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Theory in Biosciences

, Volume 136, Issue 3–4, pp 153–167 | Cite as

Diversity and survival of artificial lifeforms under sedimentation and random motion

  • Nicolas GladeEmail author
  • Olivier Bastien
  • Pascal Ballet
Original Article

Abstract

Cellular automata are often used to explore the numerous possible scenarios of what could have occurred at the origins of life and before, during the prebiotic ages, when very simple molecules started to assemble and organise into larger catalytic or informative structures, or to simulate ecosystems. Artificial self-maintained spatial structures emerge in cellular automata and are often used to represent molecules or living organisms. They converge generally towards homogeneous stationary soups of still-life creatures. It is hard for an observer to believe they are similar to living systems, in particular because nothing is moving anymore within such simulated environments after few computation steps, because they present isotropic spatial organisation, because the diversity of self-maintained morphologies is poor, and because when stationary states are reached the creatures are immortal. Natural living systems, on the contrary, are composed of a high diversity of creatures in interaction having limited lifetimes and generally present a certain anisotropy of their spatial organisation, in particular frontiers and interfaces. In the present work, we propose that the presence of directional weak fields such as gravity may counter-balance the excess of mixing and disorder caused by Brownian motion and favour the appearance of specific regions, i.e. different strata or environmental layers, in which physical–chemical conditions favour the emergence and the survival of self-maintained spatial structures including living systems. We test this hypothesis by way of numerical simulations of a very simplified ecosystem model. We use the well-known Game of Life to which we add rules simulating both sedimentation forces and thermal agitation. We show that this leads to more active (vitality and biodiversity) and robust (survival) dynamics. This effectively suggests that coupling such physical processes to reactive systems allows the separation of environments into different milieux and could constitute a simple mechanism to form ecosystem frontiers or elementary interfaces that would protect and favour the development of fragile auto-poietic systems.

Keywords

Cellular automata Gravity Sedimentation Thermal noise Survival Biodiversity Interface Origins of life Prebiotic chemistry 

References

  1. Abbas L, Glade N, Demongeot J (2009) Synchrony in reaction-diffusion models of morphogenesis : applications to curvature-dependent proliferation and zero-diffusion front waves. Phil Trans Roy Soc Lond A 367:4829–4862CrossRefGoogle Scholar
  2. Adamatzky A (2017) Thirty seven things to do with live slime mould. In: Adamatzky A (ed) Advances in Unconventional Computing, vol 23. Springer International Publishing, pp 709–738Google Scholar
  3. Adami C (1995) On modelling life. Artif Life 367:4829–4862Google Scholar
  4. Adami C (1998) An introduction to artificial life. Springer-Verlag, New York IncCrossRefGoogle Scholar
  5. Barge LM, Cardoso SSS, Cartwright JHE, Cooper GJT, Cronin L, Wit AD, Doloboff IJ, Escribano B, Goldstein RE, Haudin F, Jones DEH, Mackay AL, Maselko J, Pagano JJ, Pantaleone J, Russell MJ, Sainz-Díaz CI, Steinbock O, Stone DA, Tanimoto Y, Thomas NL (2015) From chemical gardens to chemobrionics. Chem Rev 115(16):8652–8703CrossRefPubMedGoogle Scholar
  6. Bec L (2008) L’art est le vivant. La Découverte, ParisGoogle Scholar
  7. Bedau MA (1999) Can unrealistic computer models illuminate theoretical biology? In: Proceedings of the 1999 International Genetic and Evolutionary Computation Conference, GECCO 1999, pp 20–23Google Scholar
  8. Berlekamp ER, Conway JH, Guy RK (1982) Winning ways. Academic Press, New YorkGoogle Scholar
  9. Cairns-Smith AG (1990) Seven Clues to the Origin of Life: a scientific detective story. Cambridge University Press, CambridgeGoogle Scholar
  10. Castets V, Dulos E, Boissonade J, Kepper PD (1990) Experimental evidence of a sustained standing turing-type nonequilibrium chemical pattern. Phys Rev Lett 64:2953–2956CrossRefPubMedGoogle Scholar
  11. Čejková J, Novák M, Štěpánek F, Hanczyc MM (2014) Dynamics of chemotactic droplets in salt concentration gradients. Langmuir 30(40):11,937–11,944Google Scholar
  12. Cornish-Bowden A, Cárdenas ML (2008) Self-organization at the origin of life. J Theor Biol 252(3):411–418CrossRefPubMedGoogle Scholar
  13. Courbet A, Molina F, Amar P (2015) Computing with synthetic protocells. Acta Biotheor 63:309–323CrossRefPubMedGoogle Scholar
  14. Dowek G (2011) Proofs and algorithms: an introduction to logic and computability. Springer, BerlinCrossRefGoogle Scholar
  15. Feitelson DG (2006) Experimental computer science : the need for a cultural change. http://www.cs.huji.ac.il/~feit/papers/exp05.pdf
  16. Gardner M (1970) Mathematical games. The fantastic combinations of john conway’s new solitaire game “life”. Sci Am 223:120–123CrossRefGoogle Scholar
  17. Gonzàlez AE (2006) Stratification of colloidal aggregation coupled to sedimentation. Phys Rev E 74(061):403Google Scholar
  18. Grassé PP (1959) La reconstruction du nid et les coordinations inter-individuelles chez bellicositermes natalensis et cubitermes sp. la théorie de la stigmergie : Essai d’interprétation du comportement des termites constructeurs. Ins Soc 6:41–80CrossRefGoogle Scholar
  19. Ho MW, Ulanowicz R (2005) Sustainable systems as organisms? Biosystems 82:39–51CrossRefPubMedGoogle Scholar
  20. Hunding A, Képès F, Lancet D, Minsky A, Norris V, Raine D, Sriram K, Root-Bernstein R (2006) Compositional complementarily and prebiotic ecology in the origin of life. Bioessays 28:399–412CrossRefPubMedGoogle Scholar
  21. Janson AL (2007) Evolution de la biodiversité benthique des vasières subditales de l’estuaire de la seine en réponse à la dynamique sédimentaire. de l’approche descriptive à l’approche fonctionnelle. PhD thesis, Université de RouenGoogle Scholar
  22. Johnson AP, Cleaves HJ, Dworkin JP, Glavin DP, Lazcano A, Bada JL (2008) The miller volcanic spark discharge experiment. Science 322:404CrossRefPubMedGoogle Scholar
  23. Kagan JL, Peleg S, Meisels E, Avnir D (1983) Spatial structures induced by chemical reactions at interfaces: survey of some possible models and computerized pattern analysis. In: Jäger W, Murray JD (eds) Lecture Notes in Biomathematics. Proceedings of the Workshop Modelling of Patterns in Space and Time, Heidelberg, Springer Verlag, Berlin, Heidelberg, New York, Tokyo, pp 146–156Google Scholar
  24. Kaplan EL, Meier P (1958) Nonparametric estimation from incomplete observations. J Am Statist Assn 53:457–481CrossRefGoogle Scholar
  25. Kauffman S (1986) Autocatalytic sets of proteins. J Theor Biol 119:1–24CrossRefPubMedGoogle Scholar
  26. Langton CG (1984) Self-reproduction in cellular automata. Phys D 10:135–144CrossRefGoogle Scholar
  27. Langton CG (1986) Studying artificial life with cellular automata. Phys D 22:120–149CrossRefGoogle Scholar
  28. Leduc S (1911) The mechanism of life. W. Heinemann, LondonGoogle Scholar
  29. MacLennan BJ (2014) Molecular coordination of hierarchical self-assembly. Nano Commun Netw J 3:116–128CrossRefGoogle Scholar
  30. MacLennan BJ (2015) The morphogenetic path to programmable matter. Proc IEEE 103:1226–1232CrossRefGoogle Scholar
  31. Mange D, Stauffer A, Petraglio E, Tempesti E (2004) Artificial cell division. Biosystems 76:157–167CrossRefPubMedGoogle Scholar
  32. Margolis RL, Wilson L (1978) Opposite end assembly and disassembly of microtubules at steady state in vitro. Cell 13Google Scholar
  33. Martin E, Silver SA (2009) Game of life’s lexicon (update by e. martin). http://www.bitstorm.org/gameoflife/lexicon/
  34. Mason OU, Nakagawa T, Rosner M, Nostrand JDV, Zhou J, Maruyama A, Fisk MR, Giovannoni SJ (2010) First investigation of the microbiology of the deepest layer of ocean crust. PLOS One 5(e15):399Google Scholar
  35. Maturana H, Varela F (1988) The tree of knowledge. New Science Library, Shambhala, BostonGoogle Scholar
  36. Maturana H, Varela FJ (1974) Autopoiesis: the organization of living systems, its characterization and a model. Biosystems 5:187–196CrossRefGoogle Scholar
  37. Müller SC, Venzl G (1983) Pattern formation in precipitation processes. In: Jäger W, Murray JD (eds) Lecture Notes in Biomathematics, Proceedings of the Workshop Modelling of Patterns in Space and Time, Heidelberg. Springer Verlag, Berlin, Heidelberg, New York, Tokyo, pp 254–278Google Scholar
  38. Norris V, Hunding A, Képès F, Lancet D, Minsky A, Raine D, Root-Bernstein R, Sriram K (2007) Question 7: the first units of life were not simple cells. Orig Life Evol Biosph 37:429–443CrossRefPubMedGoogle Scholar
  39. Pattee HH (2015) Cell phenomenology: the first phenomenon. Prog Biophys Mol Biol 1–8Google Scholar
  40. Ray TS (1994) Evolution, complexity, entropy and artificial reality. Phys D 75:239–263CrossRefGoogle Scholar
  41. Rennard JP (2002) Vie artificielle. Où la vie rencontre l’informatique. Vuibert Informatique, Paris (in french)Google Scholar
  42. Rennard JP (2004) Perspectives for strong artificial life. In: Castro LD, von Zuben F (ed) Recent developments in biologically inspired computing, IGP, pp 301–318Google Scholar
  43. Rennard JP (2008) Golem numérique, vie et vie artificielle. hal-00416207 pp 1–13 (in french)Google Scholar
  44. Ricotta C (2007) A semantic taxonomy for diversity measures. Acta Biotheor 55(1):23–33CrossRefPubMedGoogle Scholar
  45. Ronald EMA, Sipper M, Capcarrère MS (1999) Testing for emergence in artificial life. In: Proceedings of the 5th European Conference on Advances in Artificial Life. Springer-Verlag, London, UK, ECAL ’99, pp 13–20Google Scholar
  46. Rothemund PWK, Ekani-Nkodo A, Papadakis N, Kumar A, Fygenson DK, Winfree E (2004) Design and characterization of programmable DNA nanotubes. J Am Chem Soc 126(50):16,344–16,352Google Scholar
  47. Ruff SW, Farmer JD (2016) Silica deposits on mars with features resembling hot spring biosignatures at el tatio in chile. Nat Comm 7(13554)Google Scholar
  48. Sayer RMP (2007) Self-organizing proto-replicators and the origin of life. Biosystems 90:121–138CrossRefPubMedGoogle Scholar
  49. Sims K (1994a) Evolving 3d morphology and behavior by competition. In: Brooks M (eds) Artificial Life IV Proceedings. MIT Press, pp 28–39Google Scholar
  50. Sims K (1994b) Evolving virtual creatures. In: Computer Graphics, Siggraph 94 Proceedings, pp 15–22Google Scholar
  51. Smith CR, Baco AR (2003) Ecology of whale falls at the deep-sea floor. Oceanogr Mar Biol Ann Rev 41:311–354Google Scholar
  52. Turing AM (1952) On the chemical basis of morphogenesis. Phil Trans Roy Soc Lond B 237:37–72CrossRefGoogle Scholar
  53. Ulanowicz RE (2001) Information theory in ecology. Comput Chem 25:393–399CrossRefPubMedGoogle Scholar
  54. Vanag VK, Epstein IR (2003) Segmented spiral waves in a reaction-diffusion system. Proc Natl Acad Sci USA 100(25):14,635–14,638Google Scholar
  55. Varela FJ (1989) Autonomie et connaissance: Essai sur le vivant. Seuil, ParisGoogle Scholar
  56. Varenne F, Chaigneau P, Petitot J, Doursat R (2015) Programming the emergence in morphogenetically architected complex systems. Acta Biotheor 63:295–308CrossRefPubMedGoogle Scholar
  57. Varetto L (1993) Typogenetics: an artificial genetic system. J Theor Biol 160:182–205CrossRefGoogle Scholar
  58. Varetto L (1998) Studying artificial life with a cellular automaton. J Theor Biol 193:257–285CrossRefPubMedGoogle Scholar
  59. Vavilin VA, Zhabotinsky AM, Krupyanko VI (1967a) Dependence of the behaviour of an oscillating chemical reaction on the concentration of the initial reagents ii. oxidation of bromomalonic acid. In: Frank GM (ed) Oscillating processes in biological and chemical systems, Science Publ., MoscowGoogle Scholar
  60. Vavilin VA, Zhabotinsky AM, Yaguzhinsky LS (1967b) Dependence of the behaviour of an oscillating chemical reaction on the concentration of the initial reagents i. oxidation of malonic acid. In: Frank GM (ed) Oscillating processes in biological and chemical systems, Science Publ., MoscowGoogle Scholar
  61. Wentworth TD (1942) On growth and form. Cambridge at the University Press, CambridgeGoogle Scholar
  62. Whitfield J (2009) Origin of life: Nascence man. Nature 459:316–319CrossRefPubMedGoogle Scholar
  63. Zak JC, Willig MR, Moorhead DL, Wildman HG (1994) Functional diversity of microbial communities: a quantitative approach. Soil Biol Biochem 26:1101–1108CrossRefGoogle Scholar
  64. Zeng W, Thomas GL, Glazier JA (2004) Non-turing stripes and spots: a novel mechanism for biological cell clustering. Phys A 341:482–494CrossRefGoogle Scholar
  65. Zhabotinskii AM (1974) Kontsentratsionnye Avtokolebaniya [Russian] (Concentration Self-Oscillations). Nauka, MoscowGoogle Scholar
  66. Zhabotinsky AM, Zaikin AN (1973) Autowave processes in a distributed chemical system. J Theor Biol 40:45–61CrossRefPubMedGoogle Scholar

Copyright information

© Springer-Verlag GmbH Germany 2017

Authors and Affiliations

  1. 1.TIMC-IMAG LaboratoryUniversité Grenoble Alpes - CNRS UMR 5525La TroncheFrance
  2. 2.Cell and Plant Physiology Laboratory (LPCV)CNRS UMR 5168 - CEA - Université Grenoble Alpes, Institut de Recherche en Sciences et Technologies pour le Vivant, Commissariat à l′Energie Atomique GrenobleGrenoble Cedex 9France
  3. 3.LaTIM, INSERM UMR 1101 - Université de Bretagne OccidentaleBrest CedexFrance

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