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I don't think it's really helpful by trying to establish the existence of God by pointing to various errors, gaps, discrepancies in a scientific theory such as evolution.

Probably true. I just don't see ID trying to do that. At least not in the effort to develop ID as science. As a political movement, a different story.

If say in a hundred years science is able to fill in those gaps, or create an alternative theory which better explains the facts, then that would mean God doesn't exist.

That conclusion is not warranted

So the real problem with Behe's logic isn't that he can presumably tear apart current theories of evolutionary biology--I will assume that he can, and let's say evolution is a worthless theory--it's that he's basing his argument for the existence of God on that refutation.

Behe is trying to develop ID as a science. So Behe does not base his argument for God on ID, because he doesn't use ID-as-science to argue for God in the first place. Any theological implications of his work are outside of science, and he is careful to distinguish the two. Yes, he believes the designer is God, but it is not because science tells him so.
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