January 2010 Archives

Butterstick Goes Wild

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Tai “Butterstick” Shan, the panda born at the National Zoo in Washington DC and displayed up above, is going back to China. CNN has a report on his farewell party.

But it is Still a Robot!

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This months PLoS Biology contains a review article by Floreano and Keller on studies that explore evolution using robots. It is an interesting read.

Evolution of Adaptive Behaviour in Robots by Means of Darwinian Selection

Darwin suggested that adaptation and complexity could evolve by natural selection acting successively on numerous small, heritable modifications. But is this enough? Here, we describe selected studies of experimental evolution with robots to illustrate how the process of natural selection can lead to the evolution of complex traits such as adaptive behaviours. Just a few hundred generations of selection are sufficient to allow robots to evolve collision-free movement, homing, sophisticated predator versus prey strategies, coadaptation of brains and bodies, cooperation, and even altruism. In all cases this occurred via selection in robots controlled by a simple neural network, which mutated randomly.

The Glory

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The glory – seen from an airplane.

Enough of biology! Another optical phenomenon. The dark line to the right is the contrail. Contrast has been enhanced.

Thin reeds

Okay, this is classic Casey Luskin. He recently published a law review article of minimal interest in the Hamline University Law Review, about “teaching biological origins,” which as we know means, “finding some clever way to pretend that creationism is science so that we can teach it in biology classes in violation of the law.” He’s posted a couple paragraphs of the article over at DI’s blog. Here he mentions a case called Segraves, in which a California court rejected a Free Exercise Clause challenge against a school district for teaching evolution–that is to say, the court correctly held that teaching evolutionary science in a government school does not violate a person’s right to freely exercise his religious beliefs. But here’s Luskin’s interpretation: “This opinion is of minimal value as precedent, as it comes from a lower state court and was never officially published as a legal opinion. Nonetheless, it implies that evolution education policies may avoid establishing religion when they are based upon the legitimate secular purpose of avoiding dogmatism in the classroom.”

So, in other words, an unpublished, and therefore unciteable, decision by a trial court, which is therefore not precedent for anything, really, but which upheld the teaching of evolutionary science, is somehow precedent for the DI’s mission of teaching religion masquerading as science on the taxpayer’s dime. I have nothing against the trial court’s decision in Segraves, obviously, but it’s not exactly the strongest court opinion to cite for anything, least of all in the service of Luskin’s badly disguised defense of creationism.

You can read the Segraves decision here.

BCSE critiques “Explore Evolution”

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“Explore Evolution” is the latest shot in the ‘get ID creationism into the public schools’ strategy of the Discovery Institute. It’s a book aimed at home schoolers and public schools that purports to use an “inquiry-based” approach to teaching evolution. In fact what it does is use an “error-based” approach, one laden with strawman arguments and the usual creationist distortions and misrepresentations of the science. The National Center for Science Education has a detailed analysis of the trash that the book conveys to students.

Now the British Centre for Science Education has prepared a shorter pamphlet (pdf), based on the NCSE material, which is aimed mainly at British schools. An outfit named “Truth in Science” (what else?) sent the book to many schools in the UK, and BCSE is responding to that wallpapering of their schools with ID creationism.

Leaving aside the UK-specific material relevant to their national curriculum, pages 7-15 of the pamphlet (pdf) are a succinct and readable rebuttal of the glop in the book, and would be useful for anyone involved in this effort in the UK or elsewhere. It’s designed as a teacher resource and does a good job. Highly recommended.

Hat tip to NCSE on Facebook.

My Genome is Sequenced!

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panda_nature.jpg You humans have finally finished sequencing my genome—okay, not exactly mine but a cousin’s. Some of you might be thinking about using this to clone me. But I own the copyright to myself so you can’t do anything!

I’m busy clubbin’ with some seal friends of mine right now and haven’t had the time my species needs to digest such monumental work. I recommend Matthew Cobb’s take on the giant panda genome.

Last summer, I began working as a postdoc at the University of Houston. I was initially unsure about the move, but I am pleasantly surprised with the city and the university. There is a strong, core group in ecology and evolutionary biology here. Thus I pass on this student recruitment letter, with the mention that if you attend school here, you will get to hang out with Prof. Steve Steve.


The Department of Biology and Biochemistry at the University of Houston (UH) welcomes applications for its graduate program in Evolutionary Biology and Ecology for Fall 2010. The following faculty in the area of Evolutionary Biology and Ecology are seeking graduate students for their labs:

Blaine Cole ([Enable javascript to see this email address.]) — Evolution and social behavior
Dan Graur ([Enable javascript to see this email address.]) — Theoretical molecular evolution
Diane Wiernasz ([Enable javascript to see this email address.]) — Ecological genetics
George Fox ([Enable javascript to see this email address.]) — Experimental evolution and origin of life
Gregg Roman ([Enable javascript to see this email address.]) — Evolution of behavior
Rebecca Zufall ([Enable javascript to see this email address.]) — Genome and molecular evolution
Ricardo Azevedo ([Enable javascript to see this email address.]) — Evolution
Steve Pennings ([Enable javascript to see this email address.]) — Community ecology
Tim Cooper ([Enable javascript to see this email address.]) — Experimental evolution
Tony Frankino ([Enable javascript to see this email address.]) — Evolution of complex traits
Yuriy Fofanov ([Enable javascript to see this email address.]) — Evolutionary bioinformatics

For more information regarding the Evolutionary Biology and Ecology graduate program at UH see:

http://www.uh.edu/admissions/graduate/
http://www.bchs.uh.edu/graduate/
http://www.bchs.uh.edu/about/resear[…]d-evolution/

The deadline for application of prospective students is April 1st, 2010, but students are encouraged to apply as soon as possible.

Creation Opens Friday

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Creation, the true story of Charles Darwin, based on the book by Randal Keynes, Darwin’s great-great-grandson, opens in theaters this Friday in New York, Los Angeles, Boston, San Francisco, and D.C.

“His love for his wife, his observations of his children, his friendships with gardeners, schoolteachers and pigeon fanciers, his fears about death, revolution, bankruptcy, inbreeding … all these things found their way into his theory. He was the most inclusive of thinkers.” Randal Keynes, Annie’s Box

Support the film! The distributors will gladly link back to your organization from their Facebook and Twitter pages if you link to them. Help us spread the word.

Become a fan of Creation on Facebook.

Follow Creation on Twitter.

For theater information, check http://creationthemovie.com/.

This post was modified from a press release we received today.

Darwin’s finches

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Darwin’s finches – science tattoos. Photograph courtesy of Carl Zimmer, The Loom.

Freshwater: DIY Handwriting Analysis

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In my recent post on testimony on December 30 I noted that Freshwater’s attorney, R. Kelly Hamilton, engaged in some theatrics about an exhibit introduced by the Board’s attorney, characterizing it as a forgery. I also described some of the similarities in the writing on two documents. One is a copy of an article on building tall structures decorated with handwritten comments about the Tower of Babel, found in Freshwater’s classroom. The other is a lesson plan written by Freshwater in 2006 and introduced by his attorney as an exhibit. Freshwater testified that the handwriting on the lesson plan was his.

I’ve put scans of the relevant portions of both documents on the web, and I invite readers to make their own comparisons. Note that when one clicks on one or the other document there is a button towards the top right of the screen to magnify the displayed document.

For reference the similarities I noted earlier are below the fold.

Freshwater Day 31: A School Board Member’s Ethics Problem

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The 31st day of the administrative hearing on whether John Freshwater should be terminated as a Mt. Vernon Middle School science teacher was supposed to be today, but after 2 hours and 15 minutes of private conferences among the attorneys and referee the hearing was abruptly adjourned until January 22, 2010.

In addition, I have learned that a new member of the Board of Education, Steve Thompson, has started engaging in private efforts to produce a settlement without authorization or discussion by the Board of Education, thereby exposing the Board to significant legal jeopardy. Both are described below the fold.

More on Signature in the Cell

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Yesterday, I showed how the treatment of information in Stephen Meyer’s book, Signature in the Cell, contains many misunderstandings and unjustified claims.

Today, I want to focus on what I call the “dishonesty factor” of the book: claims that are misleading or just plain false. The philosopher Thomas Nagel has stated that “Meyer’s book seems to me to be written in good faith.” Perhaps, after reading these examples, he might reconsider his assessment.

Freshwater: Yet another student and yet another cross

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While the administrative hearing on the termination of John Freshwater as a Mt. Vernon, Ohio, middle school science teacher is slowly approaching a conclusion, the preliminaries to the two federal suits are in progress. Recall that the Dennis family’s suit against the school district was partly settled, with the district agreeing to pay attorney’s costs plus a small amount to the family. However, Freshwater remains a defendant in that suit. And Freshwater has sued a range of entities and people in federal court.

I recently obtained the transcript of a deposition made a year ago by another student in Freshwater’s class that academic year, 2007-2008, and that deposition corroborates two major allegations about Freshwater’s classroom behavior, the use of the Tesla coil to mark students’ arms with crosses and the showing of a creationist video, The Watchmaker in science class.

The deposition of the student, referred to in the deposition as “Student No. 5”, was taken on February 16, 2009 for the Dennis family’s federal suit. In it there are two passages of immediate interest. They’re below the fold.

A couple of months ago, I finished a first reading of Stephen Meyer’s new book, Signature in the Cell. It was very slow going because there is so much wrong with it, and I tried to take notes on everything that struck me.

Two things struck me as I read it: first, its essential dishonesty, and second, Meyer’s significant misunderstandings of information theory. I’ll devote a post to the book’s many mispresentations another day, and concentrate on information theory today. I’m not a biologist, so I’ll leave a detailed discussion of what’s wrong with his biology to others.

In Signature in the Cell, Meyer talks about three different kinds of information: Shannon information, Kolmogorov information, and a third kind that has been invented by ID creationists and has no coherent definition. I’ll call the third kind “creationist information”.

It’s been a long time since I’ve responded to an Uncommon Descent post, and I’m starting to remember why. There’s one that went up over there the other day on the fossil record that’s really almost mind numbing - starting with the title, which is “Why Not Accept the Fossil Record at Face Value Instead of Imposing a Theory on it?

Here’s what seems to be the main argument:

Here’s a simple example - extinction estimates. Darwinists will say that 99.99% of species that have ever lived have gone extinct. Well, that’s actually a bunch of B.S. There are roughly 250,000 species that have been identified in the fossil record, and well over 1,000,000 species that exist today. Taken at face value, even if every species in the fossil record has gone extinct (which they haven’t), that means that 80% of species that ever existed ARE STILL ALIVE. That’s quite a stretch. So where do Darwinists get their number? By assuming that innumerable species existed in the transitional spaces. Why? Because they _must_ have existed there for their theory to be true.

Creation, the new film about Darwin featuring Paul Bettany and Jennifer Connelly, premieres in the United States on January 22, 2010, in New York, Los Angeles, San Francisco, Washington DC, and Boston.

LA and Boston will have advance showings.

Uncia uncia (Panthera uncia)

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Photograph by Dan Stodola.

Photography contest, Honorable Mention.

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Uncia uncia (or Panthera uncia) - Snow Leopard, Brookfield Zoo, Illinois.

Once again, the Discovery Institute stumbles all over itself to crow victory over evolution, led by the inspiring figure of that squeaking incompetent, Casey Luskin. This time, what has them declaring the bankruptcy of evolution is the discovery of tetrapod trackways in Poland dating back 395 million years. I know, it's peculiar; every time a scientist finds something new and exciting about our evolutionary history, the bozos at the DI rush in to announce that it means the demise of Darwinism. Luskin has become the Baghdad Bob of creationism.

The grounds for this announcement is the bizarre idea that somehow, older footprints invalidate the status of Tiktaalik as a transitional form, making all the excitement about that fossil erroneous. As we've come to expect, though, all it really tells us is that Casey Luskin didn't comprehend the original announcement about Tiktaalik, and still doesn't understand what was discovered in Poland.

What’s an IDist to do?

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IDist Stephen Meyer’s “Signature” ID book has lately inspired this, this, this and this. Now it is Ayala’s turn to play Whack-a-Meyer. Elsewhere Dembski of all people is criticized for not being wrong enough.

Galilean Moons at 400

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400 years ago today, Galileo got the bright idea of taking his newly made telescope and pointing it at Jupiter. He saw some new stars, strangely in a straight line with Jupiter. Over the next couple of nights he kept looking, saw a fourth star, and then realized that the “stars” were moving with Jupiter, but not exactly. From his Starry Messenger:

Tetrapods are older than we thought!

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Some stunning fossil trackways have been discovered in Poland. The remarkable thing about them is that they’re very old, about 395 million years old, and they are clearly the tracks of tetrapods. Just to put that in perspective, Tiktaalik, probably the most famous specimen illustrating an early stage of the transition to land, is younger at 375 million years, but is more primitive in having less developed, more fin-like limbs. So what we’ve got is a set of footprints that tell us the actual age of the transition by vertebrates from water to land had to be much, much earlier than was expected, by tens of millions of years.

Here are the trackways. Note that what they show is distinct footprints from both the front and hind limbs, not drag marks, and all that that implies: these creatures had jointed limbs with knees and elbows and lifted them and swung them forward to plant in the mud. They were real walkers.

An Ill Wind in Tortuca

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Or: How creationism (its existence and persistence) tells us a lot about how people think, even when they’re not being creationists, and how all this affects the way freethought secularism ought to approach the bigger world.

By James Downard

In a comment on an earlier post James Downard mentioned his talk to the Kennewick Freethought Society linked below. Watching the video, it struck me that James had hit on a possible cognitive mechanism that explains the phenomenon we call “compartmentalization,” the ability of a person to apply different standards of evidence (and logic?) to propositions in different domains of inquiry. I asked James if we could publish a transcript of the talk, and he graciously provided it. It’s below, with appropriate formatting inserted for the Thumb’s requirements. —RBH

An address by James Downard, presented to the Kennewick, Washington Freethought Society on October 25, 2009.

A friend of mine and fellow member of our local Inland Northwest Freethought Society, Jason, kindly recorded my talk and the various questions afterward from the audience. The main speech itself he posted in three parts on Youtube and elsewhere (retitled for there as “The Absurdity of Religion: Tortucan Traps” to give it a bit more kick as a teaser title). I got into a pretty fast delivery speed for it, for which I apologize.

Homo nivarius

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Photograph by Dave Thomas

EvolutionSnowman.jpg

Homo nivarius – evolution of the snowman.

Signature in the Cell?

(The following is a follow-up to a comment I made in this thread.) There is much abuzz in the ID-o-sphere regarding Stephen Meyer’s new book, “Signature in the Cell: DNA and the Evidence for Intelligent Design”. The book is a lengthy recapitulation of the main themes that ID proponents have been talking about for the past 15 years or so; indeed, there will be precious little that is new for seasoned veterans of the internet discussions and staged debates that have occurred over the years.

Long though the book is, it is built around one central theme - the idea that the genetic code harbors evidence for design. Indeed, the genetic code - the triplet-amino acid correspondence that is seen in life - is the “Signature in the Cell”. Meyer contends that the genetic code cannot have originated without the intervention of intelligence, that physics and chemistry cannot on their own accords account for the origin of the code.

It is this context that a recent paper by Yarus et al. (Yarus M, Widmann JJ, Knight R, 2009, RNA-Amino Acid Binding: A Stereochemical Era for the Genetic Code, J Mol Evol 69:406-429) merits discussion. This paper sums up several avenues of investigation into the mode of RNA-amino acid interaction, and places the body of work into an interesting light with respect to the origin of the genetic code. The bottom line, in terms that relate to Meyer’s book, is that chemistry and physics (to use Meyer’s phraseology) can account for the origin of the genetic code. In other words, the very heart of Meyer’s thesis (and his book) is wrong.

For details, follow this link, where comments may be left.

Bradley Monton thinks he understands intelligent-design creationism better than either its opponents proponents or its critics. He’s about half right.

Monton, a philosopher at the University of Colorado, has recently been making a bit of a name for himself by publicly debating ID creationism and also moderating a debate between Francisco Ayala and William Lane Craig. So I decided it was time I read his book, Seeking God in Science: An Atheist Defends Intelligent Design from cover to cover. I am working from a proof copy that the author kindly sent me last spring, so I will not comment on minor errors. I thought the book was well and clearly written, if not always well argued, but I thought that if I saw one more instance of an awkward and wholly superfluous phrase such as “it is the case that,” I was going to scream or throw my shoe through the monitor.

Freshwater: 2009 (but not the hearing) drags to an end

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This week saw two more days of testimony in the administrative hearing to determine a recommendation on whether John Freshwater should be terminated as a middle school science teacher in the Mt. Vernon school district. The main witness for the two days, December 29 and 30, was Freshwater himself undergoing cross examination after his direct examination which is summarized here.

The proceedings went very slowly under both direct and cross examination because Freshwater has become much more cautious about answering questions, has begun reading all exhibits offered slowly and thoroughly, is frequently asking for clarification or rewording of questions, and in some cases repeatedly avoided answering until at a couple of points the referee intervened, instructing him to answer the question asked.

For additional coverage by reporters at the hearing I refer you to Pam Schehl’s story in the Mt. Vernon News here (29th) and here (30th), and to Dean Narciso’s stories in the Columbus Dispatch here and here. For updates by a creationist of the Kent Hovind kind who is also attending the hearing, see here.

The two days are summarized in 8,000 well-chosen words below the fold.

Rosa Grandiflora “New Year”

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Photograph by David Young.

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Rosa Grandiflora “New Year” – New Year Rose, Albuquerque Botanic Garden, Albuquerque, New Mexico.

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