Science can study the evolutionary process from a single cell to what we see today but it can't answer the question of why does the process exist in the first place.
The evolutionary process is surely a necessary element of our universe. It seems to follow from the most basic physical processes observed. If we one day find the ultimate ToE (Theory of Everything), and can somehow gain the power to follow its solution through the chaos and complexity, I believe we will see evolution, us, and our moral code all there in the formulae. All gaps will have been removed.
However, the biggest question of all will remain... WHY? That simple question is where religion, ID and atheism fit in. And that simple question is surely infintely larger than all of our understanding and all of our gaps put together? Perhaps we should give God (and ~God) the luxury of that space and stop trying to cram him into every conceivable process that psuedo-hints at meta-physicality?