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Starting with an ideologically charged example is indeed not a good way to do it. If it were up to me, I would first teach students the general principles (with politically neutral examples to assist them). Then they might be given past examples of how ideological bias could trump science (for instance, the history of genetics in the USSR). Finally, I would let them learn about present controversies (creationism, global warming etc.) by independently reading the arguments of each side.

I think Global Warming works much better as an example then creationism.

With creationism the theist side doesn't really make scientific arguments. With Global Warming you at least find a bunch of people who care about arguing within the realm of science on the skeptic side.
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