A Model of Bacterial Adaptability Based on Multiple Scales of Interaction : COSMIC

Evolution has frequently been seen as a result of the continuous or dis contin­ uous accumulation of small mutations. Over the many years since Darwin, it has been found that simple point mutations are not the only mechanism driving genomic change, for example, plasmids, transposons, bacteriophages, insertion sequences, deletion and duplication, and stress-sensitive mutation all have a part to play in directing the genetic composition and variation of organisms towards meeting the moving target that is the environmental ideal that exists at any one time. These generate the variation necessary to allow rapid evolutionary response to changing environmental conditions. Predictive models of E. coli cellular processes already exist, these tools are excellent models of behaviour. However, they suffer the same drawbacks; all rely on actual experimental data to be input and more importantly, once input that data are static. The aim of this study is to answer some of the questions regarding bacterial evolution and the role played by genetic events using an evolving multicellular and multispecies model that builds up from the scale of the genome to include the proteome and the environment in which these evolving cells compete. All these scales follow an individual based philosophy, where by genes, gene products and cells are all represented as individual entities with individual parameters rather than the more typieal aggregate population levels in a grid. This vast number of parameters and possibilities adds another meaning to the name of the simulation, COSMIC: COmputing Systems of Microbial Interaetions and Communications.