"IF 'intelligent design' is true, there must be a way of addressing design issues in our science, without having to appeal ONLY to contingency, adaptation and undirected processes. It MAY be argued that we have not yet found the right way to do it, but this does not mean that design must be banished to the realm of philosophy/theology and that we must proceed in our science as though design has no relevance to our research questions."
If as you say we have not yet found the right way to address design issues in scientific research, then how would you ask researchers to proceed? Should they leave every scientific question open until we are able to address design issues (which would have the result of effectively halting all scientific research, since no explanations could be developed until design issues could be properly addressed)? Or should they simply do what they are doing now, developing what they believe are the best explanations for scientific phenomena, then wait to see if any better explanation comes along (even if that means as you say banishing design the realm of philosophy/theology, at least until the right way to apply it to scientific questions can be developed)?
As a research scientist, I would opt for the latter option, because I want to be able to keep on working and publishing, rather than sit around with nothing to do while a group of philosophers decide how to apply design issues to scientific questions. If they ever do so, then great; I would be more than happy to begin applying design issues to scientific questions. But until they can, I will not suspend my research simply because I'm told I shouldn't rule out a concept that I can't currently use as part of my scientific research.
Kevin L. O'Brien