Abstract
Studying semantics is strongly connected to studying codes that link signs to meanings. Here we suggest a formal method to identify organic codes at a molecular level. We define a molecular organic code with respect to a given reaction network as a mapping between two sets of molecular species called signs and meanings, respectively, such that (a) this mapping can be realized by a third set of molecular species, the codemaker and (b) there exists alternative sets of molecular species, i.e., alternative codemakers, implying different mappings between the same two sets of signals and meanings. We discuss theoretical implications of our definition, demonstrate its application on two abstract examples, and show that it is compatible to Barbieri’s definition of organic codes. Our approach can be applied to differentiate the semantic capacity of molecular sub-systems found in the living world. We hypothesize that we find an increasing capacity when going from metabolism to protein networks to gene regulatory networks. Finally we hypothesize that during the chemical and Darwinian evolution of life the capacity for molecular organic codes increased by the discovery and incorporation of those reaction systems that contain many molecular organic codes.
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References
Küppers, B.O.: Information and the Origin of Life. MIT Press, Cambridge (1990)
Shannon, C.E.: A mathematical theory of communication. The Bell Systems Technical Journal 27, 379–423, 623–656 (1948) (reprinted with corrections)
Arndt, C.: Information Measures: Information and Its Description in Science and Engineering. Signals and Communication Technology, vol. 1. Springer, Berlin (2004)
Yockey, H.P.: Information Theory, Evolution, and the Origin of Life. Cambridge University Press, New York (2005)
Anderson, D.R.: Model Based Inference in the Life Sciences. Springer, Berlin (2008)
Barbieri, M. (ed.): Biosemiotics: Information, Codes and Signs in Living Systems. Nova Science Publisher, New York (2007)
Barbieri, M. (ed.): The Codes of Life: The Rules of Macroevolution, 1st edn. Biosemiotics, vol. 1. Springer, Netherlands (2008)
Favareau, D. (ed.): Essential Readings in Biosemiotics. Biosemiotics, vol. 3. Springer, Heidelberg (2009)
Barbieri, M.: The Organic Codes: An introduction to Semantic Biology. Cambridge University Press, Cambridge (2003)
Barbieri, M.: Biosemiotics: a new understanding of life. Naturwissenschaften 95(7), 577–599 (2008)
Faria, M.: Signal transduction codes and cell fate. In: Barbieri, M. (ed.) The Codes of Life: The Rules of Macroevolution, pp. 265–283. Springer, Dodrecht (2008)
Gabius, H., Andre, S., Kaltner, H., Siebert, H.: The sugar code: functional lectinomics. Biochimica et Biophysica Acta-General Subjects 1572(2-3), 165–177 (2002)
Turner, B.M.: Cellular memory and the histone code. Cell 111(3), 285–291 (2002)
Turner, B.M.: Defining an epigenetic code. Nat. Cell. Biol. 9(1), 2–6 (2007)
Fontana, W., Buss, L.W.: ’The arrival of the fittest’: Toward a theory of biological organization. Bull. Math. Biol. 56, 1–64 (1994)
Speroni di Fenizio, P., Dittrich, P., Ziegler, J., Banzhaf, W.: Towards a theory of organizations. In: German Workshop on Artificial Life (GWAL 2000), Bayreuth, April 5-7 (2000)
Szathmáry, E.: Coding coenzyme handles: a hypothesis for the origin of the genetic code. Proc. Natl. Acad. Sci. USA 90(21), 9916–9920 (1993)
Yarus, M., Caporaso, J.G., Knight, R.: Origins of the genetic code: the escaped triplet theory. Annu. Rev. Biochem. 74, 179–198 (2005)
Koonin, E.V., Novozhilov, A.S.: Origin and evolution of the genetic code: the universal enigma. IUBMB Life 61(2), 99–111 (2009)
Adami, C., Ofria, C., Collier, T.C.: Evolution of biological complexity. Proc. Nat. Acad. Sci. USA 97, 4463–4468 (2000)
Dittrich, P., Speroni di Fenizio, P.: Chemical organization theory. Bull. Math. Biol. 69(4), 1199–1231 (2007)
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Görlich, D., Dittrich, P. (2011). Identifying Molecular Organic Codes in Reaction Networks. In: Kampis, G., Karsai, I., Szathmáry, E. (eds) Advances in Artificial Life. Darwin Meets von Neumann. ECAL 2009. Lecture Notes in Computer Science(), vol 5777. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-21283-3_38
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DOI: https://doi.org/10.1007/978-3-642-21283-3_38
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