Bradley Monton, a Princeton-trained philosopher on the faculty at the University of Kentucky, has an important piece on Dover here. Though Monton is not an ID proponent (he is a philosopher of physics who in his professional work is quite critical of fine-tuning as evidence for God), he exhibits little patience for the reasoning in Judge Jones’s decision. Note especially the following paragraph from his article:
There is a problem with this idea that science should change its methodology in light of empirical confirmation of the existence of a supernatural being [[a point that Pennock had conceded in testimony]]. How does this empirical confirmation take place, if not scientifically? By PennockÃ¢â‚¬â„¢s lights, there must be some other epistemic practice that one can engage in where one can get empirical evidence for some proposition. What epistemic practice is this, and why doesnÃ¢â‚¬â„¢t it count as science? Pennock doesnÃ¢â‚¬â„¢t say. Also, note that the scientific status of that epistemic practice will presumably shift: at a time before one gets the empirical evidence that a supernatural being exists, the epistemic practice is unscientific, but after one gets that empirical evidence, the methodology of science changes in such a way that the epistemic practice (presumably) counts as scientific.
The lesson, which should be obvious to Pennock and Forrest if only it didn’t provide such a wide opening for ID, is that methodologies are tools for assisting inquiry but cannot define (or confine) inquiry.