Dan, "Intelligent design" is just another chapter in the long history of "god of the gaps" arguments.
Even Isaac Newton used god to fill the gaps he couldn't figure out. Why the planets are all on the same plane in their path around the sun puzzled him, he figured out lots of other stuff but this fact looked like design to him. Of course now we know why planets all form on the same plane, its to do with spinning cooling gas etc.
Later it was the design of the eye that got creationists all indignant about their clever designer but we worked that out as well, and pointed out that the human eye isn't all that good after all.
Now its cell biology and creationists are investing a lot of hope in biologists not working out how things like the bacterial flagella evolved. Its a short-term refuge for god.
The claim that the flagellum and the blood-clotting cascade are irreducibly complex has already been debunked. Here is a link to an article called "Type III secretion systems and bacterial flagella: Insights into their function from structural similarities" published on the website of the National Academy of Science. It shows the similarity between the flagellum and a much simpler system used by bacterium to infect cells they attack.
The scientists who wrote it spend their time pushing back the limits of human knowlede as opposed to parasites like Behe who feed off the gaps in scientific knowledge.