Nature and Origin of LifeCourse

Lecture 1What is Life

Self Evaluation• Understanding the Nature and Origin of Life

Needs material from Biology, Chemistry, Geology, Planetary Science and Astronomy, Physics.

Nobody has been taught to be an expert in all of these. Astrobiologists are all partly self-taught.

Where do you stand in each of these areas?

Which is your home area, your area of competence, your area in which you hope to make a living?

Training/Competence• For each area, Biology,Chemistry, Geology,

Planetary Science, Astronomy, Physics, assess your competence equivalent.

• That is one or more course equivalents

• L= little or none, H = high school , C= college , G= Graduate.

• In each, is your highest level of competence

self-taught or teacher taught? S or T.

One purpose of this course • To help you learn how to teach yourself new fields.

• During this semester, you will be asked to read up four topics outside your field of expertise. You will find it easier to pick narrow topics than broad ones. Do you know about life form classification? What is pH? What is a red giant star, and why? When did Earth develop an oxygen atmosphere, and how? What is thermodynamics? Or whatever you choose. Find topics that interest you, preferably course related.

Homework• Spread your work over three weeks. Then for the last

few days, decide what you have learned, and write a ½ to 1 page summary of it.

• What will you be graded on? 1) Include a list of places where you looked.2)Show that you learned the key issues of your topic?3) Show new technical terms you learn to use, and what

they mean? (quality of understanding as well as quantity)

4) Can you describe how your theme’s process works?5) Where would you follow these ideas next?

Dates for handing in this homework.• First assignment 11 Sept.

• Second assignment 2 Oct.

• Third assignment 23 Oct.

• Fourth assignment 13 Nov.

• There will be one brief take home mid semester test (for graduate students only)

• There will be a final report about a topic from the course that will be treated as a final exam.

Class Time

• Normally:

1 hour lecture followed by 15 min discussion intended, as needed, to clarify issues raised in class.

Policies (read later). All holidays or special events observed by organized religions will be honored for

those students who show affiliation with that particular religion, Absences pre-approved by the UA Dean of Students (or Dean’s designee) will be

honored. List of required texts NONE REQUIRED• Policies

– Expected classroom behavior (e.g., use of pagers/cell phones);– Plagiarism, etc., within Student Code of Academic Integrity:

http://deanofstudents.arizona.edu/codeofacademicintegrity – Threatening behavior by students:

http://policy.web.arizona.edu/threatening-behavior-students• Notification, warning students that some course content may be deemed

offensive by some students; • Disabled students must register with Disability Resources and be identified to the

course instructor through the University’s online process in order to use reasonable accommodations. For recommended language, see http://drc.arizona.edu/faculty staff/syllabus-statement

• The information contained in the course syllabus, other than the grade and absence policies, may be subject to change with reasonable advance notice, as deemed appropriate by the instructor.

Books via Amazon (Or other sellers)Deamer D.W. Origin of Life, the central concepts

4 new $24, ~10 used @$10)Sullivan and Baross, Planets and Life Too expensive new. Used $46-$35Oparin Life its Nature Origin and Developmentused, about $5.Benner Life the Universe and the Scientific Method -

$35 if you can get it.Shklovsky and Sagan Intelligent Life in the Universe~$6 also check your local bookstore.

Also, we will add pdf copies of key papers for your personal use.

• Cleland and Chyba.• Pace: Universal Nature of Biochemistry Class Ast 506 schedule

WARNINGThere is NO AGREEMENT as to either what life

is, nor about the processes that produced the origin of terrestrial life.

In these lectures, you are receiving opinions with reasons for them.

You are welcome to further explore the reasoning.

But alternate opinions exist because the reasoning is incomplete, and the experimental evidence is currently minimal.

Out of the Big Bang The concept that the entire material of the universe came

out of an immensely dense hot state has immense implications.

• Life was a development after that state.

• All those aspects we hold dear, were either emergent properties, inherent in some aspect that discriminated between earlier states, or emergent illusions.

• Plan to decide for yourself, on the basis of evidence and understanding: What is life? What is death? What is an appropriate attitude to Community? Race? Gender? Age? Humanity? Economics? Education? Freedom? Conservation? Medicine?

What is Life?This is a difficult topic, not to be confused with what

is living, or what is a life form.Life is a system whose component, living organisms

include some which do not have all the capabilities that the system requires.

In 1831 Wöhler heated ammonium cyanate, a normal chemical ingredient and produced urea, a chemical previously only known in animal urine. From this and further developments it became clear that life forms had a physical implementation in chemicals.

From Wickipedia• Élan vital was coined by French philosopher Henri Bergson

in his 1907 book Creative Evolution, in which he addresses the question of self-organisation and spontaneous morphogenesis of things in an increasingly complex manner. Elan vital was translated in the English edition as "vital impetus“…………. It is a hypothetical explanation for evolution and development of organisms, which Bergson linked closely with consciousness.

[But is better considered as a feeling about being and consciousness rather than how the physical world works] …………………………………….

• The British biologist Julian Huxley remarked that Bergson’s élan vital is no better an explanation of life than is explaining the operation of a railway engine by its élan locomotif ("locomotive driving force"). The same epistemological fallacy is parodied in Molière's Le Malade imaginaire, where a quack "answers" the question of "Why does opium cause sleep?" with "Because of its soporific power.“

Conservative vs. Dissipative• Words used by Prigogine to describe situations

without or with energy flow. In a closed system, order always decreases. When energy flows, order does not always decline. So Einstein obtained a patent for a refrigerator that used only a gas flame heat! Electrolux.

• The order that life develops can be considered as a kind of cooling, a decrease of entropy. The thermodynamic definition of life is that it is a system with decreasing entropy. But the growth of a crystal from solution does this too.

Cleland and Chyba 2002Abstract. There is no broadly accepted definition of

‘life.’ Suggested definitions face problems, often in the form of robust counter-examples. Here we use insights from philosophical investigations into language to argue that defining ‘life’ currently poses a dilemma analogous to that faced by those hoping to define ‘water’ before the existence of molecular theory. …For example, thermodynamic and metabolic definitions have difficulty avoiding counting crystals and fire, respectively, as alive.

[comment: Add evolution but see Pace’s paper]

How do you decide if something is alive?• Do various things to it to see if it has a variety of

responses.

• But some, like the hedgehog have only one trick. They roll into a spiney ball. Others like the fox have many.

• BUT hedgehogs select their food. They walk, they breathe, they urinate, they produce offspring.

• In general the things they do are those necessary to produce a certain kind of continuity called “survival”

Concept of Survival• Malthus’ use of “survival” as a concept for humans.

• Darwin’s generalization as a concept that includes diversification for all life forms

• Generalization to include the complete natural world. As e.g. “The house survived the storm.”

• The way that survival is assisted by the survivor depends on the nature of the survivor.

• This is a process akin to decision making,

Akin to IF….THEN in a computer program.

What do life forms do?

A computer is…

• Implemented in electronics

• It performs programs.

It operates a string of IF…THEN instructions.

Life forms are …• Implemented in organic

chemistry.

1) They perform a string of survival instructions.

2) They have descendants with added/changed instructions that (hopefully) assist survival.

How do life forms grow?• They use material ingredients from the

environment.

• They use energy either from the material ingredients, or directly from sunlight.

• These material ingredients are transformed to produce copies of components already there.

• Waste materials are eliminated.

• These processes are Metabolism. – Construction is anabolism

– Destruction is catabolism.

Continuity Darwin to Wallich 1882

Principle of Continuity

All terms that apply to biology are extension of processes that have a root function in physics/chemistry.

Key terms to consider are:

Metabolism (anabolism + catabolism)

Reproduction (replication)

Evolution (mutability)

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What is life?(the whole, not the parts)Principle of continuity. There is a continuum that

links biological and physical sciences.So, following it in this direction:1) Life is a process of survival selection all the way

down.In the opposite direction:2) Energy flow may drive growth and breakage,

corresponding to metabolism and replication.3) “Mutability” permits evolution by diversification

and selection.Evolution is the process that produces the transition

from non-life to life.

Mutability- Principle permitting evolution

• An old word used by Chaucer and Shelley.• How can change occur while holding on to some

former aspects?• If change occurs, it must be able to be selected.• Chemistry must recognize subtleties by shape

recognition.• At a molecular level it requires at least 4 electron

bonds to define shape retained (1 plane) and shape changed (2nd plane). (2 bonds defines 1 geometric plane).

• Is this why life uses carbon?

From Wickipedia (read later)• Silicon has several drawbacks as a carbon alternative. Silicon,

unlike carbon, lacks the ability to form chemical bonds with diverse types of atoms necessary for the chemical versatility required for metabolism. Elements creating organic functional groups with carbon include hydrogen, oxygen, nitrogen, phosphorus, sulfur, and metals such as iron, magnesium, and zinc. Silicon, on the other hand, interacts with very few other types of atoms. Moreover, where it does interact with other atoms, silicon creates molecules that have been described as "monotonous compared with the combinatorial universe of organic macromolecules". This is because silicon atoms are much bigger, having a larger mass and atomic radius, and so have difficulty forming double bonds (the double bonded carbon is part of the carbonyl group, a fundamental motif of bio-organic chemistry).

• [Pace: The Universal Nature of Biochemistry]

A number of cases in which a fly is killed.1) One billiard ball hits another, which then moves in such a speed and

direction that it strikes and kills a fly.2) A primed Venus Fly Trap plant has its leaves closed as a result of a

genetic program. This closure results in a fly being trapped and killed.

3) A spider chooses where to make its web. A fly is trapped on the web and killed.

4) We choose a place to hang a fly paper, which traps a fly and it dies.In all four there is a fork in the possible way the future will develop, and

in all four, the path is one in which the fly dies.

In (1), the path of the ball is set by mechanistic processes. In (2), the genes of the plant make an enzyme which causes the leaf to

close. In (3), the spider is using cognitive skills to kill the fly, but has no

concept of the potential global consequences of its action. In (4), we might attempt to think through the global consequences of

using fly paper.

Life is a process of survival selection all the way down.

• The lowest level of survival that can be selected is durability.

• A proton is durable. Stones are durable.

• A bricks are durable, but straw and sticks are not.

• BUT some stones in some environments are not only durable, but they also grow, and break and so replicate.

Dissipative system – Zircon CRYSTAL

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Earth is hot inside from radioactivity and from self-compression

• The interior is hotter than the exterior.

• Part way in it is hot enough to melt some minerals.

• Convection currents bring down cool material from the exterior, and raise hot matter from lower down.

• The raised material cools and becomes surface igneous rock.

• Then it is weathered and becomes sedimentary rock.

Zircons sustained by a dissipative process

• Earth heat flow carries zircons through a life cycle.• Zircons are zirconium silicate crystals. Their high

melting point lets them survive in magma pools.• Old ones grow layers, new ones are born in magma

pools when crustal rock is subducted. Re-emerging at the surface, zircons form part of

magmatic rock.• Earth processes erode them, break them in pieces

(reproduction), move them, and form them into sedimentary rock. Some are totally destroyed in the process. Then they are subducted for new growth.

• Growth = repair = metabolism.• But zircons cannot evolve. 30

The Functions and Life1) Material2) Cohesion3) Process (resisting 3, +repairing 4,

+mutable/genetic 5, + cognitive 6 + science 7)4) Sustaining (using environmental energy) (Protocells,Fire and Crystals fit here and are non-

living)5) Responding Most life forms6) Thinking Animal life forms7) Understanding Humans are headed there

Function 1 Function 2 Function 3 Function 4 Function 5 Function 6 Function 7 ExampleMatter Cohesion Process Sustaining Responding Thinking UnderstandingMolecule Valency Resisting Conservative - - - Solid

Lipid Membrane +Repairing Dissipative Historic - - Proto-cellMonomer Polymer +Mutable “ Genetic - - MicrobeNeuron Synapse +Neural “ Intentional Cognitive - SpiderTerminal

Internet +Science “ Planned Analyzed Integrative Post-human

Functions applied to Survival

Distinguishing a life form from non life 1

• Is a virus alive. It takes over the machinery of a cell to reproduce itself, so it is not an independent producer.

• Comment – a cuckoo requires the machinery of another bird feeding its young.

We require the machinery of plants using sunlight to make food for us.

We and cuckoos and viruses are parasitic.

But we are all alive.

Distinguishing a life form from non life 2

• Is a prion (protein causer of mad cow disease) alive?

It takes over the machinery of the cell to fold a protein used in the brain, so preventing cognitive processes.

• Comment – This is a uniquely one function activity. In this way it is similar to the growth of a zircon, or the way a hurricane works.

• It is not alive.

Distinguishing a life form from non life 3

• Is a Mars Rover alive?• It makes its own electricity from sunlight, and

it makes decisions about what it will do based on sensory equipment and internal program.

• Comments – Mars Rovers are produced by humans, and there is no physical link whereby the presence of a prior Mars Rover produced a new one. Also, it does not get repaired.

• Also it is not made from carbon compounds.• It is not alive.

Distinguishing a life form from non life 4

• Is the Hubble Telescope alive?• It makes its own electricity from sunlight, and it

makes decisions about what it will do based on sensory equipment and internal program.

• It has failures repaired (by humans).Comment - The missing ingredient is still

reproduction.Also it is not made of carbon compounds.It is not alive.

Distinguishing a life form from non life 5

• There are carpet cleaners that can sense their way around the floor. Also there are devices that will sense when their batteries are low, and find a socket and plug themselves in. When these are combined will the device be alive?

• Comment – as we move down this chain, the three issues that dominate are:

1)How is reproduction enabled by the device itself

2)Is it made of carbon chemistry?

3)What is its mechanism for evolving?

Reproduction• Not all life forms can reproduce.

• Simple ones just divide.

• More complex ones need a male and female.

• And sometimes the evolutionary path to the two organisms is sufficiently different that the live form produced can metabolize but not reproduce.

• Example: A mule is the product of a horse and donkey. It is infertile.

Species• The concept of a species is of the grouping that is

sufficiently similar that the offspring can itself reproduce.

• The variants of a species are called sub-species. They are different, but can produce fertile offspring. There is often a geographical spread of sub-species, in which the end groups act as separate species to one another.

• Example the American red squirrel has species “hudsonicus” and “douglasii”. There are places where sub- species of each have been reported to cross breed.