Origins and Early Evolutionof Life

Richard VannCBI 206/ANESTH 445

Physiology and Medicine of Extreme EnvironmentsSpring 2013

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Origin of Life Topics• Who, when, what, where, how, why• Discussion

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Panspermia & Spontaneous Generation

•Panspermia: life exists throughout the universe•Spontaneous generation: life forms by the action of the sun on the primordial terrestrial slime

Aristotle384-322 BC

Anaximander611-547 BC

Anaxagoras500?-428 BC

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Recipe for Mice:Jan Baptista van Helmont (1580-1644)

• Put a soiled shirt and grains of wheat in a jar and let them ferment

• Mice form after 21 days• No experimental evidence

provided

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Friedrich Wöhler & Urea (1828)

• Wöhler made urea by heating ammonium cyanate

• "I can no longer, so to speak, hold my chemical water and must tell you that I can make urea without needing a kidney, whether of man or dog."

• A founder of organic chemistry5

• Organic and non-living compounds are different (“élan vital, life force, will-to-live”)

Death of Spontaneous Generation:Louis Pasteur (1859)

• Living systems arise biotically from other living systems

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Charles Darwin (1871)

“But if (& oh what a big if) we could conceive in some warm little pond with all sorts of ammonia & phosphoric salts, - light, heat, electricity, etc. present, that a protein compound was chemically formed, ready to undergo still more complex changes …”

- letter to Joseph Hooker7

Aleksandr Oparin (1924)

•Early atmosphere was strongly reducing

•CH4, NH3, H2O , H2 (no O2)•Sunlight reacted with non-living chemicals in the “primeval soup”•Unique, abiogenic, spontaneous generation of life•No difference between a living organism and lifeless matter

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J.B.S. Haldane (1929)

“When ultra-violet light acts on a mixture of water, carbon dioxide and ammonia, a vast variety of organic substances are made, including sugars and apparently some of the materials from which proteins are built up … [B]efore the origin of life they must have accumulated till the primitive oceans reached the consistency of hot dilute soup.”

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Harold Urey1893-1981

Stanley Miller1930-2007

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Miller-Urey Ocean-Atmosphere (1953)

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Miller (1953). Production of amino acids under possible primitive Earth conditions. Science 117: 528.

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Space• Radio astronomy found evidence of organic

molecules on space dust• Laboratory simulations of deep space created

organic molecules

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• Collisions of comets with primitive Earth• Murchison meteorite in Australia 1969

contained organic molecules

Exogenesis and Mars

• Mars may have been habitable a billion years before Earth

• A meteorite from Mars recovered in 1984 was claimed to contain fossil life but this is disputed

• The question of exogenesis from Mars to Earth is unresolved

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Hydrothermal Volcanic Vents

Hydrothermal vents

DSV Alvin (1977)

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Giant Clams

Tube Worms

Corliss, Baross & Hoffman. 1981. An hypothesis concerning the relationship between submarine hot springs and the origin of life on Earth. Oceanolgica Acta 4 (Suppl): 59-69.

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Deep, Hot Biosphere

Laboratory Simulations• Reactants: N2, CO2, S, Fe• Minerals: Fe-S, Ni-S• Products: NH3, amino acids,

peptide bonds, C-fixation Fe-complexes

Rock-Eating Bacteria

Thermophiles

Yellowstone (1966)

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Origin of Primordial Molecules- Deamer (2002)

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Timeline~13.7 bya “Big Bang” (atomic evolution)~11.5 Supernovae & heavy elements ~4.6 Sun, solar system & Earth~4.4 Oceans formed~4.4-3.9 Chemical evolution~4.2-4.0 Earliest life at hydrothermal vents?4.0-3.7 Earliest life at sea level?~3.5 Earliest fossils (Apex chert, WestAus)~0.5 Organic evolution (‘naked genes’)~1 mya Social evolution (humans) 19

When was Earth Ready for Life?- Schopf (2002)

Oldest Fossils:Stromatolites

Origin ofSustained Life

Sterilizing Meteor Storms

Successof Life

4.5 4.0 3.9 3.03.5

Billions of Years Ago (bya)20

PlanetaryBirth

Life and the Atmosphere

STERILIZINGMETEOR STORMS

OLDEST FOSSILS:STROMATOLITES

SUSTAINEDLIFE

EUKARYOTESCHEMICALEVOLUTION

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BIF

OXYGENCATASTROPHE

O2 metab

3.9 – 3.5 bya

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Manyearlylife

forms(temperature,

anaerobic,radiation,arsenic,

salt)

OO22 Catastrophe Catastrophe LUCALUCA

PresentBiochemistry

(ATP, Krebs cycle,RNA, DNA)

Time

NASA Definition of Life• “A self-sustaining chemical system

capable of Darwinian evolution”–Self-sustaining (energy production)–Chemical system (cell membranes)–Darwinian evolution (replication)

• What’s the driving force that makes this system run?

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Energy and Complexity- Chaisson (2001)

Stars 2 erg/g/secPlanets 75Large animals 20,000Human brain 74,000Society 500,000

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Sagaminopteron Ornatum

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Thermodynamics• 1st Law: energy is conserved, not created or

destroyed– all forms of energy are inter-convertible

• 2nd Law: heat flows from higher to lower temp– Energy conversions are never complete

• Some energy is always lost to the environment as wasted heat (ΔQ)

– Entropy (S) = wasted heat divided by the environmental temperature (ΔS=ΔQ/T)

• Entropy is generated with each energy conversion • The entropy of a closed system always increases• Entropy is “time’s arrow”Entropy is “time’s arrow” 26

Entropy Generation Rate- Silva (2008)

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Entropy (S) and “Heat-Death”

Universe

Life

dS/dt > 0∆Suniverse > 0

Energy

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∆Slife = 0

• Life is maintained by energy input from the universe & entropy export to the universe

• Does time stop when dS/dt=0?

How Did Early Life Get Energy?

• Heterotroph – the ‘premordial soup’ provided high energy complex molecules that had been abiotically synthesized (Oparin & Haldane). – Modern heterotrophs eat other organisms.

• Autotroph – energy derived from oxidation of ammonia to nitrous & nitric acid, sulfur to sulfurate, iron to iron oxide, and methane to carbon dioxide & hydrogen.

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Reverse TCA Cycle

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2 CO2 + 4 H2 2 H2O + C2O2 (acetate)no catalyst:very slow

Iron-Sulfur World - Günter Wächtershäuser

• Life originated on mineral surfaces near deep hydrothermal vents (“primordial sandwich”)

• 1st cells were lipid bubbles on mineral surfaces

• Metabolism predated genetics with iron sulfides as energy source (chemoautotrophs)

• Photoautotrophs evolved as chemical energy was deleted

• Autocatalytic & self-replicating metabolism

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Thioester World- de Duve

• Thioester bonds are high energy & played the role of ATP in early life

• Thioesters are intermediates in the ancient processes leading to ATP

• Thioesters evolved into ATP

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Driving Force: Entropy & Probability

• Most probable configuration has greatest entropy

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Less probable (S1) More probable (S2)

S3 < S4

Less probable (S3) More probable (S4)

• Attractive & repulsive intermolecular forces determine the most probable configuration

S1 < S2

• Heat is molecular motion

Simulation of Self-Assemblyhttp://complex.upf.es/~harold/lipid_world/index.html

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Before self-assembly (low S) After self-assembly (high S)

Self-Assembly of Liposomes- Bangham (1961); Deamer (1997, 2002)

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MurchinsonMeteoriteextract

MurchinsonLiposomes

Biological Self-Assembly• Lipid bi-layer membranes

36Antibody & antigen Substrate & enzyme

• Structure guided by attractive & repulsive forces (“lock-and-key”)

Lipid World - Serge, Ben-Eli, Deamer, Lancet (2000)

• Coacervates. 1-100 μ “proto-cells” (Oparin 1932)

• Microspheres formed by heat-polymerized amino acids (Fox 1957)

• Murchison carbonaceous meteorite (Deamer 1997). Catalytic activity, replication, etc. also proposed.

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Tobacco Mosaic Virus (TMV)• TMV self-assembly from separated protein & RNA

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Darwinian Evolution- Darwin (1959)

• Modified progeny of ‘A’ are better adapted to the environment & survive

• Subsequent generations of ‘B’ – ‘F’ are unmodified & become extinct

• Track ‘A’s genealogy into deep time to find LUCA

• Fossil record too limited

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Systematics or Phylogenetics- Haeckel (1866)

• Commonality of traits– Animals – consumers– Plants – producers– Protists – reducers

• Eucaryote* – nucleus, etc.• Prokaryote* – no nucleus

* Stanier (1961) [common biochemistry]

• LUCA

• Fossils–no! Genetic code?40

Evolutionarytime

DNA Code

Cytosine

Adenine

Guanine

Thymine41

RNA World

• RNA-based life predated DNA life• RNA can act as its own catalyst (‘ribozyme’) so

proteins were unnecessary• RNA evolved into DNA which is more stable• Ribosomal RNA (rRNA) is a remnant of the

RNA World• Problems: RNA chemically fragile, difficult to

synthesize abiotically, limited catalysis

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Pre-RNA Worlds• Alternative nucleic acids

– RNA precursors: threose nucleic acid (TNA), PNA (peptose), GNA (glycol)

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• PAH (Polycyclic Aromatic Hydrocarbon) World– PAHs are amphiphilic and might

self-organize in stacks as a nucleic acid backbone

Clay World - Cairns-Smith (1985)

• Proto-life was inorganic and existed on solid surfaces such as clays

• Clays catalyzed formation of complex organic molecules

• Clays acted as template for RNA self-assembly and evolved into RNA

• Natural selection enhanced their replication potential

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Ribosome- Woese (1981)

• Site of protein synthesis in all cells– Functionally constant over time

• Ribosomal RNA 16S– RNA “dictionaries” → phylogenetic trees– Genotype → phenotype (cell membranes)

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‘progenotes’ 46

Phylogenetic Tree of Life (16S rRNA)- Woese (1990)

Horizontal Gene Transfer (HGT)

• ‘Infective heredity’• Endosymbiosis

– Mitochondria (1.7-2 bya)– Plastids (1.5 bya)

• Antibiotic resistance– Plasmids

• Viruses

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Artificial HGT (Social Evolution)- Craig Venter

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• Sequence yeast cell genome (Myoplasma mycoides)

• Synthesize M. mycoides genome from lab chemicals

• Transplant synthetic genome into recipient cell (M. capricolum)

• Test viability of synthetic cell• Next find minimal viable synthetic genome• Applications – bio-fuels, vaccines, drugs, etc.

• What are the limitations of the field?• What came first: metabolism or replication?• What would be the result if you could re-run

evolution again beginning from the Big Bang?• What would be the result if you re-ran

evolution from the Big Bang 1,000 times?• Is laboratory investigation of the creation of

some form of life valuable? • If you were in charge of an origin of life lab,

where might you focus your efforts?

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