That's one heck of a link, hcg.
First, an observation. It's really hard to understand. I mean really hard to understand. I've had one graduate level course in neuropsychology, a whole bunch of engineering, and I only partially understand it. Moral of the story: If someone else doesn't understand it, that doesn't mean they are stupid.
But let's see why it doesn't refute intelligent design, or even that specific claim made by Behe that bacterial flagella could not arise through mutation
and natural selection. Here's a quote from the link.
One plausible path for the evolution of flagella goes through the following basic stages (keep in mind that this is a summary, and that each major co-option event would be followed by long periods of gradual optimization of function):
A passive, nonspecific pore evolves into a more specific passive pore by addition of gating protein(s). Passive transport converts to active transport by addition of an ATPase that couples ATP hydrolysis to improved export capability. This complex forms a primitive type-III export system.
First, note that we are starting with an existing cell, anyway, which is already an extremely complex structure.
But, given that, how did we just happen to have a gating protein lying around? Wasn't that convenient? I mean, what are the odds that there would just happen to be an appropriate gating protein around, and that it would add its blueprint into this organism's DNA in such a way that it actually improved the organism's survival chance. I (speaking as the ID supporter) would say that's pretty astronomical, wouldn't you?
What? You, as the evolutionist, (yes, I hate that word too, but I don't know a better one) say that no it is not astronomical. It's extremely likely, in fact. A trivial example. Happens all the time.
So here we are. Stuck. One side says that it is extremely unlikely. One side says it isn't unlikely. The only way we can resolve that is to compute the probability that such a thing could happen.
We can try to do that theoretically. Perhaps someone knows how to do that. I don't.
We can try to do that by observation. How often have we seen it happen? The evolutionist might say that we have seen lots of DNA that looks like this happened, so by observation, the probability of it happening with enough cell divisions and mutations is very near 1. The IDer might say that we have never seen it happen. All that DNA that looks like it could have happened in is actually the result of design. The probability is near 0. (Do these sorts of bacteria even have DNA? Do they have nuclei? I'm not even sure. However, whatever structures they have, they pass on.)
So what we have here, and in every step of the path given, is a situation where one side will say that it is easy to see how it could happen through mutation and natural selection because it is highly probable given enough iterations of the process, and one side says it is almost impossible.
Ahh, but you might object, and Dr. K did object, the assertion of the ID crowd is that such a scenario is impossible. We have shown that it is possible, even if improbable. That refutes ID!
Well, no. The theory of evolution asserts that such a scenario is of high enough probability that it could happen without assistance. The "theory" of ID says that the probability is so low that it could not happen without assistance. To resolve the conflict, we would have to compute the probability. Since we cannot do that, we're stuck. Each is an unproven theory. ID remains neither supported nor refuted by the argument.
So, you might ask if I am saying then that ID and evolution are both unproven theories that should be given equal weight in education. No. I am not saying that. I am saying that evolution is a plausible theory that explains all the available evidence, and is the only natural theory that does so. ID, on the other hand, also is compatible with all available evidence, but that is almost a definition. No matter what is presented, the ID believer can assert that the designer wanted it that way.
To futher complicate matters, back when I was a Christian, I believed that evolution worked, but that God would, at particular times, introduce a "random" mutation, to guide the process along. I think that may even be considered a form of intelligent design, wouldn't it? And yet it is entirely compatible with Darwinism. Natural selection, which we have been told is not a random process, after all, was the means the designer employed to make his creations.
More thoughts on the implications of this for discussing ID later. I agree that ID is not really science, and doesn't belong in classrooms, and that evolution is science, and does belong there, but it isn't so clear exactly what can and can't be said about each one without going beyond real science and getting into philosophy.