microbe that borrows different mechanismsproteins from different cells Fill in the blanks with protein names and the organism that the protein was taken from
Materials Each team has a set of cards each card symbolizing a different organism On the card you will see the name of the organism a picture of the organism and proteins that is unique to them Proteins (or enzymes) convert one molecule into another
Starch amp Water Protein borrowed Protein borrowed
Input Organism Organism
Protein borrowed $ Protein borrowed $ Protein borrowed Organism Organism Organism
Protein borrowed Protein borrowed Protein borrowed Hydrogen Organism Organism Organism Output
Experiment adapted from Zhang YH Evans BR Mielenz JR Hopkins RC Adams MW (2007) High-yield hydrogen production from
starch and water by a synthetic enzymatic pathway PLoS ONE 5 e456
copy 2009 Yu-Tzu Debbie Liu 12
Organism Cards (one set)
Teachers Please make as many copies as the number of groups of students Cut the cards out and shuffle before handing to students
Source NIH
Bacteria
Rabbitbull Protein T uses [X5P] to make [S7P]
Photo US Fish and Wildlife Service bull Protein F uses [S7P] to make [NADPH] bull Protein G uses starch and water to make [G-1-P] bull Protein P uses [G-1-P] to make [G-6-P]
Yeast
Public domain image (Source Wikimedia Commons)
bull Protein D uses [G-6-P] to make [NADPH] and [R5P]
Public domain image (Source Wikimedia Commons) Spinach
bull Protein R uses [R5P] to make [X5P]
Experiment adapted from
Archea Courtesy of Angels Tapias (License CC BY)
bull Protein H uses [NADPH] to make Hydrogen
Source NIH Mouse
bull Protein X uses [T8P] to make Hydrogen
Zhang YH Evans BR Mielenz JR Hopkins RC Adams MW (2007) High-yield hydrogen production from starch and water by a synthetic enzymatic pathway PLoS ONE 5 e456
copy 2009 Yu-Tzu Debbie Liu 13
MIT OpenCourseWarehttpocwmitedu
MAS714J STS445J Technologies for Creative Learning Fall 2009
For information about citing these materials or our Terms of Use visit httpocwmiteduterms
Lesson Plan Day 2 Materials
21st century scientist case study of Jay Keasling Student notebooks or journals
Prep Step Review lesson plan background information and understanding goals Make copies of 21st century scientist case study of Jay Keasling (p 8)
Explore Step 1 What is scientific thinking Ask students to describe what they think is scientific thinking Collect a representative list of studentsrsquo thoughts on the board Ask students to explain or expound on the meaning behind what they are saying After reviewing the list ask them ldquo Do you think all scientists come to their discoveries in the same wayrdquo ldquoDo scientists display all these characteristics at all timesrdquo It is important to point out to students that scientists have various methods going about their experimentation and work and depending on the type of work they are doing scientists donrsquot always share the same methods Furthermore scientists engage in thinking patterns that are specific to its particular socio-cultural context and one of which is mechanistic thinking Engage in a discussion with students on how might the explosion of advancements in scientific knowledge and technology at the turn of the century change the way scientists at the cutting edge of research interact with their work
Step 2 Analyze case study of a 21st century scientist Let students know that they will be learning about the field of synthetic biology as a means to illustrate how modern scientists work and think Specifically they will be studying Jay Keasling one of the pioneers of synthetic biology Hand out the case study on Jay Keasling Have students work in groups of 3-4 students to identify any patterns of thinking that the scientist displays Make sure to ask students to specifically identify what part of the case study justifies their claims Have students write the class findings in their journalsnotebooks
Possible findings from case analysis Jay Keasling
Keasling is a pioneer of synthetic biologymdasha field that designs and constructs new organisms for useful purposes He is most known for creating a microbe that produces a drug to treat malaria (making drugs from bugs) Some of his characteristics as a scientist include
bull Creative and imaginative wanted to invent new tools that can turn cells into chemical plants take in something very simple and spits out something complicated and valuable coming up with other applications of synthetic biology (use microbes to break down pesticides make biodegradable plastics create fuels from plants)
bull Critical thinking thought about how to design and create microbes to produce artemisinin much quicker and cheaper how to integrate genes from different species into a microbe to fabricate the drug
copy 2009 Yu-Tzu Debbie Liu 6
bull Seek and integrate information integrated methods and concepts from engineering and biology leading to synthetic biology
bull Supported with significant resources did research at universities and received grant money
bull Practical-minded microbes will churn out anti-malarial drug for a fraction of its current cost making it accessible to much more of the world these microbes could save millions of lives
bull Strong disciplinary understanding studied biology and chemical engineering extensively leading to his PhD and professor position at UC Berkeley
Step 3 What is mechanistic thinking Introduce students to the idea of mechanistic thinking as a prominent thinking pattern in the 21st
century
Mechanistic Thinking
Mechanistic thinking is a way of thinking that has a mechanical or engineering undertone This is shown through scientistsrsquo regular use of mechanical analogies to conceptualize their work and their modular synthetic and purpose-driven approach towards their research problems The display of mechanistic thinking by scientists appears to be a result of the merging of biology and engineering practices that is increasingly observed in 21st century biology as compared to a time when most of biologymdashtraditionally known for its pure basic researchmdashremain clearly demarcated from engineeringmdasha purely applied research field A mechanistic way of thinking has come to the forefront of 21st century science because of recent developments in new technologies and knowledge that enable scientists to manipulate the object or organism they are working with more directly allowing them to engineer and create novel biological systems for practical applications
Let students know that the work synthetic biologists do often require them to think mechanistically Now that students are given a definition of mechanistic thinking have students revisit their case study analysis and explore how synthetic biologists might think mechanistically
Review Extend and Apply
Step 4 Scratch Assignment Ask students to create a mini-Scratch project to demonstrate what they have learned so far (the project does not have to be all inclusive students can choose to focus on just one thing they learned either about scientific thinking mechanistic thinking or synthetic biology) Emphasize to students that the goal is not to create a complex programming project but to use Scratch creatively as a medium for creative expressing not matter how simple the project is Encourage students to work with partners and collaborate by borrowing adapting or building upon the ideas and projects of others (this is not considered cheating)
copy 2009 Yu-Tzu Debbie Liu 7
Detailed Case Study Jay Keasling
(1964 ndash present)
Best known for pioneering the new field of synthetic biology which designs and constructs new organisms for useful purposes He is also most known for creating a microbe that produces a drug to treat malaria (making drugs from bugs)
Jay Keasling was raised on a farm and spent his childhood exploring the practical side of biology chemistry and engineering This background eventually led him to work in the rapidly growing field that uses living organisms like bacteria for various practical purposes such as food processing agriculture and medicine
In the early 1980s genetic engineering became popular because you can ldquoconvincerdquo microbes to produce insulin growth hormones and other valuable proteins by simply inserting a single gene from a different organism into bacteria However Keasling believed that genetic engineering isnrsquot harnessing the full power of these cells The production of molecules isnt always so simple it requires a complex interaction of several genes (not just one) being produced in a certain sequence So Keasling wanted to invent the tools that would allow him to create these kinds of genetic assembly lines Thus what goes on in a cell is a lot like what goes on in a chemical plant petroleum goes in and after a whole chain of reactions plastic comes out
Keasling went to college studying biology and chemical engineering extensively and got his PhD in 1991 He is now a professor at the University of California at Berkeley He spent his first 10 years at UC Berkeley building the new tools he would need to turn cells into chemical plants He also invented powerful chemical switches (like a light switch) that allowed him to control when he wanted to ldquoturn onrdquo and ldquoturn offrdquo protein production in cells This way of borrowing techniques from engineering and figuring out how to manipulate microbes came to be call synthetic biology
After years of perfecting his biological tool kit Keasling wanted to find a real-world use for it In 2002 he learned of the dire need for artemisinin a compound derived from the sweet wormwood plant which is 90 percent effective against the parasite that causes malaria and has few side effects (malaria kills some 3 million people a year) However extracting the drug from sweet wormwood is a slow and expensive process Keasling figured he could design and create microbes to produce artemisinin much quicker and cheaper Rather than wait months for sweet wormwood to grow on farms Keasling wanted to create it simply by pouring sugar in a tank full of microbes that can use the sugar to make the drug via a chemical pathway he has designedmdashhe wanted to integrate genes from different species into a microbe to fabricate the drug for malaria
copy 2009 Yu-Tzu Debbie Liu 8
In 2006 Keaslings team (comprised of graduate students post-docs and research assistants) published their success of the production of artemisinin It is expected to lower the cost of artemisinin production from a dollar per gram to just 10 cents He was awarded a $43 million grant from the Bill and Melinda Gates Foundation and awarded DISCOVER magazinersquos first ever Scientist of the Year Award
Fighting malaria is just one part of Keaslings larger agenda to explore the potential of synthetic biology In his laboratory students are engineering microbes to break down pesticides make biodegradable plastics and create ethanol and other fuels from plants
Excerpts of i interview w Jay Keasling
1 You arrived at UC Berkeley in 1992 with training as both a chemical engineer and a biologist What did you hope to do
2 Why hadnt anybody tried to engineer cells that way before
3 How did you get involved in your antimalaria project
Jay Keisling biography adapted fromZimmer C (2006) Scientist of the Year Jay Keasling Discovermagazinecom Retrieved from
httpdiscovermagazinecom2006deccover
copy 2009 Yu-Tzu Debbie Liu 9
See responses to these questions atZimmer C (2006) Scientist of the Year Jay Keasling Discovermagazinecom Retrieved from
httpdiscovermagazinecom2006deccover
Interview content removed due to copyright restrictions
Interview content removed due to copyright restrictions
Interview content removed due to copyright restrictions
Lesson Plan Day 3 Materials
Designing a New Microbe worksheet Organism cards Student notebooks or journals
Prep Step Review lesson plan background information and understanding goals Photocopy Designing a New Microbe worksheet (p 28) Cut out organism cards (each group of 3-4 students will have a set of cards) (p29)
Explore Step 1 Designing a New Microbe Introduce todayrsquos activity by saying ldquoYou will be simulating how synthetic biologists think mechanistically by doing an the activity that is actually modeled after a real experiment done by scientists in 2007rdquo Divide students into groups of 3 or 4 Each group receives a set of organism cards Each student receives a Designing a New Microbe worksheet Remind students that proteins (or enzymes) are molecules inside cells that convert one molecule into another (eg the make-believe molecule How is converted to the molecule Home by Protein T in bacteria) Following the directions of the handout have students create a kind of assembly line that integrate proteins from different organisms into a microbe that uses water and starch (inputs) to ultimately produce hydrogen (output)
Possible answers to Designing a New Microbe
There are two possible pathways that can lead to hydrogen production
1 Starch amp water Protein G Protein P Protein D Protein R Protein T Protein F Protein H Hydrogen
2 Starch amp water Protein G Protein P Protein D Protein H Hydrogen
Guide students along by encouraging students who have already figured out how to attempt the problem to reveal and share with the class how they are thinking through the problem Stop students periodically to ask ldquoHow are you thinking through this problem What is your goal and how is your thinking helping you reach that goalrdquo Students may find either working sequentially forward or backward to fill in the worksheet to be easier
Note to teachers The hydrogen production pathway from starch and water is a shorten version of the actual 2007 experiment for learning purposes The organism types and molecule names are true to the experiment Protein names are made up for simplicity
copy 2009 Yu-Tzu Debbie Liu 10
Step 2 Discuss studentsrsquo findings Have students tell you what they found as you write their findings on the board Students may have discovered by now that there are two paths that lead to hydrogen production Students might recall that Jay Keasling have done something similar by making an antimalarial drug from sugar using synthetic biology Students may have also discovered that no proteins from the mouse organism were used for the design of their new microbe Ask students ldquowhat do you think is the purpose of having a mouse organism when we didnrsquot need itrdquo Help students understand how in reality scientists have hundreds of organisms to choose from some of which are irrelevant to their work In fact a common skill that scientists share is being about to identify and pull together important and relevant information The activity allows students to discover that synthetic biology is a very mind-blowing field accomplishing things that some people never thought was possible Students will come to appreciate how seemingly impossible feats can be possible especially when scientists are thinking creatively By thinking and working mechanistically scientists have more freedom then before in designing and creating novel organisms for real-world applications
Review Extend and Apply Step 3 How do you think mechanistically Ask students to reflect on their experience with Scratch and how they might have engaged in mechanistic thinking in their own work Helps students make the connection that they themselves have been engaging in mechanistic thinking while working on their own Scratch projects The Scratch grammar is designed so that users are presented with a versatile collection of graphical programming blocks that they can be snapped together to create programs much like synthetic biology Connectors on the blocks suggest how they should be put together so that over the process of tinkering with these blocks the emerging structure can give rise to new ideas and direction to the project Not only does snapping together complimentary blocks provide an easy way into learning programming but the idea of modularization as a problem-solving and design strategy is directly relevant to mechanistic thinking Go on to discuss how they can apply scientistsrsquo patterns of thinking to our own thinking in science class and daily life
copy 2009 Yu-Tzu Debbie Liu 11
Name___________________________ Date ____________
Designing a New Microbe
Task Gas prices have reached its all time high Thus scientists are trying to think of ways to produce alternative fuels such as hydrogen gas in a much cheaper and quicker way You are a scientist and you are familiar with six different organisms Based on what you know can you come up with a way to generate hydrogen from starch and water by designing a microbe that borrows different mechanismsproteins from different cells Fill in the blanks with protein names and the organism that the protein was taken from
Materials Each team has a set of cards each card symbolizing a different organism On the card you will see the name of the organism a picture of the organism and proteins that is unique to them Proteins (or enzymes) convert one molecule into another
Starch amp Water Protein borrowed Protein borrowed
Input Organism Organism
Protein borrowed $ Protein borrowed $ Protein borrowed Organism Organism Organism
Protein borrowed Protein borrowed Protein borrowed Hydrogen Organism Organism Organism Output
Experiment adapted from Zhang YH Evans BR Mielenz JR Hopkins RC Adams MW (2007) High-yield hydrogen production from
starch and water by a synthetic enzymatic pathway PLoS ONE 5 e456
copy 2009 Yu-Tzu Debbie Liu 12
Organism Cards (one set)
Teachers Please make as many copies as the number of groups of students Cut the cards out and shuffle before handing to students
Source NIH
Bacteria
Rabbitbull Protein T uses [X5P] to make [S7P]
Photo US Fish and Wildlife Service bull Protein F uses [S7P] to make [NADPH] bull Protein G uses starch and water to make [G-1-P] bull Protein P uses [G-1-P] to make [G-6-P]
Yeast
Public domain image (Source Wikimedia Commons)
bull Protein D uses [G-6-P] to make [NADPH] and [R5P]
Public domain image (Source Wikimedia Commons) Spinach
bull Protein R uses [R5P] to make [X5P]
Experiment adapted from
Archea Courtesy of Angels Tapias (License CC BY)
bull Protein H uses [NADPH] to make Hydrogen
Source NIH Mouse
bull Protein X uses [T8P] to make Hydrogen
Zhang YH Evans BR Mielenz JR Hopkins RC Adams MW (2007) High-yield hydrogen production from starch and water by a synthetic enzymatic pathway PLoS ONE 5 e456
copy 2009 Yu-Tzu Debbie Liu 13
MIT OpenCourseWarehttpocwmitedu
MAS714J STS445J Technologies for Creative Learning Fall 2009
For information about citing these materials or our Terms of Use visit httpocwmiteduterms
bull Seek and integrate information integrated methods and concepts from engineering and biology leading to synthetic biology
bull Supported with significant resources did research at universities and received grant money
bull Practical-minded microbes will churn out anti-malarial drug for a fraction of its current cost making it accessible to much more of the world these microbes could save millions of lives
bull Strong disciplinary understanding studied biology and chemical engineering extensively leading to his PhD and professor position at UC Berkeley
Step 3 What is mechanistic thinking Introduce students to the idea of mechanistic thinking as a prominent thinking pattern in the 21st
century
Mechanistic Thinking
Mechanistic thinking is a way of thinking that has a mechanical or engineering undertone This is shown through scientistsrsquo regular use of mechanical analogies to conceptualize their work and their modular synthetic and purpose-driven approach towards their research problems The display of mechanistic thinking by scientists appears to be a result of the merging of biology and engineering practices that is increasingly observed in 21st century biology as compared to a time when most of biologymdashtraditionally known for its pure basic researchmdashremain clearly demarcated from engineeringmdasha purely applied research field A mechanistic way of thinking has come to the forefront of 21st century science because of recent developments in new technologies and knowledge that enable scientists to manipulate the object or organism they are working with more directly allowing them to engineer and create novel biological systems for practical applications
Let students know that the work synthetic biologists do often require them to think mechanistically Now that students are given a definition of mechanistic thinking have students revisit their case study analysis and explore how synthetic biologists might think mechanistically
Review Extend and Apply
Step 4 Scratch Assignment Ask students to create a mini-Scratch project to demonstrate what they have learned so far (the project does not have to be all inclusive students can choose to focus on just one thing they learned either about scientific thinking mechanistic thinking or synthetic biology) Emphasize to students that the goal is not to create a complex programming project but to use Scratch creatively as a medium for creative expressing not matter how simple the project is Encourage students to work with partners and collaborate by borrowing adapting or building upon the ideas and projects of others (this is not considered cheating)
copy 2009 Yu-Tzu Debbie Liu 7
Detailed Case Study Jay Keasling
(1964 ndash present)
Best known for pioneering the new field of synthetic biology which designs and constructs new organisms for useful purposes He is also most known for creating a microbe that produces a drug to treat malaria (making drugs from bugs)
Jay Keasling was raised on a farm and spent his childhood exploring the practical side of biology chemistry and engineering This background eventually led him to work in the rapidly growing field that uses living organisms like bacteria for various practical purposes such as food processing agriculture and medicine
In the early 1980s genetic engineering became popular because you can ldquoconvincerdquo microbes to produce insulin growth hormones and other valuable proteins by simply inserting a single gene from a different organism into bacteria However Keasling believed that genetic engineering isnrsquot harnessing the full power of these cells The production of molecules isnt always so simple it requires a complex interaction of several genes (not just one) being produced in a certain sequence So Keasling wanted to invent the tools that would allow him to create these kinds of genetic assembly lines Thus what goes on in a cell is a lot like what goes on in a chemical plant petroleum goes in and after a whole chain of reactions plastic comes out
Keasling went to college studying biology and chemical engineering extensively and got his PhD in 1991 He is now a professor at the University of California at Berkeley He spent his first 10 years at UC Berkeley building the new tools he would need to turn cells into chemical plants He also invented powerful chemical switches (like a light switch) that allowed him to control when he wanted to ldquoturn onrdquo and ldquoturn offrdquo protein production in cells This way of borrowing techniques from engineering and figuring out how to manipulate microbes came to be call synthetic biology
After years of perfecting his biological tool kit Keasling wanted to find a real-world use for it In 2002 he learned of the dire need for artemisinin a compound derived from the sweet wormwood plant which is 90 percent effective against the parasite that causes malaria and has few side effects (malaria kills some 3 million people a year) However extracting the drug from sweet wormwood is a slow and expensive process Keasling figured he could design and create microbes to produce artemisinin much quicker and cheaper Rather than wait months for sweet wormwood to grow on farms Keasling wanted to create it simply by pouring sugar in a tank full of microbes that can use the sugar to make the drug via a chemical pathway he has designedmdashhe wanted to integrate genes from different species into a microbe to fabricate the drug for malaria
copy 2009 Yu-Tzu Debbie Liu 8
In 2006 Keaslings team (comprised of graduate students post-docs and research assistants) published their success of the production of artemisinin It is expected to lower the cost of artemisinin production from a dollar per gram to just 10 cents He was awarded a $43 million grant from the Bill and Melinda Gates Foundation and awarded DISCOVER magazinersquos first ever Scientist of the Year Award
Fighting malaria is just one part of Keaslings larger agenda to explore the potential of synthetic biology In his laboratory students are engineering microbes to break down pesticides make biodegradable plastics and create ethanol and other fuels from plants
Excerpts of i interview w Jay Keasling
1 You arrived at UC Berkeley in 1992 with training as both a chemical engineer and a biologist What did you hope to do
2 Why hadnt anybody tried to engineer cells that way before
3 How did you get involved in your antimalaria project
Jay Keisling biography adapted fromZimmer C (2006) Scientist of the Year Jay Keasling Discovermagazinecom Retrieved from
httpdiscovermagazinecom2006deccover
copy 2009 Yu-Tzu Debbie Liu 9
See responses to these questions atZimmer C (2006) Scientist of the Year Jay Keasling Discovermagazinecom Retrieved from
httpdiscovermagazinecom2006deccover
Interview content removed due to copyright restrictions
Interview content removed due to copyright restrictions
Interview content removed due to copyright restrictions
Lesson Plan Day 3 Materials
Designing a New Microbe worksheet Organism cards Student notebooks or journals
Prep Step Review lesson plan background information and understanding goals Photocopy Designing a New Microbe worksheet (p 28) Cut out organism cards (each group of 3-4 students will have a set of cards) (p29)
Explore Step 1 Designing a New Microbe Introduce todayrsquos activity by saying ldquoYou will be simulating how synthetic biologists think mechanistically by doing an the activity that is actually modeled after a real experiment done by scientists in 2007rdquo Divide students into groups of 3 or 4 Each group receives a set of organism cards Each student receives a Designing a New Microbe worksheet Remind students that proteins (or enzymes) are molecules inside cells that convert one molecule into another (eg the make-believe molecule How is converted to the molecule Home by Protein T in bacteria) Following the directions of the handout have students create a kind of assembly line that integrate proteins from different organisms into a microbe that uses water and starch (inputs) to ultimately produce hydrogen (output)
Possible answers to Designing a New Microbe
There are two possible pathways that can lead to hydrogen production
1 Starch amp water Protein G Protein P Protein D Protein R Protein T Protein F Protein H Hydrogen
2 Starch amp water Protein G Protein P Protein D Protein H Hydrogen
Guide students along by encouraging students who have already figured out how to attempt the problem to reveal and share with the class how they are thinking through the problem Stop students periodically to ask ldquoHow are you thinking through this problem What is your goal and how is your thinking helping you reach that goalrdquo Students may find either working sequentially forward or backward to fill in the worksheet to be easier
Note to teachers The hydrogen production pathway from starch and water is a shorten version of the actual 2007 experiment for learning purposes The organism types and molecule names are true to the experiment Protein names are made up for simplicity
copy 2009 Yu-Tzu Debbie Liu 10
Step 2 Discuss studentsrsquo findings Have students tell you what they found as you write their findings on the board Students may have discovered by now that there are two paths that lead to hydrogen production Students might recall that Jay Keasling have done something similar by making an antimalarial drug from sugar using synthetic biology Students may have also discovered that no proteins from the mouse organism were used for the design of their new microbe Ask students ldquowhat do you think is the purpose of having a mouse organism when we didnrsquot need itrdquo Help students understand how in reality scientists have hundreds of organisms to choose from some of which are irrelevant to their work In fact a common skill that scientists share is being about to identify and pull together important and relevant information The activity allows students to discover that synthetic biology is a very mind-blowing field accomplishing things that some people never thought was possible Students will come to appreciate how seemingly impossible feats can be possible especially when scientists are thinking creatively By thinking and working mechanistically scientists have more freedom then before in designing and creating novel organisms for real-world applications
Review Extend and Apply Step 3 How do you think mechanistically Ask students to reflect on their experience with Scratch and how they might have engaged in mechanistic thinking in their own work Helps students make the connection that they themselves have been engaging in mechanistic thinking while working on their own Scratch projects The Scratch grammar is designed so that users are presented with a versatile collection of graphical programming blocks that they can be snapped together to create programs much like synthetic biology Connectors on the blocks suggest how they should be put together so that over the process of tinkering with these blocks the emerging structure can give rise to new ideas and direction to the project Not only does snapping together complimentary blocks provide an easy way into learning programming but the idea of modularization as a problem-solving and design strategy is directly relevant to mechanistic thinking Go on to discuss how they can apply scientistsrsquo patterns of thinking to our own thinking in science class and daily life
copy 2009 Yu-Tzu Debbie Liu 11
Name___________________________ Date ____________
Designing a New Microbe
Task Gas prices have reached its all time high Thus scientists are trying to think of ways to produce alternative fuels such as hydrogen gas in a much cheaper and quicker way You are a scientist and you are familiar with six different organisms Based on what you know can you come up with a way to generate hydrogen from starch and water by designing a microbe that borrows different mechanismsproteins from different cells Fill in the blanks with protein names and the organism that the protein was taken from
Materials Each team has a set of cards each card symbolizing a different organism On the card you will see the name of the organism a picture of the organism and proteins that is unique to them Proteins (or enzymes) convert one molecule into another
Starch amp Water Protein borrowed Protein borrowed
Input Organism Organism
Protein borrowed $ Protein borrowed $ Protein borrowed Organism Organism Organism
Protein borrowed Protein borrowed Protein borrowed Hydrogen Organism Organism Organism Output
Experiment adapted from Zhang YH Evans BR Mielenz JR Hopkins RC Adams MW (2007) High-yield hydrogen production from
starch and water by a synthetic enzymatic pathway PLoS ONE 5 e456
copy 2009 Yu-Tzu Debbie Liu 12
Organism Cards (one set)
Teachers Please make as many copies as the number of groups of students Cut the cards out and shuffle before handing to students
Source NIH
Bacteria
Rabbitbull Protein T uses [X5P] to make [S7P]
Photo US Fish and Wildlife Service bull Protein F uses [S7P] to make [NADPH] bull Protein G uses starch and water to make [G-1-P] bull Protein P uses [G-1-P] to make [G-6-P]
Yeast
Public domain image (Source Wikimedia Commons)
bull Protein D uses [G-6-P] to make [NADPH] and [R5P]
Public domain image (Source Wikimedia Commons) Spinach
bull Protein R uses [R5P] to make [X5P]
Experiment adapted from
Archea Courtesy of Angels Tapias (License CC BY)
bull Protein H uses [NADPH] to make Hydrogen
Source NIH Mouse
bull Protein X uses [T8P] to make Hydrogen
Zhang YH Evans BR Mielenz JR Hopkins RC Adams MW (2007) High-yield hydrogen production from starch and water by a synthetic enzymatic pathway PLoS ONE 5 e456
copy 2009 Yu-Tzu Debbie Liu 13
MIT OpenCourseWarehttpocwmitedu
MAS714J STS445J Technologies for Creative Learning Fall 2009
For information about citing these materials or our Terms of Use visit httpocwmiteduterms
Detailed Case Study Jay Keasling
(1964 ndash present)
Best known for pioneering the new field of synthetic biology which designs and constructs new organisms for useful purposes He is also most known for creating a microbe that produces a drug to treat malaria (making drugs from bugs)
Jay Keasling was raised on a farm and spent his childhood exploring the practical side of biology chemistry and engineering This background eventually led him to work in the rapidly growing field that uses living organisms like bacteria for various practical purposes such as food processing agriculture and medicine
In the early 1980s genetic engineering became popular because you can ldquoconvincerdquo microbes to produce insulin growth hormones and other valuable proteins by simply inserting a single gene from a different organism into bacteria However Keasling believed that genetic engineering isnrsquot harnessing the full power of these cells The production of molecules isnt always so simple it requires a complex interaction of several genes (not just one) being produced in a certain sequence So Keasling wanted to invent the tools that would allow him to create these kinds of genetic assembly lines Thus what goes on in a cell is a lot like what goes on in a chemical plant petroleum goes in and after a whole chain of reactions plastic comes out
Keasling went to college studying biology and chemical engineering extensively and got his PhD in 1991 He is now a professor at the University of California at Berkeley He spent his first 10 years at UC Berkeley building the new tools he would need to turn cells into chemical plants He also invented powerful chemical switches (like a light switch) that allowed him to control when he wanted to ldquoturn onrdquo and ldquoturn offrdquo protein production in cells This way of borrowing techniques from engineering and figuring out how to manipulate microbes came to be call synthetic biology
After years of perfecting his biological tool kit Keasling wanted to find a real-world use for it In 2002 he learned of the dire need for artemisinin a compound derived from the sweet wormwood plant which is 90 percent effective against the parasite that causes malaria and has few side effects (malaria kills some 3 million people a year) However extracting the drug from sweet wormwood is a slow and expensive process Keasling figured he could design and create microbes to produce artemisinin much quicker and cheaper Rather than wait months for sweet wormwood to grow on farms Keasling wanted to create it simply by pouring sugar in a tank full of microbes that can use the sugar to make the drug via a chemical pathway he has designedmdashhe wanted to integrate genes from different species into a microbe to fabricate the drug for malaria
copy 2009 Yu-Tzu Debbie Liu 8
In 2006 Keaslings team (comprised of graduate students post-docs and research assistants) published their success of the production of artemisinin It is expected to lower the cost of artemisinin production from a dollar per gram to just 10 cents He was awarded a $43 million grant from the Bill and Melinda Gates Foundation and awarded DISCOVER magazinersquos first ever Scientist of the Year Award
Fighting malaria is just one part of Keaslings larger agenda to explore the potential of synthetic biology In his laboratory students are engineering microbes to break down pesticides make biodegradable plastics and create ethanol and other fuels from plants
Excerpts of i interview w Jay Keasling
1 You arrived at UC Berkeley in 1992 with training as both a chemical engineer and a biologist What did you hope to do
2 Why hadnt anybody tried to engineer cells that way before
3 How did you get involved in your antimalaria project
Jay Keisling biography adapted fromZimmer C (2006) Scientist of the Year Jay Keasling Discovermagazinecom Retrieved from
httpdiscovermagazinecom2006deccover
copy 2009 Yu-Tzu Debbie Liu 9
See responses to these questions atZimmer C (2006) Scientist of the Year Jay Keasling Discovermagazinecom Retrieved from
httpdiscovermagazinecom2006deccover
Interview content removed due to copyright restrictions
Interview content removed due to copyright restrictions
Interview content removed due to copyright restrictions
Lesson Plan Day 3 Materials
Designing a New Microbe worksheet Organism cards Student notebooks or journals
Prep Step Review lesson plan background information and understanding goals Photocopy Designing a New Microbe worksheet (p 28) Cut out organism cards (each group of 3-4 students will have a set of cards) (p29)
Explore Step 1 Designing a New Microbe Introduce todayrsquos activity by saying ldquoYou will be simulating how synthetic biologists think mechanistically by doing an the activity that is actually modeled after a real experiment done by scientists in 2007rdquo Divide students into groups of 3 or 4 Each group receives a set of organism cards Each student receives a Designing a New Microbe worksheet Remind students that proteins (or enzymes) are molecules inside cells that convert one molecule into another (eg the make-believe molecule How is converted to the molecule Home by Protein T in bacteria) Following the directions of the handout have students create a kind of assembly line that integrate proteins from different organisms into a microbe that uses water and starch (inputs) to ultimately produce hydrogen (output)
Possible answers to Designing a New Microbe
There are two possible pathways that can lead to hydrogen production
1 Starch amp water Protein G Protein P Protein D Protein R Protein T Protein F Protein H Hydrogen
2 Starch amp water Protein G Protein P Protein D Protein H Hydrogen
Guide students along by encouraging students who have already figured out how to attempt the problem to reveal and share with the class how they are thinking through the problem Stop students periodically to ask ldquoHow are you thinking through this problem What is your goal and how is your thinking helping you reach that goalrdquo Students may find either working sequentially forward or backward to fill in the worksheet to be easier
Note to teachers The hydrogen production pathway from starch and water is a shorten version of the actual 2007 experiment for learning purposes The organism types and molecule names are true to the experiment Protein names are made up for simplicity
copy 2009 Yu-Tzu Debbie Liu 10
Step 2 Discuss studentsrsquo findings Have students tell you what they found as you write their findings on the board Students may have discovered by now that there are two paths that lead to hydrogen production Students might recall that Jay Keasling have done something similar by making an antimalarial drug from sugar using synthetic biology Students may have also discovered that no proteins from the mouse organism were used for the design of their new microbe Ask students ldquowhat do you think is the purpose of having a mouse organism when we didnrsquot need itrdquo Help students understand how in reality scientists have hundreds of organisms to choose from some of which are irrelevant to their work In fact a common skill that scientists share is being about to identify and pull together important and relevant information The activity allows students to discover that synthetic biology is a very mind-blowing field accomplishing things that some people never thought was possible Students will come to appreciate how seemingly impossible feats can be possible especially when scientists are thinking creatively By thinking and working mechanistically scientists have more freedom then before in designing and creating novel organisms for real-world applications
Review Extend and Apply Step 3 How do you think mechanistically Ask students to reflect on their experience with Scratch and how they might have engaged in mechanistic thinking in their own work Helps students make the connection that they themselves have been engaging in mechanistic thinking while working on their own Scratch projects The Scratch grammar is designed so that users are presented with a versatile collection of graphical programming blocks that they can be snapped together to create programs much like synthetic biology Connectors on the blocks suggest how they should be put together so that over the process of tinkering with these blocks the emerging structure can give rise to new ideas and direction to the project Not only does snapping together complimentary blocks provide an easy way into learning programming but the idea of modularization as a problem-solving and design strategy is directly relevant to mechanistic thinking Go on to discuss how they can apply scientistsrsquo patterns of thinking to our own thinking in science class and daily life
copy 2009 Yu-Tzu Debbie Liu 11
Name___________________________ Date ____________
Designing a New Microbe
Task Gas prices have reached its all time high Thus scientists are trying to think of ways to produce alternative fuels such as hydrogen gas in a much cheaper and quicker way You are a scientist and you are familiar with six different organisms Based on what you know can you come up with a way to generate hydrogen from starch and water by designing a microbe that borrows different mechanismsproteins from different cells Fill in the blanks with protein names and the organism that the protein was taken from
Materials Each team has a set of cards each card symbolizing a different organism On the card you will see the name of the organism a picture of the organism and proteins that is unique to them Proteins (or enzymes) convert one molecule into another
Starch amp Water Protein borrowed Protein borrowed
Input Organism Organism
Protein borrowed $ Protein borrowed $ Protein borrowed Organism Organism Organism
Protein borrowed Protein borrowed Protein borrowed Hydrogen Organism Organism Organism Output
Experiment adapted from Zhang YH Evans BR Mielenz JR Hopkins RC Adams MW (2007) High-yield hydrogen production from
starch and water by a synthetic enzymatic pathway PLoS ONE 5 e456
copy 2009 Yu-Tzu Debbie Liu 12
Organism Cards (one set)
Teachers Please make as many copies as the number of groups of students Cut the cards out and shuffle before handing to students
Source NIH
Bacteria
Rabbitbull Protein T uses [X5P] to make [S7P]
Photo US Fish and Wildlife Service bull Protein F uses [S7P] to make [NADPH] bull Protein G uses starch and water to make [G-1-P] bull Protein P uses [G-1-P] to make [G-6-P]
Yeast
Public domain image (Source Wikimedia Commons)
bull Protein D uses [G-6-P] to make [NADPH] and [R5P]
Public domain image (Source Wikimedia Commons) Spinach
bull Protein R uses [R5P] to make [X5P]
Experiment adapted from
Archea Courtesy of Angels Tapias (License CC BY)
bull Protein H uses [NADPH] to make Hydrogen
Source NIH Mouse
bull Protein X uses [T8P] to make Hydrogen
Zhang YH Evans BR Mielenz JR Hopkins RC Adams MW (2007) High-yield hydrogen production from starch and water by a synthetic enzymatic pathway PLoS ONE 5 e456
copy 2009 Yu-Tzu Debbie Liu 13
MIT OpenCourseWarehttpocwmitedu
MAS714J STS445J Technologies for Creative Learning Fall 2009
For information about citing these materials or our Terms of Use visit httpocwmiteduterms
In 2006 Keaslings team (comprised of graduate students post-docs and research assistants) published their success of the production of artemisinin It is expected to lower the cost of artemisinin production from a dollar per gram to just 10 cents He was awarded a $43 million grant from the Bill and Melinda Gates Foundation and awarded DISCOVER magazinersquos first ever Scientist of the Year Award
Fighting malaria is just one part of Keaslings larger agenda to explore the potential of synthetic biology In his laboratory students are engineering microbes to break down pesticides make biodegradable plastics and create ethanol and other fuels from plants
Excerpts of i interview w Jay Keasling
1 You arrived at UC Berkeley in 1992 with training as both a chemical engineer and a biologist What did you hope to do
2 Why hadnt anybody tried to engineer cells that way before
3 How did you get involved in your antimalaria project
Jay Keisling biography adapted fromZimmer C (2006) Scientist of the Year Jay Keasling Discovermagazinecom Retrieved from
httpdiscovermagazinecom2006deccover
copy 2009 Yu-Tzu Debbie Liu 9
See responses to these questions atZimmer C (2006) Scientist of the Year Jay Keasling Discovermagazinecom Retrieved from
httpdiscovermagazinecom2006deccover
Interview content removed due to copyright restrictions
Interview content removed due to copyright restrictions
Interview content removed due to copyright restrictions
Lesson Plan Day 3 Materials
Designing a New Microbe worksheet Organism cards Student notebooks or journals
Prep Step Review lesson plan background information and understanding goals Photocopy Designing a New Microbe worksheet (p 28) Cut out organism cards (each group of 3-4 students will have a set of cards) (p29)
Explore Step 1 Designing a New Microbe Introduce todayrsquos activity by saying ldquoYou will be simulating how synthetic biologists think mechanistically by doing an the activity that is actually modeled after a real experiment done by scientists in 2007rdquo Divide students into groups of 3 or 4 Each group receives a set of organism cards Each student receives a Designing a New Microbe worksheet Remind students that proteins (or enzymes) are molecules inside cells that convert one molecule into another (eg the make-believe molecule How is converted to the molecule Home by Protein T in bacteria) Following the directions of the handout have students create a kind of assembly line that integrate proteins from different organisms into a microbe that uses water and starch (inputs) to ultimately produce hydrogen (output)
Possible answers to Designing a New Microbe
There are two possible pathways that can lead to hydrogen production
1 Starch amp water Protein G Protein P Protein D Protein R Protein T Protein F Protein H Hydrogen
2 Starch amp water Protein G Protein P Protein D Protein H Hydrogen
Guide students along by encouraging students who have already figured out how to attempt the problem to reveal and share with the class how they are thinking through the problem Stop students periodically to ask ldquoHow are you thinking through this problem What is your goal and how is your thinking helping you reach that goalrdquo Students may find either working sequentially forward or backward to fill in the worksheet to be easier
Note to teachers The hydrogen production pathway from starch and water is a shorten version of the actual 2007 experiment for learning purposes The organism types and molecule names are true to the experiment Protein names are made up for simplicity
copy 2009 Yu-Tzu Debbie Liu 10
Step 2 Discuss studentsrsquo findings Have students tell you what they found as you write their findings on the board Students may have discovered by now that there are two paths that lead to hydrogen production Students might recall that Jay Keasling have done something similar by making an antimalarial drug from sugar using synthetic biology Students may have also discovered that no proteins from the mouse organism were used for the design of their new microbe Ask students ldquowhat do you think is the purpose of having a mouse organism when we didnrsquot need itrdquo Help students understand how in reality scientists have hundreds of organisms to choose from some of which are irrelevant to their work In fact a common skill that scientists share is being about to identify and pull together important and relevant information The activity allows students to discover that synthetic biology is a very mind-blowing field accomplishing things that some people never thought was possible Students will come to appreciate how seemingly impossible feats can be possible especially when scientists are thinking creatively By thinking and working mechanistically scientists have more freedom then before in designing and creating novel organisms for real-world applications
Review Extend and Apply Step 3 How do you think mechanistically Ask students to reflect on their experience with Scratch and how they might have engaged in mechanistic thinking in their own work Helps students make the connection that they themselves have been engaging in mechanistic thinking while working on their own Scratch projects The Scratch grammar is designed so that users are presented with a versatile collection of graphical programming blocks that they can be snapped together to create programs much like synthetic biology Connectors on the blocks suggest how they should be put together so that over the process of tinkering with these blocks the emerging structure can give rise to new ideas and direction to the project Not only does snapping together complimentary blocks provide an easy way into learning programming but the idea of modularization as a problem-solving and design strategy is directly relevant to mechanistic thinking Go on to discuss how they can apply scientistsrsquo patterns of thinking to our own thinking in science class and daily life
copy 2009 Yu-Tzu Debbie Liu 11
Name___________________________ Date ____________
Designing a New Microbe
Task Gas prices have reached its all time high Thus scientists are trying to think of ways to produce alternative fuels such as hydrogen gas in a much cheaper and quicker way You are a scientist and you are familiar with six different organisms Based on what you know can you come up with a way to generate hydrogen from starch and water by designing a microbe that borrows different mechanismsproteins from different cells Fill in the blanks with protein names and the organism that the protein was taken from
Materials Each team has a set of cards each card symbolizing a different organism On the card you will see the name of the organism a picture of the organism and proteins that is unique to them Proteins (or enzymes) convert one molecule into another
Starch amp Water Protein borrowed Protein borrowed
Input Organism Organism
Protein borrowed $ Protein borrowed $ Protein borrowed Organism Organism Organism
Protein borrowed Protein borrowed Protein borrowed Hydrogen Organism Organism Organism Output
Experiment adapted from Zhang YH Evans BR Mielenz JR Hopkins RC Adams MW (2007) High-yield hydrogen production from
starch and water by a synthetic enzymatic pathway PLoS ONE 5 e456
copy 2009 Yu-Tzu Debbie Liu 12
Organism Cards (one set)
Teachers Please make as many copies as the number of groups of students Cut the cards out and shuffle before handing to students
Source NIH
Bacteria
Rabbitbull Protein T uses [X5P] to make [S7P]
Photo US Fish and Wildlife Service bull Protein F uses [S7P] to make [NADPH] bull Protein G uses starch and water to make [G-1-P] bull Protein P uses [G-1-P] to make [G-6-P]
Yeast
Public domain image (Source Wikimedia Commons)
bull Protein D uses [G-6-P] to make [NADPH] and [R5P]
Public domain image (Source Wikimedia Commons) Spinach
bull Protein R uses [R5P] to make [X5P]
Experiment adapted from
Archea Courtesy of Angels Tapias (License CC BY)
bull Protein H uses [NADPH] to make Hydrogen
Source NIH Mouse
bull Protein X uses [T8P] to make Hydrogen
Zhang YH Evans BR Mielenz JR Hopkins RC Adams MW (2007) High-yield hydrogen production from starch and water by a synthetic enzymatic pathway PLoS ONE 5 e456
copy 2009 Yu-Tzu Debbie Liu 13
MIT OpenCourseWarehttpocwmitedu
MAS714J STS445J Technologies for Creative Learning Fall 2009
For information about citing these materials or our Terms of Use visit httpocwmiteduterms
Lesson Plan Day 3 Materials
Designing a New Microbe worksheet Organism cards Student notebooks or journals
Prep Step Review lesson plan background information and understanding goals Photocopy Designing a New Microbe worksheet (p 28) Cut out organism cards (each group of 3-4 students will have a set of cards) (p29)
Explore Step 1 Designing a New Microbe Introduce todayrsquos activity by saying ldquoYou will be simulating how synthetic biologists think mechanistically by doing an the activity that is actually modeled after a real experiment done by scientists in 2007rdquo Divide students into groups of 3 or 4 Each group receives a set of organism cards Each student receives a Designing a New Microbe worksheet Remind students that proteins (or enzymes) are molecules inside cells that convert one molecule into another (eg the make-believe molecule How is converted to the molecule Home by Protein T in bacteria) Following the directions of the handout have students create a kind of assembly line that integrate proteins from different organisms into a microbe that uses water and starch (inputs) to ultimately produce hydrogen (output)
Possible answers to Designing a New Microbe
There are two possible pathways that can lead to hydrogen production
1 Starch amp water Protein G Protein P Protein D Protein R Protein T Protein F Protein H Hydrogen
2 Starch amp water Protein G Protein P Protein D Protein H Hydrogen
Guide students along by encouraging students who have already figured out how to attempt the problem to reveal and share with the class how they are thinking through the problem Stop students periodically to ask ldquoHow are you thinking through this problem What is your goal and how is your thinking helping you reach that goalrdquo Students may find either working sequentially forward or backward to fill in the worksheet to be easier
Note to teachers The hydrogen production pathway from starch and water is a shorten version of the actual 2007 experiment for learning purposes The organism types and molecule names are true to the experiment Protein names are made up for simplicity
copy 2009 Yu-Tzu Debbie Liu 10
Step 2 Discuss studentsrsquo findings Have students tell you what they found as you write their findings on the board Students may have discovered by now that there are two paths that lead to hydrogen production Students might recall that Jay Keasling have done something similar by making an antimalarial drug from sugar using synthetic biology Students may have also discovered that no proteins from the mouse organism were used for the design of their new microbe Ask students ldquowhat do you think is the purpose of having a mouse organism when we didnrsquot need itrdquo Help students understand how in reality scientists have hundreds of organisms to choose from some of which are irrelevant to their work In fact a common skill that scientists share is being about to identify and pull together important and relevant information The activity allows students to discover that synthetic biology is a very mind-blowing field accomplishing things that some people never thought was possible Students will come to appreciate how seemingly impossible feats can be possible especially when scientists are thinking creatively By thinking and working mechanistically scientists have more freedom then before in designing and creating novel organisms for real-world applications
Review Extend and Apply Step 3 How do you think mechanistically Ask students to reflect on their experience with Scratch and how they might have engaged in mechanistic thinking in their own work Helps students make the connection that they themselves have been engaging in mechanistic thinking while working on their own Scratch projects The Scratch grammar is designed so that users are presented with a versatile collection of graphical programming blocks that they can be snapped together to create programs much like synthetic biology Connectors on the blocks suggest how they should be put together so that over the process of tinkering with these blocks the emerging structure can give rise to new ideas and direction to the project Not only does snapping together complimentary blocks provide an easy way into learning programming but the idea of modularization as a problem-solving and design strategy is directly relevant to mechanistic thinking Go on to discuss how they can apply scientistsrsquo patterns of thinking to our own thinking in science class and daily life
copy 2009 Yu-Tzu Debbie Liu 11
Name___________________________ Date ____________
Designing a New Microbe
Task Gas prices have reached its all time high Thus scientists are trying to think of ways to produce alternative fuels such as hydrogen gas in a much cheaper and quicker way You are a scientist and you are familiar with six different organisms Based on what you know can you come up with a way to generate hydrogen from starch and water by designing a microbe that borrows different mechanismsproteins from different cells Fill in the blanks with protein names and the organism that the protein was taken from
Materials Each team has a set of cards each card symbolizing a different organism On the card you will see the name of the organism a picture of the organism and proteins that is unique to them Proteins (or enzymes) convert one molecule into another
Starch amp Water Protein borrowed Protein borrowed
Input Organism Organism
Protein borrowed $ Protein borrowed $ Protein borrowed Organism Organism Organism
Protein borrowed Protein borrowed Protein borrowed Hydrogen Organism Organism Organism Output
Experiment adapted from Zhang YH Evans BR Mielenz JR Hopkins RC Adams MW (2007) High-yield hydrogen production from
starch and water by a synthetic enzymatic pathway PLoS ONE 5 e456
copy 2009 Yu-Tzu Debbie Liu 12
Organism Cards (one set)
Teachers Please make as many copies as the number of groups of students Cut the cards out and shuffle before handing to students
Source NIH
Bacteria
Rabbitbull Protein T uses [X5P] to make [S7P]
Photo US Fish and Wildlife Service bull Protein F uses [S7P] to make [NADPH] bull Protein G uses starch and water to make [G-1-P] bull Protein P uses [G-1-P] to make [G-6-P]
Yeast
Public domain image (Source Wikimedia Commons)
bull Protein D uses [G-6-P] to make [NADPH] and [R5P]
Public domain image (Source Wikimedia Commons) Spinach
bull Protein R uses [R5P] to make [X5P]
Experiment adapted from
Archea Courtesy of Angels Tapias (License CC BY)
bull Protein H uses [NADPH] to make Hydrogen
Source NIH Mouse
bull Protein X uses [T8P] to make Hydrogen
Zhang YH Evans BR Mielenz JR Hopkins RC Adams MW (2007) High-yield hydrogen production from starch and water by a synthetic enzymatic pathway PLoS ONE 5 e456
copy 2009 Yu-Tzu Debbie Liu 13
MIT OpenCourseWarehttpocwmitedu
MAS714J STS445J Technologies for Creative Learning Fall 2009
For information about citing these materials or our Terms of Use visit httpocwmiteduterms
Step 2 Discuss studentsrsquo findings Have students tell you what they found as you write their findings on the board Students may have discovered by now that there are two paths that lead to hydrogen production Students might recall that Jay Keasling have done something similar by making an antimalarial drug from sugar using synthetic biology Students may have also discovered that no proteins from the mouse organism were used for the design of their new microbe Ask students ldquowhat do you think is the purpose of having a mouse organism when we didnrsquot need itrdquo Help students understand how in reality scientists have hundreds of organisms to choose from some of which are irrelevant to their work In fact a common skill that scientists share is being about to identify and pull together important and relevant information The activity allows students to discover that synthetic biology is a very mind-blowing field accomplishing things that some people never thought was possible Students will come to appreciate how seemingly impossible feats can be possible especially when scientists are thinking creatively By thinking and working mechanistically scientists have more freedom then before in designing and creating novel organisms for real-world applications
Review Extend and Apply Step 3 How do you think mechanistically Ask students to reflect on their experience with Scratch and how they might have engaged in mechanistic thinking in their own work Helps students make the connection that they themselves have been engaging in mechanistic thinking while working on their own Scratch projects The Scratch grammar is designed so that users are presented with a versatile collection of graphical programming blocks that they can be snapped together to create programs much like synthetic biology Connectors on the blocks suggest how they should be put together so that over the process of tinkering with these blocks the emerging structure can give rise to new ideas and direction to the project Not only does snapping together complimentary blocks provide an easy way into learning programming but the idea of modularization as a problem-solving and design strategy is directly relevant to mechanistic thinking Go on to discuss how they can apply scientistsrsquo patterns of thinking to our own thinking in science class and daily life
copy 2009 Yu-Tzu Debbie Liu 11
Name___________________________ Date ____________
Designing a New Microbe
Task Gas prices have reached its all time high Thus scientists are trying to think of ways to produce alternative fuels such as hydrogen gas in a much cheaper and quicker way You are a scientist and you are familiar with six different organisms Based on what you know can you come up with a way to generate hydrogen from starch and water by designing a microbe that borrows different mechanismsproteins from different cells Fill in the blanks with protein names and the organism that the protein was taken from
Materials Each team has a set of cards each card symbolizing a different organism On the card you will see the name of the organism a picture of the organism and proteins that is unique to them Proteins (or enzymes) convert one molecule into another
Starch amp Water Protein borrowed Protein borrowed
Input Organism Organism
Protein borrowed $ Protein borrowed $ Protein borrowed Organism Organism Organism
Protein borrowed Protein borrowed Protein borrowed Hydrogen Organism Organism Organism Output
Experiment adapted from Zhang YH Evans BR Mielenz JR Hopkins RC Adams MW (2007) High-yield hydrogen production from
starch and water by a synthetic enzymatic pathway PLoS ONE 5 e456
copy 2009 Yu-Tzu Debbie Liu 12
Organism Cards (one set)
Teachers Please make as many copies as the number of groups of students Cut the cards out and shuffle before handing to students
Source NIH
Bacteria
Rabbitbull Protein T uses [X5P] to make [S7P]
Photo US Fish and Wildlife Service bull Protein F uses [S7P] to make [NADPH] bull Protein G uses starch and water to make [G-1-P] bull Protein P uses [G-1-P] to make [G-6-P]
Yeast
Public domain image (Source Wikimedia Commons)
bull Protein D uses [G-6-P] to make [NADPH] and [R5P]
Public domain image (Source Wikimedia Commons) Spinach
bull Protein R uses [R5P] to make [X5P]
Experiment adapted from
Archea Courtesy of Angels Tapias (License CC BY)
bull Protein H uses [NADPH] to make Hydrogen
Source NIH Mouse
bull Protein X uses [T8P] to make Hydrogen
Zhang YH Evans BR Mielenz JR Hopkins RC Adams MW (2007) High-yield hydrogen production from starch and water by a synthetic enzymatic pathway PLoS ONE 5 e456
copy 2009 Yu-Tzu Debbie Liu 13
MIT OpenCourseWarehttpocwmitedu
MAS714J STS445J Technologies for Creative Learning Fall 2009
For information about citing these materials or our Terms of Use visit httpocwmiteduterms
Name___________________________ Date ____________
Designing a New Microbe
Task Gas prices have reached its all time high Thus scientists are trying to think of ways to produce alternative fuels such as hydrogen gas in a much cheaper and quicker way You are a scientist and you are familiar with six different organisms Based on what you know can you come up with a way to generate hydrogen from starch and water by designing a microbe that borrows different mechanismsproteins from different cells Fill in the blanks with protein names and the organism that the protein was taken from
Materials Each team has a set of cards each card symbolizing a different organism On the card you will see the name of the organism a picture of the organism and proteins that is unique to them Proteins (or enzymes) convert one molecule into another
Starch amp Water Protein borrowed Protein borrowed
Input Organism Organism
Protein borrowed $ Protein borrowed $ Protein borrowed Organism Organism Organism
Protein borrowed Protein borrowed Protein borrowed Hydrogen Organism Organism Organism Output
Experiment adapted from Zhang YH Evans BR Mielenz JR Hopkins RC Adams MW (2007) High-yield hydrogen production from
starch and water by a synthetic enzymatic pathway PLoS ONE 5 e456
copy 2009 Yu-Tzu Debbie Liu 12
Organism Cards (one set)
Teachers Please make as many copies as the number of groups of students Cut the cards out and shuffle before handing to students
Source NIH
Bacteria
Rabbitbull Protein T uses [X5P] to make [S7P]
Photo US Fish and Wildlife Service bull Protein F uses [S7P] to make [NADPH] bull Protein G uses starch and water to make [G-1-P] bull Protein P uses [G-1-P] to make [G-6-P]
Yeast
Public domain image (Source Wikimedia Commons)
bull Protein D uses [G-6-P] to make [NADPH] and [R5P]
Public domain image (Source Wikimedia Commons) Spinach
bull Protein R uses [R5P] to make [X5P]
Experiment adapted from
Archea Courtesy of Angels Tapias (License CC BY)
bull Protein H uses [NADPH] to make Hydrogen
Source NIH Mouse
bull Protein X uses [T8P] to make Hydrogen
Zhang YH Evans BR Mielenz JR Hopkins RC Adams MW (2007) High-yield hydrogen production from starch and water by a synthetic enzymatic pathway PLoS ONE 5 e456
copy 2009 Yu-Tzu Debbie Liu 13
MIT OpenCourseWarehttpocwmitedu
MAS714J STS445J Technologies for Creative Learning Fall 2009
For information about citing these materials or our Terms of Use visit httpocwmiteduterms
Organism Cards (one set)
Teachers Please make as many copies as the number of groups of students Cut the cards out and shuffle before handing to students
Source NIH
Bacteria
Rabbitbull Protein T uses [X5P] to make [S7P]
Photo US Fish and Wildlife Service bull Protein F uses [S7P] to make [NADPH] bull Protein G uses starch and water to make [G-1-P] bull Protein P uses [G-1-P] to make [G-6-P]
Yeast
Public domain image (Source Wikimedia Commons)
bull Protein D uses [G-6-P] to make [NADPH] and [R5P]
Public domain image (Source Wikimedia Commons) Spinach
bull Protein R uses [R5P] to make [X5P]
Experiment adapted from
Archea Courtesy of Angels Tapias (License CC BY)
bull Protein H uses [NADPH] to make Hydrogen
Source NIH Mouse
bull Protein X uses [T8P] to make Hydrogen
Zhang YH Evans BR Mielenz JR Hopkins RC Adams MW (2007) High-yield hydrogen production from starch and water by a synthetic enzymatic pathway PLoS ONE 5 e456
copy 2009 Yu-Tzu Debbie Liu 13
MIT OpenCourseWarehttpocwmitedu
MAS714J STS445J Technologies for Creative Learning Fall 2009
For information about citing these materials or our Terms of Use visit httpocwmiteduterms
MIT OpenCourseWarehttpocwmitedu
MAS714J STS445J Technologies for Creative Learning Fall 2009
For information about citing these materials or our Terms of Use visit httpocwmiteduterms