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Friday, August 31, 2007

Blog Day 2007

The rules for today are that we recommend five blogs you may not be reading on a regular basis. Here are my choices. Four Canadians and one honourary Canadian. How's that for chauvinism?

One of these is the most northern blog on my blogroll. Can you guess which one? One of the bloggers is very horny. Which one? One of the bloggers was recently at Montebello protesting George Bush (and what's-his-name, the Canadian Prime Minister). Two of them are Professors. One of them has the longest hair of any blogger I've met.

Mike's Weekly Skeptic Rant

Primodial Blog

Runesmith's Canadian Content


Sex, genes & evolution

Defining Irreducible Complexity

So many IDiots, so little time ....

Granville Sewell has posted a message on Uncommon Descent asking What if we DID find irreducibly complex biological features?. He writes,
In any debate on Intelligent Design, there is a question I have long wished to see posed to ID opponents: “If we DID discover some biological feature that was irreducibly complex, to your satisfication and to the satisfaction of all reasonable observers, would that justify the design inference?” (Of course, I believe we have found thousands of such features, but never mind that.)

If the answer is yes, we just haven’t found any such thing yet, then all the constantly-repeated philosophical arguments that “ID is not science” immediately fall. If the answer is no, then at least the lay observer will be able to understand what is going on here, that Darwinism is not grounded on empirical evidence but a philosophy.
Here's how Michael Behe defines irreducible complexity in Darwin's Black Box (p. 39).
By irreducibly complex I mean a single system composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to cease functioning. An irreducibly complex system cannot be produced directly (that is, by continuously improving the initial function, which continues to work by the same mechanism) by slight, successive modifications of a precursor system, because any precursor to an irreducibly complex system that is missing a part is by definition nonfunctional.
There are many irreducibly complex systems in biology. One of my favorites is the citric acid cycle or Krebs cycle. This is a circular pathway of enzymes that oxidize acetate groups to two molecules of CO2.

If you remove any one of the enzymes then there is no cycle and it will be impossible to oxidize acetyl groups to CO2 and regenerate oxaloacetate. You cannot evolve a cycle for the complete net oxidation of acetate by starting with a more simple circular pathway then adding additional enzymes to improve the initial function; namely, the cyclic pathway of oxidation. Thus, by Behe's definition this is an irreducibly complex system whose function is to oxidize acetyl groups and regenerate the original precursor.

We have a damn good idea how the citric acid cycle evolved so the answer to Granville Sewell's original question is: no, the discovery of an irreducibly complex system does not justify the design inference. There are many ways of evolving irreducibly complex systems. This is the same answer that we've been giving for over ten years. Please try and keep up.

Now I have a question for the IDiots. If we can prove to your satisfaction that a particular system is irreducibly complex and demonstrate how it could easily have evolved, will you stop claiming that irreducibly complex systems can't evolve?

Dichloroacetate (DCA) Website Shut Down by the FDA

Dichloroloacetate (DCA) is a potent inhibitor of pyruvate dehydrogenase kinase [Regulating Pyruvate Dehydrogenase]. There have been suggestions in the scientific literature that the inhibition of this enzyme may lead to the death of cancer cells.

Over the years a minor cottage industry has grown up around the synthesis, sale, and promotion of DCA as a magic bullet for the cure of cancer. The lure of the drug is enhanced by the fact that it is so simple and can't be patented. Thus, according to its proponents, the drug companies don't want you to know about this fabulous cure because they can't make a profit. Abel Pharmboy at Terra Sigillata has written a lot about this drug [Perversion of good science].


The problem is that the clinical trials have not been done and there's some danger of toxic effects when you take too much of the drug. The websites that sell DCA claim that it's only for animals but nobody is fooled by that ruse.

Now, according to New Scientist the FDA has ordered the main DCA website to cease selling DCA ['Cancer drug' site shut down]. When you go to the site at you read the following disclaimer, " It is against US government law to sell substances with the suggestion that they are cancer treatments unless they are approved by the FDA."

A Blue Moon Is the Second Full Moon to Occur in a Single Calendar Month

Friday's Urban Legend: DEFINITELY FALSE, MAYBE

The term "blue moon" dates back to the middle ages where it meant something quite impossible. Over time the term came to be used in the phrase "once in a blue moon" to mean "it ain't ever going to happen" [Wikipedia: Blue Moon].

Gradually the phrase took on the meaning of something that happens rarely, instead of never. Following World War II there was an attempt to relate the term "blue moon" to a real astronomical event. The most common explanation was that a "blue moon" was the second full moon in the same calender month. The average time between two successive full moons is about 29.5 days. This means that you can have two full moons in any month except February. This will occur, on average, every two-and-a-half years. This year for example, you might have seen a "blue moon" in May, June, or July depending on where you live [The Blue Moon of 2007]. This interpretation of "blue moon" was promoted by Sky & Telespcope in 1946 and it was due to a misinterpretation of the Maine Farmer's Almanac of the preceding decade.

The Sky & Telescope website has a detailed explanation of the error [What 's a Blue Moon?].

So, if you accept the new definition of "blue moon" then the title statement is correct and this is an example of an urban myth that has transformed the meaning of a phrase. However, if you stick to the original meaning of the term then the title statement is false because a "blue moon" is about as likely as one made out of green cheese.

[Photo Credit: The photograph of the "blue" moon is from miramiramazing]

Where Did Sea Anemones Get Human Genes?

A recent paper by Putman et al. (2007) discusses the newly completed genome of the starlet sea anemone Nematostella vectensis. Kevin Z, a marine biology researcher, blogged about this paper last month [Cnidarian Double Whammy: Anemone Genome Completed and a Worm Thats a Jelly!].

The IDiots were also interested in the paper because it reveals that humans and sea anemones share some genes. Someone named "dacock" posted a message on Uncommon Descent revealing that Darwinism had been overturned (again) [Where Did Sea Anemones Get Human Genes?].

I was going to blog about the stupidity of the IDiots but I just don't have time. Anyway, Kevin Z beat me to it [Anemone's Raise a Tentacle in Support of Evolution]. I don't agree with everything he says about the sea anemone genome and why the Intelligent Design Creationists get it wrong but it will have to do for now. Kevin's responses to some of the IDiots who posted comments over on Uncommon Descent are well worth the visit to his blog.

[Photo Credit: The photograph of the starlet sea anemone and its description is from Summary of Professional Exchanges on Coral Genomics]

Putnam, H.M. et al. (2007) Sea Anemone Genome Reveals Ancestral Eumetazoan Gene Repertoire and Genomic Organization. Science 317: 86 - 94.

Tangled Bank #87


The latest version of the Tangled Bank has been posted on Balancing Life [Tangled Bank #87].

I really like the article on "Standing on the shoulders of giants." It explains what Newton really meant when he wrote that to Hooke. Look it up.

Thursday, August 30, 2007

THEME: Pyruvate Dehydrogenase

Pyruvate dehydrogenase is one of the most important enzymes in the cell. It catalyzes the reaction that converts pyruvate to acetyl-CoA with the release of CO2.

Acetyl-CoA is the molecule that enters the citric acid cycle (Krebs Cycle) to be broken down to two additional molecules of CO2.

April 16, 2007
Monday's Molecule #22 (pruvate). The series began with an unknown molecule that turned out to be pyruvate.

April 17, 2007
Pyruvate. A more complete description of the properties of pyruvate.

(April 18, 2007)
Pyruvate Dehydrogenase Reaction. This posting described the reaction catalyzed by pyruvate dehydrogenase.

April 18, 2007
The Structure of the Pyruvate Dehydrogenase Complex was described in some detail, including the techniques used to elucidate it.

April 18, 2007
Nobel Laureate: Aaron Klug. Aaron Klug worked out the technique used to describe the structure of the pyruvate dehydrogenase complex.

April 20, 2007
Some Bacteria Don't Need Pyruvate Dehydrogenase. There are other ways to catalyze the formation of acetyl-CoA.

April 20, 2007
Pyruvate Dehydrogenase Evolution. The evolution of the genes encoding the pyruvate dehydrogenase subunits is explained.

April 20, 2007
Human Genes for the Pyruvate Dehydrogenase Complex. Identifying the genes for the subunits of the complex.

April 23, 2007
Regulating Pyruvate Dehydrogenase. How pyruvate dehydrogenase is regulated, including the effect of the inhibitor dichloroacetate (DCA).

August 31, 2007
Dichloroacetate (DCA) Website Shut Down by the FDA

August 3, 2012
On the Evolution of New Enzymes: Completely Different Enzymes Can Catalyze Similar Reactions

Dennett on Adaptationism

I've been trying to avoid the discussion of Dawkins vs Gould until the results of the poll are in (see left-hand margin). Those of you who voted for Dawkins will need some major reorientation to bring you into the 21st century. My task is enormous. (I know who you are!)

But since I brought up Daniel Dennett in reference to the aquatic ape just-so story [Aquatic Ape Speculation], I couldn't resist quoting him from Darwin's Dangerous Idea. After outlining the main points in favor of the speculation Dennett says,
The details—and there are many, many more—are so ingenious, and the whole aquatic-ape theory is so shockingly antiestablishment, that I for one would love to see it vindicated. That does not make it true, of course.

The fact that its principal exponent these days is not only a woman, Elaine Morgan, but an amateur, a science writer without proper official credentials in spite of her substantial researches, makes the prospect of vindication all the more enticing. The establishment has responded quite ferociously to her challenges, mostly treating them as beneath notice, but occasionally subjecting them to withering rebuttal. ... I have often asked them just to tell me, please, exactly why Elaine Morgan must be wrong about the aquatic-ape theory. I haven't yet had a reply worth mentioning, aside from those who admit, with a twinkle in their eyes, that they have often wondered the same thing.
We all love an underdog but this is going too far. The fact that Dennett can't see what's wrong with the aquatic ape speculation suggests that his understanding of evolution and how it works is vastly overrated. He then goes on to prove it.
My point in bringing up the aquatic-ape theory is not to defend it against the establishment view, but to use it as an illustration of a deeper worry. Many biologists would like to say, "A pox on both your houses!" Morgan deftly exposes the hand-waving and wishful thinking that have gone into the establishment tale about how—and whyHomeo sapiens developed bipedalism, sweating, and hairlessness on the savanna, not the seashore. Their stories may not be literally as fishy as hers, but some of them are every bit as speculative, and (I venture to say) no better confirmed. What they have going for them, so far as I can see, is that they occupied the high ground in the textbooks before Hardy and Morgan tried to dislodge them. Both sides are indulging in adaptationist Just So Stories and since some story or other must be true, we must not conclude that we have found the story just because we have come up with a story that seems to fit the facts. To the extent that adaptationists have been less than energetic in seeking further confirmation (or the dreaded disconfirmation) of their stories, this is certainly an excess that deserves criticism. [my emphasis in red—LAM]
This is classic adaptationist thinking. It assumes, without evidence, that there must be an adaptationist explanation for every feature. Hairlessness, for example, must be explained by some sort of just-so story involving running on the savanna or wading by the seashore. All the stories seem silly—including the aquatic ape speculation—but since one of the stories must be true we shouldn't reject it just because it makes no sense. There's no room for a non-adaptationist explanation in such a worldview.

Let's see how a pluralist might approach this problem.
For many reasons, ranging from the probable neutrality of much genetic variation to the nonadaptive nature of many evolutionary trends, this strict construction [adaptationism] is breaking down, and themes of unity are receiving renewed attention. ... One old and promising theme emphasizes the correlated effects of changes n the timing of events in embryonic development. A small change in timing, perhaps the result of a minor genetic modification, may have profound effects on a suite of adult characters if the change occurs early in embryology and its effects accumulate thereafter.

The theory of human neoteny, often discussed in my essays (see my disquisition on Mickey Mouse in The Panda's Thumb), is an expression of this theme. It holds that a slowdown in maturation and rates of development has led to the expression in adult humans of many features generally found in embryos or juvenile stages of other primates. Not all these features need be viewed as direct adaptations built by natural selection. Many, like the "embryonic" distribution of body hair on heads, armpits, and pubic regions, or the preservation of an embryonic membrane, the hymen, through puberty, may be nonadaptive consequences of a basic neoteny that is adaptive for other reasons—the value of slow maturation in a learning animal, for example.

                        Stephen Jay Gould in How the Zebra Gets Its Stripes
If you are a Dawkins/Dennett adaptationist then your explanations are confined to the sorts of adaptationist just-so stories promoted by the likes of Elaine Morgan. If you are a pluralist like Gould, you have more choices. Some of the pluralist nonadaptationist explanations might be right. In this case I think Gould is more likely to be right about the evolution of hairlessness. Unfortunately, Dennet and his ilk can't imagine such explanations because it doesn't fit with their idea of how evolution works.

Cleopatra VII (69 BC - 30 BC)

According to some sources, Cleopatra committed suicide on this day in 30 BC [On this day: August 30]. Other sources say it was August 12th and still others claim that it was on the last day in August.

The situation was serious. The armies of Mark Antony and Cleopatra has just deserted to Octavian and Antony had committed suicide. Cleopatra was a prisoner in Alexandria. She had no hope of escaping Octavian.

Legend has it that she died after being bitten by an asp but it wasn't the modern asp, Vipera aspis, since that snake is only found in Europe. It's likely that the Romans used the word "asp" to describe all poisonous snakes. If it's true that Cleopatra used a snake to commit suicide then it was most likely the Egyptian cobra Naja haje that did the deed [Cleopatra’s Asp].

Corba venom contains a number of toxins and enzymes. For the biochemist, it's most famous for the presence of phospholipase A2, an enzyme that cleaves glycerophospholipids, the main components of cell membranes. This leads to disruption and death of cells, especially red blood cells and lymphocytes in the blood stream. A picture of cobra venom phospholipase A2 bound to a lipid molecule (left) can be found in most biochemistry textbooks.

Hyaluronidase is an enzyme found in many snake venoms. It degrades hyaluronic acid, a complex carbohydrate of the sort found in many glycoproteins. Hyaluronic acid is an important component of cartilage where it forms a central strand for attachment of proteoglycan molecules. The breakdown of cartilage lining the blood vessels leads to massive hemorhaging. The combination of phospholipase A2 and hyaluronidase could eventually lead to death but it probably wasn't the immediate cause of death for Cleopatra. As it turns out, there are other things in the cobra venom that are even more lethal.

These other components of cobra venom include various cobra venom factors that interfere with the complement pathway leading to an extreme over-stimulation similar to that seen in septic shock. The venom also includes a number of neurotoxins that gain access to the central nervous system when blood vessels break down. The combination of all these proteins can cause death within minutes of receiving a cobra bite. However, many people survive cobra bites suggesting that the Cleopatra story may not be true.

[The painting is The Death of Cleopatra by Reginald Arthur (d. 1896), 1892 [The Death of Cleopatra.]]

Genetic Discrimination in Denying Health Benefits

Hsien-Hsien Lei of Eye on DNA links to an article in the Los Angeles Times [U.S. military practices genetic discrimination in denying benefits].

The issue concerns a Marine who was discharged without medical benefits because he was found to have a genetic disease—in this case it was Von Hippel-Lindau syndrome.

Apparently the US military doesn't take responsibility for soldiers who develop medical problems as a result of a genetic pre-disposition.
The regulation appears to have stemmed from an effort to protect the armed services from becoming a magnet for people who knew they would come down with costly genetic illnesses, according to Dr. Mark Nunes, who headed the Air Force Genetics Center's DNA diagnostic laboratory at Keesler Air Force Base in Mississippi.
As you might expect, the lawyers got involved and some of these men and women have won some compensation from the US government. But some lost their case and they face bankruptcy.

Only in America.

There's a simple solution to all these disputes about health coverage and your genes. It's called universal health care. Try it. You'll like it. (Unless you're a lawyer.)

[Photo Credit: The photograph shows Dr. Mark Nunes (center) with Jay Platt, a former US Marine Corps drill instructor (left) and Susannah Baruch, senior policy analyst at the Genetics and Public Policy Center (right). The panelists are discussing Genes in Uniform: Don't Test, Don't Tell.]

Ohmygod! These photographs are faked!

Jonathan Wells, the author of one of the stupidest books on Intelligent Design Creationism (Icons of Evolution) has just posted a message on the Discovery Institute website [Exhuming the Peppered Mummy]. Wells says,
The peppered myth died several years ago when scientists discovered that photos of peppered moths on tree trunks - used in most biology textbooks to convince students of Darwinian evolution - had been faked.
In his book he reveals the extraordinary deception that has confused thousands of biology students. The photographs of peppered moths on tree trunks were staged. In some cases dead moths were pinned to the tree trunks and in other cases the moths are alive but they were carefully positioned by scientists.

Can you believe it? Look at the pictures above. I bet you thought that some photographer had set up a camera and waited for years to photograph two moths—one black and one white—to land next to each other in the camera's field. Silly you. You've been fooled. Those moths have been deliberately staged. So much for the Theory of Evolution.

Now, as it turns out there's more to the peppered moth story than this "deception." The real issue is whether the moths spend significant amounts of time on tree trunks. But that's not the point that Wells choose to make in his posting. Instead, he emphasizes the "faked" photographs as though that's the most significant aspect of the peppered moth story. Maybe it is. Maybe Wells and his friends were totally taken in by the photographs in the biology textbooks. I wouldn't be surprised. After all, that's we we call them IDiots.

[Photo Credit: The photographs are from bill.srnr.arizona. The original source is unknown.]

Wednesday, August 29, 2007

Aquatic Ape Speculation

Read all about the speculation concerning our aquatic ancestry in an impressively researched article by laelaps [Scuttling the Aquatic Ape Hypothesis]. This is a typical adaptationist just-so story. Even people who should know better, like Daniel Dennett, have fallen for it.

Animals and Research

There are lots of people who object to the use of animals in medical research. They're usually referring to warm fuzzy animals and not to fruit flies and nematodes, or even fish.

Some of these people write for prominent newspapers like The Guardian in the UK [Ivory tower mentality blamed for 50% rise in animal tests].

Nick Anthis at The Scientific Activist has exposed the myth expressed in the Guardian article [Animal Rights Activists Hijack the Brains of Three Respectable Scientists!]. So has PZ Myers over on Pharyngula [You can't replace animals with petri dishes and computers]. Now Abel Pharmboy at Terra Sigillata has jumped into the fray with a plug for the Foundation for Biomedical Research [Great Animal Research Poster]. I'm copying the poster from their website.

Normally I don't like the kind of rhetoric that's on the poster. I doubt very much that the statement is correct. However, it's an attention grabber and somebody needs to counter the animal activists with a different (gasp!) frame. My life and the lives of everyone in my building are much less comfortable because we have to worry about security on a daily basis. It's not Islamic terrorists that we fear, it's animal rights terrorists. There have been several incidents where property has been destroyed and one bomb has been exploded.

Nobel Laureate: Paul Karrer


The Nobel Prize in Chemistry 1937.

"for his investigations on carotenoids, flavins and vitamins A and B2"

In 1937, Paul Karrer (1889-1971) shared the Nobel Prize in Chemistry with Walter Norman Haworth. Karrer won the award fro his pioneering work on the structure of carotene [Monday's Molecule #40] and vitamin A (retinol).

Professor W. Palmær, Chairman of the Nobel Committee for Chemistry of the Royal Swedish Academy of Sciences, delivered the presentation speech on on December 10, 1937. Only the part addressed to Karrer is quoted below.
The Royal Academy of Sciences has decided also to award to Professor Paul Karrer in Zurich one half of the Nobel Prize in Chemistry this year in recognition of his researches concerning carotenoids and flavins, and the vitamins A and B2.

Thus these two scientists have both worked on another common field of research, the vitamins. As I have already endeavoured to elucidate at some length the importance of making clear the chemical structure of the vitamins, taking vitamin C as an example, I may be somewhat brief regarding the brilliant discoveries made by Professor Karrer.

The carotenoids form a group of yellowish-red colouring matters, widely dispersed within the vegetable kingdom, which have obtained their name from the carrot in which they were first observed. The French name of the carrot is known to be carotte, while Karotte is one of the German names thereof. Carotenoids occur in various other red or yellow parts of vegetables, such as tomatoes, hips, turnips. The examination of these numerous substances was commenced by Karrer ten years ago, and he has succeeded in making clear their chemical structure. The mother substance is in itself a hydrocarbon of very complicated composition, i.e. a chemical compound consisting only of carbon and hydrogen. Its molecule consists of no less than 40 atoms of carbon and 56 of hydrogen. Other carotenoids also contain oxygen, as is the case, for instance, with astacene, which gives the red colour to boiled crayfish and to the "cardinal of the sea", the lobster. The colour of saffron and of paprica is likewise due to carotenoids.

The splendid research concerning the carotenoids, made by Karrer, received its coronation, when it led to the isolation, the production in a pure form and the determination of the chemical structure of vitamin A. This vitamin, which had been known to exist from its biological effects already since 1906 and the synthesis of which in a pure form had been tried in vain in many laboratories all over the world, was successfully isolated by Karrer in 1931 from cod-liver oil, and it was the first of the vitamins of which the chemical structure was clarified. It forms a growth factor, i.e. a substance necessary for the growth of the body. In 1929 von Euler found the same property existing in the carotine itself, and it has been proved since then that this is dependent on the circumstance that carotine, that is the dyestuff of the carrot, is a substance from which the animal body can in itself produce the vitamin A, which has a somewhat less complicated structure. It is also a medicine, as it prevents the serious disease of the eye called "dry eye" or xerophthalmia. Hence vitamin A has received the name of axerophthol.

Some words now regarding Karrer's researches on flavins and on vitamin B2, which were commenced in 1933. Flavins are natural substances of a light yellow colour which often glisten, or fluoresce to the green. One of them is vitamin B2, also called factoflavin, which was discovered by Warburg and Christian in the yellow respiratory ferment, and which has also been disentangled in regard to its chemical structure by Karrer. It constitutes likewise a growth factor, and Karrer's method of producing this compound has led to a technical production of the substance, which is of great biological importance. It contains, besides carbon, hydrogen and oxygen and also nitrogen.

Karrer has thus succeeded in elucidating completely the nature of two of the vitamins, hitherto considered as so mysterious, and one of them is now produced artificially. A characteristic of this scientist is his open eye to the great and important problems as well as to their kernels, and the independent way in which he attacks the problems and pursues his new departures with the aid of his own methods.

There remain many questions to be studied regarding the way in which the vitamins cooperate in such processes of life as cannot be started without their presence.

A vitamin does certainly not produce the effect alone, however. The lactoflavin, for instance, combines, with the aid of phosphoric acid, with an albuminous substance, and only in this way the yellow respiratory ferment is formed. Its molecule contains about 200 times as many atoms as that of the vitamin itself. The yellow ferment is reckoned as belonging to the catalyzers, i.e. substances capable to accelerate a chemical reaction without undergoing any change themselves. Their action may be compared to that of a lubricating oil on a rusty machine. In this case the oxidation of certain substances present in the body is taking place, thus a kind of combustion, although of course much slower than for instance the burning of wood in a stove. We may perhaps compare the very effect of the vitamin to that of a key. A heavy door may thus resist the strongest blows and knocks, but can easily be opened by the aid of a small key - always provided that the right key is found.

The discoveries, which have now engaged our attention, touch upon the domain of Physiology as well as that of Chemistry, a circumstance which has found its expression in that they have been awarded Nobel Prizes in Medicine as well as in Chemistry. Often it is just within the borderland between two sciences, where efforts have been frequently made to establish demarcatory lines (although mostly in vain), that the important discoveries are to be found. In such cases it is evidently of small avail, generally speaking, to try to decide, even with the aid of the greatest acuteness, to which field of science such discovery should be properly attributed. The principal thing is, however, that the discoveries are recognized, if such be their value, and the classification of the prize awarded is a question of minor importance. In the present case it may be said, nevertheless, that the discoveries which have been awarded a prize in Chemistry are on the whole more chemically accentuated in their character than those which have received the prize in Medicine. In all the cases, however, such discoveries may be said to have "conferred the greatest benefit on mankind" in accordance with the intentions expressed in the will of Alfred Nobel....

Professor Karrer. The Royal Swedish Academy of Sciences has decided to confer upon you and Professor Haworth this year's Nobel Prize in Chemistry. In this way the Academy wishes to express to you her recognition for your brilliant investigations on carotenoids and flavins, as well as on vitamins A and B2. As a result of your work, the structure of a vitamin has for the first time been clarified. The structure of a second vitamin has also been cleared up, thus enabling its technical preparation.

I convey to you the congratulations of the Academy and request you to receive the prize from the hands of his Majesty the King.

Vitamin A (retinol)

There are four lipid vitamins: vitamin A, vitamin D, vitamin E, and vitamin K. Each of them contain rings and long aliphatic (—CH2—) side chains. The lipid vitamins are highly hydrophobic, although each possesses at least one polar group. Ingested lipid vitamins are absorbed in the intestine by a process similar to the absorption of other lipid nutrients. After digestion of any proteins that may bind them, they are carried to the cellular interface of the intestine as micelles formed with bile salts. The study of these hydrophobic molecules has presented several technical difficulties, so research on their mechanisms has progressed more slowly than that on their water-soluble counterparts. Lipid vitamins differ widely in their functions.

Vitamin A, or retinol, is a 20-carbon lipid molecule obtained in the diet either directly or indirectly from β-carotene [Monday's Molecule #40]. Carrots and other yellow vegetables are rich in β-carotene, a 40-carbon plant lipid whose enzymatic oxidative cleavage yields vitamin A.

Vitamin A exists in three forms that differ in the oxidation state of the terminal functional group: the stable alcohol retinol, the aldehyde retinal, and retinoic acid. All three compounds have important biological functions. Retinoic acid is a signal compound that binds to receptor proteins inside cells; the ligand–receptor complexes then bind to chromosomes and can regulate gene expression during cell differentiation. The aldehyde retinal is a light sensitive compound with an important role in vision. Retinal is the prosthetic group of the protein rhodopsin; absorption of a photon of light by retinal triggers a neural impulse.

From Horton et al. Principles of Biochemistry, 4th ed. © 2007, Laurence A. Moran and Pearson/Prentice Hall

[Photo Credit: The picture of the carrots is from The Food Network.]

Cows into Whales

UPDATE:The Bad Idea Blog takes issue with Berlinksi's claim that he calculated at least 50,000 changes were required to change a cow into a whale (he stopped counting) [Berlinksi, whales, and why Intelligent Design can’t get no respect]. If Berlinski took ten seconds to write down each of these changes it would take him 5 days, assuming he wrote for 24 hours each day. How's that for a mathematical calculation!
Here's one of the chief IDiots, David Berlinski, expounding on how difficult it must be to change cows into whales. Berlinksi has a Ph.D. in philosophy and has written several books on mathematics. He is a Senior Fellow at the Center for Science & Culture (CSC).

Here's a free clue for the IDiots: cows didn't evolve into whales. Instead whales are the modern descendants of a primitive carnivore that lived over 50 million years ago. See the video at the PBS site for basic information on the evolution of whales—the sort of information that you'd expect anyone to know if they were going to criticize the scientific explanation for the evolution of whales [Whale Evolution]. Berlinski knows some of this history but he's missing the big picture. Berlinksi and most of his fellow fellows at the CSC don't know much about evolution and how it works. It's all a big mystery to them; but then, that's why they are IDiots.

[Hat Tip: The video was posted on the Discovery Institute website by Robert Crowther, who presumably believes that the evolution of cows from whales (sic) is important.]

Tuesday, August 28, 2007

Where Are the Musicians and the Poets?


Over on Tangled Up in Blue there's a posting about Country Joe McDonald and his new anti-war song [1,2,3 What Are We Fighting For?]. Country Joe was at Woodstock 39 years ago. He's an old geezer. So is Neil Young who is just about the only other singer to speak sing out.

The anti-war movement of the 60's was supported by all kinds of artists and some of their songs can still stir up powerful feelings today. Where are today's singers? Why are there no protest songs about the war in Iraq? Why are there no demonstrations in the streets and on the campuses? Where are the young firebrands and their passionate speeches? What's wrong with today's younger generation?

New Seven Wonders of the World


One of my colleagues just got back from Rio de Janeiro where he visited one of the New Seven Wonders of the World. It got me thinking about the others that were recently voted in. It's not a bad list but I think the Eiffel Tower and Stonehenge should have been on the list instead of Christ the Redeemer and the Colosseum.

And what about this? When it's finished it will be one of the most impressive structures that humans have ever made—especially when you consider the location. A somewhat greater challenge than Macchu Picchu, don't you think?

The international space station may turn out to be not very useful but then the Great Wall of China, the Eiffel Tower, and Christ the Redeemer weren't very useful either.

Blog Spam: What's the Point?


There must be some advantage to spammers who litter the comments section with spurious messages. They usually have a name that links to something. For example, today there was a poster named "Viagra" who put several comments on my blog. If you click on "Viagra" it takes you to a webpage ( with a list of Viagra related items.

Can someone explain the point of all this? What advantage to spammers get out of polluting blogs?

I left an example of this spam in the comments of the thread Science Policy Forum: Framing Science.

Monday, August 27, 2007

Monday's Molecule #40


Name this molecule. There's a short common name but it's not sufficient. You have to supply the complete IUPAC name in order to win the prize. There's a direct connection between this Monday's Molecule and Wednesday's Nobel Laureate(s).

The reward goes to the person who correctly identifies the molecule and the Nobel Laureate(s). Previous free lunch winners are ineligible for one month from the time they first collected the prize. There are two ineligible candidates for this Wednesday's reward. Both of them are waiting to collect their prize when September rolls around. The prize is a free lunch at the Faculty Club.

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

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Francis Collin on CBC Radio

CBC Radio recently interviewed Francis Collins. The interview was conducted by Mary Hynes a woman who shows herself to be completely ignorant of atheism [Tapestry: Interview with Francis Collins].

You can listen to the entire interview if you dare but there's nothing new here. For the most part, Collins repeats the same old tired arguments we saw in his book The Language of God [Theistic Evolution According to Francis Collins]. One of the things he says is that when he was an atheist he began to question his lack of belief. All of his questions about God were answered on reading the first few pages of Mere Christianity by C.S. Lewis! I bet you didn't realize how easy it is to become a Christian! Neither did PZ Myers so he posted the first chapter of Mere Christianity on his blog [Get Ready fo Become a Christian]. Atheists beware, read it at your peril. You might fall down on your knees and be converted to Christianity.

Collins believes that one of the strongest arguments for the existence of God is our sense of what's right and wrong. He calls this the Moral Law. Somehow we seem to know the difference between good and evil. Collins also thinks that the concept of altruism is a major stumbling block for atheists. Here's how he puts it in the radio interview.
... because if you pursue the socio-biological explanation of altruism to its ultimate conclusion, and you say that it's really just evolution that is responsible for this sense of right and wrong, you can't get away from what that means, That means that good and evil have no absolute significance at all. They're purely arbitrary. They're evolutionary contrivances. The idea that we have in our head about something being right or wrong is just a complete illusion. And for people who want to adopt that view you have to go all the way there and embrace that. And something about that, in people I talk to, even those who .. consider themselves to be atheists or agnostics, that really troubles them. And it should.
Now many people seem to think that C.S. Lewis and Francis Collins have a very sophisticated view of religion—one that Dawkins fails to grasp when he criticizes religion. But as far as I'm concerned, if this is the best they can do then theists deserve all the criticism they get.

Evolution has given us brains and we have learned how to use them. Over thousands of years we have developed rules of behavior designed to improve our security and well-being and promote an orderly society. Accordingly, it is "bad" to take something that doesn't belong to you and it is "good" to help your neighbor. It is "bad" to lie and it is "good" to tell the truth. In the long run, if everyone does "good" things your society will be better off. Nobody like thieves and liars. They can't be trusted.

"Good" and "bad" are not arbitrary and they are not the direct product of evolution. They have "absolute signficance"—they promote social interactions and humans can achieve much more collectively than they can as individuals. Collins is way off base here. I don't know of any atheists who are troubled by this. I can't imagine who he's talking to.

Denyse O'Leary and the Blogosphere

Denyse certainly got my attention when she announced on her blog that she had some nice things to say about me and some "almost-nice" things about PZ Myers [Podcast: Why I think the blogosphere beats legacy media cold, plus heartfelt regards to Larry Moran and PZ Myers]. Listen to Casey Luskin interviewing Denyse O'Leary and decide for yourselves. The relevant questions come at 12 minutes and 45 seconds into the podcast when she's asked about PZ Myers and me [Blogophile: Denyse O'Leary and the Blogosphere]. If you don't want to follow the link to a podcast where you can skip to the end then listen to the whole thing below.

Click here to get your own player.

The Purpose of Graduate Education

There has been considerable debate about the real purpose of a graduate education. Is it just a way of training students to become university Professors? [Job Propsects for Graduate Students]. Is it true that graduate students are just indentured labour as a recent article in Nature implied?

These are interesting questions. One of the issues that often comes up in these debates is the "pressure" to publish. Supervisors will often try to persuade their graduate students to publish papers. Is this a good thing or a bad thing?

It's a good thing, in spite of what most people believe. Here's how Ryan Gregory sets up the question ...
At the base of this discussion is the assumption that most advisors actually do encourage/pressure their students to publish -- an assumption with which I will not disagree here. What remains open is the interpretation of why this might occur. There are several possibilities:
Read his blog to see why graduate students should publish papers and why this doesn't necessarily mean that the advisor is treating them like slave labor [Why would advisors encourage students to publish?].

[Photo Credit: Graduate students in the Dept. of Biochemistry, University of Toronto.]

Gene Genie #14


The 14th edition of Gene Genie has just been published on Microbiology Bytes [Gene Genie #14: Bugs and Beyond].

Friday, August 24, 2007

Top Five Dead Scientists

Robin Ince lists his top five scientists in the video. It's obviously intended to be a farce since he doesn't mention Charles Darwin. Some bloggers have asked for serious submissions. For example Peter Mc at The Beagle Project Blog wants to know who you would name for the other four spots [Top five dead scientists: list 'em]. So does James Randerson at the Guardian [Top five dead scientists].

So who would I choose besides Charles Darwin at #1? How about Isaac Newton (#2) and Albert Einstein (#3). They seem pretty obvious. I'm tempted to go with Ibn al-Haytham (965-1039) for the #4 position although I don't know as much about him as I should. At #5 I'll pick Thomas Hunt Morgan (1866 - 1945) the first geneticist to win a Nobel Prize and the founder of modern genetics. (And because nobody else has named him yet.)

Honorable mentions to Max Planck, Niels Bohr, Francis Crick and Louis Pasteur. Some of those mentioned by others don't even make the top 100 on my list.

[Hat Tip: Coturnix]

Six Days 'Till the Poll Closes

Get on over to the left-hand margin and vote for your view of evolution. The poll closes at the end of August. When it does, I'll explain the errors of your ways!

Sam Harris Gets It Right (Again)

Sam Harris has a letter in this week's Natrue where he takes the editors to task for their accommodationist approach to the fight between rationalism and superstition [Scientists should unite against threat from religion].

The immediate object of Harris' letter is a recent commentary praising Islam as an "intrinsically rational world view" that is "perfectly in harmony with scientific naturalism." Harris points out the fallacy of such a position then goes on to raise questions about a review of Francis Collin's book The Language of God. According to Harris, the review, entitled "Building Bridges," ...
... represents another instance of high-minded squeamishness in addressing the incompatibility of faith and reason. Nature praises Collins, a devout Christian, for engaging "with people of faith to explore how science — both in its mode of thought and its results — is consistent with their religious beliefs".
I agree with Harris that the Theistic Evolution version of Christianity promoted by Collins is not compatible with reason and science. I agree with Harris that Nature should be ashamed of itself for suggesting otherwise. This is an area where the editors of Nature should either avoid comment or, preferably, defend science.

Harris closes his letter with a nice jab.
There are bridges and there are gangplanks, and it is the business of journals such as Nature to know the difference.

People Living Today Outnumber all Those Who Have Died in the Past

Friday's Urban Legend: DEFINITELY FALSE

This month's issue of Scientific American addresses this popular myth [Fact or Fiction?: Living People Outnumber the Dead].
The human population has swelled so much that people alive today outnumber all those who have ever lived, says a factoid whose roots stretch back to the 1970s. Some versions of this widely circulating rumor claim that 75 percent of all people ever born are currently alive. Yet, despite a quadrupling of the population in the past century, the number of people alive today is still dwarfed by the number of people who have ever lived.
The data is supplied by Carl Haub, an expect on world demographics at the Population Reference Bureau in Washington DC (USA) [How Many People Have Ever Lived on Earth?].

The myth isn't as outlandish as it seems. If you look at the chart above it's not difficult to imagine that the area under the curve from 1950 - 1998 might be close to the area under the rest of the curve. (The start point—Adam & Eve in 5,000 BC is meant as a joke.) Nevertheless, Carl Haub points out that it just doesn't make sense once you start to think about it seriously. But, and this is a serious "but", nobody really knows how many people were alive in the past.
Any such exercise can be only a highly speculative enterprise, to be undertaken with far less seriousness than most demographic inquiries. Nonetheless, it is a somewhat intriguing idea that can be approached on at least a semi-scientific basis.

And semi-scientific it must be, because there are, of course, absolutely no demographic data available for 99 percent of the span of the human stay on Earth. Still, with some speculation concerning prehistoric populations, we can at least approach a guesstimate of this elusive number.
The guesstimate begins with a decision about when to start counting. Haub picks 50,000 BC as a somewhat arbitrary beginning of the human population. As it turns out, the exact start point may not matter very much since the human population was probably small for many tens of thousands of years.

The growth in human population can only be estimated by making guesses about the average life expectancy and birth rate at different points in time. Carl Haub is about as knowledgeable in this field as anyone so we can assume that his guesstimate is as good as it gets. Remember that we are interested in how many people have ever lived and this has to include children who died young as well as adults who lived to be 40 or 50 years old.

There are estimates of the number of people alive in 1AD based on the population of the Roman Empire and China. The consensus is about 300 million (45 million in the Roman Empire). By 1650 the world's population may have been close to 500 million even when you take into account the ravages of the Black Death.

Here's the bottom line. The people alive today represent about 6% of all the people who have ever lived.

The Rings of Uranus Viewed Edge-on

The photograph and caption from SciencDaily says it all [Astronomers Get First Look At Uranus's Rings As They Swing Edge-on To Earth].
This series of images from NASA's Hubble Space Telescope shows how the ring system around the distant planet Uranus appears at ever more oblique (shallower) tilts as viewed from Earth - culminating in the rings being seen edge-on in three observing opportunities in 2007. The best of these events appears in the far right image taken with Hubble's Wide Field Planetary Camera 2 on August 14, 2007. (Credit: NASA, ESA, and M. Showalter (SETI Institute))
As expected, Phil Plait of Bad Astronomy has much more information and lots of spectacular photographs [Yes, yes, rings around Uranus, haha]. Where does he get them?

Do You Support Our Troops?

A. Whitney Brown explains why he supports the brave American troops fighting in Iraq. His talk applies to my support of brave Canadian troops fighting in Afghanistan—or at least it raises the same questions.

[Hat Tip: Canadian Cynic]

Thursday, August 23, 2007

Job Prospects for Graduate Students


This week's issue of Nature has two short articles on the future of science in the USA. The first one refers to Indentured Labour. It talks about the fact that the number of life science researchers in the universities (tenure and tenure-track) has leveled off at about 30,000 while the number of students earning degrees in the life sciences has doubled. The pejorative reference to graduate students as indentured labour is quite unnecessary. It declares a bias and prevents rational discussion.

The second article makes a similar point [More biologists but tenure stays static] about the job prospects of Ph.D. students.

Both Nature articles are based on statistics compiled by the Federation of American Societies for Experimental Biology (FASED). The original study can be found at [Education and Employment of Biological and Medical Scientists: Data from National Surveys]. The Nature articles have stimulated considerable debate on the blogosphere, See PZ's posting and the comments [The most daunting numbers I've seen yet].

Most of the postings have failed to ask the really hard questions so that's what I'm going to do. But first, let's look at the data from the powerpoint presentation on the FASEB site.

The first graph shows the number of Ph.D. graduates in life sciences over the past 40 years. The rate was about 4,000 per year throughout most of the 1980's then jumped up to about 6,000 per year in the late 1990's. Lately there has been a further increase to about 7,000 per year. Much of the increase is due to foreign students.

The second graph shows the increase in positions for researchers with a Ph.D. in life sciences. The number of jobs has almost tripled from 1973 to 2003. Most of the increase has been in industry as a result of the expansion of biotech firms. Most of the fuss is because the number of academic jobs seems to have flattened out at about 60,000. Of these, only 30,000 are tenure or tenure-stream positions. At our university the number of positions in hospital research institutes (non-tenured) has vastly outpaced the number on the campus (tenured) so this isn't a surprise to me.

One of the questions being debated is whether we should continue to graduate far more Ph.D's than the number of academic positions that need to be filled. The answer is yes and here's why.

Assuming (incorrectly) that our primary purpose in graduate education is to train our replacements and assuming (incorrectly) that all graduates want an academic position, we should still graduate more candidates than there are positions because we will want to choose the best candidates for a position and this means that there has to be a larger supply than the demand. How large should this supply be if we were to treat graduate students as a commodity? I don't know, maybe five or ten times the number of jobs?

Now, don't get me wrong. I'm not advocating that we behave this way. I'm simply pointing out to those who do want us to adopt this point of view that there should be many more Ph.D.'s than jobs. That's something that most people don't seem to understand. They seem to think that the number of Ph.D. graduate should approximate the number of jobs available. What this would mean in practice is that the selection for tenure-stream Professors would take place mostly on admission to graduate school and whatever happens afterwards is hardly relevant (i.e., no weeding out). (Some people even think that the candidates for tenure-stream positions are chosen from graduates of their own institutions. Those people are really out of touch.)

Is the "crisis" as serious as most people think? I don't believe it is for several reasons. First, many of the foreign students will return to their native countries. This means that the graduate students who are getting Ph.D.'s in America won't all be looking for jobs in America. Second, many students want to take jobs in industry because they pay better. They won't be competing for academic positions. Third, there's a considerable lag between the expansion of student numbers and the expansions of faculty. Many universities have plans for faculty expansion in the near future. Fourth, the steady-state level of faculty positions disguises the fact that faculty hired in the 1970's expansions are now retiring. Thus, for the short term there will be more new hiring than the graphs indicate.

But behind all this debate and discussion is a more serious issue. Why do students go to graduate school? Is it only because they want to be trained for a future job? Should Professors look upon every graduate student as a job trainee and behave accordingly? I'd like to think that there are still students out there who go to graduate school for the love of science. I did.

The graduate school experience is an end all by itself and not always a means to an end. Sure, it would be nice if things work out and the student gets a nice post-doc and an academic position—if that's what they want—but there's other things to do after graduate school. I've known lots of students who went into teaching, medicine, or law for example. I've known students who choose to be full-time parents even though they did well in graduate school and enjoyed the experience.

I'm very reluctant to fall into the mindset where I view every graduate student as a trainee for a job in industry and academia and not as a young inquisitive scientist. If Professors adopt the former mindset, and some do, then the goal of graduate research is not to answer important scientific questions but to churn out enough papers in respectable journals to ensure you get a good post-doc. The fact that this goal is sometimes compatible with the ambitions of the P.I. (more papers) makes for a deadly combination.

Hugh McLachlan on Cloning Humans

Last week I posted an article on cloning humans. It was a reference to a piece in New Scientist by Hugh McLachlan, a Professor of ethics at Glasgow Caledonian University in Scotland (UK). McLachlan does not oppose the cloning of humans and neither do I.

Here are some other articles on the same topic [Ignore The Boys from Brazil - say Yes to human cloning], [Poor reasons for making human cloning illegal].

McLachlan sent me the following message in response to some of his critics. It addresses some of the issues that have come up in the comments on Sandwalk. He has given me permission to post it.
I think that the risks to the embryos are irrelevant to the issue of whether or not human cloning should be illegal. (Whether public money should be spent on human cloning if it is a very inefficient technique is another matter.) The potential mothers should be informed about the known risks and they must, of course, give their consent. The risk to the mothers is not a justification for making the technique illegal in my view.

Consider an analogy. Imagine that 100 people were trapped, unconscious in a building. They might, for instance, be hostages. A bomb might be primed to explode shortly. If they are not rescued fairly soon they will die. Suppose that the only way they could be rescued is if they were snatched by SAS. The snatch might kill them all. It might result in some being injured, impaired and disabled. It might even result in some living a life that was not worth living. However, there is a chance that one or more might survive to live a normal life. Should we take the chance and snatch them? If we are thinking only about the interests of those 100 people, we must do it even if the chances are remote that any will be saved.

To say that it should be illegal to make the snatch because of the risk to the hostages would be absurd. It is similarly absurd to say that, because of the risks to the embryos involved, human cloning should be illegal.

There is a risk to the soldiers. However, since people volunteer to be soldiers and might even volunteer for particular dangerous missions it is generally judged acceptable that soldiers are exposed to such risks. I can see no reason why we should not allow potential mothers to accept the risks of delivering clones if that is what they want to do.

The objection about the risks to the embryos/clones involved looks at the issue of risk and uncertainly the wrong way round. Suppose that some technique or other were devised to reduce the suffering of those people who had some particular relatively minor ailment. The question of the risk of the technique to these potential patients might be relevant particularly if we assume that to live with the ailment is still pleasant and worthwhile even if not as pleasant and worthwhile as life without the ailment. Suppose that, with the technique, the likelihood is that X% of the patients will be cured completely of the ailment, Y% will end up with a worse case of the condition and that Z% will die in the course of treatment.

In a situation such as this, it is important to know what numbers X, Y and Z stand for to try to judge whether the risk involved in worth taking. Ideally, we would tell the patients and let them decide for themselves. However, human cloning is quite different from this imagined scenario. For the people who might be born as a result of cloning - whether, in the event, they actually are born - cloning is their only chance of birth and life. In the absence of cloning, they will not be born. Hence, cloning is not a risk for them but an opportunity - their only opportunity. To make cloning illegal in their interests on the grounds that, in the course of the technique, not all implanted embryos will become healthy mature human bodies is absurd.

Fool me once .... shame on you ...

See Can You Hear the Drums Beating?, Bush Flubs the Message and A Prelude to War.
There's an old saying in Tennessee — I know it's in Texas, probably in Tennessee — that says, fool me once, shame on — shame on you. Fool me — you can't get fooled again.
                                                   George W. Bush 2002

[Hat Tip: John Lynch]

Rationalism vs. Superstition: The Enemies of Reason (Part 2)

Here's part 2 of Enemies of Reason, Richard Dawkins' attack on superstition. This episode focuses on medical quacks and kooks. It's very entertaining. You'll certainly like the segment on how to increase the number of strands in your DNA!

Read Orac's review at Respectful Insolence. The point to remember is that the battle is between rationalism and superstition and the atheism vs. religion controversy is only a subset of the bigger battle. And evolution vs. creationism is an even smaller subset. You are missing the point when you ask people like Richard Dawkins to align themselves with moderate theists in order to combat the extreme versions of creationism.

Justice, Texas Style

Reuters is reporting that the State of Texas has just executed it's 400th convicted criminal since 1982 [Texas executes 400th person since 1982].

The Governor's office issued a statement in response to criticism of the large number of executions in Texas.
Texans long ago decided that the death penalty is a just and appropriate punishment for the most horrible crimes committed against our citizens.
I suspect this is true. Texans probably do support the death penalty. That's not the point. The point is why are there are so many more executions in Texas compared to other states with the death penalty and why is the USA one of the few "civilized" nations to permit executions of their own citizens?

I don't know the answers to these questions. Does anyone else?