1. Chemical Evolution by Natural Selection Chrisantha Fernando School of Computer Science University of Birmingham 16th October 2006 Chrisantha Fernando School of Computer Science University of Birmingham 16th October 2006

2. 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.  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.

3. How did unlimited heredity arise?  Template replication of sequences allows unlimited heredity, 4 100 ~10 60 messages.  If a new message was produced each second for 4 billion years, we would still have only ~ 10 38 of the 10 60 possible messages.  How could template replication arise?  Template replication of sequences allows unlimited heredity, 4 100 ~10 60 messages.  If a new message was produced each second for 4 billion years, we would still have only ~ 10 38 of the 10 60 possible messages.  How could template replication arise?

4. Ribonucleotides could not have formed spontaneously.  Specific synthesis of ribose, specific phosphorylating agents.

5. 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.  “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.

6. Chemical Evolution  Miller’s non-random synthesis of formic acid, alanine, glycine etc… eventually resulted in tar; a combinatorial explosion of polymers, but no increasingly ordered chemical organizations.

7.  What modifications must be made to this protocol to allow…

8. 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).  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).

9. 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.  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.

10. Theories of Self-Organization of Metabolism are Flawed.  Eigen’s idea and Kauffman’s model of Reflexive autocatalytic sets of proteins.  Fontana’s idea of self-organization of higher order chemical organizations in a flow reactor, modeled with Lambda Calculus.  Morowitz’ idea (and recently Dewer’s arguments for) a self-organizing force due to the existence of a steady state energy flux.  Eigen’s idea and Kauffman’s model of Reflexive autocatalytic sets of proteins.  Fontana’s idea of self-organization of higher order chemical organizations in a flow reactor, modeled with Lambda Calculus.  Morowitz’ idea (and recently Dewer’s arguments for) a self-organizing force due to the existence of a steady state energy flux.

11. Reflexive Autocatalytic Sets  Each member has its formation catalyzed by one or more members of the set.

12. Kauffman Side-steps Side- Reactions 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) The system is ‘spreading’ if the problem of poisoning catalysis is not completely ignored as Kauffman did. Kauffman’s Universe Our Universe

13. Kauffman Ignores Precursor Depletion If there is depletion then… the precursors of the set must be re-cycled! In Kauffman’s universe there is constant excess of a vast diversity of precursors. In our universe, we need to assume more limited initial recycling capability. Kauffman’s Universe Our Universe

14. 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.  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.

15. 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 > 1 L1 organization present.  String > 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 Fontana’s reactor, and we reject that it would work in real chemistry since the same problem of side-reactions is ignored.  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 > 1 L1 organization present.  String > 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 Fontana’s reactor, and we reject that it would work in real chemistry since the same problem of side-reactions is ignored.

16. 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.  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.

17. 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.

18. 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.  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.

19. 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.  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.

20. 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.

21. 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 Bahinder’s work.  But no-one has demonstrated natural selection in populations of spontaneously formed phase separated individuals.  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 Bahinder’s work.  But no-one has demonstrated natural selection in populations of spontaneously formed phase separated individuals.

22. 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.  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.

23. 1 The artificial version for the lab. 1

24. (1) Basal Liposome Growth a a a a a a a a a a No chemical reactions Just phase separation

25. (2) Liposome Division a a a a a a a a a a a a a a a

26. (3) Chemical Avalanches? Pyrite

27. a b

28. b c + d a RARE (low flux) reaction

29. b c + d a c + e High flux reaction But now we must calculate the reactions of e and so on. ? C happens to be autocatalytically produced, it need not have been. This is the avalanche.

30. 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?  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?

31. 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.  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.

33. The Artificial Chemistry

34. Energy  Each species is assigned a free energy of formation, G f.  Any novel reaction must be spontaneous,  G = G products – G reactants < 0.  The equilibrium ratio of a reaction is given by K = e -  G/RT.  k b = 0.01 and k f = 0.01K  A species has an 80% chance of being lipophilic. If a product is lipophilic, the reaction is effectively irreversible.  Each species is assigned a free energy of formation, G f.  Any novel reaction must be spontaneous,  G = G products – G reactants < 0.  The equilibrium ratio of a reaction is given by K = e -  G/RT.  k b = 0.01 and k f = 0.01K  A species has an 80% chance of being lipophilic. If a product is lipophilic, the reaction is effectively irreversible.

35. Initial conditions  Food set. 100 mM: { aab, aaab, aabb, bbbb, aaaab, aaabb, aabbb, abbbb. }  G f = 1.0  Growth set. 0mM: : {abb (0.1), abbb (0.01), abbbb (1), abbbbb (2), abbbbbb (3), abbbbbbb (4), abbbbbbbb (5), abbbbbbbbb (5)}.  Food set. 100 mM: { aab, aaab, aabb, bbbb, aaaab, aaabb, aabbb, abbbb. }  G f = 1.0  Growth set. 0mM: : {abb (0.1), abbb (0.01), abbbb (1), abbbbb (2), abbbbbb (3), abbbbbbb (4), abbbbbbbb (5), abbbbbbbbb (5)}.

38. Definition of Fitness

39. Results.

46. Energy dissipation increases

47. Avalanche properties change over the course of evolution. As molecule size increases the chance of an autocatalytic product from an avalanche Decreases.

48. Mean Avalanche Properties

49. Conclusions 1.Liposome level selection maintains molecular replicators arising in chemical avalanches. 2.Autocatalytic constituents are more likely to be short molecules with few atom types (given random rearrangement reactions). 3.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. 4.Lipophobic side products drive irreversible reactions, whilst lipophilic non-reactive products prevent continued drainage. 1.Liposome level selection maintains molecular replicators arising in chemical avalanches. 2.Autocatalytic constituents are more likely to be short molecules with few atom types (given random rearrangement reactions). 3.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. 4.Lipophobic side products drive irreversible reactions, whilst lipophilic non-reactive products prevent continued drainage.

50. Conclusions 5.A more diverse food set promotes more complex autocatalytic cycles, 1,2, & 3 member cycles observed. 6.Energy flux increases over evolutionary time for two reasons; energy demands of memory, energy demands of growth. 7.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. 5.A more diverse food set promotes more complex autocatalytic cycles, 1,2, & 3 member cycles observed. 6.Energy flux increases over evolutionary time for two reasons; energy demands of memory, energy demands of growth. 7.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.

51. Acknowledgements  Jon Rowe  Eors Szathmary  Hywel Williams  Kepa Ruiz-Mirazo  Fabio Mavelli  Alvero Moreno  Xabier Barandieran  Jon Rowe  Eors Szathmary  Hywel Williams  Kepa Ruiz-Mirazo  Fabio Mavelli  Alvero Moreno  Xabier Barandieran