Lawrence VanDyke has left a comment below, which I would like to bring up here to address in more detail. Lawrence wrote:
I left out the "in support of ID" because I assumed that much was obvious in context. You make it sound like I was trying to make Leiter say ID proponents haven't published any articles in peer reviewed journals at all. If I were trying to say that, my response to Leiter's statement would have been much simpler and I wouldn't have bothered to address Pharyngula's post. Nice try.
But the two links you provided don't address what Brian said. They do not provide a single example of an article published in a peer-reviewed journal. In the first link, Dembski is responding to a letter that my friend Genie Scott sent to the Texas Board of Education. In the process, he misrepresents what Genie said, but that is another story for another day. At any rate, there is not a single example in Dembski's response of an article published by an advocate of ID in a peer-reviewed journal in support of ID. He only cites two articles therein. The first is from two mathematicians who do not support ID, who wrote an article that also does not support ID, in a mathematics journal. But since it does cite a statistical concept that Dembski uses in one of his books, he lists it. The second is Denton, Marshall and Legge's article in Nature which is merely a reference to another article they published in the Journal of Theoretical Biology about "evolution by natural law". This in now way supports ID, and Dembski is careful not to claim that it does, he merely says that ID is broad enough that it might incorporate this. But in fact, that's not the case at all. The article in question does not posit any sort of controlling intelligence that designed any natural systems.
On the basis of these two articles, neither of which addresses Leiter's claim at all, Dembski claims that "intelligent design research is in fact now part of the mainstream peer-reviewed scientific literature." That's a rather large leap, isn't it?
He also cites his own book, The Design Inference, which he says was peer-reviewed in order to get in to the monograph series of which it was a part. But nothing in that book actually supports the claim that ID is a viable alternative to evolution. TDI merely lays down the groundwork of his statistical theory that he bases his later claims on. There's lots of mathematics in it, but virtually no science. Even if his "explanatory filter", in the abstract, passes through peer review in a statistics or philosophy context (and in fact there are very good reasons to reject that as well), it still wasn't applied to living systems in that book to support the contention that living systems, either in general or in particular, must have been designed by some intelligent force. At any rate, it does not engage Leiter's demand, which was for articles in peer-reviewed journals, presumably scientific journals.
The second link that you provided was also from Dembski, citing the same 2 articles discussed above, plus the Axe article that Paul Myers answered quite well. Not only does the Axe article not support ID, but Dembski clearly distorts the conclusion of the article. Here is Dembski's description of the article:
This work shows that certain enzymes are extremely sensitive to perturbation. Perturbation in this case does not simply diminish existing function or alter function, but removes all possibility of function.
But the article shows anything but "extreme sensitivity to perturbation". It shows that you have to change out 20% of the amino acids in a given enzyme before function is impaired. There is absolutely nothing in that article that provides any support whatsoever for ID and it is simply dishonest for Dembski to continue to claim that it does.
The only other article that Dembski cites on this page is Loennig and Saedler's article on transposable elements. Notice that Dembski doesn't say that this article supports ID. He says that it is "non-Darwinian", which is a term he often uses. What it really means is "non-selective", but non-selective mechanisms are not in any way a problem for evolutionary theory. It's this little shell game that Dembski and other ID advocates like to play. They label an idea as "non-Darwinian", which simply means "non-selective" or "non-adaptationist" and then imply that since ID is also "non-Darwinian", all "non-Darwinian" ideas are a part of ID. Clearly a very silly argument, don't you think?
This is nothing new for Dembski or the Discovery Institute. In 2002, they provided a list of 44 citations to the Ohio state school board that allegedly showed problems with evolution or support for ID. But when the authors of all of those 44 papers were contacted, every single one of them said that the Discovery Institute was distorting their work, that nothing they had written provided any reason to doubt evolution or to support ID. But even after being shown the statements from every single author whose work they cited saying otherwise, the DI's Stephen Meyer still wrote an op-ed piece a month later claiming that those citations "raise significant challenges to key tenets of Darwinian evolution" - never mind that the authors of those articles themselves said that the articles did no such thing.
Their ability to distort citations seems to be matched quite well by yours. You claimed that the NCSE "grudgingly admitted that 1% of scientists doubt evolution", but the link you provided to the NCSE said the exact opposite of what you claimed. But it's nice to know that you went to the trouble of qualifying the manner in which they admitted what they didn't admit.
As far as your claim to have addressed Paul Myers' criticism of the Axe paper, here is what you wrote in that regard:
Meyerss exhibit number one to refute Axes peer-reviewed journal article - get this: Axe is a closet Intelligent Designer! Wow, thats a shocker. We were all expecting the naturalistic evolutionists to write peer-reviewed articles supporting design theory! Not only is this ridiculous genetic fallacy, it isnt very smart genetic fallacy. Meyer next does some hand-waving, pronounces the claim that the paper speaks significant[ly] to ID ludicrous (I guess were just supposed to trust him on this), and ignores the other three journal articles.
If you think this in any way refutes what Paul wrote, I can't imagine how you managed to get into law school. One would think, based on what you wrote, that Paul tried to "refute Axe's peer-reviewed journal article" by saying, "he's an ID supporter, so he must be wrong." But that isn't even close to the truth. First, Paul did not attempt to "refute Axe's peer-reviewed journal article." In fact, he specifically accepts the data that Axe provides, saying,
It's not a bad paper. It says something about the range of tolerance for change in proteins, and that even portions of the sequence remote from the active site contribute to the integrity of the enzyme; nothing surprising or unexpected, even to us evolutionists, but it is good to see the data documenting it.
Second, he did not use the fact that Axe is Dembski's friend and an ID supporter to argue in any way against the conclusions that Axe drew in his paper. What he did argue against was Dembski citing this paper as one that supports ID when it does nothing of the sort. He also points out, as I did above, that Dembski completely misrepresents the conclusions of the paper, pretending that it showed "extreme sensitivity to perturbation" when in point of fact it showed 20% resistence to perturbation. You did not address a single argument that Paul makes for why it is dishonest to cite the Axe paper as an example of a peer-reviewed article supporting ID. Yet you want to claim that your non-answer to Paul proves that your ellipses didn't make it appear that you answered the claim that Bryan made by changing the substance of that claim. Sorry, but I think I've shown pretty conclusively that this argument just doesn't fly, especially in light of your complete distortion of what the NCSE "grudgingly admitted".
Look, I frankly think that ID critics should stop bringing up the fact that no pro-ID article has ever been published in a peer-reviewed science journal. I think this claim, while true at this point, is fairly meaningless, and at some point they'll probably manage to get one through. There are, after all, hundreds and hundreds of obscure science journals and peer review is hardly a guarantee of scholarly rigor. What really matters is not whether they've ever managed to get a single article published or not, but whether they've managed to actually develop a testable, falsifiable model that explains the data well. And on that point, ID can only be described as an utter failure at this point. If you can name a single testable hypothesis that flows from the ID "theory", you'll be the first one to manage it. And until they have produced that, they simply are not doing science, they're just promising that sometime in the future they will be doing science.
"But when the authors of all of those 44 papers were contacted, every single one of them said that the Discovery Institute was distorting their work, that nothing they had written provided any reason to doubt evolution or to support ID. But even after being shown the statements from every single author whose work they cited saying otherwise, the DI's Stephen Meyer still wrote an op-ed piece a month later ..."
Two minor inaccuracies here, at least judging from the analysis on the NCSE web site. First, not all of the authors responded, although a lot of them did. Second, the analysis quoted only some of the authors' responses; presumably NCSE didn't want to bore people by including the full comments. NCSE offered to make the full set of responses available on request to members of the Ohio state board of education and the press.
Mr. Brayton - I reply to this post at Ex Parte - where I posted my original reply to Professor Leiter. That will likely be my last post on this topic: I need to get back to my neglected studies and make sure Leiter's aspirations regarding my career don't materialize for lack of diligence on my part.