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 SoberThe big picture, I think, is that common ancestry is evidentially prior to natural selection in Darwin's theory and in contemporary evolutionary biology as well.
Elliott Sober"Tiger is a natural kind" and "Tiger is a historical particular" are incompatible with each other, and evolutionary biology provides a reason for favoring the latter over the former.
Elliott SoberThe 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.
Elliott Sober