Even if the intelligent design of some structure has been established, it still is a separate question whether a wise, powerful, and beneficent God ought to have designed a complex, information-rich structure one way or another. For the sake of argument, let's grant that certain designed structures are not simply, as Gould put it, "odd" or "funny," but even cruel. What of it? Philosophical theology has abundant resources for dealing with the problem of evil, maintaining a God who is both omnipotent and benevolent in the face of evil.
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