Origins of Life and Evolution of Biospheres

, Volume 35, Issue 2, pp 111–133 | Cite as

Polymer Gard: Computer Simulation of Covalent Bond Formation in Reproducing Molecular Assemblies

  • Barak Shenhav
  • Arren Bar-Even
  • Ran Kafri
  • Doron LancetEmail author


The basic Graded Autocatalysis Replication Domain (GARD) model consists of a repertoire of small molecules, typically amphiphiles, which join and leave a non-covalent micelle-like assembly. Its replication behavior is due to occasional fission, followed by a homeostatic growth process governed by the assembly’ s composition. Limitations of the basic GARD model are its small finite molecular repertoire and the lack of a clear path from a ‘monomer world’ towards polymer-based living entities.We have now devised an extension of the model (polymer GARD or P-GARD), where a monomer-based GARD serves as a ‘scaffold’ for oligomer formation, as a result of internal chemical rules. We tested this concept with computer simulations of a simple case of monovalent monomers, whereby more complex molecules (dimers) are formed internally, in a manner resembling biosynthetic metabolism. We have observed events of dimer ‘take-over’ – the formation of compositionally stable, replication-prone quasi stationary states (composomes) that have appreciable dimer content. The appearance of novel metabolism-like networks obeys a time-dependent power law, reminiscent of evolution under punctuated equilibrium. A simulation under constant population conditions shows the dynamics of takeover and extinction of different composomes, leading to the generation of different population distributions. The P-GARD model offers a scenario whereby biopolymer formation may be a result of rather than a prerequisite for early life-like processes.


biopolymers catalytic networks compositional information dimers lipid world mutual catalysis oligomers prebiotic evolution replication stationary states 


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  1. Acevedo, O. L. and Orgel, L. E.: 1986, Template-Directed Oligonucleotide Ligation on Hydroxylapatite, Nature 321, 790–792.CrossRefPubMedGoogle Scholar
  2. Alberts, B., Johnson, A., Lewis, J., Raff, M., Roberts, K. and Walter, P.: 2002, Molecular Biology of the Cell, Garland Pub.Google Scholar
  3. Anders, E.: 1989, Prebiotic Organic Matter from Comets and Asteroids, Nature 342, 255–257.CrossRefPubMedGoogle Scholar
  4. Bagley, R. J. and Farmer, D. J.: 1991, Spontaneous Emergence of a Metabolism, in Langton, C. G., Taylor, C., Farmer, J. D. and Rasmussen, S. (eds), Artificial Life II, Addison-Wesley, Redwood City, pp. 93–140.Google Scholar
  5. Bagley, R. J., Farmer, D. J. and Fontana, W.: 1991, Evolution of a Metabolism, in Langton, C. G., Taylor, C., Farmer, J. D. and Rasmussen, S. (eds), Artificial Life II, Addison-Wesley, Redwood City, pp. 141–158.Google Scholar
  6. Bak, P. and Sneppen, K.: 1993, Punctuated Equilibrium and Criticality in a Simple Model of Evolution, 71, 4083–4086.Google Scholar
  7. Basile, B., Lazcano, A. and Oro, J.: 1984, Prebiotic Syntheses of Purines and Pyrimidines, Adv. Space Res 4, 125–131.CrossRefPubMedGoogle Scholar
  8. Briggs, M. H. and Mamikunian, G.: 1964, Organic Constituents of Carbonaceous Chondrites, Life Sci. Space Res 2, 57–85.PubMedGoogle Scholar
  9. Bujdak, J. and Rode, B. M.: 1999, The Effect of Clay Structure on Peptide Bond Formation Catalysis, J. Mol. Catal. A-Chem. 144, 129–136.CrossRefGoogle Scholar
  10. Cooper, G., Kimmich, N., Belisle,W., Sarinana, J., Brabham, K. and Garrel, L.: 2001, Carbonaceous Meteorites as a Source of Sugar-related Organic Compounds for the Early Earth, Nature 414, 879–883.CrossRefPubMedGoogle Scholar
  11. Deamer, D. W. and Pashley, R. M.: 1989, Amphiphilic Components of the Murchison Carbonaceous Chondrite: Surface Properties and Membrane Formation, Orig. Life Evol. Biosph. 19, 21–38.PubMedGoogle Scholar
  12. Dyson, F.: 1999, Origins of Life, Cambridge University Press, Cambridge.Google Scholar
  13. Eigen, M.: 1971, Selforganization of Matter and Evolution of Biological Macromolecules, Naturwissenschaften 58, 465–&.Google Scholar
  14. Eigen, M., McCaskill, J. and Schuster, P.: 1988, Molecular Quasi-Species, J. Phys. Chem. 92, 6881–6891.CrossRefGoogle Scholar
  15. Ertem, G. and Ferris, J. P.: 1997, Template-directed Synthesis Using the Heterogeneous Templates Produced by Montmorillonite Catalysis. A Possible Bridge Between the Prebiotic and RNA Worlds, J. Am. Chem. Soc. 119, 7197–7201.CrossRefPubMedGoogle Scholar
  16. Eschenmoser, A.: 1999, Chemical Etiology of Nucleic Acid Structure, Science 284, 2118–2124.CrossRefPubMedGoogle Scholar
  17. Fendler, H. J. and Fendler, E. J.: 1975, Catalysis in Micellar and Macromolecular Systems, Academic Press, New York.Google Scholar
  18. Ferris, J. P., Edelson, E. H., Mount, N. M. and Sullivan, A. E.: 1979, The Effect of Clays on the Oligomerization of HCN, J. Mol. Evol. 13, 317–330.CrossRefPubMedGoogle Scholar
  19. Ferris, J. P. and Ertem, G.: 1993, Montmorillonite Catalysis of RNA Oligomer Formation in Aqueous Solution. A Model for the Prebiotic Formation of RNA, J. Am. Chem. Soc. 115, 12270–12275.CrossRefPubMedGoogle Scholar
  20. Gomperts, B., Kramer, I. M., Tatham, P. E. R. and Gomperts, B. D.: 2002, Signal Transduction, Academic Press.Google Scholar
  21. Jain, S. and Krishna, S.: 2001, A Model for the Emergence of Cooperation, Interdependence, and Structure in Evolving Networks, Proc. Natl. Acad. Sci. USA 98, 543–547.CrossRefPubMedGoogle Scholar
  22. Jain, S. and Krishna, S.: 2002, Large Extinctions in an Evolutionary Model: The Role of Innovation and Keystone Species, Proc. Natl. Acad. Sci. USA 99, 2055–2060.CrossRefPubMedMathSciNetGoogle Scholar
  23. Kaneko, K.: 2002, Kinetic Origin of Heredity in a Replicating System with a Catalytic Network, J. Biol. Phys. 28, 781–792.CrossRefGoogle Scholar
  24. Kauffman, S.: 1993, The Origin of Order, Oxford University Press.Google Scholar
  25. Kochavi, E., Bar-Nun, A. and Fleminger, G.: 1997, Substrate-directed Formation of Small Biocatalysts Under Prebiotic Conditions, J. Molecular Evol. 45, 342–351.Google Scholar
  26. Lancet, D., Sadovsky, E. and Seidemann, E.: 1993, Probability Model for Molecular Recognition in Biological Receptor Repertoires: Significance to the Olfactory System, Proc. Natl. Acad. Sci. USA 90, 3715–3719.PubMedGoogle Scholar
  27. Lawless, J. G.: 1980, Organic Compounds in Meteorites, Life Sci. Space Res 18, 19–27.PubMedGoogle Scholar
  28. Lazcano, A. and Miller, S. L.: 1999, On the Origin of Metabolic Pathways, J. Mol. Evol. 49, 424–431.PubMedGoogle Scholar
  29. Lodish, H., Berk, A., Zipursky, S. L., Matsudaira, P., Baltimore, D., Darnell, J. and Zipursky, L.: 1999, Molecular Cell Biology, W.H. Freeman & Co.Google Scholar
  30. Maden, B. E.: 1995, No Soup for Starters? Autotrophy and the Origins of Metabolism, TIBS 20, 337–341.PubMedGoogle Scholar
  31. Maurette, M.: 1998, Carbonaceous Micrometeorites and the Origin of Life, Orig. Life Evol. Biosph. 28, 385–412.CrossRefGoogle Scholar
  32. Miller, S. L.: 1953, A Production of Amino Acids Under Possible Earth Conditions, Science 117, 528–529.PubMedGoogle Scholar
  33. Miller, S. L.: 1986, Current Status of the Prebiotic Synthesis of Small Molecules, Chem. Scr. 26B, 5–11.PubMedGoogle Scholar
  34. Mitsuzawa, S. and Watanabe, S.-I.: 2001, Continuous Growth of Autocatalytic Sets, Biosystems 59, 61–69.CrossRefPubMedGoogle Scholar
  35. Morowitz, H. J.: 1967, Biological Self-replicating Systems, in Snell, F. M. (ed), Progress in Theoretical Biology, Academic Press, pp. 35–58.Google Scholar
  36. Morowitz, H. J., Heinz, B. and Deamer, D. W.: 1988, The Chemical Logic of a Minimum Protocell, Orig. Life Evol. B 18, 281–287.Google Scholar
  37. Morowitz, H. Z.: 2002, The Emergence of Everything, Oxford University Press, New York.Google Scholar
  38. Oparin, A. I.: 1953, The Origin of Life, Dover Pub., N.Y.Google Scholar
  39. Oparin, A. I.: 1957, The Origin of Life on the Earth, Oliver and Boyd, London.Google Scholar
  40. Oró, J., Mills, T. and Lazcano, A.: 1992, The Cometary Contribution to Prebiotic Chemistry, Adv. Space Res 12, 33–41.CrossRefGoogle Scholar
  41. Ourisson, G. and Nakatani, Y.: 1994, The Terpenoid Theory of the Origin of Cellular Life: The Evolution of Terpenoids to Choloesterol, Chem. Biol. 1, 11–23.CrossRefPubMedGoogle Scholar
  42. Root-Bernstein, R. S. and Dillon, P. F: 1997, Molecular Complementarity 1. The Complementarity Theory of the Origin and Evolution of Life, J. Theor. Biol. 188, 447–479.CrossRefPubMedGoogle Scholar
  43. Rosenwald, S., Kafri, R. and Lancet, D.: 2002, Test of a Statistical Model for Molecular Recognition in Biological Repertoires, J. Theor. Biol. 216, 327–336.CrossRefPubMedGoogle Scholar
  44. Segré, D., Ben-Eli, D., Deamer, D. W. and Lancet, D.: 2001a, The Lipid World, Orig. Life Evol. B 31, 119–145.CrossRefGoogle Scholar
  45. Segré, D., Ben-Eli, D. and Lancet, D.: 2000, Compositional Genomes: Prebiotic Information Transfer in Mutually Catalytic Noncovalent Assemblies, Proc. Natl. Acad. Sci. USA 97, 4112–4117.CrossRefPubMedGoogle Scholar
  46. Segré, D. and Lancet, D.: 1999, A Statistical Chemistry Approach to the Origin of Life, Chemtracts – Biochem. Molec. Biol 12, 382–397.Google Scholar
  47. Segré, D. and Lancet, D.: 2000, Composing Life, Embo Rep. 1, 217–222.CrossRefPubMedGoogle Scholar
  48. Segré, D., Lancet, D., Kedem, O. and Pilpel, Y.: 1998a, Graded Autocatalysis Replication Domain (GARD): Kinetic Analysis of Self-replication in Mutually Catalytic Sets, Orig. Life Evol. B 28, 501–514.CrossRefGoogle Scholar
  49. Segré, D., Pilpel, Y. and Lancet, D.: 1998b, Mutual Catalysis in Sets of Prebiotic Organic Molecules: Evolution Through Computer Simulated Chemical Kinetics, Physica A: Slat. Theor. Phys. 249, 558–564.CrossRefGoogle Scholar
  50. Segré, D., Shenhav, B., Kafri, R. and Lancet, D.: 2001b, The Molecular Roots of Compositional Inheritance, J. Theor. Biol. 213, 481–491.CrossRefGoogle Scholar
  51. Sephton, M. A.: 2002, Organic Compounds in Carbonaceous Meteorites, Nat. Prod. Rep. 19, 292–311.CrossRefPubMedGoogle Scholar
  52. Shapiro, R.: 1986, Origins: A Skeptic’s Guide to the Creation of Life on Earth, Simon & Schuster, Inc., N.Y.Google Scholar
  53. Shenhav, B., Segre, D. and Lancet, D.: 2003, Mesobiotic Emergence: Molecular Assemblies that Self-replicate Without Biopolymers, Adv. Complex Sys.Google Scholar
  54. Stadler, P. F., Fontana,W. and Miller, J. H.: 1993, Random Catalytic Reaction Networks, 63, 378–392.Google Scholar
  55. Stryer, L.: 1995, Biochemistry, W.H. Freeman & Co.Google Scholar
  56. Suwannachot, Y. and Rode, B. M.: 1998, Catalysis of Dialanine Formation by Glycine in the Saltinduced Peptide Formation Reaction, Orig. Life Evol. Biosph. 28, 79–90.CrossRefPubMedGoogle Scholar
  57. Szathmáry, E.: 2000, The Evolution of Replicators, Philos. Trans. R. Soc. Lond. B Biol. Sci. 355, 1669–1676.CrossRefPubMedGoogle Scholar
  58. Wächtersh user, G.: 1988, Before Enzymes and Templates: Theory of Surface Metabolism, Microbiol. Rev., 452–484.Google Scholar
  59. Wills, C. and Bada, J.: 2001, The Spark of Life: Darwin and the Primeval Soup, Perseus Publishing.Google Scholar

Copyright information

© Springer Science + Business Media, Inc. 2005

Authors and Affiliations

  • Barak Shenhav
    • 1
  • Arren Bar-Even
    • 1
  • Ran Kafri
    • 1
  • Doron Lancet
    • 1
    Email author
  1. 1.Department of Molecular Genetics and the Crown Human Genome Centerthe Weizmann Institute of ScienceRehovotIsrael

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