Chemical Evolution by Natural Selection

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Chemical Evolution by Natural Selection

• Chrisantha Fernando
• School of Computer Science
• University of Birmingham
• 16th October 2006

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My Claim

• I claim that the spontaneous origin of a
  geophysical natural selection machine was
  necessary for the production of increasingly
  ordered chemical organizations ultimately leading
  to a nucleotide producing metabolism.
• I reject other self-organizing principles that
  have been proposed to explain the origin of
  metabolism.

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How did unlimited heredity arise?

• Template replication of sequences allows
  unlimited heredity, 4100 1060 messages.
• If a new message was produced each second for 4
  billion years, we would still have only 1038 of
  the 1060 possible messages.
• How could template replication arise?

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Ribonucleotides could not have formed
spontaneously.

• Specific synthesis of ribose, specific
  phosphorylating agents.

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The need for Self-Organization.

• Clearly, some complex chemistry must have
  self-organized on the primitive earth and
  facilitated the appearance of the RNA world.
  Leslie Orgel, (2000).
• Graham Cairns-Smith Clay Templates.
• PNAs etc.. Eschenmoser.
• Metabolic Self-Organization. I will discuss how
  metabolic self-organization could arise through
  natural selection.

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Chemical Evolution

• Millers non-random synthesis of formic acid,
  alanine, glycine etc eventually resulted in tar
  a combinatorial explosion of polymers, but no
  increasingly ordered chemical organizations.

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• What modifications must be made to this protocol
  to allow

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What do we want?

• Open ended evolution (Bedau et al 2000)
• Origin of basic autonomy, i.e. a dissipitive
  system capable of the recursive generation of
  functional constraints (Ruiz-Mirazo, 2004).
• Production of nucleotides (Maynard-Smith
  Szathmary, 1995).
• Coupled cycling of bioelements (Morowitz, 1968)
• Maximization of entropy production by the
  biosphere (Kleidon, 2004)
• The minimal unit of life Membrane, Template
  Replication, Metabolism. (Ganti, 2003)
• Autopoetic units, (Membrane, Metabolism)
  (Maturana and Verala, 1992).

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What is Metabolism?

• The set of processes (e.g. chemical reactions)
  producing the constituents of the organism.
• An organism is a spatially distinct unit.
• But some people try to define metabolism
  non-spatially, e.g. a closed and self-maintaining
  set of chemicals and reactions (Dittrich and
  Spironi, 2005, Kauffman, Fontana, etc).
• But organismal metabolism is not closed, it is
  externally recycled.
• A spatially distinct individual necessary for
  organismal metabolism, the sort which interests
  us.

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Theories of Self-Organization of Metabolism are
Flawed.

• Eigens idea and Kauffmans model of Reflexive
  autocatalytic sets of proteins.
• Fontanas idea of self-organization of higher
  order chemical organizations in a flow reactor,
  modeled with Lambda Calculus.
• Morowitz idea (and recently Dewers arguments
  for) a self-organizing force due to the existence
  of a steady state energy flux.

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Reflexive Autocatalytic Sets

• Each member has its formation catalyzed by one or
  more members of the set.

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Kauffman Side-steps Side-Reactions
The system is spreading if the problem of
poisoning catalysis is not completely ignored as
Kauffman did.
Kauffmans Universe
Calculations of probabilities about such systems
always assume that a protein may or may
not catalyse a given legitimate reaction in the
system but that it would not catalyse harmful
side reactions. This is obviously an error. Hence
the paradox of specificity strikes again -- the
feasibility of autocatalytic attractor sets seems
to require a large number of component
types (high n), whereas the plague of side
reactions calls for small systems (low n). (Eors
Szathmary, 2000)
Our Universe
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Kauffman Ignores Precursor Depletion
If there is depletion then the precursors of the
set must be re-cycled! In Kauffmans universe
there is constant excess of a vast diversity
of precursors. In our universe, we need to
assume more limited initial recycling
capability.
Kauffmans Universe
Our Universe
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Conclusion on Kauffman

• Kauffman has proposed an alternative
  self-organizing principle in addition to natural
  selection, but it does not work if
• We take side-reactions seriously.
• We assume limited diversity of recyclable
  precursors.
• No reflexive autocatalytic set has been produced.
  
• We reject this as a relevant self-organizing
  princple in the origin of life.

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Fontana and Buss Lambda Calculus.

• They claim, self-organization arises in a system
  lacking any formulation of Darwinian selection.
• Flow reactor consisting of string re-writing
  expressions, no mass or energy conservation, but
  chemical reactions are modeled as equivalence
  classes of operations.
• If self-copying is forbidden, larger (L1)
  organizations of string subsets arise that are
  self-maintaining.
• They claim NS could not happen, but it could
  since there could be gt 1 L1 organization present.
  
• String gt a maximum length are forbidden, i.e.
  again the problem of a combinatorial explosion
  producing tar is nicely forgotten.
• In conclusion We reject that any self-organizing
  principle other than natural selection acts in
  Fontanas reactor, and we reject that it would
  work in real chemistry since the same problem of
  side-reactions is ignored.

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Energy Flow Organizes a System.

• Claims that life is driven by radiant energy to
  attain complexity in the form of coupled cycling
  of material.
• Although careful to mention that complexity
  alone is an insufficient measure for
  characterizing the transition from non-living to
  living, he goes on to claim that
• Miller type experiments indicate the great
  potential for a directed energy input to organize
  a system., organization being defined as
  compressible complexity.

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The Logical Error.
The last statement does not follow from the
first. e.g.the continued steady state flux
through a cloud or a Bernard cell does not arise
because the physical properties of the system
were informationally specified (ordered) by
the energy flux itself.
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Energy Flux not a driving force for
organization.

• Only a small subset of systems driven by external
  energy become increasingly organized, in others
  the size of the sink increases, with loss of
  capacity for recycling.
• How does the subset of dissipative systems
  increase their capacity for recycling and their
  rate of entropy production?
• I propose it is the subset capable of natural
  selection that have this property. A steady-state
  energy flux is necessary for the maintenance of
  the initial natural selection machine.

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Natural Selection

• Algorithmic process occurring in populations of
  entities having multiplication, heredity and
  variation (JMS, 1986).
• What is the simplest machine capable of
  sustaining natural selection, that is likely to
  have formed spontaneously?
• The Oparin school first proposed natural
  selection as a mechanism of prebiotic evolution,
  but with little experimental success.

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Alexander Oparin 1894-1980
Coacervates spontaneously formed polypeptide
structures. He distinguished between artificial
and natural coacervates. He proposed variation in
polypeptide composition. No self-replication or
heredity was demonstrated.
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Fox Dose, Folsome, Bahinder, Weber

• Fox and Dose Polypeptide microspheres in which
  budding occurred due to potentially non-random
  polycondensation reactions. Details of heredity
  were not studied. (1977).
• Folsome observed that the thin oily scum on the
  surface of the water in the Miller experiment
  formed exponentially growing microstructures and
  then sank to the bottom of the flask (no
  continued lineage). (1979)
• Bahinder showed that formaldehyde, ammonium
  phosphate, mineral salts and ammonium molybdate
  exposed to sunlight formed spherical
  microstructured called Jeewanu.(1954).
• Weber (2005) described a synthesis of
  microspherules from sugers and ammonia without
  reference to Bahinders work.
• But no-one has demonstrated natural selection in
  populations of spontaneously formed phase
  separated individuals.

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Chemical Evolution by Natural Selection

• The origin of metabolism occurred under the
  following conditions.
• A spontaneous natural selection machine arose
  capable of
• Production of lipophilic material to replenish
  phase separated individuals formed from that
  material.
• A process of agitation to replicate a liposome
• A reaping of liposomes to impose selective
  pressure.
• The capacity for variation by chemical
  avalanches within liposomes.
• Some novel chemicals produced in an avalanche can
  aid I. liposome growth, ii. liposome division.

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1
1
The artificial version for the lab.
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(1) Basal Liposome Growth
No chemical reactions Just phase separation
a
a
a
a
a
a
a
a
a
a
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(2) Liposome Division
a
a
a
a
a
a
a
a
a
a
a
a
a
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a
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(3) Chemical Avalanches?
Pyrite
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a
b
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b
c d
RARE (low flux) reaction
a
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C happens to be autocatalytically produced, it
need not have been.
b
c d
High flux reaction
c e
a
?
But now we must calculate the reactions of e
and so on.
This is the avalanche.
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The model asks

• Is the production of increasingly ordered
  metabolism possible when variation is by chemical
  avalanches, most of which are harmful or neutral?
• What metabolic topology is evolved?
• What thermodynamic organization of metabolism is
  evolved?
• What are the fundamental constraints for natural
  selection to act in such a system?

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The Algorithm

• A hill-climbing algorithm is used to select for
  liposomes that maximize their growth after a
  fixed period.
• Parental (liposome) fitness is assessed, a child
  is produced that inherits half the parental
  material, and has experienced an avalanche. If
  its fitness is greater than the parent, it
  replaces the parent, else a new offspring is
  produced and assessed.

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The Artificial Chemistry
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Energy

• Each species is assigned a free energy of
  formation, Gf.
• Any novel reaction must be spontaneous,
• ?G Gproducts Greactants lt 0.
• The equilibrium ratio of a reaction is given by K
  e-?G/RT.
• kb 0.01 and kf 0.01K
• A species has an 80 chance of being lipophilic.
  If a product is lipophilic, the reaction is
  effectively irreversible.

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Initial conditions

• Food set. 100 mM aab, aaab, aabb, bbbb, aaaab,
  aaabb, aabbb, abbbb.
• Gf 1.0
• Growth set. 0mM abb (0.1), abbb (0.01), abbbb
  (1), abbbbb (2), abbbbbb (3), abbbbbbb (4),
  abbbbbbbb (5), abbbbbbbbb (5).

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Definition of Fitness
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Results.
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Energy dissipation increases
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Avalanche properties change over the course of
evolution.
As molecule size increases the chance of an
autocatalytic product from an avalanche
Decreases.
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Mean Avalanche Properties
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Conclusions

• Liposome level selection maintains molecular
  replicators arising in chemical avalanches.
• Autocatalytic constituents are more likely to be
  short molecules with few atom types (given random
  rearrangement reactions).
• An ecology of autocatalysts exists,
  non-competitive, competitive, parasitic,
  cross-catalytic, but all selected on the basis of
  by-product mutualism of autocatalysts within the
  same liposome.
• Lipophobic side products drive irreversible
  reactions, whilst lipophilic non-reactive
  products prevent continued drainage.

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Conclusions

• A more diverse food set promotes more complex
  autocatalytic cycles, 1,2, 3 member cycles
  observed.
• Energy flux increases over evolutionary time for
  two reasons energy demands of memory, energy
  demands of growth.
• Large generation numbers and large population
  sizes will be necessary since most avalanches are
  harmful or neutral, thus automated microfluidics
  is required, perhaps under high pressure to
  promote chemical avalanches.

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Acknowledgements

• Jon Rowe
• Eors Szathmary
• Hywel Williams
• Kepa Ruiz-Mirazo
• Fabio Mavelli
• Alvero Moreno
• Xabier Barandieran