This morning the Kansas State Board of Education is all shook up.

Last year the board voted 6-4 for much-criticised, creationism-friendly science education standards. Yesterday the primaries for the board elections took place, and on balance, the science-standards bloc lost two seats to Republic opponents. So it looks as if the balance is going to shift to 4-6, and the standards are going to go down.

The vote is all the more notable for the fact that the primaries saw a big media campaign carried out by the Discovery Institute, the main organization pushing intelligent design (a k a “the progeny of creationism”).

During the campaign, the Discovery Institute claimed over and over again that they were not actually promoting the teaching of Intelligent Design. They were simply supporting the Board’s call for the “critical analysis” of evolution. But how are teachers supposed to teach “critical analysis” according to the Board? One way is to dredge up the red herrings and other fallacious arguments that have been repeatedly invoked by creationists in the past. Another way is to consider “alternatives” to evolution, such as–surprise–intelligent design. So, despite their protestations, yesterday’s elections represent a political loss for the Discovery Institute. And, as Panda’s Thumb notes, this is the latest in a series of disappointments for them, from the polls to the courthouse.

I haven’t yet seen a reaction from Intelligent Design advocates to the new defeat. But in the past, advocates of intelligent design have brushed off their defeats as irrelevant. Apparently, despite all their press releases, op-ed columns, radio ads, court testimony, and cable news appearances, it’s all about the science.

In December, when parents in Dover, Pennsylvania, got intelligent design ejected from science classes, the lawyer for the school board scoffed to the New York Times:

“A thousand opinions by a court that a particular scientific theory is invalid will not make that scientific theory invalid,” said Mr. Thompson, the president and chief counsel of the Thomas More Law Center, a public interest firm in Ann Arbor, Mich., that says it promotes Christian values. “It is going to be up to the scientists who are going to continue to do research in their labs that will ultimately determine that.”

William Dembski, now of the Southwestern Baptist Theological seminary told the reporter, “I think the big lesson is, let’s go to work and really develop this theory and not try to win this in the court of public opinion…The burden is on us to produce.”

Those remarks came nine months ago. How has it been going in those labs?

Have these unnamed scientists been publishing a stream of papers in peer-reviewed biology journals in which they test hypotheses based on intelligent design, in which intelligent design is shown to provide a superior understanding of the world compared to other theories?

Medline, one of the world’s biggest medical and biological literature databases, reveals that the answer is no. Search for papers (not news reports) with the phrase “intelligent design,” and you get zip. Try other phrases–”Discovery Institute,” “irreducible complexity,”–and again, nothing. Try the names of Ph.D.s at the Discovery Institute–Michael Behe, Jonathan Wells, for example–and once again, zip.

By the way, claiming on a web site that someone else’s paper about gene networks supports intelligent design does not count–especially if you studiously ignore the paper’s discussion of evolution and the complete absense of the phrase intelligent design from its pages.

To put this silence in perspective, I then searched the database for papers about evolution published since December, when the Dover trial ended. The result: 4298 papers.

I’m curious to see the inside of one of those intelligent design laboratories Thompson was talking about. They seem like quite the hopping places.

Update 12:15 pm: The ID reactions are arriving. Guess what–the standards don’t matter. (See Ed Brayton for more.)

The Washington Post has an article today called And the Evolutionary Beat Goes On . . .. It is based on some interviews with scientists who are documenting evidence of natural selection in humans. I won’t be surprised if it gets emailed hither and yon, but not for the text, which is based on stuff that’s been out for some months now. No, it’s got a slick animation with the following caption: “A morphing demonstration of human evolution shows the transformation from a small lemur, up the evolutionary ladder into a human: seen here as legendary evolutionary biologist Stephen Jay Gould.”

The article goes into all sorts of contortions to accommodate this movie. In the lead, it reads,

Stephen Jay Gould would have been pleased.

No, not about his mug shot at the endpoint of evolution in the illustration above, but about the growing evidence that evolution is not just real but is actually happening to human beings right now.

But the article ends on an entirely different note…

Come to think of it, the late Stephen Jay Gould might have been upset with the above illustration. Contrary to the popular imagination, evolution is not a linear process that culminates in the triumphal ascent of humans at the top of the genetic heap. The process is analogous to a bush, where twigs and leaves push out in every direction.

So…the paper is showing something that further promotes a popular misconception about evolution–the evolutionary ladder. Nice job, folks.

In fact, of course, the movie is even more misleading. Stephen Jay Gould did not evolve from a chimpanzee, let alone a lemur. Nor did you, dear reader. I am part English, so by the Washington Post’s logic, I could make a movie showing Prince Charles morphing into me.

So much computing power, so little enlightenment…

Update: Monday 2:15. The Loom gets results (sort of): Barbara King, an anthropologist at William and Mary, first brought this movie to my attention this morning. She sent an email complaint to the newspaper, and also brought this post to their attention. She got one email from the reporter, who claimed that the last three paragraphs of the article addressed her concerns. Then she got an email from the deputy news editor, who promised to change the caption to the movie. Now the caption reads,

A lighthearted rendering of evolution imagines the transformation of a small lemur into a human in the person of legendary evolutionary biologist Steven Jay Gould.

A failure of a fix, if you ask me. A reader who is not familiar with the details of evolution will not understand why the movie is lighthearted. A reader who is will find the movie annoying in the way it gets evolution wrong. In a time when lots of people ask, “If monkeys evolved into people, why are there still monkeys?” this movie will just add to the misunderstanding, caption fix or not.

As I wrote in May, there have been some signs that scientists were gearing up to reconstruct the Neanderthal genome. Now it’s official, as Nicholas Wade reports in the NY Times. [link fixed] I’m particularly intrigued that the paleoanthropologists doing this work are teaming up with a hot little biotech company down the road from me in Branford, Connecticut called 454. They had a paper out recently showing how they can sequence DNA much faster than by conventional methods. Combine classic fossil work with the latest in genome sequencing, and voila…

Update, seconds later: Whoops, forgot to mention that 454 has set up a very nice page on the project, with fact sheets and papers.

As I browsed the new papers published this week in the Proceedings of the National Academy of Sciences, I was brought up short by this frolicsome picture. It’s a nice example of the visual display of information done right. It shows the spread of primates 55 million years ago across the Northern Hemisphere. I’m always game to learn about what primates were up to in Wyoming and Greenland. But this picture–and the paper that goes with it–have an extra value. They offer some clues to what sort of world we may be creating by pumping billions of tons of carbon dioxide into the atmosphere.

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If our genes are wired like circuits, does that mean nature is an electrician?

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Randy Olson visited the Loom a few months ago in connection with his movie about our national fun and games with evolution and intelligent design, Flock of Dodos. He provoked a lot of discussion with his main point, that biologists were doing a poor job of reaching out to the public. Some skeptics wondered whether accepting Olson’s argument would lead to dumbing science down and engaging in the same bogus PR as creationists. This morning Randy dropped me an email note to point out what he considers a depressing confirmation of his thesis.

Kansas–where the science standards have been softened up for the supernatural and are now considered the worst in the nation–is getting ready for their primaries in August. To support the board members who rewrote the standards, the Discovery Institute–which promotes Intelligent Design, a k a “the progeny of creationism”–has rolled out a big campaign, “Stand Up for Science, Stand Up for Kansas.” They’re all over the place in Kansas, apparently, with ads, meetings, and other activities. This all must cost some serious coin.

Olson, a Kansas-born biologist himself, has found that the local candidates and organizations opposing the science-softening board members have been left on their own:

They are receiving NO SUPPORT from outside organizations. In spite of all the bellyaching and agonizing of the national science organizations from AAAS to the National Academy of Science, not one dollar is coming into the state to support the Kansas Education Alliance which is the main grassroots group assembled to fight the attack on evolution

I’m wondering if other readers from Kansas would agree with this description of the situation. I’m also curious to get reactions from skeptics who thought Olson was off base. If his report is accurate, then it would seem to be exactly the sort of problem he’s been trying to get people to deal with all along.

It was eight years ago that some computer programmers got together and issued a manifesto for something they called open source software. Conventional software development–kept hidden behind walls of intellectual property, copyright, and secrecy–was clumsy and slow. It would be far better, the open source advocates declared, to make software open to all. It would foster the growth of a vast decentralized community of developers and consumers who could work together to create better software together. Individuals would grab software created by others, tinker with it, and then make it available in turn to the community for more testing and tinkering.

The open source movement may not have taken over the world yet, but it certainly has thrived. Take a look at the web site for the eighth annual Open Source Convention. Along with a vast range of talks about everything from Perl to seventeenth-century censorship, you may notice the big corporations such as IBM that are sponsoring the event. Corporate fear of the open source movement seems to be shifting to acceptance, if not enthusiasm. Another sign of the open source movement’s health is its influence beyond the world of software development, from mash-ups to Wikipedia to open source as a force for democracy to open-source biology.

Its success has drawn curious minds back to the origins of the open source movement. In a sense, people were thinking about it long before it had a name. Eric Raymond, one of the founders of the official open source movement, puts its origins four decades ago, in the hacker culture of the 1960s. Back then it was expected that each hacker would share his secrets with the rest of the hacker tribe.

I’d suggest that Raymond is not be thinking big enough. The open source movement is a wee bit older. Instead of four decades, try four billion years.

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A good article on the importances of big animals helps put the new dodo fossil discoveries in some ecological context. If you can’t bring dodos back, at least bring in the giant tortoises!

I just want to make one thing clear. When Ann Coulter talks about her Giant Raccoon Flatulence Theory, she’s talking about me. Don’t let anyone else tell you that they are a giant flatulent raccoon. They’re all just a bunch of wannabes. For I am the One True Giant Flatulent Raccoon.

Allow me to explain…

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In today’s New York Times I have an article about the discovery of a vast graveyard of dodo fossils. The fossils date back an estimated 3,000 years. Dodo fossils are exquisitely rare, and so it’s quite something to find an entire assemblage of them. But as the leader of the expedition that found them told me, that discovery alone would have been scientifically unimportant. What matters is the entire package. The scientists found fossils of lots of other animals and plants. It wasn’t just the dodo that went extinct on the island of Mauritius. It was an entire ecosystem, and these fossils may help scientists understand how that ecosystem lived and breathed. Along with the article, I also talk about the discovery on the Science Times podcast this week (I come in at 8:40). And if you need more things dodo, check out the expedition blog.

Last night I took the ferry across Long Island Sound to spend the day in Stony Brook at Evolution 2006, the joint annual meeting of American Society of Naturalists, the Society for the Study of Evolution, and the Society of Systematic Biologists. About 1500 scientists were there, and there were enough talks going on–often simultaneously–to keep me in constant motion from eight in the morning till eleven at night.

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Two hundred thousand years ago or thereabouts, an African lion killed someone. Along with a meal, the big cat got a wicked stomachache. Today a record of that unfortunate death still survives, in the bacteria that make big cats sick.

The trail of this strange story starts in the 1980s, when scientists discovered that ulcers are caused by bacteria known as known as Helicobacter pylori. H. pylori is found in people around the world, and scientists learned how to recognize the different strains they carried. Based on the patterns of the strains, a team of scientists concluded in 2003 that Helicobacter pylori must have been present early in the history of our species, and was spread across the world during the migration of humans. (I wrote a long post on H. pylori and human evolution when the scientists who discovered its link to ulcers got the Nobel Prize.)

But there were skeptics.

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