Thanks to various live-bloggers, you can read summaries of all of the University of Chicago Darwin 2009 conference presentations. The conference organizers have also promised to make video podcasts available of all the lectures shortly. By contrast, what follows below is — as they say in sports television — color commentary. This will be a longer post, because much was said that calls for comment.
Bottom line: this was an outstanding conference, where any ID theorist would have enjoyed himself, and learned a lot, if he didn’t mind a bit of mocking laughter along the way.

2009 in the Light of 1959
While both lauded Darwin, the 1959 and 2009 celebrations at the University of Chicago were strikingly different affairs. 1959 was a longer, much larger event, complete with a specially written musical and wide-ranging panel discussions for the lay public, instead of the more technical lectures of 2009.
But it is instructive to note other differences as well, and how various themes were amplified, or modified, by the 2009 event.
1. The bad guys in their black hats were not invited, but we know they’re out there.
As the video podcasts will show, in addition to the talks by Ron Numbers and Eugenie Scott that focused specifically on “anti-evolution” (which meant anything other than undirected, fully materialistic evolution), several speakers brought up ID, or dissent from Darwinian theory, if only to ridicule it.
This attention to the black hats was, I think, considerably greater than what was said about “anti-evolution” in 1959. In her detailed study of the 1959 conference, historian of science Betty Smocovitis observes that the organized attention give to doubts about Darwinian theory amounted to minor “sideshows” in 1959 (1999, p. 294). Instead, “the supremacy of natural selection was a dominant theme in all panel discussions bearing directly on the subject of biological evolution” (1999, p. 298). Evolutionary theory was seen as completely unified around natural selection and inexorably expanding in its sphere of cultural triumph.
There is something of an irony in this. One wonders what the 1959 panelists, now all deceased, would have said, not only about the Numbers and Scott 2009 lectures — “anti-evolutionists” exist in the year 2009? are you quite serious? is it really necessary to address this? — but the frequent jabs at ID in the other 2009 lectures. At the 1959 event, Julian Huxley predicted the demise of the idea of a transcendent personal cause of the universe, to be replaced by the “new religions” that were evolving to the fore. Goodbye, design.
Didn’t happen. (The fact that you’re reading this blog — well, you can do the math.) Smocovitis notes that the 1959 Darwin centennial prompted the rise of “scientific creationism” in the United States:

…the Darwin centennial had at least one noteworthy but unexpected consequence. While it promoted the respectability and legitimacy of Darwin’s evolution by natural selection to a wide audience, it also drew attention to a theory of longstanding unpopularity and controversiality. The excessive attention and promotion given to evolution by natural selection at the Darwin centennial galvanized into action the very group that most opposed it on religion, philosophical, and moral grounds. One outcome of the Darwin centennial was a regrouping of Christian evangelicals, led by individuals like Henry Morris, into the movement that came to be known as scientific creationism. No longer would they accept the rhetoric of scientific legitimacy given to evolution by means of natural selection; evolution was to remain a problematic concept subject to scientific, as well as religious and philosophical, criticism. (1999, p. 322)

When a theory is defined by what it is not — e.g., Darwinian evolution holds that a transcendent intelligence did not design living things — then that theory cannot help but cart its opposition around, wherever it goes. “Yes, I know he smells bad,” says Theory Q regretfully, about supposedly refuted Theory P, who is sitting in the back seat picking his nose, “but I am defined in opposition to Mr. P, so he has to come along, whether we want him around or not.”
Is it possible for modern evolutionary theory to wean itself from its theological predecessors? Perhaps not, if for no other reason than lampooning “creationists” is always good for a laugh to move a lecture along [see, for instance, the video podcasts of the 2009 talks by Michael Ruse and Phil Ward when they become available]. The deeper question, of course, concerns the content of the theory itself, not its rhetorical framework.
2. While evolutionary theory might have been unified in 1959, today it isn’t.
Example: Michael Ruse opened his lecture by saying that I had tweaked him, via email, about a new article by NIH scientist Eugene Koonin. Koonin argued that “the edifice of the modern synthesis has crumbled, apparently, beyond repair.” Ruse then said that I was in the habit of doing this — tossing problems with neo-Darwinism in his path, in a nah-nah-nah, ID wins fashion.
Not exactly. In fact, my point was exactly the opposite. Michael’s announced lecture topic was “Is Darwinism Past Its ‘Sell-By’ Date?” I thought he would be interested in seeing a recent expression, by a non-neoD-but-very-much evolutionary scientist, that the answer to that question was Yes. For the record, here is our email exchange, with personal material excised:

From: Paul Nelson
Sent: Wednesday, October 21, 2009 12:05 PM
To: Michael Ruse
Subject: Re: FW: Evolutionary Theory proofs
[…]
I look forward to saying hello next week, at the U of C’s Darwin’s 150th event. Your talk won on my schedule, over Joel Kingsolver on natural selection, your direct competitor in the 2:15-2:55 Sat 10/31 time slot. Attached for your amusement is Eugene Koonin’s argument that the Modern Synthesis is most certainly past its sell-by date: “all major tenets of the modern synthesis have been, if not outright overturned, replaced by a new and incomparably more complex vision of the key aspects of evolution” (p. 2).
Does that leave you two fighting over the metaphorical milk carton at the kitchen sink? What am I going to pour on my breakfast cereal if Koonin has his way? 😉
[…]
From: “Michael Ruse”
To: “Paul Nelson”
Sent: Wednesday, October 21, 2009 11:41:04 AM GMT -06:00 US/Canada Central
Subject: RE: FW: Evolutionary Theory proofs
It seems to me that koon is way over the top — more than that, if he is true little comfort there for you
See you next week
micahel
From: Paul Nelson
To: “Michael Ruse”
Sent: Wednesday, October 21, 2009 12:05:06 PM GMT -06:00 US/Canada Central
Subject: Re: Evolutionary Theory proofs
[…]
seriously: allow me a measure of sophistication in these matters. The landscape of theory has (far) more than two options: thus ~neo-D does NOT equal ID, or special creation, or whatever. I’ve belabored this point, in fact, while sharing a dais with you, at schools here and there. Some of the most outspoken critics of neo-D — such as Lynn Margulis, Stuart Newman, or Jim Shapiro — are equally contemptuous of ID. The landscape ranges 360 degrees from almost any interesting point of contention. Plenty of room to wander.
It is likely you will hear from U of C audience members who doubt neo-D, but have zero interest in promoting ID, and actively oppose it.

Just so you don’t miss it: ~neo-D does NOT equal ID. ~Democrat does not equal Republican (I’m not a Democrat, nor a Republican, but a registered independent). What seems to unify evolutionary theory today is (mostly) its opposition to ID, very much in evidence in the 2009 talks.
But I don’t want to end on that sour note. So, here’s a preview of (some of) what to watch for when the video podcasts become available:
3. Recorded a Wow in the margins of my legal pad
— David Jablonski, on the reality and uniqueness of the Cambrian Explosion.
The event took 10-15 million years, tops, Jablonski argued, and is unparalleled in the rest of the history of life. This interval is equivalent (temporally) to the isolation of cichlids in Lake Tanganyika, or to only five times the interval estimated for the speciation of the Galapagos finches (3 million years). “But give the finches more time,” continued Jablonski, “and they’d still be finches.” What was different about the Cambrian Explosion? Jablonski also stressed that the geological record is, pace Darwin, more than “good enough” for us to draw robust inferences from it.
— Phillip Ward, on the pervasiveness of convergence.
Among the many Myths of Talk.Origins ™, probably none is as influential as the so-called “Twin Nested Hierarchies,” according to which molecular data reinforce, or corroborate, the classical historical signal from morphology. The evolutionary trees built on the basis of anatomy have now been supported by molecules, says the myth, and a pretty little myth it is indeed.
Well, the hierarchies are nested, except when they’re not. After lampooning creationists — like I said, the chuckles can be useful to move things along — Ward gave several, some of them downright astonishing, examples where molecular data busted up long-accepted clades, based originally on morphology, and “distributed the groups all over the tree.” Convergent evolution is thus very widespread: “We were simply, greatly misled by morphology alone,” Ward stressed. After another example of unexpected convergence, in the insects: “We were grossly misled by morphological similarities.”
— David Kingsley’s entire lecture on sticklebacks
At a post-conference reception, chatting with PZ Myers, I agreed with his judgment that Kingsley’s lecture was hands-down the best of the conference. Just over ten years ago, Kingsley’s lab at Stanford selected stickleback fishes as a model system in which to study evolution, and they’ve succeeded to a remarkable degree. Using a combination of population genetic surveys, experimental (genetic) manipulation, and DNA sequencing, Kingsley and his co-workers have been able to isolate the genetic changes (in regulatory elements) leading to dramatic phenotypic changes, such as the loss of pelvic structures, pigment, and the like.
Great talk — beautifully illustrated, full of testable implications. If more evolutionary biology were like this, the field would have a much higher reputation among other biological disciplines.
But here’s where PZ and I didn’t agree. (He told me that, as usual, I was confused.) The evolutionary changes that Kingsley et al. have illuminated are all losses. Freshwater sticklebacks, for instance, often lose pelvic structures, and in fact have done so in parallel (with the same regulatory elements being involved) all over the world.
But really interesting macroevolution can’t be losses of this and that. Gotta build novelty, not jettison it (when the latter happens to be advantageous). Mike Behe and I have talked about this quite a bit — his reaction to the Cold Spring Harbor Darwin symposium lectures of this past summer was, “Paul, it was all breaking things and losing things.”
In any case, don’t miss Kingsley’s talk. I also recommend, for its clarity, Elliott Sober’s lecture on the structure of Darwin’s argument, and Jane Maienschein’s talk on the often unhappy relationship of embryology and evolution, for her wit.
It’s a heck of a lot of fun to attend a conference like this, if you don’t mind being the butt of jokes.