Genotypes with phenotypes: adventures in an RNA toy world

Evolution has created the complexity of the animate world and deciphering the language of evolution is the key towards understanding nature. The dynamics of evolution is simplified by considering it as a superposition of three less sophisticated processes: population dynamics, population support dynamics, and genotype-phenotype mapping. Evolution of molecules in laboratory assays provides a sufficiently simple system for the quantitative analysis of the three phenomena. Coarse-grained notions of structures like RNA secondary structures are used as model phenotypes. They provide an excellent tool for a comprehensive analysis of the entire complex of molecular evolution. The mapping from RNA genotypes into secondary structures is highly redundant. In order to find at least one sequence for every common structures one need only search a (relatively) small part of sequence space. The existence of selectively neutral phenotypes plays an important role for the the success and the efficiency of evolutionary optimization. Molecular evolution found a highly promising technological application in the design of biomolecules with predefined properties.