December 17, 2006 - December 23, 2006 Archives

Doushantuo embryos dethroned?

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Almost ten years ago, there was a spectacular fossil discovery in China: microfossils, tiny organisms preserved by phosphatization, that revealed amazing levels of fine detail. These specimens were identified as early animal embryos on the basis of a number of properties.

  • The cells were dimpled and shaped by adjoining cells, suggesting a flexible membrane—not a cell wall. This rules out algae, fungi, and plants.
  • The number of cells within each specimen was usually a power of 2. This is something we typically see in cleaving embryos, the sequence from 1 to 2 to 4 to 8 to 16 cells.
  • They were big. Typical somatic cells in animals are 5-10 µm in diameter, but ova can be a millimeter or more in diameter, and individual blastomeres (the cells in the cleavage stage embryo) can be several hundred µm across. These cells and the whole assemblage were in that size range.
  • The individual cells were uniform in size, as seen in many cleavage stage embryos, and contained organelles arranged in a consistent pattern.
  • They were often found encapsulated in a thin membrane, similar to the protective membrane around embryos.

There are some concerns about the interpretation, though. One troubling aspect of their distribution is that they are all only in the cleavage stage: we don't see any gastrulas, the stage at which embryonic cells undergo shape changes and begin to move in a specific, directed manner. Studies of taphonomy (analyses of the processes that lead to fossilization) have shown that these later stages are particularly difficult to preserve, which potentially explains why we're seeing a biased sample. Another unusual bias in the sample is that all of the embryos exhibit that regularity of division that produces equal-sized blastomeres—yet many invertebrate embryos have early asymmetric cleavages that produce recognizable, stereotyped distributions of cells. That asymmetry could be a feature that evolved late, but at the same time, some of the fossils were described as resembling molluscan trefoil embryos. Why aren't the examples of early asymmetry translated into a later asymmetry?

Now there's another reason to question the identity of the Doushantuo microfossils: they may be bacterial.

Continue reading "Doushantuo embryos dethroned?" (on Pharyngula)

Ode to the Flagellum

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The evolution of the flagellum Youtube video based on Nick Matzke's hypothesis by CDK007

History and Cobb County

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Many were taken by surprise by the Cobb County School Board’s decision to settle the Selman case, give up their practice of putting evolution “warning labels” in textbooks, and pay $167,000 in fees to the plaintiffs. They had fought this case for four years, and succeeded in getting the Court of Appeals to vacate the district court decision for a retrial. Perhaps the third time Cobb’s sticker got in front of a court would be the charm.

Well, the reality was that this was not likely at all.

In the spirit of the season, Tom Lehrer, Weird Al Yankovic and overwhelming evidence, and as we can’t do flash animations with flatulence noises, once more the Panda’s Thumb Offensive Morris Dancing Troop and Precision Yodelling Team bring you …

The Twelve days of DISCO redux:

On the first day of DISCO the DI gave to me … No original peer-reviewed work.

On the second day of DISCO the DI gave to me … A Dover Pro-Science Victory, and no original peer-reviewed work.

On the third day of DISCO the DI gave to me … Judge Jones Bashing, A Dover Pro-Science Victory, and no original peer-reviewed work.

On the forth day of DISCO the DI gave to me … More Science-Free Books, Judge Jones Bashing, A Dover Pro-Science Victory, and no original peer-reviewed work.

On the fifth day of DISCO the DI gave to me … More Sternberg Spin! More Science-Free Books, Judge Jones Bashing, A Dover Pro-Science Victory, and no original peer-reviewed work

On the sixth day of DISCO the DI gave to me … Clogging Student Blog sites. More Sternberg Spin! More Science-Free Books, Judge Jones Bashing, A Dover Pro-Science Victory, and no original peer-reviewed work

On the seventh day of DISCO the DI gave to me … Clueless Dover Denial, Clogging Student Blog sites. More Sternberg Spin! More Science-Free Books, Judge Jones Bashing, A Dover Pro-Science Victory, and no original peer-reviewed work

On the eight day of DISCO the DI gave to me … No Biologic Institute Research, Clueless Dover Denial, Clogging Student Blog sites. More Sternberg Spin! More Science-Free Books, Judge Jones Bashing, A Dover Pro-Science Victory, and no original peer-reviewed work

On the ninth day of DISCO the DI gave to me … More Judge Jones Bashing, No Biologic Institute Research, Clueless Dover Denial, Clogging Student Blog sites. More Sternberg Spin! More Science-Free Books, Judge Jones Bashing, A Dover Pro-Science Victory, and no original peer-reviewed work

On the tenth day of DISCO the DI gave to me … Conspiracy Paranoia, More Judge Jones Bashing, No Biologic Institute Research, Clueless Dover Denial, Clogging Student Blog sites. More Sternberg Spin! More Science-Free Books, Judge Jones Bashing, A Dover Pro-Science Victory, and no original peer-reviewed work

On the eleventh day of DISCO the DI gave to me … A Cheesy Flash Animation, Conspiracy Paranoia, More Judge Jones Bashing, No Biologic Institute Research, Clueless Dover Denial, Clogging Student Blog sites. More Sternberg Spin! More Science-Free Books, Judge Jones Bashing, A Dover Pro-Science Victory, and no original peer-reviewed work

On the twelfth day of DISCO the DI gave to me … A Cobb county pro-science Victory, A Cheesy Flash Animation, Conspiracy Paranoia, More Judge Jones Bashing, No Biologic Institute Research, Clueless Dover Denial, Clogging Student Blog sites. More Sternberg Spin! More Science-Free Books, Judge Jones Bashing, A Dover Pro-Science Victory, and no original peer-reviewed work

S.multipunctatus.jpg

Regular readers of my own blog may remember that I have a softspot for tropical catfish. The genus Synodontis (Cuvier 1816) is interesting for a number of reasons. For example, S. multipunctatus (the gorgeous fish pictured above) is the only fish known to practice brood parasitism: it manages to mix it eggs with those of mouthbrooding cichlids in Lake Tanganyika, its larvae grow faster than those of the host and feed on them.

Lake Tanganyika is, of course, famous for the cichlids which have been studied as an example of a rapid, recent radiation which was caused by environmental change (in this case, fluctuations in water level). It is also home to to other endemic fauna, including ten species of Synodontis. A recent study has used mitochondrial DNA to study the history of the genus in the region.

Read more over at Stranger Fruit

Barbara Forrest has written an article that will supposedly appear in January’s print edition of Skeptical Inquirer but is available online now. Titled, The “Vise Strategy” Undone, it’s a recount of the events leading up to and including the Dover trial. And it contrasts William Dembski’s pre-trial fantasies about forcing “Darwinists” to testify under oath (his self-described “vise strategy”) against what actually happened, which is that pro-science testimony carried the day while Dembski and most of his crew chickened out.

Although we’ve all been inundated with tales of Dover for the last year, this article contains a lot stuff that was new to me. This part was my fave:

Dover’s problems actually started in 2002. Bertha Spahr, chair of Dover High School’s science department, began to encounter animosity from Dover residents toward the teaching of evolution. In January 2002, board member Alan Bonsell began pressing for the teaching of creationism. In August, a mural depicting human evolution, painted by a 1998 graduating senior and donated to the science department, disappeared from a science classroom. The four-by-sixteen-foot painting had been propped on a chalkboard tray because custodians refused to mount it on the wall. Spahr learned that the building and grounds supervisor had ordered it burned. In June 2004, board member William Buckingham, Bonsell’s co-instigator of the ID policy, told Spahr that he “gleefully watched it burn” because he disliked its portrayal of evolution.

That’s so wrong on so many levels that I don’t even know where to begin.

(Cross-posted to Sunbeams from Cucumbers.)

The University of Kansas Hall Center for the Humanities has put online the videos from this fall’s “Difficult Dialogs” series. Included are talks by Ken Miller, Judge Jones, Richard Dawkins, Eugenie Scott, and Michael Behe. We had some previous discussion of the Behe talk here. (Apparently Behe was the ID guy who “discovered” that lawyers file a lot of paper with the court before, during, and after a trial, including Proposed Findings of Fact, which of course would be obvious if one had looked at the Kitzmiller documents archive that NCSE has maintained since the trial began.)

DMPC Announces the 2006 Winners of the Disease Management Intelligent Design Awards™

Hat tip to Glenn Branch on this. Here is an organization that knows how to best put the shoddy reputation of the term “intelligent design” to good use:

The Disease Management Purchasing Consortium (DMPC), the most comprehensive source of information about the disease management industry, announced today the winners of the “2006 Disease Management (DM) Intelligent Design Awards,” given annually to those contributions which most set back the evolution of the disease management and wellness fields. Just as engineers say that more is learned from a single bridge which collapses than from 100 which stay up, there are serious lessons to be learned from these often-humorous failures.

Intelligent Design™ as a phrase synonymous with failure… seems apt to me.

Spongeworthy genes

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Oscarella lobularis

What are the key ingredients for making a multicellular animal, or metazoan? A couple of the fundamental elements are:

  • A mechanism to allow informative interactions between cells. You don't want all the cells to be the same, you want them to communicate with one another and set up different fates. This is a process called cell signaling and the underlying process of turning a signal into a different pattern of gene or metabolic activity is called signal transduction.

  • Patterns of differing cell adhesion. But of course! The cells of your multicellular animal better stick together, or the whole creature will fall apart. This can also be an important component of morphogenesis: switching on a particular adhesion molecule (by way of cell signaling, naturally) can cause one subset of cells to stick to one another more strongly than to their neighbors, and mechanical forces will then sort them out into different tissues.

These are extremely basic functions, sort of a minimal set of cellular activities that we need to have in place in order to even begin to consider evolving a metazoan. Fortunately for our evolutionary history, these are also useful functions for a single celled organism, and while the metazoa may have elaborated upon them to a high degree, there's nothing novel about the general processes in our make-up. The principles of signaling and transduction were first worked out in bacteria, and anyone who has a passing acquaintance with immunology will know about the adhesive properties of bacteria, and their propensity for modulating that adhesion to build complexes called biofilms.

So let's take a look at the distribution of signaling and adhesion molecules in single-celled organisms, multicellular animals, and most interestingly, a group that is close to the division between the two (although more on the side of multicellularity), the sponges.

Continue reading "Spongeworthy genes" (on Pharyngula)

December Animalcules is up

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The latest edition of Animalcules, a monthly carnival of microbiology blogging, is up over at Aetiology.

The email exchange between Dembski and Richard Dawkins continues. Dawkins just posted an email that Dembski sent to him in 2004 (2003 actually, referring to “early next year”, which would be 2004).

It sparked a memory that I had seen it before. So I asked around. It turns out that in late 2003 Dembski sent the following email to most of the people he is spamming right now. In response to this letter in the UK Guardian by Dawkins, Dembski emailed the following. It really…well, any comment would be superfluous.

I’ve been back from the Australian Health and Medical Research Congress, a 6 day research fest, for a couple of weeks now. However, my brain is still full with the heady delights of the work I experienced there. My students gave reasonably well received talks, and I have a whole grab bag of experiments to do now (or get my students to do). While there were many things that were of deep societal interest at the conference, one of the things that struck me most was a throwaway line in a lecture about cell adhesion. Nectin, a “molecular Velcro” that helps cells stick together is a member if the Ig superfamily.

To explain why it set a light bulb off in my head, and how the knowledge that molecular Velcro shares a structure with immunoglobulins throws deep insight into the evolution of the adaptive immune system, I will beg you patience and do a very brief review of the immune system first.

The funny thing about the Discovery Institute’s Media/Judge Jones Complaint Division is how it deals with defeat. Oftentimes we will see weeks and weeks of vigorous posting about this or that political fight – but then, if they lose, they often just completely ignore it, like nothing happened.

There is another issue about L’Affaire Sternberg that I think needs to be expounded upon, one that doesn’t seem to have been addressed much at length up to this point. And that is the role of the Office of Special Council (OSC) in releasing their preliminary findings that tried to make a martyr out of Sternberg.

Below the fold I will go into a fair amount of detail about how this came to be.

Tangled Bank declares War on Christmas

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The Tangled Bank

A Tangled Bank is a good spot from which to launch an ambush—so Salto Sobrius is on the attack!

P.S. Scienceblogs had a server upgrade last night that has gone awry. Everything still looks fine, but the backend is a mess, and you won't be able to make any comments, and we won't be able to make any new entries, until it is all repaired…which will be shortly, we hope.

P.P.S. "Shortly" means it seems to have already been fixed. Hooray!

Evolution of vascular systems

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Once upon a time, in Paris in 1830, Etienne Geoffroy St. Hilaire debated Georges Léopole Chrétien Frédéric Dagobert, Baron Cuvier on the subject of the unity of organismal form. Geoffroy favored the idea of a deep homology, that all animals shared a common archetype: invertebrates with their ventral nerve cord and dorsal hearts were inverted vertebrates, which have a dorsal nerve cord and ventral hearts, and that both were built around or within an idealized vertebra. While a thought-provoking idea, Geoffroy lacked the substantial evidence to make a persuasive case—he had to rely on fairly superficial similarities to argue for something that, to those familiar with the details, appeared contrary to reason and was therefore unconvincing. Evolutionary biology has changed that — the identification of relationships and the theory of common descent has made it unreasonable to argue against origins in a common ancestor — but that difficult problem of homology remains. How does one argue that particular structures in organisms divided by 600 million years of change are, in some way, based on the same ancient organ?

One way is sheer brute force. Characterize every single element of the structures, right down to the molecules of which they are made, and make a quantitative argument that the weight of the evidence makes the conclusion that they are not related highly improbable. I'll summarize here a recent paper that strongly supports the idea of homology of the vertebrate and arthropod heart and vascular systems.

Continue reading "Evolution of vascular systems" (on Pharyngula)

The Year in ID

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What a year it has been for the Discovery Institute and the Intelligent Design movement! Over at Stranger Fruit, I detail the advances that ID has made in the short time since Judge Jones delivered his ruling in Kitzmiller v. Dover.

Update: John West has offered his version of the year for ID. Compare and contrast at your leisure

Talkorigins

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Some of you may have noticed that the Talk.Origins Archive was not accessible today. Its hosting company changed the IP address for the server that the Archive is on. The new IP address is currently propagating through the DNS network and you will be able to access the site again as soon as your ISP updates its records.

Also we’ve ordered a new server for PT and will have access to more bandwidth soon.

Update:

Current plans have us switching to the new connection tonight. This means that PT may go offline for you until your ISP picks up the new IP.

A little birdie just called to tell me that the Cobb County evolution disclaimer case has been settled, and on very favorable terms for our side. Americans United is sending out a press release which says, in part:

In an agreement announced today, Cobb County school officials state that they will not order the placement of “any stickers, labels, stamps, inscriptions, or other warnings or disclaimers bearing language substantially similar to that used on the sticker that is the subject of this action.” School officials also agreed not to take other actions that would undermine the teaching of evolution in biology classes.

It should be noted that this happens one day before the one year anniversary of the ruling in Kitzmiller, and I don’t think that is coincidental here. When the appeals court remanded this case back to the district court, not only was the case reopened for a new trial but the judge also reopened discovery and decided to allow expert witnesses to testify. I strongly suspect that this was a big influence on making the defense settle the case. After watching how effectively we used expert testimony in the Dover case, they couldn’t like that prospect. It is perhaps also worth noting that this is what real lawyers do in lieu of putting out silly “studies” based on word counts.

The AU press release is here. NCSE story is here.

The Discovery Institute is promoting a new report from a conservative Indiana Congressman about the Sternberg affair. For those who don’t recall, Richard Sternberg was the editor of the Proceedings of the Biological Society of Washington, a journal loosely associated with the Smithsonian Institution, when they published the now-infamous paper by DI Program Director Stephen C. Meyer. This is very important for their PR campaign to position themselves as victims of persecution, but the facts of the case simply do not support the conclusions of the report.

I have a detailed and comprehensive response to this report at Dispatches from the Culture Wars. Comments may be left there.

The Discovery Institute’s attempt to call Judge Jones a plagiarist for his decision in Kitzmiller was a publicity stunt, and it flopped. Nobody fell for it because it was easy to confirm the fact that judges follow proposed findings of fact all the time—that this is a routine and even a praiseworthy practice—and that the DI’s “statistics” were essentially invented, by using such weasel words as “virtually verbatim.” Moreover, we showed that their attempt to prove that courts disapprove of the practice was silliness. The cases they cited to not only did not show that Jones did anything wrong, but in some instances, were examples of routine creationist quote mining. For example, Mr. Luskin cited to Bright, but we showed that Bright said pretty much the opposite of what he claimed it said.

The DI’s position weakened further when they tried over and over again to claim that they weren’t calling Jones a plagiarist—a clumsy attempt at a paralepsis, indeed. “Oh, no,” they said, “in legal circles Jones wouldn’t be called a plagiarist”—and so forth—things that were all attempts to call him a plagiarist without actually coming out and saying it. Then they did call him a plagiarist, for a speech which had been transcribed—even though Jones had indicated that he was quoting from a published source, and even though the transcription probably didn’t reflect quote marks because spoken presentations often don’t use the word “quote….”

Anyway, now rather than admitting that this was all just an idiotic publicity stunt, Casey Luskin has a post at the DI’s blog trying to defend the idea that Jones was doing something wrong.

Tripoli 6 sentenced to death

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The 5 Bulgarian and 1 Palestinian health workers accused of having infected Lybian patients with the HIV virus were found guilty and sentenced to death today in Tripoli, despite international outcry and molecular phylogenetic evidence demonstrating their innocence. As much as it is tempting to snarkily frame this as a court victory for anti-evolution forces, the situation is too serious.

Follow the story and do what you can to add your voice to the outrage. Visit the Amnesty International web site for updates. Donate if you can.

Kenneth Miller, professor at Brown University and expert witness for the plaintiffs in the Kitzmiller v. Dover Area School District, replied to William A. ‘Divine Wind’ Dembski this morning with some suggestions for good video. I know I’d like to see it. Fortunately, he used “reply all” in responding to Dembski, so I got it in my inbox. I thought that the PT community would like to see it, too, so I asked Prof. Miller if I could get his permission to post his email, and he kindly agreed. It is appended below the fold.

DI Plagiarizes Law Review Article?

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It seems that the Discovery Institute, while disingenuously libeling a Federal judge for his routine use of findings of fact from a plaintiffs’ brief, has been engaged in plagiarism of its own work in a context where such copying is strictly forbidden. Virtually every law review has strict rules against publishing articles that substantially copy one’s own previously published works, yet the DI’s David DeWolf and Casey Luskin submitted an article to the Montana Law Review that was 95% identical to what they had written in the book Traipsing Into Evolution. Prof. Peter Irons has issued a press release concerning this, which is available at Dispatches from the Culture Wars. Comments may be left there.

Dembski’s motive

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On UncommonDescent, Dembski ‘explains’ his motivation behind the Judge Jones School of law:

Dembksi Wrote:

Just to be clear, my aim in this flash animation was not to shake up the convictions of convinced Darwinists. Rather, my aim was to render Judge Jones and his decision ridiculous in the eyes of many young people, who from here on will never take Darwinian evolution or him seriously. If the cost of accomplishing this is yet another lowering of my estimation in the eyes of PT or Richard Dawkins, that’s a price I’m only too glad to pay — heck, I regard that as a benefit of the deal.

David Opderdeck correctly observes that

The problem here is three-fold, IMHO: (1) it inculcates a disrespect for the legal system; (2) it rests on a false premise of “plagiarism”; and (3) it discredits your substantive work, particularly among those of us who really know how the legal process works.

Davescot tried to object and David responded

Molecular Clocks

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Over at Dembski & Co., there are some recent posts (here, here, and here) complaining about molecular clocks and arguing that well known and long established limitations of molecular clocks invalidate evolutionary biology.

I find it sad that a week after scientists used molecular clocks to show that the Tripoli Six did not cause an HIV outbreak, the anti-evolutionists at UD throw up some posts ignorantly questioning the well established and understood procedure. I feel like arguing that anti-evolutionists want these six innocent health workers to be executed, but I’m sure that is not the case. They just don’t get the science or even care to. But the science is important, and the ignorance engendered by anti-evolution can have life-and-death consequences.

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