Monthly Archives: August 2006

The Pope and Antievolution

The Discovery Institute Fellows are salivating over word about the upcoming confab the Pope is having:

Last week, Cardinal Christoph Schonborn of Austria revealed that evolution and creation had been chosen as the subjects for this year’s meeting of the Pope’s Schulerkreis – a group consisting mainly of his former doctoral students that has been gathering annually since the late 1970s. Other participants at the closed-door meeting will include the president of the Austrian Academy of Sciences, Peter Schuster; the conservative ethical philosopher Robert Spaemann; and Paul Elbrich [sic], professor of philosophy at Munich University.

And no wonder. The list of conference participants is pretty much a who’s who of European antievolutionists. It’s like the Catholic church wanted to take its lead from Groundhog Day here in the USA: if the Pope steps out and sees his shadow, the Catholic church will postpone coming to terms with science for another four hundred years.

If there’s at least one scientist without the antievolution baggage, there just might be a chance, though. He could sit throughout the proceedings chanting, “Galileo, Galileo, Galileo…” Pope Benedict might just take the hint.

DOL Departing UD?

Denyse O’Leary, official co-blogger at Dembski’s “Uncommon Descent”, seems to have had a posting hiatus. Her last post on UD is dated the 20th of August. This is prompting comment that perhaps Denyse, religious commentator, will be officially parting ways with UD shortly. Maybe so, maybe not; certainly a week’s posting break would be consistent with Denyse taking a vacation. But where’s the fun in that? Of the other possibilities, there are two main ideas for why Denyse might be breaking away from UD.

First, there is the idea that Denyse is not enjoying her tenure at UD. And the main cause for friction would be former UD “blog czar” and Howard Stern-alike-wannabe David “DaveScot” Springer. Springer is… well, it is difficult to say what Springer is. Springer seems to like to describe himself in terms of what he has been. He used to work for Dell Computers, and made a packet when Dell went from a little computer company to a humongous computer company. What he does now seems to be spouting insults in various online fora, which appears to be more of a Don Rickles channeling than a Howard Stern impersonation. Apparently Springer had not gotten the memo that DOL would be coming on board UD officially, and treated her to his usual spew of invective as a bolded addition to a comment that she left at UD. Between that and another comment Springer made about his penchant for adulterous impregnation, suddenly his ability to make gratuitous additions to other people’s comments was rescinded. Springer then handed in his “blog czar” propeller beanie and decamped to the UDOJ (“U Dream of Janie”) blog, there continuing intermittent castigation of DOL as a “morphodyke” and various other terms of endearment. While Springer was gone, DOL posted away at UD. But as of the 21st of August, Springer was back at UD, officially welcomed to return by William Dembski, and handed author privileges there. One suspects that Denyse wasn’t consulted about this move.

Second, there is the notion that Denyse has found even the limited scope for dissent at UD to be hotter than she wants to handle. On the 19th, she wrote a post there explaining,

First, I find the title of Shermer’s book interesting. If Darwin really mattered, Shermer wouldn’t be writing a book insisting that he does.

I mean, who writes a book called “why better gas mileage matters” or “why preventing cancer matters”? Evident benefits prompt no defence.

UD commenters, culled to be sycophantic to a fault, still couldn’t quite swallow this whole. Denyse wrote two more posts trying to shout out those who took issue with her howler. Her latest post was made the next day. Since then, nothing.

I’m thinking that the vacation hypothesis still has a lot going for it. Antievolutionists are usually quite forgiving of each other, the better to band together against the evil Darwinists, reducing the likelihood that the “huffy Denyse” hypothesis will work. And being an antievolutionist means being ironclad against embarrassment over being wrong, so it hardly makes the “chagrined Denyse” hypothesis a winner. But time will tell, I guess.

Update: Over at After the Bar Closes, commenters note that Denyse has been posting to other blogs, which discomfits the vacation hypothesis. However, she apparently did say that she would be posting less frequently while she is engaged in copy-editing a book. So the “too busy” hypothesis appears and has some confirming evidence.

Update: DOL is back on UD, breaking her hiatus with some stern admonishments for now-retired Vatican astronomer George Coyne. Stuff about keeping his private theology to himself, and not letting himself be treated as an authority on scientific issues that have nothing to do with his field of study. DOL evidently is as irony-deficient as many other antievolutionists.

Takedown of Wells’s “The Politically Incorrect Guide to Darwinism and Intelligent Design” In Progress

Over on the Panda’s Thumb, the PT Bar Crew is taking down Jonathan Wells’s new propaganda publication, The Politically Incorrect Guide to Darwinism and Intelligent Design. Reed Cartwright led off with an introduction, which will add a table of contents linking to each of the chapter critiques as they are posted to PT. Burt Humburg followed with his critique of Chapter 1, taking Wells’s to task on his vague and inconsistent use of words, and persistent refusal to say what, exactly, intelligent design is. PZ Myers weighs in with a critique of Chapter 3, wherein he reveals various quotemining by Wells and convenient overlooking of the facts of embryology.

Most of the rest of the chapter critiques will follow over the next two to three weeks. Be sure to tune in. Alan Gishlick and I are working on Chapter 2, and perhaps Mike Dunford will join us after he polishes off two other chapters himself. Mark Perakh already has a critique up at TalkReason concerning Wells’s perverse misuse of the Lysenko affair in the Soviet Union. This will be reposted to PT a bit later. Check it out.

Expert Witnessing: Daubert and Behe

In looking at other stuff online related to expert witness rules, I came across a page by Patrick Malone that offers advice to lawyers on the selection and retention of an expert witness coming under Daubert scrutiny. Daubert v. Merrell Dow resulted in a set of rules for courts to act as “gatekeepers” to expert testimony, excluding those experts who don’t produce reliable testimony by established methods. Daubert rules for experts have been adopted by many states across the country. Where Daubert isn’t used, the earlier Frye rules are the usual standard.

Something that I need to look at is that apparently the Discovery Institute’s book, Traipsing Into Evolution, tries to argue that Judge Jones did things wrong because of Daubert considerations. It sounds like a ludicrous argument on its face, but I’ll need to have a look at the specifics before I can confirm or reject that impression.

But in any case, there was a particular passage in Malone’s article that made me think of Michael Behe, defense expert witness last year in the Kitzmiller v. DASD trial.

Keeping an open mind Before Daubert, an adversary’s discovery that your expert had formed an opinion, then read the relevant literature, would amount to, at worst, a credibility point for cross-examination. Now, that kind of discovery can get an expert tossed off the case.12 Beware the expert who claims that he or she doesn’t need to read the literature on the subject because no amount of literature could change his or her mind. That is exactly what happened in Cooper. The expert rationalized his behavior, stating, “[A]after I read those two articles years ago, they didn’t affect my prior judgment—and they still haven’t—that smoking doesn’t have anything to do with healing in spinal fusion. So even if there were 10 more articles, I’m not going to change my mind about it.”13 The court was not impressed.


12. See, e.g., Mitchell, 165 F.3d 778, 783.
13. Cooper, 259 F.3d 194, 202.

Remember Behe being confronted with 58 peer-reviewed articles and several textbooks discussing the evolution of the immune system? Remember Behe admitting he hadn’t read a lot of those? And remember Behe saying that he was confident that the material just wasn’t good enough, sight unseen? It seems obvious that the Thomas More Law Center could have benefited from reading Patrick Malone’s 2003 article on expert witnesses. They could have avoided a costly mistake.

Update: Ed Brayton pointed me to the actual decision in Cooper and here is the relevant section from it:

In the face of the medical literature and Cooper’s own records, Dr. Mitchell categorically dismissed any suggestion that Cooper’s smok- ing was the cause of the nonunion. Dr. Mitchell stated that he rejected the medical articles as unpersuasive after he read just two of them. When asked if he should have considered more of the articles, Dr. Mitchell replied:

No, for the simple reason, after I read those two articles years ago, they didn’t affect my prior judgment, and they still haven’t, that smoking doesn’t have anything to do with healing in spinal fusion. So even if there were ten more arti- cles, I’m not going to change my mind about it. In this case, Dr. Mitchell did not identify specifically how he ruled out smoking and other potential causes of the nonunion. Simply asserting that he read two articles on smoking and rejected them as unpersuasive is insufficient. Such a practice offers no solid grounds for rejecting smoking as a cause of the nonunion, and renders his opinion that the Rogozinski System was the actual culprit little more than speculation. As the Supreme Court has repeatedly held, “nothing in either Daubert or the Federal Rules of Evidence requires a district court to admit opinion evidence that is connected to existing data only by the ipse dixit of the expert.” Kumho Tire, 526 U.S. at 157 (quoting Joiner, 522 U.S. at 146).

Fast forward to Behe on the stand in the Kitzmiller case:

[169]Q. You haven’t read the books that I gave you?

[170]A. No, I haven’t. I have read those papers that I presented though yesterday on the immune system.

[171]Q. And the fifty-eight articles, some yes, some no?

[172]A. Well, the nice thing about science is that often times when you read the latest articles, or a sampling of the latest articles, they certainly include earlier results. So you get up to speed pretty quickly. You don’t have to go back and read every article on a particular topic for the last fifty years or so.

[173]Q. And all of these materials I gave you and, you know, those, including those you’ve read, none of them in your view meet the standard you set for literature on the evolution of the immune system? No scientific literature has no answers to the question of the origin of the immune system?

[174]A. Again in the context of that chapter, I meant no answers, no detailed rigorous answers to the question of how the immune system could arise by random mutation and natural selection, and yes, in my, in the reading I have done I have not found any such studies.

Score another one for Santayana.

Cutting and Pasting All Over Again

Carl Zimmer has a post up about the tremendous similarity between antievolution opinion pieces published recently by Jack Kemp and Phyllis Schlafly. It is a nice catch. (There may be a possibility that some publisher mixed up bylines. I’ll post an update if that is the case here.)
However, in antievolution this sort of thing is far from uncommon. There is, after all, a playlist of arguments in the antievolution ensemble, and each antievolution advocate is essentially a “disk jockey” of screeds. They may “re-mix” an argument, adding in their own particular touches. They may play them up straight from time to time. And, just as a disk jockey would be perplexed if you accused him of plagiarism for playing a particular song, so too do antievolutionists often simply fail to grasp the concept of plagiarism as something relevant to what they are doing. In theology, providing a “proof-text” is just what you do to make a point. It doesn’t necessarily have to be referenced; the important thing is simply to make sure that the argument is made. That there are other modes of thought that put a premium on originality and paying attention to priority is essentially alien.

Update: As I noted parenthetically in my opening paragraph above, it turns out this time that the similarity is actually due to someone messing up on the byline. No plagiarism in this particular case. See Carl’s blog for the details.

Cooper’s Confusion

Seth Cooper is upset. Apparently unsatisfied with his attempt to smear the Dover, PA school board that replaced the “intelligent design” advocates whose ill-considered policy cost the district \$1M by blaming the replacements rather than those responsible, Cooper has another screed up to try to claim somebody, anybody, else may be guilty of something or other. Cooper is at least on board with the current target of choice: ID advocates have declared open season on Judge John E. Jones III’s character and skills. Cooper teams up with Leonard G. Brown III for this one.
Cooper is mainly mad about the Foundation for Thought and Ethics being excluded by Jones from direct participation in the Kitzmiller case last year. The result is a sob story with rather a lot of cock and bull in it. Given that I realize that I am mortal, I’ll just spend a bit of time with this segment of Cooper’s prose:

On April 28, 2005 Texan Jon Buell received subpoenas from the ACLU. Buell is President of FTE, the non-profit organization that publishes Pandas. Headquartered near Dallas, FTE receives revenues from sales of the textbook and has intellectual property ownership of its contents. From a handful of news stories, Buell was dimly aware of the distant Pennsylvania lawsuit. He had received no contact from the Dover Board’s attorneys. ACLU subpoenas demanded he be deposed in May, and that he turn over all documents related to Pandas. Surprisingly, the ACLU also demanded Buell turn over all unpublished working-draft materials for FTE’s as-yet-unreleased textbook, The Design of Life: Discovering Signs of Intelligence in Biological Systems.

The ACLU’s subpoenas of FTE were a broadside representing potential catastrophe for the publisher. The ACLU had secured as consultants the pro-Darwin and Oakland-based anti-ID lobby group, National Center for Science Education (NCSE). The NCSE has long been a harsh critic of Pandas, and the ACLU sought to place the important Design of Life draft into their hands.

FTE promptly filed motions in Texas and Pennsylvania for a protective order to quash the subpoenas. On May 12, 2005, Judge Jones conducted a hearing. He entered a weak protection order, denying the motion to quash. FTE was required to hand over its Design of Life manuscript and related Pandas documents. Judge Jones simply warned the ACLU and NCSE not to publicize Design of Life’s contents prior to publication and instructed the ACLU to notify FTE attorneys as to who received draft copies.

OK, so Cooper didn’t like the fact that drafts of The Design of Life were put into the hands of the plaintiffs and their lawyers and consultants. Is that the complete story, Seth? Well, of course not.

What Seth doesn’t say anywhere in his essay is the one name that must figure largely in any complete history of this event: William A. Dembski. Dembski’s involvement is more than any missing footnote, no, Dembski’s affiliations and actions were central to this little melodrama. Moreover, once one appreciates Dembski’s role in this, the entire thesis that Jones performed as an activist judge in the release of The Design of Life can be seen to be so much poppycock.

(See also Ed Brayton’s post detailing why Cooper and Grumm are wrong on the FTE “timeliness” issue.)

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Upgrades Break Things

Back when I worked at the Pacific Northwest Laboratory, we worked on a software project hosted on DEC Ultrix workstations. We were in the midst of designing a second version of a map database application when a DEC representative working on a problem with a workstation noticed that we were running Ultrix 4.0. “You should upgrade to Ultrix 4.1,” he told us, “It’s covered in your service contract.” It sounded good to us. So he came back another day, and upgraded the OS on all our workstations.

I think it was an hour or so later when one of us checked out a file, made a change, and tried to compile the system. A stream of errors was emitted, daunting in its length. Our code was all in K&R style C. The new C compiler in Ultrix 4.1 not only used ANSI style headers, but had no known means of telling it to accept K&R headers. We spent about two weeks revising the entire code base of the system to use the ANSI headers. We took to calling our recent system software change as the “operating system downgrade”.

Yesterday, a bunch of software packages got updated on the server here. Apache, MySQL, PHP, and several others were brought up to the cutting edge releases. This, predictably, caused some problems.

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Antievolutionary Objections to Evolutionary Computation

Back in 1999, I started a draft of an article about objections to evolutionary computation. It looks like now would be a good time to remind people that these arguments against evolutionary computation have long been addressed.

Creationist Objections

1. Natural selection is an inadequate theory of adaptation because it does not provide the basic rules for successful computer simulation.[1]

Natural selection turned out to be perfectly adequate as a source of basic rules for simulation. The field of evolutionary computation dates back to the late 1950’s or early 1960’s. Even when Marcel-Paul Schutzenberger assured the attendees of the mid-1960’s Wistar conference on mathematical challenges to the Neo-Darwinian synthesis that all efforts to model natural selection on computers just “jam” the machines, another attendee spoke out saying that he had successfully run such simulations, and was, in fact, impressed with how quickly they worked.

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Many Ark. Candidates Say Intelligent Design in Schools is OK

Many Ark. Candidates Say Intelligent Design in Schools is OK

Remember how Arkansas passed a law similar to Tennessee’s Butler Act in the wake of the Scopes trial? That law prohibited teaching evolutionary biology to students. In 1967, the Supreme Court struck down that Arkansas law in its Epperson v. Arkansas decision. Then, in 1981 Arkansas passed Act 590, a “balanced treatment” law that would have required teachers to present “creation science” whenever they presented evolutionary biology. A federal district court decision in McLean v. Arkansas by Judge William Overton ruled Act 590 as unconstitutional.

After the Kitzmiller v. DASD case last year, several of us who watch these things thought that “intelligent design” had had its McLean case in KvD, but that it had yet to have its Edwards case, that is, a case that would take the issue of teaching “intelligent design” as science to the Supreme Court and get a ruling that was binding across the country.

The news article linked up at the top of this post shows that Arkansas is aiming to again spend more of their taxpayer dollars in litigation over religiously motivated antievolution. Both the major party candidates for governor are saying that teachers should have the “academic freedom” to teach students about “intelligent design”.

So far as I can see, these folks haven’t gotten the memo that “intelligent design” is a label past its sell-by date. If Arkansas adopts a “maybe teach ID, maybe don’t” policy, we can expect another big legal case. And it doesn’t look like a winner for Arkansas this time, either. The KvD trial and decision show exactly how this can be approached. I don’t expect the Discovery Institute’s A-team to be any more ready to testify under oath for Arkansas than they were for Dover, Pennsylvania, and I doubt that those who did show up to testify will want a second helping of cross-examination. That will leave Arkansas with calling a bunch of second-string ID advocates as experts. I think we can be confident that many of the pro-science experts from the KvD case will answer the call to appear in Arkansas if this proceeds within the next few years. The ID advocates were seriously overmatched in KvD, and I don’t see things getting any better for them in Arkansas.

There are some nice places to visit in Arkansas within a couple of hours drive from Little Rock. I think I’ll go visit my AAA office and pick up some maps and tour books.

Bacteria can help predict ocean change

Bacteria can help predict ocean change

This study found that particular marine bacteria have well-defined niches, like many metazoan species. This means for for many bacteria, the presence or absence of them can indicate changes in the environment.

The idea of monitoring species to provide some idea of the health of an ecosystem has been around for a long time. Usually, though, researchers have looked to the opposite edge of the food web, at top predators, for instance, to fill the role of an indicator species.

There are a number of potential advantages to using particular bacterial species for this task. First, there is ubiquity. If you use a top predator, you have a lot of work ahead of you doing surveys and accounting for bias due to the level of effort put into the sampling. This isn’t a problem with bacteria. Second, there are the numbers. Lots and lots of bacteria versus exceedingly few top predators. You can make various quantitative measurements that likely just aren’t possible with rarer metzoans. Third, nobody gives a rip about the bacteria in your water samples. No paperwork, no permits required, and no PETA protesters to worry about.

Despite these considerations, I find it personally difficult to get worked up over microbial ecology. But it looks good for folks who already work in microbiology who want to get into marine science.

Behe Called on His Bluff

Over on Uncommon Descent, “BarryA” expresses his disappointment in Judge Jones. Specifically, “BarryA” thinks that Michael Behe got a raw deal during the Kitzmiller v. DASD trial last year when the topic of the immune system came up. Jones, according to “BarryA”, should not have permitted the plaintiffs’ attorneys to present the stack of papers and textbooks containing discussion of the evolution of the immune system, at least not without reading the contents of each item into the record.

Here is the passage from Jones’s decision that seems to have upset “BarryA”:

The immune system is the third system to which Professor Behe has applied the definition of irreducible complexity. Although in Darwin’s Black Box, Professor Behe wrote that not only were there no natural explanations for the immune system at the time, but that natural explanations were impossible regarding its origin. (P-647 at 139; [128]2:26-27 (Miller)). However, Dr. Miller presented peer-reviewed studies refuting Professor Behe’s claim that the immune system was irreducibly complex. Between 1996 and 2002, various studies confirmed each element of the evolutionary hypothesis explaining the origin of the immune system. ([129]2:31 (Miller)). In fact, on cross-examination, Professor Behe was questioned concerning his 1996 claim that science would never find an evolutionary explanation for the immune system. He was presented with fifty- eight peer-reviewed publications, nine books, and several immunology textbook chapters about the evolution of the immune system; however, he simply insisted that this was still not sufficient evidence of evolution, and that it was not “good enough.” ([130]23:19 (Behe)).

Tom English pointed out in comments that Behe’s unfamiliarity with the material seemed to be the point of the exercize. Here’s how “BarryA” responded to that:

Thank you for your quotations from the record. It now seems that I gave Judge Jones too much credit. If no expert testified that the books and articles were authoritative that should have been the end of it. The judge should have stopped them right there. In other words, the plaintiffs did not even make it through the first Rule 803(18) hoop, much less the second. Maybe I also gave the defendants’ lawyers too much credit. Once Behe testified that he was unfamiliar with a particular book or article they should have objected to any further reference to it or use of it.

Excuse me? “BarryA” had already in his main post stipulated that Behe had admitted that the materials presented met that hurdle:

Based on the quotes from Behe’s testimony, it is fairly clear that this step was met. Behe admitted the books and articles were learned treatises.

As to how the articles came into the record, and how familiar Behe was with them, let’s look at the trial transcript.
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A Note to Glenn Shrom

Glenn Shrom is hawking a book of his. He notes with apparent approval a statement by Art Chadwick and Robert DeHaan that would give credence to the claim that “intelligent design” can be or is a part of science. Then he notes with apparent disapproval that Creationism’s Trojan Horse by Barbara Forrest and Paul R. Gross does not approach ID in that credulous fashion. Well, OK, everyone has an opinion. But Shrom went a bit over the line:

Then in 2004, Barbara Forrest and Paul R. Gross completely ignored that first approach in their book Creationism’s Trojan Horse: The Wedge of Intelligent Design**. Instead they choose to focus, as most of America does, on the religious and philosophical approaches to ID. Their book does not delve into what ID is as a science, but addresses how ID has been used for political and ideological purposes.

It’s one thing to note that CTH doesn’t do much in the way of trying to evaluate ID claims on whatever dubious merits they may once have had. It’s another to pretend that there isn’t anything else out there relevant to the point that Shrom brings up.

So, I wrote Shrom an email to point this out. I reproduce the text of it here.

Concerning the advertisement on you wrote:


In Getting Past the Culture Wars, I appeal to both evolutionists and Creationists to drop their preconceived, visceral baggage and take a fresh look, with reason and fair-mindedness, at the first approach. Such an enlightened vision is desirable for good education, good religion, good science, and good judicial rulings.

[End Quote]

Been there, done that. “Why Intelligent Design Fails”, now available in paperback from Rutgers University Press, fills the bill. Of course, it finds that ID’s claims to science are simply overblown and pretentious. We took up the ID claims as they were and put in the time and effort to evaluate them against the relevant scientific knowledge. Uniformly, they failed to make the grade.

Intelligent design advocates has been steadily ignoring “Why Intelligent Design Fails” since its publication. The question is why you would ignore it in your advertisement, since it rather precisely meets the criterion that you state, and instead you choose to focus upon a book that never promised to deliver that sort of examination of the arguments. At best, this oversight indicates an essential ignorance of the relevant literature. At worst, it indicates a deliberate misdirection intended to mislead the reader.

Web page for Why Intelligent Design Fails


A Virus, I Think

I’ve been under the weather, which accounts for the paucity of posts here. Yes, I know, I was really under the weather when I started this weblog.

In any case, I started feeling some scratchiness in my throat last week. I started taking some zinc lozenges, which seemed to help with the symptoms at least. I made it through my workshop presentation last week and my sermon at the UU church in Walnut Creek this past Sunday all right. Monday, I could hardly talk at all. This is not a good thing for a guy whose scoutmaster used to call him “Motormouth”.

Things aren’t quite so bad today. We’ll see how things shape up for the weekend. If I’m still scratchy, I’m thinking Friday will be a good day to visit my primary care physician.