Alright, I promised to write a bit more about cosmopolitanism and theodicy, but that's still cooking somewhere in the back of my head and right now I don't have access to enough caffeine to bring it out. In lieu of that, let me point this article, via Jerry Coyne at Why Evolution is True. Coyne is discussing a recent paper (and the NY Times article about it) on recent work to discover some evolutionary changes in the human genome that may have been selected for because of cultural practices. By this they mean things such as the appearance and spread of the mutation that allows adult human to remain lactose-tolerant even after reaching adulthood. This is the partly contingent and partly human-chosen structure of culture affecting the genetic makeup of humans. Now sociologists are often deeply suspicious of genetic explanations for human qualities, and with good reason- scientific racism is not dead yet! Still, these sorts of studies are of a different sort and cautious enough, though I'm not sure if they can be useful for the social sciences.
This sort of work that should be considered in light the evidence compiled by sociology, anthropology, and history of the extreme cultural malleability of human behavior. One of my favorite prosaic examples of that is “stink heads”, salmon heads buried for a week or more in the ground to rot and considered a delicacy among the Yup'ik. Our biological inclination to avoid rotting food, so seemingly basic and undeniable, seems less like a law and more like a tendency which socialization at an early enough age can overcome. The work discussed by Coyne comes at this problem from the other direction. Looking at both we would say the relationship between culture and genetics is dialectic over the long-term, in which cultural practices can influence our physical makeup and this can in turn affect the development of culture. But again, given the very long time frames and social isolation needed for these culturally-induced genetic effects I think we have to be very careful in seeing what role they may play in cultural and social history, especially in our highly globalized modern era.
More useful to the social sciences ( and to atheists!) might be the application of phylogenetic methods to understanding human cultural development. One cool example is this paper by Steven Jay Gould's old collaborator Niles Eldredge and Ilya Temkin which traces the “evolution” of the trumpet-like cornet (NYTimes article as well). Phylogenetic trees, the “tree of life” style charting that is used to plot evolutionary history, might be a useful tool for charting the tangled path of social evolution.
Once some solid methods are hashed out, these sorts of phylogenetic approaches might be applied to things as large as the changes over time within the institutions that interact over multiple nations, civilizations and even at the level of a world-system. Types of states, economic models, even the way radical social movements organize themselves could have their development laid out phylogenetically. One could certainly apply this kind of evolutionary tree history to religion- the sort of project that I bet would show how “innovation” in religion, from directly political and tyrannical to the more mild polite forms we see today, has most often come from outside its epistemologically frozen structures. You know, from those nasty heretics/atheists/freethinkers/doubters who wouldn't just sit down and “be polite.”