Monday, November 30, 2009

The Fruitlessness of ID "Research"

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.

By contrast, let's compare Meyer's work with another paper, in the same field, of roughly the same length, and published in the same year:

W. G. Joyce, J. F. Parham, and J. A. Gauthier, "Developing a protocol for the conversion of rank-based taxon names to phylogenetically defined clade names, as exemplified by turtles", Journal of Paleontology 78 (5) (2004), 989-1013.

This paper has been cited 60 times since 2004, according to ISI Web of Science, by researchers writing in journals such as Systematic Biology, Journal of Anatomy, Bulletin de la Société Géologique de France, Proceedings of the Royal Society B - Biological Sciences, Journal of Morphology, Zootaxa, Journal of Ornithology, Naturwissenschaften, Journal of Vertebrate Paleontology, etc., etc. Clearly there is a substantial difference in opinion of this paper, versus Meyer's.

Now let's look at all 9 papers that have cited Meyer's work, as reported by ISI Web of Science. I have read every paper, except paper 4 (Luskin); for that paper I had to be content with an abstract.

1. J. Giles, "Peer-reviewed paper defends theory of intelligent design", Nature 431 (7005) (Sept 9 2004), 114. A one-column news article in the news section of Nature about the publication of Meyer's paper. Not a scientific research paper.

2. K. M. Helgen, "Meyer paper: don't hang the Soc. Wash. out to dry", Nature 432 (7020) (Dec 23 2004), 949. A letter to the editor defending the reputation of the journal that published Meyer's article. Money quote: "Given the Proceedings’ taxonomic focus, Meyer’s ID paper is clearly out of place. Its publication represents a lapse of the journal’s usual editorial policies, and has been swiftly repudiated ( However, although the publication of Meyer’s paper is lamentable, it need not be used to trivialize the Proceedings’ long, respectable and ongoing tradition of cataloguing global biodiversity." Not a scientific research paper.

3. Mark Terry, "One nation, under the designer", Phi Delta Kappan 86 (4) (Dec 2004), 264. Abstract. Full paper (subscription required). This journal is a professional journal for educators. The paper's subtitle reads, "Mr. Terry alerts readers to a new, more insidious anti-evolutionist strategy. And the redefinition of science is only the first step." Meyer's paper is discussed, as follows: "The supposed "scientific revolution" is a creation of public relations. A science teacher cannot go to any major science journal or scientific organization and find out about all this new research - because there is none. In the fall of 2004 an ID article by a Discovery Institute Fellow appeared in the Proceedings of the Biological Association of Washington, a venerable but formerly obscure journal dealing with subtle taxonomic issues. The flurry of responses to the article gives a good picture of the current state of ID as science: the governing council of the journal almost immediately disavowed the article's publication." Not a scientific research paper.

4. C. Luskin, "Alternative viewpoints about biological origins as taught in public schools, Journal of Church and State 47 (3) (Summer 2005), 583-617. First page. A journal of law and social science. Luskin is "Program Officer in Public Policy and Legal Affairs" at the Discovery Institute. Not a scientific research paper.

5. B. H. Weber, "Emergence of life", Zygon 42 (4) (Dec 2007), 837-856. Zygon is self-described as a journal of "religion and science", but I would consider it a philosophy journal. A review article. Of the nine papers, this is the one that is the closest to a scientific research article that cites Meyer approvingly: "The emergence and increase of novel, specified, functional information remains the crucial issue." He thinks that Meyer's questions have been answered by "the new science of emergent complexity".

6. J. Koperski, "Two bad ways to attack intelligent design and two good ones", Zygon 43 (2) (June 2008), 433-449. Again, Zygon is self-described as a journal of "religion and science", but I would consider it a philosophy journal. This article focuses on the rhetoric of intelligent design and its opponents. Not a scientific research paper.

7. Emilia Currás and Enrique Wulff Barreiro, "Integration in Europe of human genetics results obtained by Spaniards in the USA: A historical perspective", Scientometrics 75 (3) (2008), 473-493. This is the strangest paper of the nine. It purports to be about "the mobility of Spanish biochemists from Europe to the United States over the past 80 years". It cites Meyer as follows: "In the context of cancer research, the (chemical and reductionist) search for the molecular basis of cancer induction is combined with the holistic vision of the close relationship between form and function in physiology [Shimkin, 1974; Meyer, 2004; Marra & Boland, 1995]". Although it is about "form", Meyer's paper doesn't mention "cancer" or "physiology" at all. Perhaps the citation was really meant to refer to something completely different? In any event, this paper is more a historical discussion, not a scientific research paper.

8. S. L. Shafer, "Critical thinking in anesthesia: Eighth honorary FAER research lecture", Anesthesiology 110 (4) (2009), 729-737. Full paper here. An article criticizing various anti-scientific trends. Here is how he cites Meyer: "One can find many Web sites devoted to intelligent design. However, the story in the peer-reviewed literature is quite different. Of 99 articles identified by a PubMed search of intelligent design (on November 14, 2008), the majority are defenses of evolution against claims of intelligent design. Not appearing in the search is the single scientific article supporting the claims of intelligent design written by Stephen Meyer of the Discovery Institute. This article was published without peer review in a nonindexed journal and was subsequently retracted by the journal for insufficient scientific merit." Not a scientific research paper. [Update: Shafer's claim about "published without peer review" is not correct, and the paper was not actually formally "retracted". "Disavowed" is more like it.]

9. Juan E. Carreño, Fernando Hansen, et al., Some considerations about the theory of intelligent design, Biological Research 42 (2) (2009), 223-232. Full paper here. An article, critical of intelligent design, in an obscure Chilean biology journal. However, the topic is more about philosophy than science. Money quote: "We also reject the claim that ID is a legitimate scientific theory, because it does not exhibit the classical characteristics that a scientific kind of knowledge must have." Not a scientific research paper that cites Meyer approvingly.

The grand total: exactly 1 paper (Weber's) can be said to be a scientific paper that cites Meyer approvingly, and even that is subject to debate.* This meager record does not support the claim that ID is a scientific revolution with far-reaching consequences.

ID advocates are constantly telling us that intelligent design is a new scientific paradigm that will prove fruitful. Five years after ID's flagship "peer-reviewed" paper, that does not seem to be the truth.

* No doubt ID advocates will produce other papers, published in obscure venues, that cite Meyer, that I missed. For example, Google scholar lists a few more, including:

10. Fernando Castro-Chávez, "Hepatology Microarrays, antiobesity and the liver", Annals of Hepatology 3 (4) (Oct-Dec 2004), 137-145. Full paper here. A case of inappropriate citation. The only citation to Meyer comes in the final paragraph, which reads "... to better describe the identity and function of genes and genomes, composers of a natural, complex, and precise biological software that as a genetic program, contributes to the healthy programming and the pathological reprogramming of life." The author appears to be an intelligent design advocate. I predict that inappropriate citation -- the bogus insertion of citations to pro-ID papers in irrelevant contexts -- will become more popular in the future, as creationists attempt to bolster their case that ID is scientific.

11. Wolf-Ekkehard Lönnig, "Mutation breeding, evolution, and the law of recurrent variation", Recent Res. Devel. Genet. Breeding, 2 (2005), 45-70. Full paper here. Lönnig is a well-known creationist. The only references to Meyer appear on pages 61 and 64: "Thus, in accord with the laws of probability, examples and cases relativizing the law of recurrent variation have not been observed so far (35, 43, 46, 65, 77, 78, 88, 95, see also note 2)." and "For an additional detailed discussion of further points and possible
objections, see (see 1-9, 15, 20, 21, 23, 27, 30, 35, 38, 39, 43-57, 61, 65, 77-80, 86, 88, 90, 91, 94, 95)".

But ISI Web of Science also misses a number of articles critical of Meyer. In any event, the citations I have found do not support the extravagant claims made for ID and for Meyer's article. So far, ID is not proving frutiful for science.

Saturday, November 28, 2009

The Ol' Information Bait-and-Switch

It seems that my criticism of aging philosopher Thomas Nagel has got the folks at Uncommon Descent running scared. That's because they know their bogus claims about information are being exposed.

I gave an example that trivially refutes Stephen Meyer's claim that "information always comes from a mind": weather prediction. Meteorologists record information such as wind speed, wind direction, and temperature to make their predictions. Under both the informal definition of information used in everyday life, and the formal technical definitions of "information" universally accepted by mathematicians and computer scientists, these quantities indeed represent "information". What is the response?

Of course, it's the old information bait-and-switch trick: Dembski is now claiming that my example was "unspecified information", whereas Meyer was talking about "specified information".

Dembski is an old hand at the information bait-and-switch game, as Elsberry and I showed in detail in our peer-reviewed article. He moves from one definition to another seamlessly, as it suits him, for whatever argument is at hand. This is most apparent in his estimation of probabilities, where he switches back and forth between the uniform probability interpretation and the causal-history interpretation, depending on which one gives the answer he requires. We discuss this at length in our article.

Furthermore, the notion of "specification" comes from Dembski himself, and as Elsberry and I showed, it is completely incoherent. Nobody can say whether a given string is "specified" or not, and "specification" fails to have the properties Dembski claims it has. No mathematician or computer scientist, other than Dembski and his intelligent design friends, uses Dembski's measure or does any calculations with it. To pretend that it is meaningful is not honest.

Just to give one example, here is Dembski and his deep technical and mathematical "proof" that "the [sic] bacterial flagellum" is specified:

"At any rate, no biologist I know questions whether the functional systems that arise in biology are specified." (No Free Lunch)

So, a challenge: which, if any of the following strings constitute "specified information"? Be sure, in your answer, to give all the things that Dembski says are required before one can be sure: the space of events, the rejection function, the rejection region, the "independently-given" specification, the relevant background knowledge, the independence calculation, and so forth.


Meanwhile, Dembski needs to inform his acolyte "Joe G", who thinks that the proper definition of "information" is "the attribute inherent in and communicated by one of two or more alternative sequences or arrangements of something (as nucleotides in DNA or binary digits in a computer program) that produce specific effects". Well, by that definition, my example of the information used in weather prediction is indeed information -- there are many alternatives in wind speed, direction, and temperature, and no one can doubt that different arrangements of these quantities produce different effects -- namely, different weather.

Joe G, get with the program! Just say my example is "unspecified", and be done with it! No need to trouble yourself with actual thinking.

Friday, November 27, 2009

Discovery Institute Fellow Accused of Making Stuff Up

And in a really huge surprise, a fellow of the Discovery Dishonesty Institute, Benjamin Wiker, is accused by a young-earth creationist of making stuff up.

Why, I am simply speechless!

To be fair, Wiker has a Ph. D. in "theological ethics". You know, as distinguished from real ethics, where fibbing is considered to be in bad taste.

Thursday, November 26, 2009

A Failed-Self Reference Argument

Steven Goldberg is an American sociologist. In his book, When Wish Replaces Thought, he proposes the following argument against descriptivism, which he seems to think is completely decisive. I found the argument interesting, because it attempts to use self-reference in much the way Turing's proof that the halting problem is unsolvable does. Unfortunately, Goldberg's argument is flawed in several respects.

Here is the relevant passage, which appears on pp. 193-194:

"People with more than a passing interest in words fall into two groups, prescriptivist and descriptivist. The prescriptivist believes that there is an ideal of correctness in the use of words - shifting and temporally based as it ultimately may be. The descriptivist finds the concept of "correctness" elitist at best and, more often, incomprehensible.

"The one inviolable rule of descriptivism is this: There are no correct definitions, meanings, or usages other than those used by people-in-general; any attempt to substitute a definition, meaning, or usage for that used by people-in-general is invalid. Where the prescriptive subordinates popular usage to correct usage, the descriptivist denies to correctness
and all other criteria parity with use by people-in-general.

"Now consider what happens when you ask a descriptivist how he defines "dictionary" in his descriptivist dictionary.

"The descriptivist might, as his inviolable rule says he must, accept the definition of "dictionary" used by people-in-general. If he does this, he will define "dictionary" as people-in-general really do, as giving correct definitions, correctness being determined by a literary elite. The descriptivist must accept the view of people-in-general that there is a correct usage -- in this case correct definitions -- because his inviolable rule requires that he accept the view of people-in-general. In granting that there is a correct usage, the descriptivist grants what his inviolable rule, his basic premise, denies.

"The descriptivist might, on the other hand, reject the definition used by people-in-general and substitute the definition of "dictionary" implied by his violable rule, the definition that denies there there is a "correct" usage other than that used by people-in-general. But if he does this, he does the one thing that his inviolable rule prohibits. He substitutes a "correct" definition whose existence his basic premise denies for the only definition that his basic premise -- his inviolable rule -- grants as legitimate, the definition used by people-in-general.

"The descriptivist cannot argue that people-in-general are incorrect in defining a "dictionary" as giving correct usage because "incorrect" (or "wrong") has no meaning in the descriptivist universe (except, perhaps, to describe misrepresentation of the usage of people-in-general, which is just what the descriptivist does if he alters the definition of "dictionary" used by people-in-general; people-in-general cannot, according to the descriptivist premise, be incorrect).

"Whether the descriptivist accepts the definition of "dictionary" used by people-in-general or rejects the definition used by people-in-general, the descriptivist's descriptivism is exposed as rotten at its core. Note that the contradiction is not merely an oddity relevant only to a single definition. The problem of defining "dictionary" is but a focused view of a contradiction that infuses all of descriptivism and that can be stated without reference to a definition of "dictionary". The general contradiction is that descriptivism is founded on an axiom that accepts "A" (popular usage) and rejects "B" (any other authority or criterion for correctness) even when acceptance of "A" commits descriptivism to an accepance of "B", which is rejected by the axiom ("A") that requires its acceptance."

I think this argument is flawed for a number of reasons. Here are a few.

1. I think Goldberg caricatures what descriptivists believe. A descriptivist wouldn't say that meaning is determined the use of "people-in-general", because words don't have single meanings. For example, what if exactly 50% of "people-in-general" think a word means one thing, while exactly 50% of "people-in-general" think it means another? Then there is no one meaning held by "people-in-general" at all. For another, words have multiple meanings and shades of meaning. Sometimes these meanings can even be the opposites of each other. What, for example, do "people-in-general" mean by the word "cleave"? On the one hand, it can mean "to stick together". But it can also mean "to cut apart". Then there are words whose meanings have gradually shifted over time, such as "nubile". Originally, it meant "marriageable", but these days it seems to be used more as if it means "young and sexy".

2. I think Goldberg caricatures what "people-in-general" believe about the meaning of the word "dictionary". It may well be that "people-in-general" think of a dictionary roughly like what Goldberg claims: as a book "giving correct definitions, correctness being determined by a literary elite". But if you ask "people-in-general" whether they think a dictionary can ever contain an incorrect definition, or is it necessarily always right, I'd be very surprised if they choose the latter option. Furthermore, there is not a single dictionary accepted by all English-speaking people, but many different ones. "People-in-general" will have to concede that these many different dictionaries may disagree on the meaning of a word. So a descriptivist may well define "dictionary" as "a book containing usually-correct definitions, approved by a literary elite" and still satisfy the beliefs of "people-in-general". But then Goldberg's "contradiction" disappears.

3. The dictionary definition of "dictionary" doesn't usually claim its definitions are correct. For example, picking a dictionary at random from the web, I find the first definition of "dictionary" as "A reference book containing an alphabetical list of words, with information given for each word, usually including meaning, pronunciation, and etymology." Given that, maybe "people-in-general" don't assume what Goldberg claims they do.

4. "People-in-general" may well believe that a word has a certain definition but that does not necessarily mean that the object that the word refers to actually exists. For example, "people-in-general" might define "unicorn" as "a goat-like animal with magical powers and a single horn", but that doesn't mean that unicorns actually exist or have magical powers. Acknowledging this doesn't violate the descriptivist position; the descriptivist need not be a moron. So "people-in-general" may believe that a dictionary is a book "giving correct definitions, correctness being determined by a literary elite", but that doesn't necesssarily believe that such a book actually exists. Thus, a descriptivist can, without fear of contradiction, believe both that "people-in-general" think "dictionary" has this meaning on the one hand, and also believe that no such book as described by "people-in-general" actually exists in the real world.

So while I find Goldberg's attempt interesting, I think it is a failure.

Wednesday, November 25, 2009

Stupid Philosopher Tricks: Thomas Nagel

In a previous post, I said, "Whenever scientific subjects are discussed, you can count on some philosopher to chime in with something really stupid."

Here's another example. Thomas Nagel, a philosopher of some repute, nominates Stephen Meyer's Signature in the Cell as his pick for book of the year in the Times Literary Supplement.

Does Nagel have any biological training? None that I could see. Does he know anything about evolution or abiogenesis? Not if he thinks Meyer has any valid contribution to make. Did he bother to check if biologists think Meyer's book is a good contribution to the literature? I doubt it. Did Nagel spot all the phony claims Meyer makes about information? I doubt it again.

Just to cite one: Meyer claims, over and over again, that information can only come from a mind -- and that claim is an absolutely essential part of his argument. Nagel, the brilliant philosopher, should see why that is false. Consider making a weather forecast. Meteorologists gather information about the environment to do so: wind speed, direction, temperature, cloud cover, etc. It is only on the basis of this information that they can make predictions. What mind does this information come from?

It's sad to see such an eminent philosopher (Nagel) make a fool of himself with this recommendation.

Strange Physics Foundation

Take a look at the website for the Santilli Foundation and the International Committee on Scientific Ethics and Accountability. Strange, aren't they?

I particularly liked the reference to "moist insidious and organized plagiarisms".

A New Creationist Claim?

My barber told me, quite straight-faced, a new creationist claim. There is, he said, abundant evidence in the Torah that dinosaurs were actually demons. "No, they were just animals," I replied. Despite our disagreement, I got a good haircut.

But I've got to admit, that's a new one for me.

Tuesday, November 24, 2009

Aboard the Toronto Airport Ferry

I never flew into the Toronto Island airport before, but I did so for the first time on Sunday. After you land, a ferry takes you across 120 meters of water in 60 seconds. This is what the view looks like from the ferry. Not bad, eh?

Another Anti-Choicer Refuses to State What the Penalty Should be for Abortion

I commented about this earlier.

Here's the bishop of Providence, RI, who wants to outlaw abortion but refuses to say what the penalty should be for a woman who has an abortion.

Coma Video Shows Use of Bogus "Facilitated Communication" Technique

By now you've probably heard the story of a man, thought to be in a coma for 23 years, who was recently "discovered" to be conscious the whole time.

Maybe so. But maybe not.

As James Randi points out, a video clearly shows that the man himself is not typing. Instead, a woman is shown using a technique called "facilitated communication", where she moves his hand to type on a keyboard. He is not moving his hand independently.

Facilitated communication is a bogus technique that has been exposed as fraudulent.

This makes me very suspicious of the entire report.

Not surprisingly, at Uncommon Descent, Denyse ("The World's Crappiest Reporter") O'Leary completely buys the story.

Three Felonies a Day

That's the title of a new book by Harvey Silverglate. The subtitle is "How the Feds Target the Innocent".

There's no question that overzealous and politically-motivated prosecution has destroyed the lives of many innocent people. One prominent example discussed by Silverglate is former Alabama governor Don Siegelman, whose conviction on corruption charges was almost certainly engineered by Karl Rove and the Bush White House.

Despite this, I was disappointed by the book. For one thing, the title - based on a claim that the average "busy professional" "likely commit[s] several federal crimes" each day, is simply not substantiated. The crimes discussed in this book are mostly things like overprescription of painkillers, flawed medical device manufacture, accounting fraud, etc., which are probably not the domain of the average "busy professional". For another, the focus on federal crimes leaves out some of the most egregious prosecutions, like those for copyright violation and teenagers recording their own sex acts.

But the main flaw is that I was not actually convinced by several of the cases discussed that the people charged were actually innocent or that the prosecutions were illegitimate. Some of the cases turn on strained readings of existing law, where the people involved should have known their actions were dubious. In two cases - the prosecution of Boston pols Kevin White and Thomas Finneran - Silverglate seems to suggest that influence peddling is just a normal part of city politics, and nothing to get worked up over. I don't agree. I want all politicians to keep their decisions squeaky clean and completely removed from their financial interests. They need to avoid even the appearance of conflict of interest.

So, while I agree with Silverglate's main thesis, I think some of the cases he chose were not the best examples of overzealous prosecution. Too bad - because this is an important topic that deserves a comprehensive treatment.

Saturday, November 21, 2009

Rowing and the Thue-Morse Sequence

Here's an interesting preprint by John Barrow about the optimal configuration of rowers to minimize "wiggle". The story was picked up by Technology Review, which you should go read first.

Ultimately, the problem comes down to assigning exactly half of the numbers from 1 through N a sign of +1, and the other half -1, so that the sum of the numbers is 0. For N = 4 there is one solution

1 2 3 4
+1 -1 -1 +1

and its "reflection" that is obtained by multiplying everything by -1.

It's easy to prove that a solution exists if and only if N is a multiple of 4. For N = 8, Barrow proposes some new solutions.

There is a connection here to the Thue-Morse sequence t(i), which assigns to i either +1 or -1, according to the parity of the number of 1's in the binary expansion of i. An old theorem of D. H. Lehmer implies that

Σ0 ≤ i < 2k   t(i) p(i) = 0

for any polynomial of degree < k. So in particular, the Thue-Morse sequence gives an infinite family of solutions to the wiggle-free rowing problem, whenever N is a power of 2. In particular, for N = 8, Barrow's solution (d) is given by the Thue-Morse sequence.

As an aside, Barrow implies something about the complexity of the problem in his abstract. He says, "We show that the problem of finding the zero-moment rigs is equivalent to a version of the NP-complete Subset Sum problem." No, not really. He showed that his problem is a special case of the subset-sum problem, which says nothing at all about its complexity. After all, his problem is also a special case of the halting problem! And in any event, since it is easy to show that solutions exist if and only if N is a multiple of 4, the decision problem's complexity is trivial.

This is yet another example of the rule that says "Whenever scientists or mathematicians with no formal training in computer science talk about complexity theory, with high probability they are quickly going to say something stupid." For another example, see here. Of course, if I were to write about physics, no doubt I would say something equally stupid.

Friday, November 20, 2009

Authoritarian Creep of the Month

Kurt Greenbaum is the "director of social media" at the St. Louis Post-Dispatch. Last Friday, he posted a topic for discussion, What's the Craziest Thing You've Ever Eaten?

One not-particularly-clever commenter wrote in the answer, "pussy", and Greenbaum's authoritarian streak took over. How dare anyone refer to oral sex in his space! How shocking! How vulgar!

Greenbaum then did what every good little fascist-in-training would do: he tattletaled on the commenter to his employer:

A few minutes later, the same guy posted the same single-word comment again. I deleted it, but noticed in the WordPress e-mail that his comment had come from an IP address at a local school. So I called the school. They were happy to have me forward the e-mail, though I wasn’t sure what they’d be able to do with the meager information it included.

About six hours later, I heard from the school’s headmaster. The school’s IT director took a shine to the challenge. Long story short: Using the time-frame of the comments, our website location and the IP addresses in the WordPress e-mail, he tracked it back to a specific computer. The headmaster confronted the employee, who resigned on the spot.

Not surprisingly, the reaction to Greenbaum's misconduct was negative. What to do? Why, shut off the comments, of course!

Comments are still open on here, in case you want to pile on.

Update: the Post-Dispatch deleted my comment, although it contained no profanity - just criticism. Big surprise.

Sarah Palin: Pathological Liar

Huffington Post demonstrates that Sarah Palin's pathological liar tendencies continue in her new book.

Wow, what a surprise.

I guess now she'll have to threaten them with a lawsuit, too.

Meanwhile, you can watch this video from two clueless Palin supporters.

Wednesday, November 18, 2009

Paper Rebutting Dembski Finally Out

Back on my previous sabbatical, in 2001-2, I spent a couple of months reading WIlliam Dembski's book, No Free Lunch, which he was kind enough to send me. I chose to do that for a number of reasons: first, I was interested to see if his claims about a mathematical refutation of Darwinism were true; second, a sabbatical is the time to tackle some unusual project you don't usually have time for; and third, I have an interest in pseudoscience and pseudomathematics. Reading it led to some fun discussions with Wesley Elsberry and we eventually produced a long, 54-page refutation of many of Dembski's claims.

But then, what to do with it? I had heard Dembski and Ruse were co-editing a voume, so I briefly entertained the idea of submitting it for inclusion there. But I was worried Dembski would refuse because the paper was sharply critical of his work, and after talking to Ruse I had second thoughts and decided to look for another venue. We chose a journal whose subject matter included biology and philosophy, but the paper was eventually rejected -- not because of the quality of the paper, but because the referees felt that spending 54 pages to debunk what they perceived as anti-evolution crackpottery was not a good use of their journal's space.

Finally, we were invited to submit the paper to a special issue of the journal Synthese, and we did so. The paper went through multiple rounds of refereeing, with the referees suggesting that more and more be cut. Now that it has finally appeared, it is down to a measly 34 pages. Luckily the long version is still available online.

If you can't read the Synthese version because you don't have a subscription, just write me and I'll be happy to send you a copy.

This is the longest interval I've ever had between finishing a paper (2002) and the time it appeared (2009). And it's likely to be my only paper in a philosophy journal. I predict that the intelligent design community will continue to ignore all the criticisms (which have been available to them for years) and continue to pretend that CSI is actually a coherently-defined entity, and that the "law of conservation of information" holds. I predict lots of breast-beating, and excuses for not addressing our criticisms, but no response that deals forthrightly with all the errors we found in Dembski's work.

Creationists Handing Out Origin of Species at MIT

As you probably know, creationist moron Ray Comfort has created a new version of Darwin's Origin of Species with his own introduction, and his minions are now handing them out at college campuses in the US. Above is a picture taken 15 minutes ago at MIT, showing a creationist happily distributing this bizarre book.

While these morons are distributing Ray Comfort's sleaze, MIT researchers are getting ready for a symposium on the evolution of the eye on November 20.

Ironic, isn't it?

New Blue Pigment Discovered

Here's an interesting article about an apparently new blue pigment discovered serendipitously by chemists at Oregon State. The color is reported to arise from Mn3+ "introduced into the trigonal bipyramidal sites of metal oxides". The new pigment is said to be better than alternatives such as cobalt blue, ultramarine, Prussian blue, and azurite, because it is stable and non-toxic.

I'm a little skeptical that it's commercially viable, since the examples the chemists have produced so far are based on compounds using the rare metals yttrium, indium, lutetium, and gallium.

Perhaps it is just a coincidence, but there is exactly one known mineral that crystallizes in the trigonal bipyramidal form, and it is also known for its blue color: benitoite (BaTiSi3O9).

Monday, November 16, 2009

Stupid Creationist Letter Award for November

A creationist has responded to this post about the dirty rhetorical tricks of creationists, as follows:

There is really no scientific evidence that proves evolution happened. No animal has developed extra chromosomes that we have recorded and none of the findings of supposedly ancestors have any DNA evidence. Evidence does not hold up in court.

Darwin had a theory, based on observation. Fine.

Creationists have a theory based on the Bible.

Intelligent design mongers are clueless and belive in Star Trek.

No one knows where we come from, but the fact that Darwinism was used as en excuse to justify fascists regimes is a fact. They refer to Darwin as their substitute for God all the time in their literature, comparing fascism to "Survival of the Fittest. Why? He is dead, he can't defend himself.

Let me explain where they are wrong. Nature doesn't work by "survival of the fittest". "Survival of the species" trumps that. Observe bees, bacteria, herds of animals, even predators like lions depend on socialization for survival. Where is the "survival of the fittest?". The economists, in their greedy ways twist science to justify a consumerist society in which a few have wealth and the rest suffer.

It really is remarkable for its stupidity, ignorance, and arrogance, all rolled up into one. Isn't it?

Boston's Monument to Foolishness

This prominent building, in Boston's downtown, is probably the city's largest monument to foolishness. Although its supporters make extravagant health claims, these are not supported by evidence. Nevertheless, the group's political power has helped pass laws in dozens of states to allow it to avoid prosecution.

What building is it?

Sunday, November 15, 2009

Phony Calls for "Civility"

You know a call for "more civility" is completely phony when the person who issues it only cites examples from one side of the debate.

That's the case with this recent opinion piece by Casey Luskin, spokesman for the Discovery Institute.

Luskin lists three examples of incivility, and all of them are from the pro-science, anti-creationist side. He fails to cite a single example of incivility from a creationist, even though there are many examples to choose from. As Wesley Elsberry has documented, Luskin's friends routinely compare evolutionary biologists to Nazis, communists, the Taliban, and Satan. Luskin himself has labeled materialists an "ominous force" that will "consume" people. William Dembski proudly sponsored an animation that used fart noises to make fun of Judge Jones, who decided the Kitzmiller v. Dover case.

No one is going to be fooled by this dishonest posturing.

Authoritarian High School Principal of the Month

Our nomination for authoritarian high school principal of the month goes to Thomas Murray, principal of Danvers High School in Danvers, Massachusetts, who has chosen to ban the word "meep" from the campus.

Students reportedly had been using the nonsense word to disrupt classes. But isn't disrupting class already an offense at the school? Why would a word need to be banned, too?

Instead of using this opportunity to talk about free speech and preserving a good learning environment, the principal chose a heavy-handed and authoritarian approach to the problem. Shame on him.

NPR Examines Consciousness

An NPR series called "The Really Big Questions" has recently examined the question, "What Can the Animal Mind Tell Us About Human Consciousness?"

The people they interviewed included neuroscientist Christof Koch, ethologist Colin Allen, primatologist Frans de Waal, and philosopher Colin McGinn. Now, who do you suppose had the most moronic things to say? Take a guess.

No surprise, it was the philosopher. Whenever scientific subjects are discussed, you can count on some philosopher to chime in with something really stupid. McGinn made all sorts of dubious unsupported claims, like "There are very strong reasons to think that reductionism is not true". He said, "I think there are problems of principle. In the very project you're trying to understand how the phenomenological might arise from the organic, because we're trying to bring together two different conceptual schemes, two different types of knowledge we have of the world, knowledge which we derive from first person awareness of our own consciousness and then the knowledge we have of the physical world, and these two types of knowledge simply don't fit together." Luckily Christof Koch was there to answer some of this kind of fuzzy thinking.

Unfortunately, the interviewer, Lynn Neary, didn't help things out. Although it should be obvious to anyone who thinks about it for even a few minutes that what we call "consciousness" is multifaceted, involving things like memory, planning, anticipation, modelling of the environment, and self-awareness, it took nearly half an hour before these ideas were brought out explicitly, and even after that, Neary persisted in conflating them. She seemed to want to have some very simple definition of what consciousness is before discussing it. Is it too much to ask that interviewers do a little homework before beginning their job?

If there's any consolation, at least they didn't interview Mario Beauregard.

Thursday, November 12, 2009

Dover Trial Reunion

I attended the reunion for the Kitzmiller v. Dover trial over the weekend, which was held at Lauri Lebo's house in York Haven, PA. Lauri was a reporter for the York Daily Record at that time, and wrote the most intimate account of the trial in her book, The Devil in Dover. It is a terrific book, funny and sad at the same time, and definitely worth reading.

(As you may know, I played an extremely small role in this historic event - I had been asked to testify as a rebuttal witness against William Dembski. But Dembski withdrew from the trial, so my testimony was never needed.)

Lauri Lebo lives with the folk-rock-country musician Jefferson Pepper in two houses in rural Pennsylvania. I stayed in the famous beer can house, which houses the world's largest collection of beer cans. (I stayed in the German room, in case you want to know.)

I got to meet some of the important figures of the trial for the first time, including Vic Walczak of the ACLU, Richard Katskee of Americans United for the Separation of Church and State, and some of the plaintiffs, including Bryan Rehm, Cynthia Sneath, and Steven Stough. (There were others, but I'm bad with names.) And I got to see old friends, including the NCSE's Genie Scott, superstar biologist Ken Miller, and Behe-destroying lawyer Eric Rothschild.

Above: me with Genie Scott and some beer cans.

Above: Ken Miller.

In the evening there was a concert at the very cool Midtown Scholar Bookstore in Harrisburg, PA. (If you are ever in the area, this is definitely a place to visit. I picked up three books about snakes for my youngest son, who is a snake enthusiast, and two books about intelligent design for my anti-evolution & pseudoscience collection -- all at very reasonable prices.)

Above: ironic sign in the bookstore.

The concert featured a brief reading by Genie Scott, some terrific music by Jefferson Pepper and the Varmints of Heaven, a lecture by Kenneth Miller, and evolutionary rap by Baba Brinkman.

Above: Baba Brinkman and Eric Rothschild.

Above: rockin' out with Jefferson Pepper and the band. At right, on rhythm guitar, is York Daily Record columnist Mike Argento, who wrote some of the funniest newspaper columns about the Dover trial; he also has a blog.

Above: Baba Brinkman.

All-in-all, it was a fun weekend. Thanks to Lauri, Jeff, and the others who made it possible.

Friday, November 06, 2009

Journal Editor in Libel Suit

According to this article in the Press-Gazette, Mohamed El Naschie, former editor of the journal Chaos, Solitons, and Fractals is suing Nature because of a November 2008 article. That article, written by Quirin Schiermeier, raised the issue of the very large number of papers authored by El Naschie and published in that journal CSF, and the quality of those papers.

I don't think El Naschie has a case, but who knows in Britain, where libel laws are insane?

Monday, November 02, 2009

Misunderstood Mathematics

One of my long-term book projects is about mathematical theorems that give people fits. A good example is Cantor's theorem that the real numbers are uncountable. The proof is simple enough that you can explain it to a 10-year-old, but some adults simply don't get it, no matter how many times it is explained.

For example, see this thread over at Mark Chu-Carroll's blog. It just goes on and on, with one poster ("Vorlath") babbling away, but making no progress at all in comprehending this very simple proof.

I'd be interested in understanding the psychological mechanisms behind this kind of misunderstanding. It reminds me of the difficulty that some religious people appear to have in understanding evolution - you just go 'round and 'round with them, but they make no progress. Is it willful? That is, do they secretly know they are talking nonsense, but can't accept it because of their preconceptions? Or are they truly baffled?