Lawrence VanDyke has posted a response to me on the Exparte blog, the blog of the Harvard Federalist Society. I will reply to that as well as a comment he made to my first post on this subject.
VanDyke's response begins with Adam White saying:
Lawrence VanDyke continues to defend himself against the vicious attacks of Professor Brian Leiter and others. He posts this reply to Ed Brayton regarding Leiter's attack.
For the record, I don't think my posts on this situation can fairly be portrayed as a vicious attack. Professor Leiter's reply, I suppose, might be called such. While I agree with him on the substantive issues, I think he would do better to restrain his rhetoric and be a bit more collegial. It only distracts from the substantive issues. I understand his frustration, believe me. You get tired of hearing the same tired nonsense over and over again, and I often have to reign in my sarcasm, occasionally failing to do so.
Having said that, however, I think the reaction from Hunter Baker and VanDyke, striking the martyr pose and accusing Leiter of threatening both VanDyke's career and academic freedom, is hysterically overblown. Academic freedom does not insulate one's published writings from criticism, no matter how sharply worded that criticism is. Still, I think even the informal charge of academic fraud is over the line. I think Mr. VanDyke is guilty of wishful thinking, of badly misreading (as opposed to intentionally misrepresenting) several sources, and of swallowing a lot of nonsense that would not stand up to scrutiny. I don't think he's guilty of academic fraud, which is a serious accusation that shouldn't be thrown around casually even in an informal context. Now, to the substance of the dispute....
VanDyke's response begins:
Mr. Brayton most of your response argues that the links I provided in support of my claim regarding peer-reviewed articles dont in fact support that claim. Whether you are right or wrong, you seem to acknowledge that what I was trying to support was a claim about peer-reviewed articles in support of ID. Otherwise why even argue the point Meyers has already alleged that Axe is a closet ID supporter. But later on you seem to revert to arguing that I somehow was intentionally trying to misrepresent something with my ellipses. I wasnt.
Frankly, I have a hard time believing that the ellipses was not intention. The ellipses only replaced 4 words, for crying out loud, so there was no reason to use them in the first place, multiple times, especially when those 4 words were absolutely crucial to the claim that Leiter made. In a reply of probably several thousand words, you felt the need to take out 4 words to save space and then just happened to give an answer that, in reality, only answered your modified version of his position, not the position he actually took? That does strain credulity a bit, but I suppose I'll give you the benefit of the doubt on that. But the reality remains that Leiter's claim remains true and your links did not answer that claim substantively.
The sources I to which I linked say that there are peer-reviewed articles in support of ID, not just peer-reviewed articles by ID proponents. You are grasping at straws if you are trying to show I was trying to misrepresent Leiter.
Actually, the sources you quote don't really say that at all. In both links, Dembski certainly implies that those articles support ID, at least in his introduction to them. He says that they show that "intelligent design research is in fact now part of the mainstream peer-reviewed scientific literature." But when he introduces the actual articles he is citing, he doesn't try to claim that they "support ID", because he knows that they don't. He has been caught at this game before, as I mentioned in my previous response. More than once, the DI has been caught presenting lists of references that, by implication, allegedly support ID only to have it pointed out that those citations do not, in fact, support ID. So then they backpeddle and say, "Okay, so they don't really support ID, but they do dissent from Darwinism." But then it gets pointed out that they really don't dissent from Darwinism, they merely pose non-adaptationist or non-selective mechanisms, all of which are also well within the purview of evolutionary theory. But none of that stops them from making the same claim all over again to a different audience. They consistently misrepresent the work of scientists and they consistently get caught at it. THAT, I would suggest, is academic fraud. And a careful reading of the links you gave would have shown that none of the sources that Dembski cites actually supports ID or challenges Leiter's position on that question.
However, regarding your claims that the articles themselves dont support ID, I cant argue that directly with you. Im not a scientist. But I am quite confident that the scientists at Discovery Institute would argue (and have argued) vehemently that those articles do indeed support ID.
As I noted above, they actually don't argue vehemently that those articles do indeed support ID, they only imply it, because they know that they can't support that claim. That's why they often phrase it as "these references challenge Darwinism" (though in fact they don't). Nor do I think one has to be a scientist in order to analyze the meaning of articles. The man whose claims you cited, Bill Dembski, is not a scientist either, his degrees are in mathematics, philosophy and theology. Perhaps that explains why he so often gets it wrong when he implies that an article supports ID, but in his case I am far more inclined to blame it on dishonesty than ignorance. He has had the truth pointed out to him too many times, and he is not a stupid man by any means. But he is guilty either of being extremely sloppy or of being dishonest, and since his sloppiness always just happens to coincide with a misrepresentation that supports his position, I think dishonesty is the more reasonable, if less charitable, conclusion.
I am not a scientist either, merely an educated amateur, but I know that a paper that shows that you have to change 20% of the amino acids in an enzyme before function is impaired does not, by any sane criteria, show "extreme sensitivity to perturbation". That is an outright misrepresentation of the article, there are no two ways about it.
Which brings us back to the real issue. The issue isnt really about the peer reviewed articles. I didnt bring them up in my Note; Leiter did in his attack. You have already admitted they are a weak argument. The real questions still are: First, did I commit scholarly fraud as Leiter blatantly accused me of? Second, did Leiter have factual errors and misleading innuendo in his attack (since he accuses me of this, by his definition his post was scholarly fraud if he engaged in such in the very post he attacked me with)?
While I'm sure that is your real issue, it's not mine. I've already stated that I think that charge, even while he probably intended it in an informal manner rather than a formal one, was unnecessary and overly combative. I'll leave you and Leiter to handle the "I know you are but what am I" exchange, I'm addressing the substantive issues, the question of whether ID is a legitimate challenge to evolution and whether it has any place in a science classroom. That was the substance of Beckwith's book, the substance of your endorsement of it, and that is what interests me.
I'm also just intensely fascinated, as an observer, at the kneejerk reaction from ID advocates, immediately claiming persecution whenever anyone disputes them or disparages their work. As any historian of science will tell you, this is one of the hallmarks of crank science. Every obscure crank in the history of science has claimed to be the victim of a hidebound and dogmatic scientific establishment that fears his Truthtm and will stop at nothing to destroy him in order to preserve their favored position in academia and society. As I said before, this makes for good public relations but very poor science. If Dembski and his colleagues really have a scientific model that can withstand scrutiny, then let them put it out before the scientific community, open it up for peer review, suggest hypotheses that can be tested, and get on with the business of testing them. The fact that they have not done so speaks volumes, I think.
Finally, Ive already admitted that I made a mistake in my first post here at Ex Parte by supporting my more than two scientists point using NCSEs Steve site...
But in doing so, you misread it again. You said:
About the "Project Steve," I see what Mr. Brayton is saying. I assumed that because the site parodied supporters of "ID" as "Steve" that when it referred to "Steve" it was referring to ID supporters. I see now my misreading.
But that's just another way of misreading the article. It did not "parody supporters of ID as Steve". The Steves in question are some 400+ scientists named Steve (after Steve Gould) who do NOT support ID. So you didn't see your misreading, you merely substituted misreading #2 for misreading #1. At the very least, this is extraordinarily sloppy citing, especially for a Harvard law student. I suspect, and would hope, that such shoddy citing on a paper at that school would bring down the wrath of your professors and the very poor grade such work demands. And this has been fairly consistent. You cited Dembski's citation of allegedly peer-reviewed journal articles that support ID without bothering to read them and see if that citation was correct. You cited a list of 100 ID supporters without bothering to read the statement to which they agreed, which does not in any way question evolution or support ID. In short, you've kind of swallowed whole the rhetoric of the ID movement without taking the time to do any research on the subject, or even, it seems, to read over the text of the sources you yourself cited. And in doing so, you've opened yourself up to being accused of sloppiness and lack of rigor, at best, and dishonesty at worst. Either way, I think it's fair to expect more than this from a student at one of the finest academic institutions in the world and I certainly think it's fair to point out those shortcomings, especially in light of your desire to cast yourself as the victim of a monolithic orthodoxy.
Just a point of clarification: Axe's paper only shows "extreme sensitivity" for a very loose definition of "extreme" and "sensitivity", but that doesn't mean that the phenomenon doesn't exist. The phenotype:genotype problem is an example: very slight changes in the genotype, such as a single point mutation, can potentially trigger extreme changes in phenotype -- lethality, for instance, which is a pretty extreme effect, if you ask me.
The existence of sensitivity is not an argument against evolution, of course, nor is it any kind of argument for intelligent design.
I don't think there's any question that there are lots of examples of slight changes in genotype that can have an enormous effect on function, even to the point of lethality. But Axe's paper certainly didn't show that. Nor, as you state, would that in any way be a problem for evolution if it did. I can't for the life of me understand why anyone would cite the Axe paper as supporting ID. The implication from Dembski's description seems to be that because enzymes are "extremely sensitive" to the removal of even a single amino acid (never mind for now that the article showed quite the contrary), that means that this particular protein must be irreducibly complex, or something close to it. But if that is the case, the citation shows quite the opposite. They define an IC system as one in which the removal of any component makes the system non-functional. A protein in which you can remove 1/5 of the amino acids in certain sections before function is impaired is anything but irreducibly complex.
Furthermore, we know from the genome products that proteins can show only 30% sequence identity (or less, sometimes down to random sequence similarity) and still maintain essentially identical structures and functions. Generally there are only a few amino acids in a protein where identity is really crucial, in the active site or at some crucial structural spot. Even here, a disabling mutation can often be "rescued" by another mutation elsewhere in the protein (or in an interacting protein), indicating that there may be a huge functional space even where supposedly "fatal" mutations have occurred.
All of this indicates that proteins basically aren't all that "specified" -- an enormous amount of variability is tolerated, and there are a lot of different ways to "solve" the same chemical or structural "problem".
Analogies to English sentences, computer code, etc., are thus highly misleading in this sense.
Here's something that should have occured to me about Lawrence's reply. When he said:
I should have replied that this is exactly why Dembski gets away with this. He lists 4 citations that he implies (without directly saying so) that they support ID, knowing that the vast, vast majority of those who read his work are not in a position to evaluate whether that is true or not. He also uses a rhetorical device to gain sympathy from his readers and cast doubt upon his opponents by claiming:
So he sets up the reader by making them think he's being treated unfairly by Genie because, after all, he gave her these same citations and yet she still says they don't exist. How unfair of her! But the truth is that she doesn't count them because they don't count, for all the reasons we've already provided for why those articles do not either cast doubt on evolution or support ID as an explanation. Then he goes on to list a few citations that he implies provide support for ID, which his audience has neither access to read nor knowledge to understand, and sure enough his readers pick right up on it. Lawrence provides links to them as "proof" that ID does indeed have articles in the scientific literature to support it, and Greg even goes so far as to list them, pretend that HE found them, and on the basis of his mistaken assumption that they answer the question, puff up and get all haughty with Leiter for his "ignorance" and laziness in not going to find these holy grails of ID himself. Goal achieved.
Dembski got exactly what he wanted, he got his followers to accept what he said without bothering to read the citations, then go forth and proclaim the Truth. And when the flaws are pointed out, the followers simply say, "Hey, I'm not a scientist, so I can't argue that with you. But I'm sure these people could prove you wrong." Methinks their faith in Dembski is a tad bit misplaced.
As for the whole Axe thing goes, the best way to test Dembski's claim about "extreme sensitivity" is to mimic the process of evolution through mutation and selection, rather than doing what Axe did, which is to change a whole bunch of amino acids all at once. The literature on directed evolution makes it clear that enzymes do not have "extreme sensitivity"; they can be quite easily converted into enzymes that use different substrates or have different catalytic activity; sometimes they're converted into enzymes with completely different properties altogether. And this happens after relatively few generations. Another example are SELEX experiments that start with randomly generated polymers, and through repeated rounds of selection and mutation, come up with molecules that perform a given function highly effectively. And in this case the given function gets pulled out of a relatively small starting pool of 10^7 or 10^8 molecules.
So the most anoying thing about Dembski's repeated references to Axe (as if he were the only protein chemist on Earth) is that Axe's work is largely irrelevant. The relevant data is out there, and it is continuously ignored by Dembski. His only response is to claim that directed evolution is really just "intelligent design", because it involved researchers, which is just plain dumb.
Steve-
I agree. Contrary to the claims of Behe and Dembski, molecular systems are often highly adaptable. One lab experiment after another has shown that if you remove a component from a complex molecular system, either a protein or one or more amino acids from a protein, the organism will often coopt another protein or another amino acid sequence to preserve the function of the system as a whole. Hence the old biologist's saying "Evolution is cleverer than you". Organisms coopt components to different function all the time, and this has been observed many times. It is exactly this type of cooptive adaptation that provides plausible pathways for complex biochemical systems to evolve.