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.
Elliott SoberCurrent 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.
Elliott SoberIt is an interesting fact about model selection that the evidence at hand can indicate that a model known to be false will be more predictively accurate than a model known to be true. This opens the door to a kind of instrumentalism.
Elliott SoberI 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.
Elliott SoberI 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.
Elliott SoberDarwin 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.
Elliott Sober