Joined: June 2009
There may be some value in checking Mendel's Accountant, to see whether it really implements the model that it claims to, but I don't see much point in trying to cobble together a new program to simulate evolution here. That is a major research project, with many unknown parameters, i.e. a truly realistic simulation of evolution isn't possible yet.
The important questions about MA, assuming the program isn't simply fatally flawed, concern the model that it is implementing. For the default values, you don't have to run the program to know that it will produce genetic collapse of the population -- that's inevitable, given the assumptions of the model. The model assumes a large number of mildly deleterious mutations, so mild that they are unaffected by purifying selection. It also assumes purely hard selection, in which lower fitness translates directly into loss of fertility for the population, and few beneficial mutations (which are also of small effect), independent of the fitness of the population (i.e. no compensating mutations). Given those assumptions, the population will inevitably decline towards extinction, since there is no force counteracting the relentless accumulation of deleterious mutations. The model stands or falls on those assumptions; the code is a side-issue.