Collect. Czech. Chem. Commun. 2003, 68, 139-177

Artificial Chemistry and Molecular Darwinian Evolution in silico

Vladimír Kvasnička* and Jiří Pospíchal

Department of Mathematics, Slovak Technical University, 812 37 Bratislava, Slovakia


A simplified model of Darwinian evolution at the molecular level is studied by applying the methods of artificial chemistry. A chemical reactor (chemostat) 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. The dynamics of such an autoreplicating system is described by Eigen's differential equations. These equations have a unique asymptotically stable state, which corresponds to those strings that have the highest rate constants (fitness). Fitness of binary string is calculated as a graph-theory similarity between a folding (phenotype) of respective string and the so-called required folding. The presented method offers a detailed view of mechanisms of the molecular Darwinian evolution, in particular of the meaning and importance of neutral mutations.

Keywords: Artificial life; Artificial chemistry; Fitness landscape; Eigen theory of replicators; Molecular Darwinian evolution; Neutral mutations; Neutral evolution.

References: 45 live references.