February 4, 2007 - February 10, 2007 Archives

A little knowledge…

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Over at Uncommon Descent, the poster Pav has a post entitled “Programmers Only Need Apply”. In it, they note, but fail to discuss this paper, Xue W, et al., Senescence and tumour clearance is triggered by p53 restoration in murine liver carcinomas. Nature. 2007 445; 656-660. What gets the poster excited is not the finding that restoration of the protein p53 can stop tumor growth (which, amusingly, drives yet another nail in the coffin of Discovery Institute Fellow Jonathan Wells’s non-mutational model of cancer ), but that the authors use the word “program” to describe the cellular senescence pathway activated by p53.

The evolution of the genetic code

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Scientists from the Weizmann Institute of Science report the exiting findings of Parallel Codes In Genes

These findings are exciting since they can help further unravel the origins and evolution of the genetic code

“Our findings open the possibility that genes can carry additional, currently unknown codes,” explains Dr. Uri Alon, principal investigator on the project. “These findings point at possible selection forces that may have shaped the universal genetic code.”

These findings provide for potential answers to our ignorance, further driving back Intelligent Design, forcing it to hide it the shadows of our ignorance.

Shalev Itzkovitz and Uri Alon The genetic code is nearly optimal for allowing additional information within protein-coding sequences Genome Res. Published February 9, 2007

Abstract: DNA sequences that code for proteins need to convey, in addition to the protein-coding information, several different signals at the same time. These “parallel codes” include binding sequences for regulatory and structural proteins, signals for splicing, and RNA secondary structure. Here, we show that the universal genetic code can efficiently carry arbitrary parallel codes much better than the vast majority of other possible genetic codes. This property is related to the identity of the stop codons. We find that the ability to support parallel codes is strongly tied to another useful property of the genetic code—minimization of the effects of frame-shift translation errors. Whereas many of the known regulatory codes reside in nontranslated regions of the genome, the present findings suggest that protein-coding regions can readily carry abundant additional information.

I wonder how ID proponents will spin these results. Nothing in ID predicts nor explain these findings. But I am sure that some will spin this, despite ID being nothing more than ‘science cannot explain X’ and does not provide for any framework to make scientifically relevant predictions.

The Discovery Institute is stepping up their smear campaign against Randy Olson and Flock of Dodos, and the biggest issue they can find is their continued revivification of Haeckel's biogenetic law. They've put up a bogus complaint that Olson was lying in the movie, a complaint that does not hold up, as I'll show you.

First, though, let's simplify the debate. The Discovery Institute position is that any text that shows Ernst Haeckel's ancient diagram of various embryos is guilty of fraudulently distorting the evidence for evolution. They have accused scientists of a conspiracy of lies, of using this known false diagram to buttress evolutionary theory.

If this were the case, then the worst case of mass market fraud around would have to be Wells' own Icons of Evolution: it contains 4 versions of the Haeckelian diagram, including the original, and talks about it for 28 pages. Obviously, this is a criminal conspiracy to promote phony evidence for evolution.

Wait, wait, you protest: Wells' book was explaining that Haeckelian recapitulation was wrong, and that there were both errors and intentional misrepresentations of embryos in that old work. That should be acceptable.

I would agree, except that the textbooks Wells is damning in Icons often do exactly the same thing! Those that do mention Haeckel and his biogenetic law do so as an example of a historically significant error. Some go on to explain what was correct and what was wrong in his ideas, but basically all are merely pointing out that here was an interesting but failed explanation from the late 19th century, that nonetheless exposes an interesting phenomenon that needs to be understood.

I would add that progress in evolutionary biology has led to better explanations of the phenomenon that vertebrate embryos go through a period of similarity: it lies in conserved genetic circuitry that lays down the body plan. Intelligent Design creationism has contributed absolutely nothing to either refuting Haeckelian ideas, which was the product of working biologists at the end of the 19th century, nor has it generated any better, testable explanations for the conservation of embryonic body plans.

Now what about the Discovery Institute's claim that Olson was lying about Haeckel's representation in modern texts?

Continue reading "Wells’ false accusation against Randy Olson" (on Pharyngula)

Desperate Times for ID?

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At the Discovery’s Website for the Renewal of Science and Culture, Logan Gage proudly presents the statements by a British Scientist who claims that Intelligent Design is a valid scientific theory.

Professor of Design and Nature Stuart Burgess of Bristol University (UK) was interviewed in yesterday’s The Independent. This is a man who knows something about design. He is worth heeding:

I’ve been designing systems like spacecraft for more than 20 years. One of the lessons I’ve learnt is that complex systems require an immense amount of intelligence to design. I’ve seen a lot of irreducible complexity in engineering. I have also seen organs in nature that are apparently irreducible. An irreducibly complex organ is one where several parts are required simultaneously for the system to function usefully, so it cannot have evolved, bit by bit, over time.

Source: Independent

An engineer…

In the Yale Daily news, Michael Zimmerman responds to some of the more outrageous misunderstandings by Discovery Institute’s Jonathan Wells, author of the infamous (and wrong) Icons Of Evolution. In a historical repetition it seems that Wells got few of the details right.

Seems that the DI is truly concerned about the impact of Evolution Sunday and the Clergy Letter.

Darwin and neutrality

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Various ID proponents have shown a confusion about Darwinism and neutrality, arguing that these concepts are contradictory rather than complementary and that the existence of one negates the existence of the other. Such a false duality is commonly found in the writings and musings of ID proponents who insist on elimination to infer the existence of one of many alternatives. So lets explore in further detail the concept of neutrality and its relevance and importance to evolutionary science (and by logical extension also the vacuity of Intelligent Design).

I am inclined to suspect that we see, at least in some [cases], variations which are of no service to the species, and which consequently have not been seized on and rendered definite by natural selection…. Variations neither useful nor injurious would not be affected by natural selection, and would be left either a fluctuating element, as perhaps we see in certain polymorphic species, or would ultimately become fixed…. We may easily err in attributing importance to characters, and in believing that they have been developed through natural selection;… many structures are now of no direct use to their possessors, and may never have been of any use to their progenitors…. [On the other hand,] we are much too ignorant in regard to the whole economy of any organic being to say what slight modifications would be of importance or not.

From: DARWIN, C., 1872 The Origin of Species, 6th ed. p. 60,88,181,182,184. New American Library of World Literature, New York (1958)

Darwin Day is fast approaching! In honor of Charles Darwin’s birthday and his intellectual achievements, the Alliance for Science is starting an annual Darwin Day essay contest geared at high school students. We will be accepting essays from the 50 states, submissions sent by email. There will be cash prizes for the top entries, magazine subscriptions, and numerous signed books on evolution, creationism, or other relevant topics in biology available as prizes. Teachers, if your student is the winner then we will also kick in some money for your science labs!

Interested in finding out more and maybe donating to the contest?

Continue reading “1st Annual Darwin Day Essay Contest” (at Neurotopia)

And it's a dud. They've got two complaints against Randy Olson's Flock of Dodos posted, neither of which are particularly stunning.

Continue reading "Discovery Institute fires its first salvo in the War Against Dodos" (on Pharyngula)

In August of 2005, the Rio Rancho, New Mexico School Board adopted “Science Policy 401,” which was amended last April, after strong protests from scientists and teachers against the Intelligent-Design friendly policy.

After yesterday’s Rio Rancho school board elections, Policy 401 had better start looking over its shoulder. Even though the amended policy is basically toothless in comparison to the original version, the existence of this totally unnecessary policy still rankles many in the community. One of the policy’s original supporters, Kathy Jackson, decided not to run again, and gave her support to candidate Steve Dietzel. Dietzel, however, was crushed by strong pro-science candidate Divyesh Patel in a landslide vote. So, the creationist-leaning members of the board now find themselves in the minority, and policy 401 itself may be on the chopping block soon.

Another of the policy’s supporters, Marty Scharfglass, was able to keep his seat, but only by a few dozen votes. His opponent, pro-science candidate Sabrina Vidaurri, ran a surprisingly strong campaign against the incumbent.

Yesterday, I introduced a seminar of honors students at UNC to the science of evolution. If you go to my blog, you can read how it went and download handouts of my presentation.

De Rerum Natura: Introduction to Evolution (comments may be left there)

As I reported previously, evangelicals, led by Bishop Boniface Adoyo, Chairman of the Evangelical Alliance of Kenya, are trying to suppress a fossil display in Kenya’s National Museum. (And they’re apparently getting aid from unnamed Western groups.) The planned exhibit contains numerous hominid fossils found in that country, including the famous Turkana Boy, a nearly complete Homo erectus skeleton.

CNN has recently published an article about the museum exhibit and the evangelicals’ attempts to whisk it away to some back room where it can’t offend them. Most of the information in the article is old hat, but it’s good to see the American media finally picking up on this. There is however one part that’s new to me:

[Richard] Leakey fears the ideological spat may provoke an attack on the priceless collection, one largely found during the 1920s by his paleontologist parents, Louis and Mary Leakey, who passed their fossil-hunting traditions on to him.

The museum, which attracts around 100,000 visitors a year, is taking no chances.

Turkana Boy will be displayed in a private room, with limited access and behind a glass screen with 24-hour closed-circuit TV. Security guards will be at the entrance.

”There are issues about the security,” said Dr. Emma Mbua, the head of paleontology at the museum. “These fossils are irreplaceable and we wouldn’t want anything to happen to them.”

Insurance coverage could run into millions of dollars, she added.

Way to go creationists. You’ve successfully driven security and insurance costs through the roof because your nutty followers can’t be trusted not to destroy priceless artifacts.

(Cross-posted to Sunbeams from Cucumbers.)

Next Tuesday the Kansas state Board of Education will vote on adopting new science standards based on the work on the science standards writing committee. The committee, of which I am a member, started work in June 2004, but our work was co-opted by the Intelligent Design crowd in Kansas (remember the infamous Kangaroo Kourt “science hearings” in 2005?), and so ID-creationist standards were adopted in November 2005.

However, elections in 2006 once again brought a majority of pro-science supporters to the Board, and so now the Committee’s Recommended Standards (which we continued to work on even after we were officially dismissed in favor of the IDists) are being brought back for adoption.

Kansas Citizens for Science has issued an open letter supporting the Board in voting “Yes” to adopt the new standards. (See below the fold.)

We are asking that people in the state and around the world email Board members expressing your support for the new standards. Please keep your emails positive, even to the Board members who support the ID standards. The issue is not what is wrong with the ID standards (a subject that has been interminably discussed), but rather what is right about the Committee’s standards. Put your email in a positive pro-science, pro-education framework, not an anti-anything framework.

Help Kansas Citizens for Science stand up for science!

By the way, if you want to see for yourself the differences in the Committee’s standards and the ID standards, you can download a comparison document here. However, trust me, ours are better, :-)

Darwin’s Day Activities, February 12 at the University of Kansas Theme: We have come a long way since Darwin. See here for much prettier information at the KU website!

If you’re in the area, please join us! KCFS will buy a ticket for anyone who says you read about it here on the Panda’s Thumb!

6:00 pm Museum Activities: Special exhibits and tours of the museum and the Exploring Evolution exhibit will be given

7:30 pm Costume contest: Sponsored by Kansas Citizens for Science

Anyone dressed as Darwin (any age), Muffy Moose, or a Dodo will get in free to the movie “Flock of Dodos” (see Flock of Dodos, The Dodos Gazette and the Muffy Moose weblog), and will get to lead the crowd from the Museum to Woodruff Auditorium for the show.

$100.00 cash prize for winner of each category. $50.00 cash prize for second

7:45 pm “Flock of Dodos” showing.

The cost of the movie and event is $2.00. Tickets will be available through the Gift Shop in the museum

I always enjoy watching creationists blather about stuff that they have no knowledge about, which is of course just about anything that comes out of their mouths. I am always amazed how they can pull the most randomly backwards arguments from out of nowhere and confidently state that this one is the one that is going to trump “Darwinism”. Their arguments are really not that different from one another, but they sure can come up with some bizarre and senseless variations.

Good Math, Bad Math has a good take down of one such recent argument from Cordova on UD: Once again, Sal and Friends Butcher Information Theory.

Acting! On the web!

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Are you a voice talent? Want to participate in an online drama? Sign up for a part in a podcast recreation of parts of the Dover trial. It should be fun, if you're into that kind of thing.

I'm not volunteering, I'm afraid. I can't act, and I'm also afraid that the closest match to my voice would be Michael Behe, and I'd die of mortification.

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