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Intelligent Design doesn't go back 2000 years, but only 200, to William Paley's Natural History: or, Evidences of the Existence and Attributes of the Deity, Collected from the Appearances of Nature (1802).
Paley's book was a response to the decline of traditional religion and the rise of science. Its goal was to prop up religion by cherry-picking some of the most impressive aspects of the natural world and then claiming they were too complex to have a natural explanation.
The argument he started has raged back and forth ever since -- but every time religion has tried to draw a line in the sand, science has promptly crossed it. There are still many things science has not yet explained, but there is no reason to believe there is anything in this world which science cannot explain.
For sensible people, the argument has therefore moved to one about the origin of the universe itself -- what came before it, what comes after it, what is outside it, and so forth. And on that level of discussion, there's no problem with the fact that some people say "God" while others say :shrug:
The real problem comes with those people who aren't prepared to accept that we live in a realm of scientific causes and scientific explanations and that anything beyond that is a matter of metaphysics and not of science. Instead, they're trying to take things back to where they were 150 years ago, to poke holes in science, to dredge up obscure phenomena that they hope science won't be able to explain, even to deny science the right to examine certain areas of existence.
It's that aspect of intelligent design -- the Paleyesque claim that the inadequacy of science proves the existence of God -- that most science-minded people fear and despise. The reason is that, if accepted, it destroys the ontological basis of science itself.
For myself, I'm quite prepared to concede that there are certain aspects of nature where current mechanistic approaches fall short. But I'd be far more inclined to look for alternative explanations in Sheldrake's morphogenetic fields or even in something like a world-soul than in the archaic religious daddy-knows-best style of creator.
People have always tried to explain the world in terms of what they know. At various times in the past, this has meant imagining a goddess who birthed the world, or a god who masturbated the world into being, or an androgynous deity who dreams of an existence that continues only as long as the dream. Today, the God-believers are inclined towards an engineer-deity, who putters around in his workshop, improving a feature here and implementing an upgrade there. But as far as I'm concerned, that particular metaphor has all the sterility of laboratory science without its practical effectiveness. It's really time to move on.
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