The indispensability argument seeks to assimilate the epistemology of metaphysical statements to the epistemology of statements that are obviously empirical. I think it fails to achieve this goal. The argument does not refute the Carnapian thesis that scientific theories and metaphysical claims differ epistemologically - observations can provide evidence for the former, but not for the latter.

When one theory is simpler than its competitor, this fact is relevant to saying what the world is like.

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.

Another way to test hypotheses about adaptation is to consider trait variation across a group of species instead of focusing on the trait of a single species. Rather than seeking to explain why polar bears have fur of a certain thickness, one tries to explain why bears in colder climates have thicker fur than bears in warmer climates. The former problem is hard to solve, since it is hard to say exactly what fur thickness polar bears should have if natural selection guided the evolution of that trait.

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.

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.

Methodological naturalism gives advice to scientists about what they should include in their theories. There is a second type of methodological naturalism that gives advice to philosophers, which I call "methodological naturalismp." It says that the methods that philosophers should use in assessing philosophical theories are limited to the methods that scientists ought to use in assessing scientific theories.