June 2004 Archives

A brief overview of Hox genes

In previous articles about fly development, I'd gone from the maternal gradient to genes that are expressed in alternating stripes (pair-rule genes), and mentioned some genes (the segment polarity genes) that are expressed in every segment. The end result is the development of a segmented animal: one made up of a repeated series of morphological modules, all the same.

eve and ftz stripes

Building an animal with repeated elements like that is a wonderfully versatile strategy for making an organism larger without making it too much more complicated, but it's not the whole story. Just repeating the same bits over and over again is a way to make a generic wormlike thing—a tapeworm, for instance—but even tapeworms may need to specialize certain individual segments for specific functions. At its simplest, it may be necessary to modify one end for feeding, and the opposite end for mating. So now, in addition to staking out the tissues of the embryo as belonging to discrete segments, we also need a mechanism that says "build mouthparts here (and not everywhere)", and "put genitalia here (not over there)".

Many people have at least heard of the particular set of genes, the Hox genes, that are responsible for assigning specific regional identities on body parts (Ed Lewis won the Nobel for his work on them, for one thing). I'll just try to give a rough overview of them here, but if you want more details, check out Thomas Bürglin's Homeobox Page.

Continue reading "A brief overview of Hox genes" (on Pharyngula)

Tangled problems at the Tangled Bank

The Tangled Bank

This is a week for the Tangled Bank (which will be hosted at Johnny Logic's place) but we've had a bit of a glitch in the e-mail. Usually, we'd have you send submissions to host@tangledbank.net; however, all mail to that address is currently bouncing...someone tried to interfere with my site, I had to increase security on my server, and somehow in the process I broke the e-mail address. Sorry. I'll try to fix it this week.

Until it's fixed, though, if you have John Taylor's address, you can send those submissions directly to him; if you don't, send them to me at pzmyers@pharyngula.org and I'll send them along to the right place.

Due to this error, we may delay this week's entry a day or two. If you've had a submission bounce, send it again to me. If you forgot so far, but have some cool story relevant to natural history or medicine you'd like to share, send it to me right away.

More bad legal analysis

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A new article in the Wake Forest Law Review provides a shoddy legal which is, alas, all too common in the religion context. Beginning with a deeply flawed understanding of the roles of the Free Exercise and Establishment Clauses, the article ends up making foolish statements about creationism in the classroom.

Patrick M. Garry, Inequality Among Equals: Disparities in The Judicial Treatment of Free Speech And Religious Exercise Claims 39 Wake Forest L. Rev. 361 (2004), argues that courts tend to pay too much attention to freedom of speech, as opposed to other freedoms, and that they ought not to do this. Now, broadly speaking, this is true.

The Left Hand of Darwin

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Privileged Planet: Nature review

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In addition to my reviews and evaluation of the Privileged Planet ideas, the book has now been reviewed in Nature by Douglas A. Vakoch from the SETI Institute. Titled “Bright blue dot” NATURE VOL 429 24 JUNE 2004 p 808-809

Ed Note: This is a guest column written by Sean Starcher and JA Pourtless. You can read the original version of this column on Sean’s blog.

Casey Luskin of the IDEA Center has really had it piled on lately. We don’t want it to seem like we’re picking on him (there are certainly a healthy number of creationist websites out there that are in serious need of a reality check!), but his primer on “Problems with Evolutionary Explanations of the Fossil Record” contains some serious errors that are in immediate need of correcting.

That there are “some” errors is a bit of an understatement, but for the time being we’re going to focus in on two of his major criticisms. He says:

But what did Archaeopteryx come from? Given the similarities to therapod [sic] dinosaurs, it is usually claimed to be a nice clean relative of the therapods [sic]. The catch? These therapods [sic] are only known from one locality–the Yixian formation in China, and according to the radiometric dates, the Therapods [sic] are “at least 20 Myr younger than Archaopteryx” [sic]. To give an analogy, that’s sort of like saying that the first apes came from modern humans (which appeared out of no where 25 million years ago and then disappeared).

This passage is confused on a number of different counts. Firstly, that bird-like theropods are limited to a single locality, the Yixian, is just flat-out wrong. Dromaeosaurids are known from North America (e.g. Bambiraptor, from the Two Medicine Formation of Montana, Dromaeosaurs and Saurornitholestes from the Judith River Formation of Alberta Canada, Deinonychus from the Cloverly Formation of Wyoming), Europe (teeth, mostly undescribed, from the UK and Portugal), Mongolia (Velociraptor from the Djadoctha Formation, Adasaurus from Nemegtskaya Svita), and Africa (undescribed teeth). Oviraptorosaurs are known from North America, Mongolia, Kazakhstan and Uzbekistan. Therizinosaurs have been found in Mongolia and the United States. Alvarezsaurids are known from Mongolia and the US. This is by no means an exhaustive list.

This is the first in an ongoing series about recent discoveries and commentaries concerning aspects of evolution that affect our everyday lives. On the one hand, it’s a fun way to showcase some of the recent goings-on in the literature, and on the other, it’s a way to rebut the occasional creationist claim that evolution isn’t important to biology or to science at large. That assertion is false, and would be irrelevant even if true, but in my opinion (and I suspect this is true of most of us here), the aspects of evolution that affect our day-to-day lives are the most fascinating.

Consider the existence of man-made pollutants. Since the advent of modern chemistry, humans have found ways of making new and useful chemicals that can’t be found in nature. Unfortunately, part of what makes a chemical useful is its ability to resist breaking-down. And if it happens that such a chemical gets produced in huge quantities, and that some of this quantity manages to make its way out into our environment, it can be quite a hazard to human and environmental health. The resistance to degradation becomes a part of the problem, because these chemicals can accumulate over many years to the point where they become toxic. It’s therefore important for us to understand methods by which these compounds can be eliminated.

Fortunately, our bacterial friends have evolved ways of dealing with many of the persistent pollutants that have been dumped into the environment. In a just published review in the Journal of Biological Chemistry, Lawrence Wackett of the University of Minnesota describes some of the enzymes that microbes have evolved to digest these man-made chemicals. Unlike enzymes that evolved gillions of years ago, many of which have histories that are impossible to reconstruct, these enzymes show signs of having evolved quite recently. Wackett notes:

Another lesson being learned from biodegradation studies is that functionally significant enzyme evolution occurs on shorter time scales than previously appreciated; weeks, months and years rather than eons.

Scientists Discover Two New Interstellar Molecules: Point to Probable Pathways for Chemical Evolution in Space.

A team of scientists using the National Science Foundation’s Robert C. Byrd Green Bank Telescope (GBT) has discovered two new molecules in an interstellar cloud near the center of the Milky Way Galaxy. This discovery is the GBT’s first detection of new molecules, and is already helping astronomers better understand the complex processes by which large molecules form in space.

The 8-atom molecule propenal and the 10-atom molecule propanal were detected in a large cloud of gas and dust some 26,000 light-years away in an area known as Sagittarius B2. Such clouds, often many light-years across, are the raw material from which new stars are formed.

“Though very rarefied by Earth standards, these interstellar clouds are the sites of complex chemical reactions that occur over hundreds-of-thousands or millions of years,” said Jan M. Hollis of the NASA Goddard Space Flight Center in Greenbelt, Md. “Over time, more and more complex molecules can be formed in these clouds. At present, however, there is no accepted theory addressing how interstellar molecules containing more than 5 atoms are formed.” […]

Complex molecules in space are of interest for many reasons, including their possible connection to the formation of biologically significant molecules on the early Earth. Complex molecules might have formed on the early Earth, or they might have first formed in interstellar clouds and been transported to the surface of the Earth.

Molecules with the aldehyde group are particularly interesting since several biologically significant molecules, including a family of sugar molecules, are aldehydes.

“The GBT can be used to fully explore the possibility that a significant amount of prebiotic chemistry may occur in space long before it occurs on a newly formed planet,” said Remijan. “Comets form from interstellar clouds and incessantly bombard a newly formed planet early in its history. Craters on our Moon attest to this. Thus, comets may be the delivery vehicles for organic molecules necessary for life to begin on a new planet.”

I find this pretty interesting, because the enzyme I work with catalyzes an aldehyde dehydrogenase reaction that uses propanal (aka propanaldehyde, aka proprionaldehyde). We use propanal to assay the enzyme’s activity, so I’ve got a big bottle of propanal sitting in the fridge. I kind of like the way it smells.

If you’re wondering what propanal is, think of its little brother, acetaldehyde, which contains two carbon atoms instead of three. Acetaldehyde is something that most of us have had the joy of communing with, given that it’s the main product of ethanol metabolism. When you drink, it’s actually the acetaldehyde, and not the alcohol itself, that gets you intoxicated. A second dehydrogenation turns acetaldehyde into acetic acid, aka vinegar, which gets digested as usual.

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 here is a new one.

Dembski and Human Origins

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William Dembski has just posted an essay on human origins on www.designinference.com. If there was any doubt that the Intelligent Design movement was about religious belief rather than science, this essay dispels that doubt.

Confederate Pandas

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Zoo Atlanta is home to two giant pandas, Lun Lun and Yang Yang. Lun Lun is an avid climber who enjoys playing throughout the day, while Yang Yang is playful and easygoing.

They are both nearly seven years old and together eat about 220 pounds of bamboo a day. The zoo relies on bamboo donated from private lands to feed Lun Lun and Yang Yang. The zoo uses their own team to harvest the bamboo, but I think it would be more interesting if they simply took the pandas out to graze at the site.

Of notable interest is that the zoo has a webcam of the pandas, available from 10am to 5pm (EST) Tuesday through Friday. Of course you can guess what they spend most of the day doing.

Only three zoos in the US have pandas: Zoo Atlanta, The San Diego Zoo, and The National Zoo. Both of these latter zoos also have panda cams: San Diego and The National Zoo.

This report has just been issued: [URL =http://www.nature.com/nsu/040614/040614-11.html]Tunes create context like language: Maths shows why tonal music is easy listening.[/URL]

It set me [URL =http://evolvethought.blogspot.com/2[…]anguage.html]thinking… [/URL]

Thalassocnus on The Loom

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An aquatic sloth?


Skull of Thalassocnus yaucensis, sp. nov., holotype, MUSM 37 in lateral (A), ventral (B), dorsal (C), views; mandible in lateral left (D) and dorsal (E) views.

Carl Zimmer has the details. This is very cool—yet another series of transitional fossils, showing a set of Peruvian sloths, of all things, that adapted to an aquatic lifestyle over the course of several million years.

Hunter Baker Redux

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I didn’t know that the men’s movement had blogs until I received an e-mail this weekend from Vic (aka David) with a link to one. The subject of the blog entry, much to my surprise, was evolution and the ID movement. Is there some connection between the men’s movement and the ID movement? Many of the same people who are anti-evolution are also strongly anti-feminist, so I suppose there might be, but it still seems a bit out of place. Unfortunately, the author of this blog has no permanent links to specific posts, so you’ll just have to scroll down till you find the title Intellectuals Who Doubt Darwin.

The post was written, according to the text, “by our friend, Hunter Baker the Great”. Long time readers of this blog may remember Hunter Baker as the author of the National Review Online article about the Leiter/VanDyke brouhaha. That situation involved a book review published in the Harvard Law Review by Lawrence VanDyke, a Harvard Law student, of a book about ID and the establishment clause written by Frank Beckwith. Frank is a professor of law at Baylor and a friendly adversary in the evolution/creationism battle who has posted comments here from time to time.

It's Father's Day, and what does everyone think of on this holiday? What is one thing that we know all fathers have in common, absent dads, neglectful dads, drunk dads, abusive dads, or even caring and responsible dads like the one I had? Why, it's testicles, of course. They all had at least one. So, in honor of the generative apparatus of our paternal predecessors, without which we would not be here, I have put together a few tributes to the testes, commendations to the cojones, a big hand for the balls. There's a little anatomy and physiology, a bit of development, some evolution of the scrotum, and even <shudder> a link to some recipes.

Icons of ID: Reliability: Do we care?

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No false positives? So what? All science is tentative, isn’t it?

Such seems to be the common response of ID proponents when ID critics show that the claims about reliability of the Design Inference are unsupportable. Let’s first look again at the claims made by ID proponents as to the exact nature of the explanatory filter, the Design Inference and its reliability. Once I have established the relevance of the reliability criterion, I will explore the recent objections and arguments from ID proponents. I will use claims and observations from many resources to show how the arguments from ID proponents fail to address these issues. In addition I will show how ID critics have made a compelling argument that the theoretical foundation of ID is fundamentally flawed.

Small Treasures

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Having recently (finally!) acquired a digital camera with pretty good zoom capabilities (10x optical, 3x electronic), I’ve been lurking around the place taking pics of little things, pushing the zoom to the max. This is my favorite so far, what I think is a Celastrina of some variety/subspecies, though the notched wing is a teaser. (Is there a lepidopterist in the house?) I’m particularly taken with the pattern of alternating black and white on the antennae. Click here for a larger image (27K), and here for a still larger image (47K).

Evolution 2004

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The Evolution Conference 2004 begins in little over a week (June 26th to be exact). This year it is being held at Colorado State University in Fort Collins, CO. This yearly conference is the biggest in the field of evolutionary biology. (Next to, of course, the secret meetings in the White House basement where we worship Darwin, push our conspiracy forward, and destroy all the evidence that disproves our religion.) The Evolution Conference is jointly sponsored by the Society for the Study of Evolution, the Society of Systematic Biologists, and The American Society of Naturalists.

This year’s schedule includes symposia on estimating clade ages, adaptation during ecological invasions, biological diversity, teaching evolution, sexual dimorphism, and evolution of plant phenotypes.

I will be attending, but not presenting anything. Will any of our readers be going as well? Next year’s conference is in Alaska, and I hope to present some of my research there.

Les Lane made a comment on my site about an op-ed in the Pioneer Press. The thing is supposed to be a "rebuttal" to a lovely piece by Lisa Peters that I praised earlier this month. It isn't. It's standard creationist hackwork, a compendium of cliches and lies that we have all heard repeatedly.

Creationists have a real advantage when doing this kind of thing. They can lie brazenly, and in a single short sentence declaim something with absolute confidence that is nothing short of an outright fabrication, and it would take me an hour to adequately dissect their words and show how fraudulent they are. Take, for example, the title of the op-ed:

Evolution is a theory in crisis

It's a lie. Here, this guy, Bob Hazen, has written a fairly long piece in which he makes assertion after assertion, and he has the gall to start it with a bold lie as the title. Here I am, trying to make an honest and thorough reply to the article, and I'm finding it hard to look past the title. Shouldn't I just wad this newspaper up and throw it in the trash, not bothering to reply to such garbage? Yes. Unfortunately, it's the editors of the Pioneer Press who should have instantly canned this kind of crank nonsense, so we, the informed readers, are stuck with the pointless chore of plodding through, making note of the foolishness therein.

You see, evolution is not in crisis. It's a healthy, active science, inspiring investigators and guiding research in the field and the lab. The theory is supported with near-unanimity by biologists; the few who disagree are generally crackpots and people driven by an unscientific religious agenda. The only people who claim it is a "theory in crisis" are creationists, who want to pretend there is honest doubt where there is none.

Continue reading "Creationist lies in the Pioneer Press" (on Pharyngula)

The Tangled Bank strikes again!

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The Tangled Bank
Tangled Bank #5 is now online at Borneo Chela. This time around we have a solid evolutionary theme going, but that isn't always going to be the case: if you've written anything on biology, natural history, or medicine, send it in to host@tangledbank.net for the next edition, which will be hosted by Johnny Logic on 30 June.

Three SH’s and one D

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On April 21, 2004, a debate was conducted at the Veritas forum at UCLA. It consisted of two parts. In the first part Michael Shermer who is the editor of the Skeptic magazine and director of the Skeptic Society (based in Los Angeles, CA), argued in favor of a materialistic worldview against Jeffrey Schwartz who is a professor at UCLA and is conducting research in the human brain’s activity. In the second part Niall Shanks who is a professor of philosophy (and an adjunct professor of physics and of biology) at the East Tennessee State University debated William A. Dembski, who is an intelligent design advocate with doctoral degrees in both mathematics and philosophy plus a degree in theology. Each of the four participants of the debate has published several books. The debate which was moderated by a professor of philosophy Dallas Willard was taped and broadcast on C-SPAN 2 channel on June 12, 2004.

Anthropomorphizing Dogs

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My son-in-law, Todd, has a 2-year-old mutt named Rico. Rico may be about half Labrador retriever and half German shepherd, but he may also be a Heinz hound (57 varieties). I often tease Todd and Rachel about the way they anthropomorphize their dog.

The other day, I went to their house, and Todd was hanging clothes in the back yard. I sat on the stoop. Rico promptly came over and dropped a tennis ball at my feet. He plainly wanted me to throw it and (I thought) pantomimed turning away from me and running.

I told Todd that I had just read in Science about another dog named Rico. That dog supposedly had a vocabulary of 200 words and would fetch various toys on command from the owner. Without turning from his clothesline, Todd said, “Rico, why don’t you get the rope?”

Icons of ID: No Free Lunch Theorems

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In this installment of Icons of ID I will explore the evolution of the reliance of Dembski’s ID arguments on the No Free Lunch Theorems. While originally Dembski was suggesting that the “No Free Lunch Theorems” play a major role in his arguments against Darwinian pathways, he seems to have changed his tune when it was pointed out that his application of these theorems was flawed or as Wolpert, who is one of the original authors of the these theorems mentioned “written in jello” and “fatally informal and imprecise”.

We want to hear from you

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The Tangled Bank

Don't be shy! We're looking for new entries for The Tangled Bank, and if you've written anything about biology, natural history, medicine, etc., send a link to host@tangledbank.net. Today is the last chance to get submissions in for tomorrow's list (hosted at Borneo Chela), so send something to Jason now! It's a painless way to quickly get linked from a number of science-oriented sites.

Minions of the Discovery Institute don't restrict themselves to only fighting for the indoctrination of high school students with creationism—they've also got a wider goal of infusing society with their anti-science dogma. One Discovery Institute Fellow, Wesley Smith, has been all over the place ranting against stem cell research lately, typically with as little actual grasp of the facts as the DI usually brings to bear against evolution.

For instance, how is this for a lovely title: "Embryonic Stem Cell Research Likely Won't Cure Any Diseases"? Now that's doom-and-gloom for you. The gist of his argument is that 1) biotech companies are not getting rich on embryonic stem cell research now, and 2) it won't work anyway. The first point is irrelevant. Basic research often isn't going to be immediately profitable, which is why we need government sponsorship; that our current administration has actively crippled this kind of research might, perhaps, be contributing to the reluctance of the biotech industry to leap into it.

His second point is backed up with some incredibly dishonest quote mining. What he does is quote scientists as being discouraging about the prospects for the research, while omitting key conclusions that contradict his points.

Continue reading "Stem cells, Alzheimer's, and the contumely of the Discovery Institute" (on Pharyngula)

Metamorphosis

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The Panda’s Thumb will be going through some changes. Where we once were a bland caterpillar, we are going to emerge soon as a beautiful, elegant butterfly. (Or nasty maggot to shit-eating fly, take your pick.) Some might say that PT is evolving, but no we are developing, growing into adulthood. We will have fur where there wasn’t fur before, our voice will deepen, and might even grow a breast or two. So please bear with us as we make the changes.

Citizens of the UK, speak out!

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There is an online petition for UK citizens to protest creationism in education. Sign it if you agree with this statement:

We, the undersigned, feel it is an inappropriate use of taxpayer's money (and inappropriate within the UK National Science Curriculum) to teach religion in the science classrooms of UK schools. We feel is more appropriate that religion be taught as a separate subject from science. We want religion taught as a separate subject from science and the science taught to our (the nation's) children to reflect our scientist's current best understanding of the world & universe around us.

Say Hello to Phoebe

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I am mostly a biology person, and PT is mostly a biology blog, but I think we can all take a moment to have a gasp at the results of the first moon flyby of the Cassini-Huygens mission to Saturn.

Quite an improvement over the last few days, eh? Check the continually-updated latest images from Cassini page at JPL, where you can view the images at almost whatever resolution you desire. The Cassini team will probably be adding images rapidly from now on.

Columnist Linda Seebach of the Rocky Mountain News has written a column on Project Steve, the NCSE’s parody of creationist lists of evolution-doubting scientists. These lists, touted most prominently by the Discovery Institute, consist of scientists (and random other people) that are creationists, that doubt evolution in some way, or that are willing to put their name on a certain-to-be-abused vague statement encouraging “careful examination of the evidence”.

The first Icon I will explore is the Icon of the Explanatory Filter being reliable, or in the words of Dembski “No false positives”.

Dembski’s opinion on “false positives” seems to have evolved over time. From an initial claim of reliability and “no false positives” via an admission that if the filter erroneously attributes design, it is useless to acceptance of “false positives”, the “Explanatory Filter” evolved from reliable to useless.

Despite the fact that “false positives” are inevitable and thus the filter is not only unreliable but in fact useless, Dembski and the ID movement seems to continue to insist that the Explanatory Filter is a reliable theoretical foundation for detecting design.

Bicoid, nanos, and bricolage

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flagellum cartoon

Intelligent Design creationists are extremely fond of diagrams like those on the right. Textbook illustrators like them because they simplify and make the general organization of the components clear—reducing proteins to smooth ovoids removes distractions from the main points—but creationists like them for the wrong reasons. "Look at that—it's engineered! It's as if God uses a CAD program to design complex biological systems!" They like the implication that everything is done with laser-guided precision, and most importantly, that every piece was designed with intent, to fill a specific role in an apparatus that looks like it came out of a high-tech machine shop at a Boeing aerospace lab.

This is, of course, misleading. Real organelles in biology don't look glossy and slick and mechanical; they look, well, organic, with fuzziness and variability and, most importantly, mistakes and slop. What these biological machines look like is not the precisely engineered output of a modern machine shop, but like bricolage. Bricolage is a term François Jacob used to contrast real biology with the false impression of nature as an engineer. It's an art term, referring to constructions made with whatever is at hand, a pastiche of whatever is just good enough or close enough to the desired result to make do. It covers everything from the sculptures of Alexander Calder to those ticky-tacky souvenirs made from odd bits of driftwood and shells glued together that you can find at seashore gift shops.

The closer we look at the developmental biology of organisms, the more apparent the impromptu, make-do nature of their construction is. This is not to imply that they don't work well or efficiently, but only that the signature of intent is missing. What we see is function cobbled together out of scrap from the junkyard. One clear example of this property is a gene, nanos, in Drosophila.

Continue reading "Bicoid, nanos, and bricolage" (on Pharyngula)

(Note: Pharyngula will be inaccessible for much of the day on Sunday, 13 June, while maintenance work is done on the electrical system out here in Morris, Minnesota. Look for it to be back online in the early evening.)

Entropy continued

As I explained before, entropy may appear to be a simple concept but is easily confused. A good example is the claim made by Jerry Bauer who claims to be using Feynman’s equation to calculate the entropy of mutations.

Let’s see what Jerry claims and then compare this to what he should have said. I pointed out to Jerry that Feynman presented a hint to Jerry as to how to calculate entropy correctly:

I've written before about Casey Luskin and his IDEA club, which exists to promote Intelligent Design on college campuses. I've criticized it for having purely religious motivations (which Luskin tries desperately to conceal), and for their very poor understanding of the science they claim to criticize. Jack Krebs and Wesley Elsberry here at the Panda's Thumb have also ripped into Luskin over both of these issues.

Luskin, as you might guess, is indignant. In particular, he is irate that he was caught with a current listing at a conference that describes the IDEA club as a "ministry". It wasn't his fault, he protests. At length. At extravagant length.

But a look at the history of the IDEA club reveals a different story.

Continue reading "Casey Luskin and the evolution of an IDEA" (at Pharyngula)

Icons of ID: Introduction

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One of the characteristics of science is that it is self correcting. One of the most common and successful methods for self correction involves peer review. In case the reviewers do not catch the errors, comments from colleagues can result in a later correction of the mistake. Examples of such can be found throughout the scientific world. Relevant to evolution the following examples come to mind: Piltdown Man, Haeckel embryos, Nebraska man. (See Is Evolution Science?. Scientific theory is always tentative, open to refutation, reaffirmation, and alteration when more and more data become available.

Despite this we see ID proponents such as Nancy Pearcey speaking out against what they consider to be “defenders of falsehoods” when accusing Darwinists of refusing to correct errors in textbooks. Most of their perceived ‘errors’ are in fact overblown. What is relevant however is that ID proponents seem to expect Darwinists to be ‘self correcting’.

Paul Nesselroade similarly observes that when it comes to public trust, science should be self-correcting .

The public trust afforded to science comes, in part, from its own claim that it is self-correcting, constantly engaged with the evidence and paying tribute to no person, philosophy, or creed. But how can this basis for trust be reconciled with a refusal to hear challenges or examine its own presuppositions?

Then there is David Buckna who argues without much supporting evidence that:

Good science is always tentative and self-correcting, but this never really happens in the case of evolution.

Often the ID proponents seem to confuse legitimate debate about issues as a weakness of evolutionary theory.

Another major misconception is that science is simply the accumulation of observational fact, and theories are merely unsubstantiated guesses. This “facts only” view of science misses the core of what the scientific enterprise really is. In my opinion, nothing could be more deadly to teaching science than to divorce it from the unifying theories which give observations meaning. They make the world comprehensible. They also generate the testable hypotheses (expectations) that drive further exploration and discovery. When science is taught as only factual observation (something the standards passed by the Board would encourage), then disagreements among scientists and changing scientific views are seen as weaknesses and failings of scientific knowledge. However, the exact opposite is the case. It is the dynamic, changing, self-correcting nature of science that is its very strength. The less science is seen as a body of established knowledge, the more inherently interesting and exciting it becomes.

Keith B. Miller in The Controversy over the Kansas Science Standards

So how does the Intelligent Design movement, which claims to be a scientifically motivated movement deal with correcting its own errors and omissions ? In the next few postings that will start with the title “Icons of ID:” I intend to explore some icons of the ID movement and show how corrections are being handled. I intend to show that the ID movement is far from self correcting when it comes to their own arguments and claims.

Niall Shanks has informed me that his recent debate with William Dembski at UCLA will be broadcast by CSPAN-2 this Saturday at 9:30 A.M. I already have my VCR programmed ...

Blogger Kathy Shaidle has a review here of a new creationism book, By Design Or By Chance: The Growing Controversy On The Origins Of Life In The Universe by Denyse O'Leary.

But the review is so full of mischaracterizations and misleading statements that it's hard to know where to begin.

Pre-Cambrian coelomate!

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A hot-off-the-presses article in Science describes the discovery of bilaterian fossils in the Doushantuo Formation, from roughly 570 million years ago.

Ten phosphatized specimens of a small (<180 µm) animal displaying clear bilaterian features have been recovered from the Doushantuo Formation, China, 40 to 55 million years before the Cambrian. Seen in sections, this animal (Vernanimalcula guizhouena gen. et sp. nov.) had paired coeloms extending the length of the gut; paired external pits that could be sense organs; bilateral, anterior-posterior organization; a ventrally directed anterior mouth with thick walled pharynx; and a triploblastic structure. The structural complexity is that of an adult rather than larval form. These fossils provide the first evidence confirming the phylogenetic inference that Bilateria arose well before the Cambrian.

This is exciting news, not because it revolutionizes our understanding of evolutionary history, but precisely because it is nothing surprising at all—we expect, from molecular/phylogenetic evidence, that complex animal life arose long before the Cambrian 'explosion', and what these fossils represent is a satisfying confirmation of that expectation (and they neatly fit predictions about bilaterian evolution that Erwin and Davidson made in 2002). It is actually expected, though, that bilaterian coelomates are even older than the 570 million years of the Doushantuo Formation; the last common ancestor of protostomes (arthropods and others) and deuterostomes (vertebrates and others) is estimated to have lived somewhere between 600 and 1200 million years ago.

Continue reading "Pre-Cambrian coelomate!" (on Pharyngula)

EvolutionBlog Returns!

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I just wanted to let everyone know that after a two-week vacation, EvolutionBlog is back. I make regular posts Sunday through Thursday evenings. Stop by for a visit!

The recent anthology Darwinism, Design and Public Education, edited by John Angus Campbell and Stephen C. Meyer, is chock-full of brazen dishonesty, false science, and sloppy arguments. In the midst of all of this silliness, however, is one essay whose arguments are so absurd, so completely divorced from all semblance of rational thought, that it must be singled out for special attention. The essay is entitled “Intelligent Design Theory, Religion, and the Science Curriculum”, by Warren A. Nord. Nord is a professor of philosophy at the University of North Carolina, Chapel Hill.

Dembski’s Five Questions: Number One.

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Gary S. Hurd, Dave Mullenix

Scientific Creationism wholeheartedly embraced fundamentalist Christian dogma, particularly the notion of a six-day creation week with the inference that every ‘kind’ of life was directly and uniquely created, that a global flood covered the entire Earth in which only those life forms rescued on Noah’s Ark survived, and that the ‘ages’ associated with various biblical genealogies could be summed to obtain a chronology of creation. In the face of repeated legal losses, which excluded religious indoctrination from public schools in America, the Scientific Creationists asserted that they could use purely scientific means to “prove” that their specific biblical interpretation was literal truth. Thus, they argued their creationism was different from simple fundamentalism, and deserved to be taught as science in public schools. The origin, and (lingering) decline of Scientific Creationism are very sympathetically studied by Ron Numbers in his 1993 book, [u]The Creationists: The Evolution of Scientific Creationism[/u] (Berkeley: University of California Press). Scientific Creationism never made good on the promise to use science to ‘prove’ that their biblical interpretations were empirically correct, although there are a small number of individuals still trying. They have been reduced to making ‘scientific arguments’ more bizarre than accepting miracles, and lame efforts to attack evolution such as denying fossil evidence of evolutionary transitions, or equating “Darwinism” simultaneously with Nazis, Communists, and recently Al Qaeda. Throughout the 1980s Scientific Creationists lost legal battles. Scientific Creationists were turned away from public schools by the courts. This set the stage for the emergence of a new version of creationism, Intelligent Design.

Under the Weather

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The server that hosts the Panda’s Thumb was affected by the power outages in the Dallas-Fort Worth Metroplex area. The server was offline from about 4AM on the 2nd, and went back online around 7PM on the 3rd. As it is, we should consider it fortunate to have power restored so soon.

From the Antievolution.org Quotes and Misquotes Database home page:

Antievolutionists have a fondness for quoting authorities. Almost as strong as this fondness is their fondness for misquoting authorities.

The antievolution fascination with quotations seems to stem from the anti-science mindset of “revelation”: testimonial evidence reigns supreme in theology, thus many antievolutionists may mistake that condition as being the same in science. However, science has pretty much eschewed assigning any intrinsic worth to testimonial evidence. Quotations from some source are taken as being an indication that some condition as stated holds according to the reliability of the speaker, as seen by reviewing the evidence. Antievolutionists “get” the first part, but have real difficulty coming to terms with the second part. If some Expert A says X, then the antievolutionist expects that no lesser known mortal will dare gainsay Expert A’s opinion on X. However, such a situation is routine in science. Anyone presenting Evidence Q that is inconsistent with X then has shown Expert A to be incorrect on X. If the person holding forth shows repeatedly that they can’t be trusted to tell us correct information on, say, trilobites, then that just means that we likely don’t hold any further talk on trilobites from that source in high regard.

Misquotation comes in many forms (see the t.o. Jargon File for the list). This page is meant to display some of the most egregious misquotations engaged in by antievolutionists that have been floated in online discussions, and also the quotes that an antievolutionist is likely to inject into an argument (even if the quote has no bearing).

In one of the threads here, I commented on the poor showing an IDEA Club article made on describing aspects of punctuated equilibria. As I was reviewing the IDEA Club article on the fossil record, I noted the use of a “quote” from Steven Stanley. Stanley’s “The New Evolutionary Timetable” has proved a treasure trove for antievolutionist quote-miners. I tend to become a bit nervous when an antievolutionist uses ellipses. It makes me wonder what inconvenient text has been dropped. Well, in this particular “quote” we find four sets of ellipses. That prompted me to pull out my copy of the source book and update my quotes database. The entry for the IDEA Club quote can be seen here.

Tangled Bank #4

The Tangled Bank

Check it out over on De Rerum Natura...links to good biology stories. You can find more general information on what the Tangled Bank is about at the Tangled Bank website.

If you're inspired and have your own science writing to brag about, send submissions to host@tangledbank.net—there'll be another on 16 June at Borneo Chela.

Bruce Grant reviews “Creationism’s Trojan Horse: The Wedge of Intelligent Design”, the excellent expose by Forrest and Gross of the intelligent design movement.

I find Bruce Grant’s review particularly of interest because he provides us with some previously unknown details as to a manuscript he reviewed a while ago that ‘purported to review the literature on the evolution of melanism in peppered moths”. Bruce’s comments were scathing.

Soon thereafter the manuscript appeared on the internet and later as an op-ed piece for “The Scientist”. According to Grant this version was still “error-ridden” with many of the same errors he had pointed out as a reviewer.

Bruce Grant

“Those who cavalierly reject the Theory of Evolution, as not adequately supported by facts, seem quite to forget that their own theory is supported by no facts at all.” –Herbert Spencer, 1820-1903

ABOUT SIX YEARS AGO the editor of a national journal in the biological sciences sent me a manuscript to referee that purported to review the literature on the evolution of melanism in peppered moths. No new data were presented. The author had not published in this field previously, and had not produced any research of his own. But science is an open enterprise, and anyone who has something valid to offer should be welcomed and encouraged. So, I read it with care, and offered this commentary to the editor

In one of the comments to my recent posting, “Why Not Teach the Controversy?”, someone called “Navy Davy” repeatedly called for evolutionary biologists to provide the “best evidence … that supports the theory of evolution.” Merely by asking the question in that way, Mr. Davy displays a woeful misunderstanding of science and how science works.

Simply put, there is never a single best piece of evidence; there is no crucial experiment or observation that will validate any theory whatsoever. Theories are accepted according to whether or not they explain data better than some competing theories - a mountain of evidence, if you will.

Kids and evolution

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There was an excellent op-ed in the Pioneer Press (free registration required; I've also posted a few excerpts) that is well worth reading. It points out that creationists, despite legal setbacks at higher levels, have won at the schoolhouse door by intimidating teachers into avoiding the subject of evolution altogether.

As another issue, the author is a writer of children's books, and I believe has written this one, Our Family Tree: An Evolution Story, which is intended for 4-8 year olds. That got me wondering...when was the last time anyone saw a book on evolution for young kids? The "Bible Stories for Kids" genre seems to have a lock on pediatrician's waiting rooms, I've noticed, and this looks like another niche in the PR/indoctrination front that the creationists hold.

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