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.

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

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.

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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.]

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 (search2.site.io/index.html) 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'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)bioinfo.med.utoronto.ca) 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.


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

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?].

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[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].

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]