Evolutionary biologists often appeal to parsimony when they seek to explain why organisms "match" with respect to a given trait. For example, why do almost all the organisms that are alive today on our planet use the same genetic code? If they share a common ancestor, the code could have evolved just once and then been inherited from the most recent common ancestor that present organisms share. On the other hand, if organisms in different species share no common ancestors, the code must have evolved repeatedly.

"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.

Evolutionary biologists often avoid using the term "race" because there is so much racist baggage that comes with the term. However, they are often okay with the idea that the genealogy of human groups within our species can sometimes be inferred in much the same way as the genealogy of different species.

Darwin and his successors have railed against the fallacy of confusing the current utility of a trait with the reason the trait evolved. For example, Darwin argued that skull sutures in mammals did not evolve because they facilitate live birth; the sutures were in place well before live birth evolved. Checking the chronological order in which different traits evolved in a lineage is one way to test an adaptive hypothesis; the fact of common ancestry is what makes that checking possible.

Evolutionary theory, properly understood, does not conflict with the idea that God occasionally intervenes in nature - for example, by once or twice causing a beneficial mutation to occur. Biologists have not detected any such interventions despite the data and theory they have assembled about mutation. However, I think it is a mistake to expect biological experiments to be able to detect such one-off acts of divine intervention, especially if those acts occurred in the distant past. Science isn't in that line of work.

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).

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.