4 Literature survey

Trying to implement a biological plausible model in computer science is a difficult task. One has to be extremely careful about the way in which features of biology are to be implemented in computer science. Careful examination of the literature reveals important factors which many fail to address: 1. Understand the role of the feature\s one try to extract in the biological context. 2. Examine carefully whether there are obvious interdependencies with other features which might affect the target one\s. 3. Implement the conceptual ideas rather then the biological machinery which facilitate them. 4. Explain the possible (at least intuitive) contribution it might give to the search in Genetic Algorithm. 5. Validate that the mapping to the computer science domain makes sense. Following our discussion in the previous section we underline the most important features that every evolutionary algorithm should have: the importance of adaptive change, the consideration of the genotype-phenotype map and away to develop it. Later on, we will analyze several algorithm based mainly on these criteria. Adaptive change Both theoretical and empirical examinations of the genetic code emphasize the great importance of adaptive change. Small changes (mutation) in the genotype should result in small changes in the phenotype. The genetic code is redundant. Some point mutations will cause no change to the phenotype. This phenomenon supports the neutral theory of evolution. However the adaptivity of the transcription-translation process goes much further. Even if the change is not redundant, usually, it will code a very similar amino acid (in terms of hydrophobic) – which in turn, in most cases, won’t have a significant effect on the protein. Furthermore, even if the amino acid defers, if the change is not in the protein active sites, there is still a good chance that, given the long chain of amino acids which construct the protein, it will function properly. The genotype-phenotype map The translation process of the genotype to the phenotype plays a crucial role in the effectiveness of the genetic operators. The genome underlies a complex network of interconnection between different genes and proteins. The product of some genes (e.g. RNA polymerase) might have a considerable effect on other genes. In order to produce adaptive changes this phenomena need to be minimized