September 2011 Archives

Joe Thornton beats on Behe


Joe Thornton is a distinguished researcher who works on reconstructing ancient biomolecules to study how they evolved into their present forms. Recently ID creationist Michael Behe has commented on Thornton’s work, interpreting it to mean that the molecules couldn’t have evolved. On Carl Zimmer’s Loom Thornton eviscerates Behe’s misintepretation. A couple of quotes to give the flavor:

Behe contends that our findings support his argument that adaptations requiring more than one mutation cannot evolve by Darwinian processes. The many errors in Behe’s Edge of Evolution – the book in which he makes this argument – have been discussed in numerous publications.


Behe’s discussion of our 2009 paper in Nature is a gross misreading because it ignores the importance of neutral pathways in protein evolution.


This brings us to Behe’s second error, which is to confuse reversal to the ancestral sequence and structure with re-acquisition of a similar function.


Behe’s argument has no scientific merit. It is based on a misunderstanding of the fundamental processes of molecular evolution and a failure to appreciate the nature of probability itself. There is no scientific controversy about whether natural processes can drive the evolution of complex proteins. The work of my research group should not be misintepreted by those who would like to pretend that there is.

Read the whole thing. (And don’t miss Matheson’s remarks on natural selection at the link below.)

Hat tip to Steve Matheson for calling my attention to Thornton’s piece..



Photograph by Rachel Shannon.


Microburst, Boulder, Colorado, driving west on South Boulder Road.

Webcast: The Evolution of Religion


Another in an annual series of discussions of science and religion at Ohio State is scheduled for October 5. The announcement:

*The Evolution of Religion*
Wednesday, October 5, 7-9pm
[Enable javascript to see this email address.] Studios, 333 West Broad Street, Columbus, Ohio 43215

Where do our religious beliefs come from? Have religious beliefs served an evolutionary purpose? Join us in the [Enable javascript to see this email address.] Studios for a spirited panel discussion on the intersection of science and religion, followed by a question-and-answer session. Scheduled speakers include:

- Moderator Neal Conan, host of NPR’s *Talk of the Nation *
- Nicolas Wade, New York Times science writer and author of *Before the Dawn* and *The Faith Instinct*
- Lionel Tiger, Charles Darwin Professor of Anthropology, Emeritus at Rutgers University, and author of *God’s Brain*

The event is free but reservations are required. To register, visit this site or call 614.228.2674 for details. Supported by a grant from the John Templeton Foundation.

The series is sponsored by public TV station WOSU, by the Center for Science and Industry in Columbus, and by the Department of Entomology at the Ohio State University. I wrote about one such on the Thumb four years ago. They have had a distinctly “accommodationist” flavor, and given the Templeton Foundation’s funding of the series (via Susan Fisher of the Department of Entomology at Ohio State), I suspect this one will carry on that theme. I know little of Tiger’s or Wade’s views on that, so I may be wrong. The entire series of webcasts is archived at this site.

Tom Baillieul, a member of Ohio Citizens for Science, has a background essay on the evolution of religion available here (PDF).

(I can’t resist noting that the Department of Entomology is also home to one of the creationist “scientists,” Glen Needham, who played a significant role in the Bryan Leonard affair at Ohio State.)

Hitcher-poster180px.jpgGenetic hitchhiking is thought to be an inevitable result of strong positive selection in a population. The basic idea is that if a particular gene is strongly selected for (as opposed to selected against), then the chunk of the genome that carries that gene will become very common in the population. The result is a local loss of genetic diversity: all (or nearly all) of the individuals in the population will have that same chunk of genetic information, whereas before the selection process acted, there might have been a lot of variation in that chunk throughout the population. And this means that areas of the human genome that are less variable between people are suspected sites of recent positive selection. Within that chunk, there are potentially many genes and genetic elements that became more common in the population by virtue of their placement near the gene that was actually selected for. Those other genes are the hitchhikers. And it’s likely that some hitchhikers are bad news - they’re harmful mutations that would normally become rare or extinct in the population, but instead have become common by hitchhiking.

In the last few years, large amounts of genetic information have become available that have enabled biologists to look for evidence of such phenomena in the human genome. Specifically, two major projects have collected genetic data for the purpose of analyzing genetic variation among humans. One project, the International HapMap Project, mapped and quantified sites in the human genome that are known to vary among humans by a single genetic letter. These sites are called single nucleotide polymorphisms, or SNPs (pronounced “snips”). The project has mapped millions of these sites in a group of 270 humans representing various lineages. Another project that has made the news recently is the 1000 Genomes Project, which also seeks to provide a picture of human genetic variation using more people (more than 1000 at present) and slightly different technology. Efforts like these have taken analysis of the human genome to a new level. No longer do we merely wonder what “the” human genome is like - we can begin to learn about how genetic differences give rise to biological differences such as susceptibility to particular diseases.

And we begin to look for evidence of positive selection in the human genome.

Read a primer on hitchhiking, then read the rest of the story about harmful mutations in the human genome, at Quintessence of Dust.

Looks like the cartoonist Wiley Miller has started a series of strips on teaching the “controversy.” He’s got the age of the dinosaurs wrong, and carbon dating does not work that far back anyway, but, hell, the strip is called Non Sequitur. The money quote so far is, “Um, just as an F.Y.I., saying ‘facts’ would be a lot less offensive if you used air-quotes.”


The fifth BILL is a lively and entertaining look into modern research in evolutionary biology, presented by Hopi Hoekstra of Harvard University. Professor Hoekstra’s lab explores evolutionary mechanisms at multiple levels, moving seamlessly between the field (more precisely, the beach) and the lab.

BILL the fifth is “What Darwin Did and Didn’t Know: the Ultimate and Proximate Causes of Evolutionary Change”, a lecture by Hopi Hoekstra presented at the Darwin/Chicago 2009 conference. It’s a .mov file, which you watch streaming or download.

Hoekstra’s lecture is a superb and approachable introduction to the key questions in evolutionary genetics, and contains some fascinating surprises. Her lab website is a treat, too, with great images and access to numerous publications, including review articles.

As usual, tips and comments are below the fold. Recommendations for future BILLs should be sent to the BILL czar (BILL at pandasthumb dot org) or can be left in the comments.

Tomorrow at 1:00pm Texas Time (CST), Oscar Westesson will be presenting a Phyloseminar.

The “multiple sequence alignment” is a computational artifact. In nature there is no such thing; rather, an alignment represents a partial summary either of indel history, or of structural similarity. Here we show, via evolutionary simulation tests, that all currently-available multiple alignment tools introduce systematic biases into downstream evolutionary analysis - particularly when used to reconstruct histories of insertions and deletions.

I will present our unification of Felsenstein’s “pruning” algorithm and “progressive alignment” to build a fast, linearly-scaling approximate-maximum-likelihood phylogenetic alignment/reconstruction algorithm. Inference of evolutionary history in this framework displays a clear improvement in accuracy over non-statistical phylogenetic reconstructions and a massive improvement in performance over slow-running MCMC statistical reconstructions.

Phyloseminars are streamed live, and can be watched anywhere you have an Internet connection. To learn how to connect, visit the Phyloseminar page.

Pieris rapae


Pieris rapae – imported cabbage worms (enjoying their last meals), Boulder, Colorado.

New species of sparrow


According to the Beeb, there is a new species of sparrow, the Italian sparrow. Not the first instance of speciation within human memory, but a nice example. The species was originally a cross between the two other species, and the article notes that speciation by this mechanism may be more common than had been thought.

Photography contest winners

Sorry, I have been preoccupied lately. The winners of the photography contest are

Sky: Turkey vultures by James Rice

Sea: Fishing spider by Michael Siccha

Land: Cooling pahoehoe lava, by Andrew Cooper

In addition, I would like to award fourth place to Ammonite fossils by Amanda Brooks, because she has a good eye for fossils and composition, not to mention that she is 17 years old and a senior in high school.

If the winners, including Ms. Brooks, will send me their snail-mail addresses, I will send their copies of The Way of the Panda, by Henry Nicholls. Once again, we thank the publisher, Pegasus Books, for their generosity in providing the books.

Evolution News and Views noticed my previous post, and wrote a little reply. Unfortunately for them they completely missed the point, that Dembski claimed “Darwinists” were making stuff up, when there was good theoretical and (indirect) observational evidence to be confident that planets abounded in the galaxy.

The 55 Cnc system (excluding the outermost planet), 55 Cnc e is marked by the red cross near the sun. The 55 Cne system has features similar to our solar system.

Instead, they chose to focus on whether the planets we have found are habitable, which was beside the point [1]. Guillermo Gonzalez wrote a response for them, which included this:

The typical exoplanetary system is very different from our Solar System. Jovian planets are being discovered in very tight or highly eccentric orbits. Jovian planets in our Solar System are characterized by large nearly circular orbits. Our Solar System looks ever more like the exception, and it is exceptional in ways that are life friendly.

Distribution of orbital periods of the currently discovered exoplanets. The pink bars are “Super Jupiters” and the yellow bars are Jupiter-like planets in Jupiter period orbits.

Well, that’s sort of true, but deeply misleading. When we first started looking Super Jupiters were the norm. To explain why, and why this is no longer true, I’m going to digress for a moment to explain the main methods used to find exoplanets. The first is the radial velocity method. Here the slight wobbles produced in the position of a star by the gravitational tug of an orbiting planet are detected by Doppler shift.

In the transit method, the slight dimming in the stars light as the planet passes in front of it.

KOI-701.03, an as yet unconfirmed, Earth-like world probably in the habitable zone of its Sun. KOI-703.03 visualized in Celestia (click to embiggen).

On this Thursday at 18:00 UT NASA will hold a press conference on a recent discovery by the Kepler, the exoplanet discovery telescope. I don’t know what to expect, on the basis of past performance they will probably announce a tidally locked super-Earth in the habitable zone of a Red Dwarf as if we have found a second Earth (or maybe they will confirm KOI-701.03 really is in the habitable zone of a reasonably sun like star).

Still, despite coming hard on the heels of the 50 new exoplanets found by HARPS, the existing bonanza of Kepler worlds and discovering the atmospheric composition of some exoplanets, one can hardly suppress a thrill at the prospect of learning something new about the plethora of extrasolar worlds we have found.

One wonders how William Dembski feels after proclaiming in 1992:

“Dawkins, to explain life apart from a designer, not only gives himself all the time Darwin ever wanted, but also helps himself to all the conceivable planets there might be in the observable universe (note that these are planets he must posit, since no planets outside our solar system have been observed, nor is there currently any compelling theory of planetary formation which guarantees that the observable universe is populated with planets)”

Three years later the first exoplanet was confirmed, and the current count stands at 677.

Peter H. A. Sneath (1923 - 2011)


Word has reached me that Peter Sneath died last Friday at his home in Leicestershire. He was 87 years old. For a more complete and entertaining autobiographical account see page 77 of this Bulletin of Bergeys International Society for Microbial Systematics.

Peter was a medical microbiologist, who, in the late 1950s, began to work on numerical methods for classifying bacteria. He developed numerical clustering methods. He soon came into contact with Robert Sokal, who was doing the same. Together they wrote Principles of Numerical Taxonomy, a widely-noticed textbook advocating taking a phenetic approach to classification, basing it on measures of overall similarity rather than any inference of phylogeny. The smartest thing Sokal and Sneath did was to not fight over who invented numerical taxonomy, but to join together to promote it (Sneath was first author on the 1973 revision Numerical Taxonomy).


                 Peter Sneath with his children, about 1960. Photo by Joan Sneath, courtesy of the late Peter Sneath

Numerical taxonomy rattled the systematic establishment, then dominated by followers of Ernst Mayr and George Gaylord Simpson’s school of “evolutionary systematics”. It encouraged and stimulated many younger people to look into numerical approaches. By about 1980 phenetic approaches had been pushed aside by phylogenetic systematics, but Sneath and Sokal’s work is still regarded by mathematical clusterers as the most important founding work in their field. The most widely-used of Sneath’s methods is the UPGMA clustering method (independently also invented by F. J. Rohlf). [See comment of September 30 below for correction of this statement].

I always enjoyed meeting Peter and Joan Sneath. Peter was intrigued by any and all uses of numerical and computer methods in science, and was even willing on occasion to violate his own precepts and come up with methods for analyzing phylogenies.

He wrote a pioneering 1975 paper (with Sackin and Ambler) on detecting recombination between lineages, for example. I remember Peter telling me that as he traveled around he collected soil samples to study their bacteria. He carried no sterile vials for that – he simply went out and bought a ream of typing paper, as it was sterile, then used some to scoop up the sample and fold it into an envelope. It was a brilliant common-sense improvisation typical of the best of his generation of English scientists.

Canis lupus arctos


Photograph by Alexandra Young.

Arctic Wolf in Bear Country USA SD by Alex Young.jpg

Canis lupus arctos, arctic wolf, South Dakota.

Over at UD, the ever-amazing Denyse O’Leary (writing as “News”) has gone after me.

I am apparently a “Darwin lobbyist” whose salary is “paid for under protest by people who don’t believe it”. (Of course UD News posts never insult people, do they?)

First she quotes the paleontologist T. Berra as saying that cars, like fossils, show “descent with modification”. Then she puts words in Berra’s mouth, implying that Berra has said that cars have genes and offspring, and that Berra has called automotive engineers liars.

Then she quotes some paragraphs by me about the mysterious “digital information” that ID types like Stephen Meyer are always announcing has been found in the genome. I made the point that it is nothing very new – actually it’s just the presence of protein-coding genes, RNA genes, and regulatory sequences, which we already knew were there. (I have heard Meyer speak on this issue and he did not explain what the mysterious “digital information” was – leaving his audience to infer that it was some mysterious new pattern previously unknown to science, but which could only have arisen by Intelligent Design).

She introduces the quote from me by misdescribing it as being


on why genetic information requires no intelligence.

It of course wasn’t about that. It was reacting to Meyer’s mesmerizing phrase “digital information” and his statement that

Stephen Meyer:

the discovery of digital information in DNA provides strong grounds for inferring that intelligence played a causal role in its origin.

I was pointing out that Meyer wasn’t describing some new pattern that, by itself, proved intelligent design.

O’Leary has misunderstood my 2007 paper and which parts argue what. It is later in the paper that I take on William Dembski’s arguments for his Law of Conservation of Complex Specified Information and his No Free Lunch argument, and show (by arguments invented by others and some invented by me) that they don’t work. And of course those arguments in my paper are against Dembski’s alleged proof of Intelligent Design. They don’t prove that ID is impossible, just that Dembski has no proof that it is necessary.

I recommend that article to O’Leary.

We need your vote on the third edition of our Photography Contest. Voting ends this weekend. Last week you voted on the Sea Finalists. This week its for Sky.

Just go here to view the finalists and vote.

You have to sign in to vote, but it’s easy. We accept local accounts and Facebook, Google, Yahoo, etc. accounts.

Pimping a friend’s book


Joan L. Slonczewski, a friend and former colleague who is a microbiologist at Kenyon College and a John Campbell Award-winning science fiction author, has a new science fiction novel coming out next week titled The Highest Frontier. According to the blurb, it’s about a

… college in a space habitat financed by a tribal casino, colonized by a geocentrist church, and defended from aliens by Homeworld Security.

Sounds familiar. :)

Joan’s A Door into Ocean, with themes of ecofeminism and pacifism, won the 1987 John W. Campbell Memorial Award for Best Science Fiction Novel. All her science fiction (see Wikipedia link above) is biologically informed and is to some extent at least biologically themed.

For central Ohioans, there will be a book launch gathering and book-signing at 7:00 pm on Tuesday, Sept 13, at the Kenyon Bookstore in greater downtown Gambier, Ohio. Downtown Gambier is one block long, so finding the bookstore ain’t hard. Finding Gambier, on the other hand, can be … erm … interesting. I’ll be there.


The fourth BILL is a tour de force of scientific explanation, presented by a well-known scholar described by a colleague (who introduces him in the video) as “the principal guru to go to on evolutionary genetics in the world.”

BILL the fourth is “Why Evolution Is True”, a lecture by Jerry Coyne presented at the 2009 Atheist Alliance International convention. Coyne is the author of the excellent book and blog by the same name.

It was one of several very good lectures at that convention, some of which would make excellent future BILLs. Coyne’s lecture is a perfect BILL: illuminating and lively, basic enough for laypersons but stimulating for all.

As usual, tips and comments are below the fold. Recommendations for future BILLs should be sent to the BILL czar (BILL at pandasthumb dot org) or can be left in the comments.

The winner of the Sea category, with 29 out of 78 votes, is Fishing Spider by Michael Siccha. Ammonite Fossils by Amanda Brooks was second with 21 votes. Finalists in the Air category have been posted. Congratulations again to everyone who participated.

Note: Matt Young directed the selection of the finalists and wrote most of this text.

We received approximately 40 photographs from 20 photographers. Most of the pictures were excellent. We divided the entries into 3 categories, Land, Sea, and Sky, though we had to fudge a little bit to populate all 3 categories.

Choosing finalists was difficult. We considered what we thought were the scientific and pictorial qualities of the photographs, and also attempted to represent as many photographers and present as much variety as possible. The text was written by the photographers and lightly edited for style.

Here are the finalists in the Sky category. Please look through them before voting for your favorite. You will have to be logged in to vote on the poll. We know it is possible to game these polls. Please be responsible and vote only once. If we think that the results are invalid, the contest will be canceled. The photos and poll are below the fold.

The winner in each category will receive a copy of The Way of the Panda, by Henry Nicholls; we thank the publisher, Pegasus Books, for their generosity in providing the books.

Thanks to John Pieret, the full text of Clarence Darrow’s (1926) essay “The Eugenics Cult” is now online in text format. Clever readers could find it in Darrow anthologies at Google Books, but it’s nice to have it in plain text for the purposes of searching and general Google-tasticness. Hopefully the IDists/creationists will never be able to mention Darrow and eugenics in the same sentence again, without being sent a link to this essay.

You should go and read the essay. It is one of the most spectacular examples of polemic used-appropriately-and-for-good that you will read. And I find it fascinating that Darrow was leading a charge against eugenics (in his 1925 and 1926 essays) at exactly the same time that the Scopes Trial and appeals were going on (1925-1927). It’s rather more than William Jennings Bryan ever said against eugenics, I believe. (Did Bryan ever bash eugenics like this? My sense of it was that it wasn’t a major point of his, despite later revisionist history from creationists.)

And, I think the essay still speaks to issues we face in the 21st century. Although eugenics is almost universally despised today, many of the naive assumptions that made it seem like a good idea are still common today, amongst both liberals and conservatives. E.g., both some liberals and some conservatives think that the relative breeding of human cultural groups (religious/nonreligious, rich/poor, liberal/conservative) has great significance for the future – whereas the observed historical reality, and probably the future, is that massive cultural change is a continuous, people change cultural and religious affiliations constantly, and no safe extrapolation can be made based on uniformitarian assumptions about breeding.

Niall Shanks dies


Glenn Branch of NCSE tells us, unhappily,

Sad news from Kansas: Niall Shanks, whom many of us knew and whose God, the Devil, and Darwin all of us should know, died in July; he was only 52.

I never met Professor Shanks, but he contributed a chapter to Why Intelligent Design Fails, and I found him a pleasure to work with. I am saddened by the news. You may see NCSE’s obituary here.

Pop quiz: early eugenics critic


Pop quiz, folks. Who wrote the following in 1926? If you know the answer via, say, me, hold off a bit and let people guess. No fair googling, although it looks like a plain google search doesn’t help much. (The internets can thank me for ASCII-ifying this bit of wisdom later.)

If you figure it out, go back to google and have a look at what the IDists/creationists say about this guy and eugenics and post examples. Have they done their research?

The history of the race shows endless examples of the pain and suffering that men have inflicted upon each other by their cocksureness and their meddling.

We know something about biology. We know a little about eugenics. We have no knowledge of what kind of man would be better than the one that Nature is evolving to fit the environment which he cannot escape. We have neither facts nor theories to give us any evidence based on biology or any other branch of science as to how we could breed intelligence, happiness or anything else that would improve the race. We have no idea of the meaning of the world “improvement.” We can imagine no human organization that we could trust with the job, even if eugenicists knew what should be done, and the proper way to do it. Yet in the face of all this we have already started on the course, and the uplifters are urging us to go ahead, with no conception of where we are going, or what route we shall take!

In an age of meddling, presumption, and gross denial of all the individual feelings and emotions, the world is urged, not only to forcibly control all conduct, but to remake man himself! Amongst the schemes for remolding society this is the most senseless and impudent that has ever been put forward by irresponsible fanatics to plague a long-suffering race.

Please vote if you haven’t yet.

We need your vote on the third edition of our Photography Contest. Voting ends this weekend. Last week you voted on the Land Finalists. This week its for Sea.

Just go here to view the finalists and vote.

You have to sign in to vote, but it’s easy. We accept local accounts and Facebook, Google, Yahoo, etc. accounts.

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