Evolution of Autocatalytic Sets in Computational Models of Chemical Reaction Networks

Theoretical Modeling

Abstract

Several computational models of chemical reaction networks have been presented in the literature in the past, showing the appearance and (potential) evolution of autocatalytic sets. However, the notion of autocatalytic sets has been defined differently in different modeling contexts, each one having some shortcoming or limitation. Here, we review four such models and definitions, and then formally describe and analyze them in the context of a mathematical framework for studying autocatalytic sets known as RAF theory. The main results are that: (1) RAF theory can capture the various previous definitions of autocatalytic sets and is therefore more complete and general, (2) the formal framework can be used to efficiently detect and analyze autocatalytic sets in all of these different computational models, (3) autocatalytic (RAF) sets are indeed likely to appear and evolve in such models, and (4) this could have important implications for a possible metabolism-first scenario for the origin of life.

Keywords

Chemical reaction networks Autocatalytic sets Evolution RAF theory Origin of life 

References

  1. Ashkenasy G, Jegasia R, Yadav M, Ghadiri MR (2004) Design of a directed molecular network. PNAS 101(30):10872–10877PubMedCentralCrossRefPubMedGoogle Scholar
  2. Eigen M, Schuster P (1979) The Hypercycle. Springer-VerlagGoogle Scholar
  3. Farmer JD, Kauffman SA, Packard NH (1986) Autocatalytic replication of polymers. Phys. D 22:50–67CrossRefGoogle Scholar
  4. Gillespie DT (1976) A general method for numerically simulating the stochastic time evolution of coupled chemical reactions. J Comput. Phys. 22:403–434CrossRefGoogle Scholar
  5. Gillespie DT (1977) Exact stochastic simulation of coupled chemical reactions. J. Phys. Chem. 81(25):2340–2361CrossRefGoogle Scholar
  6. Goldberg DE (1989) Genetic Algorithms in Search, Optimization, and Machine Learning. Addison-WesleyGoogle Scholar
  7. Hordijk W (2013) Autocatalytic sets: From the origin of life to the economy. BioScience 63(11):877–881CrossRefGoogle Scholar
  8. Hordijk W, Fontanari JF (2003) Catalytic reaction sets, decay, and the preservation of information. In: KIMAS’03 (IEEE International Conference on Integration of Knowledge Intensive Multi-Agent Systems), pp 133–138Google Scholar
  9. Hordijk W, Steel M (2004) Detecting autocatalytic, self-sustaining sets in chemical reaction systems. J. Theor. Biol. 227(4):451–461CrossRefPubMedGoogle Scholar
  10. Hordijk W, Steel M (2012) Predicting template-based catalysis rates in a simple catalytic reaction model. J. Theor. Biol. 295:132–138CrossRefPubMedGoogle Scholar
  11. Hordijk W, Steel M (2013) A formal model of autocatalytic sets emerging in an RNA replicator system. J. Syst. Chem. 4:3CrossRefGoogle Scholar
  12. Hordijk W, Steel M (2014) Conditions for evolvability of autocatalytic sets: A formal example and analysis. Orig Life Evol Biospheres 44(2):111–124CrossRefGoogle Scholar
  13. Hordijk W, Kauffman SA, Steel M (2011) Required levels of catalysis for emergence of autocatalytic sets in models of chemical reaction systems. Int J Mol Sci 12(5):3085–3101PubMedCentralCrossRefPubMedGoogle Scholar
  14. Hordijk W, Steel M, Kauffman S (2012) The structure of autocatalytic sets: Evolvability, enablement, and emergence. Acta Biotheor 60(4):379–392CrossRefPubMedGoogle Scholar
  15. Hordijk W, Hasenclever L, Gao J, Mincheva D, Hein J (2014a) An investigation into irreducible autocatalytic sets and power law distributed catalysis. Nat Comput 13(3):287–296CrossRefGoogle Scholar
  16. Hordijk W, Wills PR, Steel M (2014b) Autocatalytic sets and biological specificity. Bull Math Biol 76(1):201–224CrossRefPubMedGoogle Scholar
  17. Hordijk W, Smith JI, Steel M (2015) Algorithms for detecting and analysing autocatalytic sets. Algorithm Mol Biol 10:15CrossRefGoogle Scholar
  18. Jain S, Krishna S (2001) A model for the emergence of cooperation, interdependence, and structure in evolving networks. PNAS 98(2):543–547PubMedCentralCrossRefPubMedGoogle Scholar
  19. Jain S, Krishna S (2002) Large extinctions in an evolutionary model: The role of innovation and keystone species. PNAS 99(4):2055–2060PubMedCentralCrossRefPubMedGoogle Scholar
  20. Kauffman SA (1971) Cellular homeostasis, epigenesis and replication in randomly aggregated macromolecular systems. J Cybern 1(1):71–96CrossRefGoogle Scholar
  21. Kauffman SA (1986) Autocatalytic sets of proteins. J Theor Biol 119:1–24CrossRefPubMedGoogle Scholar
  22. Kauffman SA (1993) The Origins of Order. Oxford University PressGoogle Scholar
  23. Lincoln TA, Joyce GE (2009) Self-sustained replication of an RNA enzyme. Science 323:1229–1232PubMedCentralCrossRefPubMedGoogle Scholar
  24. Mitchell M (1996) An Introduction to Genetic Algorithms. MIT PressGoogle Scholar
  25. Mossel E, Steel M (2005) Random biochemical networks: The probability of selfsustaining autocatalysis. J Theor Biol 233(3):327–336CrossRefPubMedGoogle Scholar
  26. Sievers D, Von Kiedrowski G (1994) Self-replication of complementary nucleotide-based oligomers. Nature 369:221–224CrossRefPubMedGoogle Scholar
  27. Smith J, Steel M, Hordijk W (2014) Autocatalytic sets in a partitioned biochemical network. J Syst Chem 5:2PubMedCentralCrossRefPubMedGoogle Scholar
  28. Sousa FL, Hordijk W, Steel M, Martin WF (2015) Autocatalytic sets in E. coli metabolism. J Syst Chem 6:4PubMedCentralCrossRefPubMedGoogle Scholar
  29. Steel M (2000) The emergence of a self-catalysing structure in abstract origin-of-life models. Appl Math Lett 3:91–95CrossRefGoogle Scholar
  30. Szathmáry E (2013) On the propagation of a conceptual error concerning hypercycles and cooperation. J Syst Chem 4:1CrossRefGoogle Scholar
  31. Vaidya N, Manapat ML, Chen IA, Xulvi-Brunet R, Hayden EJ, Lehman N (2012) Spontaneous network formation among cooperative RNA replicators. Nature 491:72–77CrossRefPubMedGoogle Scholar
  32. Van Santen RA, Neurock M (2006) Molecular Heterogeneous Catalysis. Wiley-VCHGoogle Scholar
  33. Vasas V, Fernando C, Santos M, Kauffman S, Sathmáry E (2012) Evolution before genes. Biol Direct 7:1PubMedCentralCrossRefPubMedGoogle Scholar
  34. Wills PR, Henderson L (2000) Self-organisation and information-carrying capacity of collectively autocatalytic sets of polymers: ligation systems. In: Bar-Yam Y (ed) Unifying Themes in Complex Systems: Proceedings of the First International Conference on Complex Systems, pages 613–623. Perseus BooksGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2015

Authors and Affiliations

  1. 1.SmartAnalytiX.comLausanneSwitzerland

Personalised recommendations