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.

Photograph by Lou Shackleton.

Photography contest, Honorable Mention.

Rabidosa rabida – rabid wolf spider.

Announcement of Microbiologist Position at UH — Announcement 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.

Tetrahymena thermophila

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.

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.

Photograph by Peter Psyhos Burns.

Photography contest, Honorable Mention.

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

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.

Photograph by Andrew Gould.

Photography contest, Honorable Mention.

Panoramic view of Grand Canyon, Arizona.

According to NCSE’s scorecard, that is what happened to most of 10 anti-science bills introduced in state legislatures. Most of the bills used the now traditional “strengths and weaknesses” or “academic freedom” ploys, but some would have allowed “teachers to ‘intelligently explore’ controversies and help wayward students ‘develop critical thinking skills,’” as NCSE puts it. Four bills attacked climate change in addition to evolution. None of the bills was enacted into law. Unfortunately, a bill to repeal the “notorious” Louisiana Science Education Act also failed.

Three years ago I became a chimera. Again. I am also geneticist. Surprisingly, the two are unrelated.

As most PT readers probably know, the National Center for Science Education (NCSE) has added climate change education to the core issues it is concerned with. I was originally dubious of that move, feeling that the focus on evolution education was enough to handle without adding another issue on which there’s public/political debate, though (as is also the case with evolution) considerably less scientific debate.

I’ve come around, though, for a couple of reasons. One, of course, is the increasing trend on the part of anti-evolutionists to lump climate change in with evolution in their “controversial issues” and so-called “academic freedom” legislation. These are part of the more general anti-science movement that Kenneth Miller warned against in Only a Theory, and I share Miller’s apprehensions in that respect. I do not think Miller exaggerates the threat to science literacy and support in the U.S.

Mario Livio definitely does not pick on someone smaller than he. Indeed, when he decided to write about what he considers scientific blunders, he went after Darwin, Kelvin, Pauling, Hoyle, and Einstein.

The full title of his latest book is Brilliant Blunders: From Darwin to Einstein – Colossal Mistakes by Great Scientists That Changed Our Understanding of Life and the Universe, which is more of an abstract than a title. It would be incorrect to claim that Livio has not laid a glove on any of his subjects, but neither, it seems to me, are all of the errors “colossal.” Still, the book was well worth reading and contains excellent introductory material for those who are not experts in the subjects and even for those who are. The organization of the book is also interesting in that every chapter relates in some way to evolution, whether of life or the earth or the universe, and the transitions from scientist to scientist are relatively seamless.

Not stated is whether they manage to lose weight, nor whether they still get cavities or develop diabetes. But a recent article in Science shows that cockroaches evolved an aversion to glucose after glucose was used for a number of years as a poisoned bait. That is, the cockroaches developed an aversion to the bait rather than a resistance to the poison. The Science article is kind of written in Greek

In response to the anthropogenic assault of toxic baits, populations of the German cockroach have rapidly evolved an adaptive behavioral aversion to glucose (a phagostimulant component of baits).

but The New York Times has a nice summary and notes, almost as a throw-away, that the result might have application to diseases, such as malaria, that are spread by mosquitoes.

Memo to potential trolls: Yes, yes, we know—they are still cockroaches!!

Yesterday, I received a letter and a booklet from an organization called Day Star Research. The booklet was written by the president of Day Star, Fred Heeren, who writes, among other things,

Day Star Research is committed to

* Promoting healthy dialogue between the religious and non-religious.

* Fighting irrational extremism with rationality.…

* Encouraging Christians to reverse their reputation for anti-intellectualism, insensitivity, and judgmentalism.…

Photograph by Huajin Sun.

Grus japonensis – red-crowned crane. This photograph, which adorns the dust jacket of The World’s Rarest Birds, earned second prize in the “endangered or data-deficient” category of a worldwide photo contest. I will review the book briefly, below the fold.

Note added May 21, 11:00 a.m., MDT: You may see the contest winners here and the winners of a second contest here.

Angelina Jolie wrote about her decision to have a double mastectomy after learning that she carries a version of the BRCA1 gene with mutations that are significantly associated with developing breast cancer, speaking with her doctor, and considering the risks and benefits to herself, and for her family.

By ILA-boy

Many people have reacted, but I particularly like this response from Judith Soal that introduces the complexity of understanding the genetic component of diseases. We still have quite a lot to learn about the relationship between genes, environment, and disease, but we do know that some genetic mutations increase susceptibility to disease, but also that people without known genetic mutants are often affected by diseases due to environment, to novel mutations, or, by chance.  Moreover, rarely is the culprit of a disease a single gene. But, for now, we’ll leave this to others.

I want to focus on something else. Something that is relevant to every person. Something that both of these articles touch on.

The genome from a species of bladderwort (Utricularia gibba) was recently published. Ed Yong has a wonderful summary about the bladderwort genome paper and its relationship with current debates regarding what is functional (introduction to the ENCODE project). Here’s my accessible research introduction:

The bladderwort is a carnivorous plant with beautiful yellow flowers on top:

This is a captivating “horned bladderwort” (Utricularia cornuta), by Jacopo Werther

And curious “bladders” on its roots that it uses to trap its prey.

Those who know John Searle’s “Chinese Room” critique of the possibility of genuine consciousness in artificial/machine intelligences will enjoy this:

John Searle’s homunculus announces phased retirement

After 54 years of teaching at Berkeley, the man inside John Searle’s head has announced he will be entering a three-year phased retirement after the end of the current semester. The diminutive Zhu Tao made the announcement at a press conference Monday in a rare out-of-costume appearance.

At the conference Zhu said he is retiring from his current position in order to spend more time with Searle’s family. “I have become quite attached to these people,” Zhu said through a translator. “Although, admittedly, not being able to understand a word they say has limited the intimacy of our relationships.”

…

While he expressed sadness at the end of an era, Zhu looked back with pride at his time inside John Searle’s head. Zhu is popularly credited with sparking the shift away from brain-based cognition. Today that shift continues apace, with figures such as Andy Clark and David Chalmers outsourcing their thinking to call centers in India as part of a growing movement of philosophers who believe cognition can extend beyond the boundaries of one’s skull.