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 Pennock’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 doesn’t it count as science? Pennock doesn’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.