October 2004 Archives

I’ve recently obtained permission from Science and an author of the recent paper “Evolution of Coral Pigments Recreated,” to use the splendid figures in a popular discussion of this important new work. Permission to post these figures was granted only for the NMSR page, so I can’t post them here, but here’s a link to my new article, “New Work Documents the Evolution of Irreducibly Complex Structures.”

Here’s a snippet:

Recent work on the evolution of pigments in star corals, “Evolution of Coral Pigments Recreated,” by Juan A. Ugalde, Belinda S. W. Chang, and Mikhail V. Matz, (Science 2004 305: 1433 (9/3/2004), Copyright 2004 AAAS) shows conclusively that “irreducibly complex” structures not only can evolve, but that they have evolved. This should lay to rest the “Intelligent Design” assertion that this type of complexity is forbidden to natural evolution.

And Ugalde et. al.’s conclusion:

The more complex red color evolved from green through small incremental transitions (a stepwise accumulation of improvements), each identified in our experiments by ancestral gene reconstruction (Fig 1D). This mode of evolution has been anticipated since Darwin, but has only recently been demonstrated in computer simulation experiments (5, R. E. Lenski, C. Ofria, R. T. Pennock, C. Adami, Nature 423, 139 (2003), “The Evolutionary Origin of Complex Features” )

Continue reading “New Work Documents the Evolution of Irreducibly Complex Structures” (offsite at NMSR)

In his 2004 paper “The Origin of Biological Information and the Higher Taxonomic Categories” Meyer introduces the reader to the concept of Shannon information. Despite the fact that the paper is presented as an ‘extensive review paper’ which ‘ argues that no current materialistic theory of evolution can account for the origin of the information necessary to build novel animal forms’ Meyer forgets to add the relevant scientific research showing how variation and selection can increase Shannon information in the genome.

What I find surprising is the number of references omitted in this review paper directly relevant to the origin of biological information.

December’s Backpacker Magazine has a long article about rafting the Grand Canyon in ICR style. The author, an Evangelical-Christian-turned-Agnostic describes his adventures with the group that included Tom Vail, Steve Austin, Andrew Snelling, a doctor, a pathologist, a chiropractor, a home-schooling family of four, and a pair of chicken farmers, among others. It was a nine day trip that started at Lee’s Ferry with a description of how the layer below the Great Unconformity is the closest to the land Noah walked on. As the trip continued, the author wondered if Stockholm syndrome explained why he was starting to think that the creationist geology had some sense to it. The authored described a worship service that took place before they left Marble Canyon and entered the Grand Canyon. I think it offers a good feel for the article and the trip.

The day before we descended into the canyon, we attended church services on the rim. After hymns and prayer, a preacher from ICR got to going, and brother, he could bring it. I like some good preaching, and this was that. He paced the riser, he found his cadence and he worked it. He took it up, and he took it down. He spoke of invisible things, of how man can only define God in the things He has made, which means we have all seen God, which means that we are left no excuse of disbelief. He got some mm-hmms with that one. Riffing in the area of Romans 1:22, he spoke of men so full of their own philosophy they become blind to what God has made. He mentioned Carl Sagan, and did a little billions and billions impression. Then the preacher came to a full stop, stage right, and looked out at us with his head at an impish tilt. Stood there silent for two beats, then said, “By the way, ol’ Carl knows what’s goin’ on now!” The congregation bubbled with chuckles. The preacher held a smug pose, on hand sucked aw-shucks style in a pants pocket, the other held flat beneath the splayed Bible from which he had been quoting without looking. As the chuckles spread, the preacher rolled his eyes and gave the Bible a little bounce. And I’ll tell you, he lost me right there. You want to lure me back, brother, show some compassion. Before honor is humility, if you’ll allow me a little Old Testament. Drop to your knees and pray through tears that our fellow sinner Carl might yet be redeemed. What you had there was a jig danced on a lost soul. I’d heard those chuckles before, from people of my own congregation, as they listed to one of our preachers recount how he turned his back on a struggling member after he caught her wearing shorts. From that day forward, I’ve tried to reconcile the deep goodness of my childhood church with the poisonous little seems of petty certitude. If found myself doing a similar thing in the canyon, trying to reconcile the chuckles on the rim with the sincere smiles all around me.

Don’t forget to check out the November Issue which had a little blurb about Dinosaur Adventure Land.

Cobb County update

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For those following the Cobb County disclaimer case, the law firm handling the case has informed me that trial has been set for November 8. (Court dates are, of course, always subject to change.)

Wedgie’s World: Stung not bitten

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ID proponents are stumbling over themselves in their haste to come to the defense of the Meyer 2004 review paper. But rather than defending the paper (given the critiques, an unenviable task now delegated to unnamed ‘DI Staff’), they quickly readjusted their sights and settled for strawmen to shoot down (see for instance the ‘response’ by DI Staff to Meyer’s hopeful monster. Only by creating a strawman argument as to what Gishlick et al were arguing can they even hope to make their case. And I won’t even mention the poor reading comprehension of the papers which were given to Meyer as examples of relevant papers missed by Meyer in his ‘review paper’.

Another example is a recent article by Mark Hartwig.

Although the article itself has received a share of the abuse–mostly in the form of a “critique” published on the Panda’s Thumb blog–the main target has been the editor who published the piece, Richard Sternberg. Mark Hartwig in Bitten

I understand that to ID proponents, peer review can feel like ‘abuse’ but that is mostly because typical ID ‘research’ tends to be based on appeal to ignorance and a restricted view of science. Unfamiliar with peer review, it may come as a shock when scientists expose the many flaws and shortcomings in what some may have hoped would be a glorious entry of ID into the world of science. But as the critique on Panda’s Thumb has shown, ID cannot really withstand the scrutiny of critical peer review. (A conclusion further supported by the response by the DI staff)

And that must sting…

Historically, the central dogma in molecular biology has been that the genetic information in DNA is transcribed into intermediate RNA which are translated into amino acids to form proteins. Proteins were seen as the primary regulators of the expression of genes. While this picture appears to be correct for prokaryotes, a different picture arises for eukaryotes.

Mathematical considerations have shown that while generating complexity is simple, controlling it isn’t. The amount of regulation needed tends to scale as the quadratic of the number of genes. The genome size of prokaryotes seems to be limited by these considerations.

Homo floresiensis

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Flores Man

A long-lost cousin has been discovered, Homo floresiensis, or Flores Man. It's especially dramatic for a number of reasons. It's relatively recent, with the youngest specimen only 18,000 years old, but it is most closely related to Homo erectus. This species was also minute, only 3 feet tall, and tiny-brained. Here we have a group of small, specialized human relatives, living contemporaneously with Homo sapiens, on isolated islands in Indonesia. It's like discovering that Munchkins were real. You can read more here:

An ID Curriculum?

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Over at ARN this was proposed as curriculum for Dover, PA new biology policy.

The theory of ID posits the following:

  • High information content (or specified complexity and irreducible complexity constitute strong indicators or hallmarks of past intelligent design.
  • Biological systems have a high information content (or specified complexity) and utilize subsystems that manifest irreducible complexity.
  • Naturalistic mechanisms or undirected causes do not suffice to explain the origin of information (specified complexity) or irreducible complexity.
  • Therefore, intelligent design constitutes the best explanation for the origin of information and irreducible complexity in biological systems.

reference page 92 of Darwinism, Design and Public Education

As far as I can tell, the person who posted this is serious. From a logical standpoint, the major flaw in this “theory [sic] of ID” is that it relies solely on negative argumentation. It tries to prove “intelligent design” true by disproving something else. Such an argument rarely works in science because one has to first demonstrate that both the “proved” and “disproved” explanations together make up the complete set of all possible explanations. People who rely on negative argumentation seem to always ignore the unknown.

The problems with the proposal go beyond that because number four does not follow from number three even if we grant that there is a complete set. If hypotheses X and Xc are a complete set, and X explains 90% of the data, whereas Xc explains 10% of the data, neither is sufficient. But according to the logic employed in the ID argument above, Xc would be declared the best explanation because X is not sufficient. However, X is actually the best explanation on the criterion given despite the fact that it is not sufficient.

Points one, two, and three are popular talking points of “intelligent design” activists but are not supported by any scientific research. (If you disagree, feel free to provide references to the peer-reviewed scientific papers that demonstrate any of these things.) As such they are entirely inappropriate for a secondary school science curriculum that treats them as anything other than the pseudoscience they are.

Another obvious flaw is that “information” is not defined in any biologically meaningful way (or at all). Under some definitions of “information,” high information content is the hallmark of a completely random process. “Information” as a formal concept is butchered by “intelligent design theorists” almost as badly as the Second Law of Thermodynamics is butchered by Young Earth Creationists.

If this represents what “intelligent design” activists think counts as science, then its only use in a science classroom is to point out how to not do science.

In an opinion column for the Iowa State Daily, Scott Rank, a senior in journalism and mass communication from Knoxville, addresses intelligent design, and the recent lecture where two ISU professors addressed the fallacies and problems with Guillermo Gonzalez’s and Jay Richard’s “The privileged planet” [1].

Scott Rank’s comments show some excellent examples of the shoddy research of the issues as shown in detail by two Panda’s Thumb regulars: Richard B Hoppe and Gary Hurd. With permission of the authors I am reproducing their responses here since they show clearly what is wrong with Intelligent Design and its proponents. Richard B Hoppe has already posted his comments on Panda’s Thumb so I will focus on the comments by Gary Hurd and comments by the “Faculty and Graduate Students of Ecology, Evolution and Organismal Biology”.

Journalists Against Evolution

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The parade of those whose qualifications to knowledgeably evaluate a scientific theory are non-existent continues. Last week it was real estate agents, this week a student journalist at Iowa State.

Scott Rank, Opinion Editor of the Iowa State Daily, published a column describing a recent on-campus forum in which Guillermo Gonzalez’s The Privileged Planet was critiqued by Professors Hector Avalos and John Patterson of Iowa State. Avalos is characterized as “Iowa State’s most beloved atheist,” while Patterson, a retired faculty member, is a long-time critic of creationism. (Jim Foley discusses TPP briefly here.)

I’ll not discuss in detail most of the errors in Rank’s column – they’re familiar to anyone with some passing acquaintance with IDist bloviations. Three specific aspects of the column, though, are of interest given that Rank is allegedly a senior journalism major. It’s not just that Rank is scientifically ignorant: his column displays a careless disregard for both accuracy and journalistic ethics. It’s in the best tradition of hack propaganda, complete with a fictitious quotation.

Titan flyby #1 today

Remember Cassini, the multibillion dollar spaceship we put in orbit around Saturn back in July? (If not, see the PT posts Say hello to Phoebe and First decent views of the surface of Titan, and the Cassini website).

Well, it has taken awhile for Cassini to do its first full orbit, but it is back in the inner Saturnian system, and today it completed its first flyby of Titan, the solar system’s largest moon and only moon with a thick atmosphere made of nitrogen and organic compounds.

Cassini will pass within 746 miles of Titan – a mere 10 hour drive on the freeway – and snap up close photos, and image the surface in detail with atmosphere-penetrating radar.

In a Letter to Nature, Vladimir Svetlov makes the following observations talking about the Meyer 2004 paper:

Your News story Peer-reviewed paper defends theory of intelligent design” (Nature 431, 114; 2004) suggests that getting an intelligent-design paper into a peer-reviewed journal is a huge achievement for creationism. I am more surprised it took so long to get one in.

Dr Svetlov continues to observe:

The paper in question presents no new arguments and is unremarkable in any way except in that it has been published. It appeared in a journal that, until this particular editorial decision, enjoyed much-deserved obscurity. Proponents of intelligent design would have us believe that this publication is a testament to the scientific legitimacy of their theory – although the editor has since left and the journal has disowned the paper as “inappropriate” (see Nature, 431, 237; 2004).

In my opinion it is yet another testament to the rampant proliferation of scientific publications, resulting in a flood of inconsequential papers appearing in those thousands of journals that exist on the fringes of scientific publication. The real dirty secret of academic publishingNature 431, 897 (21 October 2004)

Politics and evolution

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A [URL = http://www.pandasthumb.org/pt-archi[…]/000568.html]recent blog by Matt Young[/URL] has more than a few folk upset. I am not upset, exactly, but I do not agree with the way he characterised the political spectrum, or the general features of the parochial duopoly he has drawn from American party politics. Most of all, though, I object to the notion that biology, in particular evolution, has any warrant in such debates at all.


A while back I posted about the school district in York, Pennyslvania, which decided to add the creationist book From Pandas To People to their classrooms. The school board chose not to require it as part of the curriculum, but did place it in classes for teachers to use, which I said was inappropriate.

It turns out the school district has decided to go farther.

green spotted pufferfish

The fugu is a famous fish, at least as a Japanese sushi dish containing a potentially lethal neurotoxin that was featured on an episode of The Simpsons. Fugu is a member of the pufferfish group, which have another claim to fame: an extremely small genome, roughly a tenth the size of that of other vertebrates. The genome of several species of pufferfish is being sequenced, and the latest issue of Nature announces the completion of a draft sequence for the green spotted pufferfish, Tetraodon nigroviridis, a small freshwater species.

Tetraodon has about the same number of genes as we do, 20,000-25,000, but they are contained in a total genome length of 340Mb vs. our huge 3.1Gb. One major difference is that in Tetraodon, transposable elements are rare: they have 73 types, present in less than 4000 copies, but humans have about 20 different types present in millions of copies. Transposable elements may be reverse transcriptases that blindly copy RNA sequences back into the DNA (called LINES) or shorter sequences that are processed by LINES, called SINES. These really are parasitic bits of selfish DNA, and somehow, pufferfish seem to be largely free of them.

One of the interesting things one can do with a pair of genome sequences is to start mapping synteny. Synteny represents the preservation of small regions of order within a chromosome; while the overall organization may have been scrambled by millions of years of chromosome breaks and fusions and duplications and deletions, we can still identify smaller blocks that maintain the same series of genes within them. For example, if we look on a chromosome of one organism and we see the series of genes A-B-C-D-E-F, and we look in another organism and find a chromosome with the genes W-X-C-D-E-Y-Z, we can see that the C-D-E chunk can be mapped directly to one region of that second organism's chromosome.

Continue reading "Pufferfish and ancestral genomes" (on Pharyngula)

Real Estate Agents Against Evolution

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Peter and Helen Evans, identified as real estate agents who “teach a philosophical approach to conservatism,” published a response to Evan Ratliff’s Wired article about the ID Movement. The column was published on Mullenax News, a far-right wing Web site that advertises itself as “Always Tough” and “Always Honest.” Pity the same can’t be said about its columnists.

Happy 6000th Birthday, Earth!

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Yes, folks, today is the Earth’s 6000th birthday, according to the famous Bishop Ussher. In 1650, he famously calculated the age of the Earth using the biblical timeline based upon the ages at which various people were begat and came up with October 22nd, 4004 BC. At around 6 pm. Technically, the 6000th birthday was actually in 1997, owing to odd lineups in various calenders, but such pedantry would just ruin a good party.

She looks pretty good for 6000, don’t you think? A little bigger around the equator, perhaps. The smog has made her a little more gray around the temples, and global warming a little thinner on top. But all in all, not a bad planet to call home. So raise a glass and sing “For she’s a jolly good planet”, something nobody can deny, and bust out the cake. What do you get for the planet that has everything?

The human genome project has reached another landmark, the effective completion of the euchromatic sequence. It's still not 100% done, but the remaining small bits are going to require some new tricks to ferret out. You may recall announcements all over the place back in 2001 that the genome had been sequenced, but that was the draft sequence; 90% of the euchromatic genome was done, but there were still about 150,000 gaps scattered through it. You have to think of this project as something like assembling a colossal jigsaw puzzle—when the draft was done, we had a pretty good idea of the structure of the picture, and maybe had the borders done, but there were still these broad patches of solid colors that hadn't been pieced together yet. At this point, though, most of those have been filled in and the gaps are smaller and sparser.

Some numbers: the completed sequence so far consists of 2,851,330,913 nucleotides. There are only 341 gaps left in the sequence. and 33 of those are in the heterochromatin (the mildly boring, repetitive chunks of the genome, which correspond to those regions of solid color in a jigsaw puzzle), representing 198 megabytes of stuff that still has to be sequenced. In the euchromatin (the more interesting and complex stuff) there are more gaps, 308, but they are much smaller, so only 28 Mb of mystery remains. The total length of the genome is 3.08 Gb, with 2.88 Gb of it in the form of euchromatin.

The new, better defined sequence allows for a more accurate count of total gene number, and that number has dropped once again. We're down to 20-25,000 protein-coding genes. Some may think that knocks us off our pedestal a bit more, but that sounds like plenty to me.

One thing that leaps out at anyone reading the announcement is the importance of evolution in analyzing and understanding the genome. They used alignment with the chimpanzee draft sequence, for instance, to search for deletions. They are identifying recent duplications by their degree of divergence from neighboring genes, and have found 1,183 new genes that have arisen since the human and rodent lineages split. They're tracking the death of genes by identifying sequences with small numbers of disabling mutations (we seem to be losing olfactory genes at a rapid clip, relative to rodents).

The bottom line is that the HGP has provided us with a better tool for all kinds of research.

Nonetheless, the euchromatic human genome can now be regarded as effectively known. The accuracy and completeness of the current near-complete human genome sequence has important consequences for biomedical research. It allows systematic searches for the causes of disease—for example, to find all key heritable factors predisposing to diabetes or somatic mutations underlying breast cancer—with confidence that little can escape detection. It facilitates experimental tools to recognize cellular components—for example, detectors for mRNAs based on specific oligonucleotide probes or mass-spectrometric identification of proteins based on specific peptide sequences—with confidence that these features provide a unique signature. It allows sophisticated computational analyses—for example, to study genome structure and evolution—with confidence that subtle results will not be swamped or swayed by noisy data. At a practical level, it eliminates tedious confirmatory work by researchers, who can now rely on highly accurate information. At a conceptual level, the near-complete picture makes it reasonable for the first time to contemplate systems approaches to cellular circuitry, without fear that major components are missing.

International Human Genome Sequencing Consortium (2004) Finishing the euchromatic sequence of the human genome. Nature 431:931-945.

Tangled Bank #14 exists!

The Tangled Bank

We have another Tangled Bank—#14 is online at Prashant Mullick's Weblog. He had me worried for a while that darn few submissions were coming in, but as usual, there was a last-minute flurry and we have an entertaining and diverse assemblage of biology posts.

There will be more to come at The Sixth International in two weeks, so send us those links. Also, I'm still looking for more hosts, so if you're willing to collect and organize a few web links, volunteer!

Development of cavefish eyes

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astyanax

Here's a story that Darwin got completely wrong. He had observed that certain species had profoundly reduced or rudimentary organs, and he explained them not as a consequence of natural selection, but as evidence of the inheritance of acquired characters.

But we learn from the study of our domestic productions that the disuse of parts leads to their reduced size; and that the result is inherited.
It appears probable that disuse has been the main agent in rendering organs rudimentary. It would at first lead by slow steps to the more and more complete reduction of a part, until at last it became rudimentary,- as in the case of the eyes of animals inhabiting dark caverns, and of the wings of birds inhabiting oceanic islands, which have seldom been forced by beasts of prey to take flight, and have ultimately lost the power of flying.

It's easy to feel mildly embarrassed for Darwin on reading this now; it was an honest error, though, and since he had no good model for inheritance, he fell back on an old idea, that the use or disuse of an organ in the parent would have an effect on its progeny. Blind fish lost their eyes because Mom and Dad fish lived in the dark and never used their eyes, so Junior inherited weaker eyes.

As it is difficult to imagine that eyes, though useless, could be in any way injurious to animals living in darkness, their loss may be attributed to disuse.

Well, actually, Charles…it's not difficult to imagine at all. Eyes are fragile, pulpy things that represent a significant investment in energy. I could imagine that there would be a slight selective advantage to jettisoning something an animal isn't using, that costs it effort to develop or is a weak or sensitive point of attack. Since we've long discarded the hypothesis of the inheritance of acquired characters, that's one of the primary explanations for the loss of eyes in cave animals—their absence was an advantage.

Another explanation is that eyes are effectively a neutral character in dark environments, and that there is therefore no selective advantage in maintaining them. Cave organisms acquired mutations that knocked out the eyes, and in the absence of selection to maintain sight, these mutations accumulated until the entire population was lacking eyes.

There is a third possibility, now supported by observations in blind cave fish of the genus Astyanax. Despite being wrong on the mechanisms of inheritance, Darwin was no dummy, and he almost figured this one out. If he'd had just a little more intuition about development, he might have suggested this idea. Here's the tantalizingly close passage:

By the time that an animal had reached, after numberless generations, the deepest recesses, disuse will on this view have more or less perfectly obliterated its eyes, and natural selection will often have effected other changes, such as an increase in the length of the antennae or palpi, as a compensation for blindness.

The third possibility requires that one recognize that development is not infinitely plastic, that characters are linked in development, and that maybe the only way to develop these compensatory structures is at the expense of the eyes—that is, that there is a selective advantage to developing long antennae or palpi or other organs, but that the simplest developmental process to do so involves cannibalizing eye tissue. This explanation is an example of the way knowledge of developmental biology can inform our understanding of evolutionary biology.

Continue reading "Development of cavefish eyes" (on Pharyngula)

Dick Armey, the former House majority leader has famously (or infamously) remarked that liberals are not very bright (Johnson, 2004). The claim is as arrogant as it is wrong: neither faction has a monopoly on intelligence. The difference is in the gut.

Steven Johnson, in “The Political Brain,” notes that people become Republicans or Democrats before they learn what those parties stand for. He argues that people with like outlooks congregate and that party affiliation initially results from whom you hang around with rather than from dispassionate consideration of the issues.

Johnson notes further that you cannot make a so-called rational decision without emotional involvement, and that is what I want to amplify on here.

Privileged Planet, Mk. 1

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Alfred Russel Wallace, the co-discoverer of natural selection, published a book in 1903 called “Man’s Place in the Universe: a Study of the Results of Scientific Research in Relation to the Unity or Plurality of Worlds”. Stephen Jay Gould wrote about it in one of his Natural History columns, and later reprinted it as the essay “Mind and Supermind” in his book The Flamingo’s Smile. Gould summarizes Wallace’s argument thus:

…Wallace examined the physical structure of the earth, solar system, and universe and concluded that if any part had been built ever so slightly differently, conscious life could not have arisen. Therefore, intelligence must have designed the universe, at least in part that it might generate life.

Sound vaguely familiar? Compare it to a synopsis of Privileged Planet, a book currently being hyped heavily by the Discovery Institute. (Gould, however, was writing his essay in response to proponents of the ‘anthropic principle’, especially Freeman Dyson.)

Tangled Bank is on its way

The Tangled Bank

Remember! The next edition of the Tangled Bank will be at Prashant Mullick on Wednesday. Send your submissions directly to Prashant, to host@tangledbank.net, or to me.

Good for Derbyshire

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I'm very far from being an admirer of John Derbyshire, and I'm sure that there are other things in this article which will bother people, but conservatives tend to be so willing to accommodate the creationists that I was really pleasantly surprised that Derbyshire would say

Human beings must have their consolations in this cold world, and wishful thinking is by no means only found on the political left, as Creationism and the "Intelligent Design" flapdoodle illustrate. Science ought to be trusted. Careful, peer-reviewed science--even human science!--ought to be read with respect, and with calm objectivity, and with the yearning to understand this strange universe, shot through as it is with mystery and wonder.

It's refreshing to see that not all of the National Review crowd are under the ID illusion.

Del Ratzsch

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Del Ratzsch presented a lecture “Could ‘Intelligent Design’ be Legitimate Science?” Tuesday, Oct. 12, at 7 p.m. in the Benton Auditorium in the Scheman Building (Iowa State Center) as part of the Areopagus Lecture Series ISU (corrected from an earlier reference to God at Work at ISU) While Del Ratzsch argues that ID may hold promises, he also remarks that so far ID has failed to make much of a case. Not surprising since ID lacks any scientifically relevant hypotheses.

The Iowa State Daily reported under the headline Intelligent design theory merits regard, speaker says

Ratzsch’s speech was based on the question, “Could Intelligent Design be Legitimate Science?” His conclusion was that intelligent design deserves attention in the scientific community as it competes with naturalistic evolution as a possible explanation for why things are the way they are.

He stipulated that he didn’t mean he espoused the claims of intelligent design theorists.

“I don’t think the design case has yet been convincingly made,” Ratzsch said. “I think that design advocates have raised some intriguing issues. Intelligent design theory merits regard Iowa State Daily

While researching the hot topic of ALU repeats for my posting on evolvability, I ran across the following paper

Alu elements and hominid phylogenetics by Abdel-Halim Salem, David A. Ray, Jinchuan Xing, Pauline A. Callinan, Jeremy S. Myers, Dale J. Hedges, Randall K. Garber, David J. Witherspoon, Lynn B. Jorde, and Mark A. Batzer published in PNAS October 28, 2003 vol. 100 no. 22 12787-12791

Let me add a disclaimer that I am a novice when it comes to evolutionary biology. While I am familiar with the term such as ALU repeats, SINE and retroposons, I am not by any means an expert. Nevertheless, I like to share my research and learning with the readers of Panda’s Thumb, in the hope that 1) people like me who are similarly interested in learning more about “what is hot” in evolutionary theory can learn about some of the details 2) others, more capable than me, can add their comments, suggestions and objections.

War of Reviews

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In this essay I will discuss some of the devices intelligent design (ID) advocates and purveyors of other brands of creationism employ in what they refer to as the “cultural war” which they intend to “win” at any cost regardless of whose side the truth is on.

The term “cultural war” was, for example, used by one of the most prolific advocates of “intelligent design,” theologian William Dembski in his lecture at the Fellowship Baptist Church in Waco, TX, on March 7, 2004. 1 The intention to win that war regardless of whose side the truth is on, was, for example, clearly stated by Dembski in his post. 2

I will refer here mainly to the reviews posted to the Amazon.com website which serve as one of the devices creationists often employ to achieve their goals, in particular to denigrate the books critical of the ID literary production.

One example illustrating my thesis is how the ID advocates have reviewed my book, Unintelligent Design, as well as the anthology Why Intelligent Design Fails (edited by Matt Young and Taner Edis), the book Creationism’s Trojan Horse by Barbara Forrest and Paul R. Gross, and the book God, the Devil and Darwin by Niall Shanks.

Mei long, the sleeping dragon

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mei long

Those new fossils just keep pouring out of China. Here's a new troodontid dinosaur with the lovely name of Mei long, which was discovered intact as if caught abruptly in the instant of its death. Troodontids are long-necked bipedal dinosaurs that look rather ostrich-like. This one is a juvenile that died suddenly in its sleep, and is presumably in its normal resting posture.

Continue reading "Mei long, the sleeping dragon" (on Pharyngula)

The DI Strikes Back

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True to their word, the DI staff has begun their rebuttal to Gishlick et al.’s PT critique of Meyer’s 2004 paper in PBSW. The DI reply is entitled “Neo-Darwinism’s Unsolved Problem of the Origin of Morphological Novelty.” For a history and (almost) comprehensive links, see The “Meyer 2004” Medley.

Rather than responding in this initial post, let me recommend a strategy for those of us that might wish to make a few counterpoints to the DI (after you’ve finished repairing your irony meters). Folks may follow these recommendations or not as this is something of an experiment.

If you are itching to comment on a particular point on the DI page, then give your comment a title (using bold tags: [bold]text[/bold] with “b” instead of “bold”) indicating what it is about. Then continue with your comment on that topic. If you comment on another topic, give it another title.

If you comment on the DI piece elsewhere (e.g., another PT post or an online forum), please add a link or carbon copy the text into the comments on this page.

The idea behind this is that rather than just have the usual disorganized commenting free-for-all, the comments page will be semi-organized so that people can find various topics and see which ones have been addressed, and which not. If a fair number of people do this, we will end up with a point-by-point critique (that might end up as e.g. a talkorigins FAQ) much faster than one person can write something. I’ll post an example in the comments to start it off.

Like I said, this is an experiment, but hey, this is the blogosphere, right?

by Ian F. Musgrave, Steve Reuland, and Reed A. Cartwright

“There’s precious little real biology in this project,” Mr. Behe said. For example, he said, the results might be more persuasive if the simulations had operated on genetic sequences rather than fictitious computer programs.

Michael J. Behe was commenting in The Chronicle of Higher Education (Kiernan 2003) on a paper reporting that digital organisms could evolve irreducibly complex systems without intervention (Lenski et al. 2003). Ironically, Behe has just coauthored a theoretical paper with David W. Snoke on the evolution of complex molecular adaptations that has “precious little real biology” in it. William Dembski has already stated that Behe and Snoke’s research “may well be the nail in the coffin [and] the crumbling of the Berlin wall of Darwinian evolution” (Dembski 2004). Despite the common claim made by “intelligent design” activists that evolution is in trouble, they have so far been unsuccessful in presenting their arguments to the scientific community. Is this the long-awaited peer-reviewed publication which will finally do it?

School Board May Censor Books, Hand Out Bibles

Young supports a recent board recommendation that calls for “removing anything (from reading lists) that provides a neutral or positive view of immorality or foul language.”

But some in the southern Maryland county are upset, fearing that some board members are attempting to impose personal religious and moral beliefs on the public schools.

They point to the book list and a proposal that recommends distributing Bibles in schools, removing science books “biased towards evolution” and teaching sexual education classes focused exclusively on abstinence.

“They’re basically trying to skew the curriculum, to teach their own conservative Christian values,” said Meg MacDonald, a representative from the Charles County Education Association.

A Voyage to Lawrence, Kansas

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Jay Manifold of A Voyage to Arcturus has a series of posts summarizing The Panda's Thumb's own Jack Krebs' recent talk on the Kansas science standards. It's thorough; consider it a kind of independent review.

Here's the list of articles on the talk:

(Good news: I think Jack passed the review.)

More on Dennett and Wright

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Over at EvolutionBlog I have just posted a series of entries dealing with the recent bru ha ha over Robert Wright's interview with Daniel Dennett.

I wrote those entries before reading Timothy Sandefur's marvelous post on the same subject here. I came to many of the same conclusions as Timothy. He also made a number of points I wish I had thought of! Hopefully he will have the same reaction to my thoughts on the subject...

What is it really about?

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A high school student doing an article on evolution and Intelligent Design for her school newspaper asked me for a summary “in simple language of what the issue between intelligent design and evolution in Kansas really is.” This was a good but challenging suggestion.

In response I sent her the following:

The Ascent of Man

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I see the Discovery Science channel is showing Jacob Bronowski's 1973 miniseries The Ascent of Man. It's a classic work of science, history, and philosophy, eloquently and beautifully created, and certainly Bronowski's masterpiece, despite several small flaws. I'm a great admirer of Bronowski (about whom I wrote for Liberty magazine in December, 2002). One astounding thing about this 13-hour miniseries is that it was almost entirely performed extemporaneously: the director pointed the camera at Bronowski, and he just talked. It's a magnificent achievement, and I encourage our readers to tune in!

On the subject of debates about ID

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After my speech at the University of Kansas a few weeks ago (see Kansas Citizens for Science), a number of ID supporters complained that even though both Chancellor Hemenway and I referred to the discussion as a debate, my speech just represented one side of the issue. In response to a post on a local discussion forum, I promised I would address this complaint, which I will now do here.

Breakthrough in Pest Control?

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There’s a new article out about a new breakthrough in controlling pesticide resistant insects in Australia, one which involes trying to shut down their ability to resist pesticides:

Australian and British scientists have achieved a technical breakthrough to help control insects that have developed resistance to common agricultural pesticides, the New South Wales state government said on Thursday.

[…]

“Developed by the NSW Department of Primary Industries and Rothamsted Research in the UK, the technique relies on the use of naturally occurring enzyme inhibitors to disarm an insect’s defense system,” Macdonald said.

“The enzyme inhibitor acts first to shut down an insect’s resistance mechanisms. A few hours later, while the bug’s defenses are still low, the pesticide kicks in.”

Gotcha!…?

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Daniel Dennett is among the foremost writers on the philosophical issues surrounding evolution. Indeed, I consider him the greatest philosopher alive. Among his books are Darwin's Dangerous Idea, Consciousness Explained, and Freedom Evolves. He's attacked creationism and its surrounding notions time and time again. But--gasp!--he's admitted that Intelligent Design makes sense!

No, not really.

Newest NAGPRA News

The Center for the Study of the First Americans has issued their comment on the amendment to NAGPRA. This amendment, as I've blogged before, would appease creationists by seriously curtailing the ability to do research on ancient skeletons in America. More on how you can help protect science here.

Urochordates and neural crest

urochordates

The neural crest is an example of a profound evolutionary innovation in vertebrates. It seems to be something simple—it's a population of cells that are 'left over' at the closure of the neural tube, and that wander out into the other tissues of the body—but it has been co-opted in numerous ways to provide major vertebrate features. You wouldn't have much of a face without the neural crest, for instance; this plastic population of migrating cells get recruited to build much of what lies below your eye sockets, along with some radical reorganization of branchial arches. These cells also form the myelin sheaths of your peripheral nerves, and most visibly, form all of the pigmentation in your skin. Having neural crest in the embryo, obscure as it is to most people, is considered to be one of the hallmarks of being a vertebrate.

One particularly pressing question, then, is where the neural crest came from (and no, divine prestidigitation or alien tweaking aren't under consideration, at least not until someone comes up with actual evidence for such designer intervention.) Where should we look? In lineages that branched off of the chordate line before the evolution of vertebrate neural crest. One such lineage is the urochordata.

Continue reading "Urochordates and neural crest" (on Pharyngula)

Another DNA discoverer dies

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Maurice Wilkins, whose X-ray photographs of DNA were central to Watson and Crick's later elucidation of the structure of DNA, and who shared the Nobel Prize with them, died in London Tuesday.

Why, it looks like a big chicken!

Here are some closeups of some fossilized bones from the early Cretaceous. Look closely:

tyrannosaurid

They've got fine filamentous feathery hairs all over them—it's a dinosaur with feathers. One very cool thing about it is that this is a basal tyrannosaurid, a new species named Dilong paradoxus.

Continue reading "Why, it looks like a big chicken!" (on Pharyngula)

Tipler on Peer Review

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I have resumed my analysis of the essays in William Dembski's anthology Uncommon Dissent. I am currently working my way through Frank Tipler's contribution, entitled “Refereed Journals: Do They Insure Quality or Enforce Orthodoxy?” This essay seems especially important in light of Stephen Meyer's recent paper, reported on extensively at this site and others.

My first two posts, over at EvolutionBlog, can be found here and here, I discuss four examples of Tipler distorting other's people's work or telling dubious anecdotes. For example, he suggests that the criticisms of neo-Darwinian theory offered by Lynn Margulis in her book Acquiring Genomes: A Theory of the Origin of Species are effectively equivalent to those being made by Behe and Dembski. He further asserts that Ernst Mayr, in his foreward to the book, agrees that neo-Darwinism has the flaws Margulis (and by extension Behe and Dembski) describe. I show that both of these claims are nonsense.

Tipler's essay is long on arrogance and dubious generalities, but very short on substance. His bombast has to be cleared out of the way before his arguments can be addressed. I have not yet addressed his arguments on peer review, but that is coming in a later posting. Enjoy!

The Tangled Bank

Tangled Bank #13 is online at Preposterous Universe, and it contains 19 entries. Wow—that's our record so far. And while you're over there, be sure to send belated birthday greetings to Sean.

And there's more to come! The next edition will be at Prashant Mullick on October 20th. Send your submissions directly to Prashant, to host@tangledbank.net, or to me.

Creationists like to say that evolution's influence is dying and that it is of little importance to doing biology. They take advantage of the layperson's lack of familiarity with the scientific literature to argue that evolution has little relevance, or that Dobzhansky's aphorism that "nothing makes sense in biology except in the light of evolution" is false. Anyone who actually reads the biological literature, though, will come away with exactly the opposite impression: the journals are full of references to evolution, even in disciplines and journals that don't have "evolution" in their title. The concept is central; it's as ubiquitous as references to "genes".

To demonstrate, I've carried out a quick exercise, similar to one I've done before. The latest copy of one of the major journals in my field, Developmental Biology, just arrived in my mailbox. It's a top-notch journal, affiliated with our biggest organization, the Society for Developmental Biology. It's not evolutionary biology directly, but there has been an increasing awareness of the significance of evolution to our field, so it's a good representative of an expanding, hot field which is experiencing some synergy with other disciplines.

What I did was to quickly skim through each of the 21 articles in Volume 274, Issue 2, of Developmental Biology, and ask myself how much each article depended upon or discussed the topic of evolution. I categorized and color-coded each one by the following criteria:

Blue articles are explicit in their discussion of evolution, proposing evolutionary connections or even testing evolutionary hypotheses. The evolutionary aspect may not be the major point of the paper, but it is discussed.
Green articles treat evolution as implicit; they may work with molecules homologous between different species, but they don't specifically address evolutionary ideas. This is not to say that they have a lesser commitment to evolution, but more that they take it for granted.
Gray articles don't say anything one way or the other about evolutionary relationships. Most often these are papers that are tightly focused on analysis of data from a single species. It's entirely possible to imagine a creationist writing these, but of course there is no implication that the authors deny evolution.
Black articles would be ones that directly discuss Intelligent Design or other anti-evolutionary ideas about science. This is a hypothetical category; none were found.

Here is my classification of each of those articles, with a brief justification for why I put each in its particular category.

Continue reading "How often do biologists talk about this evolution stuff, anyway?" (on Pharyngula)

I was extremely disappointed to see that the Society for American Archaeology has issued a statement supporting the amendment of NAGPRA which, if passed, would severely limit the ability of scientists to study ancient remains found on federal land. (More on this amendment below.) SAA says that they're just fine with the destruction of ancient skeletal remains, intended to appease American Indian creationists; they just oppose the way the amendment was introduced (rather quietly, and without substantial public comment). More on how you can help protect science at the Friends of America's Past.

Update: Thanks to inappropriate response, here is what the American Association of Physical Anthropologists has to say.


The school district in York, Pennsylvania has come to a compromise of sorts on the use of the book Of Pandas And People (1989) in the classroom. This book is controversial because it includes various ID elements. I haven't read it, but glancing through it, there are some pretty objectionable statements--statements that show how illusory is the attempted distinction between creationism and ID.

Phillip Johnson has once again “clarified” his position on the age of the Earth. You can read my previous comments about this issue here.

On the comments page of Touchstone magazine, we’re treated to an email that Johnson sent to his list. (Note: this is not a permanent link, it will eventually be archived.) Johnson is apparently touring the U.K. with Andrew Snelling from the Institute for Creation Research, a fervently YEC outfit. So does this mean Johnson is showing his true colors as a YEC? This is what he has to say:

I received the message below, forwarded from from [sic] a theistic evolutionist Christian College professor (the explanations in brackets are mine, not Phil’s):

The following paragraph comes from a post on the ASA list, citing information in a publication from ICR. This would tend to support John Wilson’s implicit suggestion in his Christianity Today article, that Phil is moving toward a YEC [young earth creationist] position. If Phil has any comments, I’m all ears. The latest issue of ACTS AND FACTS arrived today. I see that Phillip Johnson and Andrew Snelling (of ICR [the Institute of Creation Research, I think]) will be making a joint speaking tour in England from 10/26 to 11/13. The tour is being underwritten by Elim Churches and several “evangelical alliances.”

I have consistently said that I take no position on the age of the earth, and that I regard the issue as not ripe for debate yet. I have also rejected all suggestions that I should denounce the YECs and instead have said that I regard high-quality YECs like Andrew Snelling as respected allies.

I am not upset when YECs criticize me for not embracing their position, nor am I upset when theistic evolutionists or progressive creationists criticize me for being overly friendly with YECs. For now I am standing right where I want to stand. When developments make it appropriate for me to clarify or adjust my position, I will not hesitate to do so.

One wonders just what developments could possibly make Johnson make up his mind about the age of the Earth. Is he holding out for some new and improved radiometric dating technique? Waiting for new ice core results? I somehow doubt it. He’s probably referring to political, not scientific, developments. The scientific case for an old Earth is quite overwhelming, as can be seen by any open-minded person willing to invest some time researching it. But Johnson’s “Big Tent” strategy requires him to do the exact opposite of what he pretentiously claims to be doing, which is following the evidence wherever it leads. Instead, he has to sweep the evidence under the rug when it’s politically incorrect to do otherwise.

It’s funny that ID advocates have been known to deride evolutionary theory as “19th century science”, even though the modern synthesis was developed in the 20th century. Perhaps, previously, I didn’t appreciate what they meant by that. Maybe instead of insinuating that evolutionary theory is old and stale, they meant that it’s futuristic and scary. Because anyone who thinks that the age of the Earth is “not ripe for debate yet” is living in a bygone era, well before Darwin.


NAGPRA is a federal law which requires that any skeleton found on federal land or in a federal museum which is the skeleton of an American Indian, must be returned to that person's tribe, usually for burial or other form of ceremonial destruction. Archaeologists are troubled by some of the extreme implications of this law, which has already cast a dark shadow over attempts to study ancient skeletons, such as Kennewick Man. Now there is a possibility that NAGPRA will get even worse.

Axel and Buck win the Nobel Prize

The announcement is on the Nobel site. Carl Zimmer has the summary.

Axel's and Buck's work was on odorant receptors, and what they accomplished was to demonstrate on the molecular level how your nose works. It's very nifty stuff from a physiological standpoint, showing how an olfactory signal is transduced via G protein coupled receptors into a change in cyclic AMP levels, which then opened membrane channels to change the electrical potential of the cell. It also turned out to have evolutionary significance, because what they discovered was a huge gene family; every different class of odorant has its own unique receptor molecule, and roughly 3% of our genome is dedicated to this one task that we take for granted. We aren't even particularly well endowed with odorant receptors, and our genome is further riddled with broken odorant receptor pseudogenes, relics of the more discerning noses of our distant ancestors.

Testing fundamental evolutionary hypotheses by David Penny, Michael Hendy and Anthony Pool was published in Journal of Theoretical Biology volume 223, pages 377-385 in 2003. Penny et al show that ‘Intelligent Design’ can be formulated as a testable hypothesis but this requires us to formulate motivation(s), means and/or opportunity to restrain the explanatory power of an ‘intelligent designer’. Additionally, they show why various potential ID hypotheses can be rejected based on the experimental evidence. Until ID proposes other hypotheses, common descent seems to remain the best hypothesis available. Since the Geoscience Research Institute (GRISDA) proposes an alternative theory of ID (multiple independent origins) I will explore this hypothesis and show that again the data do not bode well for ID.

The Tangled Bank

We're looking for more submissions to the next edition of the Tangled Bank, which will be at Preposterous Universe on Wednesday. Send links to your science writing to carroll [at] theory.uchicago.edu, to pzmyers@pharyngula.org, or to host@tangledbank.net. Get 'em in as soon as you can!

William Dembski has posted a revised version of his essay on human origins on www.designinference.com. This was way back in August, but I’ve been busy. In the acknowledgements he thanks me, amongst others, for helpful criticism. Now I’m quite chuffed that I could help the greatest philosopher of our time with his essay, but it might have been nicer if he actually had acted on my criticisms.

As before, there are still numerous biological mistakes Dembski makes in this essay. He didn’t take my advice to get a real biologist to look over it carefully. What about my specific criticisms?

Report on KU Speech

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Last Tuesday, September 28, 2004, about 300 people attended my speech “Kansas Science Standards 2004: Will It Be 1999 All Over Again?”, sponsored by the Chancellor’s Office and all the natural science departments at the University of Kansas. Generally the audience was supportive and appreciative, although a few ID advocates and supporters were there (including Intelligent Design managing director John Calvert.)

If you are interested, links to some materials, including mp3’s of the speech, are on the Kansas Citizens for Science website www.kcfs.org. Even if you aren’t particularly interested in Kansas, much of this talk is pertinent to anyone interested in the ID movement.

1) The Powerpoint presentation is here.

2) A Word version of the Powerpoint text, with cues to the mp3 files is here. This is a more useful (and much smaller) document.

3) The speech itself is separated into a small mp3 files corresponding to the Powerpoint presentation, which you can either listen to directly or download to listen to consecutively later. I recommend listening while following the Word document. The files are all here.

The reaction by the IDists was strong - perhaps even a little over-the-top.

Denyse O’Leary has posted an entry on her weblog at Christianity.ca on the controversy surrounding the 2004 Meyer paper titled Darwinism - An Intellectual Scandal in Science?. O’Leary makes several claims and accusations about various critics of Meyer’s 2004 paper as well as some general accusations towards Panda’s Thumb. In this posting I will go through her major claims and show how they are based on various errors, such as getting the order of events wrong. O’Leary is author of the book By Design or by Chance and a freelance writer as well a columnist for various Christian resources.

I recently acquired O’Leary’s book “By Design or by chance” and have started to review the book. My overall impression of the book is that it presents the ID argument without much skepticism, and presents a strawman argument of Darwinism and its supporters. For instance Darwinism is often presented as relying on chance alone, or even as what remains after design is eliminated. The author is clear that she is on the supportive side of intelligent design and considers herself a ‘post-darwinist’, meaning that she accepts evolution but doubts that Darwinism is an adequate explanation. Her stated reasons are that “Darwin did not anticipate the complexity of the problems so his theory is not likely the solution”.

The National Museum of the American Indian has opened in Washington, D.C. I haven't seen it, so I can't offer my own perspective, but this article in the Washington Post gives grounds for concern. According to Joel Achenbach, the great virtue of the Museum is that it does not attempt a scientific or technical understanding of the history or cultures of American Indians.

The Bathroom Wall

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With any tavern, one can expect that certain things that get said are out-of-place. But there is one place where almost any saying or scribble can find a home: the bathroom wall. This is where random thoughts and oddments that don’t follow the other entries at the Panda’s Thumb wind up. As with most bathroom walls, expect to sort through a lot of oyster guts before you locate any pearls of wisdom.

The previous wall got a little cluttered, so we’ve splashed a coat of paint on it.

I Was a Token Darwinist

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I was the “Opposing View” at last week’s Darwin, Design and Democracy V conference, held on September 24th and 25th in Albuquerque, New Mexico. The title of this post is derived from one of the videos sold at the conference, “I was a Teenage Darwinist”, which in turn was derived from the 1957 Michael Landon horror movie “I was a Teenage Werewolf.”

planula

One of many open questions in evolution is the nature of bilaterian origins—when the first bilaterally symmetrical common ancestor (the Last Common Bilaterian, or LCB) to all of us mammals and insects and molluscs and polychaetes and so forth arose, and what it looked like. We know it had to have been small, soft, and wormlike, and that it lived over 600 million years ago, but unfortunately, it wasn't the kind of beast likely to be preserved in fossil deposits.

We do have a tool to help us get a glimpse of it, though: the analysis of extant organisms, searching for those common features that are likely to have been present in that first bilaterian; we're looking for the Last Common Bilaterian by finding the Least Common Denominators among living species. And one place to look is among the flatworms.

A recent paper by Bagun and Riutort examines one specific subgroup of the flatworms, the acoelomorphs (pronounced a-seel-o-morphs). These are tiny marine worms that have long been grouped under the platyhelminthes, but molecular work has been revealing that the platyhelminths have been a victim of our "worm is just a worm" bias, and are almost certainly polyphyletic. Bagun and Riutort argue that the acoels ought to be recognized as a separate phylum of their own, and further, that they represent basal bilaterians. They propose on the basis of molecular data that most of the Platyhelminthes belong in the protostome clade, and that they've secondarily lost characters common to most members of that group, such as segmentation. and that the acoelomorph flatworms are an early branch off the bilaterian root.

Continue reading "Acoelomorph flatworms and precambrian evolution" (on Pharyngula)

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