January 2012 Archives

Science Foundation Arizona is sponsoring a postdoctoral scholar program at Arizona State University that offers a really sweet deal:

Bisgrove Scholars will receive an annual stipend of $60,000, benefits and an additional $20,000 per year for research expenses. The Bisgrove appointment is renewable on a year-to-year basis for a maximum initial term of two years, contingent upon the availability of funds.

This program is only open to individuals who have no prior post-doctoral experience and obtain a PhD prior to appointment, i.e. doctoral students in their last year of studies. So while you may be now eating ramen every night in the lab while trying to finish up the last experiment you need to graduate, this time next year, you could be eating ramen sprinkled with gold dust and angel tears, while trying to finish up the last experiment you need for a grant proposal. (Did I mention that rent is cheap here?)

Another qualification is that your research has to fit with the Science Foundation Arizona’s mission: “Areas include, diagnosis and prevention of disease, sustainable energy and the environment, and information and communications technologies at the human interface.”

You will also need to specify possible mentors for your research project. (Hey, I’m available!)

For instructions on how to apply, see http://graduate.asu.edu/bisgrove.

Applications due Feb 15th.

Ark Park Still in Kentucky Budget


The governor of Kentucky plans budget cuts of $350 million over two years, including $50 million from public education and substantial cuts to higher education – but has managed to find $11 million to build an interchange to a phantasmical Ark Park, according to LEO Weekly, a Louisville alternative newspaper. Presumably the interchange, which will connect to a 1-mile road between Interstate 75 and a town of 3500, will go to roughly the same place as the Bridge to Nowhere or one of its brethren.

The governor, Steve Beshear, reportedly understands that his state “struggles due to the lack of an educated labor force” and admits that his proposed budget “is inadequate for the future needs of our people.” Maybe he should read a recent editorial in Science magazine and ponder whether the poor performance of US students in science and mathematics can be traced to politicians who cut education budgets and pander to anti-scientific crackpots.

Alces alces


Photograph by Arthur Rosen.


Alces alces – moose, Denali National Park, Alaska.



Press release: Genetic data expert to bolster ASU’s high-throughput DNA analytics

Unfortunately, they forgot to mention my collaborator, Prof. Steve Steve.

PS, we are still looking for a postdoc and students.


Nest of bushtitPsaltriparus minimus – Walden Ponds, Boulder, Colorado. The nest to the upper right may be an oriole’s nest. Identifications courtesy of Wild Bird Center, Boulder.

Do you know of any graduating or recently graduated baccalaurate students who are considering graduate school? Do they come from disadvantaged backgrounds or belong to underrepresented groups in biomedical sciences? If so, then ASU has a program built for them: ASU PREP.

PREP scholars spend 75% of their time working as technicians on a research project under the direction of an experienced ASU faculty mentor, in a laboratory with PhD graduate students and/or postdoctoral fellows. The program director and faculty advisory committee help scholars identify the research area and mentor that best matches the interests and goals of each scholar. Scholars receive a salary of $21,000 per year. Scholars participate in a one to two year program, dependent on each individualized development plan.

Applicants must be U.S. citizens or permanent residents that have completed their undergraduate degree from an accredited U.S. college or university within the last three years. Applicants must intend to apply to a Ph.D. graduate program within two years. Individuals who contribute to the diversity of the graduate student community and to the biomedical or behavioral sciences, at ASU and nationally, are strongly encouraged to apply.

Application deadline is March 30, 2012

See http://graduate.asu.edu/prep for full details and application instructions.

Freshwater: The main briefs in the appeal


Update: The Dennis family’s amicus brief is now up on NCSE.com.

The two main briefs in John Freshwater’s appeal of the Knox County Court of Common Pleas’ decision to uphold Freshwater’s termination by the Mt. Vernon Board of Education are now up on NCSE’s site. The two amicus briefs, from NCSE and the Dennis family, have not yet been accepted by the court. NCSE’s brief is on the site linked above; the Dennis’ brief is not yet available online, though I’ve read a copy.

I’ll briefly (!) summarize what I see as the core arguments of the briefs here, and go into more detail below the fold.

Freshwater’s appeal brief: Basically argues that (a) Freshwater only taught “alternative scientific theories”, (b) there are good pedagogical reasons to do so, and (c) he has free speech and academic freedom rights to do so. Also argues that the moves against Freshwater are motivated by religious animus, though it’s silent about specifically who feels that animus.

Board’s response brief: Argues that because student attendance is required and the public school has an interest in protecting itself against the consequences of illegal actions by teachers, Freshwater, as an agent and employee of the public school, does not have unfettered free speech or academic freedom rights. Also argues that the Common Pleas court did not abuse its discretion when it elected to not hold public hearings in view of the extensive record generated by the administrative hearing.

NCSE amicus brief: Puts Freshwater’s behavior in the context of the history of attempts to teach creationism in the public schools, and argues that his teaching was both pedagogically and scientifically unsound.

Dennis family brief: Reviews Freshwater’s impermissible injection of religion into his teaching, and disputes his de-emphasis of the Tesla coil incident, pointing out the inconsistencies in Freshwater’s stories about the incident.

The case is not yet scheduled for oral arguments. I’m told that Freshwater requested an expedited hearing, which I understand means that there will be no back-and-forth, no rebuttals and rejoinders, in the paperwork. What’s there now is what the appeals court will use to make its decision.

Some remarks and elaborations below the fold

My high school, Athens Academy in Athens, GA, is currently offering an Evolutionary Genetics course to 11th graders (16–17 year olds). They are mostly using an curriculum from the University of Georgia funded through a grant for K-12 evolutionary education development.


Take that creationists.

Sticklebacks, Manatees, and Creationists


The other night our local PBS station re-aired a NOVA two-hour special, What Darwin Never Knew. It was pretty cool stuff, and incidentally featured Sean Carroll of UW Madison. I mention that because I want to digress for a moment. I live in Madison and since July of 2009 have been organizing Madison Science Pub. Every month I invite a different UW science professor to come to Brocach Irish Pub on the downtown square and talk about their field to a very interested, attentive, and inquisitive audience. I have an open invitation to Dr. Carroll to come talk, but he always seems to be too busy or something. Yes, yes, I know he runs a lab, and is Vice President for Science Education at the Howard Hughes Medical Institute, teaches, publishes, has a family, etc., etc., but come on, Sean… free beer! There. I’ve said my piece, back to the matter at hand.

The Cartwright Lab at Arizona State University is seeking Postdoctoral Research Associates in the area of Computational Evolutionary Genetics (broadly defined). The Cartwright Lab is part of The Center for Evolutionary Medicine and Informatics (CEMI), one of 10 research centers in the Arizona State University’s Biodesign Institute.

Research in the Cartwright Lab covers many different questions in population genetics and molecular evolution, at the interface of biology, statistics, and computer science. A majority of our research involves developing, implementing, and applying novel methodologies to study genomic datasets. Potential research topics for postdoctoral research associates include

  • The study of mutation patterns between human families and across species, using data from next-generation sequencing. This includes both indel and point-mutation patterns.
  • Models of frequency-dependent selection, with applications to genomic data.
  • New methods for alignment and phylogeny reconstruction that take into account the uncertainty of genomic data.
  • New methods for simulating homologous sequences that can be optimized to mimic natural datasets.

For more information see http://scit.us/ or http://labs.biodesign.asu.edu/cartwright/.

To apply, forward one document that includes a cover letter, detailed CV, and 3 references to [Enable javascript to see this email address.]. Please put the job title in the subject line of the letter. The initial closing date is January 31, 2012, Applications will continue to be accepted and considered until the job is filled/closed. A background check is required for employment. ASU is an EO/AA employer and is committed to excellence through diversity.

See full ad at http://www.biodesign.asu.edu/jobs/p[…]-12-15-11-54

Contact Dr. Cartwright at [Enable javascript to see this email address.] or 480-965-9949 for more information.

Photograph by David Young.

Darwin Day Is February 12


Charles Darwin in 1816. Detail of a painting by Ellen Sharples. Public domain.

And the Center for Inquiry provides a short list of resources for campus organizations or anyone else who wants to sponsor an event. In particular, you may contact their speakers bureau to find speakers on evolution, creationism, and intelligent-design creationism (it is a complete mystery why hardly anyone from Panda’s Thumb is on that list, but we will not go into that now). Additionally, Center for Inquiry directs you to the International Darwin Day Foundation, where you may find a list of activities near you, and, of course, the National Center for Science Education.

CFI recommends that you try to teach someone about evolution or other scientific principles and notes that the Public Broadcasting System has a wealth of material on evolution, science, and Darwin. The Understanding Evolution Web page is likewise an excellent resource.

Finally, not mentioned by CFI, the Clergy Letter Project lists 400-odd religious congregations that plan Evolution Weekend activities, February 10-12. Indeed, it may be of interest to some that Science can help church keep its young folk.

Freshwater: Appeal documents flowing in


As I reported a month ago, the Rutherford Institute, acting on behalf of John Freshwater, appealed Judge Otho Eyster’s decision in the Court of Common Pleas to the Ohio 5th District Court of Appeals. Eyster ruled that the Mt. Vernon Board of Education’s termination of Freshwater was justified on the evidence of the administrative hearing.

Now additional documents are becoming available. The first to be publicly available is NCSE’s amicus brief (pdf). Yet to come are an amicus brief being filed by the Dennis family and the school board’s brief. The deadline for filing is today, January 13, and I expect that final copies will be publicly available soon. When they are I’ll write a longer post summarizing them after I have a chance to read them all.

The case is not yet scheduled for oral arguments before the Court of Appeals. The Court’s schedule is published through February, 2012.

Upcoming television series on PBS: Inside Nature’s Giants, begins January 18th at 10 PM.

Professor Joy Reidenberg is an unlikely TV star. She’s a comparative anatomist with the Mount Sinai School of Medicine in New York. Physically, she is diminutive, dark-haired and dark-eyed, and not the sort of slender sylph in morphotype that TV producers seem to favor. But Joy has deep anatomical knowledge and a gift for communicating what she knows, and that led the producers of the documentary series, “Inside Nature’s Giants”, to feature Joy in their program.

(Originally posted at Austringer)

James F. Crow 1916 - 2012


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

CrowMishima72.JPG CrowKimura72g.JPG

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

His father was a cytologist 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 as a Foreign Member 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, 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 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, Rocky Mtn Natl Park.jpg

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.

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