Tangled Bank #72

 
Tangled Bank #72 has been posted at Ouroboros.

Buy a Conservative T-shirt

 
Here are three of my favorites. See the rest at ThoseShirts.com. Please tell me this is sarcasm.

Should Christians Be Armed?

 
While checking out Pat Boone's IDiotic statements about evolution [Charles Darwin's Funny Joke] I noticed this icon in the sidebar. Naturally I couldn't resist clicking on it.

I ended up at a site advertising the book Shooting Back. Here's what I read,

What would you do if armed terrorists broke into your church and starting attacking your friends with automatic weapons in the middle of a worship service?

Would you be prepared to defend yourself and other innocents?

Would you be justified in doing so?

Is it time for Americans to consider such once-unthinkable possibilities?

There is one man in the world who can address these questions with first-hand experience.

His name is Charl van Wyck – a South African who was faced with just such a shocking scenario.

In "Shooting Back: The Right and Duty of Self-Defense," van Wyk makes a biblical, Christian case for individuals arming themselves with guns, and does so more persuasively than perhaps any other author because he found himself in a church attacked by terrorists.

Wow! That's all we need. IDiots with guns. In church.

Don't you just love America?

Recognize This Guy?

 
Of course you do. That's PZ Myers of Pharyngula in a photo taken by a very talented photographer in someone's back yard in Oxford, UK.

PZ just got a nice write-up in the University of Minnesota at Morris News [PZ visits friend].

I get a mention too but no pictures of me.

Nobel Laureates: Deisenhofer, Huber, and Michel

 
The Nobel Prize in Chemistry 1988.

"for the determination of the three-dimensional structure of a photosynthetic reaction centre"

Johann Deisenhofer, Robert Huber, and Hartmut Michel received the Nobel Prize in 1988 for working out the structure of the first photosystem—the photosynthetic reaction centre from the purple bacterium Rhodopseudomonas viridis. We now know that this is a Photosystem II-type complex with a type II reaction center. Its chlorophyll molecules absorb a photon of light and catalyze the transfer of electrons from an electron donor (usually cytochrome c) to quinone.

The photosystem structure was one of the most complex structures ever solved by X-ray crystallography. Even today there are only a handful of solved structures that are as complicated as this one.

The complex is normally embedded in a lipid bilayer that surrounds the vertical α-helices shown in the figure. The large gray space-filling molecules in the middle are the chlorophyll molecules that absorb light. Excited electrons are released from the chlorophylls and transferred down toward the bottom of the molecule to reduce a bound quinone near the iron atom (brown dot).

The cytoplasm on the inside of the cell is at the bottom of this picture and the intermembrane space between the inner and outer bacterial membranes is at the top.

The reaction center chlorophylls need to be resupplied with electrons and these come from a type c-like cytochrome (purple) that's attached to the top of the photosystem. This particular cytochrome is unusual since it has multiple heme groups. In most other species the electron donor is cytochrome c.

As noted in the presentation speech, by solving the structure of a bacterial photosystem Deisenhofer, Huber, and Michel not only contributed to our understanding of photosynthesis but also to our understanding of all membrane proteins and of electron transfer reactions in general.

The structural determination awarded has led to a giant leap in our understanding of fundamental reactions in photosynthesis, the most important chemical reaction in the biosphere of our earth. But it has also consequences far outside the field of photosynthesis research. Not only photosynthesis and respiration are associated with membrane-bound proteins but also many other central biological functions, e. g. the transport of nutrients into cells, hormone action or nerve impulses. Proteins participating in these processes must span biological membranes, and the structure of the reaction center has delineated the structural principles for such proteins. Michel's methodological contribution has, in addition, the consequence that there is now hope that we can determine detailed structures also for many other membrane proteins. Not least important is the fact that the reaction center structure has given theoretical chemists an indispensable tool in their efforts to understand how biologic electron transfer over very large distances on a molecular scale can occur as rapidly as in one billionth (American English, trillionth) of a second. In a longer perspective it is possible that such research can lead to important energy technology in the form of artificial photosynthesis.

Poor IDiots, Wrong Again

 
GilDodgen over at Uncommon Descent has put his foot in it once again. This time the IDiots have jumped all over the book Chance & Necessity by Jacques Monod. The book was written 36 years ago but that doesn't seem to faze the IDiots. Anything that conflicts with their worldview is a target. See [Classic Darwinian Texts — (soon to be, if not already) On the Ash Heap of History].

Here's what GilDodgen has to say,

Read Monod’s book — a foundational Darwinian text. Nowhere in it does he ever address probabilistic resources; he just assumes on faith that random mutation and natural selection can produce everything.

Now I've seen some pretty stupid things over at the Dembski headquarters but calling Monod's book "a foundational Darwinian text" just about takes the cake. This is not classic Darwinism. Classic Darwinism tries to deny the role of chance as much as possible. What Monod does is emphasize the importance of chance and contingency.

The entire book is devoted to addressing the probability of evolution—something that seems to have escaped the notice of IDiots like GilDodgen. Here's a short excerpt from pages 43-44 where Monod explains his view of probability and the inability of natural selection to make predictions.

The thesis I shall present in this book is that the biosphere does not contain a predictable class of objects or of events but constitutes a particular occurrence, compatible indeed with first principles, but not deducible from those principles and therefore essentially unpredictable.

Let there be no misunderstanding here. In saying that as a class living beings are not predictable on the basis of first principles, I by no means intend to suggest that they are not explicable through these principles—that they transcend them in some way, and that other principles, applicable to living systems alone, must be invoked. .... All religions, nearly all philosophies, and even a part of science testify to the unwearying, heroic effort of mankind desperately denying its own contingency.

That ain't Darwinian, baby. Can you imagine Richard Dawkins ever saying that we are here by chance? And it sure as heck ain't intelligent design either—that's the part that annoys the IDiots.
The classic quote from Monod's book can be found on page 112. He discusses the various kinds of mutations that had been discovered by 1971. Then he concludes,

We call these events accidental; we say that they are random occurrences. And since they constitute the only possible source of modifications in the genetic text, itself the sole repository of the organism's hereditary structure, it necessarily follows that chance alone is at the source of every innovation, of all creation in the biosphere. Pure chance, absolutely free but blind, at the very root of the stupendous edifice of evolution: this central concept of modern biology is no longer one among other possible or even conceivable hypotheses. It is today the sole conceivable hypothesis, the only one that squares with observed and tested fact. And nothing warrants the supposition—or the hope—that on this score our position is ever likely to be revised.

You know what surprise me the most about the IDiots? It's not that they are ignorant about evolution, after all there are many scientists who cling to the old-fashioned Darwinian worldview as well. No, the thing that surprises me is that the IDiots are completely incapable of recognizing the different points of view within evolutionary biology. Here we have an example of an IDiot who has read Chance & Necessity but still calls it "a foundational Darwinian text." The mind boggles at such stupidity.

Memo to IDiots: there's more to evolution than Darwinism.

Of course GilDodgen can't resist taking a few other potshots at Monod. After all, Monod is French, an atheist, and (gasp!) a socialist to boot. Those evil socialist evolutionists, where do they get off caring for the downtrodden and the oppressed?

Footnote: GilDodgen begins his rant with,

I just pulled out my 1972 edition of Jacques Monod’s “classic” work, Chance and Necessity, subtitled A Philosophy for a Universe without Causality.

He can't even get the subtitle right. What he's quoting is a blurb on the cover that says "A philosophy for a universe without causality—by the Nobel Prize-winning French biologist." The actual subtitle is "An Essay on the Natural Philosophy of Modern Biology."

What Is a Valid Argument?

 
As part of the basic concept series, Janet Stemwedel explains arguments [Basic concepts: arguments]. For example, she says,

Here's an example of a valid argument:
1. Britney Spears is from Mars. (premise)
2. Martians have astounding vocal range and are great dancers. (premise)
3. Hence, Britney Spears has astounding vocal range and is a great dancer. (conclusion)

Are you convinced that this is a valid argument?

DNA Packaging and DNA Replication

 
The first part of this video shows how long strands of DNA are packaged in eukaryotic cells. It's pretty good. The second part is a demonstrating of how the replisome works. The replisome is a little molecular machine that copies DNA. The animation doesn't do a very good job of conveying the idea that the various components of the replisome interact with each other to form a compact blob at the replication fork.

The concept of a "molecular machine" was promoted by Bruce Alberts who worked on DNA replication. It gets the IDiots all in a tizzy whenever we talk about molecular machines. They think we're advocating intelligent design!



[Hat Tip: Living the Scientific Life]

A Typical Graduate Course in Biochemistry

 
Vince LiCata was kind enough to publish a generic course syllabus that applies to most graduate courses—and many senior undergraduate courses. Read it at MY NEW GRADUATE COURSE OFFERING.

[Hat Tip: The World's Fair]

Student Evaluations Don't Mean Much

Inside Higher Ed has just commented on a new study of student evaluations [New Questions on Student Evaluations]. The results are not surprising. They confirm all previous studies showing that student evaluations aren't what everyone thinks they are.

Previous studies suggested that students are rating generosity and personality and not quality of teaching. For example, a study of ratings on RateMyProfessor [‘Hotness’ and Quality] showed that,

... the hotter and easier professors are, the more likely they’ll get rated as a good teacher. As far as students — or whoever is rating professors on the open Rate My Professor site — are concerned, nothing predicts a quality instructor like hotness.

The new study from Ohio State University finds "... a strong correlation between grades in a course and reviews of professors, such that it is clear that students are rewarding those who reward them." Duh!

Now a cynic might say that this simply means that good teachers are doing such a good job that their students get higher grades. Thus, the evaluations truly represent the quality of the teacher and not how easy they mark. Well, that's not what the study suggests,

The Ohio State study, however, provides evidence for the more cynical/realistic interpretation — namely that professors who are easy (and aren’t necessarily the best teachers) earn good ratings. The way the Ohio State team did this was to look at grades in subsequent classes that would have relied on the learning in the class in which the students’ evaluations were studied. Their finding: no correlation between professor evaluations and the learning that is actually taking place.

The authors of the report show that student evaluations are practically worthless but in the interest of appeasing students they close with a mealy-mouthed sop as reported on the Inside Higher Ed site,

The authors stress that there are many ways — such as adjusting for student bias for easy graders or bias against certain groups of instructors — to continue to use student evaluations as one tool for measuring professors’ performance. But they write that, used alone and unadjusted, they appear highly questionable.

Let's see if I understand this logic .... student evaluations are biased and useless but instead of abolishing them we continue to use them to measure Professor's performance as long as we use other criteria as well.

Why? Why not get rid of student evaluations? We've known for decades that they don't work. Let's try and find another way for students and Professors to work together to improve university education. Student evaluations are ignored by all responsible Professors and they give students the false impression that their opinion is valued.

There has to be a better way. I believe that university students can provide useful and constructive criticism but only if they give up on the popularity contest and stop pretending that it has anything to do with quality of learning.

(As I write this, I'm supposed to be making up exam questions. I think I'll make some of them a bit easier .... )

[Hat Tip: Uncertain Principles]

Engineers Learn Workplace Skills

 
From the University of Toronto website comes this press release about how engineers learn workplace skills that will help them in their careers. The first two paragraphs are,

Gathered in the main dining room of the Faculty Club on the evening of Jan. 17, more than 100 engineering students sat down for an important professional lesson: dining etiquette. Led by Faculty Club manager Leanne Pepper, students were taken through the dos and don’ts of a five-course meal.

Organized by the Leaders of Tomorrow (LoT) program in chemical engineering and applied chemistry, the dining etiquette session was one of a series of talks and workshops that aim to develop the broader skills needed for engineers in the workplace.

Leanne is a friend of mine so I'll resist commenting.

Guernica

 
Remember Guernica? Thanks to the team of senior public health scientists and practitioners at Effect Measure for finding this video.

Is Nutritional Science Really a Science?

 
I have my doubts, and so does Jonah Lehrer [Why is Nutritional Science So Bad?].

John Kasich Interviews Atheist Brian Flemming about the Blasphemy Challenge

 
We don't get FOX News up here so I've never seen this John Kasich dude in action. Watch him interview Brian Flemming, the originator of the Blasphemy Challenge, at [onegood move]. With people like John Kasich around we have a long way to go before the majority gives up their supersitutions and becomes rational.

Kasich just doesn't get it. One is left with the distinct impression that Kasich has never, ever, questioned his religious beliefs. In other words, he has been so thoroughly brainwashed that alternative viewpoints just don't exist for him. Disgusting.

[Hat Tip: RichardDawkins.NET]

Monday's Molecular #11

 
Name this molecule. You must be specific. We need the correct common name.

This is another easy one for everyone who has ever taken biochemistry. This compound is one of the most important energy molecules in living cells. We will discuss the very important reactions that result in synthesis of this molecule after you've been given a chance to identify it.

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

What Is a Gene?

(Other definitions are at Discovering Biology in a Digital World, Pharyngula, and Greg Laden.)

The concept of a gene is a fundamental part of the fields of genetics, molecular biology, evolution and all the rest of biology. Gene concepts can be divided into two main categories: abstract and physical. Abstract genes are the kind we refer to when we talk about genes “for” a certain trait, including many genetic diseases. Most geneticists and many evolutionary biologists use an abstract gene concept.

Philosophers have coined the term “Gene-P” for the abstract gene concept. The “P” stands for “phenotype” indicating that this gene concept defines a gene by it’s phenotypic effects and not its physical structure.

Physical genes consist of stretches of DNA with a beginning and an end. These are molecular genes that can be cloned and sequenced. Philosophers call them “Gene-D” where “D” stands for “development”—a very unfortunate choice.

This essay describes various modern definitions of physical genes (Gene-D). I like to define a gene as “a DNA sequence that’s transcribed” but that’s a bit too brief for a formal definition. We need to include something that restricts the definition of gene to those entities that are biologically significant. Hence,

A gene is a DNA sequence that is transcribed to produce a functional product.

This eliminates those parts of the chromosome that are transcribed by accident or error. These regions are significant in large genomes; in fact, the confusion between accidental transcripts and real transcripts is responsible for the overestimates of gene number in many genome projects. (In technical parlance, most ESTs are artifacts and the sequences they come from are not genes.)

We could refine the definition by including RNA genes but that’s such a insignificant percentage of all genes that the refinement is hardly worth it. As we shall see, there are more significant limitations to the definition.

This "DNA sequence that's transcribed" definition describes a physical entity. Let’s examine a simple molecular gene to see how the definition applies.

This is a simple bacterial protein-encoding gene. The horizontal line represents a stretch of double-stranded DNA with the rectangular part being the gene. The gene is copied into RNA as shown by the arrow below the gene. This process is called transcription. Transcription begins when the transcription enzyme (RNA polymerase) binds to a promoter region (P) and starts copying the DNA beginning at the initiation site (i). The DNA is copied until a termination site (t) is reached at the end of the gene. According to my preferred definition of a gene, it starts at “i” and ends at “t.”

The part of the gene that’s transcribed includes the coding region, shown in black. This is the part of the gene that contains sequential codons specifying the amino acid sequence of the protein. At the beginning of the gene, called the 5ʹ (5-prime) end, there’s a short stretch of sequence that will be transcribed but not translated into protein. This 5ʹ untranslated region (5ʹ UTR) will contain various signals for starting protein synthesis.

The other end of the gene is called the 3ʹ (3-prime) end and there’s almost always a stretch that’s transcribed but not translated (3ʹ UTR). The 3ʹ UTR contains signals that cause transcription termination and also signals that regulate translation.

There are regions upstream of the promoter that control whether or not the gene is transcribed. These regions are called regulatory regions. They may contain binding sites for various proteins that will attach there in order to enhance the binding of RNA polymerase to the promoter. One of the differences between my preferred definition of a gene and others is that some other definitions include the promoter and the regulatory region.

There are two problems with such definitions. First, they’re not consistent with standard usage when we talk about the regulation of gene expression. We don’t say that only “part” of a gene is transcribed, which would be correct if we included the regulatory region in our definition of a gene. How often have we heard anyone say that regulatory sequences control the expression of part of the gene? That doesn’t make sense.

Second, by including regulatory sequences in the definition of a gene the actual extent of the gene becomes ill-defined. For most genes, we don’t know where all the regulatory sequences are located so we don’t know for sure where the gene begins or ends. Furthermore, there are some regulatory sequences, especially in eukaryotes, that are not contiguous with the gene and this leads to “genes” that are split into various pieces. It’s much easier to use a definition like “a DNA sequence that’s transcribed” because it defines a start and an end.

The organization of a typical eukaryote gene is shown below.

The main difference between this type of gene and a typical bacterial gene is the presence of introns and exons. These genes are transcribed from an initiation site to a termination site just like bacterial genes. When the RNA transcript is finished it undergoes an additional step called RNA processing. In that step, parts of the original transcript are spliced out and discarded. These parts correspond to the introns in the gene—shown as thinner rectangular region within the genes.

Note that the coding region (black) can be interrupted by these introns so the final messenger RNA (mRNA) cannot be translated until RNA processing is completed. The important point for our purposes is that the introns are part of the gene since they are transcribed.

My preferred definition has been used by molecular biologists for many decades but there are several other definitions that have been popular over the years. All of them have good points and bad points. I’ve already dealt with the definition that includes regulatory regions.

Some people still prefer a gene definition that corresponds to one used over half a century ago; namely, a gene is a sequence that encodes a polypeptide. This is the so-called one gene:one protein definition. It’s very old-fashioned. We’ve known for years that there are genes that do not encode proteins in spite of the fact that we commonly show protein-encoding genes whenever we describe typical genes. (As I did above.) There are genes for transfer RNA (tRNA), genes for ribosomal RNA, and genes for a large heterogeneous class of small RNAs. None of them have coding regions. The transcript is the functional product, often after RNA processing.

Because this old-fashioned definition is rarely used, the examples of alternative splicing producing different proteins pose no problem for modern definitions. These modern definitions refer to the transcript as the important product and not a protein.

There are exceptions to every generality in biology. Here’s a short list of gene examples that do not conform to my preferred definition.

Operons: In some cases adjacent “genes” are transcribed together to produce a large initial transcript containing several coding regions. In other cases the primary transcript is subsequently cleaved to produce multiple functional RNAs. In these cases it doesn’t make sense to refer to the co-transcribed genes as a single “gene.” Instead, we identify the stretches of DNA that correspond to a single functional unit as the “gene.” Thus, the lac operon contains three “genes” and the ribosomal RNA operons contain two, three, or four genes.

Trans-splicing: There are examples of “genes” that are split into pieces. The transcript from one piece is joined to the transcript from another to produce a functional RNA.

Overlapping Genes: Some “genes” overlap. This means that a single stretch of DNA can be part of two, and in at least one case, three genes.

RNA Editing: In some cases the primary transcript is extensively edited before it becomes functional. In the most extreme cases nucleotides are inserted and deleted. What this means is that the information content of the “gene” is insufficient to ensure a functional product and the assistance of other “genes” is required.

The Richard Dawkins Definition of a Gene Is Seriously Flawed

 
(This is an updated version of a article that I originally posted to talk.origins on Sept. 6, 1999)

We are interested in the correct definition of a "gene" (see ...). Part of the confusion is due to popular science writers who don't get it right. For example, Richard Dawkins does some serious handwaving in The Selfish Gene and he compounds it in The Extended Phenotype.

Dawkins knows that his defintion of "gene" in the Selfish Gene is unusual so he returns to the subject in The Extended Phenotype in his discussion of the selfish replicator. Dawkins is forced to concede that his use of the word "gene" is incorrect. That's why he says,

I am happy to replace 'gene' with 'genetic replicator where there is any doubt.

Nevertheless, he tries very hard to defend his point of view by claiming that geneticists and molecular biologists can't come up with a good definition of gene either. This leads him to make some very silly statements about genes and cistrons. He defines his genetic replicators in terms of alleles which means that they don't exist unless there is variation in the genome. He then goes on to restrict his discussion of changes in frequency to the results of natural selection, which means that his "genes" are effectively defined by the mechanism he prefers. This is why he quotes George Williams,

This is the rationale behind Williams's definition: 'In evolutionary theory, a gene could be defined as any hereditary information for which there is a favorable or unfavorable selection bias equal to several or many times its rate of endogenous change.'
                ....The Extended Phenotype p.89

The hand-waving in The Selfish Gene is even more obvious,

In the title of this book the word gene means not a single cistron but something more subtle. My definition will not be to everyone's taste, but there is no universally agreed definition of a gene. Even if there were, there is nothing sacred about definitions. We can define a word how we like for our own purposes, provided we do so clearly and unambiguously. The definition I want to use comes from G.C. Williams. A gene is defined as any portion of chromosomal material that potentially lasts for enough generations to serve as a unit of natural selection.
                ....The Selfish Gene p.28

In the new version of The Selfish Gene (1989) Dawkins adds a footnote where he again addresses his critics, especially Sewall Wright. Dawkins defends his definition of a gene as a unit of selection.

More handwaving,

I am using the word gene to mean a genetic unit that is small enough to last for a number of generations and to be distributed around in many copies. ... The more likely a length of chromosome is to be split by crossing-over, or altered by mutations of various kinds, the less it qualifies to be called a gene in the sense I am using the term.
                ....The Selfish Gene (1989) p.32

I said that I preferred to think of the gene as the fundamental unit of natural selection, and therefore the fundamental unit of self-interest. What I have now done is to *define* [Dawkins' emphasis] the gene in such a way that I cannot really help being right!
                ....The Selfish Gene (1989) p.32

The fact that Dawkins uses the word "gene" in such a non-standard way is not an issue as long as one recognizes that the Dawkins "gene" has nothing to do with the genes that molecular biologists and geneticists talk about. It's not an issue as long as one doesn't try and pretend that Dawkins has avoided handwaving and "clearly" refuted the problems raised by his critics.

The most reasonable definition of gene is that it is a piece of DNA that is transcribed but there are exceptions to everything in biology. Some genes are made of RNA, for example, and sometimes it's better to define a gene in terms of the protein it encodes. In no case is it reasonable to define a gene in terms of its ability to be selected or whether recombination can occur within it.

Jane Fonda Is Back

 
It's about time. Jane Fonda spoke at the Washington rally for peace yesterday. She said "I haven't spoken at an anti-war rally for 34 years. But silence is no longer an option." Jane is right. Silence is no longer an option. We need to get out of Iraq and Afghanistan.

Many of us will remember when "Hanoi Jane" visited North Vietnam in 1972. Is it time for her to visit Iraq?

[Photo Credit: According to Wikipedia "This photograph was shot by a public affairs officer of the Peoples Republic of Vietnam, and released worldwide for distribution."]

Psychic Sylvia Browne Is Nothing but a Con Artist and a Fake

 
Anderson Cooper on CNN does something right. He exposes Sylvia Browne as a con artist. She told the parents of a missing boy that their son was dead but he turned up alive after four years. James Randi takes part in the debunking.

Now, if only we could get Larry King to admit that psychics are frauds ....

Free Love, the '60's, and Protein Synthesis

 
Most of us have seen this video of protein synthesis. It was made in 1971 (close enough to the '60's) at Stanford University and narrated by Paul Berg. This is a classic. Every student has to see it. (Much of the science is outdated but you don't watch it for the science.)

You have to wait until 5 minutes into the video to start seeing the student participation section on the outdoor field. This sort of thing was easy to organize back in 1971 but I can't imagine my students doing it today. Perhaps I'm wrong. Would any of you be interested in making an updated version?

All mimsey was the mRNA, and protein chain outgrabe ....

Thanks to Living the Scientific Life for finding it on YouTube.

Should We Pity America, or Hate It?

 
The Maher Arar case came to a close yesterday when the Canadian government agreed to a $10.5 million dollar settlement. The Prime Minister apologized for Canada's role in the sorry saga [`I wish I could buy my life back'].

In case you don't know, Arar is a Canadian citizen. He was arrested by the FBI in New York in 2002 on suspicion of terrorism and send to Syria to be tortured. He was released after almost a year and returned to Canada. Since then he has been cleared of all charges by a judicial inquiry.

The American government refuses to admit they made a mistake (a lawsuit is pending). Even more extraordinary, they refuse to remove Arar from their "no-fly" list in spite of the fact that the Canadian system has found him innocent. The FBI file has been reviewed by the Canadian government and there's nothing in there to warrant further suspicion.

All this is well known in Canada and Canadians are angry. Here's an excerpt from an article by Thomas Walkom on the font page of today's Toronto Star [U.S. security trumps freedom].

Ottawa's decision to compensate Canadian Maher Arar for its role in his unlawful imprisonment and torture contains a warning and a lesson.

The warning is that Canada and the U.S. are on fundamentally different paths when it comes to matters of terrorism and human rights. The lesson is that until Ottawa gets more aggressive with our friends in the war on terror, a Canadian passport won't mean much.

First the warning. The U.S. has chosen to subordinate the principles of individual freedom to what it sees as its security needs. It jails people indefinitely without charge, utilizes interrogation methods that the United Nations describes as torture, wages illegal wars and commits the very crimes against humanity it once helped to prosecute.

For America's friends, this is heartbreaking to watch.

Yes, it's heartbreaking and I feel sorry for my American friends who know what's going on (e.g., Ed Brayton). But enough is enough. The refusal to admit that they, like we, were wrong about Maher Arar does not deserve our pity. It's just plain stupid and wrong.

America seems to have lost its way after 9/11. Its leaders are willing to sacrifice basic human rights in order to imprison and torture people who they suspect of terrorist activities. Most of them are innocent but that doesn't seem to matter.

Furthermore, America has no respect for its friends. Canada's system of justice is just as good as America's—probably better. If we find Arar innocent then America should have the decency to respect our decision and remove him from their list of suspect terrorists.

BMCR REVIEW of Heinz Heinen, Vom hellenistischen Osten zum römischen Westen.

Heinz Heinen, Vom hellenistischen Osten zum römischen Westen. Ausgewählte Schriften zur Alten Geschichte. Historia Einzelschriften 191. Stuttgart: Franz Steiner Verlag, 2006. Pp. 553. ISBN 3-515-08740-0. €80.00.


Reviewed by Michael Hesse, Witten (sallustius-crispus@gmx.de)
Word count: 250 words

Der anlässlich des 65.Geburtstags des Trierer Althistorikers und Bengtson-Schülers Heinz Heinen erschienene vorliegende Band stellt ein pietätvolles sincerae pignus amicitiae für den langjährigen Mitherausgeber (1971-2003) der Zeitschrift Historia dar.

Ziel der Herausgeber des Bandes --der Heinen-Schüler Andrea Binsfeld und Stefan Pfeiffer-- ist es, eine Auswahl der "Kleinen Schriften" ihres Lehrers zu bieten, welche die Forschungsschwerpunkte Heinens (griechisch-römisches Ägypten, Trier und Trevererland in römischer Zeit, Christentum und Spätantike, antike Sklaverei,1 bosporanisches Reich und der nördliche Schwarzmeerraum in der Antike und die russische Historiographie) repräsentiert und gleichzeitig seine inter-disziplinäre Arbeitsweise vorzustellen, die sich durch die Einbeziehung von Philologie, Archäologie, Papyrologie, Epigraphie und Ägyptologie auszeichnet. Phänomene der Akkulturation finden ebenso Berücksichtigung wie sozialhistorische Fragestellungen besonders in den "Randgebieten" des Römischen Reiches. Ein ausführliches Schriftenverzeichnis Heinens ist dem Band vorangestellt. Die hier vorgelegten 29 Beiträge werden unverändert geboten; wenige Corrigenda finden sich im Anhang. Die Entscheidung für eine Reproduktion der Beiträge in ihrer ursprünglichen optischen Form unter Beibehaltung der ursprünglichen Paginierung ist sicherlich richtig. more at BMCR

Publisher: Franz Steiner Verlag

"Anlässlich des 65. Geburtstages von Heinz Heinen bietet der Band eine repräsentative Auswahl seiner Kleinen Schriften, die das Spektrum seiner Forschungen veranschaulichen. Neben grundlegenden Beiträgen zum griechisch-römischen Ägypten und zur Geschichte des Schwarzmeerraumes finden sich auch wichtige Arbeiten zum Christentum, zur Spätantike und zur Sklaverei forschung. Hierdurch kommt die inter disziplinäre Ausrichtung Heinz Heinens im Schnittpunkt der Fächer Alte Geschichte, Klassische Philologie, Archäologie, Ägyptologie und Papyrologie klar zum Ausdruck. Phänomene der Akkulturation finden ebenso Berücksichtigung wie sozialhistorische Fragestellungen besonders in den „Randgebieten“ des Römischen Reiches."

1. Auflage 2006. XXVIII, 553 S., 34 s/w Abb.
Frontispiz, Gebunden.

Historia-Einzelschriften Band 191
Franz Steiner Verlag
lieferbar

Martine Leguilloux, Les objets en cuir de Didymoi

Martine Leguilloux
Les objets en cuir de Didymoi. Praesidium de la route caravanière Coptos-Bérénice. Praesidia du désert de Bérénice III

Le fort de Didymoi, construit par l’armée romaine sur la piste Coptos-Bérénice en 76/77 apr. J.-C. et occupé jusqu’au second quart du IIIe siècle, a livré une collection de plus de 700 objets en cuir. Fragments de vêtements, chaussures et sandales, outres, gourdes, guides, sangles, pièces de harnachement et de sellerie, étuis, fourreaux offrent un panorama des emplois du cuir. La découverte de chutes de cuir atteste la présence régulière de cordonniers ou au moins d’individus sachant travailler le cuir. Les objets proviennent des couches de détritus rejetés devant le fort au cours des Ier et IIe siècles et du comblement des casernements dans la première moitié du IIIe siècle. Grâce à une stratigraphie fixée chronologiquement par des critères intrinsèques (ostraca) et extrinsèques (mise en relation de certaines strates avec des travaux commémorés par des inscriptions), le matériel en cuir est daté avec une grande précision. L’exceptionnel état de conservation en fait une des plus importantes collections d’objets en cuir de l’époque romaine et rend aisée la comparaison avec les ensembles découverts dans des milieux immergés du nord de l’Empire, tels que les camps du Limes de Germanie.

IF 936 FIFAO 53
ISBN 2-7247-0409-6
2006 48 €

REVIEW of Hélène Cuvigny, Ostraca de Krokodilô

Hélène Cuvigny, Ostraca de Krokodilô. La correspondence militaire et sa circulation (O. Krok. 1-151). Praesidia du désert de Bérénice II. Fouilles de l'IFAO 51. Le Caire: Institut français d'archéologie orientale, 2005. Pp. 283. ISBN 2-7247-0370-7. €35.00.


Reviewed by Thomas Kruse, Ruprecht-Karls-Universität Heidelberg
Word count: 2653 words

Hélène Cuvigny is a distinguished expert on the area of the Egyptian Eastern desert between the Red Sea and the valley of the Nile in the Roman period. Since 1994 in the context of a research project which is funded by the Institut Français d'Archéologie Orientale in Cairo she has been entrusted with the exploration of the network of the small Roman forts (praesidia) along the 180 km road leading from Qift (ancient Koptos) to Qusayr on the Read Sea. Almost at the beginning of this project it turned out that Qusayr or (to be more precise) the ancient site of Qusayr al-Qadîm, 5 km north of the modern town, is the ancient sea port of Myos Hormos, which had until then been located in historical maps of the region about 160 km further to the north along the Red Sea coast. more at BMCR

publisher: IFAO

Science blogger Bora Zivkovic

 
The Nature interview with Bora Zivkovic is out [here]. I want to take this opportunity to thank Bora and everyone else for organizing the 2007 North Carolina Science Blogging Conference. It was lots of fun, I'm looking forward to next year already.

Here's a photo that Bora took of me and my daughter Jane at dinner on Friday night (January 19th). That's Cathy Davies (The Lab Cat) on my right. Bora tells me [here] that we were right under the John Edwards campaign headquarters. I wish I known, I would have popped up to say "hello."

Praying before City Council Meetings

 
Following up on a previous posting [Reciting the Lord's Prayer at City Council] I note that the Durham city council (west of Toronto) voted on Wednesday to make prayers before the meeting "voluntary." There was an excellent news clip about this on CityTV and you can watch it here. I'm particularly impressed with Mayor Bob Shapherd of Uxbridge (a member of the council) who declared that he is a non-believer and doesn't want to be a hypocrite when he's forced to recite something he doesn't believe.

I'm embarrassed that there are Canadian politicians who are stupid enough to think that public recital of a Christian prayer is a good thing. I'm proud of those who challenged them.

My own city council in Mississauga also prays before meetings. I've written to my councillor, Katie Mahoney, but she hasn't replied.

[Hat Tip: Richard Dawkins]

Let's Help America: Make Florida the 11th Province

 
America is in trouble. I urge all Canadians to sign the petiton at Florida11 to make Florida the 11th province of Canada. We need to do our bit to prevent a repeat of the 2000 election crisis that got America in such trouble in the first place.

Lead in Lipstick Will Cause Cancer

 

Friday's Urban Legend: FALSE

There's an email message circulating that warns women against the dangers of lead in lipstick.

It's currently #9 on the 25 Hottest Urban Legends. (Incidently, the Barack Obama myth has moved up to #1; see Baracl Obama Is a Closet Muslim).

The message claims that lead causes cancer. This is not true. The message claims that lipstick contains lead. This is correct but the levels are way below those allowed by health rules in civilized countries [Easily Lead].

[Photo credit: Wikipedia, Creative Commons]

IDiots and the War

 
Yesterday Ed Brayton posted on DaveScot's silly notions about the war in Iraq [DaveScot's Ridiculous Arguments]. Ed goes into much more detail than I did on Wednesday [The IDiots Understand the War in Iraq]. The most interesting thing about Ed's posting is his description of the censorship imposed on the thread over at Uncommon Descent. If you go there you'll notice that the comments are closed. But they weren't closed yesterday. Find out from Ed what Mike Dunford did to force DaveScot to delete all comments.

And you wonder why we call them IDiots?

Toyota RAV4 Jousting

 
This is too cool. Anyone want to try it with me? I'll drive. We can challenge a team of IDiots.

Teaching Ethics in Science: Science v Technology (Part 2)

[Larry Moran: Part 1] [Janet Stemwedel: Part 1, Part 2]

The issue is whether we should be teaching "ethics" in science classes. The particular examples that we've mentioned are debating whether GM food is good or bad and discussing the consequences of the human genome project.

My concern is not so much whether these issues are topical or fun—they certainly are. I'm worried about the fact that they detract from my main purpose, which is to get students to appreciate science for it's own sake and not just because of some application it might have.

Janet Stemwedel responds,

I'm very sympathetic to Larry's worry here -- as a philosopher, how could I not be? -- that students aren't grasping the beauty inherent in a coherent model of a piece of the world, in a piece of knowledge that is valuable primarily because it satisfies our curiosity. Teachers get burnt out on the "What are we ever going to use this for?" question almost as rapidly as the even more discouraging "Is this going to be on the test?" For us, knowledge scratches a particular kind of itch. It distresses us to think that our students might not have that itch. Thus, maybe our teaching ought to be directed at making our students feel itchy -- helping them see what's cool about the knowledge we're trying to convey even if we table all questions of how the knowledge might be applied to solving various practical problems in the real world.

Yes, I think we ought to pay more attention to making our students feel itchy rather than pandering to their pre-conceived notions that technology is more important than science. If we don't make the attempt then the current situation will never change. As adults, the students will still demand that scientific research be directed toward betterment of the human species.

On the other hand, even if the discussion is restricted to the science content, the "What is this good for?" questions are already part of the storyline in many courses. We teach students about the more refined models that came to replace the earlier and clunkier ones, models that are good because they make better predictions or have clearer connections to empirical data or other useful models. We teach students about particular experimental techniques that are good for answering particular questions or adjudicating between different accounts of what's going on in a system. Organic chemistry students have to learn a truckload of reactions that are good for producing this kind of compound from this kind of starting material in this set of conditions.

I'm not opposed to teaching the technology of scientific research. That's part of learning about science. I think it's overdone in many cases but it's still useful for students to do some experiments in the lab.

A laundry list of isolated facts is not the kind of thing the students want to learn, nor the kind of thing the science teachers want to teach. What keeps the facts from being isolated -- what imposes a coherent structure where they're connected to each other -- almost always involves a storyline about what various bits of the knowledge are good for.

The trick, I suppose, is to keep the students focused on that question within the bounds of the discourse about the knowledge and its production -- at least as long as the students are taking a biochemistry class, rather than a biochemical ethics class.

Yes, that's the trick. You avoid overwhelming students with irrelevant facts and concentrate on the basic concepts of science. The emphasis is on the big picture idea of how cells work and not the nit-picky details that nobody cares about.

Introducing "ethics" debates about the application of technology makes the job more difficult. The problem is that not all science teachers share my goal of trying to interest students in how nature works rather than what it it good for. And even among those that do, there's a lack of appreciation of the downside of "ethics" debates.

One little response to Larry's comments on my grant-writing claim: I'm inclined to agree that B.S. is not something we want to be a necessary part of requesting and securing funds to support scientific research -- whether research aimed at solving a well-defined practical problem or research on the basic questions about which scientists are most curious. However, there's a difference between overselling the likely applications of a piece of research and pointing out its relevance to things non-scientists might take to be important as well. And, pointing out the relevance of a line of research is important for the simple reason that scientists come to non-scientists asking for money. It would be lovely if the people controlling the research funds (and the tax payers whose money provides those funds) were already sold on the idea that building scientific knowledge is a good thing in its own right. Surely, getting more people to come around to this way of thinking seems to be part of what Larry would like to accomplish. However, even if everyone agreed that scientific knowledge is to be cultivated, the research that makes this happen wouldn't always get prioritized ahead of the other practical things for which tax dollars must pay. Pointing out relevance isn't so much admitting that knowledge can't be good just to have as it is showing additional ways our society benefits from having that knowledge beyond just getting smarter.

I agree that it would be lovely if the people controlling the money appreciated science for its own sake. Everyone I know agrees. But nobody is trying very hard to change this when we teach our science classes. It's like they've given up the fight because it's hopeless.

Well I'm not yet ready to give up. I try to get my students to stop thinking about "relevance" every time they learn a new concept. I long for the day when the general public prioritizes knowledge over relevance. Maybe that will mean more money for philosophers.

Finally, Larry closes with these comments:

If you really want to teach ethical reasoning then you need training in ethics. This probably means a degree in philosophy or at least hanging out with philosophers for several years.

I don't want to chase away the scientists who might want to hang out with the likes of me, but is it really the case that scientists who are themselves ethical practitioners of science are unable to teach their students anything useful about the ethical use and conduct of science? To the extent that this is true, what's up will all the scientific training programs where there isn't a formal ethics component at all, let alone one overseen by a credentialed philosopher? Are you folks in need of more help than you let on?

Here's a question. Notice how I've put "ethics" in quotation marks. That's because I'm not sure whether some of these so-called ethical questions are really ethical questions. What about the debate over genetically-modified food?

To me that seems to be a straightforward debate about safety. That's not ethics. What's the ethical problem? Are there some people who are ethically opposed to the genetic manipulation of plants? We've been doing it for 5000 years.

After hanging out with philosophers for ten years or so, I realize they have special training in logic and reasoning. They usually know things like how to present a correct argument and they usually know the proper meanings of terms like "ethics" and "morality."

I've seen science teachers try to explain the difference between ethical relativism and absolutism. I've seen them get confused about the difference between religion and morality. I've seen them mistaking their personal biases for logical arguments.

So, in answer to your question, yes we need help.

The Next Leader of the Free World?

 
The blogosphere is all abuzz with debate over who's going to be the next leader of the free world. I have a question. Who's the current one?


If I had a vote, I'd vote for the guy in the middle. Anyone who has a blog and supports universal health care coverage for all Americans can't be all that bad. Besides, he lives in Chapel Hill and that's a very nice place.

CODEPINK Women for Peace

 
 
Read Dariana's blog if you have two X chromosomes or want to support those who do.


[Hat Tip: Greg Laden]

I'm not a Darwinist, but I Ain't Signing

Bill Dembski continues to demonstrate his ignorance of evolution by ranting against Darwinism. In his latest posting [Dissenting from Darwin] he urges those of us who are skeptical about the exclusivity of Darwinian evolution to sign a petition.

Increasinginly I find that those with doctorates in the natural and engineering sciences are asking, “What can I do to help in the fight against Darwinism?” For some this will involve research bearing directly on Darwinian theory. But there is also another way to help. Many in the media and the public still do not know that there is scientific dissent from Darwinism. They have no idea that MANY scientists are skeptical of neo-Darwinian theory.

So one way you can help is to put your head on the chopping block and voice your skepticism of Darwinism (if you do, trust me, Darwin’s dogmatic defenders will try to chop off your head). This is why Discovery Institute created their statement “A Scientific Dissent from Darwinism.” It states: “We are skeptical of claims for the ability of random mutation and natural selection to account for the complexity of life. Careful examination of the evidence for Darwinian theory should be encouraged.”

There's nothing wrong with the statement. I am skeptical of claims that natural selection accounts for all of the complexity of life. There are lots of other things going on during evolution.

But I will not sign this petition because Dembski and the IDiots will deliberately misinterpret my intentions. They have no idea what dissent from classical Darwinism really means. They have no idea that someone like me could (mostly) agree with the statement while, at the same time, referring to all Intelligent Design Creationists as IDiots. I suspect that some of those who signed the petition would feel the same way about Intelligent Design.

The list of dupes and IDiots is [here]. There are 686 names and two of them claim the University of Toronto as their affiliation. They are,

            Stephen J. Cheesman Ph.D. Geophysics
            Alfred G. Ratz Ph.D. Engineering Physics

Neither of them are listed in the phone directory and they have no affiliation with the university according to a search of the website. Chessman was involved in writing some software for an undergraduate lab back in 1992.

Eva Amsen's Cocktail Recipe

 
Eva Amsen is a graduate student in my department and a blogger (easternblot.net). She was at the 2007 North Carolina Science Blogging Conference last weekend and now she's written an article about it at Inkling Magazine [Science Bloggers Avoid the Spinach Dip Brush-Off].

Ageism in Science

 
I'd like to address a thorny issue; namely, discrimination on the basis of age. The focus of this particular posting is the widespread belief that "young" investigators are more valuable to the research community than "old" ones.

By "young" I mean scientists who have graduated with a Ph.D. and completed several years of post-doc. They are either about to be hired as principle investigators for the first time or have already been hired within the past 7 years. Typically, they are under 40 years old and if they have a university position it will be as an Assistant Professor. They do not have tenure.

"Old," or senior, investigators are those over 40. There are two sub-categories: those between the ages of 40 and 55 who are thought to be in their prime and those over 55 who are thought to be well past their prime.

I was prompted to bring up this issue by the recent funding crisis in Canada and especially by some comments made in an open letter from Alan Bernstein, the President of CIHR (but see Old Professors). Alan's opinion, as expressed in the letter, is not that much different from the opinion of most of my colleagues. The difference is that Alan is in a position to act on his view of Canadian scientists. He can redirect funding.

Here's what Alan says about young investigators,

I am very concerned about the impact this situation will have on all members of the research community - new investigators, mid-level established investigators and Canada's most senior researchers. And I am particularly concerned about the impact on new investigators who are at the beginning of their careers. These new investigators represent the future of health research in Canada. Failure to secure grant support for their research in those critical first years can have a lasting detrimental effect on their subsequent careers. Clearly, all of us need to think about how to improve the situation for the very group of investigators who are bringing their energy, superb training and new approaches to health research.

At first glance this seems like a typical harmless motherhood statement that nobody questions. After all, doesn't everyone agree that youth represents the future? Doesn't everyone agree that energy and new approaches come from young investigators and not from old ones? Doesn't everyone agree that failure to get a grant can threaten the careers of young investigators?

Yes and no. There's a lot more going on than what's implied by such facile statements. Let's try and unpack Alan's paragraph and see what we can learn.

Like Alan, I am very concerned about the impact of the funding crisis on all members of the research community. Unlike Alan, I don't reserve any special concerns for young investigators at the expense of older ones. The loss of a grant in the middle of a promising career is just as devastating as the failure to get one in the first place. Perhaps more so, since the mid-career investigator has a lab full of graduate students, post-docs, and research assistants who have to be let go or moved. Given the choice between funding a mid-career investigator with a decent publication track record and a young investigator with no track record, why should we favor the unproven over the proven? Does such a bias make sense?

I question the common belief that young investigators represent the "future" of research. It suggests that a 45-year old doesn't have a future even though they may still have 20-30 years of productive research ahead of them.

Are young investigators more energetic? Perhaps, but I know lots of enthusiastic and energetic investigators who are no longer young. Besides, wisdom and maturity can often beat out energy in a head-to-head competition to do good research.

What about the idea that youth is more innovative? Is there any truth to that myth? Not really. There are lots and lots of senior investigators who are right up there on the cutting edge of science. I daresay there's more innovative work done in the labs of senior investigators than in the labs of young investigators, at least in my field. Part of this is due to the system. You can't take too many risks until you've become established. Part of it is due to experience. Experience is a good teacher—you can see productive new directions once you've mastered the old ones.

None of this means we should abandon young investigators in favor of senior investigators. But, by the same token, we shouldn't sacrifice senior investigators in order to fund younger ones. The excuses used to promote the "youth" strategy need to be questioned to see if they are truly valid. I don't think they are.

In the recent grant competitions, there was a tilt toward funding young investigators at the expense of renewing the grants of senior investigators. That's not right. It's discrimination on the basis of age and it must stop now.

(In the interests of full disclosure, I am not competing for grants from any granting agency. I do not have a direct stake in this issue other than to promote what's good for research and good for my colleagues. If we don't have enough money to support our current crop of researchers then it's stupid to hire more.)

Front Page News: CIHR Funding Crisis

 
Last week the Canadian Institutes of Health Research (CIHR) Funding crisis made the front page of the Globe and Mail (lower left corner)[Cash crunch spurs research warning]. I blogged about this earlier (Massacre in Canada) in order to publicize the effect it was having on my colleagues. We need to do something before we destroy researchers in the most productive part of their careers.

The President of the CIHR is Alan Bernstein. He responded to the crisis by publishing a President's Message to the Research Community - January, 2007. The message does not inspire confidence. The current mess was caused by a downturn in government funding but that downturn might have been foreseen. It could have been managed better.

The crisis is also due, in part, to the diversion of basic research money to new goals; namely, "relevant" research that might lead directly to improvements in health.

Alan has just published a article in an online magazine where he explains his philosophy [Publicly-Funded Research and Innovation: Canada’s Key to the 21st Century]. He says,

The world is in the midst of profound social, scientific, and technological change. How Canada responds to these changes will determine our future quality of life, career opportunities for young Canadians, and whether we will be globally competitive and productive.

Our future success as a nation will depend on our ability to attract and retain top scientific talent (what The Economist magazine recently called “The world’s most sought-after commodity on the planet”), to generate new ideas and transfer them into new products, new policies, and new services.

Real, cutting-edge research is tough to do. But, transforming research into action is even tougher. This process, called knowledge translation or innovation, involves meaningful interaction between researchers and the users of research.

It's the conflict between "knowledge translation" (God, how I hate buzzwords) and pure basic research that's causing angst. I don't see any evidence that the President of CIHR is willing to stand up for curiosity motivated research—the kind done on university campuses across the nation. He talks a lot about competitiveness and new products but not about knowledge and understanding.

This is very disappointing. It suggests that Alan has lost touch with the goals of his former colleagues (he used to be a research scientist at the University of Toronto). If the President of CIHR won't stand up for basic research then we're in big trouble. Maybe it's time to look for a new President who understands that support for basic science is crucial.

Nobel Laureate: Peter D. Mitchell

The Nobel Prize in Chemistry 1978

"for his contribution to the understanding of biological energy transfer through the formulation of the chemiosmotic theory"

Peter D. Mitchell (1920-1992) received the Nobel Prize in 1978 for developing the Chemiosmotic Theory to explain ATP synthesis resulting from membrane-associated electron transport [Ubiquinone and the Proton Pump].

Mitchell is the last of the gentleman scientists. He first proposed the chemiosmotic principle in a 1961 Nature article while he was at the University of Edinburgh. Shortly after that, ill health forced him to move to Cornwall where he renovated an old manor house and converted it into a research laboratory. From then on, he and his research colleague, Jennifer Moyle, continued to work on the chemiosmotic theory while being funded by his private research foundation. [Peter Mitchell: Wikipedia]

The Chemiosmotic Theory was controversial in 1978 and it still has not been fully integrated into some biochemistry textbooks in spite of the fact that it is now proven. The main reason for the resistance is that it overthrows much of traditional biochemistry and introduces a new way of thinking. It is a good example of a "paradigm shift" in biology.

Because he was such a private, and eccentric, scientist there are very few photos of Peter Mitchell or his research laboratory at Glynn House . The best description of him is in his biography Wandering in the Gardens of the Mind: Peter Mitchell and the Making of Glynn by John Prebble, and Bruce Weber. A Nature review by E.C. Slater [Metabolic Gardening] gives some of the flavor and mentions some of the controversy.

Many scientists believe that the Chemiosmotic Theory was the second greatest contribution to biology in the 2oth century (after the discovery of the structure of DNA). The case is strong, I think they're right.

The IDiots Understand the War in Iraq

 
DaveScot didn't like the short speech by Senator Jim Webb. Apparently Webb just doesn't get it about Iraq. According to DaveScot, there's a really good reason for being in Iraq [[Off Topic] Senator Jim Webb: Clueless.

Did you know that the real reason is to train the marines?

Here’s the deal Jim. In order to have an effective force in fighting guerilla and urban wars in Arab countries we need actual combat veterans seasoned in that type of warfare leading the unseasoned troops. Use your head, Jim. Now we have an effective force led by NCOs who know how to survive urban and guerilla wars in Arab countries. And Bush managed to build that force without losing 58,000 American lives as were sacrificed in Vietnam but rather limited the losses to 3,000. Use your head for something other than a place to put your hat, Jim. We needed a veteran ground combat force for the Middle Eastern theater. Now we have one. Now what happened to Russia in Afghanistan won’t happen to us.

Clueless.

I can't help but notice some glaring deficiencies in current military training. There are no veterans with experience in colder climates like those we find in Canada. There's also a lack of experience in the European theater—almost all the veterans from World War II have retired. And let's not forget China or India. Nobody in the Marines has ever fought in China or India.

Maybe the USA should start a war in one of those theaters in order to get some veterans?

What Is a Species? John Wilkins Knows

 
As part of the ongoing basic concepts posts, John Wilkins has described Species. John is one of the world's leading authorities on this topic so you can be sure to learn something if you jump over to Evolving Thoughts.

For those of you that don't want to learn about all the various definitions of species here's the bottom line from John ....

So, after all that, what is a species? I think, and this is very much my own opinion, that there is no ....

How to Fix NIH and NSF

 
I recently commented on the funding crisis in Canada. Less than 20% of grants will be funded in the latest CIHR competition. Canadian scientists are trying to see what needs to be done to fix the problem.

There's a similar problem in the USA. At the 2007 Science Blogging Conference we received a flyer from Geoff Davis and Peter Fiske asking people to go to their blog and get involved in the discussion about how to fix NIH and NSF. Here's the site: [Zerhouni for a Day: A challenge].

So far the main suggestions under discussion are to limit the size of grants and to cut back on funding interdisciplinary centers. Both suggestions are worth serious consideration.

Ubiquinone and the Proton Pump

Yesterday's molecule was ubiquinone, also known as coenzyme Q or just plain "Q." Ubiquinone is a lipid soluble cofactor that accepts and donates electrons in oxidation-reduction reactions. These are reactions in which electrons are transferred from one molecule (oxidation) and accepted by another (reduction).

Ubiquinone is confined to lipid membranes where it diffuses laterally. It is synthesized in reactions catalyzed by membrane-bound enzymes. Bacteria contain a structurally similar molecule called menaquinone and photosynthetic organisms have plastoquinone.

All of these quinones play a role in pumping proteins across a membrane in order to create a proton gradient that's used to make ATP. If you understand how this works then you can understand how life first arose 3.5 billion years ago.
Quinones can carry up to two electrons per molecule and they are added one-at-a-time in the reaction shown below.

The reason why ubiquinone is so important is because the ring structure stabilizes the negatively charged semiquinone anion allowing for the addition of another electron to create ubiquinol (QH₂). Note that when two electrons are taken up, two protons (H⁺) are added to neutralize the negative charge. In the reverse reaction (ubiquinol to ubiquinone: bottom to top) two protons are released when the electrons are given up.

The key to understanding the importance of ubiquinone is recognizing that protons can be taken up from one side of the membrane during the reduction of ubiquinone and they can be released on the other side of the membrane when ubiquinol is oxidized in the reverse reaction.

The enzymes responsible for this differential uptake and release are part of the membrane-associated electron transport chain found in mitochondria and in the membranes of bacteria. There are several different reactions that take place as shown in the simple schematic diagram below.

The red line traces the path of electrons released from a molecule called NADH. The electrons pass through three different membrane complexes called complex I, complex III, and complex IV. At each step, protons are pumped across the membrane. In complex IV the electrons are passed to oxygen (O₂) to make water. This final step is why you need oxygen to live.

We are mostly interested in the middle complex (complex III) because that's the one found in all species. It also takes part in photosynthesis, which is a similar process for producing a proton gradient.

The protons accumulate in the intermembrane space between the outer and inner membranes of mitochondria and bacteria. The complexes are located in the inner membrane. (The outer membrane isn't shown in the diagram.) Because there's a higher concentration of protons in the intermembrane space compared to inside the cell, there's pressure to return protons down the concentration gradient to restore the balance. This pressure is called the protonmotive force. It's used to drive ATP synthesis by coupling the transport of protons to the phosphorylation of ADP. ATP is the main energy currency in the cell. It can be used to make other molecules or cause muscles to contract etc.

The idea that electron transport is mainly used to create a proton gradient which is then used up in the synthesis of ATP is known as the Chemiosmotic Theory. It was championed in the 1960's by Peter Mitchell (see tomorrow's Nobel Laureate).

The role of quinone in complex III is complicated. Here's a schematic (left) showing the uptake of protons (H⁺) from the cytoplasmic side (bottom) to form QH₂ and their release on the other side when QH₂ is converted back to Q. This complicated set of reactions is known as the Q cycle and it is responsible for the generation of protonmotive force in all species. Since the protonmotive force is what drives ATP synthesis, this makes the Q cycle one of the most important reactions in biochemistry.

The structure of complex III has been solved. In addition to being one of the most important enzymes, it is also one of the most beautiful. You can easily see the two b heme groups that form the catalytic sites for oxidation and reduction of QH₂ and Q. The iron-sulfur center (Fe-S) helps in the transport of electrons to heme c₁ and eventually to cytochrome c.

This is such a fabulous molecule that I put it on the cover of my biochemistry book.

Students often wonder how the earliest forms of life created energy before the invention of photosynthesis. Once you understand the Chemiosmotic Theory, it isn't difficult to see how this worked 3.5 billion years ago. All you need is a source of energetic electrons to drive the reduction of quinone. In the presence of a cytochrome complex, like complex III, you'll get a protonmotive force generated by the Q cycle. This will power ATP synthesis.

Here's a simplified version of how it's done in chemoautotrophic bacteria that can use hydrogen as an energy source. There are many other possible sources of energy, such as H₂S or NH₄⁺. They are obvious candidates for the kinds of energy production that was common when life first began.