May 2011 Archives

Grease your shutters!


Yes, we will run a photography contest again this year. And thanks to all who submitted suggestions for a theme. Many of those were clever, and many were very funny (deliberately, that is). Some of the better suggestions were unfortunately too narrow, since we want to exclude almost nothing in the natural world. Thus, the theme of the third Panda’s Thumb photography contest will be

Land, Sea, Sky

Entrants should specify one of these categories for each photograph submitted. We will allow a two-week period for submitting entries, beginning the third or fourth week in July, depending on various people’s schedules. The rules will be about the same as last year’s, possibly with minor modifications. These rules will be announced at the beginning of the submission period.

Athene cunicularia


Photograph by David Young.


Athene cunicularia – burrowing owl, Badlands National Park, South Dakota.

ResearchBlogging.orgA few months ago, we were looking at the concept of a fitness landscape and how new technologies are creating opportunities for biologists to look in detail at relationships between genetics and fitness. The first post discussed the concepts of a fitness landscapes and adaptive walks, with some focus on the limitations of the metaphor. The second post summarized some recent work on bacterial fitness and mutation rates, with the concept of a fitness landscape as a theme, and the third post reviewed another recent paper, one that described techniques for studying fitness landscapes in detail by linking protein function (which can be screened and/or selected) and genetic information. Here we’ll look at yet another approach to the problem, in which the subject of the analysis is not an organism (as in the first paper) or a protein (as in the second paper) but an RNA molecule.

The New Scientist reported yesterday that U. S. Muslim clergy have signed an Imam Letter to the effect that evolution is compatible with their Muslim beliefs. I cannot find any information yet as to the number of signatories, but they will join approximately 13,000 Christian clerics, 500 rabbis, and 250 Unitarian-Universalist clerics when they affirm

that the timeless truths of the Qur’an may comfortably coexist with the discoveries of modern science. As Imams we urge public school boards to affirm their commitment to the teaching of the science of evolution. We ask that science remain science and that religion remain religion, two very different, but complementary, forms of truth

99.9% Wrong


by Joe Felsenstein,

Over at Uncommon Descent, “niwrad” is back with more calculations showing that conventional figures for comparing sequences of genomes are all wrong. Last time “niwrad” showed that humans and chimp genomes match only about 62% of the time. The usual figure given is 98.77%. Niwrad did this by taking 30-base chunks of one genome, finding the best match in the other genome, and then asking what fraction of the time there was a perfect match of all 30 bases. That’s where the 62% figure comes from. I immediately pointed out here at PT that this was expected and did not represent some insightful new way of calculating these figures.

Now Niwrad has turned to comparing two human genomes. The figure for 30-base perfect matches is about 96%. The conventional figure is about 99.9%. Let’s see what is expected. If a single base position has a 0.999 probability of matching, two bases have a 0.999x0.999 probability, three bases a 0.999x0.999x0.999 probability. 30 bases then have a probability that is 0.999 raised to the 30th power. Which turns out to be (ta-da!) 0.97. Not a bad fit.

Niwrad proudly notes that in the previous discussion

it seemed to me that the general feeling at the end was that my statistical method for performing genome-wide comparisons might have some merit, after all.

(Niwrad must have missed the discussion over here).

It does have merit: It’s a way of taking a close match and making it sound much less close – without changing anything. I have a suggestion: why not try 100-base chunks? That way human/chimp match will drop to only about 29%, while human/human will drop to 90%. Or how about 1000-base chunks? (human/chimp would be only about 0.00042 of a percent, and human/human would be down to about 37%). Where will this all end?

Fossilized palm fronds


Fossilized palm fronds, Triceratops Trail, Dinosaur Ridge, Golden, Colorado.

Freshwater: Back and Forth on the Admonishment


As I posted in March, the Ohio Department of Education issued a Letter of Admonishment to John Freshwater (PDF of the letter) for using a Tesla coil on middle school students.

Freshwater, through his attorney R. Kelly Hamilton, objected to the Letter of Admonishment. In a lengthy (188 page PDF!) objection, he argued that the local district’s action settled the issue, that Zachary Dennis was lying in his testimony, and that the Letter of Admonishment was “erroneous, defamatory and unwarranted.” (Mount Vernon News story.)

The Dennis family recently filed a rebuttal (PDF) arguing not only for the retention of the Letter of Admonishment but also that Freshwater’s teaching certificate (which expired last year) should not be renewed. (Mount Vernon News story.)

Still pending are Freshwater’s appeal of his termination in the Knox County Court of Common Pleas and his complaints to the Ohio Civil Rights Commission and to the federal Equal Employment Opportunity Commission. I have no information on their progress (or lack thereof).

World ends tomorrow!


I guess everyone knows it by now, but the world ends tomorrow. I anticipate a headline the day after tomorrow, “The world ended yesterday.”

Nevertheless, this human-interest article in the Times was disturbing. For example,

Intelligent design news from the 28th of April to the 18th of May, 2011.

Finally! It’s back again, your fix of ID news and discussion. To make up for my three-week-long absence, this post will cover five of the top ID blog posts from the past three weeks. Lucky for me then that it hasn’t been an especially busy time for the ID community during my break - otherwise I’d have a much bigger job on my hands.

Anyway, enough grovelling, let’s get into it.

Today’s posts are about Osama bin Laden and junk DNA, Oxford University and evolutionary mathematics, dissent in the evolutionary ranks, enzyme evolution, and, of course, junk DNA.

Andrew Weil practices “alternative” medicine, that is, medicine for which there is no evidence of efficacy. Now, according to an article in the Los Angeles Times, he recommends that evaluations of the efficacy of a treatment include “[p]atient factors – including how patients felt about the treatment, whether they can afford it and any evidence of a placebo response” (the words are those of the reporter, not Weil).

Some of Weil’s other recommendations, such as consideration of the funding source and possible unintended consequences, make sense, but “how patients felt about the treatment” is an invitation to peddle snake oil - maybe we should perform all clinical trials using red pills to get the best outcome.

Paraphrasing Weil, the article goes on to say,

Medicine has become enslaved to “evidence-based” approaches that rely on randomized, clinical trials as the only measure of whether a treatment is valuable[.]

Enslaved to evidence-based approaches? Reminds me of nothing more than William Dembski’s pathetic level of detail.


Trace fossils Raindrop impressions, Triceratops Trail, Dinosaur Ridge, Golden, Colorado.

One of the goals of the intelligent design (ID) movement is to show that evolution cannot be random and/or unguided, and one way to demonstrate this is to show that an evolutionary transition is impossibly unlikely without guidance or intervention. Michael Behe has attempted to do this, without success. And Doug Axe, the director of Biologic Institute, is working on a similar problem. Axe’s work (most recently with a colleague, Ann Gauger) aims (in part, at least) to show that evolutionary transitions at the level of protein structure and function are so fantastically improbable that they could not have occurred "randomly."

Recently, Axe has been writing on this issue. First, he and Gauger just published some experimental results in the ID journal BIO-Complexity. Second, Axe wrote a blog post at the Biologic site in which he defends his approach against critics like Art Hunt and me. Here are some comments on both.

Read the rest at Quintessence of Dust.

So, apparently, do some robots. Well, simulated robots, anyway.

I think this is sort of like an open letter to our readers:

We are thinking of running a third photography contest in the summer. The theme of the first contest, which was frankly decided in arrears, was animal, mineral, and vegetable. The theme of the second contest was threatened, endangered, and invasive.

Would anyone like to suggest a theme for a third contest?



Photograph by Wesley Elsberry.


Pyrite, or iron pyrite – fool’s gold.

After watching an episode of the Jon Stewart show, a frustrated Chris Rodda has decided to make her book Liars for Jesus available free as a pdf file. Ms. Rodda is senior research director for the Military Religious Freedom Foundation, which I recently discussed here.

The TalkOrigins Archive has two articles (here and here) on observed instances of speciation. Now a recent PNAS paper describes speciation in Aspidoscelis, a genus of whiptail lizards. The paper is titled “Laboratory synthesis of an independently reproducing vertebrate species.” From the abstract:

Here we report the generation of four self-sustaining clonal lineages of a tetraploid species resulting from fertilization of triploid oocytes from a parthenogenetic Aspidoscelis exsanguis with haploid sperm from Aspidoscelis inornata. Molecular and cytological analysis confirmed the genetic identity of the hybrids and revealed that the females retain the capability of parthenogenetic reproduction characteristic of their triploid mothers. The tetraploid females have established self-perpetuating clonal lineages which are now in the third generation.

Read more at Nobel Intent, to which we tip our hat.

My research doesn’t have an easy outreach component. There is only so much you can do to get K-12 students interested in the bioinformatics of indels. My colleague Dan Ksepka has a much better time getting the public interested in his research. Of course, he works on the giant fossil penguins of Peru ( He recently gave a talk on penguin evolution to open NC State’s seminar series for research professionals. Luckily it has been archived online. So grab the munchkins, sit them in front of the monitor, and let them marvel the awesomeness of penguins the size of Danny Devito.

Fossil Penguins: A 60 Million Year Journey From Wings to Flippers


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Specimen unearthed by Todd Shannon.


Barite crystal on limestone, Grand Junction, Colorado.

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