James F. Crow died peacefully in his sleep in Madison, Wisconsin on January 4^th at the age of 95, having nearly reached his 96^th birthday. Jim, as everyone who knew him called him, was one of the most important population geneticists of the 20^th century, a major figure in the generation that followed Fisher, Wright, and Haldane.

Jim Crow in Mishima, Japan, 1972               Crow and Kimura in discussion, Mishima railroad station, 1972            photos by J.F.

His father was a cytogeneticist who did graduate work soon after the rediscovery of Mendel’s work. Jim did his graduate work in the 1930s at the University of Texas, where he had gone in hopes of working with H. J. Muller (who had, however, already left). He later had opportunities to work with Muller, and always considered himself primarily influenced by Muller. After working at Dartmouth College during and after World War II, he moved to the University of Wisconsin - Madison, where he spent the rest of his career. His many honors included election to the National Academy of Sciences and the Darwin Medal of the Royal Society.

He was famous as a teacher and mentor of numerous population geneticists, of whom I am one. In the 1950s he started traveling to Japan; he had many Japanese collaborators and students. Motoo Kimura was his Ph.D. student, and began a longtime collaboration with him. In 1970 they published An Introduction to Population Genetics Theory, which became the standard textbook of that field. Jim’s plain and folksy speaking style was the same as his writing style – he was enormously prolific and famous for his clear exposition. Among its many effects on the field, the book popularized Gustave Malécot’s way of defining inbreeding coefficients and using them to compute covariances among relatives for quantitative characters.

Jim’s many papers included major work on mutational load and other forms of genetic load, clarification of the concepts of inbreeding and variance effective population number, and expanding on R. A. Fisher’s and H. J. Muller’s theory of the evolutionary advantage of recombination. In the 1950s and early 1960s he was a major participant in the debate over genetic variation in natural populations, arguing against Theodosius Dobzhansky’s view that attributed it largely to balancing selection. With Motoo Kimura, in 1964 he derived the expected heterozygosity brought about by neutral mutation, and he played a major role in assisting Motoo Kimura in effectively presenting his case for neutral mutation. He helped bring Sewall Wright to Madison in 1955, and Jim and Ann Crow were important as friends during Wright’s later years.

In addition to these he contributed numerous insights in his many papers. He was interested in all of genetics, and read its literature widely. As an invariably polite, surprisingly modest, and easily approachable mentor who was always interested in clarifying and simplifying models, he had a great effect. Through his lab passed much of a generation of theoretically-inclined population geneticists. If your name was Morton, Kimura, Maruyama, Hiraizumi, Kerr, Sandler, Hartl, Langley, Gillespie, Ewens, Li, Nagylaki, Aoki, Lande, Bull, Gimelfarb, Kondrashov, Phillips, or Wu, you were among the many who were in Jim’s debt, and remember him warmly as friend and role model.

Photograph by David Young.

Nymph Lake – the lake is a short hike above Bear Lake. The water lily is (I presume) Nymphaea polysepala. And welcome back to Reed, who (I also presume) is happily ensconced in Arizona.

The blog 11 Points has a hilarious look at the creationist textbook Science 4 For Christian Schools.

I’m moving to Arizona tomorrow to start my faculty position at ASU. The main PT server will be taken offline during that time.

We will move most of this site to a backup machine during the move, but comments will be offline until further notice.

Do not send me any notices about stuff being broken. I expect that many features will not work over the next week or so.

A couple of years ago the late Lynn Margulis generated a flap in the Proceedings of the National Academy of Sciences by shepherding a paper through PNAS’s editorial process that advocated the notion that butterflies are the result of an ancient symbiotic relationship between “worm-like and winged ancestors.”

I was reminded of that flap the other day while I was reading Alfred Russel Wallace’s autobiography. Wallace mentions an 1872 talk he gave to the Entomological Society in which he described Herbert Spencer’s hypothesis that segmented insects are the result of an aggregation of once-separate ancestors:

In 1872, in my presidential address to the Entomological Society, I endeavoured to expound Herbert Spencer’s theory of the origin of insects, on the view that they are fundamentally compound animals, each segment representing one of the original independent organisms. (Volume II, Chapter XXVI, unpaginated in my Nook version)

The reference is to Spencer’s The Principles of Biology, Volume II, Chapter IV, where the proposal is developed on pp 93ff. The link is to Spencer’s 1899 revision of the 1867 first edition; Wallace would have used the 1867 edition as the basis for his talk.

So the preacher in Ecclesiastes was right: there’s nothing new under the sun.

By James DeGregori and Michael Antolin

The journal Evolution: Education and Outreach (EVOO) had dedicated the December issue to evolutionary medicine, with articles on how evolutionary theories are critical for understanding human disease and why thorough classroom instruction in evolution is essential. The publisher Springer has made the journal freely available through the end of December. Many of the articles are written for a broad audience and should be of interest to specialists and non-specialists alike.

The special issue was edited by Kristin Jenkins of the National Evolutionary Synthesis Center and Michael Antolin of Colorado State University, and in part follows a symposium organized for the 2011 annual meetings of the Society of the Study of Evolution held June 19 in Norman, Oklahoma. The purpose of that symposium broadly overlaps the EVOO special issue: to make biologists who teach evolution at every level from secondary school to medical school aware of how much biomedical science gains from understanding human evolution and our continued vulnerability to disease. An additional goal is to increase understanding and acceptance of evolutionary science in biomedical research and to help doctors become better practitioners.

LEO Weekly, an alternative weekly published in Louisville, Kentucky, reports that fundraising for the Ark Park has gone virtually nowhere since last May. Groundbreaking, if it was ever planned at all, has been postponed and postponed and postponed until next spring at the earliest.

LEO Weekly reports that the Ark Park has raised only about $1 million since last May and has raised a total of $4 million altogether. Its goal is to raise approximately $25 million. A representative of the Ark Park says, “Funding is progressing, a little slower [sic] due to the very slow economy.” He says further that they are 3-4 months behind schedule and adds, “We are considering a few options to help speed up the construction and possibly open to guests earlier than our original schedule. Once we have more information developed I’ll update you – probably by the first of the year.” LEO Weekly estimates that at the present rate groundbreaking might be scheduled for 2024.

My own estimate is that their timescale is skewed by their belief that the Earth is around 5000 years old. It is in fact more like 5 billion years old. Thus, if we take 3-4 months and multiply it by the ratio of 5 billion years to 5000 years, we estimate that the groundbreaking ceremony will take place in 3 million months, or 250,000 years.

Anyone who wonders where the money may be going in the meantime might consider the review by a volunteer named Roxy, posted at Charity Navigator. Additionally, comments to the LEO article claim that the Ark Park itself is a for-profit venture, but the Ark Encounter Website is not completely clear (to me, at least), and I cannot independently verify the claims. I cannot, however, find Ark Encounter in IRS Publication 78 .

A favorite creationist mantra these days, and one you especially hear from young earthers, is that creationists and scientists both have the same facts, they just look at them differently. To laypeople that may sound reasonable. The handful of guys at Answers in Genesis look at the Grand Canyon and say it was formed by a flood about 4400 years ago when God got all pissed off at humans. The 24,000 members of the Geological Society of America (and virtually every member of the literally dozens of geological organizations listed at their web site*) look at the Grand Canyon and say it was formed over millions of years by natural processes that continue today.

Same facts; different conclusions. Some of us laypeople often hear these two positions and see them as equally valid positions on either side of a debate. But some of us scratch the surface, and it doesn’t take a very deep scratch to see a significant difference. Scientists do science and creationists don’t.

As mentioned, I have a couple of pro-ID books that need to be read and reviewed these holidays: Signature in the Cell: DNA and the Evidence for Intelligent Design by Stephen C. Meyer, and Intelligent Design Uncensored by William Dembski and Jonathan Witt. While I’ve done preliminary readings of both books, in order to grasp their overall structure and scope, I recently started reading the latter in a greater level of detail.

What I’ve found has not been pretty.

Yes, Intelligent Design Uncensored is not a very healthy book to read, if you get angry at slick rhetoric in place of rigorous argumentation, blatant strawman arguments, and an easily digestible style of writing that doesn’t at all match with the supposed gravity of the topic at hand. Unfortunately, those are some of the things that push my buttons, so I’m not a happy little “Darwinist”. No sir.

In fact, it has been so infuriating so far that I’m seriously considering not doing a proper review of it: it may not be worth my time nor my effort. Meyer’s Signature is a much more worthy target - it’s held up by the ID community as some shiny tome of pure knowledge, blessed to humanity from the heavens, whilst Dembski and Witt’s book is a barely-mentioned teaching tool for prospective members.

According to The New York Times, the United States government has asked the journals Science and Nature “not to publish details of certain biomedical experiments, for fear that the information could be used by terrorists to create deadly viruses and touch off epidemics.” The experiments involved the development of a lethal and highly transmissible form of the H5N1 avian flu virus, a virus that so far has been transmitted mostly from birds to humans, but not from humans to humans. The government fears that if certain details are published, then terrorists could get hold of them and manufacture viruses used for biological warfare.

Update, December 22: Carl Zimmer reports that Science has issued a statement along the lines of, “We haven’t made up our minds yet, but we may do so when you tell us how ‘responsible’ scientists can actually get hold of the data.” In the meantime, Science reports that the authors of the papers have “grudgingly” decided to “redact” their papers.

Quote mining is ubiquitous amongst the creationists, to the point that TalkOrigins maintains an extensive database of mined quotes. Now there’s a new candidate. Gary Hurd calls our attention to Rabbi Moshe Averick, who quotemines Jack Szostak, a prominent origin of life researcher (added in edit: and 2009 Nobel winner!).

What’s most fun is that Szostak’s wife, Terri-Lynn McCormick, shows up in the comments and calls Averick on his dishonesty. I’ll reproduce her whole comment here. It’s delicious!

How dare you misrepresent my husband. Your quote from the Scientific American article blatantly distorts his meaning. It is virtually impossible to imagine the cell we know now to emerging from the pre-biotic earth. He and others have, over many years, been showing incrementally how an RNA cell might have been created on early earth. There is nothing in my husband’s work that suggests otherwise. It is quite sickening that you would try to make him, a steadfast rationalist and atheist, into a propopent for I.D. You are in complete disagreement with Prof. Jack Szostak. Unfortunately for you his opinion is backed up by facts and mountains of results from peer reviewed research.

Please refrain from misrepresenting his opinions or work again. We consider it slander.

Nice!

Can you believe it’s been SIX YEARS since Judge Jones issued a devastating anti-“Intelligent Design” ruling?

Ah, the memories of Kitzmas past. Remember “Waterloo in Dover”? “Cdesign proponentsists.”? The “breathtaking inanity of the Board’s decision”?

Merry Kitzmas, everyone!

Humans have a unique form of complex communication called language. While some academics have argued that language is a purely cultural invention—Humans used their brilliant brains to reason that language was the best way to communicate.—there is ample evidence that language is a biological adaptation that evolved after our ancestors split from the ancestors of chimpanzees. For example, the face, mouth, and throat contain adaptations for the physical production of spoken language. Children acquire language through an innate ability, not using their higher reasoning skills. And regions of the brain have been shown to be critical locations for cognition specifically associated with language.

As a complex adaptation, there must be some genes underlying our language ability. However, the evolutionary dynamics of language-associated genes is poorly understood. Earlier this year, I published some research that I hope will help fill this gap. (I’ve been working on this research off and on for nearly 10 years.) The paper is entitled “Bards, Poets, and Cliques: Frequency-Dependent Selection and the Evolution of Language Genes” and appeared in the Bulletin of Mathematical Biology. The journal is offering free access this month, so you can download the paper for free.

As a complex adaptation, language did not miraculously evolve all at once. As the saying goes, natura non facit saltum (nature does not do “poof”). Likely the communication ability of our ancestors passed through several stages eventually producing moden language ability. Some well studied transitions are the origin of combinatoric language from holistic communication and the replacement of hand gestures with vocal communication.

Now imagine that you have a human population that contains two different language phenotypes. “Bards” have the ancestral phenotype, and “Poets” have a new phenotype that is potentially more efficient and fitter.—Two Poets interacting have a higher fitness than two Bards.—This increase in fitness can come from the ability of poets to confer more information to one another, communicate more accurately, or many other things. Note, we are talking about biological differences in language faculty, not cultural differences like whether Bards speak French and Poets speak Cajun.

Photograph by James Rice.

Photography contest, Honorable Mention

Underground lake, Chapat Cave, Belize. This lake is the home of cave-adapted fish, crabs, and other life. Scientists are interested in the hydrology of Chapat Cave, since it is known to flood as much as a hundred feet above the normal level shown here. The timing and cause of the floods is not yet known.

Here’s a new video from NCSE that features Genie Scott talking about the latest theme/tactic of creationists, “academic freedom” (for which one could substitute “academic anarchy” with no loss of meaning).

Hat tip to Greg Laden.

Intelligent design news, commentary and discussion from the 9^th of December to the 16^th of December, 2011.

It’s nearing Christmas, and here in Australia the weather is heating up, causing the ground to bake beneath our thong-covered feet - and a kind of cognitive dissonance sets in as the “White Christmas” imagery fed to us by popular culture and jolly old Christmas tunes conflicts with the harsh reality of Summer in December. Such is the Southern Hemisphere.

Of course I could, at this point, easily compare that tale with the cognitive dissonance present in the intelligent design movement as they wiggle around, both in cyberspace and in the real world, evading effective criticism and being ambiguous about many a topic. But I won’t.

That would be a bit forced, wouldn’t it?

No, I just wanted to let you all know about the wonderful Christmas we Australians will be having. Enjoy your Winter Wonderland, Northern Hemispherians: I’ll be cooking sausages, avoiding swarms of flying insects and trying my best not to get terribly sunburnt.

Anyway, this week we have blog posts about biomimetics, the potential predictive powers of Judaism/Christianity when it comes to the origin of humanity, using my words to pump money into the ID movement, and Richard Dawkins brainwashing poor, poor children.

As I noted in October, 2011, John Freshwater’s termination by the Mt. Vernon City Schools was appealed to the Knox County Court of Common Pleas. That court denied Freshwater’s request for additional hearings and ruled that “…there is clear and convincing evidence to support the Board of Education’s termination of Freshwater’s contract(s) for good and just cause,…”.

Subsequently, the Rutherford Institute announced that it would support Freshwater’s appeal of the Common Pleas Court’s decision to the Ohio 5^th District Court of Appeals. Now the brief supporting that appeal is available on NCSE’s site.

The brief purports to be from R. Kelly Hamilton, Freshwater’s lawyer, “in conjunction with The Rutherford Institute.” Having read way too much of Hamilton’s prose over the last three years, I’d say that Rutherford Institute staff wrote the brief and Hamilton’s main contribution was to sign it.

More below the fold

The superintendent of schools of Hart County, a small county in the middle of Kentucky, has written to the Kentucky Board of Education, complaining about the emphasis on evolution. Specifically, Ricky Line, the superintendent, writes in a long and somewhat rambling letter,