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A theory needs to be able to be disproved in order for it to be valid scientifically and there's simply no way to prove or disprove intelligent design short of the Almighty Himself weighing in on the issue. Therefore, whether it's swaddled in religious trappings or not, intelligent design simply doesn't belong in a science classroom.
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The problem is that the theory of evolution itself remains, as yet, unproven. In fact, there is some evidence that may disprove it, although the nature of that evidence is in itself relatively circumstantial at best (or at worst, fallacious).
I don't see anything unscientific about saying, "we don't know why" or even "we can't prove why". Science is about asking questions, not about disproving answers. If God did create the Universe and set it up a certain way, is there anything unscientific about analyzing that Universe to see how and why it works?
I don't see how "it just happens" is a valid scientific answer. Scientific discourse should open itself to many theories in an effort to prove any of them better than another. And in the absence of genuine evidence, we have only to keep asking the questions again of future generations and never stop looking for the answers. I don't think its fair to shut someone up just because you don't like the reprecussions of the questions they are asking, or because you have no means of answering them.
"Where did we begin?" and "Why do we exist?" are some of the key fundamental questions of science. You don't currently have any way of proving or disproving something, so the domain of science is the one area where proposing and analysing these issues is most relevant and appropriate. The only thing unscientific is the very assumption (hypothesis?) that it can't be proven or disproven at all.