Here's the challenge: science does not deal in the abstract; science deals in reality. While religion/philosophy deals in largely existential questions of meaning and purpose, science deals in observable, quantifiable facts.
The problem is that when it comes to the origins of life, those origins are fundamentally unknowable because they are unobservable.
So when it comes to the origins of life, while science can study fossil records and the like, fundamentally they are studying the effects of evolution. Science can't explain the causation. It can make projections about the causes of life's origins, but it can't make fundamental decisions, because the causes are unobservable.
It's at the causation level where science and philosophy start to mix, in part because one cannot theorize about the origins of life without trying to understand the cause. I'm not saying that "God" even needs to be a part of the answer, but the fundamental question "what caused the cause" is as much a philosophical as a scientific one.
There is no problem with, in a science class, postulating a theory of everything, or postulating a cause behind the cause. But once we get into such postulations, various theories seem to come into play -- all philosophical in nature.
ETA:
The challenge is for scientists to admit they don't have all the answers, in the same way that the challenge for religionists is to admit the same (the Bible is not a science textbook). In a fundamentally defensive world such as ours, where both science and religion are being challenged, there is naturally a tendency to close ranks and see the other side as the problem, which tends to create polarization. Naturally the nature of scientific inquiry means that answers are going to be sought, but I don't believe everything has a scientific explanation.....and I think there is a way for people of science and people of faith (who are much closer than they perhaps would care to admit, since a recent survey showed that 43% of scientists are also religious) to create an open-minded dialogue, rather than a polarizing one. I don't think science and God are opposites, and I don't think it's helpful to create an either/or scenario. (The Bible doesn't discuss the minute details of HOW God created the universe -- I read a fascinating book a while ago called "The Science of God" by Gerard Schroeder, which shows how a rapidly expanding universe, complete with the volume and force required for such spontaneous expansion, can be reconciled with a reading of the Hebrew scriptures of the Genesis account.)
I'm not sure where EXPELLED lands in all this. Knowing some of the filmmakers behind the film, I know that they are not rabid creationists. At the same time, in the rush to make a movie that will make money for its investors, and to hit a niche audience, even if the film is fundamentally about the need for a bigger tent as far as scientific inquiry goes, the flash-points of ID/creationism may ultimately sink the desire for a greater dialogue, as it has seemed to polarized the discussion.