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I understand the scaffolding argument. However it assumes a lot of complexity that I just don't think is needed to explain how certain features (like the bacterial flagellum) evolved (unless there are linked intermediate forms that demonstrate the scaffold).

Scaffolding may not be exactly what happened in the case of the flagellum. That's not really the point. The point is that Behe defines Irreducible Complexity to have a particular meaning, and then claims that IC structures cannot have evolved in small incremental steps. Scaffolding is simply one example of how an IC structure can evolve, and apparently *does*, in some cases.

There are other examples, such as that a system which serves one function sometimes evolves to perform some totally different function. The specifics don't really matter that much; the point is that Behe claims that IC (as he defined it) precludes evolution. One counterexample is enough to disprove the claim. It may be that there are other definitions of IC that do rule out evolution, but Behe hasn't proposed one, nor has he come up with a test for proving that anything is IC.
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