Artificial Chemistry and Molecular Darwinian Evolution of DNA/RNA-Like Systems I - Typogenetics and Chemostat

Abstract

Summary: Two simplified models of Darwinian evolution at the molecular level are studied by applying the methods of artificial chemistry. First, a metaphor of a chemical reactor (chemostat) is considered. It contains molecules that are represented by binary strings, the strings being capable of replication with a probability proportional to their fitness. Moreover, the process of replication is not fully precise, sporadic mutations may produce new offspring strings, which are slightly different from their parent templates. In the framework of this approach we postulate a folding of binary strings into a secondary 2D structure. The proposed chemostat method offers a detailed view of mechanisms of the molecular Darwinian evolution, in particular of the meaning and importance of neutral mutations. Second, a simplified formal system Typogenetics, introduced by Hofstadter, is discussed. Concepts of replicators and hypercycles, defined within Typogenetics, belong to the basic entities in current perception of artificial life. A metaphor of chemical reactions is applied to study an emergence of replicators and hypercycles.