More Recent Comments

Wednesday, December 05, 2007

Sandwalk Readers Are Left of Center

 
The results of last month's poll show that 70% of Sandwalk readers tend to be liberals or left wingers. I suppose that's not a big surprise. Most of us tend to read blogs that reflect our point of view on the world. This blog is not likely to appeal to those from the right wing of the political spectrum.




Nobel Laureate: Hugo Theorell

 

The Nobel Prize in Physiology or Medicine 1955.
"for his discoveries concerning the nature and mode of action of oxidation enzymes"


Axel Hugo Theodor Theorell (1903 - 1982) received the Nobel Prize in Physiology or Medicine for his work on biological oxidation-reduction reactions. These reactions are catalyzed by oxidoreductases and they often involve the oxidation and reduction of various cofactors. One of these cofactors, FMN, was Monday's Molecule #54. Near the beginning of his scientific career, Theorell worked with "yellow enzyme." The yellow color was due to the presence of riboflavin which turned out to be the cofactor FMN. It was possible to follow the oxidation and reduction of the cofactor by observing the change in color from yellow to white as it was reduced.

Later on he worked with alcohol deydrogenase, an enzyme that couples the oxidation of organic molecules to the reduction of NAD+. At the time this cofactor was known as DPN+. Theorell developed fluorescence spectroscopic methods to measure these very fast reactions.

Theorell also worked with cytochrome c, a heme-containing electron carrier involved in oxidation-reduction reactions that transfer electrons from complex III to complex IV during membrane-associated electron transport in mitochondria. Theorell was aware of the α-helix discovered by Pauling & Corey and his first X-ray images of cytochrome c confirmed that the heme group was completely surrounded by α-helices.

The Nobel Prize is awarded by the Karolinska Institute and Theorell was the first scientist from that institute to receive a Nobel Prize.

THEME:

Nobel Laureates
The presentation speech was given by Professor E. Hammarsten of the Royal Caroline Institute.
Your Majesties, Your Royal Highnesses, Ladies and Gentlemen.

The Collegium of Karolinska Institutet has this year awarded the Prize in Physiology or Medicine to Professor Hugo Theorell for his discoveries concerning the nature and mode of action of oxidative enzymes.

More than a hundred years ago the vast field of research within which Theorell's work has been carried out was opened up by a Swedish investigator, Berzelius, who advanced the concept of catalysis and postulated that vital reactions were brought about by means of catalysts, subsequently called enzymes.

Let us as an example consider sugar, dissolved in water. It is not acted upon by oxygen outside the organism, but in living cells it is rapidly broken down by means of oxygen and enzymes, with the simultaneous liberation of energy in a form suitable for use in further reactions.

During the latter part of the 19th century the catalysts postulated by Berzelius were detected - enzymes that quicken dull and sluggish molecules such as oxygen and sugar which will not spontaneously interact. The enzymes bring about this change in the behaviour of the sluggish molecules, called activation, by contacting them for a moment and then releasing them - now in an active form - into the whirls of the molecular dance where they originate new compounds. The enzyme will contact one molecule after another without itself being changed or directly participating in the dance. It is like a tool in a production line, activating the inert material delivered to it by the belt so that a maelstrom of rapid reaction is created beyond it. But such a maelstrom can never come to rest since other tools are soon encountered, each of which maintains the motion and adapts it to a new rhythm. Thus the substances to be metabolized are brought into a sequence of rapid transformations by a versatile machinery built up of strictly specific units, the enzymes.

It is of fundamental importance to know the nature and mode of action of everyone of these truly life-giving enzymes. Their number is still unknown but it is certainly very great - Berzelius' intuitive idea has been fully confirmed in this respect.

In this field a Swedish investigator has once again substantially enlarged our knowledge.

Hugo Theorell realized from the first the importance in scientific investigation of seizing and keeping the initiative. He has realized, too, that «live and let live» is a fertilizing principle for teamwork. The able must not for long remain mere collaborators. They must themselves show initiative and become independent activators. An enzyme can give life to sluggish material in such a way that a new independent enzyme is created. Theorell's scientific work deals with active enzymes, but he is himself an efficient activator on the more complex human level.

His first discovery was made during the period 1933-1935 which, as a Fellow of the Rockefeller Foundation, he spent with the foremost pioneer in enzyme research, Otto Warburg. He arrived with his own idea and with his own technical means of substantiating it. He now made his great classical discovery of the splitting and recombination of the yellow enzyme. «Meister der Enzymforschung», Warburg called him after this scientific achievement. Since then Theorell has illuminated and clarified our understanding of several of the enzymes necessary for life, and in a passionate search for truth and fact in science has spared neither thoroughness nor effort.

Following a logical plan of investigation and with continuous refinement of technique he has clarified and enlarged that field of knowledge in which he is an outstanding leader.

The iron atoms built into many oxidative enzymes constitute functional centres, and many aspects of their intricate linkages to other parts of the enzyme have been revealed, as well as other important routes for the transport of electrons involved in the functioning of oxidative enzymes. He and his collaborators have shed light on the iron-containing enzymes called peroxidases. Before Theorell began his investigations, our knowledge of these substances was little more than guesswork. The extremely high velocity of their reactions demanded the skilful application of a range of advanced technique. It can safely be predicted that the profound analyses thereby performed will be decisive for the future integration of the role of the peroxidase system into the pattern of action of living organisms. The function of another group of iron-containing enzymes, the cytochromes, began to emerge towards the end of the last century, and here again Theorell has achieved an incisive analysis. The nature and function of the muscle pigment were also established through his investigations. He showed it to be an oxygen reservoir which comes into action when the oxygen content of the blood is depleted. It is a source of a «second wind».

A most important part of Theorell's researches has been concerned with the velocities of enzyme reactions and the factors which influence them, factors which determine the directions into which the enzymes force the processes in living organisms. These experiments are not only of basic importance but may be considered model investigations in enzymology.

Professor Hugo Theorell. A fertile imagination. An undeviating and critical accuracy. An astonishing technical skill.

All scientists possess some of these attributes. Very few have all. You are one of these few. In accordance with your gifts you have chosen the most important of all tasks in biology. The purification and the characterization of enzymes are essential prerequisites for progress within the realm of biological research. You have managed to bring about a decisive advance in this fundamental field, and in so doing you have brilliantly taken up and tended the heritage from Berzelius.

On behalf of Karolinska Institutet I ask you to receive your Nobel Prize for Physiology or Medicine for 1955 from the hands of His Majesty the King.


[Photo Credit: Karolinska Institute]

Does Blogging Hurt Your Chances of Getting Tenure?

 
Here are two examples of academics who blog and who didn't get tenure [Too Much Information?]. Neither of them are certain that their blogs had any effect on the tenure committee but who knows for sure?

There are many blogging Assistant Professors who got tenure so it can't be all that bad. My own feeling is that blogging takes up a lot of time and those who are up for tenure might be able to make better use of that time.


[Hat Tip: Joshua Rosenau at Thoughts from Kansas (Science educator "Expelled!," Disco Inst remains silent)]

Sherri Shepard Is Doing It Again

 
Remember Sherri Shepherd of The View? She's the one who never thought about whether the Earth was flat [Sherri Shepherd of The View Doesn't Believe in Evolution].

Well, she's at it again. This time she claims that Christians pre-date the Romans and the Greeks. (You better watch this while you can because it will surely be removed as soon as ABC finds out about it.)




[Hat Tip: Mike's Weekly Skeptic Rant]

A Simplistic Explanation of Evo-Devo

 
This is a one minute explanation of evo-devo by Chris Mims, Editor of Scientific American. According to Mims, evo-devo is the idea that there are regulatory genes making proteins that control the expression of other genes. Many species have homologous regulatory proteins.

Whaaaaa? If that's all there is to evo-devo then what the hell is all the fuss about?

PZ Myers seems to think it's pretty cool [Evo-devo in 60 seconds]. Apparently PZ even helped with the script [What Is Evo-Devo?]. Maybe PZ can explain why evo-devo is so important if this is all there is.


Maybe you can't read it in 60 seconds but I think the description of evolutionary-developmental biology on the Wikipedia site is far better than this video.

Of course no definition will excuse some of the nonsense that's being spouted in the name of evo-devo [Evo-Devo: Innovation and Robustness in Evolution].


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.


Tuesday, December 04, 2007

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!




[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.


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.


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.


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?


[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.


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?


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

Monday, December 03, 2007

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!


[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.