Recently in Intelligent Design Category

(The following is a follow-up to a comment I made in this thread.) There is much abuzz in the ID-o-sphere regarding Stephen Meyer’s new book, “Signature in the Cell: DNA and the Evidence for Intelligent Design”. The book is a lengthy recapitulation of the main themes that ID proponents have been talking about for the past 15 years or so; indeed, there will be precious little that is new for seasoned veterans of the internet discussions and staged debates that have occurred over the years.

Long though the book is, it is built around one central theme - the idea that the genetic code harbors evidence for design. Indeed, the genetic code - the triplet-amino acid correspondence that is seen in life - is the “Signature in the Cell”. Meyer contends that the genetic code cannot have originated without the intervention of intelligence, that physics and chemistry cannot on their own accords account for the origin of the code.

It is this context that a recent paper by Yarus et al. (Yarus M, Widmann JJ, Knight R, 2009, RNA-Amino Acid Binding: A Stereochemical Era for the Genetic Code, J Mol Evol 69:406-429) merits discussion. This paper sums up several avenues of investigation into the mode of RNA-amino acid interaction, and places the body of work into an interesting light with respect to the origin of the genetic code. The bottom line, in terms that relate to Meyer’s book, is that chemistry and physics (to use Meyer’s phraseology) can account for the origin of the genetic code. In other words, the very heart of Meyer’s thesis (and his book) is wrong.

For details, follow this link, where comments may be left.

A pen-pal of mine sent me the following message regarding Stephen Meyer’s Signature in the Cell:

The Dishonesty Institute is mounting a campaign in support of Meyer’s book over at Amazon.com. In the past day there have literally been scores of new positive 5 star reviews posted by those who have seen the Dishonesty Institute’s e-mail appeal. Please vote Nay on each of these reviews and Yea on the negative ones, especially mine and Donald Prothero’s, since ours are the most comprehensive negative one star reviews posted at Amazon.com.

By Don Prothero http://faculty.oxy.edu/prothero/index.htm

Don Prothero is a paleontologist and Professor of Geology at Occidental College in Los Angeles, and Lecturer in Geobiology at the California Institute of Technology in Pasadena, and author of Evolution: What the Fossils Say and Why it Matters, in my opinion the very best book on fossils and evolution for the general reader. Last night, Monday, November 30, Prothero debated (along with Michael Shermer) ID advocates Stephen Meyer (longtime head of the Discovery Institute’s Center for the Renewal of Science and Culture) and Richard von Sternberg (the former editor who in 2004 published Meyer’s pro-ID article in the last issue of the Proceedings of the Biological Society of Washington (D.C.) which Sternberg was scheduled to edit, despite the article being wildly off-topic for an alpha taxonomy journal, substantially copied from other Meyer publications, badly inaccurate, and just weird in several ways). Sternberg is now, I believe, an employee of the Discovery Institute.

Prothero wrote these remarks directly after the debate and emailed them to me. I have added links where relevant. — Nick Matzke

My mind is a bit fuzzy from the loss of sleep, and the two hours of “debate” went by very quickly, so I cannot recall all the details, let alone recount them. Here are my morning-after thoughts about last night’s “Battle in Beverly Hills.” I don’t know when they’ll release the video recording of the event, but when it does come out, hopefully it will be possible to post it so you can all see for yourself how it went. My subjective summary of it is that our side did very well: I caught them off-guard with new arguments they had no answer for; Shermer pushed them hard repeatedly to state who the “Designer” was (and Meyer finally conceded it was God), while we both pushed them hard on the fact that neither of them ever addressed the topic of the debate, “Origins of Life.” I could tell that they were rattled a number of times, and I definitely shook up Meyer and got under his skin with my answers. Several times Meyer and Sternberg were arguing with each other, leaving the moderator, our side, and the audience wondering who runs their show. The best sign of my effect on them was Meyer trying to challenge MY credentials, or dodging a tough question by playing the sympathy card and calling me “condescending” — and the virulent post on the Discovery Institute site this morning, full of lies and spin. Of course, the event is staged so that no one will really “win”. Their supporters turned out and dominated the audience, but I had a LOT of people come up to me during the book signing (we sold a LOT of books) and congratulate me, or discuss points further with me. And we got just as much applause and sympathetic laughter at our well-turned phrases as they did.

Scientists point out, quite rightly, that the religio-political charade known as “intelligent design” (ID) is not good science. But how do we know this?

One of the hallmarks of science is that it is fruitful. A good scientific paper will usually lead to much work along the same lines, work that confirms and extends the results, and work that produces more new ideas inspired by the paper. Although citation counts are not completely reliable metrics for evaluating scientific papers, they do give some general information about what papers are considered important.

ID advocates like to point to lists of “peer-reviewed publications” advocating their position. Upon closer examination, their lists are misleading, packed with publications that are either not in scientific journals, or that appeared in venues of questionable quality, or papers whose relationship to ID is tangential at best. Today, however, I’d like to look at a different issue: the fruitfulness of intelligent design. Let’s take a particular ID publication, one that was trumpeted by ID advocates as a “breakthrough”, and see how much further scientific work it inspired.

The paper I have in mind is Stephen Meyer’s paper “The Origin of Biological Information and the Higher Taxonomic Categories”, which was published, amid some controversy, in the relatively obscure journal Proceedings of the Biological Society of Washington in 2004. Critics pointed out that the paper was not suited to the journal, which is usually devoted to taxonomic issues, and that the paper was riddled with mistakes and misleading claims. In response, the editors of the journal issued a disclaimer repudiating the paper.

Putting these considerations aside, what I want to do here is look at every scientific publication that has cited Meyer’s paper to determine whether his work can fairly said to be “fruitful”. I used the ISI Web of Science Database to do a “cited reference” search on his article. This database, which used to be called Science Citation Index, is generally acknowledged to be one of the most comprehensive available. The search I did included Science Citation Index Expanded, Social Sciences Citation Index, and Arts & Humanities Citation Index. Even such a search will miss some papers, of course, but it will still give a general idea of how much the scientific community has been inspired by Meyer’s work.

I found exactly 9 citations to Meyer’s paper in this database. Of these, counting generously, exactly 1 is a scientific research paper that cites Meyer approvingly.

Read more at Recursivity.

Just last week over at the Thinking Christian blog there was a huge stink raised over the alleged inappropriateness of linking ID to creationism. After much argument the anti-linkage people more or less conceded that there were some good reasons to link ID to a somewhat generic definition of creationism (relying on special creation), but still protested loudly about how inappropriate it was to make the linkage, because most people (allegedly) would assume that creationism = young-earth creationism, and linking ID to young-earth creationism was oh-so-wildly unfair.

Well, it’s now a week later, and, what do you know, but right there on the latest blogpost on William Dembski’s Uncommon Descent is a big fat advertisement for a straight-up young-earth creationist conference. And who is endorsing the conference? Dean Kenyon, Discovery Institute fellow, coauthor of Of Pandas and People, and one of the most-cited inspirational figures in the whole ID movement, who is mentioned dozens of times in Stephen Meyer’s new book Signature in the Cell. Here he is, endorsing young-earth garbage:

According to US biophysicist Dr. Dean Kenyon, “Biological macroevolution collapses without the twin pillars of the geological time-scale and the fossil record as currently interpreted. Few scientists would contest this statement. This is why the upcoming conference concentrates on geology and paleontology. Recent research in these two disciplines adds powerful support to the already formidable case against teaching Darwinian macroevolution as if it were proven fact.”

…proving that, yep, he’s still YEC, as has been his consistent position since at least 1980, even though this was widely doubted over on the Thinking Christian blog, and even though Stephen Meyer and all other ID advocates systematically obscure this fact.

So who is the one confusing ID and YEC? Not me. They do it themselves.

We have a twofer! In his account of his visit with Stephen Meyer to Norman, Oklahoma, a couple of weeks ago, Jonathan Wells made another totally stupid remark just following the one for which he got an earlier award. This one contains a deceptive analogy that the ID creationists have grown fond of lately. Recall that their recent mantra has been ‘evolution can’t increase “biological” information.’ That’s the shorthand gloss of Dembski’s so-called Law of Conservation of Information.

In the Q&A Wells ‘explained’ to a questioner that HOX genes are remarkably non-specific, and burped up the egregiously stupid remark for which he got the earlier award:

If evolutionary changes in body plans are due to changes in genes, and flies have HOX genes similar to those in a horse, why is a fly not a horse?

To win his second award, Wells went on to write another truly dumb thing.

It was a tough call given Casey Luskin’s stupidity about Ardipithecus, but we have a winner. In an account of Stephen Meyer’s talk at the University of Oklahoma last week, Jonathan Wells wrote

Furthermore, the similarity of HOX genes in so many animal phyla is actually a problem for neo-Darwinism: If evolutionary changes in body plans are due to changes in genes, and flies have HOX genes similar to those in a horse, why is a fly not a horse?

Hat tip to John Pieret.

With all the hagiography going on for conservative “intellectual” Irving Kristol, who died on September 18, let’s not forget one of his many idiotic statements: that Darwinism is on the way out because it “is really no longer accepted so easily by [many] biologists and scientists.”

As Glenn Morton has exhaustively shown, the trope that “more and more scientists doubt evolution” is one of the oldest falsehoods in creationism. But then, Kristol believed that not all truths were suitable for all people, an echo of Martin Luther’s view that lying for his god was acceptable.

Anti-evolution idiocy seemingly ran in the family. In 1959, Kristol’s wife Gertrude Himmelfarb wrote a terrible book, Darwin and the Darwinian Revolution, demonstrating a lack of understanding of biology and a warped view of Darwin’s influence. One perceptive reviewer penned that Himmelfarb had “an advanced case of Darwinitis, a complaint that afflicts those of a literary bent and strong attachments to pre-scientific culture, who find in the theory of evolution a disturbing and mysterious challenge to their values”. Kristol wrote a favorable review of Himmelfarb’s book for Encounter, without bothering to mention that he was Himmelfarb’s husband. So much for Kristol’s ethics.

Read more at Recursivity…

As most readers know, William Dembski and Robert Marks recently published a paper in an IEEE journal that purports to show that

In critiquing his [Dawkins’] example and arguing that information is not created by unguided evolutionary processes, we are indeed making an argument that supports ID.

Various science bloggers have critiqued it; see here, here, and here for examples.

Now the Metropolis Sampler has published a more technical analysis of the paper, concluding that

The fundamental lesson here is that the Dembski-Marks approach to evaluating model assumptions is both arbitrary and a poor reflection of scientific reasoning. Model assumptions are not accepted or rejected based on a numerical measure of how many logical possibilities that are ruled out or how far probability distributions deviate from uniform measures. Rather, model assumptions are accepted or rejected based on predictive and descriptive accuracy, domain of applicability, ability to unify existing models and empirical knowledge, and so on.

ID creationists persistently use models that misrepresent theories (or in the case of the WEASEL hoorah, misrepresent what the model is intended to represent), and then conclude (on the basis of syntactic manipulations of the model) that the theories are invalid. Dembski, of course, is a serial offender in this respect, and it’s a pity that he’s inveigled Marks into sharing his delusions.

As everybody should be aware by now, Denyse O’Leary is offering a prize for the original code for Dawkins’ Weasel program which illustrates cumulative selection [1]. O’Leary’s offer arises from people challenging Dembski’s misrepresentation of the Weasel program, as he has misrepresented it yet again in a trivial non-id paper. To get some much needed perspective, read Joe Felsenstein’s excellent article (and its follow-up) and those of Chris Mark Chu Carroll (here and here)

Seriously, arguing over whether Dawkins “weasel” program implements locking is a bit like arguing over whether the measuring cylinder in the Measuring Cylinder/Tap model of drug clearance is emptied by a tube or a bloke with a cup. Both are simplified systems that make demonstrating a concept easy, and do much the same thing.

The point is that a leading light of the cdesignproponentsits has spent an enormous amount of time critiquing a toy demonstration of selection, and can’t even get the toy example right. Not only that, they can’t admit when they were wrong. Heck, no one in the cdesign proponetsists can admit Dembski is wrong about a toy program, even when presented with video evidence.

Let’s emphasise this again. It’s a non-issue except for the way it highlights the determined cluelessness of cdesign proponetsists. To use the metaphor of the Measuring Cylinder/Tap model of drug clearance again, Dembski is effectively arguing that Dawkins said the measuring cylinder is emptied by a man with a cup in his book, but anyone can go to Dawkins original book, read how he set it up, and understand that Dawkins specified a tube. Dawkins doesn’t specify how big the tube, or the flow rate of the tap, but it’s sort of obvious and you can easily make an analogous system which demonstrates the same things that Dawkins does. Everyone understands except Dembski who then makes a convoluted argument over the whole thing (see www.evoinfo.org and read their “explanation” of Dawkins program if you have a spare half-hour of your life you don’t mind wasting).

Now there is a video showing a measuring cylinder with a tube (metaphorically, see www.youtube.com/watch?v=5sUQIpFajsg (go to 6:15) for the real video showing the weasel program), Dembski goes “oh, Dawkins must have REALLY have used a cup in his book, then swapped to a tube for the video”. Aside from the convoluted mentality involved in this staggering piece of “reasoning”, it goes to the heart of the cdesign proponentists reliability.

When Dembski claims that Lenski et al., have “smuggled in information”, explaining why they are wrong can get quite technical, but when they claim Dawkins has “smuggled in information”, one can simply point to how deeply they have misunderstood Dawkins model, and if they can’t get Dawkins right (after being told repeatedly, having it explicitly demonstrated to them and being shown a video), what hope is there that they got Lenski right.

For more information on Dembski’s denial of the video evidence, see Dembski Weasels Out, for a wide compendium of Weasel programs old and new, including head to head comparisons of Dawkins version vs Demski’s locking version see Weasels on Parade (note it took over 23 days for the Uncommon Descent people to come up with any programs themselves). To see where I completely reconstruct the output shown in Dawkins book, see here.

[1] Why doesn’t O’Leary just ask Dawkins? The whole concept of running a competition to get Dawkins code instead of asking Dawkins is rather bizarre. While he may not have the original code, he can tell her how he did it.[2] [2] People have asked Dawkins before. It no longer exists. Just like the AppleBasic programs I wrote to calculate stimulation-induced radioactive outflow for our laboratory. Used for years but vanished into the mists of time. Seriously, even if there was a disk around with AppleBasic finding a machine to run it and make copies would be an adventure in itself.

Over at Uncommon Descent Dr. Dembski has replied to commentators who pointed out he misrepresented climate science, especially his claim that in the 70’s

The scare back then was global cooling!

In response, Dr. Dembski quotes an article which proves he did misrepresent climate science. If that’s not enough, he goes on to make stuff up.

Dear Dr. Dembski, in your recent post on Uncommon Descent “H.L. Mecken on the urge to save humanity”, you quote approvingly from an article at the Investors Business Daily.

A new scientific paper [McLean, de Freitas, and Carter, 2009] says that man has had little or nothing to do with global temperature variations.…..Their research, published in the Journal of Geophysical Research, indicates that nature, not man, has been the dominant force in climate change in the late 20^th century.

As a mathematician Dr. Dembski, you will certainly be able to effortlessly analyse the McLean, de Freitas, and Carter, 2009 paper (the full paper can be found here).

Your challenge, Dr. Dembski, is to show exactly how this paper supports the statements in the Investor Business Daily article. Please pay particular attention to the smoothing and bandpass filtering analysis in your explanation. Oh, and you may also like to explain why the lead author John McLean states:

The paper by McLean et al (JGR, 2009) does not analyse trends in mean global temperature (MGT); rather, it examines the extent to which ENSO accounts for variation in MGT.

and what his statement means for the Investors Business Daily piece. You may also wish to consult these articles at Open Mind, Only in it for the Gold and More Grumbine Science, which do an in-depth analysis of the paper.

Given your interest in the role of science in policy decisions, this challenge is a valuable opportunity for you to use your expertise to show how this paper refutes many decades of climate research.

John Lynch, an evolutionary morphologist and historian of anti-evolutionism, dissects the selective history of ID propounded by the Disco ‘Tute’s new faith and evolution site. The pull quote:

If I engaged in such non-contextualized presentation in my classroom, I would rightly be accused of being a bad teacher. More importantly, the audience would receive no indication of how the argument ceased to be scientifically and philosophically tenable and instead became an issue of interest solely to apologists and theologians.

Read the whole thing.

I will send an autographed copy of the book Why Evolution Works (and Creationism Fails), by me and Paul K. Strode, to the first person who can correctly find a quotation that accurately describes evolution by natural selection and predates Darwin, Wallace, and even Erasmus Darwin by hundreds of years. To enter, just post a comment. To win, you will have to state the quotation, its author, and the approximate year. I have a specific quotation in mind, but I will consider others, as long as they clearly describe natural selection.

For the table of contents and other information about the book, go here.

In a day or so, I will declare the winner and explain why the quotation is so interesting. In the meantime, below the fold, more about Why Evolution Works (and Creationism Fails).

The Disco ‘Tute has announced the opening of a new site, Faith+Religion, which purports to discuss the relationship between evolution and religion. A brief survey of the site shows that it has two objectives. First, of course, is the traditional ID goal of denigrating evolutionary theory. Right up on the home page we see a review of Collins’ The Language of God by Moonie Jonathan Wells that says

Collins’s defense of Darwinian theory turns out to be largely an argument from ignorance that must retreat as we learn more about the genome–in effect, a Darwin of the gaps.

Sure thing, Jonnie. Wells knows more about the scientific implications of new genetic knowledge than the former head of the Human Genome project. Yup.

William Dembski and Robert Marks have written a paper. No it won’t be going in the peer reviewed literature, but into another of Dembski’s anthologies. Mark C. Chu-Carroll of Good Math, Bad Math explains what is mind-bogglingly wrong with it here and here.

Casey Luskin is once again hard at work in the Discovery Institute quote mines. In his latest effort, he tries to make the case that a recent review article by Kevin Padian and the Panda’s Thumb’s own Nick Matzke contains “veiled threats” designed to intimidate cdesign proponentsists. Casey dives into the quote mines in the first paragraph of the post:

It’s always amusing how evolutionists continually proclaim, and then re-proclaim, the apparent demise of intelligent design (ID) (i.e. ‘no really, this time ID actually is dead!’!). We’re pretty used to that, but then it gets a little creepy when they exude what appears to be an unhealthy pleasure in ID’s (purported) demise. Such was recently the exact case when National Center for Science Education (NCSE) president Kevin Padian and former NCSE spokesman Nick Matzke, in a January issue of Biochemical Journal, published a “review article” claiming that the “case for ID” has “collapsed,” gleefully asserting that “no one with scientific or philosophical integrity is going to take [Discovery Institute or ID] seriously in future.”

Whenever someone from the Discovery Institute quotes a scientist, it’s a good idea to go back to the original source. That’s particularly true in cases like this, where the quoted material consists of several sentence fragments. Unsurprisingly, when we check the original source, we find that the quoted passages occur several paragraphs apart.

.. I might add a few brief notes. After Carl Zimmer’s Unicycle-bicycle transitional form, the detailed rebuttal by Keith Ken Miller (Part 1, Part 2 and Part 3), and Nick Matzke revealing that Behe wrote the Pandas’s clotting chapter that Luskin dismisses, there is not much left for me to add*.

I want to highlight two things though. One is a quote that keeps turning up in discussions of Behe’s concept of Irreducible Complexity.

Just as none of the parts of the Foghorn system is used for anything except controlling the fall of the telephone pole, so none of the cascade proteins are used for anything except controlling [he formation of a blood clot. Yet in the absence of any one of the components, blood does not clot, and the system fails. (Behe 1996, pp. 85-86)

Actually, the clotting cascade proteins do have functions other than clotting, indeed Casey’s so-called “Irreducible Core” proteins have other important functions. I go into greater detail in this post about how these functions may have pre-adapted the clotting proteins for their role in clotting. This exposes a major flaw in the concept of irreducible complexity (read the post for the full argument).

Casey also chides Miller for not doing any knock-out experiments on blood clotting systems. This is heavily ironic as no ID proponent, not even Behe, has done any experiments on the blood clotting system. As I point out in my post Behe vs Lampreys+, it’s the evolutionary biologists that have been doing all the heavy lifting in regard to understanding the clotting system. In fact I issued a challenge to the ID proponents, the Amphioxus genome had just been published at http://genome.jgi-psf.org/Brafl1/Brafl1.home.html. Amphioxus is a primitive chordate, more primitive than lampreys, that clot their haemolymph. I challenged the ID proponents to predict which coagulation factors are present in Amphioxus, search the Amphioxus genome database and report on whether the genes found match their predictions.

Since then, silence. I can tell you one thing for sure. The Amphioxus has no gene for fibrinogen, the final step in the modern clotting cascade, yet it still clots its haemolymph. So the very basis of the “Irreducible Core” that Casey goes on about is absent in these animals, and one of Behe’s iconic pathways is exposed as reducible.

Notes:
UPDATE: Yeah, yeah: I can’t spell when writing at 1 am in the morning. But the most embarrassing bit was I got Ken Miller’s name wrong (sorry Ken). Still, the science is right.
* I could have contributed sooner, but I could be playing frisbee on the beach with my kids or surfing the internet. Guess which one I chose.
+This post also has a very nice diagram of the reducibly complex clotting system that Ken Miller discusses (section 4, “An Irreducible Core”). This diagram looks eerily similar to the diagram that Casey uses, as he copied the diagram that I provided for Barbara Forrest and Paul Gross for “Biochemistry by design,” Trends in Biochemical Sciences, Vol. 32(7):301-310 (2007). He’s made a few minor modifications (hint Casey, the correct citation method is “diagram redrawn from” not “information obtained from”), but if he asked nicely, I could have given him the original diagram.

Creationists think information theory poses a serious challenge to modern evolutionary biology – but that only goes to show that creationists are as ignorant of information theory as they are of biology.

Whenever a creationist brings up this argument, insist that they answer the following five questions. All five questions are based on the Kolmogorov interpretation of information theory. I like this version of information theory because (a) it does not depend on any hypothesized probability distribution (a frequent refuge of scoundrels) (b) the answers about how information can change when a string is changed are unambiguous and agreed upon by all mathematicians, allowing less wiggle room to weasel out of the inevitable conclusions, and (c ) it applies to discrete strings of symbols and hence corresponds well with DNA.

All five questions are completely elementary, and I ask these questions in an introduction to the theory of Kolmogorov information for undergraduates at Waterloo. My undergraduates can nearly always answer these questions correctly, but creationists usually cannot…