Acta Biotheoretica

, Volume 61, Issue 2, pp 203–222 | Cite as

Living is Information Processing: From Molecules to Global Systems

  • Keith D. Farnsworth
  • John Nelson
  • Carlos Gershenson
Regular Article


We extend the concept that life is an informational phenomenon, at every level of organisation, from molecules to the global ecological system. According to this thesis: (a) living is information processing, in which memory is maintained by both molecular states and ecological states as well as the more obvious nucleic acid coding; (b) this information processing has one overall function—to perpetuate itself; and (c) the processing method is filtration (cognition) of, and synthesis of, information at lower levels to appear at higher levels in complex systems (emergence). We show how information patterns, are united by the creation of mutual context, generating persistent consequences, to result in ‘functional information’. This constructive process forms arbitrarily large complexes of information, the combined effects of which include the functions of life. Molecules and simple organisms have already been measured in terms of functional information content; we show how quantification may be extended to each level of organisation up to the ecological. In terms of a computer analogy, life is both the data and the program and its biochemical structure is the way the information is embodied. This idea supports the seamless integration of life at all scales with the physical universe. The innovation reported here is essentially to integrate these ideas, basing information on the ‘general definition’ of information, rather than simply the statistics of information, thereby explaining how functional information operates throughout life.


Complex system Entropy Biocomplexity Evolution Network 



This work was enhanced by very thoughtful and creative reviews by anonymous referees. It was supported by a Science Technology Research and Innovation for the Environment grant from the Environmental Protection Agency of the Republic of Ireland: 2007-PhD-SD-3. C.G. was partially supported by SNI membership 47907 of CONACyT, Mexico.


  1. Adami C, Ofria C, Collier TC (2000) Evolution of biological complexity. Proc Natl Acad Sci USA 97(9):4463–4468CrossRefGoogle Scholar
  2. Annila A, Annila E (2008) Why did life emerge. Int J Astrobiol 7(3–4):293–300CrossRefGoogle Scholar
  3. Annila A, Kuismanen E (2009) Natural hierarchy emerges from energy dispersal. Biosystems 95(3):227–233CrossRefGoogle Scholar
  4. Balleza E, Alvarez-Buylla ER, Chaos A, Kauffman S, Shmulevich I, Aldana M (2008) Critical dynamics in genetic regulatory networks: examples from four kingdoms. Plos One 3(6):e2456. doi: 10.1371/journal.pone.0002456
  5. Bates M (2005) Information and knowledge: an evolutionary framework for information science. Inf Res 10(4):paper 239. Accessed from Oct 2012
  6. Bateson G (1972) Form, substance, and difference. In: Bateson G (ed) Steps to an ecology of mind. University of Chicago Press, Chicago, pp 448–466Google Scholar
  7. Bitbol M, Luisi P (2004) Autopoiesis with or without cognition: defining life at its edge. J R Soc Interface 1(1):99–107CrossRefGoogle Scholar
  8. Bowen N, Jordan I (2002) Transposable elements and the evolution of eukaryotic complexity. Curr Issues Mol Biol 4:65–76Google Scholar
  9. Bray D (1995) Protein molecules as computational elements in living cells. Nature 376(6538):307–312CrossRefGoogle Scholar
  10. Bray D (2009) Wetware: a computer in every living cell. Yale University Press, New Haven, CTGoogle Scholar
  11. Butler MH, Paton RC, Leng PH (1998) Information processing in tissues and cells, chapter Information processing in computational tissues. Plenum Press, New York, pp 177–184CrossRefGoogle Scholar
  12. Cairns J, Overbaugh J, Miller S (1988) The origin of mutants. Nature 335:142–145CrossRefGoogle Scholar
  13. Camazine S, Deneubourg JL, Franks N, Sneyd J, Theraulaz G, Bonabeau E (2001) Self-organization in biological systems. Princeton University Press, Princeton, NJGoogle Scholar
  14. Carroll S (2001) Chance and necessity: the evolution of morphological complexity and diversity. Nature 409(6823):1102–1109CrossRefGoogle Scholar
  15. Chaitin G (1990) Information, randomness and incompleteness. Papers on algorithmic information theory, volume 8 of series in computer science, 2nd edn. World Scientific, SingaporeGoogle Scholar
  16. ConantR Ashby W (1970) Every good regulator of a system must be a model of that system. Int J Syst Sci 1(2):89–97CrossRefGoogle Scholar
  17. Cowling R, Knight A, Faith D, Ferrier S, Lombard A, Driver A, Rouget M, Maze K, Desmet P (2004) Nature conservation requires more than a passion for species. Conserv Biol 18(6):1674–1676CrossRefGoogle Scholar
  18. Cummins R (1975) Functional analysis. J Philos 72(20):741–765CrossRefGoogle Scholar
  19. Curtis T, Sloan W, Scannell J (2002) Estimating prokaryotic diversity and its limits. Proc Natl Acad Sci USA 99(16):10494–10499CrossRefGoogle Scholar
  20. Davidson EH (2001) Genomic regulatory systems: development and evolution. Academic Press, San Diego, USAGoogle Scholar
  21. Davidson EH, Levin M (2005) Gene regulatory networks. Proc Nat Acad Sci USA 102(14):4935CrossRefGoogle Scholar
  22. Denning PJ (2007) Computing is a natural science. Commun ACM 50(7):13–18CrossRefGoogle Scholar
  23. Dunne J, Williams R, Martinez N (2002) Food-web structure and network theory: the role of connectance and size. Proc Natl Acad Sci USA 99(20):12917–12922CrossRefGoogle Scholar
  24. Faeder JR (2011) Toward a comprehensive language for biological systems. BMC Biol 9:68CrossRefGoogle Scholar
  25. Farnsworth K, Lyashevska O, Fung T (2012) Functional complexity: the source of value in biodiversity. Ecol Complex 11:46–52CrossRefGoogle Scholar
  26. Favareau, D (eds) (2009) Essential readings in biosemiotics: anthology and commentary. Springer, BerlinGoogle Scholar
  27. Floridi L (2003) Information. In: Floridi L (ed) The Blackwell guide to the philosophy of computing and information. Blackwell Publishing Ltd, New York, pp 40–61CrossRefGoogle Scholar
  28. Floridi L (2005) Is semantic information meaningful data? Philos Phenomenol Res 70(2):351–370CrossRefGoogle Scholar
  29. Galtin LL (1972) Information theory and the living system. Columbia University Press, New YorkGoogle Scholar
  30. Geard N, Wiles J (2005) A gene network model for developing cell lineages. Artif Life 11:249–267CrossRefGoogle Scholar
  31. Gell-Mann M, Lloyd S (1996) Information measures, effective complexity, and total information. Complexity 2(1):44–52CrossRefGoogle Scholar
  32. Gell-Mann M, Lloyd S (2003) Effective complexity. In: Gell-Mann M, Tsallis C (eds) Nonextensive entropy—interdisciplinary applications. Oxford University Press, OxfordGoogle Scholar
  33. Gershenson C (2010) Computing networks: a general framework to contrast neural and swarm cognitions. Paladyn J Behav Robot 1(2):147–153CrossRefGoogle Scholar
  34. Gershenson C, Fernández N (2012) Complexity and information: Measuring emergence, self-organization, and homeostasis at multiple scales. Complexity, Early ViewGoogle Scholar
  35. Goldman R, Pollack R, Hopkins N (1973) Preservation of normal behavior by enucleated cells in culture. Proc Nat Acad Sci USA 70:750–754CrossRefGoogle Scholar
  36. Gregory T (2001) Coincidence, coevolution, or causation? DNA content, cell size, and the C-value enigma. Biol Rev 76(1):65–101CrossRefGoogle Scholar
  37. Griffiths PE (1993) Functional analysis and proper functions. British J Philos Sci 44:409–422CrossRefGoogle Scholar
  38. Hinegardner R, Engelberg J (1983) Biological complexity. J Theor Biol 104:7–20CrossRefGoogle Scholar
  39. Hopfield JJ (1994) Physics, computation, and why biology looks so different. J Theor Biol 171:53–60CrossRefGoogle Scholar
  40. Jiang Y, Xu C (2010) The calculation of information and organismal complexity. Biol Direct 5:59CrossRefGoogle Scholar
  41. Kaila VRI, Annila A (2008) Natural selection for least action. Proc R Soc A Math Phys Eng Sci 464(2099):3055–3070CrossRefGoogle Scholar
  42. Karnani M, Annila A (2009) Gaia again. Biosystems 95(1):82–87CrossRefGoogle Scholar
  43. Kauffman SA (1993) Origins of order: self-organization and selection in evolution. Oxford University Press, OxfordGoogle Scholar
  44. Kohl P, Crampin EJ, Quinn TA, Noble D (2010) Systems biology: an approach. Clin Pharmacol Ther 88(1):25–33CrossRefGoogle Scholar
  45. Kornberg A (1991) Understanding life as chemistry. Clin Chem 37(11):1895–1899Google Scholar
  46. Kravchenko-Balasha N, Levitzki A, Goldstein A, Rotter V, Gross A, Remacle F, Levine RD (2012) On a fundamental structure of gene networks in living cells. Proc Natl Acad Sci USA 109(12):4702–4707CrossRefGoogle Scholar
  47. Lee K (2004) There is biodiversity and biodiversity. In: Oksanen M, Pietarinen J (eds) Philosophy and biodiversity. Cambridge University Press, Cambridge, pp 152–171CrossRefGoogle Scholar
  48. Lehn J-M (1990) Perspectives in supramolecular chemistry—from molecular recognition towards molecular information processing and self-organization. Angewandte Chem Int Edition English 29(11):1304–1319CrossRefGoogle Scholar
  49. Lepot K, Benzerara K, Brown G, Philippot P (2008) Microbially influenced formation of 2,724-million-year-old stromatolites. Nat Geosci 1:118–121Google Scholar
  50. Li M, Vitányi PMB (2008) An introduction to Kolmogorov complexity and its applications, 3rd edn. Springer, BerlinGoogle Scholar
  51. Lorenz DM, Jeng A, Deem MW (2011) The emergence of modularity in biological systems. Phys Life Rev 8(2):129–160Google Scholar
  52. Lovelock JE, Margulis L (1974) Atmospheric homeostasis by and for the biosphere: the Gaia hypothesis. Tellus 26(1):2–10Google Scholar
  53. Lyashevska O, Farnsworth KD (2012) How many dimensions of biodiversity do we need. Ecol Ind 18:485–492CrossRefGoogle Scholar
  54. MacKay DM (1969) Information, mechanism and meaning. MIT Press, Cambridge, MAGoogle Scholar
  55. Magurran A (2004) Measuring biological diversity. Blackwell Publishing, New YorkGoogle Scholar
  56. Margulis L (1970) Origin of eukaryotic cells. Yale University Press, New Haven, CTGoogle Scholar
  57. Maturana H, Varela FJ (1980) Autopoiesis and cognition: the realization of the living. D. Reidel Publishing Company, Dordrecht (Translation of original: De Maquinas y seres vivos. Universitaria Santiago)Google Scholar
  58. Maus C, Rybacki S, Uhrmacher AM (2011) Rule-based multi-level modeling of cell biological systems. BMC Syst Biol 5:166CrossRefGoogle Scholar
  59. McAllister J (2003) Effective complexity as a measure of information content. Philos Sci 70(2):302–307CrossRefGoogle Scholar
  60. McGill BJ (2011) Linking biodiversity patterns by autocorrelated random sampling. Am J Bot 98(3):481–502CrossRefGoogle Scholar
  61. Menconi G (2005) Sublinear growth of information in dna sequences. Bull Math Biol 67(4):737–759CrossRefGoogle Scholar
  62. Montoya J, Pimm SL, Solé RV (2006) Ecological networks and their fragility. Nature 442(7100):259–264CrossRefGoogle Scholar
  63. Mora C, Tittensor DP, Adl S, Simpson AGB, Worm B (2011) How many species are there on earth and in the ocean? PLoS Biol 9(8):e1001127. doi: 10.1371/journal.pbio.1001127
  64. Morowitz HJ (1992) Beginnings of cellular life. Yale University Press, New Haven, CTGoogle Scholar
  65. Neander K (1991) Functions as selected effects: a conceptual analysts defense. Philos Sci 58(2):168–184CrossRefGoogle Scholar
  66. Neander K (2011) Routledge encyclopedia of philosophy (Online). RoutledgeGoogle Scholar
  67. Nekola J, White P (1999) The distance decay of similarity in biogeography and ecology. J Biogeogr 26(4):867–878CrossRefGoogle Scholar
  68. Norton B, Ulanowicz R (1992) Scale and biodiversity policy—a hierarchical approach. Ambio 21(3):244–249Google Scholar
  69. Orchard S, Hermjakob H, Apweiler R (2005) Annotating the human proteome. Mol Cell Proteomics 4(4):435–40CrossRefGoogle Scholar
  70. Orgel L, Crick F (1980) Selfish DNA: the ultimate parasite. Nature 284:604–607CrossRefGoogle Scholar
  71. Prigogine I (1977) Self-organization in non-equilibrium systems. Wiley, New YorkGoogle Scholar
  72. Prigogine I, Stengers I (1984) Order out of chaos: man’s new dialogue with nature. Flamingo Collins Publishing Group, LondonGoogle Scholar
  73. Robertson M, Joyce G (2010) The origins of the rna world. Cold Spring Harbour Perspectives In BiologyGoogle Scholar
  74. Rodbell M (1995) Signal transduction: evolution of an idea. Biosci Rep 15:117–133CrossRefGoogle Scholar
  75. Salthe S (1985) Evolving hierarchical systems: their structure and representation. Columbia University Press, New York CityGoogle Scholar
  76. Schneider TD (2000) Evolution of biological information. Nucleic Acids Res 28:2794–2799Google Scholar
  77. Schrödinger E (1944) What is life? The physical aspects of the living cell. Accessed online Oct 2012
  78. Scott J, Carr W (1992) Subcellular localization of the type II cAMP-dependent protein kinase. Physiology 7:143–148Google Scholar
  79. Shannon C (1948) A mathematical theory of communication. Bell Syst Tech J 27(3,4):379–423, 623–656Google Scholar
  80. Smith E (2008) Thermodynamics of natural selection I: energy flow and the limits on organization. J Theor Biol 252(2):185–197CrossRefGoogle Scholar
  81. Smith E, Morowitz HJ (2004) Universality in intermediary metabolism. Proc Nat Acad Sci USA 101(36):13168–13173CrossRefGoogle Scholar
  82. Szostak JW (2003) Functional information: molecular messages. Nature 423(6941):689–689CrossRefGoogle Scholar
  83. Tuomisto H (2010) A diversity of beta diversities: straightening up a concept gone awry. Part 1: defining beta diversity as a function of alpha and gamma diversity. Ecography 33(1):2–22CrossRefGoogle Scholar
  84. Turing A (1936) On computable numbers, with an application to the entscheidungs problem. Proc Lond Math Soc 42:230–265Google Scholar
  85. Turing A (1952) The chemical basis for morphogenesis. Philos Trans R Soc Lond Ser B Biol Sci 237:37–72CrossRefGoogle Scholar
  86. Ulanowicz R (1980) An hypothesis on the development of natural communitiesl. J Theor Biol 85:223–245CrossRefGoogle Scholar
  87. Ulanowicz R, Baird D (1999) Nutrient controls on ecosystem dynamics: the chesapeake mesohaline community. J Mar Syst 19:159–172CrossRefGoogle Scholar
  88. Valentine J (1994) Late precambrian bilaterians: grades and clades. Proc Natl Acad Sci USA 91(15):6751–6757CrossRefGoogle Scholar
  89. Valentine J (2003a) Architectures of biological complexity. Integr Comp Biol 43(1):99–103CrossRefGoogle Scholar
  90. Valentine J (2003b) Cell types, cell type numbers, and body plan complexity. In: Hall B, Olson W (eds) Keywords and concepts in evolutionary developmental biology. Harvard University Press, Cambridge, pp 35–43Google Scholar
  91. Valentine J, Collins A, Meyer C (1994) Morphological complexity increase in metazoans. Paleobiology 20(2):131–142Google Scholar
  92. Veitia RA, Bottani S (2009) Whole genome duplications and a ‘function’ for junk DNA? Facts and hypotheses. Plos ONE 4(12):e8201. doi: 10.1371/journal.pone.0008201
  93. von Foerster H (1960) On self-organizing systems and their environments. In: Yovits M, Cameron S (eds) Self-organizing systems.. Pergamon Press, OxfordGoogle Scholar
  94. Wessler SR (2006) Transposable elements and the evolution of eukaryotic genomes. Proc Natl Acad Sci USA 103(47):17600–17601CrossRefGoogle Scholar
  95. Wicken JS (1979) The generation of complexity in evolution: a thermodynamic and information-theoretical discussion. J Theor Biol 77:349–365CrossRefGoogle Scholar
  96. Wiener N (1948) Cybernetics; or, control and communication in the animal and the machine. Wiley and Sons, New YorkGoogle Scholar
  97. Yockey H, Platzman R, Quastler H (eds) (1958) Symposium on information theory in biology (1956: Gatlinburg, Tenn.). Pergamon Press, New YorkGoogle Scholar
  98. Zepik H, Blochliger E, Luisi P (2001) A chemical model of homeostasis. Angewandte Chemie Int Edition 40(1):199–202CrossRefGoogle Scholar
  99. Zhou J, Deng Y, Luo F, He Z, Tu Q, Zhi X (2010) Functional molecular ecological networks. MBio 1(4):e00169–10. doi: 10.1128/mBio.00169-10

Copyright information

© Springer Science+Business Media Dordrecht 2013

Authors and Affiliations

  • Keith D. Farnsworth
    • 1
  • John Nelson
    • 1
  • Carlos Gershenson
    • 2
  1. 1.School of Biological SciencesQueen’s University BelfastBelfastUK
  2. 2.Instituto de Investigaciones en Matemáticas Aplicadas y en SistemasUniversidad Nacional Autónoma de MéxicoMexico, DFMexico

Personalised recommendations