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.

The racial categories that are used in a given society (for example, in contemporary America) are biologically meaningless, but sometimes it turns out that a vernacular racial category has biological reality.

Deism is compatible with evolutionary theory.

Current organisms have a higher probability of sharing a single code if the common ancestry hypothesis is true than they'd have if the hypothesis of separate ancestry were true. That is, the simpler hypothesis has the higher likelihood in the technical sense of "likelihood" used in statistics.

Deism is logically compatible with evolutionary theory for the simple reason that the theory says nothing about the origin of the universe or of the laws of nature.

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.

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.