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.

When one theory is simpler than its competitor, this fact is relevant to saying what the world is like.

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.

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.

It 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.

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.