June 2013 Archives

Under the heading Creationism Follies, Heather L. Weaver, an ACLU staffer, recalls the infamous fourth-grade science quiz that we described here on May 1. Being an ACLU staffer, Weaver notes that “religious schools are well within their First Amendment rights to indoctrinate students in this manner.” Not being an ACLU staffer, I note that they may have a legal right to teach students any kind of garbage that they like, but they have no intellectual right to do so, and schools that teach creationism as if it were truly science should lose their accreditation. Indeed, recent court decisions have upheld the University of California’s right to require remedial courses for students who have been miseducated at religious high schools.

But what about the public schools? Weaver outlines what she calls “just a few examples of creationism advocates working their influence in the public schools during the 2012-2013 school year”:

Things To Do This Weekend


zacknote.jpg As a public service, here are a few suggestions on how to entertain yourself this weekend, and support science education at the same time! If you are in the New Mexico area, come out the the annual meeting of the Coalition for Excellence in Science and Math Education (CESE), which is hosting Louisiana’s spunky young Zack Kopplin (now a student at Rice in Houston). Time: 1:00 PM Saturday, June 29th. Place: Room 122, Northrop Hall, on the UNM campus. There is a map and a flyer. Zack’s topic is “Why we need a Second Giant Leap.”

Secondly, you can act on Genie Scott’s suggestion to support the excellent indie film “The Revisionaries” by voting for it at the PBS website. Genie writes “I know which one I’m voting for: The Revisionaries – the film about Don McLeroy and the Texas Board of Education. I give it 5 stars. It’s so well done and deserves to win.” Vote here.

Finally, here’s a petition at the White House to Ban Creationism and Intelligent Design in the science classroom as federal law. As my cousin wrote me offline, there’s a fat chance such a law will ever pass, but if the petition gets 100,000 signatures, Obama will have to publically address the request.It’s about a third of the way there, but the July 15th deadline looms. If you’re so inclined, add your voice to the petition here

Luskin’s Hopeless Monster


I’m checking in from the airport on the way back from Evolution 2013. For me, highlights of the meeting included presenting my BioGeoBEARS R package and some Ph.D. results at the Ernst Mayr Symposium, hearing about all the cool things going at NIMBioS, anticipating and thus having a seat in the room while observing the Felsenstein Effect, and meeting Jerry Coyne in person for the first time, and having a friendly conversation rather than an argument. (What will our respective readers think of us? We have reputations to uphold!)

Padian on getting evolution right in textbooks


Open access in Evolution: Outreach and Education. The abstract:

Topics related to evolution tend to generate a disproportionate amount of misunderstanding in traditional textbooks, other educational materials, and the media. This is not necessarily the fault of textbook and popular writers: many of these concepts are confusingly discussed in the scientific literature. However, faults can be corrected, and doing so makes it easier to explain related concepts. Three general areas are treated here: ideas and language about evolution, historical and philosophical aspects of evolution, and natural selection and related concepts. The aim of this paper is to produce a template for a more logical, historically and scientifically correct treatment of evolutionary terms and concepts.

It’s a valuable resource not only for textbooks but for science writers and journalists.

Hat tip to NCSE on Facebook

Pandion haliaetus


Photograph by Paul Burnett.

Photography contest, Honorable Mention.


Pandion haliaetus – osprey.

Postdoc Positions Available

The Cartwright Lab at Arizona State University is hiring a postdoc in bioinformatics. The Zufall Lab at the University of Houston is hiring a postdoc in microbiology. Both postdocs are to work on an NIH-funded project to study mutation accumulation lines in Tetrahymena. The Azevedo Lab at UH is also involved in the project.

For a full description of the openings, read this post.

Note: I am extremely busy this summer, finishing grad school and moving to a postdoc. But when I got this book, I realized I wouldn’t be able to focus on my real work without having gotten my 2 cents in. This is a rough-and-ready piece, so typos and missing references, and missing explanations of technical terms are to be expected, although I’m sure they can all be figured out with a wee bit of googling. I am off to Evolution 2013 tomorrow and will be incognito, writing, after that. So I may not comment much. However I expect commenters to be reasonable discussants and polite and will ban people who break the spirit of this expectation. Cheers, Nick

Review of Stephen C. Meyer’s Darwin’s Doubt: The Explosive Origin of Animal Life and the Case for Intelligent Design

This week, a new book came out by Stephen Meyer, Darwin’s Doubt: The Explosive Origin of Animal Life and the Case for Intelligent Design. Having followed the ID movement and specifically its arguments on the Cambrian ‘Explosion’ for a long time, as well being somewhat up on the recent literature, and especially on phylogenetics, I feel that I have a pretty good sense of what to look for in any work purporting to be a capable commentary on the topic. As I read through Meyer’s book, though, in case after case I see misunderstandings, superficial treatment of key issues which are devastating to his thesis once understood, and complete or near-complete omission of information that any non-expert reader would need to have to make an accurate assessment of Meyer’s arguments.

Don't you hate it when you get up in the morning and the first thing you read on the internet is the news that your entire career has been a waste of time, your whole field of study has collapsed, and you're going to have to rethink your entire future? Happens to me all the time. But then, I read the creationist news, so I've become desensitized to the whole idea of intellectual catastrophes.

Today's fresh demolition of the whole of evolutionary theory comes via Christian News, which reports on a paper in the journal Molecular Biology and Evolution which challenges the ape to human evolutionary theory. Wait, that's a journal I read regularly. What did I miss?

Rabidosa rabida


Photograph by Lou Shackleton.

Photography contest, Honorable Mention.


Rabidosa rabida – rabid wolf spider.

Announcement of Microbiologist Position at UHAnnouncement of Bioinformatics Position at ASU


The Cartwright Lab at Arizona State University (Tempe, AZ) and the Zufall and Azevedo Labs at the University of Houston (Houston, TX) are hiring two evolutionary genomics postdocs to work on an NIH-funded project to utilize the unusual nuclear architecture of ciliates to study the rate, types, and fitness effects of spontaneous mutation.

Ciliates are really, really cool beasties.

Unlike most eukaryotes, ciliates have two nuclei. That’s two nuclei in a single celled organism.

It gets cooler than that. One nucleus, the micronucleus, pretty much does nothing, sitting around and waiting for the ciliate to have sex. The other nucleus, the macronucleus, is a copy of the micronucleus and manages all the daily activity of the cell (i.e. transcription). During sex, the macronucleus disappears, and the micronucleus goes through meiosis creating haploid nuclei which get exchanged with another cell. This forms a new micronucleus from which a new macronucleus will be generated. This is why the micronucleus is considered the germline nucleus and the macronucleus the somatic nucleus.

It gets cooler than that. In Tetrahymena thermophila the micronucleus is diploid and has 10 chromosomes. The macronucleus is 45x and has over 20,000 chromosomes; during macronucleus development, the chromosomes basically shatter, duplicate, and reassemble a bunch of times. Like magic!

All this makes Tetrahymena thermophila a nearly perfect system in which to study spontaneous mutation. By maintaining Tt lines in asexual growth, mutations will accumulate in the germline nucleus without any selection operating on them. Thus at the end of 1,500 generations, we will be able to express these mutations and measure their phenotypes and impact on fitness.

For this project we are looking for a wet-lab postdoc to be based in the Zufall lab at UH and a dry-lab postdoc to be based in the Cartwright lab at ASU, but also working with the Azevedo lab at UH. The wet-lab postdoc will be primarily responsible for generating the mutation accumulation lines, while the dry-lab postdoc will be primarily responsible for identifying mutations from genomic data and analysing the phenotypic data. Full descriptions and instructions on applying are below.

But they also ruled that cDNA sequences may be patented. The argument is something like this: DNA is found in nature, hence not patentable. But cDNA, or DNA stripped of its introns, is not found in nature, hence potentially patentable. See Adam Liptak’s article in The New York Times.

The outcome means (or seems to mean) that Myriad Genetics will no longer have a monopoly on testing for the breast-cancer genes, BRCA-1 and -2. Liptak suggests that competition will now drive the cost of such tests down from the present price of around $3000. Myriad’s stock nevertheless had gone up at the time of Liptak’s report.

Photography contest, V

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Polish your lenses again (but not dry, please) – this post announces the fifth Panda’s Thumb photography contest. We encourage entries in a single, general category, which includes pictures of just about anything of scientific interest. If we get enough entries, consistently with the rules, we may award additional prizes, presuming, of course, that we can find more prizes.

We dedicate this contest to the memory of our colleague Mark Perakh. First prize will be a copy of his book Unintelligent Design.


4 x 5 film holder (2 exposures), Tri-X film (24 exposures), SD memory card (>1000 exposures).

The rules will be substantially the same as last year’s and will be posted in detail on Monday, July 8, at noon, Mountain Daylight Time (UTC - 6 h). We will accept entries from July 8 through 22, inclusive.

We will leave this post in place for one week.

Uca pugilator


Photograph by Peter Psyhos Burns.

Photography contest, Honorable Mention.


Uca pugilator – sand fiddler crab, Wellfleet, Massachusetts, July, 2003.

Atheist in a foxhole


I hope this is not too far off task, but two years ago, on June 4, 2011, at approximately 8 a.m., I took my wife to the emergency room. I did not bring her home again till November 18.

Grand Canyon


Photograph by Andrew Gould.

Photography contest, Honorable Mention.


Panoramic view of Grand Canyon, Arizona.

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