May 2007 Archives

DDOS Slowdown

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The slowdown seen today was the result of a DDOS “attack” on PT. I’ve banned nearly 50 IP addresses that I think were the cause of it. Let me know if there is any collateral damage.

The previous thread, “Is Creationism Child’s Play?”, was closed by an admin because it was getting so long that it was loading slowly or not at all. A contributing factor is that PT has apparently been experiencing some kind of denial-of-service attack which is also slowing things down.

I have been out of town and not able to contribute to the thread much, or even read all of it, but apparently it has evolved from mudslinging into a reasonable dialog with a young-earth creationist, Mark Hausam, who actually wants to discuss the issues. Mark has pretty much acknowledged that his belief is based on a literal, inerrant interpretation of the Bible, and that he is willing to invoke miraculous “appearance of age” arguments to explain away physical evidence that conflicts with his interpretation of the Bible. Usually this sort of person is about six months away from complete deconversion from creationism. With the appearance-of-age argument, they have already admitted that the physical evidence on its face is totally against them, and that they have admitted that Last Thursdayism is as well-supported as young-earth creationism (Last Tuesdayism, of course, is unspeakable heresy). Once they’ve gone this far, most people can’t maintain the necessary doublethink for very long (Paul Nelson, John Mark Reynolds, Kurt Wise, and Marcus Ross are about the only exceptions, and they each have the peculiar ability to remorsely drown their scientific conscience whenever reality intrudes upon their textual interpretation).

This sort of discussion should be encouraged so I am starting a new thread for those who wish to discuss the issues. I will be watching the thread to ensure that it remains courteous.

My wife says she will disown me if I continue to describe every human behavior and every human trait as adaptive. I had better get a separate bank account, because I have just read David Sloan Wilson’s splendid book, Evolution for Everyone: How Darwin’s Theory Can Change the Way We Think about Our Lives (Delacorte, 2007).

Professor Wilson begins by showing how intuitive evolutionary theory really is: Variation plus consequences of that variation plus heredity. A population of moths varies in color (the variation), and some are more subject to predation (the consequence). The offspring of the more cryptic (camouflaged) moths resemble their parents (heredity), so gradually the color of the population drifts toward more crypsis. That’s it. To show his students that they are now experts, Professor Wilson pairs them up and has them conceive possible reasons why infanticide may be adaptive. If you answered lack of resources, poor quality of offspring, and uncertain parentage, you are an expert evolutionist and ready to read the book.

Behe’s bad math

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Review copies of Michael Behe’s new book The Edge of Evolution are now out – the book is officially coming out on June 5 – and now the reviews are starting. Mark C. Chu-Carroll at Good Math, Bad Math, has beat us all to the punch. I perceived many of these problems while giving The Edge of Evolution my own read-through, but it takes a mathematician to comment on Behe’s abuse of fitness landscapes and probability arguments with the appropriate sense of outrage.

I am sure we will have much more on Behe’s latest starting in June. My first take is that The Edge of Evolution is basically an incompetent attempt to provide a biological foundation for the silly assumptions that were made in Behe and Snoke’s (2004) mathematical modeling paper in Protein Science. (You will recall that it received its most thorough critique here at PT and also in a rebuttal written in Protein Science by Michael Lynch; and a biological rebuttal in this 2006 paper in Science – see also summary by Adami.)

Sam Brownback has an op-ed in the NY Times today, in which he explains with much straining at gnats why he was one of the Republicans who did not believe in evolution. Short summary: he reveals his own misconceptions about the biology, and mainly pounds the drum on how important Faith and Religion and God are. It will be persuasive to people who are already convinced that God is the most important thing in the universe, right down to what they do in the privacy of their bedrooms, but it underscores my conviction that faith is the enemy, the source of many of our problems…such as the promotion of incompetent politicians to positions of power on the fuel of the ethereal Spirit.

Get ready. It's a whole succession of reiterated platitudes about how important faith is, with no evidence that it actually is — we are, apparently, supposed to take that on faith.

Continue reading "Sam Brownback, defender of the faith" (on Pharyngula)

Presidential candidate Sam Brownback was one of three Republican candidates who raised their hands when asked if they didn’t believe in evolution.

Today he has an op-ed piece in the New York Times wherein he explains his stance. If you’re looking for something original, meaningful, or interesting, it’s not for you. It’s your standard “I’m a creationist but am too cagey to come out and say it so I’m going to dance around the issue and exude platitudes about faith…” There’s a fair chance it was ghost written by a member of the Discovery Institute. Consider this:

The question of evolution goes to the heart of this issue. If belief in evolution means simply assenting to microevolution, small changes over time within a species, I am happy to say, as I have in the past, that I believe it to be true. If, on the other hand, it means assenting to an exclusively materialistic, deterministic vision of the world that holds no place for a guiding intelligence, then I reject it.

And what if evolution means what it really means, namely that various species (say, humans and great apes) share common ancestry? Brownback totally dodges that one.

The great thing about the internets though is that new-fangled things call blogs allow people to let it all out and say what they really think, the kinds of things they would never publish in the New York Times. You know, unhinged, stream-of-consciousness rantings. Things like this:

Senator Brownback is among a tiny handful of 2008 potential Presidential candidates who understand that ANNUIT COEPTIS is what makes America great. Senator Brownback’s belief in a Higher Power goes far beyond reasonable belief. We know beyond any and all possible doubt that gravity had to have come from somewhere and by inference that this “Intelligent Designer” has favored our undertakings.

Brownback apparently didn’t get the message that the “Intelligent Designer” is an unknown entity that might well be an evil space monster, because ID is not a religious belief no sir it’s not, but he’s hardly unique in that regard. Putting that aside, what the heck was that about gravity? Here it is again:

It would take a miracle from God himself to convince non-believers that patterns statistically beyond random chance that prove an “Intelligent Designer” to be behind the creation of gravity. Maybe this miracle, or series of miracles has already happened. Belief in a Higher Power taught to our school children will increase discipline in our public schools, thus increase our economy. Reasonable belief that gravity had to have come from an “Intelligent Designer” is just the kind of miracle that America needs.

Brownback is a proponent of Intelligent Falling! We knew there had to be one out there somewhere. And apparently gravity is coming in for quite a shellacking, because they’ve even created their own category for it on the blog:

Tags : Gravity, Higher Power, ID, ethics, morals

Sadly, this is the only post under “Gravity” for now.

(Cross-posted to Sunbeams from Cucumbers.)

Waxing indignant: pointless?

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In the comments to a post I have up at Aetiology discussing the recent XDR-TB case in the U.S.,, Scott suggested that bloggers were putting too much emphasis on whether the TB patient was stupid/arrogant/self-centered/whatever, and later that “waxing indignant is pointless.” I started this as a response to those comments, but thought instead it might be an interesting conversation to have–is such indignation pointless? Certainly indignation about this guy’s behavior won’t change what’s happened. Indignation about creationists’ abuse of science won’t make them stop or change their mind. Indeed, some would suggest that even mild rants that don’t necessarily outright insult an opponent still hurt our cause in the long run. So, does such indignation have a point? If so, what? What do you think? Feel free to comment here; I have my own thoughts on it over at Aetiology.

[Edited to add: while the TB story is what spawned this musing, don’t limit it to that…certainly we here do this a lot with creationists and science teaching/literacy in general as well, so feel free to address those topics too.]

Non-sequitur in five parts

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After having retired from a university where I taught physics, I was approached by some friends who requested that I reply to a number of very popular books whose authors diligently tried to prove the compatibility of the biblical story with science. Among the writers subjected to my critique happened to be both religious preachers (like Grant Jeffrey) without any scientific credentials, and also holders of advanced degrees, sometimes from prestigious institutions, for example from MIT (Gerald Schroeder), or from some other good universities (Hugh Ross) and even professors currently teaching physics at quality universities (like Nathan Aviezer). However, there was little difference between writing of either Jeffrey or, say, Aviezer, in that both not only offered plainly fallacious arguments, but also displayed sometimes amazing lack of knowledge and understanding of even seminal concepts of science in general and physics in particular. It was easy to dismiss pseudo-arguments of, say, Schroeder, by pointing to such absurd claims as his statements that masers emit atoms, or that mass and weight are the same, or, say, by revealing the misinterpretation of probabilities by Aviezer. What credibility could be afforded their pro-biblical “arguments” if they obviously were confused about elementary facts of science and/or math?

Recently a friend wrote to me about another book written by a professional physicist, a professor of physics, thus my younger professional colleague, Stephen M. Barr, which seemed to also promote the thesis about modern science allegedly supporting faith. Unlike the likes of Schroeder or Ross, Barr seems to be indeed a well qualified scientist, with a real knowledge of modern science, and a talent for offering seemingly strong arguments in favor of his position.

Barr’s book was reviewed a number of times, mostly in religious periodicals (like First Thing) and on websites (like Metanexus) where it was acclaimed in superlative terms. The religious reviewers unanimously praised Barr’s “accessible” writing, stressed his impeccable scientific credentials and asserted that he has brilliantly proved his thesis about the supposed “fall” of “materialism” as a consequence of scientific discoveries of the 20th century.

In this review I shall discuss Barr’s opus from the standpoint of a secular scientist, thus estimating whether or not Barr’s arguments sound convincing for a skeptic.

Continue reading Non Sequitur in Five Parts at Talk Reason.

Tonight's edition of the Fox News chat show The O'Reilly Factor featured a segment on the big Creation Museum. Lawrence Krauss defended science and reason against the crazed rantings of Answers in Genesis frontman Ken Ham. Guest host John Kasich was sitting in for Bill O'Reilly. I have posted the full transcript, along with some brief remarks, over at EvolutionBlog. Comments can be left there. Enjoy!

by Martha Heil, Editor, American Institute of Physics

Scientists fared well in national news about the opening of the Answers in Genesis Creationism exhibit. The scientific process would not recognize the proposition in the creationism exhibits as science-based, because the displays began with a certain conclusion * that the Christian Bible can be interpreted as literal fact * and then found facts and logic to support that idea. This, of course is not how science works * science begins with observations or hypotheses and leads to conclusions, often unpredictable from the beginning of the experiment.

National newspapers correctly reported that scientists are concerned about this Kentucky attraction because it misrepresents scientific thought, and uses deliberate untruths about science to make a specific point. The Washington Post, New York Times, and the country’s best selling paper, USA Today, all recognized that the displays were unscientific. The national newspapers also reported that scientists were concerned about this museum because of its potential to confuse students as to the nature of science.

Zachary Lynn, a student at Eastern Kentucky University was able to tour the $27 Million Lie before the grand opening on “family day”. (He knows the son of one of the AiG leaders.) He has posted his photos on his website. If you don’t want to wait for Prof. Steve Steve’s photos, you can go see Zachary’s.

In The Perimeter of Ignorance, Neil deGrasse Tyson, explains in no uncertain terms why Intelligent Design is scientifically vacuous.

Another practice that isn’t science is embracing ignorance. Yet it’s fundamental to the philosophy of intelligent design: I don’t know what this is. I don’t know how it works. It’s too complicated for me to figure out. It’s too complicated for any human being to figure out. So it must be the product of a higher intelligence.

Most notable quote

And what comedian designer configured the region between our legs-an entertainment complex built around a sewage system?

Neil deGrasse Tyson is the Frederick P. Rose Director of the Hayden Planetarium at the American Museum of Natural History and holds a PhD in Astrophysics and has an impressive CV

What is remarkable is how scientists come to realize more and more how ID is scientifically vacuous, as evidenced fully by its proven inability to contribute in a non-begging manner to our scientific knowledge beyond ‘poof’ and asking for more will quickly be dismissed as ‘pathetic’. Such is the life of an ID proponent…

Hat tip: Red State Rabble (watch the video)

The Creation Museum

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The long-gestating and expensive monument to creationism's folly, the Creation "Museum" of Ken Ham and Answers in Genesis, is having its grand opening tomorrow. We've collected the blogosphere-wide reaction to this amazingly inane edifice at Pharyngula, in an article called simply The Creation Museum.

We do not take a conciliatory or encouraging view to this development.

By Martha Heil, an editor at the American Institute of Physics

Answers in Genesis, the biblical literalist ministry had a local advance opening of its young-earth creationism museum today. It claims that the museum scientifically proves the Word: that the earth was created in six days, that dinosaurs with pointy stabbing teeth ate only plants before the fall of humankind, and that dinosaurs and humans lived at the same time. They also would not let scientists in their gates today.

Today was for the believers. Today was also a carefully orchestrated event for people who would carry their message to the citizens of the nation. A huge press conference was planned and drew reporters from all over the country. Tomorrow, in another post, we’ll look carefully at the news stories those messengers carried and see the impact that this ministry had on the conversation about a museum that purports to do science, but deliberately misleads its visitors using scientific terms and hand-picked facts.

In defense of Hector Avalos

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On Higgaion, a Religion Scholar and Christian named Christopher Heard (Associate Professor of Religion) has responded to the attacks by the Discovery Institute on Hector Avalos.

Have I mentioned that I disagree with Hector on a number of points? He’s an atheist and I’m a believer; that alone will tell you that we don’t see eye to eye. But I am outraged by the DI’s attempts to slander a reputable and ethical scholar just because they’re upset that he got tenure when their pal didn’t.

Once again we learn how desperate the Discovery Institute has become now that most of the news media have failed to respond to their virtual onslaught of ‘press releases’. Probably because the media was quick to appreciate the level of inflationary ‘logic’ so common in Discovery Institute ‘press releases’.

What is ironic to me is that while objecting to what they believe to be religious discrimination, viewpoint discrimination and attacks on academic freedom (of speech), the DI is quick to abandon such concepts when it comes to Hector Avalos.

Avalos responds and Dembski too…

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On Pharyngula, PZ provides a comment response by Hector Avalos

The Discovery Institute has mounted the latest in a long string of creationist smear campaigns against me in Iowa. While I have never called for Dr. Guillermo Gonzalez to be fired, or even to be denied tenure, there are plenty of creationists who blatantly direct our university to fire me.

After all the Discovery Institute had decided to attack Avalos based on some pretty poor logic.

Determined not to be outdone by his fellows at the Discovery Institute, Dembski responds as well

Noticable quote:

Third, if Avalos has fudged on the status of this article—and has done so in a very public way—his CV may loaded with this type of fluff. Perhaps it’s time to start hunting for the real witch.

How are these kinds of ‘arguments’ going to help their fellow IDist Guillermo Gonzalez?

Fascinating… ID under pressure actually inflates…

Stanley Miller Dies

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Stanley Miller, who practically invented the scientific study of the origin of life, died Sunday at 77. For an article in the LA Times, see http://www.latimes.com/news/science[…]news-science and also http://www.ncseweb.org/resources/ne[…]_23_2007.asp .

The Alliance for Science has put up the final results from their 1st Annual Evolution Essay Contest! Here’s a copy of their press release, in case you didn’t know about it and want to find out more:

High School Student Cites Disease Tracking and Antibiotic Resistance in Winning Evolution Essay

For Immediate Release

May 16, 2007

Arlington, Va. –Why should doctors study evolution? High school students from all over the nation answered this question with an essay in a contest sponsored by the Alliance for Science, a national non-profit that promotes good science teaching.

“The essay contest is part of our effort to bring together scientists, teachers and supporters of science education with the many religious bodies that have found no conflict between religion and science, said Dr. Irving W. Wainer, the chair of Alliance for Science. “Our goal is to reawaken America’s love of science.”

Gregory Simonian, of Los Angeles, CA, an 11th grader at Los Angeles Center for Enriched Studies, won the grand prize for his essay, which cites disease tracking and antibiotic resistance as two important contributions of evolutionary biology to medicine. Simonian will receive a $300 cash prize.

His teacher, Ms. Gloriana Chung, also receives prizes: $250 for classroom use; GeoSpiza, an interactive biology learning program, and a DVD on evolution from the Howard Hughes Medical Institute.

Merve Fejzula, of Garfield, NJ, won second place for her entertaining essay about visiting her doctor’s own waiting room and considering the role of evolution there. Fejzula is a senior at [Enable javascript to see this email address.], in Englewood, NJ. She receives $250; her teacher Ms. Clare Kennedy wins the evolution DVD.

Third Place: Shobha Topgi, Palatine, IL, an 11th grader at Illinois Mathematics and Science Academy wins $150, and teacher Dr. Richard Dods wins the evolution DVD.

Fourth Place: Linda Zhou, River Edge, NJ, 9th grader at the Bergen County Academies wins $100, and teacher Dr. Judith Pinto wins the evolution DVD.

“I hope this contest has helped students see that evolutionary science is not a matter of personal philosophy or worldview,” said Dick Lessard, AfS Essay Contest Director.”It’s hard, evidence-based science that directly affects our lives individually, as well as having major implications for public policy.”

Not half bad, considering we had the idea in late 2006 and threw the contest together at the last minute so as to try and correspond with Darwin Day 2007. A HUGE thank-you to all our donors for making this possible, and remember that this is just the tip of the iceberg! We’ll be back next year with most of the kinks ironed out, and hopefully some great prizes and new twists!

Also, if anybody is familiar with Drupal content management systems and wouldn’t mind offering up a bit of technical advice, please drop me a line at neurotopia AT gmail dot com.

In their desperate flailing to rescue their golden boy at Iowa State, Guillermo Gonzalez, the Discovery Institute has made another mistake: they tried to do a hatchet job on another Iowa State faculty member, Hector Avalos—he was attacked because he was promoted when Gonzalez wasn't, and he also happens to be an atheist, never mind that these were completely different departments and completely different people. Avalos has responded directly to the DI attacks at Pharyngula.

Once again, the DI has exposed itself as a nest of bumbling incompetents. I'm actually beginning to feel some sympathy for Gonzalez—how would you like to be volunteered to be a martyr for the cause? That's actually what's happening now: the kind of circus being erected around a fairly ordinary tenure case is going to be deeply counterproductive to Gonzalez's future career.

The Fishing Cat

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A recent conversation brought up the subject of one of my favorite animals—and one of the more remarkable examples of evolution: the Fishing Cat (Prionailurus viverrinus). The Fishing Cat is just that—a cat that subsists on fish, and that swims naturally. In fact, the Fishing Cat actually has webbed paws.

They’re a little bigger than a bobcat, about three and a half feet long (including tail), and are native to southeast Asia, where they live beside rivers, hunting for fish. They don’t just scoop the fish out with their paws; they swim and dive under the water to catch fish. There are several zoos that have Fishing Cats, including the National Zoo in Washington; you can watch a video of Fishing Cats hunting at their website. Personally, I’m fond of the cats at the Exotic Feline Breeding Compound in Rosamond, California; they have some adorable pictures of Fishing Kittens on their website.

Happy Linnaeus Day!!

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Today is the 300th birthday of Linnaeus, aka Carl Linnaeus, Carolus Linnaeus, Carl von Linn̩, Carl Linn̩, etc. etc. Oh, heck, just call him Carl. Happy birthday, Carl! NPR reports that more than 600 birthday parties/science education events are going on around the planet this week Рnone bigger than in Sweden:

This month marks the 300th birthday of Carl Linnaeus, Sweden’s beloved botanist who gave order to the plant and animal kingdoms.

The Swedes will celebrate on Wednesday with a jubilee in Uppsala, complete with Linnaeus cream cakes.

And well they should, “Carl Linnaeus is by far the most internationally well-known Swede that has ever lived”!

Tangled Bank #80

The Tangled Bank

The latest edition of the Tangled Bank is at geek counterpoint. Lotsa linky, have fun!

Ascidian evo-devo

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Here are three animals. If you had to classify them on the basis of this superficial glimpse, which two would you guess were most closely related to each other, and which one would be most distant from the others?

ascidian.jpg amphioxus.jpg fish_larvae.jpg

On the left is a urochordate, an ascidian, a sessile, filter-feeding blob that is anchored to rocks or pilings and sucks in sea water to extract microorganismal meals. In the middle is a cephalochordate, Amphioxus, also a filter feeder, but capable of free swimming. On the right are some fish larvae. All are members of the chordata, the deuterostomes with notochords. If you'd asked me some years ago, I would have said it's obvious: vertebrates must be more closely related to the cephalochordates—they have such similar post-cranial anatomies—while the urochordates are the weirdos, the most distant cousins of the group. Recent developments in molecular phylogenies, though, strongly suggest that appearances are deceiving and we vertebrates are more closely related to the urochordates than to the cephalochordates, implying that some interesting evolutionary phenomena must have been going on in the urochordates. We'd expect to see some conservation of developmental mechanisms because of their common ancestry, but the radical reorganization of their morphology suggests that there ought also be some significant divergence at a deep level. That makes the urochordates a particularly interesting group to examine.

Continue reading "Ascidian evo-devo" (on Pharyngula)

The Chronicle of Higher Education has an article that casts a great deal of doubt on the DI’s persecution claim by examining Gonzalez’ publication record in detail. The DI makes a big deal out of the fact that Gonzalez has 68 published articles, but the Chronicle examined his publication record and found that virtually all of those papers were from research projects that he did prior to coming to ISU when he was a postdoc:

Continue Reading at Dispatches from the Culture Wars. Comments may be left there.

Show me the money.

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The Discovery Institute is (still, and predictably) in an uproar over Iowa’s decision to reject Intelligent Design proponent Guillermo Gonzalez’s tenure application. The DI is claiming that the decision could not possibly be anything other than an example of discrimination against a brave non-Darwinian scientist by the Darwinian Orthodoxy. Personally, I think it’s something different. I think it’s about the money.

According to an article that was just published in the Chronicle of Higher Education, Gonzalez has not received any major research grants since arriving at Iowa. Casey Luskin of the DI points out that the tenure guidelines written by the department do not specifically mention funding as a requirement for research. That is true, but irrelevant. I’ve never heard of a tenure committee at a research university that does not look at outside funding.

Casey claims that if Iowa is using funding, it’s clearly just an ad-hoc reason invented to deny an otherwise qualified candidate tenure. It’s not. A professor’s ability to get outside research funding is a very good indicator of how well they will perform at a research university. Here’s why:

Read more (at The Questionable Authority):

Rekha Basu at the Des Moines Register has written an opinion on ISU’s denial of tenure to Guillermo Gonzalez. She raises some good issues:

In the past 10 years, a third of the 12 tenure applicants in the physics and astronomy department have been denied. Asked if Gonzalez’s Intelligent Design views were considered, department head Eli Rosenberg replied, “Only to the extent that they impact his scientific credentials.”

One hopes the ISU president’s response to the appeal will answer any lingering questions about bias toward Gonzalez for his personal beliefs. But Intelligent Design proponents are wrong to equate the exclusion of their theory from the classroom with academic bias. Professors are entitled to their own beliefs, but not to teach as science something that is not.

It is important to remember that the Tenure requirements are more extensive than suggested by some ID proponents who limit their argument to what the department requirements specify (and even there seem to mangle the requirements)

The university maintains the tenure denial was based on the professor’s teaching, service, scholarly publications and ability to get research funding, and not his Intelligent Design advocacy.

So let’s look at Gonzalez’s publication record, compare his record before joining ISU to his record after he joined, remembering that the customary 7 year period is of a probationary nature. During this period one has to show that the promise for success based on which one was originally hired for a tenure track position is actually playing itself out, This includes the ability to continue and expand the research, the ability to attract external sources of funding, and so on.

In this light, the responses by the Discovery Institute seems quite puzzling. Are they really interested in the best outcome for Gonzalez? Sometimes I wonder.

Of flies and free will

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On Uncommon Descent Denyse comments on a paper which found how flies have ‘free will’. While ID proponents are quick to argue that (Darwinian) evolutionary pathways cannot explain ‘free will’, I will show, in a future posting, that this is a fallacious argument based on the common appeal to ignorance found amongst ID claims. In this specific case, I will present how science explains the evolution of Levy flight patterns.

In the mean time I would like to invite any ID proponent to step forward with ID’s best explanation for the existence of ‘Levy flight patterns’ as found in these fruit flies.

The New York Times has a good story on the Darwin Correspondence Project, which now has 5,000 Darwin letters online. Some good bits are in there. Darwin when he was 12:

Just as I was going, she said she must ask me not a very decent question, that was whether I wash all over every morning — no — then she said it was quite disgustin — then she asked me if I did every other morning, and I said no — then she said how often I did, and I said once a week, then she said of cour you wash your feet every day, and I said no, then she begun saying how very disgusting and went on that way a good while. …so then I went and told erasmus, and he bust out in laughing and said I had better tell he to come and wash them her self, besides that she said she did not like sitting by me or Erasmus for we smelt of not washing all over, there we sat arguing away for a good while.

Just in from the New York Times:

The National Association of State Boards of Education [NASBE] will elect officers in July, and for one office, president-elect, there is only one candidate: a member of the Kansas school board who supported its efforts against the teaching of evolution.

Who would that be? Ken Willard, someone you may remember.

For you flagellum wonks in the audience, an interesting and fairly detailed discussion of some of the science issues and, for lack of a better word, etiquette issues, took place over here at T. Taxus in “JCVI Evolutionary Genomics Journal Club on Liu-Ochman.”

(The discussion is also good for Esperanto wonks.)

Cover of Science, behavioral science issue, May 18After you have been in the habit of creationism-watching for a few years you become extremely familiar with all of the usual creationist arguments, half-baked talking points, unchecked assertions taken as obviously true, etc. If you really get into it you learn the creationist movement’s long and specific history, and you learn that whatever form of creationism you are studying at the moment inevitably traces back basically to American protestant fundamentalism, and before that to something sometimes called “naive Biblicism.”*

But there comes a point when you don’t think you can learn anything much new about the creationists. You might stumble on a new mutation of a creationist urban legend or quote mine, or a new bit of creationist history like Dean Kenyon actually being a young-earther despite this fact being carefully hidden by the ID movement for 15+ years. But basically, you don’t expect to find out much that is new.

Well, if you thought you were at this point, you would be wrong. A review article in this week’s Science magazine (with a special focus on behavioral science) shows that scholars can ring out yet another twist in creationism studies.

San Francisco’s adoption campaign for older children is featuring “Intelligent Design”, and they have this great “Heather Has Two Mommies” sort of poster.

(Original post at the Austringer)

This just in from Randy Olson. Free to forward:

FLOCK OF DODOS airing on Showtime Thursday May 17 at 8:30 EST/PST

It looks like Wendell Bird‘s lawsuit against the University of California is going to trial. This is the lawsuit bought by some private Christian high schools (Association of Christian Schools International et al., or ACSI) against the U.C. (Roman Stearns, special assistant to the U.C. president, et al.), protesting the fact that the U.C. doesn’t give credit for certain courses taught at these private schools. Not all of the classes involved are science classes, but the science classes at issue make use of Bob Jones University textbooks which are full of fake fundamentalist “science.” Private religious high schools have the right to teach whatever silliness they want (although even many private Christian schools teach evolution without problems), but it is rather dubious to assert that a top institution like the U.C. should be forced to drop all of its standards and give credit for classes that teach creationist falsehoods.

NCSE is not involved in this case so I don’t know much more than anyone else about the details of it. The legal issues are rather different than in Kitzmiller v. Dover – here, the creationists are the plaintiffs, and as I understand it, the constitutional issue is not the Establishment Clause but the Free Exercise Clause. ACSI asserts that the U.C.’s standards amount to religious discrimination. However, I do have a rather direct interest in the case myself, since I will be a Ph.D. student at U.C. Berkeley this fall, and will be a teaching assistant in the evolution course. Will the undergraduates that the U.C. admits be prepared, or will they require tedious remedial education to re-do all the biology they were taught incorrectly the first time around?

Through the grapevine, I have heard a few tidbits about the case that will interest people. It looks like the trial will be another battle of the experts:

Let’s say that you are counsel for the Association of Christian Schools. You are looking for an expert witness to stand up before the court and say that the biology and physics textbooks from Bob Jones University and A Beka are just peachy, and students taught from them should be accorded credit in biology and physics sufficient for admission to the University of California system. Who do you turn to? Naturally, you won’t bother with a biologist and a physicist for this matter; what you obviously need is a biochemist. Fortunately, you know where to find one, and, hey, presto! Discovery Institute Center for Science and Culture Senior Fellow Michael Behe files an expert report on your behalf.

Here’s a sample:

General conclusions concerning viewpoints and biology textbooks

All biology textbooks that were examined, both the approved texts and the Christian texts, contain material which is not strictly science, but which includes viewpoints, and all texts asked students to discuss non-scientific topics, such as religious, legal, political, ethical, or moral topics. In my opinion in this unanimous practice is pedagogically sound. Science does not exist in a vacuum, and students will naturally have questions about how science relates to other aspects of their world. Discussion of how scientific and other topics impinge on each other and interrelate with each other can equip students to integrate seemingly separate areas into a more coherent whole.

Darwin’s Black Box and Icons of Evolution are cited by Behe in support of his expert report. He has a section extolling a “strengths and weaknesses” approach. And, Behe is going to get a cool $20,000 for his participation in the case.

What I’d like to suggest is a little competition for the readers… how many instances of issues raised in the Behe expert report correspond to items in Mark Isaak’s Index to Creationist Claims? Please use the comments to add sightings.

Tinkle%20Giant%20Beaver.jpgAs many have noted, the Intelligent Design movement’s echo chamber has been recently belaboring the connection between Darwinian evolutionary ideas and eugenics. That’s not surprising: the Discovery Institute-headed machine has been on the ropes for a while, unable to make any significant scientific, legal or political headway against evolution science (a.k.a. “Darwinism” in ID/Creationist parlance), and it has naturally turned to what it does best, that is media-based attack campaigns on straw-man stand-ins for evolutionary biology.

The transparent goal of this new P.R. offensive is to tarnish 150 years of scientific discovery with the stain of one of its aberrations, the logical equivalent of attacking experimental medicine by claiming that it is based on analogous principles as Josef Mengele’s experiments in Nazi concentration camps. Oblivious to logic and intellectual honesty, the “Darwinism = eugenics” meme nevertheless has been widely promoted by several ID advocates, most prominently by John G. West, Associate Director of the Discovery Institute’s Center for the Renewal of Science and Culture.

Facts regarding status of tenure case at Iowa State

Partial quote:

Why was tenure not granted to Guillermo Gonzalez?

Dr. Gonzalez was evaluated for tenure and promotion to associate professor by the tenured faculty in the Department of Physics and Astronomy. That evaluation was based on an assessment of the excellence of his teaching, service, scholarly research publications and research funding in astronomy, using standards and expectations set by the department faculty. The consensus of the tenured department faculty, the department chair, the College of Liberal Arts and Sciences, the dean of Liberal Arts and Sciences, and the executive vice president and provost was that tenure should not be granted. Based on recommendations against granting tenure and promotion at every prior level of review, and his own review of the record, President Gregory Geoffroy notified Gonzalez in April that he would not be granted tenure and promotion to associate professor.

You may know by now that Guillermo Gonzalez, the pro-ID astronomer, was just denied tenure at Iowa State. If you know that then you also know that the ID crowd is in full cry and wail at this outrageous persecution. That was predictable, of course; the ID movement, being primarily about public relations and not science, has a long history of false or unsupported claims of persecution (which shouldn’t surprise us, I suppose; after all, their religion has its origin in an act of alleged martyrdom).

Continue Reading at Dispatches from the Culture Wars. Comments may be left there.

Today’s New York Times has an article wherein Republican Presidential candidate Mitt Romney clarifies (somewhat) his position on evolution. Recall that in the last Republican debate only three candidates, none of them top-tier, raised their hands when asked if they didn’t believe in evolution. Romney wasn’t one of them. And now he says why:

“I believe that God designed the universe and created the universe,” Mr. Romney said in an interview this week. “And I believe evolution is most likely the process he used to create the human body.”

This of course is the standard theistic evolutionist response. Boilerplate, banal, and politically safe… but also essentially pro-science. Of course there is room in the details for the devil to hide:

He was asked: Is that intelligent design?

“I’m not exactly sure what is meant by intelligent design,” he said. “But I believe God is intelligent and I believe he designed the creation. And I believe he used the process of evolution to create the human body.”

Translation: I’m not touching ID with a ten-foot pole.

Romney goes on to say that he believes that evolution should be taught in science class, and that other “theories” belong in religion or philosophy class. Again, this is banal and politically safe, but most importantly, it’s correct.

Unfortunately it’s almost impossible for the mainstream media to print an article on evolution without something irritating me. And here it is:

Intelligent design is typically defined as the claim that examination of nature points to the work of an intelligent designer, as opposed to the utterly random, naturalistic processes that are taught as part of evolutionary theory.

Utterly random? When are people going to learn that evolution contains an extremely powerful deterministic process known as selection? I’m afraid the author got his idea about what evolution is from the IDists.

Dodos on cable and DVD

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If you haven't seen Flock of Dodos yet, here's some good news: you can catch it on Showtime next week, on 17 May.

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If you don't get Showtime, the DVD will be released on 28 August, and you can also catch a short from the DVD extras on YouTube, a clip I've put on my site. Be sure to see why Michael Behe isn't worried about compromising science education in the public schools.

The PNAS Early Edition webpage has just posted a series of papers from the December 2006 National Academy of Sciences Sackler Colloquium, “In the Light of Evolution: Adaptation and Complex Design,” organized by Francisco Ayala and John Avise. The series of papers, on topics ranging from color vision to beetle horns, is now available (I will post the list below the fold). Eugenie C. Scott (aka Genie) was invited to speak at this meeting about evolution education and the history of opposition to it, and the speakers wrote papers to be published in PNAS and a forthcoming NAS volume.

Genie brought me on as a coauthor on the paper she was asked to write. This became:

Now that’s a stretch

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The Discovery Institute’s Casey Luskin is all atwitter about a new web article from German creationist Wolf-Ekkehard Lönnig [1] about how the giraffe is some kind of massive problem for evolution. Major planks [2] include the alleged lack of transitional fossils between the different fossil giraffe genera (never mind that creationists elsewhere typically accept that the differences between mammalian genera are small, and put the “created kind” or “basic type” at a higher taxonomic level), some confusion about whether one of the giraffe vertebrae is cervical or thoracic or something in between (note to creationists: read about homeotic shifts), and the allegation that there is no evidence for a feeding advantage for tall giraffes, relying on the fact that male giraffes are taller than female giraffes and a 1996 paper in American Naturalist (Simmons & Scheepers 1996, “Winning by a Neck: Sexual Selection in the Evolution of Giraffe”) that attempted to buck conventional wisdom and suggest that sexual selection was the cause of long necks in giraffes.

Sadly, the last plank is particularly bogus, since it completely ignores and displays no knowledge of a massively relevant and quite brilliant paper, published just back in January 2007 in American Naturalist, that constitutes an experimental demonstration of the relative feeding advantage of giraffe height:

John Wise, a biology professor at SMU has written an opinion on Intelligent Design

John Wise Wrote:

Quoting Johnson’s own words, “The objective is to convince people that Darwinism is inherently atheistic, thus shifting the debate from creationism vs. evolution to the existence of God vs. the non-existence of God.” In other words, don’t allow this to be about creationism-ID versus science. Make people think this is all about a choice they have to make between God and science. This is deceptive at best.

ending with a brilliant reminder

The foundations of Intelligent Design are in politics and religion, not science. The nature of what we have learned about our physical world does not have to conflict with our faith and understanding of the spiritual domain. Don’t let your faith become dependent on the politics of flawed pseudoscience.

Tangled Bank #79

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The Tangled Bank

The latest edition of the Tangled Bank is live at Epigenetics News.

Over at Uncommon Descent Paul Nelson tries to argue that because we can detect fraud, humans (or at least their actions) aren’t natural. Peculiar as that may be, the argument he uses is well, so loopy that you may be forgiven for thinking Paul has gone off the deep end.

The Hovind Saga Continues

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This was recently posted on CSEblogs.com – the blogs of Creation Science Evangelism, i.e. Kent Hovind’s ministry. It comes from Paul Abramson who is a longtime supporter and associate of Hovind. I will post it without further commentary, since it is pretty shocking by itself. We don’t know anything more about it than this. It could indicate anything from Hovind committing some sort of serious infraction of prison rules, all the way down to a Hovind fan’s histrionic misinterpretation of some routine event such as a prison transfer. It seems a little hard for me to believe that Hovind would do something worthy of solitary, so who knows.

Anyway, here it is… (from the comments section)

The American Enterprise Institute has an interesting discussion title Darwinism and conservatism: Friends and Foes? with Larry Arnhart, from the Northern Illinois University and John Derbyshire, from the National Review, and George Gilder, and John West, from the Discovery Institute.

Gilder ended with a particularly ironic comment about emergent properties

George Gilder Wrote:

When people talk about emergence, it’s a new popular way of saying “I have no clue”.

Does Gilder realize how this describes ID far better?

As a side note: West repeated the specious claim that Doug Axe’s probabilities were relevant to a working protein.

John Derbyshire’s contribution is excellent.

As you have no doubt heard by now, there was a brief exchange on evolution at last night's Republican debate. Senator John McCain was asked bluntly whether he “believed in” evolution. After a moment of hesitation he answered, simply, “Yes.” Moderator Chris Matthews then asked the ten candidates whether any of them did not believie in evolution. Representative Tom Tancredo, Senator Sam Brownback and Governor Mike Huckabee raised their hands.

I provide some further details over at EvolutionBlog. I've also assembled some reactions to the creationist hand-raisers from around the web. In this post and and this post I have discussed some other portions of the debate addressing cultural or scientific issues. Comments to all of this may be left at EvolutionBlog.

We have the brains of worms

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Way back in the early 19th century, Geoffroy St. Hilaire argued for a radical idea, that vertebrates and most invertebrates were inverted copies of each other. Vertebrates have a dorsal nerve cord and ventral heart, while an insect has a ventral nerve cord and dorsal heart. Could it be that there was a common plan, and that one difference is simply that one is upside down relative to the other? It was an interesting idea, but it didn't hold up at the time; critics could just enumerate the multitude of differences observable between arthropods and vertebrates and drown out an apparent similarity in a flood of documented differences. Picking out a few superficial similarities and proposing that something just looks like it ought to be so is not a persuasive argument in science.

Something has changed in the almost 200 years since Geoffroy made his suggestion, though: there has been a new flood of molecular data that shows that Geoffroy was right. We're finding that all animals seem to use the same early molecular signals to define the orientation of the body axis, and that the dorsal-ventral axis is defined by a molecule in the Bmp (Bone Morphogenetic Protein) family. In vertebrates, Bmp is high in concentration along the ventral side of the embryo, opposite the developing nervous system. In arthropods, Bmp (the homolog in insects is called decapentaplegic, or dpp) is high on the dorsal side, which is still opposite the nervous system. At this point, the question of whether the dorsal-ventral axis of the vertebrate and invertebrate body plans have a common origin and whether one is inverted relative to the other has been settled, and the answer is yes.

That raises more questions, of course. One is where the nervous system fits into this scheme.

Continue reading "We have the brains of worms" (on Pharyngula)

Lately there has been a lot of posts in the blogoshere about whether doctors need to know anything about evolutionary science. Today I got drawn into this discussion over on Uncommon Descent: I posted on a thread for another reason (see Ed Brayton’s post Sal Cordova’s Rank Dishonesty for that story), and a commenter there replied to me:

You are on record as being pro Darwinist and active in promoting Darwinism. Why don’t you take a crack at supporting Darwinism here for students in general and medical students in particular. And in the process enlighten us.

Well, I spend some time responding to this person here, and in doing so told a story that I’d been thinking about writing up for the Panda’s Thumb.

So I’m going to duplicate-post my comment there as a post here. Here’s what I wrote at Uncommon Descent:

Although many have read the transcripts of the Kitzmiller v. Dover trial (HTML version | PDF version) and found them interesting, reading the transcripts does not give the full sense of what it was like to be in the Kitzmiller courtroom. In real life, in addition to the witness answering questions, the lawyers and witnesses were constantly referring to exhibits that were digitally projected onto a large screen on the right wall of the courtroom. Usually the exhibits were just documents, but when the science witnesses testified, their powerpoint presentations contain fossils, flagella, and everything else in between. I think it is safe to say that the testimony is much easier to understand when read with the demonstrative exhibits available (the exhibit lists and a few exhibits are available online).

However, it takes a lot of work to convert the slides to web format, add captions, embed them in HTML, etc. But as a first step, I and others at NCSE have done this for Kevin Padian’s testimony (testimony+slides | just slides).

I’d like to direct you all over to Red State Rabble to read Pat Hayes’ post this morning entitled “Discovery’s Disturbing Legacy.”

The ID movement has failed scientifically (never having got off the ground), in the courts, and at the ballot box in school Board elections at the state and local level. This has not fazed the Discovery Institute, which is now concentrating on the culture war tactic of associating science (“Darwinism”) with Nazism, eugenics and other cultural evils.

I have just read the latest post of young-earth creationist/Discovery Institute fellow/Biola professor/blogger John Mark Reynolds. I think I am just going to have to occasionally serve the role of his guilty conscience in matters scientific. He has apparently thrown his own scientific conscience down a well somewhere, or he wouldn’t be able to say the wildly hypocritical things he does.

Sal Cordova’s Rank Dishonesty

I know we’re all used to seeing creationists dishonestly quoting something written by scientists, but folks I’m about to show you one of the most egregious examples you will ever see of it. This is as bad as Morris and Whitcomb’s famous distortion of Ross and Rezak’s paper on the Lewis overthrust, where they literally quoted a paragraph and stopped just before the sentence that began, “However.….”, to give the impression that the authors were saying the exact opposite of what they actually said. Go read this post by Sal at UD and you will see the following quote:

Continue Reading at Dispatches from the Culture Wars. Comments may be left there.

by Bora Zivkovic

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As the 2007 Science Blogging Conference was such a great success, we are already in full swing in organizing the 2008 conference and hoping to make it even bigger and better than the first one.

Our beta-version wiki is up—check out the homepage and the first, rough outlines of the program (feel free to edit the page and add your idea at the bottom or in the comments). At this point we are trying to get more sponsors so if you and your organization/company/magazine is interested, let us know soon.

Check out out blog for updates.

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Last time, almost in time for the conference, we edited and published the first-ever science blogging anthology, the Open Laboratory 2006, which was an instant hit. Thus, we are already collecting nominations for the next years’ edition. Send us your best posts (or best posts written by others) of the year by using this submission form and help us spread the news by adding this code to your blog or website.

There has been a spate of interest in the blogosphere recently in the matter of protein evolution, and in particular the proposition that new protein function can evolve. Nick Matzke summarized a review (reference 1) on the subject here. Briefly, the various mechanisms discussed in the review include exon shuffling, gene duplication, retroposition, recruitment of mobile element sequences, lateral gene transfer, gene fusion, and de novo origination. Of all of these, the mechanism that received the least attention was the last – the de novo appearance of new protein-coding genes basically “from scratch”. A few examples are mentioned (such as antifreeze proteins, or AFGPs), and long-time followers of ev/cre discussions will recognize the players. However, what I would argue is the most impressive of such examples is not mentioned by Long et al. (1). Below the fold, I will describe an example of de novo appearance of a new protein-coding gene that should open one’s eyes as to the reach of evolutionary processes. To get readers to actually read below the fold, I’ll summarize – what we will learn of is a protein that is not merely a “simple” binding protein, or one with some novel physicochemical properties (like the AFGPs), but rather a gated ion channel. Specifically, a multimeric complex that: 1. permits passage of ions through membranes; 2. and binds a “trigger” that causes the gate to open (from what is otherwise a “closed” state). Recalling that Behe, in Darwin’s Black Box, explicitly calls gated ion channels IC systems, what the following amounts to is an example of the de novo appearance of a multifunctional, IC system.

Twisty maze of duck oviducts

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I'm sure you've already heard about it, so I'm a little redundant to bring it up — Carl Zimmer has a spiffy article in the NY Times about duck phalluses. No, that's not quite right; the most interesting part of the story was the bit about duck oviducts. Female ducks have been evolving increasingly convoluted oviducts to baffle the efforts of duck rapists to inseminate them, and male ducks have been evolving concomitantly long phalluses to thread the maze and deliver sperm to the ovaries.

I'd heard about these huge intromittent organs in ducks before, but this is another fascinating revelation: it took a woman scientist to suggest that maybe, just maybe, they also ought to look at what's going on in the female ducks, and then the whole wonderful story of coevolution of these structures emerged. It's actually a rather embarrassing instance of a scientific blind spot, where the biases of the investigators led them to overlook an important component of the story.

A downside of successful vaccines

A few weeks back during the whole Egnor kerfuffle, I mentioned how important an understanding of evolutionary biology was to many areas of epidemiology, and specifically, for vaccine development and implementation. As one example, I brought up the phenomenon of serotype replacement, which can occur due to the use of what are called “multi-valent vaccines.” Essentially, these vaccines include strains of pathogens which are either the most common, or the most likely to cause disease–thereby protecting individuals from infection with these specific serotypes, but not making the recipient immune to infection with other strains that aren’t included in the vaccine formulation. The concern is, then, that once those types are reduced in the population via vaccination, other serotypes can come along and fill the niche that they’ve vacated. A recent story by Helen Branswell notes that this is exactly what’s happening with pneumococci:

(Continued at Aetiology)

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