The fundamental mechanisms of biological evolution have fascinated generations of researchers and remain popular to this day. The formulation of such a theory goes back to Darwin (1859), who in the The Origin of Species presented two fundamental principles: genetic variability caused by mutation, and natural selection. The first principle leads to diversity and the second one to the concept of survival of the fittest, where fitness is an inherited characteristic property of an individual and can basically be identified with its reproduction rate. Wright [530, 531] first recognized the importance of genetic drift in evolution in improving the evolutionary search capacity of the whole population. He viewed genetic drift merely as a process that could improve evolutionary search. About a decade later, Kimura proposed [317] that the majority of changes that are observed in evolution at the molecular level are the results of random drift of genotypes. The neutral theory of Kimura does not deny that selection plays a role, but claims that no appreciable fraction of observable molecular change can be caused by selective forces: mutations are either a disadvantage or, at best, neutral in present day organisms. Only negative selection plays a major role in the neutral evolution, in that deleterious mutants die out due to their lower fitness. Over the last few decades, there has been a shift of emphasis in the study of evolution. Instead of focusing on the differences in the selective value of mutants and on population genetics, interest has moved to evolution through natural selection as an abstract optimization problem. Given the tremendous opportunities that computer science and the physical sciences now have for contributing to the study of biological phenomena, it is fitting to study the evolutionary optimization problem in the present volume. In this chapter, we adopt the following framework: assuming that selection acts exclusively upon isolated phenotypes, we introduce the following compositum of mappings . . . Genotypes→ Phenotypes →Fitness . . . . We will refer to the first map as to the genotype-phenotype map and call the preimage of a given phenotype its neutral network. Clearly, the main ingredients here are the phenotypes and genotypes and their respective organization. In the following we will study various combinatorial properties of phenotypes and genotypes for RNA folding maps.
A Hands-on Exercise to Demonstrate Evolution by Natural Selection & Genetic Drift
