self-organization and irreversibility: consequences for...
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Self-organization and irreversibility: consequences for the origin of life
Robert PASCAL Institut des Biomolécules Max Mousseron
UMR5247, CNRS - Universités Montpellier 1 & 2
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The Miller-Urey’s experiment
2
May 15th, 1953
Miller Science, 1953, 117, 528.
Organic building blocks can be formed abiotically
Under conditions postulated for the primitive Earth. – Amino acids – Nucleic bases, sugars…
In the interstellar medium. In hydrothermal systems. In many places…
3
… except on the surface of the present day Earth (because of oxidizing conditions).
60 years later, the above mentioned lesson of Miller’s experiment remains valid.
The double-helix structure of DNA
4
April 25th, 1953
Watson & Crick Nature, 1953, 171, 737.
The origins of life: by chance only?
Origin of life
Biology Prebiotic chemistry
5
There is almost no possibility for life to emerge.
« S'il fut unique, comme peut-être le fut l'apparition de la vie elle-même, c'est qu'avant de paraître ses chances étaient quasi nulles. L'Univers n'était pas gros de la 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 ? »
J. Monod, Le hasard et la nécessité, Editions du Seuil, Paris, 1970
Violation of the 2nd Law of thermodynamics
Biology Prebiotic chemistry
A driving force for the emergence
Origin of life
Driving force
Replicators dynamics: Growth capacity Selection
Driving force = Dynamic Kinetic Stability
A. Pross J. Syst. Chem. 2011, 2:1
Replicator dynamics Natural selection
‘Regular’ chemistry
R C2 P2 C1 P1
[C1] = 0 ou [C2] = 0
Replicator dynamics
[P1] / [P2] = k1 / k2 = Cte
R P1 P2 k1 k2
S. Lifson J. Mol. Evol. 1997, 44, 1-8
Replicator (1)
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[Replicator]
t
A. Pross, R. Pascal Open Biology 2013, 3:120190
Reactant(s) + Replicator Replicator + Replicator
K =[Replicator] [Replicator]
[Replicator] !([Reactant])
Reactant(s) + Replicator Replicator + Replicator
Replicator (2) : Irreversibility and exponential growth
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[Replicator]
t Non-sustainability
A. Pross, R. Pascal Open Biology 2013, 3, 120190
A driving force for the emergence
Origin of life
Driving force
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Replicators dynamics: Growth capacity Selection
Irreversibility Far from equilibrium state Supply in energy
Replicator dynamics Proto-metabolism
Natural selection Metabolism
R. Pascal J. Syst. Chem. 2012, 3:3; ; A. Pross, R. Pascal Open Biol. 2013, 3, 120190
Self-organization
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Requirements
Distance from equilibrium
Nonlinearity
➮ Systems Chemistry
➮ Far from equilibrium state (energy-rich reactants / activating agents)
➮ Replication / autocatalysis
G. Nicolis, I. Prigogine, Self-organization in nonequilibrium systems 1977
Metabolism and irreversibility
In an environment rich in abiotically formed organic building
blocks,
the main role of metabolism would not be anabolism…
…but maintaining the system in a far from equilibrium state by
irreversibly coupling an energy source to the system.
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Condition for the origin of life:
An irreversible protometabolism
Catalytic cycles and catalysis S
M1
P
M4
M2 M3
M5M6
M. Eigen Naturwissenschaften 1971, 58, 465-523; M. Eigen, P. Schuster, Ibid. 1977, 64, 541-565.
Mn+1
Mn
Autocatalytic cycles and autocatalysis
S
P·S
P
P·P
P
S
M1
P
M4
M2 M3
M5M6
S
C·S
C
C·P
P
(Proto)-metabolism = irreversibility
... Ai ... An M1 ···Mi Mn Pn
Pi
Mj···
G
!
An
M1Mi Mn
PnPi
"G!
MjMn
The development of a metabolism requires the system to be held far from equilibrium by kinetic barriers
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SPi
TS≠
Mi ΔΔG≠
ΔΔG
Transition state theory
k = κ kB T
h e – (ΔG≠/RT)
The Eyring equation
A. Eschenmoser, Orig. Life Evol. Biosph. 1994, 24, 389; Angew. Chem. Int. Ed. 2011, 50, 12412.
An M1
SPiSPn SP1
···Mi Mn Pn
Pi
Mj···... Ai ...
Graphical representation of Eyring equation
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0
25
50
75
100
125
150
175
200
1,E-06 1,E-03 1,E+00 1,E+03 1,E+06 1,E+09 1,E+12 1,E+
1 s 1 d 1 yr 103 yr 10–3 s
400 K
300 K
100 K
50 K
!!G! / kJ mol–1
t1/2 / s
200 K
10–3 1 103 106 109 1012 10–6
Kinetic barriers t1/2
T
ΔG≠ = RT ln( t1/2) kBT
h ln(2)
R. Pascal, J. Syst. Chem. 2012, 3, 3. R. Pascal, In Smith, Cockell, Leach, Astrochemistry and Astrobiology: Physical Chemistry in Action, Springer, 2013.
0
25
50
75
100
125
150
175
200
1,E-06 1,E-03 1,E+00 1,E+03 1,E+06 1,E+09 1,E+12 1,E+
1 s 1 d 1 yr 103 yr 10–3 s
400 K
300 K
100 K
50 K
!!G! / kJ mol–1
t1/2 / s
200 K
10–3 1 103 106 109 1012 10–6
At 300 K ΔΔG≠ ~ 100 kJ mol–1
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Energy carriers and metabolites that accumulate in the course of a metabolic process have to be stable for periods consistent with the timescale of the progress of the whole system.
R. Pascal, J. Syst. Chem. 2012, 3, 3. R. Pascal, In Smith, Cockell, Leach, Astrochemistry and Astrobiology: Physical Chemistry in Action, Springer, 2013.
100 kJ mol–1 corresponds to a significant fraction of the energy of a covalent bond (350 kJ mol–1 for a C–C bond).
Structures based on covalent bonds are likely candidates.
The source of free energy
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Free energy ≥ ΔG≠ + ΔG ~ 150 kJ mol–1
A0
ΔΔG≠
ΔΔG An
~ 100
~ 50
R. Pascal, J. Syst. Chem. 2012, 3, 3. R. Pascal, In Smith, Cockell, Leach, Astrochemistry and Astrobiology: Physical Chemistry in Action, Springer, 2013.
Electromagnetic radiations
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Free energy ≥ 150 kJ mol–1
E = hc / λ
Wavelength ≤ 800 nm
UV Visible IR
R. Pascal, J. Syst. Chem. 2012, 3, 3. R. Pascal, In Smith, Cockell, Leach, Astrochemistry and Astrobiology: Physical Chemistry in Action, Springer, 2013.
Heat: black body radiation
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T ~ 3600 K (λmax = 800 nm)
© Wikipedia
R. Pascal, J. Syst. Chem. 2012, 3, 3. R. Pascal, In Smith, Cockell, Leach, Astrochemistry and Astrobiology: Physical Chemistry in Action, Springer, 2013.
21 Adapted from Lineweaver and Chopra, Ann. Rev. Earth Planet. Sci. 2012
Cost of irreversibility
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23 Autotrophic hypothesis
24 Autotrophic hypothesis
Concentration Cost of irreversibility
ATPase: the proton pump
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An complex molecular machine is needed to convert the potential energy of proton gradient across the membrane into ATP.
ATPase (proton pump) couples the translocation of several protons across the membrane to the synthesis of an ATP molecule.
Self-organization of life
– Need for irreversibility.
– Self-organization must not lead to a violation of the Second Law of thermodynamics.
– Need for self-organization to be coupled with irreversible transformation of chemical carriers of energy.
Organic matter and self-organization Organic building-blocks
– In reducing environments (presence of H2, H2S, FeS…) organic matter does not correspond to a far-from-equilibrium state.
– No special need for irreversibility for the formation of organics.
Prebiotic chemistry
Systems chemistry
Ludlow & Otto, Chem. Soc. Rev. 2008, 37, 101.
Consequences for space research
Meteorites and comets contain organic matter that has been stored for periods exceeding hundreds of millions of years. Activated functional groups (e.g. cyano groups) are no longer present in high extent.
It is then highly improbable (violation of the 2nd Law) that these materials could directly give rise to a proto-metabolism fulfilling the irreversibility conditions for self-organization.
How to get activated/activating species from these materials ? – Re-activation during impacts.
– Photochemistry in a planetary environment. 27
“Habitability” for the origin of life
The constraints for the origin of life are different from the constraints for life.
Life in extreme environments has no obvious relationship with the origin of life.
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T ~ 300 K
λ ≤ 800 nm
Light, lightning,
re-activation during impacts
Acknowledgements
The DSBC group of IBMM – Dr. L. Boiteau
– Dr. J.-C. Rossi
Collaboration – Dr. G. Danger (University of Marseille)
– Prof. A. Pross (Ben Gurion University of the Neguev)
Interdisciplinary program EPOV
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– Dr. G. Danger
– Dr. R. Plasson