October 2008 Archives

Nature Endorses Obama


Updated: Disclaimer appears below. Link to journal endorsement is here.

This journal does not have a vote, and does not claim any particular standing from which to instruct those who do. But if it did, it would cast its vote for Barack Obama.

Politics impacts science. From which research emphases get funded to which school board member to vote for, science and politics often cross paths. PT’s supporters come from all walks of life and bring to the pro-evolution discussion opinions on other matters that span everything from conservative to liberal. To the extent possible, PT tries to avoid overtly being political, partly because we don’t want to needlessly alienate those supporters, but mainly because it’s beyond the charter of this website and that there are many other blogs that serve that purpose better than ours. Occasionally, though, this blog encounters a crossroads between science and politics, entailing posts that necessarily make political statements. This is one.

During this election, there is a difference between the candidates running for president. Palin is a creationist of the first water. Her disbelief that money spent in support of autism research was going to labs in France that used fruit fly models, reported at Pharyngula, speaks volumes.

At least from the standpoint of science advocacy and at least to this PT contributor, the decision during this election appears straightforward. Nature’s endorsement is timely and appropriate.


PS - And novel! According to this post from DailyKos.com, it would appear that this is first time Nature has endorsed a candidate.

Zombies in Texas!

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Day 5 of the Freshwater hearing was today, but my post on it won’t be up until tomorrow night at the earliest. Tonight my seminar on the history of the controversies surrounding the theory of evolution is going to a Chautauqua performance about Clarence Darrow, and then I’m going to bed.

As a consolation prize read Glenn Branch’s Zombie Jamboree in Texas in the Beacon Broadside. Texas is heading for a potential disaster in science education.

Cucurbita pepo


Cucurbita pepo — Carving Pumpkins

Tangled Bank #117

The Tangled Bank

The latest edition of the Tangled Bank is at Neural Gourmet.

Freshwater Day 4: “Science can’t be trusted”


Preceding posts: Day 3 and Days 1 & 2. This summarizes Day 4, October 29, 2008.

I’ll take a slightly different approach in this post for several reasons. First, I’m short of time and sleep. Second, much of the day was given over to cross examination of the middle school principal by Kelly Hamilton, Freshwater’s attorney, and Hamilton’s approach to cross examination does not lend itself to any sort of narrative flow. Therefore I’ll summarize the main themes of the testimony with some examples of Q&A rather than attempting to reproduce the exact sequence of questions through hours.

The bulk of the testimony today was from Bill White, Principal of the Mt. Vernon Middle School. Another student, a former student of Freshwater who is currently a senior at Mt. Vernon High School, also testified.

More below the fold.

Freshwater Hearing: 3rd Day


This is a summary of Day 3 of the administrative hearing to determine whether John Freshwater will be terminated as a middle school science teacher in the Mt. Vernon, Ohio, City Schools. Days 1 and 2 are here.

Three witnesses testified today, Zachary Dennis, the boy who was (allegedly) burned with a Tesla coil, his mother Jenifer Dennis, and Freshwater. We’re still in the stage where the Board of Education is presenting its case for termination; later Freshwater will be allowed to put on a defense.

Summaries below the fold.

Interview with mother in the Freshwater cross-burning affair


The mother of the boy at the center of the Freshwater affair, Jenifer Dennis, has given her first interview to the Columbus Dispatch. Two excerpts:

Zachary Dennis, now a high-school freshman, told his mother that his eighth-grade teacher, John Freshwater, held his arm down Dec. 6 and used an electrical device used to test gases to burn a cross on his forearm during a science class demonstration.

“He said ‘Mr. Freshwater said this cross will be here for awhile; it’s like a temporary tattoo,’ “ recalled Jenifer Dennis, Zachary’s mother.


“We never intended to go in to get Mr. Freshwater in trouble,” said Mrs. Dennis. “I send my child to school and expect my child not to come home with an injury to his arm.”

I know the Dennis family, and know that they originally wanted only to assure the safety of Zach and the other children in Freshwater’s classes. Freshwater’s other behaviors at issue came to light in the aftermath of his burning the child and his subsequent publicity seeking via demonstrations outside the schools and on the Mt. Vernon public square.

The termination hearing on Freshwater resumes tomorrow (Tuesday). I’ll be there.

Danaus plexippus


Danaus plexippus — Monarch caterpillar feeding on milkweed, Ohio

Euastacus sulcatus


Euastacus sulcatus — Lamington spiny cray, Lamington Plateau, southeast Queensland, Australia

Information content of DNA


The information content of DNA is much harder to determine than merely looking at the number of base pairs and multiplying it by 2 to get the size in bits (remember that each site can have up to 4 different nucleotides, or 2 bits). However, this approach can provide us with a zeroth order estimate of the maximum possible information that can be stored in said sequence which for the human genome with 3 billion base pairs would amount to 6 billion bits or 750 Mbytes.

After 20 days, Religulous has grossed more than Expelled during its six months in US theatres.

TitleLifetime GrossTheatresOpening GrossTheatres
Religulous $9,201,458 568 $3,409,643 502
Expelled: No Intelligence Allowed $7,720,487 1,052 $2,970,848 1,052

Funny how despite give aways, pre-screenings and discounts, and much marketing to the religious, Expelled did not manage to attract more audience than Religulous. What is even more ironic is that Religulous outperformed Expelled from the opening weekend with half the theatre count.

Loxodonta africana


Loxodonta africana — African Bush Elephant, North Carolina Zoo

In a hilarious posting on UcD, our dear friend Davescot, who is best known for his failed predictions 1, explains why recent research into the Lactose digestion of E. coli, undermines the findings of Lenski regarding E. coli evolving the ability to digest citrate. The reason? Our friend Davescot confused citrate with the Lac Operon

Davescot Wrote:

This is contrary to Lenski’s hypothesis that a series of dice throws, each making a small change towards ability to digest lactose citrate, accumulate until lactose citrate digestion is fully switched on. Darwinian gradualism is denied once again and we see a front loaded genome switch to a new mode of operation through a saltational event.

In other words, Davescot made two mistakes in a single posting: first he confused citrate with the Lac operon and secondly, he incorrectly claims that ‘Darwinian gradualism’ is denied once again, because, after all, a stochastic event affects whether E. coli can digest lactose versus glucose.

According to the ID ‘argument’, since chance and regularity can in fact explain the Lac Operon’s switch, any design inference has been prevented. Which is why Davescot, calls it ‘front loading’ or a ‘saltational’ event.

By Dave Wisker, Graduate Student in Molecular Ecology at the University of Central Missouri.

Creationists The Discovery Institute must have drooled when they heard a paper had been published by the respected journal, Animal Behaviour, which apparently reported that peahens did not prefer peacocks with more elaborate trains. Takahashi et al. (2008) appears to contradict several well-known studies that reported the opposite, and which have been cited as evidence for sexual selection in peafowl. Since the peacock’s tail is a venerable symbol of runaway selection for a secondary sexual trait, the DI ARN jumped on the story, crowing, with breathless excitement:

The alleged amazing powers of natural selection are much diminished as a result of these findings. The argument that it is “powerful enough” to maintain the feather display against the negative effects of attracting predators must be dropped. Furthermore, it appears not powerful enough to remove the display when it becomes an “obsolete signal”. Darwinists need to think very hard about the way they do science. This is a clear example of how a Darwinian hypothesis has become accepted as scientific fact, yet now has been disproved by some rigorous empirical research. This is a falsified prediction. This means that numerous textbooks and web sites need to be revised. More importantly, Darwinists should cease giving the impression that they have the keys to understand the natural world. So much of this ‘understanding’ is like peacock feathers - lots of show and no substance. Richard Dawkins extols Darwinism as a beautiful theory, but whenever we look closely, it fails to account for the observed data.

Unfortunately for the DI ARN, their enthusiasm for this paper may be premature, as I noted in a guest entry on Denis Ford’s “This Week in Evolution”. Essentially, the paper has two major problems (my article deals with some other minor ones as well):

  1. The authors used a different methodology to determine male reproductive success than the other studies, which makes comparing them very difficult. While the British and French studies measured male reproductive success by observed successful copulations, the Japanese one estimated the number of successful copulations, based on female pre-copulatory behavior.
  2. The genetic variance in tail morphology in all of the studies was very low (Takahashi et al.’s study had the lowest), which only magnifies the differences in methodology. Small differences in number of successful copulations have greater weight because the very low variation makes determining any kind of selection very difficult.

The main thrust of my article is that the differences in methodology for determining male reproductive success were magnified by the very low variance in the trait, invalidating comparison between the studies. It should be noted that Marion Petrie and Adriane Loyau, primary authors of two of the three major studies confirming peahen’s preference for more elaborate male trains, are in the process of publishing a reply to Takahashi et al’s paper. One wonders if the DI ARN will mention that.

Blogging on Peer-Reviewed Research

While Steve Jones might think human evolution has stopped, I have to say that that is impossible. If human technology removes a selective constraint, that doesn't stop evolution — it just opens up a new degree of freedom and allows change to carry us in a novel direction.

One interesting potential example is the availability of relatively safe Cesarean sections. Babies have very big heads that squeeze with only great difficulty through a relatively narrow pelvis, so the relationship in size between head diameter and the diameter of the pelvic opening has been a limitation on human evolution. We know this had to be a factor in our evolution: the average newborn mammal has a cranial capacity that is roughly 50% of the adult size, chimpanzee babies have heads about 40% of the adult size, but human babies have crania that are only 23% of what they will be in adults. While our brains have gotten larger over evolutionary time, they have not gotten proportionally larger in utero, because large-headed babies increase the difficulty of labor and cause increased mortality in childbirth. If childbirth could bypass the pelvic bottleneck, that would allow for fetal heads to grow larger without increasing the risk of killing mother and/or child.

And childbirth is a risky proposition for women; 529,000 die every year from this natural process (although only about 1% of those deaths occur in places where women have access to good, modern medical facilities — hooray for modern medicine). About 8% of those deaths occur from obstructed labor, where the fetus is unable to proceed through the birth canal for various reasons, and these are the kinds of birth problems that can be circumvented by C-sections. In practice, teaching health care workers how to carry out emergency C-sections has been tested in regions in Africa, where it has actually worked well at reducing maternal mortality.

This is the subject of an article by Joseph Walsh in the American Biology Teacher, which suggests that C-sections will have an effect on human evolution.

"Nothing in biology makes sense except in the light of evolution." This was the title of an essay by geneticist Theodosius Dobzhansky writing in 1973. Many causes have been given for the increased Cesarean section rate in developed countries, but biologic evolution has not been one of them. The C-section rate will continue to rise, because the ability to perform a safe C-section has liberated human childbirth from natural selection directed against too small a maternal pelvis and too large a fetal head. Babies will get bigger and pelves will get smaller because there is nothing to prevent it.

The evidence so far is entirely circumstantial, but Walsh makes an interesting case. There are several correlations that imply an effect, but I can't help but think there are alternative explanations that may swamp out any heritable, evolutionary effect. The kinds of evidence he describes are:

  • A known trend for increasing birth weight in the US, by about 40 g over 18 years in one study. It's there, all right, but these studies don't demonstrate a genetic component to increased size — it could be a consequence of better nutrition and medical care.

  • An increasing frequency of C-sections. Again, this isn't necessarily genetically based at all, but could be a consequence of fads in medicine, or social factors, such as an increase in the likelihood of medical malpractice suits making doctors more cautious.

  • Walsh describes a couple of studies that seem to show that cephalopelvic disproportion (small pelvis or large babies or both together) does have a genetic component. So at least it is likely that there are heritable variations in these parameters that could influence the likelihood of obstructed labor.

  • There is statistical variation in neo-natal mortality that varies with birth weight in a suggestive way. Low birth weight clearly puts infants at risk, and there is an optimum weight around 3600 grams for newborns that minimizes mortality. Death rates also rise with increasing birth weight above the optimum. There is some data that suggest that availablity of modern medical care and C-sections reduces infant mortality at larger birth weights.

That increasing availability of C-sections might lead to an evolutionary shift towards increasing cranial capacity at birth is a reasonable hypothesis, but I'm not convinced that it has been convincingly demonstrated yet. There are too many variables that effect brain size at birth to make a clean analysis possible; in addition, many of the measures are indirect. Often, we use birth weight as a proxy for cranial capacity, and that means the numbers and correlations are sloppier than they should be. Many of the measurements made are of factors that are readily influenced by the environment, which makes it difficult to imply that these are the product of genetics.

So the idea is weakly supported, but tantalizing. Even as a purely theoretical exercise, though, what it does say is that it is obvious that human culture cannot end human evolution…all it can do is shape the direction in which it can occur.

Walsh J (2008) Evolution & the Cesarean Section Rate. The American Biology Teacher 70(7):401-404.

Blogging on Peer-Reviewed Research

We all know the story of the Miller-Urey experiment. In 1953, a young graduate student named Stanley Miller ran an off-the-wall experiment: he ran water, methane, ammonia, and hydrogen in a sealed flask with a pair of electrodes to produce a spark, and from those simple building blocks discovered that more complex compounds, such as amino acids, were spontaneously produced. Stanley Miller died in 2007, and in going through his effects, the original apparatus was discovered, and in addition, several small sealed vials containing the sludge produced in the original experiment were also found.

This isn’t too surprising. I’ve gone through a few old scientists’ labs, and you’d be surprised at all the antiquities they preserved, all with notes documenting exactly what they are. It’s habit to keep this stuff.

Now the cool part, though: the scientists who unearthed the old samples ran them through modern analysis techniques, which are a bit more sensitive than the tools they had in the 1950s. In 1953, Miller reported the recovery of five amino acids from his experiment. The reanalysis found twenty two amino acids and five amines in the vials. He was more successful than he knew!


Moles (relative to glycine = 1) of the various amino acids detected in the volcanic apparatus vials. Amino acids underlined have not been previously reported in spark discharge experiments. Values for amines are minimum values because of loss due to their volatility during workup.

Yes, I know that Miller’s reducing atmosphere is no longer considered to be an accurate representation of the ancient earth’s atmosphere. However, the experiment still supported a key idea: that the synthesis of these organic compounds did not require any kind of guiding hand, but would naturally emerge from unassisted chemical reactions. Furthermore, the authors of this paper argue that while it was not a good model of the global atmosphere, it might still model local conditions in isolated areas.

Geoscientists today doubt that the primitive atmosphere had the highly reducing composition Miller used. However, the volcanic apparatus experiment suggests that, even if the overall atmosphere was not reducing, localized prebiotic synthesis could have been effective. Reduced gases and lightning associated with volcanic eruptions in hot spots or island arc-type systems could have been prevalent on the early Earth before extensive continents formed. In these volcanic plumes, HCN, aldehydes, and ketones may have been produced, which, after washing out of the atmosphere, could have become involved in the synthesis of organic molecules. Amino acids formed in volcanic island systems could have accumulated in tidal areas, where they could be polymerized by carbonyl sulfide, a simple volcanic gas that has been shown to form peptides under mild conditions.

So good work, Dr Miller!

Johnson AP, Cleaves HJ, Dworkin JP, Glavin DP, Lazcano A, Bada JL (2008) The Miller Volcanic Spark Discharge Experiment. Science 322(5900):404.

In a Press Release, the National Association of Biology Teachers (NABT) announced that it will “recognizeDr. Randy Moore, a professor of biology at the University of Minnesota, with the 2008 Evolution Education Award during the NABT annual conference to be held 15-18 October 2008 in Memphis, Tennessee.”

Congratulations to Dr Moore.

Geochelone nigra


Geochelone nigra, 2 — Gal�pagos tortoise. Upper, emerging from shell. Lower, a couple of weeks old.

The New York Times’s science pages discuss a research study of Tiktaalik. The study in question has been published in the Journal Nature (1)

It was Neil Shubin’s team that found the Tiktaalik, as they had predicted.

Dr. Shubin said Tiktaalik was “still on the fish end of things, but it neatly fills a morphological gap and helps to resolve the relative timing of this complex transition.”

For example, fish have no neck but “we see a mobile neck developing for the first time in Tiktaalik,” Dr. Shubin said.

Some creationists have raised some pretty foolish (1) claims about evolutionary theory:

Who Is Your Creator Wrote:

1. Evolution predicts that genetic complexity is gained gradually, but specific genetic material for creating advanced features appeared “long before” in organisms that supposedly evolved millions of years earlier:

“Long before animals with limbs (tetrapods) came onto the scene about 365 million years ago, fish already possessed the genes associated with helping to grow hands and feet (autopods) report University of Chicago researchers … The capability of building limbs with fingers and toes existed for a long period of time, but it took a set of environmental triggers to make use of that capability… ‘It had the tools,’ he said, ‘but it needed the opportunity as well.’”

Source: Hox gene research and new data on how fish grew feet

The paper in question is

Davis, M.C., Dahn, R.D., Shubin, N.H. An autopodial-like pattern of Hox expression in the fins of a basal actinopterygian fish. Nature. 2007. Vol. 447. Pages 473 - 476.

Tangled Bank #116

The Tangled Bank

The latest edition is at Pro-Science. Toddle on over and see what’s new in science blogging!

In other news, Kim Jong-il was appointed an expert reviewer of the standards related to economics…

Science curriculum reviewers criticized

By Kate Alexander | Wednesday, October 15, 2008, 11:31 AM

Some of the State Board of Education’s appointments to a new panel appointed to review the state’s science curriculum standards has drawn quick fire.

Two authors of a textbook called Explore Evolution have been named to the six-member panel.

The textbook is distributed by the Discovery Institute, which promotes intelligent design. The book is described as presenting “the scientific evidence both for and against key aspects of Darwinian evolution.”

Here’s a snippet about textbook from its Web site:

The purpose of Explore Evolution, is to examine the scientific controversy about Darwin’s theory, and in particular, the contemporary version of the theory known as neo-Darwinism. Whether you are a teacher, a student, or a parent, this book will help you understand what Darwin’s theory of evolution is, why many scientists find it persuasive, and why other scientists question the theory or some key aspects of it.

The Texas Freedom Network criticized the appointment of the textbook authors, Stephen Meyer, vice president of the Discovery Institute, and Ralph Seelke, a biology and earth sciences professor from the University of Wisconsin-Superior.

“Texas universities boast some of the leading scientists in the world,” said Kathy Miller, executive director of the Texas Freedom Network. “It’s appalling that some state board members turned to out-of-state ideologues to decide whether Texas kids get a 21st-century science education.”

PS: More on pharyngula

In a book review by Christopher Heard, Pepperdine University of Stewart, Robert B., ed. Intelligent Design: William A. Dembski and Michael Ruse in Dialogue Minneapolis: Fortress, 2007, we read how Dembski’s attempts to have design be a place holder for our ignorance, are doomed to fail.

Blogging on Peer-Reviewed Research

How can I respond to a story about zebrafish, development, and new imaging and visualization techniques? Total incoherent nerdgasm is how.

Keller et al. are using a technique called digital scanned laser light sheet fluorescence microscopy (DSLM) to do fast, high-resolution, 3-D scans through developing embryos over time; using a GFP-histone fusion protein marker, they localize the nucleus of every single cell in the embryo. Some of the geeky specs:

  • 1500x1500 pixel 2-D resolution

  • 12 bits per pixel dynamic range

  • Imaging speed of 10 million voxels per second

  • Complete scan of a 1 cubic millimeter volume in 3µm steps in 90 seconds

  • Efficient excitation (5600 times less energy than a confocal, one million times less than a two-photon scope) to minimize bleaching and photodamage

Fossil daisy-chain

Blogging on Peer-Reviewed Research

Here's a very strange fossil from the Chengjiang Lagerstätte, an early Cambrian fossil bed from 525 million years ago. It's a collection of Waptia-like arthropods, nothing unusual there; these are ancient creatures that look rather like headless shrimp. What's weird about it is the way the individuals are locked together in a daisy chain, with the telson (tail piece) of each individual stuck into the carapace of the animal behind. It's not just a fluke, either — they have 22 fossil chains, and just one animal all by its lonesome.

(Click for larger image)

Waptia-like arthropod, Lower Cambrian, Haikou, Yunnan. (A) Individual with twisted abdomen, part of chain, Yunnan Key Laboratory for Palaeontology, YKLP 11020a. (B) Chain, about 20 individuals, various dorsoventral-lateral orientations, composite image (joined at cpt/p arrow), YKLP 11020a and YKLP 11020b. (C) Individual linked to carapace behind, lateral view, part of chain of nine individuals, YKLP 11021. (D) Isolated individual, subventral view, YKLP 11019. (E to G) Reconstruction shown in dorsal, ventral, and right lateral views, respectively. Scale bars in (A), (C), and (D) indicate 1 mm; in (B) and (E) to (G), 5 mm. b, s, and t indicate bent, stretched, and telescoped individuals, respectively; cpt, counterpart; f, facing direction; p, part; and tw, twisted.

They do not look like animals that were constrained in a burrow, or that were crawling over the surface. Rather, they had been swimming together in a chain at death, and the whole chain fell to the sea bed, bending and kinking but still remaining firmly locked together.

Why were they doing this? My first thought was of sex; everyone knows how dragonflies and damselflies lock together for mating, but of course that would predict pairs of individuals, not 20 at a time. It also reminded me of the Drosophila mutant fruitless, in which male flies court other male flies, and they spontaneously form conga lines in the culture bottles. That's also unlikely, since that kind of behavior doesn't lead to a consistent pattern of successful reproduction, but maybe if these animals were hermaphroditic, it might work. It's not a behavior that any modern arthropods show, however.

The authors consider the possibility it is a feeding strategy, but that's even worse: they're locked basically mouth to anus, which would mean the fellow at the end of the line gets a very unpleasant diet. They conclude that the most likely explanation is that this represents a migratory behavior, perhaps involved in daily vertical migration. It may have been that strings of these animals would link up and paddle together to move to new feeding sites, where they separated and dispersed until the time came to move elsewhere.

Hou X-G, Siveter DJ, Aldridge RJ, Siveter DJ (2008) Collective Behavior in an Early Cambrian Arthropod. Science 322(5899):224.

Loxodonta africana

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Loxodonta africana — African Bush Elephant, North Carolina Zoo

Why Evolution is True


I hope Jerry Coyne will forgive me that my frequent thought as I was reading his new book, Why Evolution Is True(amzn/b&n/abe/pwll) was, “Wow, this sure is easier to read than that other book.” That other book, of course, is Coyne and Orr’s comprehensive text on Speciation(amzn/b&n/abe/pwll), which is a technical and detailed survey of the subject in the title, and that I wouldn’t necessarily recommend to anyone who wasn’t at least a graduate student in biology. We all have our impressions colored by prior expectations, you know, and Jerry Coyne is that high-powered ecology and evolution guy at the University of Chicago whose papers I’ve read.

The new book is simple to summarize: just read the title. It’s aimed at a lay audience and answers the question of why biologists are so darned confident about the theory of evolution by going through a strong subset of the evidence. It begins with a discussion of what evolution is, then each subsequent chapter is organized around a class of evidence: fossils, embryology and historical accidents, biogeography, natural selection, sexual selection, speciation, and human evolution. If you want a straightforward primer in the experiments and observations that have made evolution the foundational principle of modern biology, this is the book for you.

Why Evolution is True makes an almost entirely positive case for evolution; it has an appropriate perspective on the current American conflict between science and religious fundamentalism that avoids dwelling on creationist nonsense, but still acknowledges where common misconceptions occur and where creationist PR, such as the Intelligent Design creationism fad, has raised stock objections. It’s a good strategy — the structure of this book is not dictated by creationist absurdities, but by good science, and creationism is simply noted where necessary and swatted down efficiently. It’s a more powerful tool for it, too — creationists can lie faster than anyone can rebut them, so the best strategy is to focus on the real evidence and force critics to address it directly.

You all really ought to pick up a copy of this book if you don’t already have a sound understanding of the basic lines of evidence for evolution (or, if you do, you could always get Speciation to get a little more depth). I recommend it unreservedly. Oh, except for one little reservation: it won’t be available until January. Go ahead and put it on your Amazon pre-order list, then.

George Coyne, a Jesuit priest and formed director of the Vatican Observatory has never hidden his dislike of “Intelligent Design”. Father Coyne holds a doctorate in astronomy from Georgetown University as well as a bachelor’s degree in mathematics from Fordham University.

Father Coyne also has spoken out strongly against Cardinal Schoenborn’s comments on evolutionary theory.

Cardinal Christoph Schoenborn claims random evolution is incompatible with belief in a creator God. Here, in an exclusive rebuttal of that view, the Vatican’s chief astronomer says that science reflects God’s infinite purpose

I discussed Coyne’s position in 2006

Pavo cristatus


By RPM, http://scienceblogs.com/evolgen/


Pavo cristatus — Indian Peafowl, Barcelona Zoo

Tamias minimus


Tamias minimus — Least chipmunk, Yellowstone National Park

The case of ID v ID


We are all familiar with the claim by Intelligent Design proponents that ID is a robust theory and yet, as I will show, even ID proponents seem to strongly disagree with this. Combine this with the logic applied by Judge Jones and others and we come to realize that ID indeed is doomed to remain without scientific content

And yet we continue to hear such arguments as:

Robert Crowther Wrote:

From our point of view, Intelligent Design is not a legal strategy, it’s a scientific theory. It’s a robust theory and we’re getting more and more interest in it all the time.

Source: Robert Cowther, Newsday: Science panel aims at evolution, Newsday, 4th March 2006

In a hilarious posting, William Dembski presents most likely an email from a colleague who argues that

I encourage you to take a look at the Panda’s Thumb and follow the entire thread devoted to the optimality of the genetic code. It is simply priceless. Someone styling himself Chunkdz dominates the discussion and by virtue of a very considerable gift for profane abuse, succeeds in doing what I never thought possible, and that is reducing the entire PT crowd to sputtering, dim-witted incoherence. You must link to it.

here is the link

Let’s link to this as well as to the response by us dim-wits.

PS: I wonder if Bill even bothered to look at the threads in question. Yes, they are full of profane abuses while ignoring the science involved. What is even more fascinating is how Bill points to a thread in which ChunkDZ’s profanity has been minimized in order to focus on his ‘arguments’ to show how they lack support and a thread in which ChunkDZ has not participated. Given Bill’s somewhat juvenile pleasures in making a judge pass gas, I am wondering in what other unexplored pleasures he indulges. Funny how so few ID proponents are willing nay able to defend ChunkDZ, other than marvel at his gift of profanity. Needless to say, ID may be scientifically vacuous but it does attracts people with remarkable gifts. Well, at least it’s more entertaining that Denyse O’Leary’s continued whining and DaveScot’s denial of the fact of global warming and the large human component of global warming. Ignorance does love company.

By Bora Zivkovic

First, there was the First NC Science Blogging Conference. Then, there was the Second NC Science Blogging Conference. And yes, we will have the Third one - renamed ScienceOnline’09 to better reflect the scope of the meeting: this time bigger and better than ever.


ScienceOnline’09 will be held Jan. 16-18, 2009 at the Sigma Xi Center in Research Triangle Park, NC.

Please join us for this free three-day event to explore science on the Web. Our goal is to bring together scientists, bloggers, educators, students, journalists, writers, publishers, Web developers and others to discuss, demonstrate and debate online strategies and tools for promoting the public understanding of science.

The conference is organized jointly by BlogTogether, the North Carolina bloggers’ group, and WiSE @ Duke, the Women in Science and Engineering organization at Duke University, with help from Sigma Xi and other sponsors.

The people behind the organization are Anton Zuiker, Bora Zivkovic (aka Coturnix) and Abel Pharmboy, with additional generous help by Brian Russell and Paul Jones.

The conference homepage/wiki is now live! Go and explore!

Registration is free and it is now open - go and Register right now!

See who has already registered.

Help us develop the Program.

Perhaps your organization/company would like to be a sponsor? Or you’d like to volunteer?

Just like last two times, we are preparing the publication of the Science Blogging Anthology and, this time, we’ll try to really have it ready and up for sale at the conference itself. This year’s Guest Editor is Jennifer Rohn and you should really start submitting your entries now.

For news and updates about the conference (and anthology), follow the ScienceOnline09 blog, or the Facebook Event page, or the FriendFeed room or check Bora’s SO’09 category on his blog.

Hope to see many of you in January!

Geochelone sulcata


Geochelone sulcata — African Spurred Tortoise, North Carolina Zoo

The continued rise of ignorance


On evolutionnews.org, lawyer Casey Luskin, ‘argues’ that Tiktaalik as an evolutionary icon is poor, in a retrospective confession of ignorance. Let’s see how he reached such a ‘conclusion’.

Casey Luskin Wrote:

The Rise and Fall of Tiktaalik? Darwinists Admit “Quality” of Evolutionary Icon is “Poor” in Retroactive Confession of Ignorance

How did Luskin reach this ‘conclusion’? Because he read an interview with the lead-researcher who made the following claim:

Boisvert Wrote:

Previous data from another ancient fish called Tiktaalik showed distal radials as well – although the quality of that specimen was poor. And the orientation of the radials did not seem to match the way modern fingers and toes radiate from a joint, parallel to each other.

A logical conclusion would be to accept the observation that the quality of the specimen was ‘poor’ regarding the details of ‘distal radials’, but instead Luskin decided to mine the statement to mean that the quality of Tiktaalik was poor.

Casey Luskin Wrote:

The “quality” of Tiktaalik as a fossil specimen was “poor”? When did we see Darwinists admit this previously? Never. They wouldn’t dare make such admissions until they thought they had something better.

But in fact, the ‘Darwinists’ had already admitted that the fossil specimen for Tiktaalik poorly resolved the distal radials.

Freshwater Hearing: Day 1 + DAY 2 Summary

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Day 2 update at the bottom

October 2, 2008

The hearing on John Freshwater’s termination began today before an external referee. It’s expected that it will go on for 7 or 8 days, split between early October and late October. I’ll post updates on those sessions I can attend. There is very limited seating for spectators and press – just 21 seats – so one has to get there very early to get in. A number of people failed to be admitted on account of space.

In today’s session the morning had some innocuous preliminaries and then some fireworks. In the course of having the Superintendent of Schools (Steve Short) identify documents, the Board of Education’s attorney (David Millstone) submitted a letter from the Does, parents of the boy who was burned, with their names redacted to preserve their anonymity. R. Kelly Hamilton, Mr. Freshwater’s attorney, objected to the redaction, and moved to hold an evidentiary hearing to determine whether there was a credible threat if anonymity was breeched. After a 25 minute sidebar and a 2-hour adjournment for a cage match among the half-dozen attorneys involved, the hearing resumed with the Does’ attorney Jessica Philemond agreeing to restoring the redaction and identifying the family. So they’re no longer anonymous.

On direct examination Millstone led Superintendent Short through a narrative of the various events that culminated in the BOE’s resolution to initiate termination proceedings. It was a straightforward recital of a series of problems: the original complaint about burning the boy with a Tesla coil, displays of religious materials in Freshwater’s classroom, Bibles stored in his classroom and allegedly distributed to students, inappropriate behavior in his role as monitor of the Fellowship of Christian Athetes (FCA), using ID creationist materials and handouts in his teaching, and problems with parental permission slips for participation in FCA.

Cross examination and Day 2 below the fold

Geochelone nigra


Geochelone nigra — Gal�pagos tortoise in the wild. Note especially the modified carapace, which allows it to fully extend its neck.

Tangled Bank #115

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The Tangled Bank

The latest edition of the Tangled Bank is online at Evolved and Rational. Say hooray for collections of science posts, and go read!

The “best possible code”


A paper written by Knight et al in 2000 has created some confusion as to the nature of the genetic code, leading some design proponents to jump to the conclusion that these findings show evidence of ‘design’ when in fact, the findings, in proper context show strong support for an evolutionary thesis of the origin and evolution of the genetic code. Let me explain.

Bison bison


Bison bison — American Buffalo, Yellowstone National Park

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