John Polkinghorne was Professor of Mathematical Physics at the University of Cambridge before becoming an Anglican priest. He played an important role in the discovery of the quark. I just spent some time sitting outside at our Boston hotel reading Polkinghorne's essay "The Universe as Creation" (in Peterson, Hasker, et. al., eds, Philosophy of Religion, 551 ff.).
Polkinghorne the brilliant scientist writes of the limitations of science. "Science's success has been purchased by the modesty of its explanatory ambition. It does not attempt to ask and answer every question that one might legitimately raise. Instead, it confines itself to investigating natural processes, attending to the question of how things happen. Other questions, such as those relating to meaning and purpose, are deliberately bracketed out. This scientific stance is taken simply as a methodological strategy with no implication that those other questions, of what one might call a "why" kind, are not fully meaningful and necessary to ask if complete understanding is to be attained." (551)
I'm now thinking of a recent discussion I had with an atheist (of the philosophical naturalist variety) on the question of why bad things happen to people. In dialogue with me he said he gets his answers to this kind of question from science. My response to him was that science cannot, in principle, answer such a question. Science can tell us about the physics of, e.g., a tornado, but it cannot tell us anything about "badness."