Origin of life and biogeological evolution
Philippe Claeys
http://we.vub.ac.be/~dglg/Web/Teaching/Teaching.html
Origin of life
a scientific question for sure but also much more...
«It is often said that all the conditions for the first production of a living organism are now present, which could ever have
been present. But if (and oh! what a big if!) we could conceive in some warm little pond, with all sorts of ammonia and
phosphoric salts, lights, heat, electricity, etc. present, that a protein compound was chemically formed ready to undergo
still more complex changes, at the present day such matter would be instantly devoured or absorbed, which would not
have been the case before living creatures were formed» (Darwin C.R., letter to J.D. Hooker, [1 February] 1871, in Darwin F.,
ed., "The Life and Letters of Charles Darwin," [1898], Basic Books: New York NY, Vol. II, 1959, reprint, pp.202-203)
«We never question the origin of kinetic energy, likewise we should get used to the idea that life always existed and that
questioning its origin is futile» (Svante Arrhenius, 1909 Nobel Price, Panspermia believer)
«L’Univers n’est pas gros de vie, ni la biosphère de l’homme. Notre numéro est sorti au jeu de Monte Carlo. Quoi
d’étonnant à ce que, tel celui qui vient d’y gagner un milliard, nous éprouvions l’étrangeté de notre condition» (Jacques
Monod, 1970, Nobel Price Medicine 1965)
«La vie appartient à la trame même de l’Univers. Si elle n’était pas une manifestation obligatoire des propriétés
combinatoires de la matière, il eut été absolument impossible qu’elle prenne naissance naturellement» (Christian de
Duve, 1990, Nobel Price Medicine 1974)
In the last few years, I have become increasingly interested in the origin and evolution of life. I have written three books,
which have been translated in a number of languages: A Guided Tour of the Living Cell (1984); Blueprint for a Cell
(1991); and Vital Dust (1995). I plan to devote my remaining years to further probing what, if anything, our growing
understanding of life and mind can tell us about the structure and meaning of the universe (Christian de Duve, 1997)
Define life ?
Life: common properties of all living being that differentiate them from non-living systems/things.
Very basic definition and not very meaningful even if we dare to add C-based
Life: open structured system where chemical reactions take place and that is capable of regulating
its exchanges with the environment and to divide itself into two other systems, each with identical
properties, not necessarily similar to those of the initial system (Jacques Reisse, 2006).
Life: is an open or continuous phenomena able to decrease its entropy by processing free energy
extracted from its environment, life feeds on negative entropy in contradiction to the Second Law
of Thermodynamics (What is life ? Erwin Schroedinger, 1944)
What is alive :
Virus ?
Artificial life in the computer ?
Life: 2 basic cell structures
Procaryote
Eucaryote
The cell: chemistry & information
The cell: metabolism
Energy sources
= e- acceptor
Life in the universe
Terrestrial
Traces
•fossil
•sediments
•isotopes
•organic
Origin
•primitive
Extraterrestrial ?
Limits
oceans
•building
blocks
components
•life in test
•homochirality tube
•temperature
•salinity
•pH
•pressure
•deep
Solar system
Extrasolar
Pamspermia
•Mars
•exoplanets •always existed,
•Europa
•signature of transfer between
extrasolar life planets, comets,
•Titan
dust, etc.
•Ganymede
biosphere
Earth a “special” place
➡
Sun: middle size star implies long life time
➡
Ideal distance from Sun: 3 phases of H2O coexist
➡
Moon stabilizing effect
➡
Large Jupiter shield
Origin of life : facts
Age of the Earth 4.567 Ga
No rock record until 3.8 Ga
Early Earth anoxic atmosphere
First proven unicellular organisms around 2.7 Ga
Microbial life only for ~ 2 Ga
Development of O2 = major pollution for anaerobic organisms,
opportunity for the survivors
First multicellular organisms around 1 Ga
3 domains of life
http://www.tolweb.org/tree/
Virus ?
Based on RNA structure in ribosomes
Which came first ?
Tree of life
Classic tree of life based on rRNA
sequence comparison (Woese 1987)
One of many possible revisions
(see Brinkmann & Philippe, 2005)
Position of the root is open question
Concept of LUCA
Last Universal Common Ancestor or Cenancestor
(Forterre and Philippe 1999)
What did LUCA look like ?
Two approaches :
• Top - down: from current organism to LUCA
• Bottom - up from atoms and molecules to LUCA,
pre-biotic chemistry
What did LUCA look like ?
Extrapolation
possible
Top - Down ?
Extrapolation
impossible
Prebiotic chemistry
20 amino acids, transition from abiotic to RNA world, peptide world,
multiple scenario’s
Miller-Urey experiment 1953 (http://www.ucsd.tv/miller-urey/) showed that organic
compounds such as AA, which are used to make proteins that are indispensable for
life, could be made easily under atmospheric conditions of Early Earth.
CH4,
NH3,
H2,
H2O
Production of HCHO, HCN
HCN + NH3 (Strecker reactions)= Adenine, base in RNA & DNA, and ATP
Adenine
Stepwise pre-biotic chemistry
with increasing complexity
1) Synthesis of the building blocks (AA, nucleic bases, nucleotides etc.)
Primordial soup, Miller-Urey experiments: basic chemical components and
energy available as pre-requisites
2) Formation of polymers (nucleic acids, peptides..)
Resulting from interactions (random ? catalyst?, activating agents?) between
building blocks, repetition to replication capability of polymers
3) Emergence of supra-molecular architectures, first membranes and individual cells
Individualization, self-replication and carrier of information
Stepwise pre-biotic chemistry
with increasing complexity
1) Synthesis of the building blocks (AA, nucleic bases, nucleotides etc.)
Primordial soup, Miller-Urey experiments: basic chemical components and
energy available as pre-requisites
2) Formation of polymers (nucleic acids, peptides..)
Resulting from interactions (random ? catalyst?, activating agents?) between
building blocks, repetition to replication capability of polymers
3) Emergence of supra-molecular architectures, first membranes and individual cells
Individualization, self-replication and carrier of information
How do random sequence of improbable reactions
lead to a self-replicated system?
The peptide world
CO-NH bond forms from amino acids under dehydration conditions
Pre-biotic soup of AA polymerization
Peptide self-replication
How convert AA sequence
into genetic information ?
Peptide double role catalyst + info carrier
Peptide world
with peptide nucleic acid equivalent
Evolution of genetic code + translation
No trace preserved of old peptide
genetic information system
Why change to nucleic acid base?
Protein and nucleic acid world
The RNA world
Pre-biotic soup of nucleotide synthesis and replication
No pre-biotic pathways to synthesize
mononucleotides
Nucleic acids both info storage and catalysts
RNA world
Translation apparatus
RNA + protein world
Evolution of ribonucleotide reductase
RNA + protein + DNA world
Co-evolution peptide - RNA
More complex
Prebiotic chemistry of AA + nucleotides
Coded peptide synthesis
+ nucleic acid replication
Peptide + nucleic acid world
Several biochemical processes seem compatible with co-evolution scenario: catalytic AA, peptide
+ AA stereo-selective catalysis (explain homochirality?), bonds AA & tRNAs, some AA involved in
both peptide and nucleic acid oligomerization (N-phosphoryl), reaction AA with inorganic PO4--
Early (hypothetical) metabolism
Most primitive cell must have had metabolism for synthesize macromolecule and energy for
cellular functions
Present metabolism too complex with various transporters, e- carriers, enzymes, pigments, and
genome with protein encoding
Early cell used simpler process to gain E from environment and make macromolecules
No trace preserved of this old / initial process but most likely took place under anoxic
conditions
Anoxic photosynthesis or fermentation/respiration too complex: chemolithotroph pathway’s
possible for energy source
Chemolithotroph organisms today are also autotroph’s CO2 into Corg. they use complex
pathways such as Calvin cycles, which seem complex for early organisms.
Better use already formed organic molecules
Early Energy source ?
Madigan et al. 2003
- Molecular H2 is an ideal e- donor reduction potential E0’ = -0.42 for 2H+/H2 2e- (E source
for procaryots in geothermal and hyperthermophilic ecosystems black smokers,
Yellowstone)
- Elemental S is an ideal e- acceptor S/H2S 2e- E0 = -0.28 also commonly used today by
procaryots
Metabolism will evolve other ways to derive E and use C
Timing and time scales differences
(Bio)Chemical reactions of life < 1 sec.
Generation time: bacteria min. to years multicellular organisms
Ecosystem development / evolution: > 10 - 1000 years
Evolution of species: kyr to Myr
Evolution of planets: > Myr to Gyr
Timing and time scales differences
(Bio)Chemical reactions of life < 1 sec.
Generation time: bacteria min. to years multicellular organisms
Ecosystem development / evolution: > 10 - 1000 years
Evolution of species: kyr to Myr
Evolution of planets: > Myr to Gyr
How long between building blocks to first cell and then to LUCA?
What about environmental conditions ?
When can this start : concept of planet habitability ?