March 21, 2004 - March 27, 2004 Archives

Stones, Bones, and Groans

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Creationist Ph. D. Joe Lary in the March 03, 2004 Tuscaloosa News wrote in support of the notion that Alabama teachers should teach intelligent design creationism. As a matter of fact, he shows us that "intelligent design" is nothing but gud ol' "creation science" warmed over. Lary started with a lengthy blather about why evolution is impossible because of 140 year old experiments, and 50 year old false quotes that I delt with over the last two days. He next launched into a "discussion" of the fossil evidence for evolution.

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LaTeX Support

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The Panda's Thumb now has $\mbox{\LaTeX}$ support based on a plugin I developed. I chose to go with converting the equations to pngs because MathML support is not where I'd like it in today's browsers. I'd like to thank Wesley for updating some software on the server to allow this to work. *Mutation-Selection Balance* $${\Delta}q \approx \mu-sq^{* 2} \approx 0 \Rightarrow \mu \approx sq^{* 2} \Rightarrow q^* \approx \sqrt{\frac{\mu}{s}}$$

The phrase "complex specified information" is a core concept in the lexicon of the World's Greatest Information Theorist William Dembski, but it was not invented by him. In fact, it comes from a book published in 1973, by Leslie Orgel, entitled The Origins of Life: Molecules and Natural Selection. It is odd to think that this notion, which is supposed by Dembski to demonstrate that life, or LIFE as he like to refer to it in his The Design Inference of 1998, cannot be the result of natural selection, was coined in the context of a discussion how it actually could.

What does Orgel actually say about complex specified information, then? He didn't actually use the complete phrase "complex specified information", but the ideas are there. Perhaps in reading him, we may get a hint of how Dembski developed his reaction to Darwinian evolution, and more to the point, perhaps we'll be able to make sense of some wider, and more important, ideas in evolution.

A response to Francis Beckwith's claim that "methodological naturalism (MN) entails philosophical naturalism (PN)" A central claim of the ID movement is that science's use of methodological naturalism means that for all practical purposes science accepts a commitment to philosophical naturalism. For instance, Discovery Institute fellow Francis Beckwith recently wrote, ID theorists maintain that contemporary science's repudiation of intelligent agency as a legitimate category of explanation is not the result of carefully assessing ID's arguments and finding them wanting, but rather, it is the result of an a priori philosophical commitment to methodological naturalism (MN),(n4) an epistemological point of view that entails ontological materialism (OM) [Beckwith's term for philosophical naturalism in this paragraph],(n5) but which ID proponents contend is not a necessary condition for the practice of science.(n6) (p. 457, "Science and Religion Twenty Years after McLean v. Arkansas: Evolution, Public Education, and the New Challenge of Intelligent Design." Harvard Journal of Law & Public Policy 26.2 (Spring 2003: 455-499) In a discussion of this quote on the internet forum at the Access Research Networks (ARN), this proposition was shortened to "MN entails PN." It is really the central claim of the Wedge strategy as advanced by the ID movement.

I'm sure you'll hear more from my colleagues in the next week about the appalling and amusing cover article in World magazine. The magazine did something that is remarkably perverse:

WORLD asked four leaders of the Intelligent Design Movement to have some fun: Imagine writing in 2025, on the 100th anniversary of the famous Scopes "monkey" trial, and explain how Darwinism has bit the dust, unable to rebut the evidence that what we see around us could not have arisen merely by time plus chance.

I've only addressed one of the articles, by Jonathon Wells. It's stunning in both its hubris and the deficiencies of intellect and imagination demonstrated by its author.

Continue reading (at Pharyngula)

Dembski invited specific questions and criticisms to his latest book. I have chosen to address his claims about "No free lunch" and the displacement hypothesis. In order to make my argument I will start with Mark Toussaint's thesis found at:

Toussaint's thesis and other relevant papers.

Ontogenetic depth

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One of the serious shortcomings of Intelligent Design is that it does nothing to provide any new or productive insights into the workings of biology. ID proponents seem to be at least vaguely aware of this failure, in that they do frequently claim to be thinking about working on a preliminary, tentative approach towards the beginnings of a potential research program (my paraphrase), but most of the effort has been directed towards political and legal enforcement of their ideas, rather than actually testing those ideas. One advantage of pursuing only legalisms is that they don't give scientists anything to grapple. Invariably, when ID proponents do dip their toes in the scientific waters, they end up getting eaten by the sharks that lurk there.

One example: Paul Nelson, of the Discovery Institute, has been peddling a peculiar idea he calls "ontogenetic depth" as a scientific concept that emerges from Intelligent Design. To his credit, he has been presenting this idea in legitimate science venues, at the Geological Society of America and Society for Developmental Biology meetings. Note that getting on the program at these meetings is not subject to peer-review, so it is not automatically a recognition of merit that this work has been presented publicly. It is a good sign that Nelson is willing to expose his work to criticism, though.

I'm going to give it some criticism here. "Ontogenetic depth" is a developmental idea, and I'm a developmental biologist. Today I also get to play shark.

My book Unintelligent Design became available from Amazon in the middle of December 2003. On December 22 those curious observers who watch the sometimes funny exchange of opinions regarding books offered by Amazon, already could read a review of my book signed "A reader from Waco, Tx." The opinion of that anonymous and very prompt reviewer was that my book was bad because it was published by a bad publisher - Prometheus Books. The anonymous reviewer recommended instead a forthcoming book by William Dembski titled The Design Revolution (which presumably must be good because of being published by a good publisher - InterVarsity Press). The reviewer from Waco promised that Dembski's book would answer all my concerns.
Of course, the fact that Dembski holds a non-teaching position at Baylor university which is located in Waco, Tx, was supposed to be a mere coincidence.

Down in the Quote Mines

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Creationist Joe Lary, Ph. D. wrote a argument that Alabama schools should teach intelligent design in science classes that appeared in the Tuscaloosa News on March third of this year. What I found the most stiking feature of Lary's argument is that he makes crystal clear that there is no substantive difference between "intelligent design" and the "creation science" of the 1970s and '80s. His arguments are lifted straight from standard young earth creationist sources, as are his methods. The false, or out-of-context quote is a favorite tactic of professional young earth creationists' efforts to undermine science and reason. This is so widely recognized among those who follow these efforts that it has come to be called "quote mining" and a compilation of many examples, and their corrections has been published on-line at: The Quote Mine Project. The Answers in Genesis Ministries, formerly the Creation Science Foundation of Brisbane, Australia, even produced a book of quotes called The Revised Quote Book (copyright 1990) that has been debunked at Cretinism or Evilution? No. 3 .

Further "quote-mine" information and examples dating as early as 1905 are found in Ron Numbers' book The Creationists (1992, pg. 50-53), and an large library of quotes are analyzed at Quotations and Misquotations .

Lary shows himself to be well versed in quote mining as I'll now examine.

A beautiful friendship?

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"Of all the gin joints in all the towns in all the world, she walks into mine."
As every film buff knows, that's what Humphrey Bogart glumly says in Casablanca, after his ex-lover (Ingrid Bergman) shows up at his Rick's Café Americaine. Bogart's Rick Blaine is of course justified in his astonishment - it certainly looks like a rather uncanny coincidence. However, most of us in the audience plainly realize that had Bergman chosen another joint, or another town, we'd simply be watching a different movie. In other words, if you are the main character in a movie, chances are you are part of an unusually interesting story: that's a so-called "observation selection" effect.

For reasons that I can't comprehend, however, this basic logic seems to escape a lot of fairly intelligent people, the most recent entrants on the list being astronomer Guillermo Gonzalez and philosopher Jay Richards. Their recently released book "The Privileged Planet" (TPP), argues not only that Earth is uniquely endowed for life forms just like us to appear (an old idea), but that our planet is also just right for those life forms to develop the scientific method, and to apply it to discover the fundamental Laws of the Universe. The series of coincidences behind these simple observations is so amazing, they say, that just a Cosmic Screen-writer could have come up with it.

Predictably, the book (and its spin-off documentary) is being hailed by Intelligent Design advocates as the best thing since, well, their last book and spin-off documentary. The National Review Online, which when ID is concerned seems to quickly shed any semblance of critical sense and journalistic standards, hosts a raving review, complete with tabloid-style bullet points and claims of (post-)Copernican Revolutions. I think all these apologists should be more cautious, as Gonzalez's and Richards' thesis seems to raise more problems for ID than it solves.

When we talk about the legal problems of creationism, we tend to focus on the fundamentalist Christian churches, but there are other varieties of creationism out there. There are even creationists among Indian tribes, and they are also causing problems for scientists. The Native American Graves Protection and Repatriation Act ("NAGPRA," 25 U.S.C. §§ 3001-3013), is a federal law which says that if a skeleton is discovered on federal land, and that skeleton is related to an Indian tribe, then the government must give that skeleton to the Indian tribe.

The law was written to address the graverobbery and other abuses of 19th century archaeologists, who often raided Indian burial grounds. But in a recent case, the law was almost used to shut down research on a 9,000 year old skeleton discovered in Washington, which was never shown to have any relationship to any modern Indian tribe. Instead, the Clinton Administration's Department of the Interior declared that the skeleton--called "Kennewick Man"--was an Indian skeleton simply because it was found in American soil and it predated the arrival of Columbus. Umatilla tribe religious leader Armand Minthorn explained that the tribe hoped to rebury the skeleton and thus remove it from scientific scrutiny; it did not want experiments performed on the bones because "[f]rom our oral histories, we know that our people have been part of this land since the beginning of time. . .. We already know our history. . .. My people have been here since time began. . .. I know how the world began, and I know how the world will end."

A group of scientists sued, arguing that this was an irrational, politically-motivated decision. After years of litigation--which included many very shady tactics on the government's part--a federal court agreed with the scientists that the government's decision was arbitrary and irrational. Bonnichsen v. United States, 217 F.Supp.2d 1116 (D.Or. 2002) A few months ago, the Ninth Circuit Court of Appeals affirmed. 357 F.3d 962 (9th Cir. 2004). (I filed a friend of the court brief in support of the scientists, on behalf of the Pacific Legal Foundation.) Tribes have asked for en banc rehearing of that decision, but it looks as though scientists will be allowed to research the skeleton. Unfortunately, NAGPRA has led to the destruction of several ancient skeletons. And it, and proposed state versions of the act, require universities to go through their collections, perform studies on the skeletons, and turn them over to tribes for burial and destruction. (England is considering a similar requirement). This threat to science needs to be addressed.

The comments to my earlier post on neutrality suggest that I have not been entirely clear. Matt Brauer says that "the issue is of the state ‘preferring' rationality to non-rationality, as it should." I agree it ought to. But if we're talking about the Constitution, then we aren't talking about what the state ought to do; we're talking about what the state may or must do. The state certainly ought to prefer rationality. But the First Amendment, even as incorporated to the states through the Fourteenth, does not clearly say that the state must do that; indeed, it doesn't even clearly say that the state may do that.

Coevolution and Dynamic Fitness Functions

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Work in evolutionary computing, evolutionary algorithms, and genetic algorithms seems to be a thorn in ID's side. In a number of places William Dembski has argued that various computer simulations of evolutionary processes tell us nothing useful about biological evolution. By modest extension, of course, computer modeling in any science is tossed out. (Too bad for the physicists in the crowd.) But Dembski's argument fails once again, for a familiar reason: profound ignorance of the relevant literature.

For those new to this subject, the current iteration of creationism-in-the-classroom goes by the name "Intelligent Design." It differs from earlier strains of "scientific creationism" in a number of ways. First, it is scrupulously vague, allowing the movement to attract supporters with a wide range of beliefs (see Nic's entry on Rael below) while avoiding any whiff of commitment to a testable hypothesis. Second, it avoids like the plague any reference to religion. Finally, it is extremely well-funded and organized on a national level.

Barbara Forrest and Paul Gross have examined the religious origins and political life of the movement (which has come to be known, somewhat ominously, as "The Wedge.") Their book, Creationism's Trojan Horse: The Wedge of Intelligent Design (1) is scrupulously researched and very well written.

In his review of the book Michael Cavanaugh, president of the Institute on Religion in an Age of Science (IRAS), discussed why it is so important to understand the origins and motivations of the ID movement:

Finding Your Niche

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A common misunderstanding of evolution is that it is all about genes. Genes are important, but organisms do a lot, too. One of the things they do is modify their environment to suit themselves, and to suit their progeny. This is called "niche construction", and I came across this rather nice essay on Jim Harrison's inanis et vacua blog on the topic, which I am posting here with his permission.

A note to add to this is the book of essays published a few years ago on this and related topics, putting the discussion in a more general context:

Oyama, Susan, Paul E. Griffiths, and Russell D. Gray, eds. 2000. Cycles of contingency: Developmental systems and evolution. Cambridge, MA: MIT Press.

There is a revolution in the thinking of evolutionary theory right now. It may take, as Jim notes, a while to become widely known...

Site Referrals

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According to Blogdex right now, The Panda's Thumb is the 11th most referenced blog today. We were 15th yesterday.

According to Blogpulse, we're #8.

And according to Technorati, we now have 111 links from 68 blogs, which is enough to push us into "marauding marsupial" territory. I've never seen a marsupial maraud before, but it can't be a pretty sight.

Here we go again

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"One only has to contemplate the magnitude of this task to concede that the spontaneous generation of a living organism is impossible. Yet, we are here as a result, I believe, of spontaneous generation." - George Wald,

"The Origin of Life", George Wald, Scientific American 191:48 (May 1954).

Alabama is considering legislation to allow teachers to include intelligent design
creationism in their daily instruction. The March 03, 2004 Tuscaloosa News carried a guest editorial by Joseph M. Lary, Ph.D. which is headed "Schools should teach intelligent design, too." Dr. Lary makes the implicit claim that his education and professional background give him special authority on the creationist debate and the consequences this has to education. Because of this claim, it is appropriate to consider if this is true. Lary has very few publications, either statistical manipulations of historical data, or those where he is third or fourth author. This is adequate for a non-academic epidemiologist, but unfortunately demonstrates no actual understanding of evolution or its role in understanding disease. Nor does Lary have a strong background in education other than as a student. In fact, Lary has no more credibility as an expert than any other citizen. Lary even fails to show a deep understanding of the issues involved as his editorial is largely a paraphrased rehash of very dated creationist sources.

I do think that it is very telling that Lary presented "classic" young earth creationist arguments of the type that have specifically been found to be unconstitutional, hiding behind an "intelligent design" fig leaf.

I'll take Lary's editorial apart nearly line by line in about three sections; first his error of equating evolution and the origin of life, second his use of bogus, and out of date "quotes" known as quote mining, and last his lack of familiarity with the fossil record and its evolutionary significance.

The Quixotic Message

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Hi all, Wesley suggested I blog this for the entertainment of the surprisingly large number of visitors we've been getting, thanks to links from several big time bloggers.

This is fun because you don't have to be a scientist or very familiar with the ID movement to get a kick out of it. About a year ago, I posted a list of contradictions and absurdities that are common from the ID movement. These are the kinds of things that make your jaw drop to the floor and your eyes jump out of their sockets, at least if you're one of those who keeps up with the shenanigans of the ID movement. People with only passing familiarity, on the other hand, might miss them. So I drew some of them up into simple statements, taking some inspiration for a similar list that Mike Huben did for libertarianism. (Note that it's not my intent to compare libertarianism to ID or vice versa.) I originally posted the list to the discussion board, whereupon I received some suggested additions, especially from Nic, and then decided to write the whole thing up for an article on Because some of the contradictions might still be lost on a lot of people, it was suggested that I make a references page to explain and document some of these. Kieran over at Crooked Timber was nice enough to link to them yesterday, so at least I know someone is reading them. :)

So here is is:

"The Quixotic Message", or "No Free Hunch" (In the tradition of Rocky and Bullwinkle, it has an alternate name.) And then there are the...

Quixotic References. Go read them right now.

Anyway, here's an example of one of the entries:

  • ID is a program for research into the science of design, nothing more. Part of our research plans are to produce coloring books for preschoolers, and to make ourselves more likeable at parties.

Sadly, this is not a joke. (I have it fully referenced here.) Bill Dembski really did say that coloring books for preschoolers are an example of what the ID movement should do rectify the imbalance between it's "cultural successes" and it's lack of scientific research. I mean, WTF? In a speech supposedly dedicated to getting the ID movement to focus its attention on actual research (instead of, you know, propaganda), this is the kind of stuff he comes up with? If you think I'm cherry picking, you're right. This is probably the most jaw-droppingly absurd bit of "scientific research" he lists, but it's hardly the only one. Among them, he also suggests "concentrating forces" of "troops" (his words), by which he means gathering the ID advocates under one banner to take advantage of a "key principle of military tactics" (also his words). Aside from the fact that this has nothing whatsoever to do with research, just what is the deal with warrior metaphors and Christian fundamentalism? Do they really perceive the rest of us as The Enemy, towards whom their attitude is kill or be killed? Anyway, he also suggests putting together laundry lists of "Fundamental Facts" and "Correcting Misinformation" (by which he apparently means Jonathan Wells' misinformation). These are nice and all, but they don't exactly qualify as research in the sense of using ID to formulate testable hypotheses, and then going about and testing them. And then of course he wants ID advocates to be more likeable at parties, despite the reputation that evangelicals already have for being wild and uninhibited party animals. As it turns out, there is very little, if anything, in Dembski's speech which comes close to qualifying as scientific research.

The lesson in all of this is that if the leading light of the ID movement gets up and speaks to the home team about ideas for scientific research, and this is the kind of stuff he comes up with, one should really start to suspect that ID simply cannot be used to generate a real scientific research program. It might be different if they were willing to make ID something other than the vague mish-mash that it is, but the ID movement has a "big tent" that it seeks to keep intact for political expediency. That should tell you where their real interests lie.

Anyway, please enjoy the rest of the Quixotic Message. And please feel free to suggest any additions in the comments below. (I'm about due for an update, but out of the dozen or so great additions I've thought of, I can only remember one.)

Now that the Raelien UFO cult has come out firmly in support of intelligent design, perhaps it's time for the Discovery Institute (DI) to finally bite the bullet and come clean about how they really feel regarding the "Marvin the Martian as Creator" hypothesis. However, as former DI Director of Media and Public Relations Mark Edwards told the Sacramento Bee on June 22, 2003, ID advocates are willing to posit even wilder, and frankly more ridiculous, claims:

"[A] person could logically argue that some sort of human has been able to design features of life working through time travel," he said. "And some people say aliens are the designer."

So in addition to getting cozy with the Raeliens, here we have a spokesman for the DI claiming the designer might be some sort of super-intelligent, time-traveling human.

What would Phillip Johnson say about this? I think he'd probably say something like, "The tent may be big, but it's not THAT big!"

Everybody better get down to Vegas. The International Raelian Movement is planning a press conference tomorrow.

A paper published online in Molecular Biology and Evolution claims to have "rigorous proof that [junk DNA was] added to DNA 'late' in the evolution of life on earth--after the formation of modern-sized genes, which contain instructions for making proteins" according to a press release from the National Institute of Standards and Technology, whose Center for Advanced Research in Biotechnology (CARB) was involved with the research (link)

The press release states:

Research from the CARB group appears to resolve a debate over the "early versus late" timing of the appearance of introns. Since introns were discovered in 1978, scientists have debated whether genes were born split (the "introns-early" view), or whether they became split after eukaryotic cells (the ones that gave rise to animals and their relatives) diverged from bacteria roughly 2 billion years ago (the "introns-late" view). Bacterial genomes lack introns. Although the study did not attempt to propose a function for introns, or determine whether they are beneficial or harmful, the results appear to rule out the "introns-early" view.

The CARB analysis shows that the probability of a modern intron's presence in an ancestral gene common to the genes studied is roughly 1 percent, indicating that the vast majority of today's introns appeared subsequent to the origin of the genes. This conclusion is supported by the findings regarding placement patterns for introns within genes. It long has been observed that, in the sequences of nitrogen-containing compounds that make up our DNA genomes, introns prefer some sites more than others. The CARB study indicates that these preferences are side effects of late-stage intron gain, rather than side effects of intron-mediated gene formation.

Ref: Wei-Gang Qiu, Nick Schisler, and Arlin Stoltzfus, "The Evolutionary Gain of Spliceosomal Introns: Sequence and Phase Preferences" MBE Advance Access published March 10, 2004, 10.1093/molbev/msh120

One thing you may notice toward the bottom of the lefthand sidebar is something that reads:

Some explanation is probably a good idea. This is a ranking system for blogs developed by N.Z. Bear, the owner of the Truth Laid Bear website, based upon the number of other blogs that are linking to that blog or to articles found on it. The more incoming links from other blogs a given page gets, the higher it ranks. Ah, but here comes the irony...

The TLLB ecosystem divides the rankings into taxonomic categories, just like biology does with plants and animals. The categories go as follows:

Higher Beings
Mortal Humans
Playful Primates
Large Mammals
Marauding Marsupials
Adorable Rodents
Flappy Birds
Slithering Reptiles
Crawly Amphibians
Flippery Fish
Slimy Molluscs
Lowly Insects
Crunchy Crustaceans
Wiggly Worms
Multicellular Microorganisms
Insignificant Microbes

Anyone familiar with biology will of course recognize that this is, roughly, the order of appearance of these various life forms on the planet. Every blog begins as an "insignificant microbe" and progresses up the scale to "higher beings" (if they become extraordinarily popular). The irony, for a blog that focuses on evolution, is that this ranking system is based upon a popular but nonetheless false conception of evolution as an inexorably progressive march toward some goal. In reality, a reptile is no more "advanced" or "evolved" than an amphibian, both are well adapted to their environments. Evolution deals with fitness for a local environment, not with some overall state of "more evolved" or "less evolved". Indeed, one could make the case that those insignificant microbes - bacteria - are "more evolved" than humans. After all, they've survived far longer, occupy a far more diverse set of environments, and evolve at a rate that often exceeds the ability of humans to combat them through antibiotics.

Another irony is that if one accepts this "great chain of being" concept of evolutionary progress, this blog seems to be moving rapidly up the scale. At this point, The Panda's Thumb is listed as an "insignificant microbe", but the number of incoming links and the number of daily visits, after only 2 days, actually places us in the middle of the "adorable rodents" taxon. Talk about rapid speciation! Even in Gould and Eldredge's wildest imaginations, they could not have foreseen the equilibrium being punctuated at a rate of 10 major saltational leaps in a mere 2 days. Perhaps The Panda's Thumb is really a hopeful monster after all.

Whether one may be attempting to apply William A. Dembski's "explanatory filter/design inference" (EF/DI) to an event to find rarefied design (see Wilkins and Elsberry 2001), or "specified anti-information" (SAI) to make an ordinary design inference (see Elsberry and Shallit 2003), you are likely to be in need of a calculating aid that can handle both very large and very small numbers. I have such a tool available online, the Finite Improbability Calculator. In addition to pointing to this (IMO) valuable resource, I also want to take up a couple of issues from Dembski's new book, The Design Revolution: Answering the Toughest Questions About Intelligent Design concerning question-begging and the proffered support for the claim that the "specified complexity" identified by use of Dembski's EF/DI is a "reliable" empirical marker of "intelligent design".

Grist for the EF mill

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Dembski's "Explanatory Filter" (EF) claims to be a reliable technique for detecting design. To date, the EF is the only method presented by the "science" of ID. How well does it do? Nobody knows. It has been applied precisely once, by Dembski in his book No Free Lunch. And that application was a dismal failure.

Before going into the reasons that the EF is a psuedo-algorithm, I'd like to present an example of what Dawkins calls a "designoid," that is, something that appears designed but isn't. A "false positive" for the EF, if you will.


Brain vaccinations

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I can't resist adding one little bit to the dogpile on VanDyke. So far as I know, none of the many critics of the book review seized on the catchy conclusion to the article, which also managed to get something wrong. VanDyke writes that "the most ironic aspect of this debate is that Darwinists are even opposed to the inclusion of ID in the public school curriculum," because evolution's "fundamental tenet" is "that competition leads inexorably to progress[.]" Thus defenders of science ought not "fear. . .a little rivalry," because the fittest argument will win. 117 Harv. L. Rev. at 971.

Of course, Dawkins and Dennett have written extensively on the question of just why false claims to truth manage to survive in this "competition." This is the subject of memetics, which VanDyke does not mention or cite to. The fact is that the best argument does not always win. If a theory (or "memeplex") is true, then it will have a competitive advantage, but other memeplexes have other advantages. Nazi bookburners had such a competitive advantage over Jewish scientists like Einstein or Szilard that they were forced to evacuate the country--but Nazism certainly wasn't popular because of its truth value. Science has much to fear from "rivalry," where that rivalry is based on methods and ideas which do not pursue and cannot reach, the truth. It has much to fear from dogma, superstition, coercion, censorship, ignorance, illiteracy, fanaticism, or blind adherence to tradition. These things all have their competitive advantages in the great cultural competition. But the simple fact is that evolution does not teach that "competition leads inexorably to progress," if by progress we mean improvement, or the attainment of the good. The late Stephen Jay Gould spent a large portion of his life attacking that notion. Evolution leads only to the next step, not necessarily to a "higher" step. In seeking the truth, therefore, we must be constantly on guard for those memeplexes that "rival" the rational pursuit of the truth.

I finally got around to reading the infamous student article by Lawrence VanDyke, Not Your Daddy's Fundamentalism: Intelligent Design in The Classroom, 117 Harv. L. Rev. 964 (2004). Most of the criticism leveled at the article was based on the fact that ID creationism is scientifically baseless, as indeed it is, as well as on the intellectual dishonesty of several of VanDyke's statements, both in the article and in the ensuing ruckus. But right as these criticisms are, I think they overlook the main problem of VanDyke's argument. That problem is one that goes to the heart of the legal aspects of the debate over the place of evolution in public schools.

A paper just published in the March 25th issue of Nature (1) suggests that a mutation in a single gene (MYH16) may have been responsible for many of the cranial difference between Homo and other primates. "A gene responsible for a majority of jaw musculature was lost from human ancestors, presumably 2.4 million years ago, according to the study. Drastic reductions in these muscles may have lifted significant physical constraints on braincase volume, allowing primates with weak jaws and big brains to eventually think about their origins." (link) While support from genetics researchers seems forthcoming (link), the anthropological community seems less convinced by the results. Owen Lovejoy states "[s]uch a claim is counter to the fundamentals of evolution, [t]hese kinds of mutations probably are of little consequence." The mutation would have reduced the Darwinian fitness of those individuals," said Bernard Wood. "It only would've become fixed if it coincided with mutations that reduced tooth size, jaw size and increased brain size. What are the chances of that?" (link).

Whether or not these results pan out in the long run, they are a powerful indication of the possible effects of single mutations and should spur further comparisons of human & ape genomes.

(1) H.H. Stedman et al., “Myosin gene mutation correlates with anatomical changes in the human lineage,” Nature, 428:415-418

...and now a link from Carl Zimmer!

Dang it, now I've got to get to work and post something substantial here.

The Northern Lights blog has posted a link to us, for which I certainly thank them. But the article linking to us contains some specious reasoning that I feel the need to reply to. To wit:

Clearly, this weblog results from design of some sort, not random combination. ID advocates must be flattered that so many people consider them a serious threat to Western civilization as we know it. I'm no defender of ID as a scientific theory, but the question of what should be included in the science curriculum of a public high school is not a scientific question, it's a public policy question. This point seems lost on biologists and the growing horde of blog commentators who feel constrained to weigh in on this subject.
I would argue that the public policy question is a scientific question. That is, the public policy criteria for what should be in the science curriculum should be essentially scientific criteria. Non-scientific alternatives to scientific theories that lack explanatory power and are not testable or falsifiable should not be a part of public school science curricula. This seems so obvious to me as to be axiomatic, but if the author of the above blog has a better standard I'd like to hear it.

Kevin Drum, the legendary CalPundit, parlayed his blogging success into a job for the Washington Monthly. In a post today, he reviews the battle between Lawrence VanDyke and Brian Leiter (and myself, ultimately) and comes to a somewhat surprising conclusion:

I've been following the whole thing with one eye, and while I have no sympathy for the ID jihadists I admit that all along I've had a sneaking feeling that, in fact, maybe it really was a bit inappropriate for an influential, tenured law professor to write such a blistering attack on a lowly student. Positions of power and all that, you understand.

Today, though, I finally got around to reading VanDyke's note (warning: large, slow-loading file) and I immediately changed my mind: Leiter probably went too easy on this cretin. Here's the damning sentence:

...while lumping ID with creationism may be a good rhetorical strategy for ID's opponents, it only detracts from an independent and rigorous evaluation of the merits of ID's claims against those of naturalistic evolution.

This sentence could be written only by someone entirely ignorant of both the history and substance of ID (which VanDyke surely isn't) or someone who is simply a shill for creationism.

But Drum isn't done yet. He continues:
I expected that VanDyke's book note (and Beckwith's book) would claim that schools should be allowed to teach ID on the basis of some kind of abstract legal or philosophical basis, which might be a perfectly publishable argument. Not so. Instead they argue on the obviously specious grounds that (a) ID isn't creationism and (b) ID is perfectly plausible science.

Leiter was right both on the facts and in the tone he took: it was scholarly fraud. The Harvard Law Review should be ashamed of itself.

While this is still more harshly than I would put it, the truth remains, as I said here and here, that on the substantive issues, Leiter was correct and VanDyke was guilty, at the very least, of absurdly sloppy pseudo-scholarship.

One last note on Drum's article. He says:

It turns out there's one silver lining to this whole dark cloud: it has apparently inspired a group of scientists to start a blog called The Panda's Thumb, dedicated to debunking the daily assaults on evolution from the ID zealots and the religious right. It's only a day old but already appears to be a terrific source. Check it out.
While we certainly appreciate the plug, it should be noted that the formation of this blog was not inspired by this incident at all. It is a mere coincidence that one followed on the heels of another, though I'm quite certain that some of our friends from the Discovery Institute could put together a compelling Argument from Really Big Numbers showing the staggering implausibility of those two things occuring in that specific order by random chance alone.

The battle-cry of the IDists, "teach the controversy!" strongly presupposes that there is a controversy worthy of teaching. It is true that there is a controversy in evolutionary biology, in the political sense. But this is not what legal scholars DeWolf (et al.) mean when they use the term. They would like to convince the majority of citizens (or the minority that sit on school boards) that this is an issue of fairness. According to the truism there are two sides to every coin, why not "teach the controversy" and let the students make reasoned opinions for themselves? Why not use "the controversy" to teach about the process of science?

The best reason not to teach the "origins controversy" is that it simply is nowhere to be found. Genuine scientific controversies -- the important and useful ones -- take up a huge volume of space in the scientific literature. Even the controversies sparked by wrong ideas can be tracked as they generate discussion among the members of the scientific community. If no-one is talking about it, it's not controversial.

On January 12, 2004 the Georgia Department of Education publicly released draft standards of a new "performance curriculum" for the state's public schools. The science standards were based on the Project 2061 benchmarks developed by the American Association for the Advancement of Science (AAAS) by way of the Council for Basic Education's Standards for Excellence in Education. Although based on these standards, the science standards proposed by the Georgia Department of Education contained many omissions or corruptions of important concepts. Despite what department representatives told educators and the public, these omissions involved more than the replacement of the central biological term "evolution" with "biological change over time."

Our First Links

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The Panda's Thumb is already getting some notice around the blogosphere. Our first few links:

Kieran Healy of Crooked Timber recommends us as a follow up to a brief review of the Brian Leiter/Lawrence VanDyke controversy.

Brian Leiter has also given us a plug, along with his usual plainspoken bluntness.

And Tim Sandefur of the Freespace blog gives us a push, while taking us to task, as a self-declared "hardcore Dawkins fan", for choosing a Gouldian title. I know that Tim is also a major Daniel Dennett fan as well, but I didn't tell him that one of the possible names I was bandying about for this blog was "Darwin's Dangerous Idea Logs".

Thanks for the links, folks.

Update: Thanks also to Skeptical Notion for their mention of The Panda's Thumb.

And add Catallaxy to the list.

The Panda’s Thumb is the collaborative effort of a large group of people from all over the world. The contributions of a diverse range of individuals will hopefully add up to a valuable resource for our readers.


As a general disclaimer, please understand that the views expressed by each individual poster here at The Panda’s Thumb are their own. Each contributor is solely responsible for the content of their posts and they do not represent the views of the various organizations and businesses they may be affiliated with.

The opinions expressed in opening posts are those of the author only, and do not reflect the opinions of other authors, other organizations, or itself. does not review or approve material before it is posted. Contact the author if you have a concern about content or the site administration if the authorship of an opening post is unclear. Links to other sites do not imply approval or endorsement of the content at those links by Linked content may be altered by other parties, and thus issues with linked content should be taken up directly with the creators of that content. Commenting is generally open to the public, and the opinions expressed there are solely those of the commenters. Panda’s Thumb has a Comment Integrity Policy for dealing with the content of comments.


This is a list of the contributors to The Panda’s Thumb, with some brief biographical information about each one:

Andrea Bottaro is an immunologist and molecular biologist at the University of Rochester School of Medicine.  [Email]

Matthew Brauer is a postdoctoral research fellow at the Institute for Integrative Genomics at Princeton University, where he is studying the evolutionary responses of metabolic networks in eukaryotes. He holds a B.A. in biochemistry from U.C.-Berkeley, an M.S. in statistics and a PhD in biological sciences from the University of Texas at Austin. He wrote a chapter in Robert Pennock’s book Intelligent Design Creationism and its Critics.  [Email]

Ed Brayton is the co-founder of Michigan Citizens for Science. He is the group’s resident non-academic, being a businessman and concerned citizen with a longstanding interest in this issue.  [Email]

Reed Cartwright holds a PhD in genetics at the University of Georgia, a B.S. in genetics, and an A.B. in Latin from UGA as well. He has written extensively on evolution and Intelligent Design and is active with Georgia Citizens for Integrity in Science Education.  [Email]

Mike Dunford has been a contributor to for so long that he almost doesn’t feel like the new kid on the block any more. Currently, Mike is an Nth year senior at the University of Hawaii at Manoa, where he is (finally) completing his B.S. in Zoology. Following completion of his undergraduate work, he plans to continue to study evolution in island environments (especially ones with good beaches). Current interests include speciation processes in sympatric populations, and the evolution of introduced species. In the past, he has worked as a paleontological lab technician. Other interests include the history of geology, especially in 19th century England.

Wesley R. Elsberry is a biologist with an eclectic academic and work history. He holds a B.S. in Zoology (U. Fl.), an M.S.C.S. (Computer Science, U. Tx. at Arlington), and a Ph.D. in Wildlife and Fisheries Sciences (Tx. A&M U.). He has worked in biological, medical, and veterinary research; software design and development for military contractors; and photojournalism and studio photography. His research interests include the physiology and bioenergetics of dolphin biosonar sound production, the hearing of marine mammals, bioacoustics, animal behavior, and emergent computation (artificial neural systems, evolutionary computation). He became interested in the evolution/creation controversy in 1986 after attending a young-earth creationist lecture at the University of Florida. Since then, Wesley has become more involved in the issue, finally “turning pro” late in 2003 by becoming the Information Project Director for the National Center for Science Education. His views as expressed at The Panda’s Thumb are his own and are not necessarily shared by NCSE, its employees, or its supporters.  [Email]

Jim Foley is a software engineer from Canberra, Australia, who has been fascinated by creationism since encountering it at university. His main interest is the intersection of human evolution and creationism, and he is the author of the Fossil Hominids website which explores these subjects. He is married with four children and enjoys reading, squash, and tae kwon do.

Alan Gishlick – [Bio pending.]

Paul R. Gross is University Professor of Life Sciences, emeritus, at the University of Virginia. His baccalaureate and doctoral degrees are from the University of Pennsylvania. He holds honorary degrees from Brown University and the Medical College of Ohio. He is a developmental and molecular biologist who has taught at Brown, Rochester, MIT, and the University of Virginia. A Fellow of the American Academy of Arts and Sciences, he served from 1978 to 1988 as President and Director of the Marine Biological Laboratory in Woods Hole, MA, and was Vice President and Provost of the University of Virginia, where he helped to found and served as Director of the Molecular Biology Institute. He is co-author with Norman Levitt of Higher Superstition (Johns Hopkins, 1994, 98) and with Barbara Forrest of Creationism’s Trojan Horse: The Wedge of Intelligent Design (Oxford, 2004).

Richard Hoppe is an Affiliated Scholar in Biology at Kenyon College, and CEO of Intellitrade, Inc., which uses evolutionary algorithms to model market systems. His Ph.D. in experimental psychology is from the University of Minnesota.  [Email]

Burt Humburg is a graduate of and lab assistant at the University of Kansas School of Medicine. In the summer of 2005, he will begin a residency in internal medicine at Penn State University – Hershey Medical Center. He is a former board member with Kansas Citizens for Science.

Arthur Hunt – [Bio pending.]

Gary S. Hurd received a doctorate in Social Science from the University of California, Irvine in 1976. He subsequently served on the faculties of the California College of Medicine (UCIMC), the Medical College of Georgia (Psychiatry), and held numerous adjunct appointments. Since 1985, he has returned to archaeology, the principle focus of his early research. He has received several honors for teaching and research and has over one hundred publications, including abstracts and technical reports, ranging from topics in psychiatry, mathematics and chemistry to frass, fish digestion, prehistoric ceremonialism and forensic taphonomy. Hurd became actively involved in the creationist anti-science debate while the Curator of Anthropology, and Director of Education for the Orange County Museum of Natural History.  [Email]

Matt Inlay is currently a post-doc at UCSD, where he received his Ph.D. in Biology in 2003. His research focused on the regulation of V(D)J recombination by enhancers and enhancer elements.  [Email]

Jack Krebs is the vice-president of Kansas Citizens for Science. After receiving his undergraduate degree in anthropology, with an emphasis on religion and belief systems, he began a long career in secondary public education that has included being a math teacher, technology director and curriculum director. Jack has had extensive experience with curriculum standards in a wide range of areas. He also has long-standing interests in science, philosophy, and religion.  [Email]

John Lynch is an evolutionary biologist in Barrett Honors College at Arizona State University, where he also is affiliated with the Institute of Human Origins, the Center for Biology & Society, and the Center for the Study of Law, Science & Technology. He holds a PhD in biology from University College in Dublin, Ireland, and continues to do biological research into morphological evolution in mammals, most recently into temporal bone variation in great apes and fossil hominds.  [Email]

Nicholas Matzke is a Public Information Project Specialist with the National Center for Science Education. He holds bachelor’s degrees in biology and chemistry from Valparaiso University, and an M.A. in geography from U.C.-Santa Barbara. His views as expressed at The Panda’s Thumb are his own and are not necessarily shared by NCSE, its employees, or its supporters.

Pim van Meurs – [Bio pending.]

Ian Musgrave is a biomedical researcher and University lecturer from Australia. His current area of research is into a protein so obscure that only four other people actually belive it exists. He is also researching Alzheimer’s disease, for reasons he can’t currently remember. In a career that has spanned 25 years, Ian has counted kangaroo poo in western Queensland, dug up beet root in the Darling Downs, lost an entire herd of cattle in an experimental tropical grass paddock, and measured the hight of sand dunes on Frazer Island. It is generally felt that he can do the least harm studying obscure proteins away from normal people. When not researching obscure proteins or obsessively tracking down long out-of-date publications on peppered moths, Ian is an amateur astronomer, bushwalker and aficionado of folk music, often combining all 3 three activities at folk music camps in the bush.  [Email]

PZ Myers is an associate professor of biology at the University of Minnesota-Morris. He holds a B.S. in zoology from the University of Washington and a PhD in biology from the Institute of Neuroscience at the University of Oregon. He has previously taught at the University of Utah and at Temple University.  [Email]

Henry Neufeld – [Bio pending.]

Mark Perakh is a professor of physics (emeritus) and perhaps by far the oldest (agewise) contributor to this blog. He got his two doctoral degrees (one in technical/engineering physics and the other in electrochemistry) in the former USSR. He has taught physics and related disciplines for more than half a century in four countries, and lives in the US since 1978. He has authored about 300 scientific papers, four books, and scores of articles on political and sociological topics published in several languages, no to mention a novel and short stories published both in Russian and English. He was awarded prizes for his scientific work, including those from the Academy of Sciences in the USSR, DAAD (the German authority on R&D) and the Royal Society of London. He became interested in debunking first the Bible code fallacy, then the publications of religious writers purportedly proving the compatibility of the Bible with science, and finally the ID concepts, after his retirement. So far he has published several articles and a book Unintelligent Design (Prometheus Books, 2004) in this vein. His lifelong hobby has been mountain climbing (Pamir, Alai, Tien-Shan, Caucasus), plus collecting Russian (and occasionally non-Russian) oral jokes, and writing a little of poetry in Russian.

Steve Reuland is a PhD student in biochemistry and molecular biology at the Medical University of South Carolina. He holds a B.S. in Biology from the College of Charleston.

Jason Rosenhouse received his PhD in mathematics from Dartmouth College in 2000. He spent three years as a post-doc at Kansas State University and is currently an assistant professor at James Madison University in Harrisonburg, Virginia. He has written essays on Evolution/ID for several journals including BioScience, Evolution, and The Mathematical Intelligencer.

Timothy Sandefur is an attorney in Placerville, California, specializing in constitutional law. He is a contributing editor for Liberty magazine, and blogs regularly at Freespace. He holds a JD from Chapman University School of law and a BA in Political Economy from Hillsdale College. He is a fellow in the College of Public Interest Law at the Pacific Legal Foundation, and was a 2002 Lincoln Fellow at the Claremont Institute. In law school, he wrote a student note on the Establishment Clause implications of the accreditation of the Institute for Creation Research’s graduate school. (Dinosaur TRACS: The Approaching Conflict between Establishment Clause Jurisprudence and College Accreditation Procedures, 7 Nexus J. Op. 79 (2002)). His views as expressed on Panda’s Thumb are solely his own and do not in any way represent those of the Pacific Legal Foundation, its employees, clients, or supporters.

Jeffrey Shallit received his AB in Mathematics from Princeton University in 1979 and his Ph. D. in Mathematics from the University of California, Berkeley, in 1983. Since then he has taught at the University of Chicago and Dartmouth College. He is currently Professor of Computer Science at the University of Waterloo in Ontario. He has a long interest in pseudoscience and pseudomathematics and has written about the intelligent design movement in Reports of the NCSE and the forthcoming book, Why Intelligent Design Fails(Edis and Young, eds.)

Tara C. Smith is an assistant professor of Epidemiology at the University of Iowa. She holds a B.S. in Biology from Yale University. A “temporary” stint as a technician led to a Ph.D. in microbial pathogenesis and virulence factor regulation in Streptococcus pyogenes (group A streptococcus) at the Medical College of Ohio in Toledo. She completed post-doctoral training in molecular epidemiology at the University of Michigan. Her current research centers on investigation of hypervariable proteins in the group B streptococcus, S. agalactiae. Other interests include microbial ecology, emerging diseases, zoonoses, and infectious causes of chronic disease. In addition to publishing in scientific journals, she has written books on the topics of group A strep and Ebola. She lives in rural Iowa with her husband and 2 young children. [Email]

Dave Thomas is a physicist and mathematician, employed at a small high-tech testing firm in Albuquerque, NM. He received bachelor degrees in mathematics and in physics, and a master of science in mathematics, from the New Mexico Institute of Mining and Technology, where he was awarded the Brown Medal. Dave is president of the science group New Mexicans for Science and Reason, and also is a Fellow of CSICOP (Committee for Scientific Investigation of Claims of the Paranormal), the publishers of Skeptical Inquirer. He has published several articles in Skeptical Inquirer on the Roswell and Aztec UFO Incidents, as well as on the Bible Code. Dave has also published in Scientific American (Dec. 1980 cover article), and has several patents. He received the National Center for Science Education’s Friend of Darwin Award in 2000. Dave is married, and has two sons. He enjoys playing bluegrass, and and performs juggling and magic shows for elementary schools and other groups.

John Wilkins is a philosophy of science PhD graduate who has contributed various FAQs to the TalkOrigins Archive and numerous puns to the newsgroup. His primary interests are the evolution of culture and in particular of science, and in philosophical issues surrounding taxonomy, but he has an Opinion on everything. He has two children and a wife, all of whom know more than he does.  [Email]

Matt Young was a physicist with the National Institute of Standards and Technology and now teaches physics and engineering at the Colorado School of Mines. He is coeditor, with Taner Edis, of Why Intelligent Design Fails: A Scientific Critique of the New Creationism (Rutgers, 2004) and author of No Sense of Obligation: Science and Religion in an Impersonal Universe (1stBooks Library, 2001), and two other books.

The Beauty and The Beast

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Mediterranean orchid photo by A. Scrugli, in Biology LettersOrchid flowers are amazing. Science journalist and top blogger Carl Zimmer recently wrote a blog on orchids, "Orchid Hacks," commenting on a paper by Florian Schistl in the Journal of Evolutionary Biology that showed how orchids "hack" into the mate-recognition systems of male wasps. However, there is more than one way to "hack" a bug.

I'm interested in teaching / facilitating a public discussion course for interesting community members, with the tentative title "Evolution: What's controversial about, why and to whom?" There are issues related to evolution in science, of course, as well as in religion and theology, philosophy, politics and culture, law and education. More specifically, there is also the anti-evolution movement itself, which argues against the theory and teaching of evolution in all the above fields. Here is an outline of issues that would need to be addressed in such a course if it were to be truly thorough.

Specified Complexity: Darwin’s Panic?

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On a radio show Benjamin Wiker of the Discover Institute makes the following claim:

Specified Complexity: Darwin's Panic 03/20/2004

Recently the Ohio State School Board voted to allow discussion of challenges to evolutionary theory in Ohio's schools. Despite claims that intelligent design is religion in disguise, Darwinists are nervously shuttling around, trying to avoid confronting the scientific impediments "specified complexity" presents to evolutionary theory. They won't be able to keep the "barbarians" out forever. Benjamin Wiker of the Discover Institute ( Discovery Institute ) in Seattle guests.


I find Wiker's arguments somewhat interesting in the light of the vast amounts of scientific criticisms of specified complexity and other scientific ID 'fables'.

Speaking of the Ohio lesson plan, the brief "challenging answer" for endosymbosis ends with the following quote.

Although some bacterial cells (prokaryotes) can occasionally live in eukaryotes, scientists have not observed these cells changing into organelles such as mitochondria or chloroplasts.

Scientists also have not observed my parents having sex. Therefore, I must be a robot like Dembski.

Ohio Moth Myths

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The Ohio year 10 high school lesson plan "Critical Analysis of Evolution" was recently accepted amid a great deal of controversy. Detailed criticisms of the lesson plan as originally proposed are here:

One of the key criticisms was thta the lesson plan included non-scientific material from creationist and anti-evolutionary sources. The lesson plan was revised, and the proponents claim that the revised plan is good science, and does not contain either creationism or "intelligent design". However, these claims are incorrect, as I will show with an analysis of the peppered moth example.

William A. Dembski recently published a book, The Design Revolution: Answering the Toughest Questions About Intelligent Design. The subtitle offers a promissory note, and so do several of the blurbs on the dust jacket and front matter to the effect that Dembski covers herein all the criticisms that have been offered about "intelligent design" and Dembski's particular contribution, "specified complexity". This is untrue, as I will attempt to demonstrate.

"The Panda's Thumb" is many things...

First, it is an example of jury-rigged evolutionary adaptation made famous by the late Stephen Jay Gould in an essay of the same name. Second, it is the legendary virtual bar serving the community of the legendary virtual University of Ediacara somewhere in the Ediacaran hills of southern Australia, growing out of the lore of the Usenet newsgroup. And now it is a weblog giving another voice for the defenders of the integrity of science, the patrons of "The Panda's Thumb".

Much as in any tavern serving a university community, you can expect to hear a variety of levels of discussion, ranging from the picayune to the pedantic. The authors are people associated with the virtual University of Ediacara (and thus the newsgroup), and various web sites critical of the antievolution movement, such as the TalkOrigins Archive, TalkDesign, and

So, here's a virtual pub crawl that you might actually learn something from. We hope you find your time spent here pleasant and rewarding.

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