Unfortunately, philosophers of science usually regard scientific realism and scientific anti-realism as monistic doctrines. The assumption is that there is one goal of all scientific inference - finding propositions that are true, or finding propositions that are predictively accurate. In fact, there are multiple goals. Sometimes realism is the right interpretation of a scientific problem, while at other times instrumentalism is.

"Methodological naturalism" and "metaphysical naturalism" are terms that often surface in the continuing battle between evolutionary biology and creationism/intelligent design. The methodological thesis says that scientific theories shouldn't postulate supernatural entities; the metaphysical thesis says that no such entities exist. In this debate, God is the supernatural entity at issue; the question isn't whether science gets to talk about mathematical entities if Platonism is correct.

The big picture, I think, is that common ancestry is evidentially prior to natural selection in Darwin's theory and in contemporary evolutionary biology as well.

Just as thought experiments can't show that vitalism is true (or that it is false), they also can't show that dualism is true (or that it is false).

If you have evidence that C1 is a cause of E, and no evidence as to whether C2 is also a cause of E, then C1 seems to be a better explanation of E than C1&C2 is, since C1 is more parsimonious. I call the version of Ockham's razor used here "the razor of silence." The better explanation of E is silent about C2; it does not deny that C2 was a cause. The problem changes if you consider two conjunctive hypotheses.

I have spent a lot of time arguing that the theory of group selection is not the stupid, pernicious doctrine that many biologists once claimed it to be. The theory is not just conceptually coherent; there are adaptations out there in nature (like reduced virulence in some viruses) that evolved because there was group selection.

One influential philosophical position about the use of probability in science holds that probabilities are objective only if they are based on micro-physics; all other probabilities should be interpreted subjectively, as merely revealing our ignorance about physical details. I have argued against this position, contending that the objectivity of micro-physical probabilities entails the objectivity of macro-probabilities.