Rather than look for a gap in the scientific account, perhaps
what is needed is openness to another kind of causal explanation, viz.
agent causation (or "personal explanation"). Certainly archaeology is a
science where persoanl explanation features large in explanatory
accounts. And as Doug Geivett argues in _Evil and the Evidence for God_
(Temple Univ. Press), personal explanation can play a large role in
natural theology. While not philosophically uncontroversial (what is?),
agent causation/personal explanation would seem to be a non-naturalistic
kind of explanation which is perhaps too often overloked in the natural
sciences.