January 2008 Archives

Determining where a genome has been produced or altered by an intelligent designer is a matter of some importance. Consider the claims that the HIV virus was engineered as a biowarfare weapon, or the concern that virulence genes from other organisms could be inserted into viruses and bacteria to “weaponise” them. For example the engineered mouse pox virus that turned lethal (Nature. 2001 May 17;411(6835):232-5 see also Nat Genet. 2001 Nov;29(3):253-6) and limits on the sequencing of the 1918 strain of the flu to stop flu from being weaponised (Fed Regist. 2005 Oct 20;70(202):61047-9,). A method that could reliably detect the action of human intelligent design in the genomes of microorganisms would be of significant advantage.

Thus we issue the “Intelligent Design Challenge”. Below the fold are 6 gene sequences. At least one of them has been produced by a human designer. All you have to do is to determine which one(s) have been acted on, what the designed sequence does, and explain the method you used to determine this (in sufficient detail to replicate your determination eg. if you used an approximation of Chaitin information, a brief description of the algorithm you used).

I’ve re-written the contest rules slightly as some people were confused as to what designer they were supposed to detect.

To win, you have to:

1) Identify which sequences have been produced by a human designer
2) Describe how you identified the sequence as being designed (eg. I used PKZip to compress the sequences as an approximation of Chaitin information and ordered the output according to the following criteria etc. etc.)
3) Describe what the sequence does (eg. “This is the active site of a triose phosphate isomerise engineered into a riboprotein – this due to the catalytic triad signature” real example BTW: this isn’t as hard as it sounds once you have the designed sequences)

Obviously, the groups who produced these sequences are not eligible to enter, and if you walked down the corridor and asked the groups who produced these sequences what they did, you are also not eligible. You need to have done some actual work related to the sequences presented here. Simply looking up all journal references to “designed sequences” in Pubmed doesn’t count (obviously this is all public domain, I’m not going to release the engineered killer mousepox virus sequence am I).

If you are in an emergency ward, trying to discover if the superflu screaming through the population is a bioweapon, you won’t find the answer that way. And you won’t have the luxury of having a full viral sequence to BLAST against known genes [thus discovering that the M2 ion channel had been replaced with the amandatine-insensitive Vpu ion channel, so that your antiviral drugs won’t work], but short sequences like the ones above.

Remember, in a real biowarfare situation, everyone will be short of time and resources. A simple, reliable procedure to determine if a sequence has been human-engineered is of the utmost importance.

So, in the spirit of the Robot Soccer Challenge and the NASA Spacecraft Challenge, look at the sequences below the fold and off you go.

The first successful determination of the designed sequence(s) and their function will win a copy of OpenLab 2007.

Comments will be will be opened for your entries at 10:30 pm Australian Central Daylight Saving Time (GMT +10:30), 1 February.

The comments are now live, write in your entries. The first correct answer fulfilling the conditions will receive a copy of OpenLab 2007. As tonight is my sons’ birthday, and I have an occultation to observe as well, don’t expect much input from me for a while.

My article “Reason And Common Ground: A Response to the Creationists’ ‘Neutrality’ Argument” will appear in the next issue of the Chapman Law Review, which subscribers should receive in the mail in a week or so. You can download it on SSRN. The article is a reply to a creationist article that the Chapman Law Review published last year, entitled “Evolution, Science, And Ideology: Why The Establishment Clause Requires Neutrality in Science Classes,” by Stephen W. Trask.

Read an excerpt from the opening of my article at Freespace…

Roger Ehrenberg dissects Ben Stein’s shaky grasp of markets in “How to Lie With Statistics” a/k/a Ben Stein’s Modus Operandi. So Stein’s an Evil Darwinist Conspiracy theorist and an Evil Traders Conspiracy theorist. I wonder if he’s an HIV denialist or a global warming “skeptic” to complete a woo trifecta.

Michael Shermer of Scientific American fame has a new book out (which will be arriving in the mail soon, I hope) about evolution and economics, called The Mind of The Market: Compassionate Apes, Competitive Humans, And Other Tales from Evolutionary Economics. His theme is how the market, like evolution, is a process of spontaneous order—a “self-organized emergent order.” He read an excerpt from the book and commented on it at the Cato Institute this month, and here’s a video excerpt from that talk. You can watch the entire event here.

One thing that really pisses me off is when lawyers abuse their status as lawyers to frighten people without justification. Casey Luskin, whose ignorance and intellectual dishonesty have been repeatedly documented on Panda’s Thumb and elsewhere, did this in a particularly amusing way, as S.A. Smith of the ERV blog points out: suddenly, it appears, an ID spokesman is worried about copyright infringement.

Read the rest at Freespace…

Some may know that one of my ‘hobby’ aspects of evolution involves the evolution of evolution, aka evolvability and how neutrality is a necessary requirement for evolvability. Let’s walk through an example which helps explain my position.

I will use a recent paper by Andreas Wagner “Hypothesis: Robustness, evolvability, and neutrality” FEBS Letters 579 (2005) 1772–1778

Our friend Abigail Smith aka ERV provides us with an entertaining posting about who else but Behe

Remember Behe’s crusade for Intelligent Design at KKMS 980AM, a Christian radio station?

For those who cannot stand the torture of listening to Michael Behe making claims that science can reliably detect ‘design’, let’s first explain what exactly Intelligent Design is all about and reject ID’s hollow claims.

Very early this morning, the Discovery Institute’s Rob Crowther posted an article over at the DI’s “why’s everyone always picking on us” blog. I’m not exactly sure what inspired Rob to get some work done late on a Saturday night, but the result is an article that’s so chock full of hysterically absurd misrepresentations and bizarre claims that it’s impossible to resist the urge to comment.

The apparent cause for Rob’s rant was his displeasure with an op-ed that was published in the Austin American-Statesman on Friday. The op-ed was written by the past-president, president, and president-elect of The Academy of Medicine, Engineering and Science of Texas, on behalf of the entire Board of Directors of the organization. In the op-ed, they noted that recent events in Texas have caused many scientists in the state to become more concerned about attacks on science education, and stated that the position of their organization is that Intelligent Design is not science, and should not be taught as such. The authors’ position is clearly stated and their tone is reasonable. That’s what I thought when I read it, anyway.

Rob Crowther disagrees. In fact, he thinks that the authors of the op-ed compared the Intelligent Design movement to Nazis. His reasoning is so completely and utterly insane that it defies the imagination.

Read more at The Questionable Authority, where comments may be left.

Evolution Weekend has approximately 750 participants from 50 states, the District of Columbia, and 9 other nations; last year, Evolution Sunday garnered a bit over 600 participants (see my earlier posting at http://www.pandasthumb.org/archives[…]sunda-3.html ). Here, for anyone willing to help publicize Evolution Weekend, is part of an e-mail I received from the organizer, Michael Zimmerman:

By way of GrrlScientist, I notice that Fieldiana (the journal of the Field Museum is now freely available online. For us here at the Panda’s Thumb, it means that DD Davis’ classic study “The giant panda: a morphological study of evolutionary mechanisms” of 1964 can now be enjoyed by one and all. Over three hundred pages, detailing everything you’d want to know about giant panda morphology. Steve Steve urges you all to check it out!

Florida Citizens for Science have posted another article showing what is the real motivations behind the opposition to the Florida science standards.

Norris, who is also a Lutheran minister, has stated that evolution should not be taught as fact and that students should be able to discuss creationism in class.

…

School Board Vice Chairman Andy Tuck said Thursday, “as a person of faith, I strongly oppose any study of evolution as fact at all. I’m purely in favor of it staying a theory and only a theory.

Help us educate these school boards. They seem to be confused that the standards call evolution a fact when it doesn’t. They also seem to believe that there may be competing theories of evolution; there are none.

And keep those postings coming, as they are documenting a clear religious component to the resolutions passed.

Zimmer interviews Shubin on Bloggingheads discussing how Tiktaalik was correctly predicted and eventually found by the researchers. The video which lasts over 50 minutes discusses many aspects of the find and also touches on Dover. Remember that Dover involved a creationist book called Of Pandas And People which implied that fossils like Tiktaalik had never been found and likely would never have been found.

Another gap closed.

Enjoy the video.

Latest Count Confirmed in support of science (1) Unknown (46) On Watch List (8) Anti Science Resolution Passed (6) Resolution on future Agenda (5)

Highlands County Educate a school board school board contact information Norris, who is also a Lutheran minister, has stated that evolution should not be taught as fact and that students should be able to discuss creationism in class. Source

Washington County joins the list
Madison County joins the list
Three new additions: Jackson County, Nassau County, and Putnam county. More on this below the fold

Brevard County first to reach green status

The St Petersburg Times has another great article on what the school boards really mean when they want to teach alternative theories.

Evolution is “going to be taught as fact, and everyone knows it’s not fact,” said Dennis Bennett, the superintendent in Dixie County, west of Gainesville. “There’s holes in it you can drive a truck through.

Philip Ball reports in Nature on new findings that show how the slime mo[u]ld can anticipate periodic events.

The actual paper is published as Amoebae Anticipate Periodic Events in Phys. Rev. Lett. 100, 018101 (2008) by authors Tetsu Saigusa, Atsushi Tero, Toshiyuki Nakagaki and Yoshiki Kuramoto

Abstract:

When plasmodia of the true slime mold Physarum were exposed to unfavorable conditions presented as three consecutive pulses at constant intervals, they reduced their locomotive speed in response to each episode. When the plasmodia were subsequently subjected to favorable conditions, they spontaneously reduced their locomotive speed at the time when the next unfavorable episode would have occurred. This implied the anticipation of impending environmental change. We explored the mechanisms underlying these types of behavior from a dynamical systems perspective.

For more information, see what Bora and I have written.

On Pharyngula, PZ Myers shows how Intelligent Design continues to be a scientifically vacuous concept.

Desperate to show that evolution can be detrimental to scientific inquiry, ID proponents have been arguing not only that junk dna was a prediction by ID, a statement which is logically flawed, but also that evolution and particularly Darwinism was the reason why people called non-coding DNA and pseudogenes ‘junk’.

The latter assertion has been more than once corrected on this blog but it seems that ID remains dogmatic in its claims, unable to learn from its own mistakes.

The same applies to the creationist understanding of the meaning of vestigial which they somehow believe to be equivalent to ‘no function’.

Wikipedia explains:

Vestigiality describes homologous characters of organisms which have lost all or most of their original function in a species through evolution.

Original function…

Over at the Discovery Institute’s blog, Rob Crowther is playing up the “Dissent from Darwinism” list. Again. The list is nothing new. They’ve been working on it for several years now, and have managed to accumulate “over 700” signatures from around the world. Given the number of scientists on the planet, and the degree to which the DI folks have relaxed their definition of “scientist”, it’s hardly a stellar performance on their part. As much as I’d like to ignore the list for being the laughable public relations gimmick that it is, I’m not going to this time. Crowther managed to punch one of my buttons with his latest attempt to describe the reasons that people sign this list:

Read more at The Questionable Authority, where comments may be left:

Florida Citizens for Science presents us with yet another newspaper editorial supporting science, making the count at least 11.

They also remind us that

This is a reminder that the Nassau County school board will be meeting tomorrow (Thursday), and one item on the agenda is an anti-evolution resolution. If you are in the area, please attend.

The meeting is at 6:30 p.m. at the School Board District Office, 1201 Atlantic Avenue, Fernandina Beach, Florida 32034 (Map). (904) 491-9900. Here is contact information for the school board members.

Wired‘s blog has a post by Brandon Keim on the situation in Florida. Andrew Coulson offers some further thoughts.

Discovery Magazine reports on a continuation of experiments involving evolvable robots, communication and concepts such as altruistic cooperation and lying.

By the 50^th generation, the robots had learned to communicate—lighting up, in three out of four colonies, to alert the others when they’d found food or poison. The fourth colony sometimes evolved “cheater” robots instead, which would light up to tell the others that the poison was food, while they themselves rolled over to the food source and chowed down without emitting so much as a blink.

Some robots, though, were veritable heroes. They signaled danger and died to save other robots. “Sometimes,” Floreano says, “you see that in nature—an animal that emits a cry when it sees a predator; it gets eaten, and the others get away—but I never expected to see this in robots.”

Fascinating how simple processes of variation and selection can explain the evolution of altruism, cooperation as well as cheating. What has ID done recently that increases our understanding of how cooperation, cheating and altruism arose?

Nothing really

Remember the memorandum by Gibbs III ‘arguing’ that teaching evolution as a foundational principle for biology would violate the establishment clause?

As reported by our diligent friends at Florida Citizens for Science, FSU law Professor Steven G. Gey, a leading scholar on religious liberty issues calls this a hollow threat. Grey’s full comments can be found here.

In the mean time, enjoy the following excerpt

Does science disprove religion?

Again, the National Academy of Sciences is clear with a resounding no. Although, religion can be foolish enough to make claims which are at odds with scientific facts by rejecting scientific findings and methods, science can only address these minor concepts of religion while it remains unable to address the larger issue of ‘is there a God”.

Science can neither prove nor disprove religion. Scientific advances have called some religious beliefs into question, such as the ideas that the Earth was created very recently, that the Sun goes around the Earth, and that mental illness is due to possession by spirits or demons. But many religious beliefs involve entities or ideas that currently are not within the domain of science. Thus, it would be false to assume that all religious beliefs can be challenged by scientific findings.

As science continues to advance, it will produce more complete and more accurate explanations for natural phenomena, including a deeper understanding of biological evolution. Both science and religion are weakened by claims that something not yet explained scientifically must be attributed to a supernatural deity.

Theologians have pointed out that as scientific knowledge about phenomena that had been previously attributed to supernatural causes increases, a “god of the gaps” approach can undermine faith. Furthermore, it confuses the roles of science and religion by attributing explanations to one that belong in the domain of the other.

Many scientists have written eloquently about how their scientific studies have increased their awe and understanding of a creator (see the “Additional Readings” section). The study of science need not lessen or compromise faith.

Is Evolution a Theory or a Fact?

In a recent book titled “Science, Evolution, and Creationism”, the Committee on Revising Science and Creationism (A View from the National Academy of Sciences, National Academy of Sciences and Institute of Medicine of the National Academies), explains why evolution is both a fact and a theory. Although these distinctions have caused much confusion amongst creationists who insist that we teach alternative theories of evolution, the simple fact is that there exist no alternative theories. And while a skeptic attitude is important in science, skepticism is reduced when the facts end up supporting the theory time after time and when the theory can be used to make successful predictions.

David Gibbs III has released a second document which was sent to the Florida State Board of Eduction ‘suggesting’ that teaching evolutionary theory would have a negative impact on religious faith and thus would violate the establishment clause.

More on the document later since it presents some claims from Kenneth Miller’s book which I feel are taken out of context.

Although various school boards have somewhat recklessly passed resolutions asking the Florida State Board of Education to revise the proposed standards to include ‘alternative theories of evolution’, the final decision rests in the hands of the following people at the Florida State Board of Education. You may want to remind them of the simple fact that there are no competing theories, as admitted to by several leading Intelligent Design proponents or that Intelligent Design has no predictive powers. It is important that these people as well as the media come to realize that Intelligent Design is scientifically vacuous as it provides no competing explanations.

Check the Florida Citizens for Science Call to Action Pages for latest information

Remember that the ‘offending text’ in the draft standards describes evolution as follows

Standard 2. Evolution and Diversity
A. Evolution is the fundamental concept underlying all of biology and is supported by multiple forms of scientific evidence.
B. Organisms are classified based on their evolutionary history.
C. Natural selection is the primary mechanism leading to evolutionary change.

REP. Dan Gelber, D-Miami Beach, has written the following letter to the editor which was published in the Palm Beach Post: Intelligent design teachings not smart for public schools

Florida is in the midst of determining whether intelligent design and creationism should be taught alongside evolution in our public schools. It would be a great mistake to give intelligent design, or any other faux science, a home in Florida’s science classes.

The state Board of Education will soon vote to accept or reject new science standards for teachers that must be updated to comply with the federal No Child Left Behind Act, and the culture wars are heating up. When the Department of Education released its proposed standards in October, for the first time the word evolution was included as a standard to the agreement of many in the educational and scientific community.

The Board of Education is likely to vote on the new science standards in February. No matter what the outcome, legislators will have an opportunity to have their say when the legislative session convenes the following month. I fear the worst.

It’s one thing for ID creationists to misrepresent evolutionary theory (and they do, of course). It’s quite another to read misrepresentations, or at least incomprehensible representations, from what are allegedly science news sources. Case in point: Today, Science Daily has a story on some research on nematodes performed at the Technion-Israel Institute of Technology. The Science Daily story reproduces a press release from the American Technion Society, an organization that supports higher education in Israel.

Now, consider just the first two paragraphs of the press release:

According to Charles Darwin’s theory of evolution, individuals in a species pass successful traits onto their offspring through a process called “deterministic inheritance.” Over multiple generations, advantageous developmental trends - such as the lengthening of the giraffe’s neck - occur.

An opposing theory says evolution takes place through randomly inherited and not necessarily advantageous changes. Using the giraffe example, there would not be a common neck-lengthening trend; some would develop long necks, while others would develop short ones.

An opposing theory? What opposing theory? Can someone parse those paragraphs for me? Is that supposed to be making some sort of contrast between adaptive evolution and neutral drift? I can’t figure it out.

Today is the 100^th birthday of one of my greatest intellectual heroes, Jacob Bronowski, the mathematician, poet, philosopher, historian, and author of The Ascent of Man. I paid tribute to him a few years ago on the Thumb. I also wrote about him for Liberty magazine.

Here is a famous scene from The Ascent: the most moving in this whole marvelous show.

At 4:00 Eastern time today (Jan 18), Michael Behe will be on Christian radio KKMS in Minneapolis. It’ll be streamed live – I haven’t yet figured out whether it will be archived. It’s advertised as

Dr. Michael Behe, Professor of Biological Sciences at Lehigh University will explain why Darwinism just isn’t factual and why Creationism is a very plausible reality.

I’ll be interested to see just how (or whether) they integrate Behe’s self-professed acceptance of an old earth and common descent into their young earth worldview, and how they treat his view that malaria was intentionally designed.

RBH

(There ought to be a hat tip here, but I can’t remember where I read about it the other day – Pharyngula, maybe?)

One of our visitors (DC) left a description of what happened in Clay County. Keep those reports coming. On a somewhat more somber note, rumors have it that “some folks may have been receiving threats and personal attacks”.

Such attacks and threats are not only illegal but also very counter productive. I hope that those people reading PT can focus on the scientific vacuity of Intelligent Design, the fact that many ID proponents agree that ID does not provide an alternative theory and the fact that many of these people seem to be confused by the meaning of such terminologies as theory and fact. Educate not alienate…

DC Wrote:

The Clay County School Board just approved a modified form of the resolution by a vote of 5-0. 22 of the 27 speakers at the meeting opposed the resolution and they covered pretty much all the bases. Some were quite eloquent, including several retired pastors. The five supporters said nothing we hadn’t heard before although the word dogma and its variants showed up a lot when referring to Darwinism. Two (Including a teacher at my own school. Sigh.) emphasized teaching all the “facts” and letting students decide. I was surprised that the local churches didn’t try to pack the meeting room until someone pointed out that this didn’t start to get publicity until after last Sunday’s services.

The Colorado Daily reports that Michael Korn, the person who emailed death threats to biology faculty at Colorado University - Boulder was sent a restraining order in email on December 6^th, and agreed to its terms in minutes. They apparently used email because no one seems to know just where Michael Korn might reside.

The article relies in part upon material quoted here on Panda’s Thumb.

Brandon Haught at Florida Citizens for Science reports on the likely source of the anti-evolution resolutions.

A lengthy article in the Florida Baptist Witness doesn’t come right out and say it, but the source of the anti-evolution resolutions seems to be:

Speaking of brazen antics, PT commenter Glen Davidson over on the AtBC forum blew the whistle by posting the “Expelled Challenge” FAQ. Apparently, these folks are running scared that their project will be little more than one step up from “direct to video” projects, and are coordinating mass attendance of students and their parents from literalist-Christian schools. They are providing what amounts to a kickback to school administrators for movie ticket stubs from attendees who go to the “Expelled” movie during its first two weeks in the local theater.

(Continue reading at the Austringer.)

Darwin Day is fast approaching, and we’ll be celebrating with 2 and a half days’ worth of festivities here in Iowa next month, on February 14-16. We’re featuring talks by Dr. Massimo Pigliucci, Dr. Martha McClintock, and University of Iowa paleontologist Dr. Christopher Brochu, as well as a dinner social Friday night (tickets required, and they’re already going fast!). Head over to Aetiology for all the details.