April 2007 Archives

Shelley Batts over at Retrospectacle was contacted yesterday by a representative of Wiley Interscience, who objected to her fair use of part of one figure from a paper. (Wiley has a record of acting dubiously.) Shelley has posted the exchange on her blog and has called for a blog-swarm.

Wiley’s legal threats are baseless because fair use allows people “to freely use portions of copyrighted materials for purposes of commentary and criticism.”—Ironically, Wiley publishes Patents, Copyrights & Trademarks For Dummies.—In addition, this move by Wiley is very stupid given that Shelley was promoting a paper published in one of their journals. She was providing good press for them. But in one stupid move Wiley has turned that good press into bad press.

Because of this I will not be publishing in any Wiley journal for the foreseeable future, and I call on others to do the same.

If you want to email the journal about this, here is the contact information.

Update: An apology has been issued to Shelley.

Aqua Teen Take Two

I went and saw Aqua Teen Hunger Force Colon Movie Film for Theaters again today. It was well worth a second viewing. I urge everyone of my readers to go see it, if you can. (It is only playing in a limited number of theaters.) You should go see it if for no other reason than because you dislike the Yankees in Boston and love the Rednecks in Atlanta.

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In my last post to Dr. Michael Egnor, an intelligent-design activist for the Discovery Institute, I pointed out that he had contradicted himself, blaming both evolution and intelligent design for eugenics: “Backed into a Corner, Egnor Cannot Keep His Arguments Straight.” He has responded, “Pseudo-Darwinism: Dr. Cartwright’s Error and Eugenics,” deciding to resolve the contradiction, like ID activist Dr. William Dembski, in favor of blaming intelligent design politics for eugenics. (See Orac for more commentary.)

Yeap, you read that correct. Creationists and intelligent-design activists, who for years have been calling evolution morally corrupt for spawning the “anti-Christian” politics of eugenics—The Discovery Institute’s Dr. Richard Weikart even wrote a book entitled From Darwin to Hitler.—have now decided that eugenics reflects the power of intelligent design and not the “amorality” of evolution. Of course, not all creationists and intelligent-design activists are happy with this change in message; the Discovery Institute’s John West has issued a brief response to Egnor, “Darwinism and Eugenics Revisited,” where in he resorts to academic dishonesty to maintain the message. (See Pieret for the truth.)

If the creationists and intelligent-design activists want to credit intelligent design for eugenics, I’m not going to stop them. Nevertheless, their turn-about is not motivated by the history of eugenics, but rather the desire to label anything done by humans as representing intelligent design. That is of course silly, but it is the “logic” motivating the change in message. According to Dembski and Egnor, artificial selection is not a “Darwinian” process and—I guess—not evidence for evolution.

Despite their seemingly 180° flip, Dembski and Engor still have their biology wrong, a point that Orac, Pieret, and Rosén, have not commented on. Take this passage from Egnor:

Dr. Cartwright is right. The experimental selection of “desirable” bacterial variants is bacterial eugenics, using the same empirical principles that eugenicists applied to human breeding. Eugenics is human breeding, and is every bit as much of a misapplication of Darwin’s theory as are Dr. Cartwright’s examples of bacterial breeding.

Is artificial selection, i.e. “breeding”, really a “misapplication” of Darwin’s theory in the way that the ID activists claim? According to them, “Darwin’s theory”, which they never describe accurately, only concerns natural selection, not artificial selection. Of course to answer that we are going to have to see what Darwin said about his theory of evolution by natural selection:

Owing to this struggle for life, any variation, however slight and from whatever cause proceeding, if it be in any degree profitable to an individual of any species, in its infinitely complex relations to other organic beings and to external nature, will tend to the preservation of that individual, and will generally be inherited by its offspring. The offspring, also, will thus have a better chance of surviving, for, of the many individuals of any species which are periodically born, but a small number can survive. I have called this principle, by which each slight variation, if useful, is preserved, by the term of Natural Selection, in order to mark its relation to man’s power of selection. We have seen that man by selection can certainly produce great results, and can adapt organic beings to his own uses, through the accumulation of slight but useful variations, given to him by the hand of Nature. But Natural Selection, as we shall hereafter see, is a power incessantly ready for action, and is as immeasurably superior to man’s feeble efforts, as the works of Nature are to those of Art.

As described by Freeman and Herron (2004) in their textbook, Darwin’s theory rests on four postulates:

The postulates, which apply to populations of organisms, are as follows:

1. Individuals within populations are variable.

2. The variations among individuals are, at least in part, passed from parents to offspring.

3. In every generation, some individuals are more successful at surviving and reproducing than others.

4. The survival and reproduction of individuals are not random; instead they are tied to the variation among individuals. The individuals with the most favorable variations, those who are better at surviving and reproducing, are naturally selected.

If these four postulates are true, then the composition of the population changes from one generation to the next. The logic is clear: If there are differences among the individuals in a population that can be passed on to offspring, and if there is differential success among those individuals in surviving and/or reproducing, then some traits will be passed on more frequently than others. As a result, the characteristics of the population will change slightly with each succeeding generation. This is Darwinian evolution: gradual change in populations over time.

(Freeman and Herron (2004) Evolutionary Analysis pp. 72-73)

It is plainly obvious from this that Darwin’s theory does cover artificial selection; Egnor and Dembski are wrong.

So where does that leave eugenics? Was it the height of Darwinian politics and medicine, or was it the success of intelligent-design activism?

While I’m happy to see the creationists and intelligent-design activists take credit for eugenics, it had nothing to do with either of them. Eugenics was a political movement powered by early geneticists that thought that it would be possible to eliminate genetic diseases and other “bad” traits from humans though selective breeding and forced sterilization. Of course such politics were serious violations of individual liberty. These early geneticists were scientific descendants of traditional plant and animal breeders, and in fact many of them worked in agriculture. Thus, making a long story short, these geneticists, and therefore eugenics itself, owed more to selective breeders than to naturalists like Darwin.

While it is true that eugenicists advocated artificial selection of humans, which is a Darwinian mechanism of evolution (see above), it is also true that Darwin wrote against the artificial selection of humans, citing that the natural selection of humans was more powerful. (See Pieret for discussion.) In an ironic twist of science, these early geneticists would ultimately produce the modern synthesis of Darwinian evolution and Mendelian genetics, which would demonstrate that eugenics was not practical.—Those damn recessive, disease alleles are hard to get rid of, and we all carry our share of them.

So while it is fun to let the creationists and intelligent-design activists take credit for eugenics, it is not historically or scientifically accurate. Of course, asking them to be scientifically accurate is like asking a house cat to bark at the moon.

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Over two years ago Tiffany and I came up with Prof. Steve Steve to be the champion of science and science education in the stead of the departed Stephen Jay Gould. He serves as the official/unofficial mascot of NCSE, citizens for science groups, the Talk Origins Foundation (including The Panda’s Thumb), and science lovers everywhere.

He has been around the world, to multiple scientific conferences, rafting down the grand canyon (twice), to the headquarters of ICISD, to North Pole to meet Santa Claus, an expert in the Dover Trial, a voice of reason at the Kansas Kangaroo Kourt, fossil-hunting in New Mexico, fought pirates in Minnesota, and dinosaurs in Berkeley.

Recently he popped up at AIG’s spanking new museum to ignorance, and the BBC has the story: “Creationist museum challenges evolution.”

As we prepare to leave [AIG’s museum], Eugenie Scott quietly slips a panda glove puppet from her handbag and photographs it among the dinosaurs.

It is introduced to me as Professor Steve Steve. Creationists are fond of lists of “scientists who doubt Darwin”.

Many thousands more support evolution, but rather than play the same game, Eugenie has parodied the lists by concentrating on scientists named Steve (Stephanies are also eligible).

So far, more than 700 have signed up. Their mascot is a panda because of a notorious creationist text entitled “Of Pandas and People”.

Steve was picked in honour of the late evolutionary biologist Stephen J Gould. Steve Steve because—well, all pandas have double names.

Actually, Prof. Steve Steve is a panda because of the title for our group blog: The Panda’s Thumb, which is the title of a SJG book. Of Pandas and People was involved with the decision, but not as directly as PT.

More Prof. Steve Steve Links:

P.S. I need to note that Ed Brayton deserves credit for suggesting that we use a double name, which is considered cute in China, and thus most zoo pandas have one.

ATHF Movie Poster

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(Click for larger version.)

Tiffany and I drove to the Mall of Georgia today in the ‘burbs of Atlanta to see Aqua Teen Hunger Force Colon Movie Film for Theaters. All I can say is Freakin’ Awesome. Well worth the most expensive movie tickets I have ever purchased.—Of course, it may not be as funny to those who have never seen the show. As I described the audience to Tiffany, “these are my people.”—I’ll probably see it again when I go back to Raleigh because it is also playing at the theater next to NCSU in Raleigh. In perhaps one of the dumbest moves, the movie did not open in Athens, which happens to be the college town closest to Cartoon Network headquarters.

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Don’t show up late or you will miss the funniest opening of any movie in years (or perhaps ever). Also stay after the credits if you want to see an additional scene.

P.S. Neil Peart of Rush makes a guess appearance.

ATHF : MFFT Tomorrow!

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Aqua Teen Hunger Force Colon Movie Film For Theaters comes out tomorrow.

Sweet!

Tiffany already said that she’d go with me; however, the movie is not opening in Athens. I hope I can convince her that it is worth a drive to the Mall of Georgia to see it.

I decided to join Youtube and post some animations I made during my dissertation research. These animations were made in the early stages of my third-chapter research. The model eventually changed and no longer produced simple, pretty animations. However, I’ll post two videos and explain what is going on.

This is an animation of a continuous “plant” population evolving with local dispersal. Each square is an individual. Blue squares have marker genotype AA, green Aa, and yellow aa. The point to take home is how local dispersal decreases the genetic variation locally, producing patches of homozygotes. If I still had my longer movies, then you would be able to see much larger patches evolving in later generations. Note that there is no selection on this marker. However, things are different in the next animation.

This animation is similar to the previous one, except that the marker locus is now linked to a gametophytic self-incompatibility locus, 20 centimorgans away. Whereas, local dispersal promotes localized inbreeding and patchiness, a self-incompatibility system facilitates outbreeding and decreases patchiness. By comparing the first movie to the second, you can see the difference, and don’t have to bother with understanding the statistics that I used in my third chapter to measure patchiness. Unlike the previous model, this model involves selection because self-incompatibility loci are under balancing selection, and the marker locus experiences a bit of that selection because it is linked to the self-incompatibility locus. We in the business call that hitchhiking.

Note: I’m sorry for the slow loading of these movies. I’m not sure why Youtube doesn’t like them.

Dr. Michael Egnor, the Discovery Institute’s new noise maker and inspiration for successful April Fools’ pranks, has responded to my demonstration that evolution was very crucial to the deduction of the genetic code:

Dr. Cartwright is mistaken. Darwin asserted that all natural biological complexity arose by random undesigned variation and natural selection. The intentional alteration and intentional selection of microorganisms is a nice example of designed variation and artificial selection. Dr. Cartwright’s application of Darwin’s theory to intentional design and breeding of bacteria is pseudo-Darwinism.

That emphasis was in the original because, as you know, putting words in boldface and italics makes them more true. But in truth, Egnor is just playing word games and in the process completely contradicts his most favorite argument: that Darwin was responsible for eugenics.—More on that later.

I guess one could forgive Egnor for being ignorant about the molecular genetic experiments involved in deducing the genetic code. After all, he is a surgeon with little training in experimental biology. However, one should not forgive his arrogant insistence of speaking authoritatively on subjects that are clearly out of his expertise. (In his honor, I have previously dubbed such behavior egnorance.) Take for instance his claim that the experiments used “designed” variation. Now since Egnor neglects to define and/or describe what “designed” variation is, I’m going to have to assume that he means that the variation in these experiments were created directly by the scientists. This is intended contrast with “random”, natural variation that exists in biological populations.

However in deducing the genetic code, the scientists used variants that in no sense could be considered “designed” by them. For starters, they did not have the technology in the 1950’s to design organisms (unless Egnor wants to claim that evolution is equivalent to design). Genetic engineering simply did not exist. (Heck, the structure of DNA wasn’t published until 1953.) Second, the early variants were spontaneous mutations, isolated from laboratory cultures. Only later in the research program did scientists use mutagens, which of course still did not design organisms. Reading the papers that developed and used the T4 phage system, one encounters “spontaneous” a lot in the description and discussion of the variants. The variants are never once called “designed”. In fact, many of the famous amber and ochre mutations, which helped discover the stop codons, UAG and UAA, were spontaneous mutants. So to claim that the scientists who deduced the genetic code worked with “designed” variation not random “undesigned” variation, is completely ahistorical and pseudoscientific. Perhaps Egnor should have bothered to read and understand the literature instead of bearing false witness about it.

Egnor also plays word games with selection, trying to contrast natural selection with artificial selection. However, the contrast is not what Egnor thinks it is. Both are selection; both follow the same basic principles that Darwin wrote about nearly 150 years ago; both follow the same mathematical models that formed a basis for the modern synthesis of evolution and genetics nearly 75 years ago. The fact is that the distinction between artificial selection and natural selection is purely, if you will allow, artificial. It is a rhetorical distinction that is much stronger than the biological distinction.

The fact that Egnor is willing to confidently declare that Darwin’s theory of evolution via natural selection is not applicable to artificial selection reveals his egnorace about evolutionary biology. He is arguing based on terminology without bothering to understand the concepts behind them. I would never let one of my students get by on such superficial and sophomoric arguments.

Egnor also asserts that biotech is just breeding microorganisms using ancient farming traditions—like the Amish. However, animal husbandry and biotech use very different selection regimes. Whereas, a breeder may pair up cattle by evaluating the physical attributes of each individual, a biotechnician is unable to evaluate individual microorganisms and instead alters their environment to select for desired gene products. In this sense, relying on the environment to evolve a population of organisms in a specific direction, biotechnology is closer to what happens in nature than what happens in stables.

Now in making the argument that artificial and natural selection are completely distinct things, Michael Egnor is in obvious conflict with other creationists and ID activists that have built arguments on artificial selection being natural selection and thus Darwinian, e.g. the recent examples of Leisola and Turunen and Egnor.

Wait, did I just say that Egnor is in conflict with Egnor? Hmm, Yes I did.

For you see, one of Egnor’s passions since he appeared on the anti-evolution scene over a month ago is to blame Darwin for the eugenics movement. For example, he ended a post on the DI’s blog with,

The single incontrovertible Darwinian contribution to the field of medical genetics was eugenics, which is the Darwinian theory that humans can be bred for social and character traits, like animals. The field of medical genetics is still recovering from eugenics, which was Darwin’s only gift to medicine.

Egnor has now contradicted himself because, as educated people should know, eugenics was a program, favored by many early geneticists, to selectively breed more fit humans (or better described as breeding less less fit humans), similar to how farmers had breed more fit livestock. Eugenics is therefore artificial selection and, according to Egnor’s dichotomy, absolutely distinct from Darwin’s natural selection. (See I can put those words in boldface and italics too.)

In Egnor’s latest opinion, such things are not attributable to Darwin or “Darwinism”, but rather are “pseudo-Darwinism”. According to Egnor, it is “the antithesis of Darwin’s theory”. In those paragraphs where Egnor criticizes me for promoting pseudo-Darwinism, he is actually criticizing himself. So how can Egnor argue that eugenics was Darwin’s curse on medicine while days later argue that eugenics and other artificial selection regimes are the antithesis of Darwin’s theory?

The answer is simple: integrity, consistency, and honesty matter little to ideologically driven activists. They play word games with rhetoric built on flashy quicksand. When backed into a corner, facing facts they cannot handle, they try anything and everything hoping something will land, but only demonstrating that they have lost. That, my friends, is Michael Egnor, M.D.

P.S. I see that Egnor has used the longest running lie in creationism. Desperation, indeed.

I’m Going to be on the Radio

A couple of colleagues of mine have a radio show out in New Mexico. I’m going to be on it this afternoon talking about my blog paper and other things. The show starts at 4:00 EST (2 MST) on AM 1350 KABQ.

Sorry, but there does not appear to be an internet stream available.

If your institution has access, you can now read the story about me (and other bloggers) in this month’s the Scientist: “Scooped by a Blog.” (Sadly, it looks like NCSU’s subscription ran out this month.) If you can’t get access, drop me an email, and I can privately send you a copy. They ran the image that I sent; however, Prof. Steve Steve was airbrushed out of the photo like some Stalinist purge.

Oh well, I’m still giddy about the success of our April Fool’s prank yesterday, so I’ll let this one slide.

One day in March 2005, Reed Cartwright jotted his thoughts on his blog, De Rerum Natura, after reading a paper that had just been published in Nature. Cartwright, then a PhD student in genetics at the University of Georgia, was skeptical. …

That wasn’t the end of it, however. Six months later, Cartwright received an E-mail from Luca Comai, a plant geneticist from the University of California, Davis, who had independently come up with the same idea and was in the process of publishing it in Plant Cell. “A friend of mine just brought to my attention your blog on hothead,” Comai wrote. “I have developed an explanation for the described phenomenon that is nearly identical to the one you posted … I think that I should acknowledge your work in some way. One way would be for you to be a coauthor.”

Read Scooped by a Blog (if you have access).

April Fools on Me

| 2 Comments

We’ve been had.

It sucks being the butt of an April Fools’ joke.

PZ is right. The DI needs to put some THIS IS A JOKE warning labels on their posts.

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