Theodosious Dobzhansky[2] defined evolution as the change in allele frequencies over time, a definition that appears to be more applicable to fine-scale population genetics questions than, necessarily, to between-species evolutionary relationships. However, it turns out that we can learn a lot about the broad-scale process by carefully specifying the fine-scale one, and for this we need some kind of model describing the change in allele frequencies within populations. In the context of molecular evolution, this model should be stochastic. The necessary ingredients for any such model can be summarized as: mating, mutation, and selection. In other words, in order to describe the dynamics of the alleles, we need to know how individuals in the population are reproducing, how the genetic material is passed on (or passed on in a changed form), and finally how the genetic material influences the survival and reproduction of the next generation of individuals. As alluded to above, the first stop in any theory of molecular evolution is selective neutrality, and so our initial model of selection is very simple-- there is no selection, and we have reduced the problem to one of reproduction of individuals and their genes. There is a conceptual justification for this apparently wild assumption of selective neutrality. A short digression on this conceptual justification follows.