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In Darwin's Black Box: The BiochemicalChallenge to Evolution I argued thatpurposeful intelligent design, rather thanDarwinian natural selection, better explainssome aspects of the complexity that modernscience has discovered at the molecularfoundation of life. In the five years since itspublication the book has been widely discussedand has received considerable criticism. Here Irespond to what I deem to be the mostfundamental objections. In the first part ofthe article I address empirical criticismsbased on experimental studies alleging eitherthat biochemical systems I discussed are notirreducibly complex or that similar systemshave been demonstrated to be able to evolve byDarwinian processes. In the remainder of thearticle I address methodological concerns,including whether a claim of intelligent designis falsifiable and whether intelligent designis a permissible scientific conclusion.