Self-organization and irreversibility: consequences for...

Self-organization and irreversibility: consequences for the origin of life

Robert PASCAL Institut des Biomolécules Max Mousseron

UMR5247, CNRS - Universités Montpellier 1 & 2

rpascal@univ-montp2.fr

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The Miller-Urey’s experiment

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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…

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  … 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

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April 25th, 1953

Watson & Crick Nature, 1953, 171, 737.

The origins of life: by chance only?

Origin of life

Biology Prebiotic chemistry

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  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