Darwin's Garden

 
In order to walk on the sandwalk you have to pass through Darwin's garden behind Down House. Most visitors take advantage of the opportunity to pass through the greenhouses and the potting shed as well. Darwin was a passionate gardener and he did many experiments with plants. Some of his original varieties are still growing in the garden.

The New York Botanical Garden has mounted an exhibit of Darwin's experiments on plants [What Darwin Saw Out Back]. I'll have to see if Mrs. Sandwalk wants to take a trip to New York to see it with me.

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[Hat Tip: Don Henry]

Ben Stein Meets Charles Darwin

 
Do you remember this image from the Expelled trailer? [Expelled: The Movie] It's a picture of Ben Stein looking at the statue of Charles Darwin in the cafeteria of the Natural History Museum in London (UK).

The group over at the The Beagle Project ran a contest to come up with a funny caption for the photo and the result has just been announced [Caption (absolutely no) contest!]. It's excellent—very close to what I would have said if I had the wit and talent to enter the contest.

A fortnight ago we launched a caption contest for the provocative image below, originally taken from Time's negative review of Expelled. We received twenty-six highly humorous entries, but there was one that towered, marble head and shoulders, above the rest, both for its comic value and also for the amount of work involved in realising it.

I'm not going to give away the answer because you all need to scoot on over to The Beagle Project log and donate some money while you're there.

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Fibrin and Blood Clots

 
The formation of blood clots in mammals is an example of a complex pathway that does not seem to be very well "designed." This hasn't stopped the intelligent design creationists who often use it as an example of irreducible complexity. They conclude that the clotting pathway cannot possibly have evolved.

Last year I posted a bunch of articles on blood clotting because I needed to learn about it myself. Since then I've kept an eye on the literature but I've been too lazy to write up all the new information that comes out on a regular basis. Fortunately, André Brown has come to the rescue. He published a paper on the elastic properties of fibrinogen last year (Brown et al. 2007) and now he reviews a recent paper by his collaborator, John Weisel, that has just come out in Science. André's blog is Biocurious, a blog about biology written by two physics graduate students. The post url is New Perspective on Blood Clot Mechanics.

Theme

Blood Clotting
The image above shows blue strands of fibrin trapping red blood cells (red) and platelets (pink) to form a clot. It is from Yuri Veklich and John W. Weisel, University of Pennsylvania School of Medicine [Building better clots]. The structure of fibrinogen (below) hints at the complexity. Follow the link in the "Theme Box" to learn more.

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Brown, A.E.X., Litvinov, R.I. Discher, D.E. and Weisel, J.W. (2007) Forced Unfolding of Coiled-Coils in Fibrinogen by Single-Molecule AFM. Biophys J. 92: L39–L41. [doi: 10.1529/biophysj.106.101261]

Fun with Polls

 
The Expelled website has a poll asking "Do you think the theory of Intelligent Design should be taught in our education system?"

When PZ Myers discovered it, the "yes" voters were ahead three to one. Now that the Pharyngula readers have voted [Crash this poll], the results are very different. Eat your heat out Ben Stein!!

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Do We Need Genetic Counselors?

 
The blogs promoting genetic testing usually think that we don't need genetic counselors to interpret the results and advise on what to do. For the most part, they seem happy to leave it up to the individual to decide on a course of action if they discover they have a particular genetic trait. I don't agree. I think this is much more complicated and I'm pretty skeptical about the motives of the private, personal genetics, for-profit, companies.

The Sciphu Weblog has an interesting posting on this issue [Now this is why we need genetic counselors]. It's worth reading.

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Top 100 Public Intellectuals

 
The Foreign Policy website has a list of the top 100 public intellectuals from around the world [The Top 100 Public Intellectuals: Bios].

The Canadians are: Malcolm Gladwell, Michael Ignatieff, Steven Pinker, and Charles Taylor. I would have included Irshad Manji, Bob Rae, and Don Cherry.

I included Don Cherry because he would fit right in with David Petraeus who is listed as a top 100 public intellectual.

There are several scientists and people who write about science and religion: Pope Benedict XVI, Noam Chomsky, Richard Dawkins, Daniel Dennett, Jared Diamond, Christopher Hitchens, James Lovelock, Lee Smolin, Harold Varmus, J. Craig Venter, E.O. Wilson. It's interesting that Francis Collins and Ken Miller aren't on the list since the main criterion for inclusion seems to be that the person has written a book and they have Miller & Collins have both written books.

I would have included Richard Lewontin, Bruce Alberts, and David Suzuki. Are there any others who should be on the list? Who should be deleted to make room?

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[Hat Tip: Sean at Cosmic Variance]

Writing with Amino Acids

 
Eva has a picture of a bracelet that spells out "I am starstuff" using the structures of several amino acids and their single-letter identifier. Some of you may be wondering exactly how that phrase is written since there seems to be an unusual letter in there. Check out Etsy Wednesday - I Am Starstuff for the answer.

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Nobel Laureate: Lord Alexander Todd

 

The Nobel Prize in Chemistry 1957.

"for his work on nucleotides and nucleotide co-enzymes"

Lord Alexander Todd (1907 - 1997) was awarded the 1957 Nobel Prize in Chemistry for his work on the the chemical structure of nucleotides and nucleic acids, particularly the phosphate derivatives. Todd is best known for working out the linkage between nucleotides in RNA and DNA but he is also responsible for proving that the sugar moieties are particular ring structures called β-D-ribofuranosides and β-D-deoxyribofuranosides [Monday's Molecule #68]. His lab in Cambridge (UK) synthesized all of the common nucleotides.

The chemical structure of DNA was known by the time Watson & Crick began working on the three-dimensional structure in 1952.

The presentation speech was delivered by Professor A. Fredga, member of the Nobel Committee for Chemistry of the Royal Swedish Academy of Sciences.THEME: Nobel Laureates

Your Majesties, Your Royal Highnesses, Ladies and Gentlemen.

Nucleotides and nucleotide coenzymes are words that may seem strange and abstruse, but these compounds are of great importance to all of us. We have such substances everywhere in our bodies and they regulate many of the processes of life. The term is derived from nucleus, which here refers to cell-kernels or nuclei. The Nobel Prize of this year has nothing to do with atomic nuclei, nuclear fission or hydrogen bombs. Nucleotides are regularly found in the chromosomes of the cell-kernels, where they are connected with the units of heredity, but also in the cell plasma. In combination with proteins they constitute the virus molecules and many coenzymes are nucleotides of low molecular weight but with a special structure. Thus they are a group of substances of very great biological importance, perhaps the most important of all.

The nucleotides have been known for nearly 90 years and they have been frequently studied by both chemists and biologists, but for a long time they were, from the chemist's point of view, an underdeveloped field of research. The difficulties were too great. Gradually it was established that they are built up of three different kinds of "building-stones" of quite different chemical character: phosphoric acid, a sugar, and a heterocyclic base containing nitrogen. I cannot express it more popularly, except to mention that these bases are compounds related to caffeine. Two different sugars are found, ribose and desoxy-ribose, and about half a dozen different bases. The simple building-stones may then be combined in hundreds or thousands to form macromolecules, the nucleic acids.

It is, however, not enough to know the building-stones; we must also know how they are connected to each other. The building-plan, the pattern or whatever you prefer to call it, must be very essential for the behaviour of the macromolecule in chemical and biological processes. The sugars and the heterocyclic bases are both somewhat complicated molecules, which may be connected to each other in several different ways, and finally it must be established how the phosphoric acid is bound. The task is very difficult; the combination of three quite different kinds of building-stones in one macromolecule gives it a very special character and neither the traditional methods of organic chemistry, nor those of inorganic chemistry are directly applicable. It is, however, pre-eminently a task for an organic chemist, and for more than ten years Sir Alexander Todd has held a leading position in this field.

Some idea of the building-plan may be obtained by examining the products formed by partial degradation of the macromolecule into small fragments containing a limited number of building-stones. Conclusive evidence can, however, only be obtained by synthetic methods, by building up possible combinations of sugars and bases - with or without phosphoric acid and comparing them with the degradation products. It is of course imperative to use such methods that the structure of the synthetic products is irrefutable.

The work has been very comprehensive, and many special methods have been evolved, but it is hardly possible to give a non-chemist a clear idea of the brilliant experimental work accomplished. Perhaps I should specially mention the methods for introducing phosphoric acid, the phosphorylation. In recent years, the fundamental role of phosphoric acid in the biochemical processes has become more and more evident, and the new phosphorylation methods - now approximating to those used in the biosynthetic procedures - are also of interest outside the special domain of nucleotide chemistry.

The building-plan of the nucleic acids is now established, at least in its outlines. We have a long chain, where the links are alternately sugar and phosphoric acid, and to each sugar molecule is attached a heterocyclic base as a small pendant. Thus there is an equal number of acid and basic groups. The different building-stones are always connected according to the same pattern and the difference between various nucleic acids must therefore be due to the kinds of bases and their relative arrangement. The number of different types is small - in a certain chain usually only four different bases occur - but in a macromolecule with thousands of appendant base molecules the number of possible combinations must be very great. We are familiar with the coding potentialities of the Morse alphabet, which has only two symbols, dots and dashes.

Through Sir Alexander's work a solid foundation is laid for the future development in this field. Starting from this work, other scientists have advanced very fascinating theories as to the arrangement of the chains; it seems that they may be coiled up as a helix with the bases inside. This model can perhaps explain how a nucleic acid chain can bring about the formation of another similar chain or even of a protein. We are here approaching very fundamental biological questions.

The synthetic methods have also been successfully applied to the preparation of low-molecular nucleotide coenzymes, for instance the cozymase, which plays a part in alcoholic fermentation and other biochemical processes. The ways are now open for synthetic preparation of the different types occurring in nature. It is also possible to synthesize coenzymes with slightly modified structure and study the effect of these modifications on the activity, and hence gain better insight into the mode of action of the enzymes.

Sir Alexander Todd. Some fifteen years ago you started your work in nucleotide chemistry. You saw the great importance of this topic and you did not underrate the difficulties. Today the chemical structure of these compounds is established - in any case in its outlines - and a solid foundation is laid for future work by biochemists and biologists. Results of utmost interest have already been reported and others will follow.

An organic chemist is perhaps most impressed by your studies in phosphorylation. We know today that phosphoric acid is engaged in most biochemical processes, but we know rather little of how it works. Some years ago, you expressed the opinion that the methods used by the living organism owe their air of magic largely to our lack of knowledge of the simple chemistry of the esters of phosphoric acids. You have learned to handle these esters with amazing skill, and I am sure that in due time the air of magic will disperse.

In recognition of your services to chemistry and to natural science as a whole, the Royal Swedish Academy of Sciences has decided to bestow upon you the Nobel Prize for Chemistry for your work on nucleotides and nucleotide coenzymes. To me has been granted the privilege of conveying to you the most hearty congratulations of the Academy, and of inviting you to receive your prize from the hands of His Majesty the King.

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Why Do People Laugh at Creationists?

 
This video asks the question and gives a pretty good answer.

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[Hat Tip: Mike's Weekly Skeptic Rant]

Carl Zimmer at Carleton University

 
Carl Zimmer recently gave the Discovery Lecture at my alma mater, Carleton University in Ottawa (Ontario, Canada).

Carl has been experimenting with posting the video on his blog [Slouching Towards Total Video Immersion]. See his successful attempt at [Slouching Toward Total Video Immersion, the Next Step]. Carl's talk is about new developments in evolutionary biology. I'm pleased to report that Carl's talks are as interesting as his writing.

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Saving Drosophila

 
According to all the normal rules of taxonomy, the name of the species Drosophila melanogaster should be changed to Sophophora melanogaster [Sophophora, the New Model Organism.

As reported by evolgen there is a movement underway to save Drosohila. Here's the actual proposal from the International Commission of Zoologial Nomenclature [Case 3407].

Case 3407

Drosophila Fallén, 1823 (Insecta, Diptera): proposed conservation of usage

Kim van der Linde
Department of Biological Science, Florida State University, Tallahassee, Florida 32306–1100, U.S.A.
(e-mail: kim@kimvdlinde.com)

Gerhard Bächli
Zoological Museum, Winterthurerstraße 190, 8057 Zürich, Switzerland
(e-mail: baechli@zm.uzh.ch)

Masanori J. Toda
Institute of Low Temperature Science, Hokkaido University, N19 W8, Kita-ku, Sapporo 060–0819, Japan

Wen-Xia Zhang
College of Life Sciences, Peking University, Beijing, 100871, China Toru Katoh COE for Neo-Science of Natural History, Hokkaido University, N10 W8,
Kita-ku, Sapporo 060–0810, Japan

Yao-Guang Hu
Institute of Low Temperature Science, Hokkaido University, N19 W8, Kita-ku, Sapporo 060–0819, Japan

Greg S. Spicer
Department of Biology, San Francisco State University, 1600 Holloway Avenue, San Francisco, California 94132–1722, U.S.A.

Abstract. The purpose of this application, under Article 70.2 of the Code, is to conserve the current usage of the widely used name Drosophila Fallén, 1823 (a genus of flies widely used in biological research, particularly in genetics and developmental biology) by the designation of Drosophila melanogaster Meigen, 1830 as the type species of Drosophila. Detailed phylogenetic studies show that the genus Drosophila as currently defined is paraphyletic. Splitting the genus requires that the subgenus Sophophora Sturtevant, 1939 must be ranked as a separate genus. The type species of
Sophophora is by original designation Drosophila melanogaster Meigen, 1830. Ranking Sophophora as a genus and changing the name of Drosophila melanogaster to Sophophora melanogaster would result in major nomenclatural instability due to the breadth and vast number of publications, using this combination. In addition, many refer to ‘Drosophila’ when ‘Drosophila melanogaster’ is actually meant; the two names are used interchangeably. It is therefore proposed that Drosophila melanogaster Meigen, 1830 is designated as the type species of Drosophila.

Keywords. Nomenclature; taxonomy; DROSOPHILIDAE; Drosophila; Sophophora; Drosophila melanogaster; Drosophila funebris; fruit flies.

Join the worldwide protest on April 31st and march to your capital city to save Drosophila!!!!

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Monday's Molecule #68

 
This is an easy one. Your task for today is to identify the molecule shown on the right. Be as specific as possible.

In addition you have to identify the Nobel Laureate who was awarded a Nobel Prize for—among other things—working out the chemical structure of this molecule.

The first person to correctly identify the specific molecule and name the Nobel Laureate wins a free lunch at the Faculty Club. Previous winners are ineligible for one month from the time they first collected the prize. There are two ineligible candidates for this week's reward.

THEME:

Nobel Laureates
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 names the Nobel Laureate(s). Note that I'm not going to repeat Nobel Laureates so you might want to check the list of previous Sandwalk postings.

Correct responses will be posted tomorrow along with the time that the message was received on my server. I may select multiple winners if several people get it right.

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

UPDATE: This was much harder than I expected. The winner is Marc Perry, co-author of the textbook from which the drawing is taken. He recognized it as a strand of DNA—I assume everyone got at least that far. Marc figured out that the Nobel Laureate had to be Sir Alexander Todd. He adds,

This was an excellent quiz because it forced me to learn a relevant fact that I was previously ignorant of. I never recall learning of this individual and his work, but based on the fact that there would be no repeats on the list of Sandwalk Laureates, _and_ on my intimate use of the website for NobelPrize.org (for my course on personalities in science, HMB305--shameless plug here), I was able to use the power of a search engine and the process of elimination to inform my guess.

If you're a student at the University of Toronto take Marc's course next year. You can also take the course that we teach together: HMB210H "Popular Scientific Misconceptions."

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Prince Charles

 
Having watched six episodes of John Adams, I'm thoroughly immersed in anti-monarchy rhetoric. Usually, I defend my Queen as a viable alternative to a system of government that doesn't make a distinction between a head of state and political leader. I like the idea that the head of state is ceremonial and non-political.

However, the presumptive heir to the current monarch leaves a lot to be desired. Now he's gone and published more superstitious nonsense that clearly demonstrates his deficiency in the intelligence category¹ [Prince of Wales's guide to alternative medicine ‘inaccurate’].

The Prince of Wales is being challenged today to withdraw two guides promoting alternative medicine, by scientists who say that they make misleading and inaccurate claims about its benefits.

The documents, published by the Prince and his Foundation for Integrated Health, misrepresent scientific evidence about therapies such as homoeopathy, acupuncture and reflexology, say the authors of a new evaluation of alternative treatments.

In a letter to The Times, Edzard Ernst, Professor of Complementary Medicine at the University of Exeter, and Simon Singh, a science writer and broadcaster, call on the Prince to recall the publications, one of which was produced with a £900,000 grant from the Department of Health.

You know you're in big trouble when a Professor of Complementary Medicine thinks your documents are inaccurate!

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1. Fortunately, his sons seem to have gotten a good dose of intelligence genes from their mother. That's saying a lot.

[Hat Tip: Skepchick]

Overthrowing the Central Dogma

I believe that the Central Dogma of Molecular Biology is widely misunderstood [Basic Concepts: The Central Dogma of Molecular Biology]. It is usually interpreted to mean that information must flow exclusively from DNA to RNA to protein. But he original definition by Francis Crick was ...

... once (sequential) information has passed into protein it cannot get out again (F.H.C. Crick, 1958)

Fig. 1. Information flow and the sequence hypothesis. These diagrams of potential information flow were used by Crick (1958) to illustrate all possible transfers of information (left) and those that are permitted (right). The sequence hypothesis refers to the idea that information encoded in the sequence of nucleotides specifies the sequence of amino acids in the protein.

I think we should retain the original definition.

A biology teacher has been discussing this issue with me and he points out that the term "Central Dogma" is defined by consensus. If the vast majority of scientists define it incorrectly, then that becomes the new definition. I agree, but I'm not yet prepared to concede defeat.

My correspondent made an interesting observation. He noted that the Nobel Prize committee has awarded three Nobel Prizes for, in part, overthrowing the Central Dogma of Molecular Biology. This is very interesting. What's the value of continuing to refer the the "Central Dogma" if it has, indeed, been refuted?

Here are the three examples. The first is from a 1975 press release announcing the Nobel Prizes to Howard Temin, David Baltimore, and Renato Dulbecco [The Nobel Prize in Physiology or Medicine 1975].

Howard Temin was since the end of the 1950ies concerned with studies of tumour viruses which contain the alternative type of genetic material, i.e. RNA. He noticed that certain characteristics of tumour cells arising after infection with this type of virus suggested a possible persistence of virus genetic material in them. It was very difficult however to understand how the genetic information of viruses containing RNA could form a part of the hereditary material of the tumour cells. In order to explain this Temin postulated that the genetic information of an RNA virus capable of giving transformation could be copied into DNA, and that this DNA in a manner similar to that described for a DNA tumour virus could become integrated into the genetic material of cells. This proposal by the overall majority of scientists was considered as heresy since it was in conflict with the central dogma accepted in the field of molecular biology in those days. This dogma implied that information transfer in nature occurred only from DNA to RNA and not in the other direction.

Note that Crick's original paper (see above) allowed for information flow from RNA back to DNA so Temin's work did not overthrow the original concept of theoretical information flow. It did conflict with the incorrect version of the Central Dogma that had been promoted by Jim Watson. It was Temin's work, and the subsequent hype about the Central Dogma, that prompted Crick to publish his 1970 paper.

The second example comes from the press release for 1989 Nobel Prizes to Sydney Altman and Thomas Cech in 1989 [Ribonucleic acid (RNA) - a biomolecule of many functions].

The genetic information in the DNA strand is arranged as a long sentence of three-letter words (e.g. CAG ACT GCC), each corresponding to one of the twenty amino acids which build the proteins. This means that there is a flow of genetic information from the DNA to the proteins, which in turn provide the structural framework of living cells and give them their different functions in the organism. However, this flow of genetic information cannot occur unless the DNA code is transcribed to another code in another type of nucleic acid - RNA (ribonucleic acid). This connection between the nucleic acids (the molecules of heredity) and the proteins (the molecules of structure and function) is what has been called the central dogma of the biosciences.
The genetic information in the DNA molecules determines the composition and function of the proteins. Altman and Cech have now modified this by showing that the RNA molecules not only transmit the genetic information but can also function as biocatalyst.

The third example comes from the press release of the 2006 Nobel Prize to Andrew Fire and Craig Mello for thier work on intrefering RNA [The Nobel Prize in Physiology or Medicine 2006]. In this case, the press release does not claim that Fire and Mello overthrew the Central Dogma but it does give an incorrect version of the Central Dogma of Molecular Biology. This is ironic since, according to the Noble Prize committee, the Central Dogma had been called into question in 1975 and 1989.

The genetic code in DNA determines how proteins are built. The instructions contained in the DNA are copied to mRNA and subsequently used to synthesize proteins (Fig 1). This flow of genetic information from DNA via mRNA to protein has been termed the central dogma of molecular biology by the British Nobel Laureate Francis Crick. Proteins are involved in all processes of life, for instance as enzymes digesting our food, receptors receiving signals in the brain, and as antibodies defending us against bacteria.

It is not true that Francis Crick referred to this process of information flow as the Central Dogma.

Is any of this important? Yes, I think it is. I think there is too much sloppiness in science these days. There are too many instances where sloppy thinking is acceptable. On this particular issue you can't have it both ways. Either the Watson definition of the Central Dogma of Molecular Biology was correct, in which case it has been discredited to such an extent that it's no longer useful. Or, the original Crick version is correct, in which case the work of Temin, Altman, Cech, Fire, and Mello have nothing to do with the Central Dogma.

If a scientist is going to write about the Central Dogma of Molecular Biology then they better be damned sure that they understand it. If they are going to quote the original papers (Crick 1958, 1970) then it might be a very good idea to read them.

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Crick, F.H.C. (1958) On protein synthesis. Symp. Soc. Exp. Biol. XII:138-163

Crick, F. (1970) Central Dogma of Molecular Biology. Nature 227, 561-563. [PDF file]

Discovery Institute Praises Expelled

 
The President of the Discovery Institute, Bruce Chapman, has posted a message extolling the virtues of the movie expelled [Discovery Salutes Expelled].

The producers of Expelled have high hopes as the film opens today.

Practical questions of theater exposures and audience awareness are things that we, as a think tank, cannot assess, of course. But we are cheering the filmmakers on. First signs look positive. The over-the-top attacks of most official reviewers--offended by the film's message, not its quality--may turn out to help in some quarters. These are the exact same reviewers who commonly tell us not to object to offensive Hollywood products, but just to judge a film for its production quality. By now a large share of the population is wise to such hypocritical standards.

So, how is the film doing so far? Not so good. You can read the reviews of Expelled on the "Expelled Exposed" website created and maintained by the National Center for Science Education (NCSE). The reviewers ratings are making this one of the worst films ever.

The people at NCSE have been working hard to debunk all the false claims in Exposed and so far they're doing an excellent job.

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