November 2011 Archives

On the web: science education and the presidential candidates


Jonathan Smith, VP of Florida Citizens for Science, will be interviewed by RadioExiles about teaching good science in schools, what is bad science, and the knowledge (or lack thereof) of the presidential candidates. The program “The seven day challenge” will be here at 11:30 am Eastern on Friday, December 2. It looks like the podcast will be available a bit later.

Tabanus subsimilis


Photograph by Richard Hughes.

Photography contest, Honorable Mention.

Hughes.Tabanus subsimilis - Striped Horse Fly.jpg

Tabanus subsimilis – striped horsefly, likely a male who landed there to drink juices from the surrounding berries, Jackson, Tennessee. For more images of bug eyes see[…]-close-ups/1

Evolution: Education and Outreach free in December


From the NCSE:

Evolution: Education and Outreach – the new journal aspiring to promote accurate understanding and comprehensive teaching of evolutionary theory for a wide audience – will be freely available through December 31, 2011, thanks to the generosity of its publisher, Springer.

Get ‘em while they’re hot!

Lynn Margulis dies


The eminent biologist Lynn Margulis has died at 73. Dr. Margulis is best known for promoting the theory, now generally accepted, that organelles such as the cell nucleus mitochondrion (I knew that!) and the chloroplast are the result of symbiosis between different species. You may read the Times obituary here.

Zea mays


Zea mays – maize, or Indian corn.

I have read the entirety of Hamza Andreas Tzortzis' paper, Embryology in the Qur'an: A scientific-linguistic analysis of chapter 23: With responses to historical, scientific & popular contentions, all 58 pages of it (although, admittedly, it does use very large print). It is quite possibly the most overwrought, absurdly contrived, pretentious expansion of feeble post hoc rationalizations I've ever read. As an exercise in agonizing data fitting, it's a masterpiece.

Here, let me give you the short version…and I do mean short. This is a paper that focuses with obsessive detail on all of two verses from the Quran. You heard me right: the entirety of the embryology in that book, the subject of this lengthy paper, is two goddamned sentences, once translated into English.

We created man from an essence of clay, then We placed him as a drop of fluid in a safe place. Then We made that drop of fluid into a clinging form, and then We made that form into a lump of flesh, and We made that lump into bones, and We clothed those bones with flesh, and later We made him into other forms. Glory be to God the best of creators.

Seriously, that's it. You have just mastered all of developmental biology, as taught by Mohammed.

Gobind Khorana 1922-2011


I just found out that Gobind Khorana died November 9 at his home in Concord MA. Khorana won the Nobel in 1968 (along with Nirenberg and Holley) for deciphering the genetic code. Before his work, nobody knew how a DNA sequence could “encode” the information necessary to make a protein macromolecule. His experiments were carried out in the classic bacterial system Escherichia coli. The realization that the genetic code in a single-celled bacterium is the exact same code used in humans is what finally convinced the biological community that all life, from trees to bacteria to elephants, shares common ancestry.

Khorana was also the first person to artificially synthesize a synthetic gene and use it to make a protein. It is not an exaggeration to say that these twin feats form the basis of all modern work on proteins.

Later, Khorana went on to use these techniques to investigate in detail the structure and mechanism of bacteriorhodopsin, which has to be one of the darn coolest proteins in the biosphere (full disclosure — I’m biased, since my lab now studies the evolution of bacteriorhodopsin). Photosynthesis evolved twice, with two very different mechanisms: plants use chlorophyll, and many bacteria use bacteriorhodopsin. While chlorophyll wins in terms of efficiency, bacteriorhodopsin is much simpler and more elegant.


Phalacrocorax carbo


Photograph by Marilyn Susek.

Photography contest, Honorable Mention


Phalacrocorax carbo – cormorant, dolomite stone quarry at Stainton, near Tickhill, S. Yorkshire, UK.

Oh no! It’s Granville Sewell again. At Uncommon Descent he has posted his 2nd law of thermodynamics argument against evolution, yet again. I have twice pointed out that (here and here) that, if true, it would prove that plants can’t grow.

Is Sewell’s argument unanswerable? No, because long before I made those posts, Sewell’s argument had been thoroughly demolished by Jason Rosenhouse and by Mark Perakh. Game over, even if you don’t know that plants can grow.

But Granville Sewell’s argument over at Uncommon Descent is unanswerable. At least there … because he has the comments turned off.

Morinda citrifolia

| 1 Comment

Morinda citrifolia – noni, Marquesas Islands, 2010. This picture is not an endorsement of noni juice.

Ford’s Theater National Historic Site has banned removed from sale Bill O’Reilly’s book on the Lincoln assassination from its bookstore because the book is not historically accurate. Can it be any worse than Grand Canyon: A Different View, which is still on sale at the Grand Canyon National Park Bookstore?

According to a group called Public Employees for Environmental Responsibility, the book has been moved to an apparently ad hoc Inspirational section of the bookstore, and the National Park Service has delayed issuing instructions on how to deal with creationist questions.

Is pseudoscience based on religion somehow privileged over pseudohistory? Apparently, yes.

Thanks to Walter Plywaski for the link to the Post article.

Illuminated Origin of Species


We just received the following letter from calligrapher Kelly Houle:

I am a natural history artist and calligrapher, and I’m creating a large-scale illuminated manuscript based on The Origin of Species. I’m looking for ideas and advice from biologists and evolution experts like you who might be willing to offer feedback on the scientific accuracy of my illustrations and possibly contribute to the project. I am designing each page as an individual work of art, writing out the entire text by hand and illuminating the realistic natural history illustrations with iridescent watercolors and 23-karat gold. The Illuminated Origin of Species will be nearly 300 pages, each measuring 22x30 inches, with over 500 illuminations. I would appreciate any constructive advice that will help make The Illuminated Origin of Species as good as it can be. Please contact me if you would be willing to serve as a science advisor for the project.

Gaythia Weis has just sent me the following announcement:

Associated Students of Aims Community College invite the public to a free program to discuss evolution

The public is invited to attend a discussion on the theory of evolution, led by Richard Bond, Ph.D. “Science, Theories, Stories: The Real Issue,” will be presented on Nov. 14 from noon to 1:30 p.m. in Ed Beaty Hall Theater on the Aims Community College Greeley campus. Bond is a former president of Morgan Community College and the University of Northern Colorado, where he holds President Emeritus status as well as Professor Emeritus of Zoology. He has also served three terms in the Colorado Legislature in addition to eight years on the Aims Board of Trustees. He also occasionally teaches adult education at First Congregational United Church of Christ.

Mt. Vernon: Creationists clobbered for BOE


Today voters in the Mt. Vernon, Ohio, City School District firmly rejected two creationist candidates for the Board of Education. The overt creationists, Jeff Cline and Steve Kelly, were among six candidates running for three slots on the 5-member board. Two incumbents, Margie Bennett and Jodi Goetzman, both of whom voted to terminate John Freshwater’s teaching contract, were also running. With all precincts reporting, these are the unofficial results from the county Board of Elections:

Goetzman: 4,296; Bennett: 3,973; Feasel: 3,704; Curry: 3,652; Cline: 2,963; Kelly: 2,541

Cline and Kelly, the two overt creationists in the race, placed dead last, while the two incumbents, who defended the teaching of honest science and faced down the fundamentalists, placed first and second. Nice!

In addition, a 1.38 mill emergency levy for the school district passed. It appears that in spite of all the Sturm und Drang of the Freshwater affair, voters in the District value education and in particular honest science education. I’m considerably cheered by these results.

Colorado front range


Photograph by Gaythia Weis.


Colorado front range – looking west … The photograph shows Long’s Peak, as seen from Pella Crossing Ponds, Hygiene, Colorado.


… and looking east, showing the infamous brown cloud. Photograph taken on Colorado Route 93, between Boulder and Golden, near Rocky Flats.

I’d like to thank Douglas and everyone for their kind words about my “cloning experiment” and impending appointment to Arizona State in Tempe.

I will be part of the Center for Evolutionary Medicine and Informatics in the Biodesign Institute and the Evolutionary Biology Program in the School of Life Sciences. I was hired as part of a genomics cluster, which is currently still hiring (Initial deadline is this Friday. See the ad below.) You could have the office next to me and Prof. Steve Steve.

I am looking to take students and graduate recruitment is underway. I’m looking for students with a background in biology, computation, mathematics, and/or statistics and interested in studying evolution theory and bioinformatics. I work on a variety of topics in computational evolutionary genetics, with most of my research dealing with mutations and developing analysis methods for detecting it from genomic data and high-throughput sequencing. I also have research programs in frequency-dependent selection and scientific computing with Javascript. If you are interested, you can check out my full CV, but I’ve appended a list of recent papers to this post. I can send anyone reprints if desired.

I’m also looking for undergraduate students to join my lab next semester as well. So if you are a current or future ASU undergrad and want to work along side Prof. Steve Steve, send me an email at [Enable javascript to see this email address.].

The application deadline for the graduate program is December 15th, and the process is described here.

Rice University is also looking for a postdoc to fill my vacated Huxley Fellowship. See the ad below the fold.

Mt. Vernon: An open letter to a school board candidate


Mt. Vernon, Ohio, as most PT readers know, has been the site of three years of legal maneuvering over John Freshwater. As a consequence of that, several creationists are running for school board here. There are three vacancies with six candidates, including two incumbents who voted to terminate Freshwater. One candidate is Steve Kelly, an official with the local Salvation Army.

Kelly is obviously a creationist. In an email response to a questioner, he wrote

I do not believe that the opening chapters of the book of Genesis belong in a science classroom. I do, however, believe that there is considerable scientific evidence that challenges the assumptions of the old-earth/evolutionary model. There is also significant scientific evidence for which the theory of an intelligent designer seems to fit the evidence better than random chance over a lengthy period of time. (I will be happy to cite some examples if you so desire.)

Our students deserve to have all theories of the origin of the world and species presented, along with evidence for and against each theory. (Quotes from religious texts do not constitute “evidence”.) All presentations should be consistent with the Scientific Method. Students can then decide for themselves which evidence seems more convincing. This is teaching our children to be independent thinkers rather than just absorbers of official dogma.

That said, the School Board has no right to abridge or abrogate any curricular requirements set by the State of Ohio. Where requirements exist, I will , if elected, follow the law.

That last sentence is all well and good, but the preceding two paragraphs are real problematic. So another person pressed Kelly about those “examples.” In response Kelly wrote

Here is a link to a page at While I do not necessarily endorse everything on that website, this is a helpful compilation of counterexamples to an old earth. See all of the references at the bottom of the page for source material. > >[…]an_Old_Earth

Gack! So I was forced to respond to Kelly’s claim in an open letter first published on Facebook (Parts 2-4 are in the comments to Part 1: Facebook posting limits and formatting regularly defeats me). I’ll reproduce that open letter below the fold with very light editing to correct a couple of typos and more substantial editing to correct an error.

Well, it had to happen sometime. Yet another one of our own, veteran TO-poster, long-time PT contributor, hacker, and guru Reed Cartwright, has taken the academic plunge and accepted a tenure-track appointment. (As if it wasn’t enough being the current Huxley Faculty Fellow at Rice University!) Reed starts this coming January 2012 as an Assistant Professor with the Biodesign Institute (does that have the D-word in it?) at Arizona State University. He will be sharing his lab space with Prof. Steve Steve, of course.


Word also has it that, as all good geneticists should, Reed has successfully replicated himself (albeit quite imperfectly, only 50% genetic identity by descent). As you can plainly see above, these life-changing events have had quite an effect on the poor Reed.

Congratulations Prof Cartwright!

Carnival of Evolution 41


CoEButton.jpgThe 41st Edition of the Carnival of Evolution is now up at The Mermaid’s Tale. This month’s carnival is typically diverse in its topics and contributors, and is typically excellent. Watch for cuckoos and other parasites, learn about flapping before wings, explore historical concepts like uniformitarianism, and read about the origins of the human hand. Eyes, nurseryfish, trade-offs, Barbara McClintock. And the suggestion that “evolutionary biology needs better PR.”

Head over to The Mermaid’s Tale and sample the bounty.

About this Archive

This page is an archive of entries from November 2011 listed from newest to oldest.

October 2011 is the previous archive.

December 2011 is the next archive.

Find recent content on the main index or look in the archives to find all content.



Author Archives

Powered by Movable Type 4.381

Site Meter