Elliott Sober, an atheist and distinguished philosopher at the University of Wisconsin, posted a paper that shows science can not rule out the possibility that some mutations had been engineered by God across the deep time of evolutionary history. Or, from a theistic position, science cannot rule out that possibility that God intervened to guide evolution such that humans came into existence.
You can find the paper here (it’s a pdf file) and here is a key excerpt:
Evolutionary theory does not entail that God never intervened in the mutation process, but the theory, when supplemented by auxiliary assumptions, does have implications about divine intervention. Here are some possible auxiliary assumptions. The list is not exhaustive:
(Deism) God created the universe, the laws that govern the universe, and the initial conditions of the universe, but he never intervenes in natural processes after that first moment.
(The Theology of the Unhidden God) If God ever intervened in the mutation process, then we’d have scientific evidence that mutation probabilities change in beneficial directions when the environment changes.
(Evidentialism) If you lack scientific evidence as to whether X is true, then you should suspend judgment about whether X is true.
(Fideism) You should believe that God guides the mutation process whether or not you have scientific evidence that he does so.
The first two of these, when added to our best scientific picture of what causes mutation, entails that God never intervened in the mutation process. The third, when conjoined with what biology tells us about mutations (properly understood), entails that we should be agnostic about divine mutational intervention. And the fourth, of course, entails that we should believe that God intervenes in the mutation process. It is beyond the scope of this essay to consider which of these auxiliary assumptions we should adopt (or whether there are other candidates that are even better). My present point is that none of these auxiliaries is part of evolutionary theory; they are ─ all of them ─ philosophical theses. My Duhemian claim is that evolutionary theory has consequences about divine intervention in the mutation process only when evolutionary theory is supplemented by further assumptions. (emphasis added)
And appropriately ends his argument with:
Atheists who think that evolutionary theory provides the beginning of an argument for disbelieving in God should make it clear that their arguments depend on additional premises that are not vouchsafed by scientific theory or data. Philosophy is not a dirty word.