December 2010 Archives

Synthese Reminder: Two days left


A reminder that the papers in the special issue of Synthese edited by Glenn Branch and James A. Fetzer are available online free for just two more days, today and tomorrow. After the 31st they disappear behind the Springer paywall. Get ‘em while they’re free!

A week ago, physicist Mark Perakh posted a short attack on Michael Ruse. He prefaced it with the following:

I dare to claim that the sole value of philosophy of science is its entertaining ability. I doubt that all the multiple opuses debating various aspects of the philosophy of science have ever produced even a minute amount of anything that could be helpful for a scientist, be he/she physicist, biologist, geologist, you name it. It can, though, be harmful, as the case of Ruse seems to illustrate.

This struck a few of us involved with PT as being a profoundly nonsensical statement. Now, philosopher John Wilkins offers a defense of philosophy.

A Full Genome from Denisova, Siberia


Last week a paper was published on the DNA sequencing of the complete genome of an approximately 40,000 year old finger bone from Denisova in Southern Siberia (Reich et al. 2010). There are a number of very significant findings in the paper.

1) The results showed that the Denisova individual was more closely related to Neanderthals than to modern humans. However, the Denisovan does not fall within the range of Neanderthal variation. There are a few lines of evidence suggesting that the Denisovan and Neanderthal lineages had separate histories once they diverged and did not form a single population. The Neanderthal genomes sequenced so far have low genetic diversity, indicating that Neanderthals passed through a genetic bottleneck after splitting from the Denisovans. With only one Denisovan genome available as yet, we don’t know how diverse they were.


2) Even more spectacular was the finding that the Denisovan genome appears to have made a genetic contribution of about 4.8% (+/- 0.5%) to the genomes of living Melanesians. Interestingly, they did not contribute to the genomes of modern populations such as Han Chinese and Mongolians which live near Denisova now. The Denisovans obviously interbred with the ancestors of modern Melanesians at some point, but it seems unlikely to have happened at Denisova, which suggests that the Denisovans lived over a considerable area of eastern Asia.

This finding recalls another major discovery made earlier this year, which was that Neanderthals appear to have contributed from 1% to 4% of the genome of all living non-Africans (Green et al. 2010; Panda’s Thumb blogged about it in June). This was not expected, given that earlier mitochondrial DNA (mtDNA) results showed no evidence of any genetic mixing between Neanderthals and modern humans (but did not exclude the possibility either). The new Reich et al paper has improved the precision of this estimate; they calculate that Neanderthals contributed 2.5% (+/- 0.6%) to the genome of modern non-Africans. That means that the Neanderthals and Denisovans together account for an impressive 7.5% of the ancestry of modern Melanesians.

How to afford a big sloppy genome

Blogging on Peer-Reviewed Research

My direct experience with prokaryotes is sadly limited — while our entire lives and environment are profoundly shaped by the activity of bacteria, we rarely actually see the little guys. The closest I've come was some years ago, when I was doing work on grasshopper embryos, and sterile technique was a pressing concern. The work was done under a hood that we regularly hosed down with 95% alcohol, we'd extract embryos from their eggs, and we'd keep them alive for hours to days in tissue culture medium — a rich soup of nutrients that was also a ripe environment for bacterial growth. I was looking at the development of neurons, so I'd put the embryo under a high-powered lens of a microscope equipped with differential interference contrast optics, and the sheet of grasshopper neurons would look like a giant's causeway, a field of tightly packed rounded boulders. I was watching processes emerging and growing from the cells, so I needed good crisp optics and a specimen that would thrive healthily for a good long period of time.

It was a bad sign when bacteria would begin to grow in the embryo. They were visible like grains of rice among the ripe watermelons of the cells I was interested in, and when I spotted them I knew my viewing time was limited: they didn't obscure much directly, but soon enough the medium would be getting cloudy and worse, grasshopper hemocytes (their immune cells) would emerge and do their amoeboid oozing all over the field, engulfing the nasty bacteria but also obscuring my view.

What was striking, though, was the disparity in size. Prokaryotic bacteria are tiny, so small they nestled in the little nooks between the hopper cells; it was like the opening to Star Wars, with the tiny little rebel corvette dwarfed by the massive eukaryotic embryonic cells that loomed vastly in the microscope, like the imperial star destroyer that just kept coming and totally overbearing the smaller targets. And the totality of the embryo itself — that's no moon. It's a multicellular organism.

Milky Way galaxy


Photograph by Dan Stodola.

Photography contest, Honorable Mention.


Milky Way rising, Boundary Waters Canoe Area Wilderness, Minnesota. Mr. Stodola writes, “For this picture it’s the darkness of the night sky, essential to taking a picture like this, that I’m calling endangered. There appears to be no location in my entire state with night skies as dark as I was able to get in the BWCA, and even at that I could still see some light pollution on the horizon. The nearest location with similarly dark skies may be about 250 miles away from where I live.”

Ilex sp. Mahonia sp.


Ilex sp. – holly. Mahonia sp.

Ediacaran roots extend deeper into geologic time?


By Joe Meert,

Several years ago while working in south Kazakhstan, my colleagues and I were stuck at a place called Maly Karatau just north of the Kyrgyzstan border. The geology of the region is interesting and was once of economic importance during the days of the Soviet Union. It is rich in early Cambrian age phosphorites which were mined for phosphorus. The geologic section is fairly complete and covers much of the Neoproterozoic (~850–542 million years ago). Our initial target focused on a sequence of volcaniclastic red and green sediments as part of a larger effort to track the initial stages of Central Asian assembly. The younger part of the section was fairly well-constrained in age from Cambrian to Ordovician, but the lower part of the section was not known. Since the section included the Ediacaran Period (635–542 Ma), we also hoped to find some evidence for Ediacaran fossils. We succeeded in a way we hadn’t imagined.

by Paul S. Braterman, University of Glasgow; Professor Emeritus, University of North Texas

As you know by now, Behe has actually had a paper published in a peer-reviewed scientific journal (Behe M.J., Quarterly Review of Biology 85(4), 2010, 419-415). Well, not exactly a paper, more of a literature review. Well, not exactly a literature review, more a review of previous reviews, reinterpreting their findings according to his own criteria. The publication itself is shoddy piece of work. I have written numerous reviews myself, and would never have dreamed of basing them on earlier reviews, rather than my own up-to-date literature search. But let that pass.

Behe constructs an elaborate apparatus for classifying mutations as “gain”, “modification”, or “loss” of what he calls a Functional Coded Element (FCT). The definition is skewed to make “gain” as difficult to prove as possible. The process needs to be understood at the molecular level, rather than simply in terms of phenotype expression. This enables him to dismiss as of unproven relevance the Lenski group’s famous demonstration of E.Coli acquiring the ability to metabolise citrate under anaerobic conditions. Moreover, advantageous removal of inhibition is treated as “loss”, but advantageous disruption of a function by IS duplication and insertion is classified as “modification”, rather than “gain”. Using these restrictive and asymmetric criteria, Behe classifies most sufficiently well-understood mutations in laboratory-bred bacteria as loss or modification, although he does recognise a few gains.

Why bother with this eccentric-seeming enterprise? Here we need to look at the broader context of Behe’s involvement with the Discovery Institute.

Like I just said – as DI guy David Klinghoeffer posted yesterday, the origin of hundreds of new genes in Drosophila is just microevolution. This is a direct deduction from their own ID/creationist logic, where small amounts of change “within the kind” are no problem for normal evolutionary processes. Too bad for Behe, Luskin, etc. Here’s the full quote for when they realize the problem and take the post down:

In a post already noted by Mark Perakh below, Michael Ruse is floating an argument that those of us who argue against the compatibility of evolution and Christianity are endangering the constitutionality of teaching evolution. He writes:

So my question (and it is a genuine one, to which I don’t have an answer) to David Barash is this. Suppose we agree to the conflict thesis throughout, and that if you accept modern science then religion–pretty much all religion, certainly pretty much all religion that Americans want to accept–is false. Is it then constitutional to teach science?

The first amendment of the U.S. Constitution separates science and religion. (Don’t get into arguments about wording. That is how it has been interpreted.) You cannot legally teach religion in state schools, at least not in biology and other science classes. That was the issue in Arkansas and Dover. (I am not talking about current affairs or like courses.) But now ask yourself. If “God exists” is a religious claim (and it surely is), why then is “God does not exist” not a religious claim? And if Creationism implies God exists and cannot therefore be taught, why then should science which implies God does not exist be taught?

Interestingly, Ruse closes his post with this:

I should add that when I raised this worry with Eugenie Scott, her response was that I am just plain “dumb.” But while that may indeed be so, I am not sure that it is an argument.

Now, it seems very unlikely that Genie would have said any such thing. Far more likely is that she called Ruse’s idea dumb. And since she is pretty much omniscient on this issue that’s an assessment that ought to be taken seriously. In this post over at EvolutionBlog I have taken my stab at providing the argument Ruse overlooked. Comments can be left there.



Well this is pretty cool. And apparently they interbred with modern humans, also. I can’t wait to see what Reasons to Believe has to say…

Philosopher Ruse as an entertainer


In a post (see here) the renowned philosopher of science Michael Ruse offered the notion that seems to equalize, in a certain respect, creationism with science.

Jerry Coyne reports on a new paper in Science by Manyuan Long and colleagues on the origin and history of new genes in a large group of Drosophila that have recently had their full genomes sequenced.

Having this much phylogenetic and genomic information allows researchers to estimate the phylogenetic position of the origin of a new gene (566 new genes amongst the group of 12 fully sequenced genomes, actually), and the periods of time in which directional selection, stabilizing selection, or drift were the dominant regime that the new genes were evolving under. In many cases, there is a period of high selection after the origin of the gene, which weakens later – which is just what you would expect if the well-known, standard model for the origin of new genes is correct.

Two additional points are worth mentioning: (1) in some cases (about 30%, 59 out of the 195 they targeted for knockout studies), these new genes have become essential to viability for the species in question – even though they are totally absent in other, basically similar, flies that do just fine without them! This is strong support for the notion that one way “irreducible” systems evolve is by evolving parts that are helpful at first, but later become essential as other parts coadapt to become dependent on them. (2) I’m sure Luskin, Ewert, and other DI people would like to dismiss this as just another case of evolutionists “illegitimately” inferring common ancestry from “mere” sequence similarity, and that “common design” could be the explanation. However, in any other context, these creationists, and virtually any creationists including the young-earthers, would easily say that all of these Drosophila are just different varieties of the Drosophila kind, and that whatever variety exists between them (minor, in the grand scheme of biology) is “merely” “microevolution within the kind!” (And in the Edge of Evolution, Behe clearly puts his estimated “edge” well above the genus level.)

What’s that? Standard boring microevolutionary processes can produce new genes with modified sequences and new functions, which is clearly new information on anyone’s definition, even the creationists’ and even (explicitly so) Michael Behe’s definition? Oh my goodness, someone better call the DI news blog to put out this fire and reassure the faithful!


Chen, S., E. Zhang, and M. Long. 2010. New genes in Drosophila quickly become essential. Science 330:1682-1685.

A previous bit of ranting on this topic by me (responding to Luskin’s ridiculous critique of another famous paper by Manyuan Long, entered into evidence in the Kitzmiller case as exhibit P-245, actually: Long et al. (2003), Nature Reviews Genetics, “The origin of new genes” (free online in many places).

Heh, five years later and Casey Luskin is still trying to refute the immune system cross:[…]_042001.html

Never mind that Luskin’s one immunologist, Donald Ewert, admits that most of his colleagues, even his coauthors, are against him and use homology and comparative evidence everywhere all the time; admits that there is a mountain of literature on the evolution of the immune system; and admits (although he barely stammers it out) that there actually is an evolutionary model for the origin of receptor rearrangement in adaptive immunity and that the researchers themselves interpreted this as confirmation of the basic transposon-origins model (although Ewert somehow thinks this was just a “classification” of the RAG genes as bacterial transposons, ignoring, (a) how damned odd that is to find in vertebrate immune system genes and (b) how this was suspected ever since the 1970s and was deliberately tested in the 1990s-2000s).

Ewert’s reply basically boils down to vague denial of vast amounts of detailed work in evolutionary immunology, raw assertions that sequence similarity doesn’t suggest common ancestry (I dare Ewert/Luskin to do a survey of comparative immunologists on that point), and complaints about the literature not being detailed enough. Unfortunately for them, Behe made all these same points at trial. When you make these kinds of claims in the teeth of an entire specialized subfield which refutes you, it’s your credibility that’s shot, on the stand or anywhere else. So, try again. Give us a better, more detailed explanation of the origins of the immune system, Luskin and Ewert. Good luck!

Merry Kitzmas +5!!


My, how the time has flown! NCSE has linked to several 5-year anniversary articles in Pennsylvania papers, including the York Dispatch and the Philadelphia Inquirer. I liked this bit:

Michael Behe said he doesn’t hear anybody talk about Kitzmiller v. Dover anymore.

Behe, a biochemist and professor at Lehigh University, testified as an expert witness in support of intelligent design. “I don’t hear anybody talk about it … except the guys on the side who won,” Behe said.

“It’s an interesting legal event,” he said in reflection. “But it doesn’t affect the science. The scientific case for intelligent design keeps getting stronger.”

In the five years since, Behe said scientists are discovering how complex cells are beyond previous understanding, and he believes that helps support intelligent design as a valid scientific theory.

Not that any of that would have affected Jones’ ruling, Behe said.

“It didn’t seem to me the judge understood any of the scientific evidence anyway,” Behe said.

Jones discounted Behe’s testimony, Behe said.

“There was a disconnect between how I thought I did on the witness stand, and how my testimony was characterized by the judge,” he said. “It really soured me on the legal system.”

If presented with the opportunity again, though, he’d be back on the stand. Intelligent design supporters have to participate, he said, or “people will think we were afraid to show up.”

Of course, the majority of ID experts were, but that’s all history now…

Just let us know when your argument improves beyond “I won’t believe evolution unless someone gives me every single mutation and every single selective step, literal piles of peer-reviewed literature on the evolution of e.g. the immune system aren’t good enough.” Then maybe you’ll have something ready for prime time…

Merry Kitzmas!

Sciurus carolinensis


Photograph by Tom Faller.

Photography contest, Honorable Mention.

Faller.Brevard White Squirrel.jpg

Sciurus carolinensisBrevard white squirrel, Brevard, North Carolina. Mr. Faller writes, “Not albino; descendants of a white squirrel pair, protected in Brevard, N. C. limits.”

Looking for any last minute gifts for the Feast of Prof. Steve Steve (Dec. 26th)? I highly recommend the two books put together this fall by ZooBorns. If you know anything about the ZooBorns website, you know that it is an overdose of cuteness. The books do not disappoint.

The book with the tiger on the cover is geared to children between the ages of 2–7. It is a large-format book, suitable for reading to young children. Although the text in the main body of the book is simple, the appendix has lots of information about the animals, including their conservation status.

The book with the fennec fox on the cover is for all ages and would make a good “stocking stuffer.” It covers more species and contains more pictures and information about the animals and zoos.


So if you like cute animals, zoos, and science, you can’t go wrong by picking up copies of both.

ResearchBlogging.orgGiven that disputes over the existence and meaning of the phylotypic stage and the hourglass model have simmered in various forms for a century and a half, the remarkable correspondence between the hourglass model and gene expression divergence discovered by Kalinka and Varga and colleagues would be big news all by itself. But amazingly, that issue of Nature included two distinct reports on the underpinnings of the phylotypic stage. The other article involved work in another venerable model system in genetics, the zebrafish.

The report is titled "A phylogenetically based transcriptome age index mirrors ontogenetic divergence patterns" and is co-authored by Tomislav Domazet-Loso and Diethard Tautz. To understand how their work has shed light on the phylotypic stage and the evolution of development, we’ll need to look first at an approach to the analysis of evolutionary genetics that these two scientists pioneered: phylostratigraphy.

I don’t have time to do a serious blog entry, but I would just note that Jerry Coyne has been blogging Behe’s QRB paper, and the scandalous abuse of it by ID proponents (well, I’m sure the abuse was intended by Behe, but what he could actually establish in a peer-reviewed paper does not support even a smidgen the claims that Behe and other ID fans are making about the paper on the blogs).

In the latest thread, Paul Nelson popped up with another promise for another piece explaining why something that’s obviously wrong is actually reasonable (in this case, why ID advocates are allowed to disdainfully ignore the massive evidence that gene duplication + divergence is the main source of new genes with new functions, and why they are allowed to claim that the origin of new functional sequence is a big problem, when in fact it’s basically a solved problem, with the answer – gene duplication + divergence – known across biology, tested and verified in numerous different ways, and written down for beginners in the textbooks). We’ll see if he ever comes up with it. But in the meantime, here are a few irate comments from me:

Like RBH said, the new special issue of Synthese is free for the moment. I would like to highlight one article in particular, Robert Pennock’s:

Robert T. Pennock (2009, 2011). Can’t philosophers tell the difference between science and religion?: Demarcation revisited. Synthese 178(2), 177-206. DOI: 10.1007/s11229-009-9547-3

Pennock reviews the debate over “demarcation” in philosophy of science, particularly what happened after the 1981 McLean v. Arkansas case. After that case, a fairly famous philosopher of science, Larry Laudan, criticized the court, and one of the experts who testified, Michael Ruse, for (allegedly) relying on naive and long-discredited attempts to “demarcate” science from pseudoscience and from religion. Laudan basically claimed that Ruse/McLean boiled down to Popperian falsificationism, that Popperian falsificationism was hopelessly wrong, and that the verdict and its supporters were guilty of philosophical crimes for even daring to make a distinction between science and pseudoscience, or between science and religion. Or something.

Synthese issue on “Evolution and its rivals”


The news is out (see John Pieret) but I’ll repeat it here. Synthese, An International Journal for Epistemology, Methodology and Philosophy of Science, has an entire issue devoted to the topic of the title edited by Glenn Branch. It includes papers by names we know like Robert Pennock, John Wilkins (of TO fame), Wes Elsberry and Jeff Shallit on Dembski’s info theory foibles, Sahotra Sarkar, Barbara Forrest, and others. Best of all, all the articles are free online until December 31. Get ‘em while they’re hot!

So, shortly after the first post on the hourglass model went up here on the Panda’s Thumb, the senior author of one of the two featured papers (the article using fruit flies, titled "Gene expression divergence recapitulates the developmental hourglass model") contacted me, clearly enthused about our interest in the story. He’s Pavel Tomancak, and together with the co-first author on the study, Alex Kalinka, he offered some useful feedback as well as some cool images. Here are some of their further thoughts, posted with their permission and edited slightly by me. Let’s think of them as honored guest bloggers.

Panthera leo krugeri


Photograph by Ed Neubaum.

Photography contest, Honorable Mention.

Neubaum_Lioness and cubs Game Perserve SA.jpg

Panthera leo krugeriwhite lion, Mokwalo White Lion Breeding Project (now closed), Hoedspruit, South Africa. The lion is considered vulnerable, or likely to become endangered. The controversy about the existence of the phylotypic stage is more than some bickering about whether one blobby, slimy fish-thing looks more like a Roswell alien than another one does. It’s about whether the phylotypic stage means something, whether it tells us something important about development and how developmental changes contribute to evolution. To answer such a question, we need more than another set of comparisons of the shape and movements of embryos and their parts. We need a completely different way of looking at the phylotypic stage, to see if something notable is going on under the hood. So vertebrates all look the same at the tailbud stage. What does that mean?

Embryos look the way they do because of the positions and behaviors of the cells that make them up. The cells in an embryo all have the same DNA, and the link between that DNA and those specific cell behaviors is the basic process of gene expression. (This is a fundamental principle of developmental biology.) And by gene expression, we usually mean the synthesis of messenger RNA under the direction of genes in the DNA. Different cell types express different sets of genes, and the orchestration of the expression of particular genes at particular times is a big part of what makes development happen. When considering the phylotypic stage, then, developmental biologists wondered: is the apparent similarity of embryos at that stage reflected by similarities in gene expression. Or, more specifically, does the hourglass model hold up when we look at gene expression? This was the focus of the two articles in last Friday’s Nature that inspired the cool cover.

Disputes and controversies in science are always a good thing. They're fun to read about (and to write about), and they're bellwethers of the health of the enterprise. Moreover, they tend to stimulate thought and experimentation. Whether scientists are bickering about evo-devo, or about stem cells in cancer, or about prebiotic chemistry, and whether or not the climate is genial or hostile, the result is valuable.

Now of course, some controversies are invented by demagogues for political purposes. The dispute in such cases is far less interesting and clearly less profitable, even if participation by scientists is necessary.

This week, two papers in Nature weighed in on a major scientific controversy that has its roots in pre-Darwin embryology, fueled by some gigantic scientific personalities and even tinged with what some would call fraud. This intense scientific dispute spawned a sort of doppelganger, a manufactured controversy that is just one more invention of anti-evolution propagandists. The Nature cover story gives us a great opportunity to look into the controversies, real and imagined, and to learn a lot about evolution and development and the things we're still trying to understand about both.

The scientific dispute is an old one, dating to when scientists first began to study embryonic development in earnest. Embryologists like the great Karl Ernst von Baer noticed that the embryos of very different animals often looked so similar that they could hardly be distinguished from each other. A chicken embryo, at some point, looks an awful lot like a human embryo. What does this mean? Two schools of thought (roughly speaking) entered into competition, with evolution as the major subtext. One set of ideas envisioned development as recapitulation: development was a sort of re-play of evolution, with the organism recapitulating its evolutionary history as it took shape. Recapitulation theory was the brainchild of Ernst Haeckel, whose view of development was codified as his Biogenetic Law and sloganeered as "Ontogeny recapitulates phylogeny." Against recapitulation were the views of von Baer and others; von Baer formulated his own set of laws, the third of which repudiates recapitulation rather directly. Everyone agreed that embryos of different animals often looked quite alike; the dispute was about what this meant. And it seems that those who opposed evolutionary explanations (like von Baer) were eager to point to difference and divergence during development, while those who championed evolutionary views wanted to emphasize the shocking similarities between, say, chickens and mammals when compared at key embryological junctures.

Haeckel, famously, went on to point to those similarities as evidence for common ancestry and, infamously, to create a certain illustration of that evidence. His picture, thought by even some embryologists to be partly fraudulent (more accurately, "doctored"), is now a staple of anti-evolution propaganda. You can read all about that elsewhere; suffice it to say that Haeckel's drawings have long since been "corrected" without creating any problems for evolutionary theory. (For a much more detailed treatment of this saga, see Richardson and Keuck, Biological Reviews, 2002.)


But interestingly, the debates about recapitulation morphed (wink) over the years into a distinct but related disagreement about whether animal development passes through a stage that is common to - or typical of - the lineage of the organism. Because although Haeckel's recapitulation idea didn't survive, it remained clear that development seemed to reflect evolutionary commonalities. Consider the photos on the right. (The figure was created by Michael K. Richardson, who led the research group that critiqued Haeckel's drawings in 1998.) While the various embryos shown all end up looking quite different - looking like the adult form, in other words - they seem to "start" at a place that's notably similar. (Compare the embryos in the first row.) That starting point is not the beginning of development, and in fact those different kinds of embryos got to that starting point via rather different beginnings. In other words, it seems that animal embryos pass through roughly three phases of development: an early phase that can vary from group to group (say, between birds and mammals), a late phase in which group-specific forms are established, and a middle phase that is eerily similar among groups. That middle phase has come to be known as the "phylotypic stage" of development, meaning that it is a stage at which the embryo looks like a typical example of its evolutionary group. For insects, this is thought to be the "extended germband" stage; for vertebrates, it's roughly the tailbud stage. The point is that there is a middle phase of development during which animal embryos of varying morphological destinies look very similar, even if their earlier stages seemed very distinct. This model of developmental trajectories, compared across groups, is known as the "hourglass model," nicely depicted by Richardson and colleagues in the cartoon on the left.


Why all the controversy? Well, the disputes all seem to be related to the fact that the model is mostly descriptive. And so, one criticism is that the model is based on what embryos look like, and not strongly anchored in carefully-defined and -measured characters. Moreover, some critics have noted that the comparisons were often restricted to popular laboratory species, such that when the analysis was expanded to include a broader set of species, the similarities in the waist of the hourglass become less striking. In other words, the dispute centered on the basis of the model. Critics were disputing the very existence of the phylotypic stage.

Oh, and while this interesting scientific debate was ongoing, some propagandists were shadowboxing with Haeckel's ghost, shrieking about fraud while creating in the minds of their dupes the illusion of a different debate: one about whether development and evolution are conceptually linked. Along the way, these busy demagogues suggested that the phylotypic stage is an illusion, cherry-picking their data more shamelessly than Haeckel ever did. In any case, these folks were exploiting the real scientific dispute: whether the phylotypic stage can be defined more rigorously, in a way that links the similarities (whatever they are) to common ancestry.


And that brings us to the cover story in this week's issue of Nature. The cover image depicts a version of Haeckel's infamous illustration. The issue includes two reports, very different in their approach and in the animals they examined. Both reports provide striking support for the hourglass model, by showing that the phylotypic stage is indeed characterized by distinctive and fascinating patterns of gene expression. Part II will explore those two papers.


Image credits: 1) embryo images from Gilbert, Developmental Biology, 6th Edition, online at PubMed; 2) cartoon from Richardson et al. 1998.

December issue of Evolution: Education and Outreach out


Adrian Thysse flags the December issue of Evolution: Education and Outreach and provides links to individual articles that are easier (for me, at least) to navigate than those on the journal site. Some good stuff there.

Correction: Turns out that Adrian’s post came up in my reader this morning and I blasted right ahead not noticing that for some reason the reader had displayed Adrian’s 2009 post on that issue. Sorry, folks. (There’s still some good stuff there, though.)

I’ve created a new web site,, to track the progress and construction of Answers in Genesis’s latest assault on common sense and good taste, the Ark Encounter theme park. I’ll aggregate news stories, blog posts, and other coverage on one site where visitors can survey reactions from the media, the public, and other sources.

Anyone coming across information related to Ark Encounter can forward it to me for posting, skip (AT) penguinsites (DOT) com.

Also on the site is a modest challenge. Mr. Ham, why not spend that hundred million plus proving what you’ve so adamantly insisted all these years: prove the Ark is physically possible. If you can build the vessel using the same methods Noah is supposed to have used, load it up with approximately the same number of animals, and eight people can successfully care for them on the water for the same length of time the flood was supposed to have taken I’ll be the first to start tithing to your museum.

And we’ll even grant you success even in calmer waters than must have existed if the catastrophic flood really happened. On the other hand, if the eight people die from suffocation under massive piles of every kind of animal poop imaginable, they will be honored martyrs for the cause, no matter how bad they smell at their funerals.

Macaca sinica


Photograph by Siromi Samarasinghe.

Photography contest, Honorable Mention.


Macaca sinicatoque macaque, or temple monkey, Bundala National Park, Sri Lanka. Ms. Samarasinghe writes that this is an old-world monkey endemic to Sri Lanka. Its conservation status is endangered.

This week’s issue of Science has a news article and a podcast about a USGS researcher who bred bacteria to live in an arsenic environment. If you do not subscribe to Science, you may read only slightly breathless articles in the New York Times and the Los Angeles Times.

I’m very proud to see that my alma mater, Chapman University, has become the newest site for the Evolution Education Research Center’s network. The announcement came last month at an event featuring Eugenie Scott of the NCSE. Congratulations to Prof. Brian Alters.

I’m particularly happy to see this because a few years ago, as readers will recall, the Chapman Law Review published a terrible creationist article. As an alumnus, I was so embarrassed to see the school’s name on such a piece of tripe that I responded with an article of my own. It’s nice to see Chapman step up for science!

Freshwater: Signed the settlement (Updated)


Just a note to say that I’ve learned that John Freshwater did sign the settlement agreement with the Dennis family prior to it being approved (insofar as the terms relating to Zachary are concerned) by Licking County Juvenile Court Judge Hoover. While the settlement agreement was negotiated by the Board’s insurance company attorneys, Freshwater as the defendant had to sign off on it, and he did.

AFAIK all that’s left now is Federal Judge Gregory Frost’s overall approval of the settlement and, of course, the concluding acts–referee’s recommendation and Board of Education action on it–of the administrative hearing. Then at last perhaps this sorry episode can be closed.

Update: Judge Frost has signed off on the settlement. See comment below.

Kentucky Jumps the Ark


by Daniel Phelps

Answers in Genesis ministries has partnered with Ark Encounters, to build an 800 acre theme park in Grant County, Kentucky (a rural part of the north central Bluegrass). The theme park will feature a “full scale replica” of Noah’s Ark as well as other “attractions” as proposed here.

The project has received support from the highest levels of the Commonwealth of Kentucky’s government. On Wednesday, December 1, Governor Beshear held a press conference with officials from AIG and Ark Encounters to announce that the state is giving the creationists a tax incentive to bring jobs to the cash strapped region. Up to $37.5 million of the $150 million total cost could go to the creationists in the form of tax breaks under Kentucky’s Tourism Development Act. Apparently, the theme park can withhold 25% of the sales tax it collects up to 25% of the total cost for building the park under the Tourism Development Act.

Stuck in moderation at Coyne’s place


Apropos of Matt’s post just below, in a post titled “NCSE becomes BioLogos” Jerry Coyne has thrown a hissy fit over NCSE noting the upcoming Webcast on ‘Evolving Christianity’ featuring a number of theists of varying stripes speaking on how they accommodate their theism and science in general and evolution in particular.

I commented on Coyne’s site more than five hours ago but my comment is still labeled (after hard refreshes) as “Awaiting moderation” while several comments posted later than mine have appeared. So I’ll reproduce my comment below the fold, warts and all.

Evolutionary Christianity


I just got an announcement to the effect that “The Clergy Letter Project has just become a co-sponsor of a free on-line series hosted by Michael Dowd and entitled ‘The Advent of Evolutionary Christianity: Conversations at the Leading Edge of Faith.’ This exciting series begins this Saturday, 4 December.” As a Nice Jewish Boy, not to mention a nonbeliever, I doubt I will participate, but I noticed several panelists of whom I think highly – not least John Shelby Spong, John Haught, and Ian Barbour. Additionally, biologist Ken Miller is on the panel, as are physicists Charles Townes and my former colleague at NIST, Bill Phillips, and astronomer Owen Gingerich. In case any of our readers are interested, I will post the gist of the announcement, which I got from Michael Zimmerman, below the fold.

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