Philosophers of biology generally recognize that evolutionary fitness (roughly, an organism's ability to survive and reproduce in its environment) is multiply realizable.
The upshot is that most philosophers of biology now hold that biological properties supervene on physical properties (where supervenience is taken to include some kind of "in virtue of" relation), and that fitness and other biological properties are not identical with physical properties.
"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.
"Tiger is a natural kind" and "Tiger is a historical particular" are incompatible with each other, and evolutionary biology provides a reason for favoring the latter over the former.
I disagree with those who argue that evolutionary biology and the existence of God are incompatible.
This is not to deny that there are versions of theism that do conflict with evolutionary biology. Young Earth Creationism is an example; it claims that God created life on earth within the past 10,000 to 50,000 years. But other types of theism are different.
I don't endorse deism or interventionist theism. My point is just that evolutionary biology is logically compatible with the former and with some versions of the latter.
The more evolutionary theory gets called an atheistic theory, the greater the risk that it will lose its place in public school biology courses in the United States. If the theory is thought of in this way, one should not be surprised if a judge at some point decides that teaching evolutionary theory violates the Constitutional principle of neutrality with respect to religion.
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.
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