Now that I've transcribed my notes in my first post, leaving out as much opinion as is humanly possible, I'll get into my reactions to it.
First and foremost, Behe isn't a bad speaker. He's not the best of the Difficult Dialogues series, but he's definately up there on the ones I attended. As far as the ID crowd goes, this is an oddity. Dembski came off horribly last spring and every time I've read or watched something by ID proponents, it comes off pretty hollow, as if they're just trying to make a convenient list of sound bytes with no real substance. But Behe was genuinely a good speaker.
However, by no means does this suggest that his content was wothwhile, nor free of rhetorical flaws. Stating that he was going to present evidence and then rebuke earlier arguments and then preceeding to do the exact opposite was rather confusing and not the best way to start.
Behe's insistance that there was something wrong with Judge Jones liberally quoting from Rothschild's proposed statement of fact was cute. However, it's been torn apart many times already. So the first major portion of his speech is a wash.
The only other part in his Dover rant was to claim that Jones hadn't understood a thing. The entire argument for this rested on a single quote of Judge Jones saying that the process was "mind-numbingly technical". The other quote Behe used ("the highly technical scientific testimony… is rapidly becoming a distant memory.") was from his KU talk and had no bearing on the actual ruling. Cute rhetorical trick, but no substance.
Behe, in the "rebuttal" phase of his talk also admitted that God was supernatural and thus the question "Who designed God?" is irrelevant. I'd agree with that. The important question is, "Who designed the Designer?" This is the question Behe should have answer and the fact that he substitutes "God" for "Designer" like this is rather telling.
But's let's suppose the question really was about such a designer. How does Behe answer that question?
Behe: "By “intelligent design” (ID) I mean to imply design beyond the simple laws of nature
...at some point a supernatural designer must get into the picture.
...it is not plausible that the original intelligent agent is a natural entity.
...input from beyond nature was required." (Source)
Looks like Behe claims the same exemptions for the Designer that he does for God; Once you invoke the supernatural, all bets are off. Too bad it also disqualifies that as science.
But don't think that such things will stop Behe from talking out both sides of his mouth given that his first point regarding the "positive" evidence for design was "Design is not mystical." Sure thing pal.
His second point (that everyone agrees that aspects of biology appear designed) is rather beside the point. Things aren't always as they "appear". Thus, this point is another cute rhetorical trick, but is about as worthwhile as saying, by looking around, the earth appears flat.
The third point about structural obstacles was mostly an argument about semantics of Irreducible Complexity which boiled down to him whining that evolution proponents weren't using his definition of IC (his definition being that it must still function as the same system). The reason for this is that Behe's requirement that it must function as the same system is a stipulation with no merit. It's just tossed in there. Anyone can require stipulations that can't be met and then claim that if they're not, it must be wrong. But that's rather dishonest. Not that I expect any better from the ID crowd.
And even when it is just tossed in, many of Behe's systems still don't hold up to scrutiny as being IC. Foremost among them is the blood clotting system. Other species have components missing but still have a functional blood clotting system. Thus, it's not IC. But Behe doesn't let that stop him from making his claims.
For his fourth point, I was amused to see Behe admit that his entire argument was an argument from ignorance. So how did he try to combat this? Change the subject of course. Don't ever be introspective. Always put the opponent on the defensive. Thus, Behe changes the subject to claim that evolution proponents fall prey to arguments from credulity in which they accept anything.
In physics, we have some very nice laws of gravity which handily explain forces between objects. Even a moderately competent high school student can do calculations involving two objects. But add a third, and the problem becomes extremely complicated with differential equations and chaotic solutions.
So what's the point? The three body problem is much like the case of the evolution of these systems. It's notoriously difficult to solve, and the more you add, the harder it gets. But that doesn't invalidate the theory of gravity. Nor should it, as Behe suggests, invalidate the theory of evolution. We have many small steps, but just because we can't replicate every step in the full process at any given instance as creationists demand, doesn't mean that there is reason to doubt the underlying principles.
This is how science works. We test what we can and extrapolate. If we couldn't do such things, entire branches of science would wither, given that we'll never be able to create solar systems in labs to test out theories of gravity. So I, like most scientists, do not see that evolution, anymore than gravity, is an argument from credulity in any inappropriate manner.
Meanwhile, Behe still hasn't defended his argument beyond "we can't figure out how thid happened, thus it didn't."
His final point about things looking designed, thus they are designed (his inducktive reasoning) is still rather weak. Quantitative analysis of design is still non-existant. Dembski's taken stabs at it, but fallen flat repeatedly.
The trouble is that it's hard to pin down the requirements for design. Generally arguments hinge around complexity. But complexity isn't always a great test for design. Good design is often elegant and simplistic. Thus, there's no limit to the range of things that can be labeled designed based on this criteria.
So ultimately, ID comes up short yet again. Behe's a good speaker, but all bark and no bite when it comes right down to it.