February 2005 Archives

Not a German Piltdown

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It has recently been reported (Telegraph, Guardian) that German scientist Reiner Protsch had committed a number of scientific frauds. Protsch apparently could not even operate his own carbon-dating equipment, and routinely made up dates for bones that had been sent to him for dating, often giving recent specimens dates that were much too old. Many webpages have repeated the following quote about the significance of these frauds:

Chris Stringer, a Stone Age specialist and head of human origins at London's Natural History Museum, said: "What was considered a major piece of evidence showing that the Neanderthals once lived in northern Europe has fallen by the wayside. We are having to rewrite prehistory."

Stringer, however, says that he never said that:

The Tangled Bank

In a horrendous and unfortunate spamfilter accident, many articles were lost from the last edition of the Tangled Bank. Join us now in a desperate rescue attempt, in Tangled Bank #22½: The Quest for the Lost Articles.

Penis evolution

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Here's a brief teaser:

Amniote penises have had a complex history. They have evolved independently multiple times, and perhaps most troubling to the male ego, they have been secondarily lost at least a few times. And every time they have evolved, they converge on a remarkably similar morphological solution.

If you want to find out more, read the rest on Pharyngula.

Why are there still Monkeys?

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We’ve all heard the Creationist refrain (also a Dennis Miller joke), “If humans evolved from Monkeys, Why are there still Monkeys?”

See http://our.homewithgod.com/whereeag[…]e/darwin.htm for a badly spelled example:

Darwin claims that because we are similar to monkeys in some ways, then we must have evolved from them. So whay are there still monkeys around then?

This aphorism is also discussed here, here, here, here, here, and most bizarrely here.

As a Friday Treat, I’m posting a Torte and a Re-Torte about this curious argument.

Have a great weekend! -Dave

George Diepenbrock is a reporter for the Southwest Daily Times, a newspaper in Kansas. At the conclusion of this recent article about the latest evolution dust-up in Kansas, he offers the following challenge to those who wish to keep ID out of science classrooms:

This scares opponents to death because they are more worried about Kansas gaining criticism from national media as it did in 1999.

Instead opponents should come up with a good argument on why teaching only the evolution theory does not violate the state education science mission statement to make all students lifelong learners who can use science to make reasoned decisions.

Presenting only one life science theory in classes without alternatives breeds ignorance and violates the mission statement.

I have answered his challenge in this blog entry over at EvolutionBlog. Whether I have answered successfully I will leave to others to decide.

Apparently, the regular procedures for science standards revisions in Kansas have not been going well for ID advocates. They lost on the science standards committee – the group of Kansas scientists and educators that were appointed to revise Kansas’s science standards.

And they lost in the four public hearings on the science standards that occurred in Kansas during February. At these hearings, it became clear that the only people who favored the 20+ pages of revisions promoted by the Kansas “Intelligent Design Network” were straight-up creationists who want God inserted into biology classes.

Now, at the last minute, they have hatched a plan to put evolution on trial for 10 days, with no standards of evidence, none of the rules found in a normal trial, no rules for what counts as a “scientist” or an “expert”, and no limitation that the “witnesses” be from Kansas. Undoubtedly what is planned is that the Discovery Institute circus of philosophers, lawyers, and a few scientists who’ve never managed to publish original research confirming “intelligent design” will invade Kansas and attempt to give their pseudoscience some thin illusion of respectability.

Unfortunately, I’m not making this up…Read the news story:

Tangled Bank #22

The Tangled Bank

The 22nd edition of the Tangled Bank is now up and ready for reading!

There was one unfortunate problem this time around. It seems that gmail decided that this bozo (umm, me) who was constantly forwarding links to Selva must be some kind of spammer, and started filtering me out. A small heap of recent submissions got thrown into the junk mail pile, so if you sent something in and it isn't there, don't worry, it wasn't that anyone thought you weren't worthy…it was gmail deciding that I wasn't worthy.

Anyway, they have all been recovered. What I think I'll do is put them into a special post this weekend, a kind of temporary tributary of the Tangled Bank, so you'll actually get two collections of science posts this week. Hooray!

New submissions should be sent to grrlscientist@yahoo.com, me, or host@tangledbank.net, for appearance at Living the Scientific Life on 9 March.

9 March is my birthday, by the way, and if anyone wants to get me something special, a link to a lovely science article on the web would be just perfect!

There’s an interesting piece by Jim Holt in the February 20th, 2005 issue of New York Times magazine, entitled “Unintelligent Design.” Holt makes some interesting observations, like this one:

In mammals, for instance, the recurrent laryngeal nerve does not go directly from the cranium to the larynx, the way any competent engineer would have arranged it. Instead, it extends down the neck to the chest, loops around a lung ligament and then runs back up the neck to the larynx. In a giraffe, that means a 20-foot length of nerve where 1 foot would have done. If this is evidence of design, it would seem to be of the unintelligent variety.

He also says something quite curious about Michael Behe:

But what if the designer did not style each species individually? What if he/she/it merely fashioned the primal cell and then let evolution produce the rest, kinks and all? That is what the biologist and intelligent-design proponent Michael J. Behe has suggested. Behe says that the little protein machines in the cell are too sophisticated to have arisen by mutation – an opinion that his scientific peers overwhelmingly do not share. Whether or not he is correct, his version of intelligent design implies a curious sort of designer, one who seeded the earth with elaborately contrived protein structures and then absconded, leaving the rest to blind chance. (emphasis added)

I’m curious, Thumbers and Lurkers - do you think this is a correct statement of Behe’s views?

Thanks, Dave

From our friends at the NCSE

Chris Mooney reports in The American Prospect that John H. Marburger III, director of the White House’s Office of Science and Technology Policy, denounced “intelligent design” as unscientific. Mooney writes:

Speaking at the annual conference of the National Association of Science Writers, Marburger fielded an audience question about “Intelligent Design” (ID), the latest supposedly scientific alternative to Charles Darwin’s theory of descent with modification. The White House’s chief scientist stated point blank, “Intelligent Design is not a scientific theory.” And that’s not all – as if to ram the point home, Marburger soon continued, “I don’t regard Intelligent Design as a scientific topic.”

In March 2004, when asked about the Bush administration’s scientific credibility in light of the president’s reported skepticism about evolution, Marburger similarly got it right: “Evolution is a cornerstone of modern biology.”

Michael Behe’s book Darwin’s Black Box is one of the most popular and extensively reviewed books promoting intelligent design “theory.” The concept of “irreducible complexity” propagandized in that book has been touted by Behe and other intelligent design advocates as a great discovery and used as one of the main tools in their efforts to “destroy Darwinism” (the goal openly announced by such “leading lights” of intelligent design as Phillip Johnson [1991] and Jonathan Wells [2002]).

Irreducible complexity, according to “design theorists,” implies intelligent design of biological system. In fact, such a conclusion lacks a logical foundation. Irreducible complexity can even more reasonably be construed as an argument against intelligent design.

Evolution of the jaw

jaw evolution

What do you know…just last week, I posted an article dismissing a creationist's misconceptions about pharyngeal organization and development, in which he asks about the evidence for similarities between agnathan and gnathostome jaws, and what comes along but a new paper on the molecular evidence for the origin of the jaw, which describes gene expression in the lamprey pharynx. How timely! And as a plus, it contains several very clear summary diagrams to show how all the bits and pieces and molecules relate to one another.

The short summary is that there is a suite of genes (the Hox and Dlx genes, which define a cartesian coordinate system for the branchial arch elements, Fgf8/Dlx1 genes that establish proximal jaw elements, and Bmp4/Msx1 genes that demarcate more distal elements) that are found in both lampreys and vertebrates in similar patterns and roles, and that vertebrate upper and lower jaws are homologous to the upper and lower "lips" of the lamprey oral supporting apparatus.

Continue reading "Evolution of the jaw" (on Pharyngula)

Plaque–evidence for Design!

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Every now and then, I check in over at The Institute for Genomic Research (TIGR) to see what new projects they’re up to, as well as to see if they’ve released a particular genome sequence I’m waiting on. Yesterday I noticed this project:

Innovative Metagenomics Strategy Used To Study Oral Microbes

Rockville, MD - The mouth is awash in microbes, but scientists so far have merely scratched the surface in identifying and studying the hundreds of bacteria that live in biofilm communities that stick to the teeth and gums.

In an innovative new project that could help improve the detection and treatment of oral diseases, scientists are now using a metagenomics strategy to analyze the complex and difficult-to-study community of microbes in the oral cavity.

***

In recent years, molecular methods have indicated that there are well over 400 species of bacteria in the oral cavity. But, so far, only about 150 of those species have been cultured in laboratories and given scientific names. Using a metagenomics sequencing strategy, TIGR scientists will be able to identify bits and pieces of the DNA of many of those oral microbes that so far have not been grown in labs and studied.

Now, I know that there are an insane amount of microbes in the mouth, but 400 species? Holy cow.

The usual creationist suspects are babbling in the comments to my article on textbook stickers, and throwing aside the usual empty apologetics and assertions that they are promoting secular atheism and weird claims about Jefferson and bizarre ideas that Einstein 'proved' Newton wrong, the only interesting argument is that scientists ought not to be distressed at a declaration that our knowledge is provisional and subject to revision, and that students should keep an open mind. The answer is that we aren't distressed at all by that; in fact, our textbooks already say it over and over, and typically have long chapters that introduce the scientific method and describe how it works and what its limitations are.

For instance, Campbell's Biology, fourth edition, has an extensive section on the hypothetico-deductive method, and comes right out and says it explicitly:

Even the most thoroughly tested hypotheses are accepted only conditionally, pending further investigation.

The Tangled Bank wants more submissions!

The Tangled Bank

The next edition of the Tangled Bank will be posted at The Scientific Indian on Wednesday, 23 February…so this is the time to send your links to Selva, me, or to host@tangledbank.net.

Also, while we've got our future hosts booked up into May, we're always looking for new volunteers. Send me a note if you'd like to get on the roster.

Science journalism panel

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We often complain about the awful state of science journalism. Turns out there's a panel discussion on the subject in Washington D.C. on Sunday, and the public is all invited. (On the panel, one of my favorite science writers, Reason's Ronald Bailey.)

Evolving textbook stickers

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Yet another school board is contemplating defacing science textbooks with warning stickers (Memphis Commercial Appeal, free reg. req.). Yet again, it's driven by religious interests rather than any desire to improve the quality of science teaching.

The same school board member who helped establish a Bible class in Shelby County Schools is pushing for a creation message on high school biology books.

County school board member Wyatt Bunker, who believes the Bible is the inerrant word of God, said he's concerned that students are being taught only scientific theories such as evolution and the Big Bang.

Good News From Georgia

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Georgia’s House Bill 179 was tabled by the education committee after hearing comments from the bill’s sponsor, a couple of biologists, and some education groups. Most of the education committee are former educators and didn’t like the anti-science content of the bill, its opposition to local control, its unfunded mandate, and the need to buy new textbooks and write a new curriculum to match the bill.

Although many people spoke against the bill, the education committee only asked questions from Rep. Bridges, its lone supporter. He argued that schools should teach facts not theories. (Although, that is not in his bill, that is how he describes his bill. Go figure.) The education committee questioned him on his (mis)use of scientific terminology and whether he had issues with hypotheses.

See that wasn’t hard; was it?

What Good is Half an Eye?

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Creationist Hate Mongering

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An editorial in the “The News Record,” a student newspaper associated with the University of Cincinnati by Scout Foust was brought to my attention late in the afternoon on 15 Feb. I was both insulted, and saddened at the gross incompetence and ignorance it represents. Mr. Foust, a fourth year student in German Literature, titled his editorial, Evolution perpetuates racist ideologies: Blacks shouldn’t back evolution.

Scout Foust was allowed to publish a baseless slander of not evolution, which as a science will take no notice, but of the hundreds of thousands of scientists who work and teach in disciplines related to evolutionary theory. Evolution is such a powerful truth that this encompasses nearly every science discipline. The Editors of “The News Record” have failed their responsibility to their readers. Further, such an incompetent article reflects very badly on their newspaper, the University of Cincinnati, and the Department that had the dubious task of educating Mr. Foust. Nor have the Editors done Mr. Foust personally any favor, as he now is exposed as an incompetent on a national level. A few hours of internet research reveals that Mr. Foust’s editorial is little more than a string of creationist sites’ propaganda weakly edited together and presented without attribution. In other words, Mr. Foust is not only incompetent on matters relating to history and science, he is also exposed as a plagiarist.

The Texas Tech Law Review recently published an article about evolution disclaimers, which contains some interesting arguments about the creationism/evolution controversy generally. Chad Edgington, Disclaiming Darwin Without Claiming Creation: The Constitutionality of Textbook Disclaimers And Their Mutually Beneficial Effect on Both Sides of the Origins Debate, 5 Tex. Tech L. Rev. 135 (2004). Edgington (whose article was published before the Cobb County decision) argues "not only...that disclaimers which call for a critical approach to evolution are constitutional, but that a liberal policy allowing for their placement in textbooks is the most satisfactory solution to controversy surrounding the teachings of origins." Id. at 138.

Koufax Awards End Tomorrow

The voting for the Koufax awards ends tomorrow. The Panda’s Thumb is a finalist in the Best Group Blogs cateogry. If you like us and haven’t already voted, please vote for The Panda’s Thumb to help us win.

The election is over, but creationism isn’t.

P.S. You can also vote for PZ’s Pharyngula as the Best Expert Blog.

Creationists come up with the weirdest criticisms. Serge at Imago Dei disagrees with my claim that humans build their face using "the same embryonic foundation that fish use to build gills", calling them "pharyngeal phantasies". He bases this on the peculiar notion that there ought to be a simple one-to-one mapping of cranial nerves to pharyngeal arches, and that by his understanding of the arrangement, the cranial nerve that innervate the derivatives of the first pharyngeal arch in us (the trigeminal nerve) ought to innervate the first gill arch in teleosts.

These are both false assumptions. I'll explain why.

Continue reading "Creationist Confusion about pharyngeal homologies" (on Pharyngula)

Response to Bobby Maddex

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Bobby Maddex, senior editor of Crux magazine, has replied to my criticism of inaccuracies that were present in accounts of the Sternberg/Smithsonian situation written by him and by John Coleman. While Coleman responding reasonably and graciously, thanking me for pointing out the inaccuracies and making the requisite corrections, Maddex chooses instead to complain, without justification, about his mistreatment. Along the way, he also adds a few more inaccurate statements to the ones initially criticized. For a full fisking of his reply, see this post at Dispatches from the Culture Wars.

In the same vein as Don Boudreaux's recent comments, Will Wilkinson has this article on markets and evolutionary psychology.

Wanted: Comments on Kansas Standards

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Opportunity to comment on the Science Curriculum Standards Draft and the Intelligent Design/creationist Proposals (Minority Report) on the Kansas Department of Education’s (KSDE) website.

From Kansas Citizens for Science:

One part of the Kansas state Board of Education’s recent Resolution concerning the science standards was to “collect comments from the public regarding the various proposed changes to the Science Curriculum Standards, either contained within the Science Curriculum Standards Draft or contained within the Minority Report.” KSDE has set up a webpage where one can offer comments on either or both of these.

Furthermore, the Resolution instructed KSDE to “make the raw data available to the members of the Board, and to deliver to the KSBE a report that will organize the data into categories of (a) how many respondents were within Kansas; (b) the number of respondents that generally supported and generally opposed the various areas of input.”

We urge you to go to here and comment. We understand that science is not established by public vote, and that this survey is merely a vehicle for trying to legitimize inserting Intelligent Design creationism-influenced claims into the standards. However, as long as the survey is there, we need to respond.

Creationism in Kentucky

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Pop quiz: name the state that still has, officially on the books, an “equal time” provision for creationism, in defiance of the 1987 Supreme Court decision Edwards v. Aguillard and much additional case law? No, not Alabama, although they do still have Evolution Warning Labels mandated in all biology textbooks.

That’s right, it’s Kentucky, future home of the $25 million dollar creationism museum run by Answers in Genesis. We are actually coming up on the 15th anniversiary of Kentucky Revised Statute 158.177, which has been in place since July 13, 1990. If you don’t believe me, read this article in the Cincinnati Enquirer.

The Enquirer quotes the statute, which I reproduce below:

Tucson Weekly story

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I would like to alert readers to a feature story that came out today in the Tuscon Weekly. “Evolution Revolution” reviews the evolution/creationism issue nationally and in Arizona, and takes the time to explore issues in a bit of depth. Project Steve gets a mention, always a bonus.

Lynn, Cooper and Dean

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There is a truly excellent op-ed from Barry Lynn today in The Houston Chronicle. Here's an excerpt I especially liked:

Phillip Johnson, a former law professor who pioneered intelligent design, told a conservative religious audience a few years ago that his goal is to use intelligent design to spread doubts about evolution and then introduce people to “the truth” of the Bible and “the question of sin.” Ultimately, Johnson said, he wants people to be “introduced to Jesus.”

If the end result of what you are doing is aimed at religious conversion, then it's evangelism, not science. It belongs in a house of worship, not a public school.

Well said.

Alas, not everyone agrees with Lynn. The Discovery Institute's Seth Cooper has weighed in with a sulky blog entry about it.

But Cooper allows blogger Darrick Dean do the heavy lifting for him. Over at EvolutionBlog I have posted entries about Lynn, Cooper and Dean, available here, here and here, respectively. Enjoy!

The Bathroom Wall

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With any tavern, one can expect that certain things that get said are out-of-place. But there is one place where almost any saying or scribble can find a home: the bathroom wall. This is where random thoughts and oddments that don’t follow the other entries at the Panda’s Thumb wind up. As with most bathroom walls, expect to sort through a lot of oyster guts before you locate any pearls of wisdom.

The previous wall got a little cluttered, so we’ve splashed a coat of paint on it.

Life on Mars?

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Here’s a provocative exclusive from Space.com:

Exclusive: NASA Researchers Claim Evidence of Present Life on Mars.

A pair of NASA scientists told a group of space officials at a private meeting here Sunday that they have found strong evidence that life may exist today on Mars, hidden away in caves and sustained by pockets of water.

The scientists, Carol Stoker and Larry Lemke of NASA’s Ames Research Center in Silicon Valley, told the group that they have submitted their findings to the journal Nature for publication in May, and their paper currently is being peer reviewed.

What Stoker and Lemke have found, according to several attendees of the private meeting, is not direct proof of life on Mars, but methane signatures and other signs of possible biological activity remarkably similar to those recently discovered in caves here on Earth.

If confirmed, this could have some serious ramifications for evolution on the early Earth. Did living things go from Mars to Earth or vice versa? Are we talking about multiple origin of life events? Interesting stuff. I guess we’ll have to live with a mere teaser for now.

Upcoming Dennett speech

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Daniel Dennett, author of such brilliant books as Darwin's Dangerous Idea and Consciousness Explained, will be giving the W.D. Hamilton Memorial Lecture at the University of New England in April.

Homo floresiensis on Darwin Day

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For Darwin Day (Feb 12th), the Canberra Skeptics arranged a talk by paleoanthropologist Colin Groves at the National Museum of Australia on the subject of Homo floresiensis, the “Hobbit”. It’s clearly a popular subject; the small lecture theatre was filled to capacity with a few hundred people.

Some scientists have disputed the idea that floresiensis is a new species, suggesting instead that the skeleton is a pathological modern human - Maciej Henneberg, for one, has claimed that it closely resembles a 4000-year-old microcephalic skull found on Crete. Groves showed pictures of that skull and compared it to the hobbit. They did not look very similar to my unqualified judgement, nor, apparently, to the judgement of many qualified scientists. The hobbit femur also has differences from that of any other hominid, and the pelvis flares more than in H. sapiens or H. erectus.

While ID ‘scientists’ vociferously object to being labeled creationists, they share one notable feature with the creation scientists of the 80s: their frequent use of discredited sources. In a 1983 PBS special, Duane Gish of the Institute for Creation Research (ICR), a YEC institution, claimed that certain human proteins were more similar to bullfrog proteins than chimpanzee homologues, a claim that would be nearly inexplicable if our current understanding of evolution was correct. However, despite countless public and private requests spanning the last 20 years, Gish has never provided a source for that claim, nor retracted it (see here for more). A few years ago, Bill Dembski claimed that there was evidence of a biochemical system for which any slight modification would not only destroy the system’s current function, but any possible function of that system whatsoever. He concluded that such a system could not have evolved through ‘Darwinian’ evolution, because of the supposed lack of functional intermediates between the current system and any hypothetical precursor. However, as I document in this post, not only is Dembski’s claim unsupported by his lone source, Dembski admits this, and yet he continues to assert that claim, even strengthening it in recent writings. One of those writings was even published in the IDists’ “peer-reviewed” journal PCID, despite the editors’ knowledge that this claim was unsupported. The intention of this blog entry is to add yet another example to the list of shoddy scholarship inherent in IDist writings.

Someone stole my idea.

In celebration of Darwin Day, someone has set the Origin of Species to Dub, a kind of music related to Reggae. No, really.

This new artistic endeavor is the creation of the Genomic Dub Collective, a group which aims to “create a new musical genre… that celebrates recent successes in the field of genomics and evolutionary biology.” Why someone didn’t think of this before, I’ll never know. The group draws talent from a Microbial Genomicist and a Jamaican scientist of some sort.

Each track is named after or takes inspiration from a chapter of the Origin, and you get two bonus tracks, the Dobzhansky Dance Trance and Ras Darwin. (For all you Sheriff John Browns, Ras refers to Erasmus Darwin, Chuck’s grandfather.)

You can listen to some samples here, or you can order the entire thing for £3.99 (about the price of a dime bag). These chaps are just trying to recoup their costs, so don’t kill the seed before it grows.

Telling it straight

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The “telling it straight” award today goes to James Gibbons, an editor at the Houston Chronicle. A short letter that Gibbons sent to the Discovery Institute in 2003 (during the textbook adoption battle in Texas) was quoted by the Discovery Institute Media Complaints Division today. They called it “one of the tackiest letters we’ve received from the media.” Readers can judge for themselves:

An extended phenotype

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Don Boudreaux on whether markets are an "extended phenotype."

Update:
More at Inclination to Criticize.

The Kansas Department of Education (KSDE) recently posted a complete transcript of the public hearing on the science standards held on February 1 at Schwagle High School in Kansas City, Kansas. If you are interesting in seeing for yourself the kinds of concerns and arguments the public has about evolution and Intelligent Design creationism, you might want to read some of the transcript (here).

Also, as I reported in the post Creationist Power Play in Kansas, this week the state Board of Education created a special Science Hearings committee, comprised of three creationist Board members, to hear testimony from “scientific experts” concerned the two “opposing views” (evolution and Intelligent Design creationism-based anti-evolution) - essentially giving the Intelligent Design creationists the “equal-time” platform they desire to try to give Intelligent Design creationism credibility as science and to deflect criticism that it is really disguised religion.

These two events, the public hearings that are an established part of the standards development process and the creation of this kangaroo-court Science Hearings committee, are related in an interesting way, I think. Let me explain.

IDist “Just Not-So Stories”

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Intelligent design creationists have made rhetorical hay out of Stephen Jay Gould’s use of Kipling’s title, when Gould said that adaptationist accounts of biological phenomena sometimes seem to be “just so stories.” John Wendt on ARN has made the perfect riposte. An ID creationist claimed

Not really. You can for instance learn a lot about bacteria flagellum from ID proponents because they are reasoning from its detailed exposition. It is much more substantive than the just so stories that have been so popular among Darwinists.

Wendt responded

Evolutionary arguments are based on observable processes. All ID has is “just not-so stories”. (Emphasis added; typo corrected)

I love that phrase! “Just not-so stories.” It perfectly captures the content-free explanations offered by ID “theory.”

RBH

Alberts on Behe

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Behe's op-ed piece in the NY Times of 7 February, which was rebuked here earlier, has been given an even more stinging setback. One of the authorities Behe cited, Bruce Alberts, has also come out in the pages of the NY Times with a forceful response.

The pro-science side of the blogosphere responds with fierce glee, with comments at Lloydletta's Nooz and Comments, EvolutionBlog, and Pharyngula. It's the perfect fillip for our Darwin's Day celebrations.


Carl Zimmer also weighs in.

We’re a Koufax Award finalist

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The Panda's Thumb has made it into the final voting for Best Group Blog. If you're a fan of evolution, leave a message to vote.

P.S. You can also vote for Pharyngula in the Best Expert Blog category.

Evolving spots

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Here's what seems to be a relatively simple problem in evolution. Within the Drosophila genus (and in diverse insects in general), species have evolved patterned spots on their wings, which seem to be important in species-specific courtship. Gompel et al. have been exploring in depth one particular problem, illustrated below: how did a spot-free ancestral fly species acquire that distinctive dark patch near the front tip of the wing in Drosophila biarmipes? Their answer involves dissecting the molecular regulators of pattern in the fly wing, doing comparative sequence analyses and identifying the specific stretches of DNA involved in turning on the pigment pattern, and testing their models experimentally by expressing novel gene constructs in different species of flies.

gompel et al.

The particular gene of interests is calledl yellow (y), which is required for the production of black pigments (why is a gene for black pigments called yellow? Because genes are often named for their effect when mutated. Break the yellow gene with a mutation, and the resulting mutant animal can't make dark pigments, and looks yellowish.) Yellow is normally turned on at a low level everywhere in the fruit fly wing, pigmenting the wing an overall light gray. In D. biarmipes, there is an additional patch of elevated yellow expression in one corner of the wing. What activates this gene in just that one place?

Continue reading "Evolving spots" (on Pharyngula)

Best op-ed yet: “The E Word”

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Extra kudos to Ben Fulton of the Salt Lake City Weekly for his perceptive op-ed piece, “The E Word.” Many op-eds have pointed out that “intelligent design” is simply creationism with a new coat of paint, that ID proponents are trying to “cut in line” and get ID into the public schools before it gains scientific acceptance, that there is no ID research program, no “ID theory”, and that it is really all one big misguided exercise in conservative evangelical Christian apologetics.

However, Fulton puts his finger exactly on the point that really drives most of us science fans at PT:

Just imagine that, for every question you presented to someone in power, they answered with the words, “We don’t really know. It’s a mystery.” Now imagine if you or your child asked a question about the origin of the human species in a science class, only to have a learned instructor tell you, “We don’t really know. It’s a mystery.” Would anyone dare call that education?Ben Fulton, “The E Word,” Salt Lake City Weekly

From the [u]Biology is Cool[/u] division at the Thumb. According to [Enable javascript to see this email address.]:

Canopy-dwelling ants in the tropical forests of the Americas have adopted a neat way of averting disaster should they fall from their perch. They glide to safety, steering towards their home trunk rather than plummeting to the ground, where they might never see their nest-mates again.[Enable javascript to see this email address.]

If you don’t believe it, read the news article, the far-too uncreatively-named Nature paper “Directed aerial descent in canopy ants”, or better yet, watch the video.

How was this fascinating discovery made?

The discovery was an accident, [Stephen] Yanoviak recalls. “About two years ago I was climbing trees to collect mosquitoes when I was attacked by these ants. I brushed 20 or 30 of them off; they fell down and made a nice J-shaped curve back to the tree.”[Enable javascript to see this email address.]

Thus a Nature paper was born…

Since you asked, Stephen P. Yanoviak is indeed a Project Steve Steve.

Creationist Power Play in Kansas

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Today in Kansas the creationist majority on the state BOE brought an unannounced resolution, which they passed 6-4, that created a special Board committee to hold as yet unspecified hearings “to investigate the merits of the two opposing views [evolution and presumably some form of Intelligent Design/creationism] offered by the Kansas Science Curriculum Writing Committee.”

This action bypasses the established procedures already in place (the writing committee itself and the public hearings now going on), and gives the creationists a special forum to air there views. The resolution appointed Board chair Steve Abrams as well as Board members Connie Morris and Kathy Martin to the Hearing Committee. All are creationists, and Abrams was the Board member who secretly collaborated with the creationists back in 1999 to produce those infamous standards.

You can see the resolution itself at www.kcfs.org

The Board also voted to link to the ID/creationists minority report (which has already been voted down by the writing committee) on the state website here for public discussion.

Bailey bashes Behe

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An excellent article from Ronald Bailey on Michael Behe, and the creationism battle in general.

Barbara Forrest, a philosopher at Southeastern Louisiana University and co-author of Creationism’s Trojan Horse, reviews Darwin, Design, and Public Education, an ID anthology that was published as part of Michigan State University’s “Rhetoric and Public Affairs” series.

Her extensive review is available for free at RedNova.com, which is nice because the original publication of the review, in the journal Integrative and Comparative Biology, requires a subscription. You should get the pdf from the journal if you want the authoritative text, since it looks like the RedNova text was scraped from the pdf and therefore has a few conversion errors.

Tangled Bank turns 21

The Tangled Bank

Lots of links to science writing can be found at Tangled Bank #21 on About Town today.

The next edition will be at The Scientific Indian on 23 February. Send your science links to Selva Kumar, me, or host@tangledbank.net.

Crux Magazine Off to Bad Start

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Crux magazine is a new publication with a virtual who's who of ID advocates as contributors and editors. It also has three blogs associated with it, with contributions from those same people. While declaring itself the "last bastion of Truth" (yes, they even capitalized it), their contributors seem to have a little difficulty grasping the non-capitalized variety of truth in two articles about the Sternberg/Smithsonian situation. The first, written by Crux senior editor Bobby Maddex, repeats the accusations in the David Klinghoffer WSJ piece as gospel truth, but adds one bit of falsehood to it:

Though still an employee of the museum, Sternberg, who is not even an advocate of Intelligent Design himself, has since been shunned by former colleagues throughout the United States, and his office still sits empty as "unclaimed space."

Don’t forget: Tangled Bank tomorrow

The Tangled Bank

This is your last chance to beat the deadline: send your science-related links to me, to host@tangledbank.net, or to Xavier if you want your weblog to get mentioned in the Tangled Bank at About Town tomorrow.

PT Spam Blocker

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Salvador is making some noise on ARN about a comment of his being rejected by our spam filter. This post is to clarify things.

Spammers target blogs with comments. These attacks can be harsh. At times spammers will go through every single post in the blog and post three comments containing scores of links advertising every thing from child rape to internet bingo.

To counter such horrid spam, we employ a blacklist plugin that searches every comment for certain patterns and rejects any that fit. Unfortunately sometimes non-spam also gets blocked. Users are sent a message informing them of the bad content so they can change the post. (Robotic spammers ignore such messages.)

Our typical cycle of spam control went like this:

  • Spam gets through the filter.
  • We recognize the spam.
  • Add the urls from the spam to the blacklist.
  • Delete the messages that got through.

Of course, the time between 1 and 4 can be hours or days, which can lead to a lot of naughty messages sitting around the blog for a while.

I finally got fed up with this reactionary technique a few months ago, and decided if there was a better option. I tried the explanatory filter but it was unable to detect links designed by spammers. So I had to fall back to old methodology and took links from our blacklist, which I already knew had been designed by spammers, and tried to deduce some megarules from them. I ended up deciding to block urls that contained multiple hyphens, since about 75% of the spammers’ urls went something like “hot-chicks-want-to-hottub-with-you.ruky.net.” (I also blocked all .info addresses since we were only getting spam from them.)

The multi-hyphen megarule has worked very well. However, it is still experimental and has been modified more than once. If you have a problem with getting a url past the spam blocker, you can simply use tinyurl.com to create a replacement url. That is what Wesley did in this comment to link to ISCID. (Contrary to some claims we did not change the blacklist for Wesley.)

We do make our blacklist publicly available, blacklist.txt, so anyone can check if we are banning sites critical towards us. Sorry, would-be martyrs, we do not censor your favorite sites from comments, unless you’re into mature mamas or something. Besides if we wanted to censor you, we’d ban your IP, not add you to our spam blocker.

Today’s Guardian has an article on creationism in American public schools. Most of the article will be familiar to those versed in the subject matter, but what turned my stomach was this quote:

But the largest applause of the evening was reserved for a silver-haired gentleman in a navy blue blazer. “I have a question: if man comes from monkeys, why are there still monkeys?”

You poor, poor Kansans…At least they should supply your creationists with some new material every now and then.

The article further fleshes out the reasoning behind the attacks on evolution:

“They believe that the naturalistic bias of science is in fact atheistic, and that if we don’t change science, we can’t believe in God. And so this is really an attack on all of science. Evolution is just the weak link.”

I’m always surprised when they say this type of thing. Evolution is more strongly supported than many other theories in science. I’ve said before that religionists ought to target the germ theory of disease instead: the mere existence of a carrier state could have been used as the death knell to Koch’s postulates, for example. But I’ve not yet seen any takers. At least they must see the absurdity in challenging some well-established theories. For now.

Behe jumps the shark

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Nick Matzke has also commented on this, but the op-ed is so bad I can't resist piling on. From the very first sentence, Michael Behe's op-ed in today's NY Times is an exercise in unwarranted hubris.

In the wake of the recent lawsuits over the teaching of Darwinian evolution, there has been a rush to debate the merits of the rival theory of intelligent design.

And it's all downhill from there.

An editorial by Mike Behe is in the Monday New York Times – you remember, that liberal legacy media we were all supposed to forget about.

None of the claims are new, but at least the text is (commonly not the case in ID op-eds). The op-ed is short, so my reply is interspersed.

Michael Ruse on Ernst Mayr

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Over on the Philosophy of Biology blog Michael Ruse has just written an extensive eulogy of Ernst Mayr. It includes an excellent summary of the importance of Mayr as well as many entertaining anecdotes.

I recently expressed the view that I would be proud to be kicked by Ernst Mayr. It seems that Ruse felt the same way:

But Mayr had many more years of active life. Even last year he was scrounging one of my books from our shared publisher, Harvard University Press, so that he could put the boot into me one more time before he was done. Michael Ruse, Ernst Mayr Eulogy

I have quoted some of the important points and good bits below, but you should really read the whole thing.

Avida in Discover Magazine

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Our congratulations go out to Carl Zimmer. Discover magazine published one of Carl Zimmer’s articles as a cover article. The article was titled “Testing Darwin” (Published in Discover Magazine Feb 2005)

Zimmer explores the relevance of work on Avida to evolution

One thing the digital organisms do particularly well is evolve.” Avida is not a simulation of evolution; it is an instance of it,” Pennock says. “All the core parts of the Darwinian process are there. These things replicate, they mutate, they are competing with one another. The very process of natural selection is happening there. If that’s central to the definition of life, then these things count.”

The work based on Avida is not well received by creationists who argue that Darwinian theory cannot explain the complexity of life. Although others have already shown that complexity and information in the genome can increase under the processes of variation and selection., Avida has recently been used to address the concept of irreducible complexity. (Note: Mark Perakh has addressed some the ever changing definitions of irreducible complexity in ID’s irreducible inconsistency revisited)

Ernst Mayr

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Sad news:

Dr. Ernst Mayr, the leading evolutionary biologist of the 20th century, died on Thursday in Bedford, Mass. He was 100.

Dr. Mayr's death, in a retirement community where he had lived since 1997, was announced by his family and Harvard, where he was a faculty member for many years.

He was known as an architect of the evolutionary or modern synthesis, an intellectual watershed when modern evolutionary biology was born. The synthesis, which has been described by Dr. Stephen Jay Gould of Harvard as "one of the half-dozen major scientific achievements in our century," revived Darwin's theories of evolution and reconciled them with new findings in laboratory genetics and in field work on animal populations and diversity.

One of Dr. Mayr's most significant contributions was his persuasive argument for the role of geography in the origin of new species, an idea that has won virtually universal acceptance among evolutionary theorists. He also established a philosophy of biology and founded the field of the history of biology.

"He was the Darwin of the 20th century, the defender of the faith," said Dr. Vassiliki Betty Smocovitis, a historian of science at the University of Florida in Gainesville.

In a career spanning eight decades, Dr. Mayr, the Alexander Agassiz Professor Emeritus of Zoology at Harvard, exerted a broad and powerful influence over the field of evolutionary biology. Prolific, opinionated and dynamic, Dr. Mayr had been a major figure and intellectual leader since the 1940's. Setting much of the conceptual agenda for the field, he put the focus just where Charles Darwin first placed it, on the question of how new species originate.

Though Dr. Mayr will be best remembered for his role as a synthesizer and promoter of evolutionary ideas, he was also an accomplished ornithologist. In fact, it was with the sighting of a pair of very unusual birds that Dr. Mayr's long career in biology began in 1923 at 19.

Evolution on Television. Help!

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I am gathering up transcripts of television segments that deal with evolution, and I need some help. I watch a truly ludicrous amount of television, and follow the cable news chat shows pretty closely, but I'm sure there are many segments out there that I have missed. I'd appreciate it greatly if people could provide links to television segments they might have seen in the last few months.

Truth in advertising: IDEAcenter

| 12 Comments

FAQ: Why isn’t intelligent design found published in peer-reviewed science journals?

Before reading further, we recommend that if you are interested in seeing the scientific underpinnings of intelligent design, that you read our article, “The Science Behind Intelligent Design to become familiar with the scientific basis for intelligent design.

Link

I have a request from Benjamin Temchine, a producer with the program Your Call on KALW in the bay area—it's a daily political affairs and cultural call-in show. He is looking for teachers who are facing increasing difficulties in teaching evolution in the way they feel is scientifically justified, and would like to interview you live on the program on Monday, 7 February, at 10-11 AM PT, 1-2 PM ET. If you are interested in being interviewed, call him at (415) 516-5971.

The rest of us can also call in and give our opinions during the show at (866) 798-TALK, and listen in via the KALW RealAudio stream. Except for me, darn it. That hour is right in the middle of my lecture, and I think I'll be talking about codominance and blood antigens at that time.

This is a cautionary tale about the dangers of leaping to grand conclusions on the basis of hearsay. It started back with the publication of Stephen Meyer's article in the August 2004 issue of the Proceedings of the Biological Society of Washington, which we took note of in the post Meyer's Hopeless Monster. In that post, we considered the political ramifications of that publication, leading us to say then:

The important issue is whether or not the paper makes any scientific contribution: does it propose a positive explanatory model? If the paper is primarily negative critique, does it accurately review the science it purports to criticize? The fact that a paper is shaky on these grounds is much more important than the personalities involved. Intemperate responses will only play into the hands of creationists, who might use these as an excuse to say that the "dogmatic Darwinian thought police" are unfairly giving Meyer and PBSW a hard time. Nor should Sternberg be given the chance to become a "martyr for the cause." Any communication with PBSW should focus upon the features that make this paper a poor choice for publication: its many errors of fact, its glaring omissions of relevant material, and its misrepresentations of the views that it does consider.

But martyrdom of Sternberg has been a topic of discussion for the past week... and the person accused of martyring him, Jonathan Coddington, has spoken out in a comment posted to a thread here on Panda's Thumb.

An historical example of Design Theory

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Doing Things With Words quotes a beautiful example from Carl Sagan:

Most curious is [Kepler's] view of the origin of the lunar craters, which make the moon, he says, "not dissimilar to the face of a boy disfigured by smallpox." He argued correctly that the craters are depressions rather than mounds. From his own observations he noted the ramparts surrounding many craters and the existence of central peaks. But he thought that their regular circular shape implied such a degree of order that only intelligent life could explain them. He did not realize that great rocks falling out of the sky would produce a local explosion, perfectly symmetric in all directions, that would carve out a circular cavity--the origin of the bulk of the craters on the moon and the other terrestrial planets. He deduced instead "the existence of some race rationally capable of constructing those hollows on the surface of the moon. This race must have many individuals, so that one group puts one hollow to use while another group constructs another hollow."

At least the Discovery Institute can take solace from the fact that they've now actually been compared to a scientist. It's far more flattering than they deserve, even though it was a scientist who was wrong

Robert Crowther from the Discovery Institute’s Media Complaints Division seems to be quite content to reference an ID friendly blogsite by Denyse O’Leary

If misreporting were a concern to Robert, he would certainly have pointed out the various problems with Denyse’s arguments. But like ‘teach the controversy’, it seems that correcting errors in reporting is mostly one sided.

Some of you may be wondering why none of us Thumbites have commented on David Klinghoffer’s op-ed about Richard Sternberg filing a complaint with U.S. Office of Special Counsel claiming discrimination at the Smithsonian. We have discussed it at length, but there is too little information to form an opinion about the complaint.

Is it possible that the Smithsonian over reacted to Sternberg’s abuse of his editorial power at PBSW? Sure. It is also possible that they didn’t. Although, Klinghoffer makes clear his opinion, he has failed to provide enough information in his op-ed to objectively determine and judge what has happened.

Because of the way the law typically works, it will probably be impossible to get the Smithsonian’s side of the story. Sternberg and his supporters can say virtually whatever they want to the media, and Smithsonian will have little ability to set the record straight. (The Discovery Institute’s Media Complaints Division will be of little help.)

However, it is interesting to note that Sternberg is a staff scientist for NCBI/NIH and is not employed by the Smithsonian. He is a research associate, which is an unpaid, “formal scholarly affiliation” with the Smithsonian. Since he is not an employee, he might not even be protected by the OSC.

Who can be protected by the OSC from prohibited personnel practices?

General. OSC has jurisdiction over prohibited personnel practices committed against most employees or applicants for employment in Executive Branch agencies and the Government Printing Office.

Sponge relationships

| 1 Comment
Spongebob!

Sponges have been in the news lately, so how could I resist writing about a recent paper on sponge relationships? Sponges (phylum Porifera) are found in three classes: the Demospongia, the Calcarea, and the Hexactinellida, all of which are quite ancient with forms identified from the Cambrian. Fossil sponges can be identified by the arrangement of their skeletons, which consist of collections of spicules with characteristic shapes and chemical constitutions. Spicules of various sizes are organized into an interlocking meshwork that generates the supporting framework of the animal. Two characteristics of the spicules that are used to classify them are 1) shape, in particular the angle that the rays diverge from one another, and 2) the chemical structure, whether they are based on calcium or on silicon.

  • Demospongia. Spicules are siliceous, with a triradiate symmetry—the spicule rays typically diverge at 60° or 120°. Individual spicules may look like a caltrop, with points to the corners of an imaginary tetrahedron.
  • Calcarea. Spicules are made of calcite, with a triradiate or tuning fork shape.
  • Hexactinellida. Spicules are siliceous, with a hexactine or tetraradiate symmetry—the spicule rays diverge at 90° angles. Picture a child's set of jacks clustered together.

Our understanding of the relationships between these three, however, has been getting juggled about. My copy of Clarkson's Invertebrate Palaeontology and Evolution, for instance, groups the Demospongia with the Calcarea in the subphylum Gelatinosa on the basis of the organization of the soft tissues and spicule shape, and sets the Hexactinellida apart in the subphylum Nuda, while admitting that there are complications that make the groupings prone to radical revision. One alternative is to group them by whether their spicules are made of calcareous or silicaceous, which would mean that the Hexactinellida and Demospongia are sister lineages, with the Calcarea the odd man out.

Bitting and Butterfield are attempting to resolve these relationships by examining a Cambrian sponge, Eiffelia globosa. Eiffelia is a member of a somewhat problematic group of sponges called the heteractinids which have been classified in the Calcarea because they have spicules made of calcium carbonate, and hexaradiate spicules that are at least close in shape to those of calcareans. What the authors suggest, though, is that Eiffelia is actually a good transitional form that also has tetraradiate spicules and two mineralogically distinct layers to their spicules that may represent both a calcareous core and a silicaceous outer rind.

Continue reading "Sponge relationships" (on Pharyngula)

The best creationism website ever

| 33 Comments

Check out Darwinsucks.com:

Welcome to Darwin Sucks Where we fish for the truth on the theory of evolution

Before you visit, make sure you:

  • Turn up your speakers
  • Read a bit about the bacterial flagellum
  • Remember, the theory of relativity is just a theory
  • Ponder the fact that the earth-sun distance varies about 3.4% within a single year. How many million miles this represents will be left as an exercise for the reader

An important story on the front page of Tuesday’s New York Times Science section documents the widespread phenomenon of teacher self-censorship – teachers avoid the “E-word” because of pressure from parents or administrators. The story is by Cornelia Dean. Here is the story: “Evolution Takes a Back Seat in U.S. Classes.” See discussion/commentary at NCSE News, Jason Rosenhouse’s EvolutionBlog, Pharyngula, and Chris Mooney’s blog.

But, the most entertaining comments were over at the Discovery Institute’s Media Complaints Division. See especially the bit about “the local amateur hour”:

Irony of the Month

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From the Thomas More Law Center, which is defending Dover, PA’s inclusion of intelligent design in biology class:

According to Richard Thompson, President and Chief Counsel for the Law Center, “It’s a common tactic for the ACLU to pile-on plaintiffs to give the impression that more people support their position than actually do. In this case, a recent poll of Dover residents shows that a majority support the school district.”

Christian Wire Service: Court Asked to Dismiss Several Plaintiffs From Evolution Lawsuit

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