Uncommon Descent has a nice commentary on the recent paper on this subject in Cell Biology International (2004), discussing some foundational definitions in the Intelligent Design debate (Explanatory Filter, Proof by Contradiction, Displacement Theorem), and does a good job of discussing the unlikelihood of evolution by chance, or chance + necessity, while answering the questions below:
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How can we be sure we won’t make some discovery in the future that will invalidate the design inference?
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How can we be sure we’ve eliminated all possible naturalistic causes, particularly since we have so few details of what happened so long ago when no one was around?