Genetic channel capacity revisited

Bionetics 2011, 6th International ICST Conference on Bio-Inspired Models of Network, Information, and Computing Systems, 5-6 December 2011, York, EnglandWe revisit previous analyses on the computation of the maximum mutual information between a genetic sequence and its mutated versions down the generations, taking into account the protein translation mechanism of the genetic machinery. This amounts to the application of Shannon's capacity to the study of the transmission of genetic information. Studies on this subject were started by Yockey and then followed by a number of researchers. Here we refine prior analyses employing the Kimura model of base substitution mutations, which is more realistic than the Jukes-Cantor model used by all previous research on this topic. Furthermore we undertake exact computations where prior works just used approximations, and we propose two practical applications of genetic capacity.Science Foundation IrelandConference detailshttp://www.bionetics.org/Check if published then EMBARGO for 12 months - OR 16/12/11 12M embargo - NYP, should appear in LNICST http://icst.org/lnicst-guidelines-for-authors/ - AV 15/11/2011 ti - kpw2/12/1

Composing life

Textbooks often assert that life began with specialized complex molecules, such as RNA, that are capable of making their own copies. This scenario has serious difficulties, but an alternative has remained elusive. Recent research and computer simulations have suggested that the first steps toward life may not have involved biopolymers. Rather, non-covalent protocellular assemblies, generated by catalyzed recruitment of diverse amphiphilic and hydrophobic compounds, could have constituted the first systems capable of information storage, inheritance and selection. A complex chain of evolutionary events, yet to be deciphered, could then have led to the common ancestors of today’s free-living cells, and to the appearance of DNA, RNA and protein enzymes

Self-organisation of symbolic information

Information is encountered in two different appearances, in native form by arbitrary physical structures, or in symbolic form by coded sequences of letters or the like. The self-organised emergence of symbolic information from structural information is referred to as a ritualisation transition. Occurring at some stage in evolutionary history, ritualisation transitions have in common that after the crossover, arbitrary symbols are issued and recognised by information-processing devices, by transmitters and receivers in the sense of Shannon's communication theory. Symbolic information-processing systems exhibit the fundamental code symmetry whose key features, such as largely lossless copying or persistence under hostile conditions, may elucidate the reasons for the repeated successful occurrence of ritualisation phenomena in evolution history. Ritualisation examples are briefly reviewed such as the origin of life, the appearance of human languages, the establishment of emergent social categories such as money, or the development of digital computers. In addition to their role as carriers of symbolic information, symbols are physical structures which also represent structural information. For a thermodynamic description of symbols and their arrangements, it appears reasonable to distinguish between Boltzmann entropy, Clausius entropy and Pauling entropy. Thermodynamic properties of symbols imply that their lifetimes are limited by the 2nd law