Just a couple random thoughts on evolutionary biology...
One of the most annoying things about evolutionary biology, as Rakesh notes, is a kind of reductionism. Richard Dawkins is probably the most well known in this case: "genes have only one goal: to make more copies of themselves." For those wondering if positivist is alive and well - it certainly seems to be. For the most part scientists are still using the langauge of "discovery." The twit/physicist Richard Feynman, perhaps untypically, once said that "after the fundamental laws are discovered, physics will succumb to second-rate thinkers, like philosophers" just after noting that ""you only discover America once."
What is most astonishing to me, other than the language of discovery, is a complete lack of understanding regarding creation. That we (yes, we) don't "discover" fundamental laws... we create them - we posit and institute them. It is just assumed, time and time again, that language is a completely self-reflective medium. Even when some people are aware that this isn't the case, they often turn to mathematics as a pure language - as if math solves the problem by conveying truth in its purest form (seemingly unaware that math is an artificial creation - something which Gadamer, rightfully I suspect, identifies as a violence against communication and understanding).
For my pennies, Stephen Jay Gould is probably one of the best theorists regarding this. At least he's emphasized the importance of contingency (a la Hegel and Marx) better than most.
What I still find frustrating though, esp. with people like Dawkins, is unbelievably imprecise formulation of theoretical models: "genes have a goal..." or "the a species that does not reproduce is a failed species." This is most annoying. I think that the social sciences have adopted a far better and less alienated (if I can say that) approach: the logic of systems... that kind of thing. The ideas are pretty much the same, but there is a tendency for theory to get less abused if one talks about logics than success and failure. And I suspect the difference in language here has a lot to do with the overwhelming tendency to reduce social phenomena to genetics (the gay gene, ie. what would be termed a failed gene in evolutionary biology). It's almost as if these researchers think of themselves in an apolitical bubble (and don't get me started on the idea of objectivity!).
The best example of this is the idea of superstring. "It must be true, because it it beautiful" (Edward Witten). I love it. Beauty is a criteria of truth... reversing the Aristotelian claim that stuff is beautiful when it is true - apparently now things are true when they are beautiful. And they say that Adorno's aesthetic theory is out of date...