Identifying molecular organic codes in reaction networks

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. © 2011 Springer-Verlag.