April 16, 2006 - April 22, 2006 Archives

Steve Jones, the award-winning geneticist and author, argued that suggesting that creationism and evolution be given equal weight in education was “rather like starting genetics lectures by discussing the theory that babies are brought by storks”.


The Game PlanHere in the pounding-nails-into-the-ID-coffin department of the Panda’s Thumb, we are still hard at work. Longtime PT posters Andrea Bottaro, Matt Inlay, and I have just published a “Commentary” essay in May 2006 issue of Nature Immunology. (Update: Subscription no longer required. Thanks to NI.) See the NCSE announcement and more background at the NCSE Evolution Education and the Law website.

The article is:

Bottaro, Andrea, Inlay, Matt A., and Matzke, Nicholas J. (2006). “Immunology in the spotlight at the Dover ‘Intelligent Design’ trial.” Nature Immunology. 7(5), 433-435. May 2005. (Subscription no longer required: DOI | Journal | Google Scholar | PubMed | Supplementary Material)

Therein, we review the now-notorious episode in the Kitzmiller case where, during Eric Rothschild’s dissection of Michael Behe, Rothschild challenged Behe’s claims about the scientific literature on the evolutionary origin of the immune system by piling up on Behe’s podium a stack of books and articles on the evolution of the immune system. Behe responded that he had not read most of it, but dismissed it out of hand, and this cavalier attitude seems to have been one (of many) factors that impressed Judge Jones and persuaded him to issue the thorough, detailed ruling that he did.

Barbara Forrest’s role in Kitzmiller

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Many people have played important roles in exposing the scientific vacuity of Intelligent Design and its religious foundations. On Red State Rabble, Pat Hayes describes the role played by Barbara Forrest in bringing down ID. Barbara Forrest and Paul Gross are the authors of the highly insightful book Creationism’s Trojan Horse: The Wedge of Intelligent Design published in 2004 by Oxford University Press

Pat Hayes Wrote:

In the months since the Dover decision, leaders of the intelligent design movement have played and re-played the trial a thousand times. The Discovery Institute and the Thomas More Law Center have had a very public falling out. Intelligent design proponents have come to refer to Judge Jones, a lifelong Republican who was appointed by George W. Bush, as an activist judge.

What they have not done, as a movement whose leaders are nearly all men, is come to grips with the great role played in their embarrassing defeat by Barbara Forrest, a tiny but very determined woman from Louisiana, who simply took their own words and turned them against them.


It's all about style. When you're out and about looking for mates, what tends to draw the eye first are general signals—health and vigor, symmetry, absence of blemishes or injuries, that sort of thing—but then we also look for that special something, that je ne sais quoi, that dash of character and fashionable uniqueness. In humans, we see the pursuit of that elusive element in shifting fashions: hairstyles, clothing, and makeup change season by season in our efforts to stand out and catch the eye in subtle ways that do not distract from the more important signals of beauty and health.

Flies do the same thing, exhibiting genetic traits that draw the attention of the opposite sex, and while nowhere near as flighty as the foibles of human fashion, they do exhibit considerable variability. Changes in body pigmentation, courtship rituals, and pheromones are all affected by sexual selection, but one odd feature in particular is the presence of spots on the wing. Flies flash and vibrate their wings at prospective mates, so the presence or absence of wing spots can be a distinctive species-specific element in their evolution. One curious thing is that wing spots seem to be easy to lose and gain in a fly lineage, and species independently generate very similar pigment spots. What is it about these patterns that makes them simultaneously labile and frequently re-expressed?

Continue reading "Evolving spots, again and again" (on Pharyngula)

The US News and World Report recently released their 2007 rankings for graduate schools. The report covers both professional and graduate programs like medical and law schools and science Ph.D. programs. The science Ph.D. programs are split into disciplines and subdisciplines. Bellow, I’ll share with y’all the rankings of the two subdisciplines most relevant for what we do here: Ph.D. programs in Ecology/Evolutionary Biology and Paleontology. These rankings are not entirely accurate because any program that is part of a medical school (like Stanford’s EEB) is not listed in these ranking but instead is considered as part of the medical school rankings. (Disclaimer: My program is listed in the EEB rankings.)

RankEcology & Evolutionary BiologyRankPaleontology
1University of California–Davis1University of Chicago
2University of California–Berkeley2Harvard University
3Harvard University3University of Michigan–Ann Arbor
4University of Chicago3Yale University
5Duke University5University of California–Berkeley
6Cornell University6University of Kansas
6University of Michigan–Ann Arbor7University of Cincinnati
8Indiana University–Bloomington8University of Iowa
8Princeton University9University of Texas–Austin
8University of Georgia10Ohio State University

So, if any of our readers are looking to go to graduate school in evolutionary biology, they should give a good look to these programs. If you want to look at genetics/genomics/bioinformatics, biochemistry, or other fields that also relate to evolution you’re going to need to pick up a copy of the US News and World Report’s rankings.

Though much of the attention to and reports of intelligent design/creationist shenanigans come from the United States, we’re certainly not the only ones inundated with deniers of evolution and other sciences. A self-described UK evolution “sceptic” is journalist Melanie Phillips, who writes for The Daily Mail. She’s annoyed many scientists in the country due to her views not only on evolution, but also on vaccination (such as this article from earlier this year), drawing the ire of many who point out that she doesn’t understand the underlying science.

She’s proven her critics correct again, with a recent article touching on everything from the Da Vinci Code, to religion/lack thereof, and to, of course, evolution.

(Continue reading at Aetiology)

The DI Denies Its Own Nature


Yesterday, the Baylor student newspaper printed an article that referred to the Discovery Institute as a “conservative Christian think tank”. The DI, as you can imagine, didn’t like that description one bit because, frankly, they’ve spent so many years selling the silly notion that they’re not a conservative Christian think tank and it’s just annoying when all that propaganda doesn’t pay dividends. They fired off a letter and the Baylor paper caved in immediately and pulled the article and made a “correction”. A brief look at the evidence will show that the paper got it right the first time.

Continue Reading at Dispatches from the Culture Wars. Comments may be left there.

The God Meter

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A week or so ago, I attended “Darwinian Evolution in the 21st Century,” the 21st Regional Conference on the History and Philosophy of Science (Friday evening and Saturday, April 7 and 8, 2006) at the University of Colorado. The conference kicked off with talks by Rob Pennock and Betty Smocovitis on Friday night and continued Saturday with eight contributed papers. Anyone who is in the Boulder-Denver area at roughly this time next year will doubtless be rewarded by attending the 22nd conference.

Victor Stenger of the University of Colorado presented a talk called “ Can Science Study the Supernatural?” He concluded, correctly in my opinion, that it can. Indeed, Professor Stenger considers that we are studying claims of the supernatural when we study ESP, near-death experiences, the Shroud of Turin, or religious visions or miracles. Some of these turn out to have plausible natural explanations, but we could not have said a priori that they would necessarily. Many people accept studies of the supernatural when “supernatural” is interpreted to mean ESP or near-death experiences but demur when the question is phrased, “Can Science Study Religion?” or “Can Science Study God?” as opposed to the broader “supernatural.” I will argue, with Professor Stenger, that science can indeed study claims of religion when those claims are factual statements about the natural world or purport to be factual statements about the natural world. But I will take issue with his contention that science has disproved the existence of God and show why I think it is a politically dangerous argument.


It's a busy time for transitional fossil news—first they find a fishapod, and now we've got a Cretaceous snake with legs and a pelvis. One's in the process of gaining legs, the other is in the early stages of losing them.

Najash rionegrina was discovered in a terrestrial fossil deposit in Argentina, which is important in the ongoing debate about whether snakes evolved from marine or terrestrial ancestors. The specimen isn't entirely complete (but enough material is present to unambiguously identify it as a snake), consisting of a partial skull and a section of trunk. It has a sacrum! It has a pelvic girdle! It has hindlimbs, with femora, fibulae, and tibiae! It's a definitive snake with legs, and it's the oldest snake yet found.

Continue reading "Najash rionegrina, a snake with legs" (on Pharyngula)

Show Up.

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How involved in politics should scientists be? What factors are important when it comes to making that decision?

For some of us, the answer to that comes fairly easily. One or two of us managed to evade the stereotype of the scientist-of-the-future, and caught the involvement bug because we were popular enough to win a role in student government early in our lives. A few of us were caught in a different stereotype - the children of the flower children - and have never known what it is like to not be involved in political causes. A bunch of scientists are just plain incapable of keeping their noses out of anything they bump into, whether it directly involves science or not.

The decision is harder for others. There are a few scientists who really do have an ivory tower mindset, and actively try to avoid anything that smacks of politics. Many put so many hours into their science that they don’t have any to spare for politics. More are apathetic to politics, or disillusioned, or simply unaware of the issues.

Both the involved and uninvolved should read a new article in PLoS Biology. The article, “Scientific Illiteracy and the Partisan Takeover of Biology,” provides some reasons to get more involved in the political process and some hints as to where the efforts of scientists might most effectively be focused.

Read More (at The Questionable Authority):

Mark Psiaki, Associate Professor at the Sibley School of Mechanical & Aerospace Engineering which is part of the Cornell University and advisor of Cornell’s IDEA club provides us with some insights into the minds of ID activists. I will leave most of his claims without comments as they speak best for themselves.

Mark Psiaki Wrote:

The principle of irreducible complexity does not give one all of biology, but if true, it serves to divert the biologist from wasting time by trying to answer a question to which there is no scientific answer.

Guest Post: Follow-up to last night’s panel discussion on ID/Evolution

How more upfront can one be about the scientific vacuity of Intelligent Design?

Of course Irreducible Complexity is flawed in many ways such as 1) it limits itself to Darwinian pathways 2) it concludes that IC systems are not just evidence against Darwinian theory but also in favor of Intelligent Design (false duality) 3) Darwinian pathways to IC systems have been identified.

How to make a bat

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or•gan•ic | ôr'ganik | adjective. denoting a relation between elements of something such that they fit together harmoniously as necessary parts of a whole; characterized by continuous or natural development.

One of the wonderful things about how development works is that organisms function as wholes, and changes in one property trivially induce concordant changes in other properties. Tug on one element, changing it's orientation or size, and during embryogenesis any adjacent elements make compensatory adjustments, so that the resultant form flows, fits, and looks organic. This isn't that surprising a feature of development, though, unless you have the mistaken idea that the genome encodes a blueprint of morphology. It doesn't; what it contains is a description of interacting agents that work together in a process to produce a complex result. Changes in genes and regulatory elements can essentially produce changes in rules of development, rather than crudely specifying blocks of morphology.

What does this mean for evolution? It means that subtle changes to the rules of development can be caused by small changes to genes (and especially, to regulatory regions of genes), and that the resulting morphological changes may be dramatic, but are still integrated organically into the form of the organism as a whole. Our understanding of how development works is making it clear that large scale macroevolutionary change may be much easier than we had thought.

Here's an example where this insight is clarifying the evolution of an organism: the fossil record of bats shows an abrupt appearance of fairly sophisticated creatures with elongated digits, clearly capable of gliding or powered flight, with no known intermediates. We expect there were less fully flight-ready predecessors, but fossil preservation is not kind to small, delicate boned animals. It's also possible that the transitional period was fairly brief; it looks like turning a paw into a long-fingered membranous wing may be a fairly simple change on a molecular level.

Continue reading "How to make a bat" (on Pharyngula)

Recent research on the origins and evolution of the genetic code have shown how “The standard genetic code enhances adaptive evolution of proteins” in a paper by Wen Zhu, Stephen Freeland, Journal of Theoretical Biology 239 (2006) 63–70

Not only is the genetic code ‘optimal’ in the sense that the effects of point mutations or mistranslations on the phenotype are minimized, a property which seems to argue for stasis, but the genetic code also speeds up the rate of adaptive evolution, a property which seems to argue for rapid change.

Again we see how the concept of robustness and evolvability are intricately linked in the genetic code.

On The Design Paradigm Salvador Cordova ‘responds’ (sic) to various claims about evolution and irreducible complexity. As I will show, the response further establishes the scientific vacuity of Intelligent Design.

Salvador Cordova Wrote:

You said, “You should also read up on existing evolutionary explanations for complexity such as scaffolding and Co-option “. No rather you should try to refute the well reasoned issues posed by the displacement theorem and the improbabilities associated with large scale co-option.

Nice redirection from examples of IC systems arising by natural pathways to yet another poorly developed concept of ID namely the displacement theorem. While the displacement theorem once again shows that ID is all about the supernatural, it also shows that as long as the system is ‘open’ to external information, there are no real issues. In other words, whether the external information is the environment or some supernatural or natural designer, it does not help ID’s cause. See Bad Math for more comments on Dembski’s claims.

As to the probabilities of ‘large scale co-option’ I notice the absence of much of any argument, calculations etc to support this claim.

While the scientific vacuity of Intelligent Design has been well documented, it does not hurt to show how Intelligent Design compares to evolutionary science.

NEW LONDON, Conn. - Phillip Barnes, associate professor of biology at Connecticut College, will explore the nature of science by contrasting evolutionary biology with intelligent design in a free and public lecture on Thursday, April 20, at 4:30 p.m. in Room 014 of the F.W. Olin Science Center.

His talk, “Evolution and Intelligent Design,” will include a discussion of the predictive power of the science of evolution “and its relevance for setting public policy in the potential avian flu epidemic, while intelligent design provides no relevant predictions or information for public policy,” Barnes said. Time for questions and discussion will follow.


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