The Lehigh University Disclaimer

 
Someone drew my attention to the note posted on the website of the Dept. of Biological Sciences at Lehigh University [Department Position on Evolution and "Intelligent Design']. This is the department where Michael Behe is a tenured Profesor. Here's the complete statement.

Department Position on Evolution and "Intelligent Design"

The faculty in the Department of Biological Sciences is committed to the highest standards of scientific integrity and academic function. This commitment carries with it unwavering support for academic freedom and the free exchange of ideas. It also demands the utmost respect for the scientific method, integrity in the conduct of research, and recognition that the validity of any scientific model comes only as a result of rational hypothesis testing, sound experimentation, and findings that can be replicated by others.

The department faculty, then, are unequivocal in their support of evolutionary theory, which has its roots in the seminal work of Charles Darwin and has been supported by findings accumulated over 140 years. The sole dissenter from this position, Prof. Michael Behe, is a well-known proponent of "intelligent design." While we respect Prof. Behe's right to express his views, they are his alone and are in no way endorsed by the department. It is our collective position that intelligent design has no basis in science, has not been tested experimentally, and should not be regarded as scientific.

This is an excellent summary of the proper way to treat Intelligent Design Creationism. There's no doubt the statement was carefully crafted and it shows. Intelligent Design Creationism isn't science. That's why it won't be taught in university except as an example of pseudoscience. We need to get the word out about this. Some people (e.g., Denyse O'Leary, Bill Dembski) still haven't got the message. We don't reject Intelligent Design Creationism because it's religious, we reject it because it ain't science.

The statement is highly relevant to the discussions we're been having about Intelligent Design Creationists. Imagine that you were trying to get a Ph.D. in this department while advocating that your thesis work refuted evolution and supported intelligent design. Since intelligent design isn't science your chances of graduating aren't great.

Imagine that you were up for tenure in this department while maintaining that intelligent design was a viable scientific option. Good luck.

On the other hand, if you already have tenure then you have jumped these hurdles and your right to say silly things is protected by academic freedom. That right must be upheld at all costs.

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Pat Condell Takes on the Atheist Accommodationists

 
Here's some of what Pat Condell says at 4:20 into the video ...

Maybe you think the way to deal with this is to engage it in polite debate, to make all your little points and counter-points and show us all what a clever dick you are. And that'll be great fun for you.

And the good news is you don't even have to worry about someone like me damaging your cause because you haven't got a a cause. What you've got is a hobby.

If God exists, and I had any reason to ask him for anything, I think I'd probably ask him to save me from the curse of polite and deferential atheists.

And that's not even the best quotation. You should hear what comes after that!

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[Hat Tip: Dr. Joan Bushwell's Chimpanzee Refuge]

Should an Intelligent Design Creationist Be Denied Tenure?

 
The quick answer is, yes.

Guillermo Gonzalez was recently denied tenure in Iowa State's Dept. of Astronomy. It seems clear that part of the decision was based on Gonzalez's promotion of demonstably bad science; namely, Intelligent Design Creationism.

Mike Dunford spells it out on The Questionable Authority [The Discovery Institute and the Gonzalez Tenure Issue: Why Should Intelligent Design be Privileged?].

It is clear from the fragments of email that the Discovery Institute released that Gonzalez's colleagues believed - correctly - that Intelligent Design is not science, and that if Gonzalez believes otherwise it casts doubts on his understanding of science. They were not arguing that his belief in ID should be used against him just because he believes In ID. They were arguing that Gonzalez's belief in Intelligent Design is evidence that he has an incorrect understanding of science.

If a tenure candidate at an astronomy department were to argue that the moon is made of green cheese, it would not be unreasonable for the tenure committee to question the candidate's scientific credentials - and that candidate would be making a scientific argument that could be examined experimentally. Gonzalez doesn't even have that much going for him.

This is an important point. As Mike points out, the Discovery Institute is fond of promoting its work as "science" and it's proud to claim Guillermo Gonzalez as a bona fide scientist.

The Discovery Institute can't have it both ways. If it's science, then Gonzalez should be judged on the quality of his science, in which case he will be found wanting and denied tenure. If it's religion, then Gonzalez should not be making claims that his work is scientific and he should not put his creationist work on his CV.

In an effort to win an appeal, Gonzalez and his backers obtained email messages fro Professors in the Astronomy Department via the freedom of information act. Here's one email comment by Eli Rosenberg, the Chair of the Astronomy Department [see More on Gonzalez tenure denial].

... on numerous occasions, Dr. Gonzalez has stated that Intelligent Design is a scientific theory and someday would be taught in science classrooms. This is confirmed by his numerous postings on the Discovery Institute Web site. The problem here is that Intelligent Design is not a scientific theory. Its premise is beyond the realm of science. … But it is incumbent on a science educator to clearly understand and be able to articulate what science is and what it is not. The fact that Dr. Gonzalez does not understand what constitutes both science and a scientific theory disqualifies him from serving as a scienceeducator.

I see nothing wrong here. I looks to me like this is grounds for tenure denial.

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Gene Genie #21

 

The 21st edition of Gene Genie has just been published on Bayblab [Welcome to Gene Genie].

The next edition (#22) will appear here on Sandwalk on December 16th. Submit your entries at Blog Carnival by clicking on the link to Submit an Article. All you have to do is fill out a short form with the URL to your posting.

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TR Gregory on Junk DNA

 
Ryan Gregory has posted another interesting discussion about junk DNA [Genome size, code bloat, and proof-by-analogy.]. You should read the entire article but I want to comment briefly on two important points.

Computer simulations rarely tell us anything about real biology in spite of the fact that computer scientists think otherwise. The main problems with most simulations is that they assume a pre-defined goal and they usually don't model random genetic drift and other non-adaptation events.

The second point is ...

Finally, it is essential to note that "non-coding elements make future evolution possible" explanations, though invoked by an alarming number of genome biologists, contradict basic evolutionary principles.

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Is Crustacea a Class or a Phylum (or something else)?

 
I was reading about Copepods on Christopher Taylor's blog Catalogue of Organisms [Taxon of the Week: Some Copepods for your Reading Pleasure].

It got me thinking about whether Crustaceans should be elevated to phylum status as proposed by Lynn Margulis and Karlene Schwartz in Five Kingdoms 3rd ed.. A quick search of the web revealed that scientists seem to be split on the issue. Several competing classifications are listed on Answers.com. The NCBI site lists Crustacea as a subclass of Phylum Arthrododa but the taxonomy on that site is notorious for being very conservative.

Are there any taxonomists out there? Is there a consensus?

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[Photo Credit: South Australian Research and Development Institute (Sardi)]

Software Developer Discusses Junk DNA

 
Randy Stimpson is a software developer who believes in Intelligent Design Creationism. He sometimes post comments on Sandwalk and Doppelganger read some of those comments. He (Doppelganger) decided to visit Randy's blog Intelligent Designer to see whether the postings on the blog were any better than the ones in the Comments section on Sandwalk.

Guess what? They aren't.

Randy Stimpson makes some incredibly stupid remarks about junk DNA and Doppelganger is more than happy to point out the many errors [Another creationist computer software-type pontificates on things he has no business pontificating on...].

Another data point for the Salem Conjecture.

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Dr. Roy Thinks about Ethical Stem Cells

 
Dr. Roy Eappen is a conservative, Christian, endocrinologist living in Montreal (Quebec, Canada). He writes a blog called Dr. Roy's Thoughts. The blog is richly decorated with all of the stereotypical symbols of the Blogging Tory that Canadian Cynic is so fond of (see example on left).

One of the thoughts Dr. Roy had recently concerns "Ethical" stem cells. This is a reference to recent work developing stem cell lines from somatic cells [see OK. Everyone take a deep breath ....].

Here's what Dr. Roy says,

This is an interesting article about Dr James A. Thomson. I have spoken to scientists on these matters before and all of them have been uneasy about using embryos for stem cells. They have said that they wanted to help the sick. While healing the sick is an admirable goal, one has to think of the moral cost as well.

Dr. Roy must hang out with a different class of scientists than the ones I see. Most of the scientists I know have few qualms about creating human stem cell lines from discarded human embryos.

This doesn't mean that there are no scientists in Canada who don't share Dr. Roy's opinions about abortion. It just means that Dr. Roy is very likely not telling the truth when he says that "all of them" are uneasy. Why is it that truthiness and Christianity don't often go together?

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[Hat Tip: Canadian Cynic ( Stem cells and reality. Because we're NOT morons.)]

Seymour Benzer (1921 - 2007)

Seymour Benzer died last Friday. In the 1950's and 1960's Benzer was a prominent member of the 'phage group founded by Max Delbrück and Salvador Luria [The Nobel Prize in Physiology or Medicine 1969.].

Benzer was best known for his detailed mapping of the rII locus in bacteriophage. Benzer was able to resolve mutants that were likely to be only a single nucleotide apart. His work on mapping deletions led directly to the conclusion that the genetic codon should consist of three nucleotides. In honor of Seymour Benzer, John Dennehy has selected his 1955 paper as this week's citation classic [Benzer, S. (1955)].

You can read about Benzer's famous experiments in the article he wrote for Phage and the Origins of Molecular Biology: Adventures in the rII region.

Later on in his career, Benzer worked with Drosophila melanogaster studying behavioral mutations, including some that affect the circadian rhythm. Since this is Coturnix's field, he has posted his own tribute to Benzer [In Memoriam: Seymour Benzer].

Other notable tributes:

Carl Zimmer [Farewell, Seymour Benzer].

PZ Myers [We've lost a great one: Seymour Benzer].

It's sad to note that most younger scientists, and almost all undergraduates, have never heard of Seymour Benzer. Mostly this is sad because it makes me realize how old I am!

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[Photo Credit: The photo shows Francis Crick (left) speaking to Seymour Benzer in 1964 (The Francis Crick Papers)]

Monday's Molecule #54

 
Name this molecule. Make sure you get the correct scientific name and the correct form of the molecule.

There's an indirect connection between this molecule and Wednesday's Nobel Laureate(s). Your task is to figure out the significance of today's molecule and identify the Nobel Laureate(s) who worked out the function of the molecule.

The reward goes to the person who correctly identifies the molecule and the Nobel Laureate(s). Previous winners are ineligible for one month from the time they first collected the prize. There are two ineligible candidates for this week's reward. The prize is a free lunch at the Faculty Club.

Send your guess to Sandwalk (sandwalk(at)bioinfo.med.utoronto.ca) and I'll pick the first email message that correctly identifies the molecule and the Nobel Laureate(s). Correct responses will be posted tomorrow along with the time that the message was received on my server. I may select multiple winners if several people get it right.

Comments will be blocked for 24 hours. Comments are now open.

UPDATE: No winner this week. Several people got the correct molecule—it's the semiquinone form of flavin mononucleotide (FMN). One person guessed the Nobel Laureate but did not get the molecule correct.

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How Does an Intelligent Design Creationist Write a Ph.D. Thesis?

 
Some of you will remember Marcus Ross. He is a Young Earth Creationist who obtained a Ph.D. in paleontology from the University of Rhode Island [Lying for Jesus]. Ross now has a faculty position at Liberty University where he teaches courses in religion and science. PZ Myers has posted an update on his career [So what's Marcus Ross up to nowadays?].

How could Ross write an acceptable Ph.D. thesis if he believes that the Earth is less than 10,000 years old? We know the answer to this question. Ross did not discuss his true beliefs in his thesis or during his Ph.D. oral exam. Instead, he wrote a thesis on the fossil record as though he accepted the scientific age of the Earth. In other words, Ross said one thing in public lectures and another in the exam room.

I was reminded of this episode while listening to Kirk Durston last week in Denyse O'Leary's course. Kirk is a Ph.D. candidate in biophysics at the University of Guelph [Kirk Durston's Proof of God]. At some point he will write scientific papers and a thesis and he will be examined on his understanding of science. I wonder what he will do?

In his talk, Kirk tried very hard to give the impression that his scientific findings point to the existence of an intelligent designer. There was a brief mention of the distinction between science and philosophy but it wasn't at all clear whether he was stepping over the line or not. He concludes that God the intelligent designer exists.

One thing was clear, however. Kirk claimed that his work demonstrated the impossibility of evolving protein folds. He presented some calculations showing the total number of mutations that could have occurred since life began (10⁴¹, if I remember correctly). Then he showed that it would take far more than 10⁴¹ mutations to evolve the known protein folds.

In his lecture he clearly states that the results refute "Darwinism." He repeated over and over again that his thesis work was scientific evidence against evolution and in favor of intelligent design creationism.

It seems to me that Kirk Durston has only two choices at this point. Either he's sincere about his "scientific" claims, in which case they go into his thesis, or, alternatively, he's willing to disguise his true "scientific" conclusion by writing a thesis that's more likely to be accepted by the scientists on his committee.

To my way of thinking, scientific integrity should not be compromised in order to get a degree by trickery. But this presents a serious problem for Intelligent Design Creationists. In their public lectures, and in articles for the popular press, they make a big deal about the "scientific" nature of their findings. If that's what they truly believe then they should have no qualms about defending it in a scientific context. In other words, it goes in the thesis and let the chips fall where they may.

But here's the rub. Intelligent Design Creationists know full well that their version of science will not pass scrutiny by other scientists. Kirk Durston will not get his Ph.D. if he's being honest about his belief in his findings. It is simply not true that protein folding is scientific proof of intelligent design and a refutation of evolution.

So, Kirk like other creationists before him, will write the thesis that his committee will pass and not the one that he would be writing if he were honest.

The next hurdle will be the Ph.D. oral exam. Members of his committee know that he has been making very vocal claims about the significance of his Ph.D. research. They know that he has been making claims that the work refutes evolution even if that's not what's in the thesis. Should they question him about the difference between what he says in the thesis and what he says on the lecture circuit? Do they have a right to fail him if they think that what's in his thesis does not reflect his true opinion about the science—and that his true opinion is scientifically invalid?

I think the committee has this right and I think that a Ph.D. candidate should be prepared to defend any "scientific" claims they make outside of the lab.

There will be a few other problems with Kirk's thesis but they are easily fixed. For example, he claimed that ancient bacteria were complex and subsequent evolution has just been degradation of the genome. In the lecture he showed us several references. We now know that he is misinterpreting these scientific papers.

I assume this will go in the thesis because Kirk seemed to be really sincere when he talked about this as scientific fact. Member of his committee will read the thesis, correct his misconceptions, and point him to other scientific papers that reveal the true nature of bacterial evolution. This will give him an opportunity to learn about good science. At the end of the process Kirk will not be making scientifically inaccurate statements in public because he will know better.

There are quite a few examples of these factual errors but I assume they will all be fixed before the oral exam.

The bottom line is can Kirk Durston get a Ph.D.? If so, how should he do it? What do you think?

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[Photo Credit: Theses from Jackson State University]

What Is Evolution?

 
Greg Laden has just posted this video on his blog [Evolution ... Its for real]. I assume Greg endorses the definition of evolution in the opening minutes.

On Tuesday and Wednesday evenings I gave lectures on Evolution Is a Theory and a Fact. The first part of the lecture was devoted to explaining What Is Evolution. Here's the minimal scientific definition of evolution.

Evolution is a process that results in heritable changes in a population spread over many generations.

I explained to the audience that the definition of evolution has to be neutral with respect to mechanism. Evolution could occur by Lamarckian or Darwinian mechanisms, or something else entirely different.

The purpose of a definition is to define what we mean by the word. If we were to define evolution as that form of change caused by meiotic drive then change by natural selection wouldn't be evolution. How silly is that?

It's just as wrong to define evolution in terms of natural selection. That means random genetic drift is not evolution, by definition. Is that right?

The opening screen of the video states "The world is full of misinformation." The second screen says, "Many of those who claim evolution is wrong have no understanding what evolution really is."

This is exactly how I begin my talk. However, from that point on my lecture diverges considerably from the video that cdk007 created. Do you agree with the definition in the video? (Natural selection + time = EVOLUTION)

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Take a Short Quiz on Cheating - Do You Agree with the First Year Engineering Students?

 
What freshman engineering students think about cheating.

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More Misconceptions About Junk DNA

 
iayork of Mystery Rays from Outer Space is upset about an article on retroviruses that appeared in The New Yorker [ “Darwin’s Surprise” in the New Yorker]. Here's what iayork says,

The whole “junk DNA” has been thrashed out a dozen times (see Genomicron for a good start). The bottom line? If you search Pubmed for the phrase “junk DNA” you will find a total of 80 articles (compare to, say, 985 articles for “endogenous retrovirus”); and a large fraction of those 80 articles only use the phrase to explain what a poor term it is. Scientists don’t use the term “junk DNA’. Lazy journalists use it so they can sneer at scientists (who don’t use it) for using it.

Wrong! Lots of scientists use the term "junk DNA." Properly, understood, it's a very useful term and has been for several decades [Noncoding DNA and Junk DNA].

Yes, it's true that journalists often don't understand junk DNA and they are easily tricked into thinking that junk DNA is a discredited concept. The journalists are wrong, not the scientists who use the term.

It's also true that there are many scientists who feel uneasy about junk DNA because it doesn't fit with their adaptationist leanings. Just because there's controversy doesn't mean that the term isn't still used by it's proponents (I am one).

I'm sorry, iayork, but statements like that don't help in educating people about science. Junk DNA is that fraction of a genome that has no known function and based on everything we know about biology is unlikely to have some unknown function. Junk DNA happens to represent more than 90% of our genome and that's significant by my standards.

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Agassiz in the Concrete and Persecution of Religious Scientists

John Pieret has a posting on possible examples of persecution of religious scientists in the nineteenth century [On the Ways of Change].

John quotes from a book by Neal C. Gillespie on Charles Darwin and the Problem of Creation. Gillespie is discussing the conflict between religion and science among academics in the mid-1800's. According to John, Gillespie says,

Antagonism against biblicism had reached such a point by the late 1850s that Agassiz suggested that fear of the wrath of the positivists was actually leading some naturalists with strong theological convictions to conform to the new science against their true judgment.

The quote refers to Louis Agassiz, a biology Professor at Harvard^1. and one of the last holdouts against evolution. John links to the upcoming Expelled movie and asks whether Agassiz is referring to persecution of religious scientists.

John posted a photograph of the statue of Louis Agassiz embedded upside down in the courtyard in front of the zoology building at Stanford University. The statue tumbled from its place above the entrance during the San Francisco earthquake of 1906.

According to legend, a passing scientist remarked that,

Louis Agassiz was better in the abstract than in the concrete.^2.

This is a clear reference to the fact that Agassiz's reputation had been severely damaged by his religious convictions and his rejection of biological evolution.

Is it true that atheist scientists discriminate against religious scientists? John has been concerned about this issue for a number of years. He thinks that atheist scientists fail to distinguish between real science and metaphysics. He thinks that much of our criticism of religious scientists is not because we're scientists but because we're atheists.

I'm posting a specific case for consideration in another message so it was quite appropriate, and fortuitous, that John Pieret brought it up today on Thoughts in a Haystack.

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1. Stephen Jay Gould held the Alexander Agassiz Professor of Zoology Chair at Harvard from 1982 until his death in 2002. Alexander Agassiz was Louis Agassiz's son. Alexander served as President of the National Academy of Sciences.

2. The story is apocryphal (a polite word for "false"). The quotation has been attributed to several men, including the President of Stanford, but all have denied it. Nevertheless, it's too good a story to abandon just because it happens to be untrue!

[Photo Credit: Wikipedia]