Science is sometimes divided into the "natural sciences" (astronomy, physics, chemistry, geology, biology) and the "human sciences" (like anthropology and psychology). The goal of the "natural sciences" is to understand the "natural order" of the physical universe. There are, of course, realities beyond the natural order and beyond the physical, but they lie outside the purview of natural science. Philosophy and theology have a much broader scope.
As I understand the "Intelligent Design movement", they are saying that certain biological phenomena can only be explained as miracles. They don't use that language, but that is in effect what they are saying. I firmly believe that miracles do happen. But a miracle, since it is something that contravenes the natural order, lies outside of natural science. I think it is quite legitimate to use scientific arguments and evidence to make out a case that some event is in fact miraculous. But that means that you have run up against the limits of what natural science can explain, and are invoking something beyond those limits. That is why I do not regard the ideas of the Intelligent Design movement as being hypotheses WITHIN natural science. Let me put it this way. Science may show that a person turned water into wine, but that would be a miracle, not a new effect in the science of chemistry. Nor was the parting of the Red Sea a new effect in hydrodynamics. I am not sure that the "design hypothesis" is a part of biological science. That is not to say that it is wrong.