PZ Meyers has an interesting (and a bit over-my-head) post on the evolution median-fins over at his blog Pharyngula. Snipping the biology and leaving the punchline, he says:

A story is beginning to emerge, though, that shows that midline fin development and evolution is a wonderful example of a general principle: modularity and the reuse of hierarchies of genes.... The redeployment of previously refined genetic modules is going to turn out to be a universal property of evolved systems, I expect.

Modularity (perhaps even hierarchical modularity) in biological systems is becoming more and more evident, and I agree that we should expect to see a lot more of it in the future. But which is a more likely source of good engineering principles like modularity? Stochastic processes, or intelligence? Might there be different sorts or degrees of modularity that could serve as predictions of one theory or the other? In particular, is there any sort of modularity that is not predicted by evolutionary theory?