hcol 185m: controversies in modern genomics office hours ...sources exploring the science, ethics,...

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HCOL 185M: Controversies in Modern Genomics

Tamara Williams, Ph.D.

Fall 2014 Syllabus

Mondays, Wednesdays 4:05-5:20pm

North Complex 016

Office Hours: By appointment

Office: HSRF 331

Email: [email protected]

___________________________________________________________

Course Summary and Goals

Following completion of the Human Genome Project, Genomics has proven a rich source

of controversy. As the applications and implications of rapid, inexpensive, and reliable

whole-genome sequencing become clearer, complex ethical, moral, and practical

questions emerge. Misuse and misunderstanding of the science behind Genomics has

clouded conversations in the public forum and polarized topics that warrant many shades

of gray. This course will focus on thoughtful, engaging, and open-minded discussions of

current controversies involving Genomics (the study of the structure, function, and

evolution of an organism’s entire genome) and Genetics (the study of specific gene

function and inheritance). Students are expected to actively participate and prepare for

each class through critical review of assigned scientific literature, documentaries, public

policy reports and documents, news articles, and other media. There is no pre-requisite

knowledge of Genetics or Genomics. Evaluation will include preparing for and actively

engaging in class discussions and projects, composing thoughtful reflection papers and a

midterm paper, and crafting a well-sourced final research report and presenting findings

as part of an expert team panel to the class for discussion.

Course Learning Objectives

Throughout this course, students will:

• Engage in thought-provoking discussions with classmates and instructor

• Increase familiarity and awareness of controversies in Genomics/Genetics

• Develop skills to critically interpret scientific literature, policy documents, and mass

media coverage of topics in Genomics/Genetics

• Expand appreciation for the ways in which science affects society and society affects

science

• Practice working in groups to dissect a topic of interest into its scientific, ethical, and

social implications

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Skills developed in this course include:

Articulate an argument or position and respectfully listen to and understand arguments or

positions of others

Write concise and thoughtful prose reflecting on complex topics spanning science, ethics,

and society

Conduct literature research to form and support positions

Work individually and collaboratively to complete projects

Increase comfort and skill with oral presentation

Challenge previous notions and impressions held through curious learning

Required Text

Atkinson, P., Glasner, P., & Lock, M. (2013). Handbook of genetics and society: Mapping the

new genomic era. London: Routledge.

(available through most online book sellers including amazon.com and bn.com and in e-

book format)

Blackboard

Assigned reading and viewing materials, excluding text chapters, will be provided on

Blackboard either by PDF attachment or web link. Please use Blackboard for updated

reading/viewing materials as changes may occur to the listed course schedule included in

this syllabus. Assignments must be uploaded to Blackboard by the listed deadline. Please

contact me prior to the deadline if you are not able to upload an assignment to

Blackboard so we can make other arrangements.

Attendance Policy

Given the importance of active discussion in attaining the goals of the class, attendance is

mandatory. Students must notify me of any University-approved absences prior to class

when possible. Any student with three or more unexcused absences will receive a failing

grade.

Grading Criteria

100 points total shall be earned as follows:

20 points- Class participation

20 points- 4 Reflection papers

20 points- Midterm paper

5 points- Research report proposal (25% individual score, 75% team score)

5 points- Participation in peer review of report proposals

10 points- Panel presentation and discussion (50% team score, 50% individual score)

20 points- Final research report (75% individual score, 25% team score)

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Assignments

Reflection Papers: Four, 2-3 page papers (excluding cover page and bibliography)

summarizing the student’s thoughts, perceptions, and lingering questions on any topic

discussed in class within its section (Life, Health, Ethics, and Society). Must cite at least 3

relevant and legitimate sources.

Midterm Paper: 4-6 page paper (excluding cover page and bibliography) citing reputable

sources exploring the science, ethics, and social implications of a controversy in

Genomics /Genetics. Must cite at least 5 relevant and legitimate sources.

Final Project: Students will work in teams of 3 to research a controversial

Genomics/Genetics topic with each student taking the lead in one aspect of the

controversy. Groups must cover the science and technology involved, ethical

considerations, and its impact on society. Individual and team grades will be given for the

proposal, the final report and the panel presentation. Individual grades will be given for

providing peer review of other teams’ proposals.

o Report Proposal: Each team will submit a proposal for their report in

outline format, identifying the key aspects that will be covered in the final

report and presentation (details provided in the assignment description).

o Peer Review: Proposals will be reviewed by the instructor but also will be

reviewed by classmates as part of a peer review process. Each student will

review and provide feedback on the other teams’ proposals.

o Final Report: Each student will independently contribute a 4-6 page section

of the final report based on the aspect of the controversy he or she

researched for the team project, citing at least 5 relevant and legitimate

sources. The team will collaboratively write the Executive Summary,

Introduction, and Conclusion sections

o Panel Presentation: Each team will form an expert panel and lead a class

discussion on the scientific, ethical, and societal considerations of the

selected topic. Students will receive copies of each team’s final report to read

prior to the class discussion to enable an engaging and well-informed

dialogue.

Classroom Environment Expectations Each student is expected to:

Actively and thoughtfully participate in class discussions

Treat others in the class with respect and dignity

Complete assigned reading materials prior to class

Turn in assignments on time

Seek out assistance from me or from classmates when needed

Behave with academic honesty and honor

Show up for class on time

Silence cell phones and put away laptops while in class

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UVM Libraries Liaison for Honors College Students

For assistance with library services and for support in research for Honors College

courses, please contact Patricia Mardeusz.

Patricia Mardeusz

Library Associate Professor

Information & Instruction Services

802.656.5718

[email protected]

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Course Schedule Subject to change- please reference Blackboard for updates and links to reading/viewing

materials

All assignments will be turned in via Blackboard unless otherwise instructed

INTRODUCTION

Monday, August 25: Course Introduction

Objectives

o Introductions by students and professor

o Discuss syllabus, course objectives and expectations

Wednesday, August 27: The American Eugenics Movement- Historical Misuse of

Genetics

Objectives

o Provide context for modern controversies in genomics by exploring the

history of American eugenics

o Discuss impact and influence of the American Eugenics Movement

Required Reading / Viewing (completed prior to class)

o Handbook of genetics and society: Mapping the new genomic era.

Chapter 30 Eugenics (Koch, L.); pp 437-447.

o Boas, Frank. "Eugenics." Scientific Monthly. 3.5 (1916): 471-478. Print.

o (Selected short essays) “Social Origins”; “Scientific Origins”; “Research

Methods”; “Traits Studied”; “Research Flaws”; “Eugenics Popularization”;

“Marriage Laws”; “Sterilization Laws”; “Immigration Restriction”. The

Eugenics Archive. Dolan DNA Learning Center at Cold Spring Harbor

Laboratory, n.d. Web. 24 Aug 2012.

<http://www.eugenicsarchive.org/eugenics/list3.pl>.

o Review the site hosting Vermont Eugenics: A Documentary History

<http://www.uvm.edu/~eugenics/>.

o (Optional) Materials posted on DNA Interactive Chronicle site hosted by

Cold Spring Harbor Laboratory

<http://www.dnai.org/e/index.html>.

LIFE Wednesday, September 3: Cloning

Objectives

o Review briefly the basic science of cloning

o Discuss the pros and cons of human cloning

o Consider ethical and moral issues

o Discern fact from fiction in popular perceptions of cloning

Required Reading/ Viewing (completed prior to class)

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Chapter 15 Human genetics and cloning in the media- Mapping the

research field (Haran, J. and Kitzinger, J.); pp 203-221.

o National Human Genome Research Initiative, National Institutes of Health.

“Cloning”.

http://www.genome.gov/25020028

o Executive Summary pages xxi-xxxviii of The President’s Council on Bioethics

(2002). “Human Cloning and Human Dignity: An Ethical Inquiry”.

o Center for Genetics and Society (2006). “Reproductive Cloning Arguments

Pro and Con”.

http://www.geneticsandsociety.org/article.php?id=282

Assignment Due

o (Optional and ungraded) Practice Reflection Paper - Students wishing

for ungraded feedback on writing may submit a Reflection Paper on

Eugenics

Monday, September 8: Designed Life and Synthetic Life

Objectives

o Review basics of the science of synthetic life

o Continue discussion on cloning with respect to “designer babies” concept

o Discuss impact of synthetic life on science and society


o Pennisi, E. (2010). Synthetic Genome Brings New Life to Bacterium. Science

Vol. 328 no. 5981 pp. 958-959.

o TED Talk (November 2010). “Paul Root Wolpe: It's time to question bio-

engineering”.

o TED Talk (May 2010). “Craig Venter unveils ‘synthetic life’”.

o Executive Summary pages 1-18 of The Presidential Commission for the

Study of Bioethical Issues (December 2010) “NEW DIRECTIONS- The Ethics

of Synthetic Biology and Emerging Technologies”. Washington, D.C.

Wednesday, September 10: Genetically Modified Organisms (GMO)

Objectives

o Review basics of the technologies and applications of genetic modification of

organisms

o Describe scientifically-based pros and cons to GMOs

o Discuss both popular and personal perceptions of GMOs



Chapter 9 Making Europe unsafe for agbiotech (Levidow, L.); pp 110-

126.

o Halper, E. (June 2014). “Vermont’s new GMO law may upend food industry

nationwide.” Los Angeles Times.

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o World Health Organization “20 Questions on Genetically Modified (GM)

Foods”.

o Act No. 120 (H.112). Consumer protection; food labeling; genetic

engineering. Summary of Act. 2014.

Monday, September 15: Genetically Modified Organisms (GMO) II, Guest Speaker

Objectives

o Engage with speaker on the pros and cons of labeling GM foods in Vermont

o Understand the broader implications of Vermont’s labeling law nationwide

o Learn about the process of political and social advocacy


o Halper, E. (June 2014). “Vermont’s new GMO law may upend food industry

nationwide.” Los Angeles Times.

o Act No. 120 (H.112). Consumer protection; food labeling; genetic

engineering. Summary of Act. 2014.

HEALTH

Wednesday, September 17: Genomics and the Healthcare Industry- Guest Lecturer

Mr. Alan French, Vice President Campbell Alliance

Objectives

o Engage with guest lecturer on genetics and the pharmaceutical industry

o Discuss drug development and pricing for the niche of genetic diseases



Chapter 11 On a critical path: genomics, the crisis of pharmaceutical

productivity and the search for sustainability (Martin, P., et al.); pp

145-162.

o Chapters 1, 3, 6 (pages 1-5, 19-25, 43-49) of Congress of the United States

Congressional Budget Office (2006). “Research and Development in the

Pharmaceutical Industry”.

o Cracking Your Genetic Code. NOVA Special documentary , Air date 03/28/12

http://www.pbs.org/wgbh/nova/body/cracking-your-genetic-code.html

Assignment Due

o Reflection Paper #1 (Life) due September 17 by 3pm

Monday, September 22: Genomics and Healthcare

Objectives

o Review the role of genomics in disease diagnosis and treatment

o Discuss the potential and limitations of personalized medicine

o Discuss cultural and social stigma of genetic disease

o Five students present 5-minute Executive Summary of Reflection Paper #1

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Chapter 6 Localising genetic testing and screening in Cyprus and

Germany: contingencies, continuities, ordering effects, and bio-

cultural intimacy (Beck, S. and Niewohner, J.); pp 76-93.

o Wertz, D.C. (2003). Ethical, social and legal issues in pharmacogenomics.

Pharmacogenomics J. 3(4):194-6.

o TEDMED (2010) “Greg Lucier, CEO Life Technologies”

http://www.tedmed.com/videos-

info?name=Greg_Lucier_at_TEDMED_2010&q=updated&year=all&sid=79&vi

d=108

Wednesday, September 24: Genetic Testing, Guest Speaker Dr. Leah Burke,

Clinical Geneticist, Director, Vermont Regional Genetics Center,Fletcher Allen

Healthcare

Objectives

o Understand the differences between genetic disease and genetic

susceptibility

o Discuss the impact and implications of increasing genetic testing on disease

diagnosis, treatment, and prevention

o Discuss issues related to genetic testing interpretation and cost


o Goldenberg, A.J. & Sharp, R.R. (2012). The Ethical Hazards and

Programmatic Challenges of Genomic Newborn Screening. JAMA

307(5):461-462.

o Bombard, Y. (2009). Perceptions of genetic discrimination among people at

risk for Huntington’s disease: a cross sectional survey. British Medical

Journal 338:b2175.

o National Public Radio (April 2012). N.Y. Preschool Starts DNA Testing for

Admission.

http://www.wbur.org/npr/149804404/n-y-preschool-starts-dna-testing-

for-admission

o TEDMED (2009) “Anne Wojcicki, CEO of 23andMe”


info?name=Anne_Wojcicki_at_TEDMED_2009&q=updated&year=all&sid=83

&vid=59

Assignment Due

o One page brief outline for Midterm Paper topic due no later than

September 24 by 3pm

Monday, September 29: Personal Genomics

Objectives

o Review concepts of personal genomics and how it is being used today

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o Discuss what personal genomics does and does not tell us about ourselves



Chapter 7 Nutrigenomics (Chadwick, R.); pp 94-104.

o Nordgren, A. (2012). Neither as harmful as feared by critics nor as

empowering as promised by providers: risk information offered direct to

consumer by personal genomics companies. Journal of Community Genetics

22 March 2012.

o TEDMED (2010) “Ozzy and Sharon Osbourne with Nathaniel Pearson”


info?name=Ozzy_and_Sharon_Osbourne_with_Nathaniel_Pearson_at_TEDME

D_2010&q=updated&year=all&sid=28&vid=2

Wednesday, October 1: Final Report Proposal Workshop

Objectives


o Work in Final Report teams to develop proposals

Assignment Due

o Reflection Paper #2 (Health) due October 1 by 3pm

ETHICS

Monday, October 6: Politics and Public Policy of Genomics

Objectives

o Introduce public policy and laws designed to protect genetic rights

o Discuss the impact of GINA on society

o Discuss the ethical implications of genetic testing in criminal justice


o (For use as a reference only, no need to read in its entirety) House

Resolution (HR-493): Genetic Nondiscrimination Act of 2008.

o Genetic Alliance, the Genetics and Public Policy Center at the Johns Hopkins

University, and the National Coalition for Health Professional Education in

Genetics. (2010). “Understanding GINA”.

o Katsanis, S. and Javitt, G. (2009). “Surreptitious DNA Testing”. Genetics and

Public Policy Center, Johns Hopkins University.

o Gram, D. (2012). “Vt. High Court to Weigh Pre-Conviction DNA Testing”. The

Boston Globe, Aug 20, 2012.

o Stempel, J. and Baynes, T. (2012). “Supreme Court May Review Case over

DNA Samples” Reuters July 30, 2012.

o The Board of Directors of the Council for Responsible Genetics (2012). “The

Genetic Bill of Rights”. The Council for Responsible Genetics.

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Wednesday, October 8: Use of Genetic Information I, Guest Speaker, Dr. Robert

Macauley, Medical Director, Clinical Ethics, Fletcher Allen Health Care

Objectives

o Understand how genetic information could be used in other contexts outside

of healthcare planning

o Discuss the ethics behind current and potential uses of genetic information

o Understand the importance of genetic information privacy, issues of

confidentiality, stigmatization, and the psychological impact of learning

about your own genetic makeup


o Harmon, A. (February 2008). “Insurance Fears Lead Many to Shun DNA

Tests”. The New York Times.

o Genetics and Public Policy Center (2007). “U.S. Public Opinion on Uses of

Genetic Information and Genetic Discrimination”.

o Sections 1-7 pages 13-46 of Health Council of the Netherlands. “The

‘thousand-dollar genome’: an ethical exploration”. Monitoring Report Ethics

and Health, The Hague: Centre for Ethics and Health, 2010.

Assignment Due

o Midterm Paper due October 8 by 3pm

Monday, October 13: Use of Genetic Information II

Objectives

o Continue discussion on the ethics behind current and potential uses of

genetic information

o Discuss the implications of genetic information in sports and in criminal

justice



Chapter 20 Forensic DNA databases and biolegality: the co-

production of law, surveillance technology and suspect bodies

(Lynch, M. and McNally, R.); pp 283-301.

o Shanks, P. (2009). “Baseball and Genetic Testing”. Psychology Today August

3, 2009.

o Miah, A. (2012). “Genetics & Sport: Bioethical Concerns”. Recent Patents on

DNA & Gene Sequences, 6, 197-202.

o Sections 8-9 pages 47-62 of Health Council of the Netherlands. “The

‘thousand-dollar genome’: an ethical exploration”. Monitoring Report Ethics

and Health, The Hague: Centre for Ethics and Health, 2010.

o Hays, D. (2008). “DNA, Forensics, and the Law”. Genetics and Public Policy

Center, Johns Hopkins University.

Wednesday, October 15: Genetic “Enhancement”

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Objectives

o Review the basic science behind inheritable genetic modification

o Discuss the potential impact of genetic modification on society

o Discuss the ethical concerns related to genetic “enhancement”



Chapter 24 Bioethics and human genetic engineering (Evans, J. and

Schairer, C.); pp 349-366.

o National Human Genome Research Initiative, National Institutes of Health.

Genetic Enhancement.

http://www.genome.gov/10004767

o Alleyne, R. (2012). “Genetically Engineering 'Ethical' Babies is a Moral

Obligation, Says Oxford Professor”. Telegraph (UK), Aug 16, 2012.

o Strong, C. (2005). Reproductive cloning combined with genetic modification.

Journal of Medical Ethics 31(11):654-8.

o Center for Genetics and Society (2006). “Inheritable Genetic Modification

Basic Science”.


o Center for Genetics and Society (2006). “Inheritable Genetic Modification

Arguments Pro and Con”.


Assignment Due

o Final Report Proposal due October 15 by 3pm

Monday, October 20: Peer Review of Research Panel Proposals I

Objective

o Engage in groups to review research panel proposals


o Read assigned set #1 team research proposals posted on Blackboard

Assignment Due

o Come to class with at least 2 questions or comments for each proposal

in set #1

Wednesday, October 22: Peer Review of Research Panel Proposals II

Objective

o Engage in groups to review research panel proposals


o Read assigned set #2 team research proposals posted on Blackboard

Assignment Due

o Come to class with at least 2 questions or comments for each proposal

in set #2

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SOCIETY

Monday, October 27: Genetic Influence of Human Behavior

Objectives

o Review evidence of genetic influence of behavior

o Discuss the implications of genetic influence on mental illness, addiction,

and personality



o Holden, C. (2008). Parsing the Genetics of Behavior. Science 7 November

2008: 892-895.

o National Institute on Drug Abuse (2008). “Genetics of Addiction”.

o Videos of Kay Jamison in DNAinteractive Chronicle “Living with Eugenics”.

o Human Genome Project Information (2008). “Behavioral Genetics” US

Department of Energy.

http://www.ornl.gov/sci/techresources/Human_Genome/elsi/behavior.sht

ml

Assignment Due

o Reflection Paper #3 (Ethics) due October 27 by 3pm

Wednesday, October 29: Human Evolution

Objectives

o Discuss implications of evolution and natural selection on society

o Discuss the role of positive selection in characterizing human-ness


o Hockenberry, J. (2007). “Beyond Human”. (Audio file)

o TEDMED Talk (2012) “Dr. Jay Lombard”


info?name=Jay_Lombard_at_TEDMED_2012&q=updated&year=all&sid=239

&vid=293

Monday, November 3: Human Evolution II and Genetic Influence of Human

Behavior

Objectives

o Engage with class regarding human evolution and the genetics of addiction

o Discuss the role of positive selection in characterizing human-ness

o Discuss the implications of genetic influence of addiction


o Vallender, E.J., et al. (2008). Genetic basis of human brain evolution. Trends

in Neuroscience 31(12):637-44.

o Wade, N. (September 2005). “Researchers say human brain is still evolving”.

The New York Times.

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o Jha, A. “Intelligence tests highlight importance of genetic differences”. The

Guardian August 9, 2011.

o TED Talk (April 2012). “Juan Enriquez: Will our kids be a different species?”.

Wednesday, November 5: Genetic Influence of Human Behavior II

Objectives

o Review evidence of genetic influence of behavior

o Discuss the implications of genetic influence on sexual orientation, risk-

taking, musical ability, and political beliefs


o Mustanski, B.S., et al. (2005). A genomewide scan of male sexual orientation.

Human Genetics 116(4):272-8.

o Fowler, J.H. & Schreiber, D. (2008). Biology, Politics, and the Emerging

Science of Human Nature. Science 7 November 2008: 912-914.

o Drayna, D. (2007). Absolute pitch: A special group of ears. Proc. Natl. Acad.

Sci. USA 11 September 2007: 14549-14550.

o Pearson, A. (2011). “Out-of-Africa migration selected novelty-seeking

genes”. The New Scientist 2811: May 6, 2011.

Monday, November 10: Workshop on Final Reports

Objectives

o Work in teams to finalize report

o Check in with instructor for guidance on any questions related to the final

report

o Four students present 5-minute Executive Summary of Reflection Paper #4

Assignment Due

o Reflection Paper #4 (Society) due November 10 by 3pm

CONCLUSIONS

Wednesday, November 12: Panel Presentations (Groups 1-2)

Objectives

o Groups 1-2 present final report findings

o Engage with students in expert panels to deepen discussion

Required Reading

o Final reports from Groups 1-2

Assignment Due

o Create at least one question to ask each of the expert panels presenting

o Final Report due November 11 by 11:59pm

Monday, November 17: No class session

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Wednesday, November 19: Panel Presentations (Groups 3-4)

Objectives

o Groups 3-4 present final report findings

o Engage with students in expert panels to deepen discussion

Required Reading

o Final reports from Groups 3-4

Assignment Due

o Create at least one question to ask each of the expert panels presenting

Thanksgiving Break November 24-28

Monday, December 1: Panel Presentations (Group 5-6)

Objectives

o Groups 5-6 presents final report findings

o Engage with students in the expert panel to deepen discussion

Required Reading

o Final report from Groups 5-6

Assignment Due

o Create at least one question to ask the expert panel presenting

Wednesday, December 3: Class Conclusion

Objectives

o Review course

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Student Learning Accommodations: In keeping with University policy, any student

with a documented disability interested in utilizing accommodations should contact

ACCESS, the office of Disability Services on campus. ACCESS works with students to

create reasonable and appropriate accommodations via an accommodation letter to their

professors as early as possible each semester.

Contact ACCESS: A170 Living/Learning Center; 802-656-7753; [email protected];

www.uvm.edu/access

UVM’s policy on disability certification and student support:

www.uvm.edu/~uvmppg/ppg/student/disability.pdf

Religious Holidays: Students have the right to practice the religion of their choice. If you

need to miss class to observe a religious holiday, please submit the dates of your absence

to me in writing by the end of the second full week of classes. You will be permitted to

make up work within a mutually agreed-upon time.

Academic Integrity: The policy addresses plagiarism, fabrication, collusion, and

cheating. www.uvm.edu/~uvmppg/ppg/student/acadintegrity.pdf

Grade Appeals: If you would like to contest a grade, please follow the procedures

outlined in this policy: www.uvm.edu/~uvmppg/ppg/student/gradeappeals.pdf

Code of Student Rights and Responsibilities: www.uvm.edu/~uvmppg/ppg/student/studentcode.pdf

FERPA Rights Disclosure: The purpose of this policy is to communicate the rights of

students regarding access to, and privacy of their student educational records as provided

for in the Family Educational Rights and Privacy Act (FERPA) of 1974.

http://www.uvm.edu/~uvmppg/ppg/student/ferpa.pdf

Promoting Health & Safety: The University of Vermont's number one priority is to support a healthy

and safe community:

Center for Health and Wellbeing http://www.uvm.edu/~chwb/

Counseling & Psychiatry Services (CAPS) Phone: (802) 656-3340

C.A.R.E. If you are concerned about a UVM community member or are concerned

about a specific event, we encourage you to contact the Dean of Students Office (802-

656-3380). If you would like to remain anonymous, you can report your concerns

online by visiting the Dean of Students website at http://www.uvm.edu/~dos/

mailto:[email protected]

http://www.uvm.edu/access

http://www.uvm.edu/~uvmppg/ppg/student/disability.pdf

http://www.uvm.edu/~uvmppg/ppg/student/acadintegrity.pdf

http://www.uvm.edu/~uvmppg/ppg/student/gradeappeals.pdf

http://www.uvm.edu/~uvmppg/ppg/student/studentcode.pdf

http://www.uvm.edu/~uvmppg/ppg/student/ferpa.pdf

hcol 185m: controversies in modern genomics office hours ...sources exploring the science, ethics,...

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