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Via The Finch & Pea

Bjørn Østman at Pleiotropy describes new research in Science that shows how duplicated genes can evolve to perform new functions. It presents

… a new model/mechanism by which duplicated genes can retain the selection pressure to not succumb to deleterious mutations. They call it the innovation-amplification-divergene model (IAD).

Basically,

IAD works like this: A gene initially has one function only (A). Then some genetic changes makes it also have a new function, b, which at first is not of too great importance. Then some environmental change favors the gene variants with the minor b-function (the innovation stage). This is then followed by duplication of the gene, such that there are now more than one copy that carries out A and b (the amplification stage). At this stage there is selection for more b, and at some point genetic changes in one of the copies results in a gene that is better at the new function, B. At this point, selection for the genes that do both A and b is relaxed, because the new gene (blue) carries out the new function. The original gene then loses the b function, and we are left with two distinct genes.

Michael Behe, of course, scoffs. Because the researchers did some manipulations that created conditions favorable to the evolution of the new function, Behe claims that

Needless to say, this ain’t how unaided nature works – unless nature is guiding events toward a goal.

Shucks. I guess every experimental manipulation ever performed has been an invalid method of studying some process. But as a PT crew member pointed out on the back channel, “this kind of shit happens all the time in nature.” See, for example, Gene duplication and the adaptive evolution of a classic genetic switch or Escape from adaptive conflict after duplication in an anthocyanin pathway gene.

According to the cartoonist Wiley, there were two Arks, and the one that carried the dinosaurs accidentally fell off the edge of the earth.

NECN.com reported today that

TOPEKA, Kan. (AP) – Carolyn Campbell lamented that she didn’t court enough voters in northeast Kansas in seeking her second term on the State Board of Education.

Her opponent, Jack Wu, was outspoken on teaching evolution and has ties to an anti-gay Topeka church notorious for picketing military members’ funerals. Campbell, a Democrat, worried GOP voters would simply follow Wu’s Republican party affiliation.

In the end, Campbell, a Topeka Democrat, received more than enough votes in Tuesday’s election, easily defeating Wu, according to unofficial results.

“I’m happy I have four more years to work for our children. That’s all I wanted to do,” Campbell said.

…

Wu, a Topeka computer programmer, made opposition to teaching evolution the centerpiece of his campaign. He described evolution as “Satanic lies” and said on a website that public schools were preparing students to be “liars, crooks, thieves, murderers, and perverts.”

Wu also raised eyebrows by saying that he was lured to Kansas from California in 2008 by Westboro Baptist. The Topeka church, led by the Rev. Fred Phelps Sr., is known internationally for picketing with anti-gay slogans and proclaiming that American soldiers’ deaths are God’s punishment for the nation’s tolerance of homosexuality. Wu is not formally a member, but he’s attended services regularly.

Here’s a bit more from Jack Wu’s own website:

My mission, in running for the Kansas State Board of Education, is to throw out the crap that teachers are feeding their students and replace it with healthy good for the soul knowledge from the holy scriptures.

Let’s be specific. Evolution should never be taught in public schools as science. Evolution is false science! God made the heaven and the earth and created humans from the dust of the earth! The very bad teachers that teach that men descended from apes via evolution need to have their teaching licenses revoked. Yes, students should be taught that God created everything.

Congratulations, Kansas!

Discuss.

Photograph by Kurt Andreas.

Photography contest, Honorable Mention.

Elateridae larva – click beetle, Glendale, New York, April 19, 2011.

Congratulations to Lou Jost, who has won both the Lab Rats and General categories, with his photographs, Orchids and Volcan Tungurahua.

On the theory that Mr. Jost does not need two copies of Among the Creationists: Dispatches from the Anti-Evolutionist Front Line, by Jason Rosenhouse, we declare James Kocher the third-place winner for his photograph Banded Iron Formation, in the Lab Rats category, and award Mr. Kocher the second copy of Mr. Rosenhouse’s book.

While the final decision hasn’t been written, the judge in the Coppedge v. Caltech and JPL case has made an order for a final ruling in JPL’s favor.

In his wrongful termination suit, Coppedge claimed he was demoted in 2009, then let go for engaging his co-workers in conversations about intelligent design and for handing out DVDs on the topic while at work. Intelligent design is the belief that life is too complex to have developed through evolution alone.

A press release we received from the Howard Hughes Medical Institute:

HHMI Premieres New Film Showcasing One of Science’s Greatest Detective Stories

Film to Debut at NABT Conference

The Howard Hughes Medical Institute will premiere, “The Day the Mesozoic Died,” a new film that chronicles one of science’s greatest detective stories, at this year’s National Association of Biology Teachers (NABT) conference.

The film retraces the extraordinary investigative work behind the stunning discovery that an asteroid struck the Earth 66 million years ago, triggering the mass extinction of dinosaurs and many other species of animals, plants and microorganisms. The Mesozoic Era, sometimes referred to as the Age of Reptiles, lasted from approximately 250-66 million years ago.

[You may see 3 short clips here.]

The Royal Society has made all its journals open access until November 29. I foresee an orgy of downloads!

Via Jerry Coyne’s blog

We received approximately 30 photographs from 14 photographers. Most of the pictures were excellent. We divided the entries into 2 categories, Lab Rats and General, though we had to fudge a little bit to populate both categories.

Choosing finalists was difficult. We considered what we thought were the scientific and pictorial qualities of the photographs, and also attempted to represent as many photographers and present as much variety as possible. The text was written by the photographers and lightly edited for consistency.

Here are the finalists in the Lab Rats category. Please look through them before voting for your favorite. You will have to be logged in to vote on the poll. We know it is possible to game these polls. Please be responsible and vote only once. If we think that the results are invalid, we will cancel the contest. The photos and poll are below the fold.

The winner in each category will receive an autographed copy of Among the Creationists, by Jason Rosenhouse, which received a very favorable review here. We are indebted to the author for his generosity in providing the books.

Acknowledgement: Reed Cartwright wrote the HTML code.

• 
  New species of orchids of the genus Teagueia, by Lou Jost—Volcan Tungurahua, Ecuador. The photographer and his students discovered a remarkable and completely unexpected evolutionary radiation of these plants, with up to 16 sympatric new species on a single mountain.
• 
  Two-headed Xenopus laevis tadpole generated by the injection of RNA encoding plakoglobin (g-catenin) into a fertilized egg, by Mike Klymkowsky. The melanocytes are contracted and extended pigment distributions in the two axes. More information.
• 
  Banded iron formation—Jasper Knob, Ishpeming, Michigan, Proterozoic eon, ~2.11 Ga, by James Kocher. Kodachrome 64, August, 1992.
• 
  E. coli by Ryan Kitko.—On the right, a test tube with Escherichia coli that appear green because they contain a plasmid to produce green fluorescent protein (GFP). The middle test tube contains the same bacteria but appears cloudy because it is missing the inducer arabinose. The left test tube is a control containing only growth medium.
• 
  Light bulb imploding inward, demonstrating that the pressure inside the bulb is less than atmospheric pressure, by Steve Switaj. Photograph was taken ~30 years ago on Kodacolor 100 with two flash units and an exposure of approximately 1/40,000 s.

As those who follow the Freshwater affair know, John Freshwater appealed his termination as an 8^th grade science teacher to the Ohio Supreme Court, filing a Memorandum in Support of Jurisdiction that induced the Court to accept his appeal, then a Merit Brief which laid out his argument for overturning the termination decision and which, not incidentally, made a different argument than that made in the Memorandum in Support; in effect, Freshwater pulled a bait and switch on the Court. The Board of Education filed a Memorandum in Response to Freshwater’s Merit Brief, and Freshwater has now filed a reply. I’ll describe some salient features of his reply below the fold.

Update, noon, October 28: Voting is now closed. We will post the finalists in the Lab Rats category on Monday, October 29, at noon Mountain Daylight Time. We will formally announce the winners on Sunday, November 4.

1000 apologies for taking so long, but here are the finalists of the 2012 photography contest. We received approximately 30 photographs from 14 photographers. Most of the pictures were excellent. We divided the entries into 2 categories, Lab Rats and General, though we had to fudge a little bit to populate both categories.

Choosing finalists was difficult. We considered what we thought were the scientific and pictorial qualities of the photographs, and also attempted to represent as many photographers and present as much variety as possible. The text was written by the photographers and lightly edited for consistency.

Here are the finalists in the General category. Please look through them before voting for your favorite. You will have to be logged in to vote on the poll. We know it is possible to game these polls. Please be responsible and vote only once. If we think that the results are invalid, we will cancel the contest. The poll may be found below the fold.

The winner in each category will receive an autographed copy of Among the Creationists, by Jason Rosenhouse, which received a very favorable review here. We are indebted to the author for his generosity in providing the books.

Acknowledgement. Reed Cartwright wrote all the HTML code.

An article in Friday’s Science magazine details how a team of scientists provided a calibration for carbon dating accurately to 50,000 years, or about 10 times the age of the earth according to many creationists.

Until now, carbon dating was accurate only to about 13,000 years, or the ages of the oldest trees. The Science article is fairly dense, but Science has provided a helpful Perspective, and Popular Science has a nice article as well.

It turns out that the concentration of ¹⁴C in the atmosphere varies from year to year, so calculations of the age of a specimen need to be corrected for this yearly variation; uncorrected calculations are not wrong, but they may be in error by hundreds of years. Until now, we have had no detailed record of the ¹⁴C concentration beyond the age of the oldest trees. Now, however, a team led by Christopher Bronk Ramsey of the University of Oxford has examined sediments in a Japanese lake and extended carbon dating to approximately 50,000 years. The lake was chosen because the bed of the lake is anoxic and its sediments are thought to have been stable and untouched by ice-age glaciers. The new calibration will be significant to archeology and studies of climate change. Read the 2 articles I have cited for more detail.

Not an earthshaking discovery, to be sure, but it shows how science progresses, step-by-step, while creationism merely stagnates.

Acknowledgment. Thanks to Rolf Manne of the University of Bergen, Norway, for alerting me to the importance of Bronk Ramsey’s article.

Afarensis, a blogger on (mostly) paleontology, has started a series of posts reviewing the Disco ‘Tute’s “Science and Human Origins.” Recall that Paul McBride also did a chapter by chapter review that hammered the book a few months ago.

It’s here. Not only does this journal have the highest rejection rate of any journal; it has no page charges. You may submit your manuscript with no anxiety, since you know it will be rejected. Unfortunately, as a colleague of mine has pointed out, if the paper is rejected immediately, you may not leave it on your resume for long; it would be better if they held your paper under review forever.

You may buy a T-shirt at their store: they claim that they will not reject your money.

Finally, if you submit a paper to a journal that will never publish it, have you created any information?

Thanks to John Scales of the Colorado School of Mines for the link.