Darwin repeatedly used the hypothesis of common ancestry as a platform on which to build his various ideas about testing hypotheses concerning natural selection. He also argued that adaptive similarities provide little or no evidence for common ancestry. Although this second claim needs to be fine-tuned, Darwin was right that ample evidence for common ancestry can exist even if none of the characteristics we observe were caused to evolve by natural selection.

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.

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.

Philosophers of biology generally recognize that evolutionary fitness (roughly, an organism's ability to survive and reproduce in its environment) is multiply realizable.

If the organisms in a species now have trait T, and this trait now helps those organisms to survive and reproduce because the trait has effect E, a natural hypothesis to consider is that T evolved in the lineage leading to those current organisms because T had effect E. This hypothesis is "natural," but it often isn't true!

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.

Deism claims that God creates the universe and the laws of nature and then is hands-off, with everything that subsequently happens in nature being due to natural processes.