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.

Group selection and individual selection are just two of the selection processes that have played important roles in evolution. There also is selection within individual organisms (intragenomic conflict), and selection among multi-species communities (an idea that now is getting attention in work on the human microbiome). All four of these levels of selection find a place in multi-level selection theory.

The rabid opposition to group selection has now considerably subsided. In the process, the conceptual structure of evolutionary theory has become clearer, as have the relationships that connect different theoretical approaches.

The more evolutionary theory gets called an atheistic theory, the greater the risk that it will lose its place in public school biology courses in the United States. If the theory is thought of in this way, one should not be surprised if a judge at some point decides that teaching evolutionary theory violates the Constitutional principle of neutrality with respect to religion.

Deism is compatible with evolutionary theory.

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).