A complete human genome contains about 1 GB of data, but only 3-4% of that information is actually used to construct and control the organism. The rest (96%) is inactive ballast. In my opinion, that extra information accumulates genetic changes, and, therefore, plays a key role in evolution. Most of the possible changes in the active part of genome are lethal, and cannot support reasonably rapid evolution. Organisms in the nodes of evolutional tree usually have enormous genomes. For example, a lungfish has about 28 GB on its chromosomes, and fraction of active DNA must be less than 0.1%.
Almost all known computer simulations of evolution use 100% active gene models. I think, that is one of the main reasons why they give quite disappointing results.
I would like to program a model, that support background evolution in inactive part of genome, to check my hypothesis. I think, the model can reveal new unexplored features of evolution, such as evolutional jumps (which cause missing links ). A simplified model can be later used as a part of educational system or game.
The model must include mechanisms of genetic exchange, mutation, and selection. I will probably implement a well known example of sorting algorithm evolution. And I will try to invent creatures, which can evolve in the system, and are interesting to observe.
Results
Algorithms used in the project
Griffiths, Miller, ... An Introduction to Genetic Analysis 1994
M.Nei Molecular Evolutionary Genetics 1987
D.Hillis *Papers about evolution simulations.
Evolution and biocomputation : computational models of evolution SERIES : Lecture notes in computer science 1995