Monday's Molecule #73

 
Today's molecule is rather large but it's made up of only two different macromolecules. It has been a favorite molecule of many famous scientists. Several fundamental advances in our understanding of biochemistry and molecular biology have come from studies of this molecules and its components.

You need to identify the molecule and give its correct common name. We don't need the formal IUPAC name in this case, because there isn't one!. Pay attention to the correct common name—you may not be able to guess it just by looking at the molecule but you should be able to deduce it knowing that it is connected to a Nobel Prize.

There's an direct connection between today's molecule and a Nobel Prize. The prize was awarded for purifying the molecule and determining its composition. The first person to correctly identify the molecule and name the Nobel Laureate(s) 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 four 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 Laureate(s) so you might want to check the list of previous Sandwalk postings by clicking on the link in the theme box.

Correct responses will be posted tomorrow. I may select multiple winners if several people get it right.

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

UPDATE: The molecule is tobacco mosaic virus (TMV). The Noble Laureate is Wendell Meredith Stanley (Chemistry 1946). There were quite a few readers who got it right but the first one was John Dennehy of CUNY New York (USA). Congratulations John! He has already declined my offer of lunch on Thursday and taken a rain check to be cashed the next time he's in Toronto.

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A Canadian Biochemist

 
This week's citation classic on The Evilutionary Biologist is really a classic. It's the Journal of Biological Chemistry paper on site-directed mutagenesis from Michael Smith's lab at the University of British Columbia.

Michael Smith, who died in 2000, won the Nobel Prize in 1993 for his work on site-directed mutagenesis.

A couple of weeks ago I pooked fun at John Dennehy's selection of a Richard Dawkins paper for his citation classic series [It Happens to All of Us Eventually]. This week John writes,

Any connection between a recent Sandwalk post, the fact that Smith is Canadian and that this article is biochemical in bent is purely coincidental.

I think we can all appreciate that this is just a coincidence. We expect you to recognize all outstanding Canadian biochemists on the grounds that they are truly excellent scientists and not just because you are pandering to your neighbors up north.¹

I'll assume that the last citation classic was just a temporary moment of insanity.

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1. Although a little pandering never hurt anyone. You never know when you might have to emigrate.

Gene Genie #32

 
The 32nd edition of Gene Genie has been posted at Highlight Health [Gene Genie #32 - Googling the Genie].

Welcome to the 32nd edition of Gene Genie, a blog carnival devoted to genes and genetic conditions. This edition includes some excellent articles on genes and gene-related diseases, genetics, genomics and personalized genetics.

Google Health launched publicly this week and to recognize the event, the last section of the carnival is devoted to articles specifically about the service. Google, financial backer of 23andMe, also funds the Personal Genome Project, which plans to unlock the secrets of common diseases by decoding the DNA of 100,000 people in the world’s biggest gene sequencing project [1]. With the vast number of genetic data points collected for each genome sequenced, a digital system for the movement and storage of personal health information is critical for the widespread use of individualized healthcare. Google’s entrance into the online personal health records market may thus help to accelerate the era of personalized medicine.

With these thoughts in mind, let’s get to to this month’s edition of the Genie.

The beautiful logo was created by Ricardo at My Biotech Life.

The purpose of this carnival is to highlight the genetics of one particular species, Homo sapiens.

Here are all the previous editions .....

1. Scienceroll
2. Sciencesque
3. Genetics and Health
4. Sandwalk
5. Neurophilosophy
6. Scienceroll
7. Gene Sherpa
8. Eye on DNA
9. DNA Direct Talk
10. Genomicron
11. Med Journal Watch
12. My Biotech Life
13. The Genetic Genealogist
14. MicrobiologyBytes
15. Cancer Genetics
16. Neurophilosophy
17. The Gene Sherpa
18. Eye on DNA
19. Scienceroll
20. Bitesize Bio
21. BabyLab
22. Sandwalk
23. Scienceroll
24. biomarker-driven mental health 2.0
25. The Gene Sherpa
26. Sciencebase
27. DNA Direct Talk
28. Greg Laden’s Blog
29. My Biotech Life
30. Gene Expression
31. Adaptive Complexity
32. Highlight Health

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Good Science Writing

 
In case you haven't noticed, there's a debate going on about the quality of science writing. Many scientists—I am one—think that the quality of science journalism is not as good as it could be.

I maintain that the top three criteria for good science writing are: 1) accuracy, 2) accuracy, and 3) accuracy. Everything else is much less important. Scientists tend to score high in accuracy when they write about science, especially if it's their field. (There are many exceptions.)

Professional science journalists tend to score high in other categories such as readability and style. These are very important features of good science writing and no scientist can be considered a good science writer without being a good writer as well as a good scientist.

What about the non-professional who writes a good story that is not scientifically accurate? Can such a person be awarded kudos for good science writing? If the awards are handed out by other journalists, and not by scientists, is accuracy of information going to count for very much?

All these questions come up in a posting on Thomas Levensen's Blog The Inverse Square Blog [More on Richard Dawkins’ Peculiar View of Science Writing]. Levensen is upset about the fact that Dawkins only selected articles by scientists in his recently published anthology The Oxford Book of Modern Science Writing.

Read Levensen's posting to see the point of view that I dispute. Note that Levinsen refers to some very popular books by science writers who were not scientists. Some of these books may be popular but they do not score high in the category of scientific accuracy. How would Levensen know this? He's turned on by a good read and not by whether or not the information is correct. Other books by science writers are excellent. They are well written and scientifically accurate. Nobody disputes that. The question we're addressing is the general quality of science writing and not the obvious counter-examples.

As a general rule, do you think that science journalists are doing a good job of presenting accurate scientific information in their books and articles? Do you think that professional scientists do a better job?

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[Hat Tip: John Wilkins]

Rating Science Blogs

 
I received the following message this morning from Amy Liu of Blogged,com.

Dear Larry Moran,

Our editors recently reviewed your blog and have given it an 8.0 score out of (10) in the Education/Science category of Blogged.com.

This is quite an achievement!

Blogged.com: Science

We evaluated your blog based on the following criteria: Frequency of Updates, Relevance of Content, Site Design, and Writing Style.

After carefully reviewing each of these criteria, your site was given its 8.0 score.

... Please accept my congratulations on a blog well-done!!

Sandwalk ranks 190th out of 822 science blogs. The top blog is Centauri Dreams an astronomy blog with a 9.8 rating. Bad Astronomy ranks 94th with an 8.9 rating.

I only recognized two blogs in the top 20: Science Blog (2nd 9.8), and Cosmic Variance (5th 9.8). In my opinion, Cosmic Variance deserves a high ranking, but so does Bad Astronomy for slightly different reasons. Science Blog is a joke, it just copies press releases.

Pharyngula (36th 9.1), The Genetic Geneologist (38th 9.0) and Aetiology (39th 9.0) make the top 40. Molecule of the Day (42nd 9.0), Discovering biology in a digital world (46th 9.0), Biocurious (47th 9.0), The Evilutionary Biologist (48th 9.0), and Sex, Genes & Evolution (49th 9.0) are in the next 20 top science blogs.

There are other ways of ranking science blogs. For example, they could be ranked by popularity as on Wilko [The Top 100 Science Blogs]. The problem with that ranking is that some of the best science blogs aren't even listed as science blogs (e.g. Bad Astrononmy).

I'm not under any illusions about the rankings of science blogs. They don't count for much in my book and I can't imagine that anyone is going to make a decision based on what Blogged.com reviewers say about a blog. But it does raise an important point. The world wide web is a mess. There's lots of inaccurate information out there and lots of blogs and web sites with hidden agendas that are not obvious. (See OpenCourseWare for one aspect of this bigger problem.)

The question is whether anything can be done about it. Is there any way to provide web users with a reliable way of determining what is accurate scientific information and what isn't? In the case of blogs, I suppose that forming clusters of blogs such as ScienceBlogs^TM or Nature Network is one way.

Both of those groups are run by for-profit science magazines. It seems a shame that we have to rely on the private sector to put their stamp of approval on good science blogs. Besides, that's only going to work if the quality of blogs on such sites is maintained at a high level so that outsiders can trust them as authorities. So far, it seems to work reasonably well although there are a few mistakes now and then (cough, Framing Science, cough).

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Fugu, Pharyngula, and Junk

 
PZ Myers writes about Random Acts of Evolution in the latest issue of Seed magazine. The subtitle says it all.

The idea of humankind as a paragon of design is called into question by the puffer fish genome—the smallest, tidiest vertebrate genome of all.

The genome of the puffer fish (Takifugu rubripes or Fugu rubripes) has about the same number of genes as other vertebrates (20,000) but its genome is only 400 Mb in size [Fugu Genome Project]. This is about 12.5% of the size of mammalian genomes.

THEME

Genomes & Junk DNA

Total Junk so far

    53%
The Fugu Genome Project was initiated by workers who wanted to sequence a vertebrate genome with as little junk DNA as possible in order to determine which sequences are essential in vertebrate genomes. The small size of the fugu genome suggests that more than 80% of our genome is non-essential junk.

Many of you might recall the results of my Junk DNA Poll from last January. In case you've forgotten the results, I'll post them again. The question was: "How much of our genome could be deleted without having any significant effect on our species?" The question was designed to find out whether Sandwalk readers believed in junk DNA or whether they were being persuaded by some scientists to think that most of our genome was essential. (Modern creationists are also promoting the death of junk DNA.) There was some dispute about the interpretation of the question but most readers took it to be a question about the amount of junk DNA.




Astonishingly, almost half of Sandwalk readers think that we need more than half of our genome to survive. This would be a surprise to a puffer fish.

I began a series of postings in order to explain what our genome actually looks like. So far we've determined that about 2.5% is essential and 53% is junk. Now it's time to finish off this particular theme and have another vote.

PZ points out that most of what we call junk DNA is not controversial. It consists of LINEs and SINES, which are (mostly) defective transposons. The pufferfish genome has a lot less of this kind of junk DNA than we do. This accounts for a good deal of the reduction n genome size that we see in modern pufferfish.

PZ also points out that we need to think differently about evolution ...

In the world of genomic housekeeping, the puffer fish is a neatnik who keeps the trash under control, while the rest of us are pack rats hoarding junk DNA.

There's a lot of thought these days going into trying to figure out some adaptive reason for such a sorry state of affairs. None of it is particularly convincing. We'd be better off reconciling ourselves to the notion that much of evolution is random, and that nothing prevents nonfunctional complexity from simply accumulating.

Well said PZ!!¹

Watch for a few more postings on the remaining 45% of our genome then get ready to vote again. I'm hoping for a better result next time!

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1. I used to know someone named Paul Myers who would never had said such a thing on talk.origins. Any relation?

[Image Credit: The junk DNA icon is from the creationist website Evolution News & Views.]

Congratulations Janet Stemwedel

 
Janet Stemwedel has just been promoted to Associate Professor with tenure at San Jose State University [The letter].

Congratulations Janet.


Here's a picture of me congratulating her in advance. Wait 'till she learns what it's really like to be a tenured Professor. She won't be smiling for long!

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Botany Photo of the Day

 
This is green green ixia or Ixia viridiflora. Go to Botany Photo of the Day to find out where it grows.

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A Chip Bus in Ottawa

 
Chip buses in Ottawa and Quebec are almost as common as Tim Horton's. You haven't really tasted poutine until you've bought it at a chip bus.

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OpenCourseWare

 
Eva Amsen has an article in this week's issue of The Bulletin—the newspaper published by the University of Toronto (not a student newspaper). You can read her description of how this article came to be published by checking out her Nature network blog [Teaching course and article on OpenCourseWare]. The article is online at The Bulletin. Scroll to the last page.

The article is about OpenCourseWare in general, and the MIT experiment in particular. MIT, and a few other schools, have made a commitment to put course material on a website and make if freely available to anyone who wants to use it. All one has to do is follow the guidelines of the Creative Commons License. MIT retains the rights to the material even though students and other lecturers are free to use it. MIT strips out all material that is copyrighted by third parties; this includes textbook figures and photographs and images taken from other websites. According to the MIT OpenCourseWare Website, it costs between $10,000 and $15,000 to publish each course. The costs will be twice as high if videos of the lectures are posted online.

Eva's article mentions some of the benefits of OpenCourseWare. Not all of them are believable; for example, one third of freshman students claim to have chosen MIT because they were influenced by OpenCourseWare. This probably doesn't mean what one might think.

Eva is a graduate student in our department so she asks, "Why is the the University of Toronto, one of Canada's leading universities, not part of the OpenCourseWare Consortium?" I'd like to address that question, making particular reference to biochemistry courses.

Let's begin by looking at the OpenCourseWare site for the Department of Biology (MIT doesn't have a Biochemistry Department) [Biology].

The first thing you notice is that most of the material is quite old. Some of the courses are from 2004, only one is 2007, and none are 2008. Let's check out the Spring 2006 course in Introductory Biology to see what OpenCourseWare is really like. Two clicks take you to complete audio lectures. You can listen to the lectures or read a transcript of the lecture. There is no supplemental material to speak of and no figures to see. I don't find this very helpful.

Contrast the MIT website with a typical university website like ours at the University of Toronto. We have more than 2000 course websites but the vast majority are restricted to University of Toronto students [Course Catalog]. If you could access the introductory biology course you would find complete powerpoint lectures with all figures and plenty of additional course material. All of it is up to date.

In some department the course material is not password protected [Dept. of Biochemistry] but it is not advertised and outsiders are not encouraged to visit the site. Complete lecture notes with figures are made available to the students. In my opinion, these notes are much more valuable to students taking our courses than the MIT OpenCourseWare lecture notes because we can post the figures without having to be wary of copyright infringement (especially if access is restricted).

Thus, one of the biggest downsides of OpenCourseWare is that the notes have to be stripped of figures. Why should our department go to great effort and expense to create a parallel site for external viewing when we know full well that the stripped down notes are practically useless? There has to be a compensating gain, right?

Eva argues that the gain is significant.

While the implementation of OpenCourseWare asks for extra work from its faculty in preparing high-quality, legally distributable course materials, this works as an incentive to produce better teaching materials. As a result, making course materials available online can not only raise an institution's visibility but also its quality.

I don't believe this for a minute. The quality of lecture material on the web is highly variable and the fact that it's freely available does not to seem to have much effect on quality. If the argument holds, we would expect the biochemistry lectures at MIT to be outstanding examples of high quality lectures.

Let's check it out. The introductory biology course from 2006 (the latest one on the web) has ten lectures on "foundations." Three of them are on biochemistry. The first one [Biochemistry 1] is all about cancer cells. The material is present at a high school level, at best. The second lecture (Biochemistry 2) is not available on the website. The third one [Biochemistry 3] is on enzymes. Here's how it begins ...

OK. So we’re going to continue with the discussion about biochemistry, and specifically focus on enzymes today. Professor Sive introduced those to you briefly in her last lecture. I’m actually covering for her today. This is one of her lectures but she has given me her material, so hopefully it will go fine. She wanted me to remind you a little bit about energetics, specifically that a negative Delta G in a reaction implies that the reaction can occur spontaneously, that is if the products have lower energy than the reactants. And so given enough time this will happen in that direction.

It's pretty much downhill from then on.

I checked out a lot of lectures on the MIT biology OpenCourseWare site and I don't see much evidence that the faculty has taken the time to prepare high quality lectures. Furthermore, if I had to evaluate the quality of teaching at MIT based on the OpenCourseWare, I don't think it would enhance the reputation of the university.

One of the main arguments for OpenCoureWare has been altruistic. The idea is that a really good university should make its lectures available to the world so that lecturers at "lesser" universities can copy it and use it in their classrooms (an argument that is also condescending). In my experience, the lecturers at smaller schools often give much better lectures in biochemistry than those at the big research intensive universities. If I'm looking for a really good textbook reviewer, for example, I'm much more likely to find one at the University of Maine or the University of Nebraska than at Harvard or Berkeley.

If every school puts up their stripped down versions of lectures, you can be assured that there will be some real gems out there. On the other hand, you can be certain there will be lots of garbage as well. OpenCourseWare may end up being just another way of cluttering up the web with useless information, or worse. If every school participates in the consortium, for example, you would probably find 100 incorrect definitions of a gene, or the Central Dogma, and 100 false conception of free energy at the top of your Goggle search. What's the point of promoting that?

Do you want to learn about enzymes on the web? Here's where you go to get free and accurate information from people who know what teaching is all about [Enzymes] [Enzymes] [Enzymes] .

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Detect Alien DNA

 
Friday's Urban Legend: TRUE!

You can buy this device from TokyoFlash. Here's what it does ...

With the threat of Alien Invasion growing ever closer & the distinct possibility that "they" are already here, it's about time we had a device to detect the humans from the human-oids. The Biohazard wrist scanner probes the immediate vicinity for Alien DNA & displays the results so that you may assess the threat level.

You will have to read the rest of the description on their website but the bottom line is that the alien detection device does exactly what it's advertised to do!

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[Hat Tip: Eye on DNA]

Lester B. Pearson

 
Lester Bowles ("Mike") Pearson (1897-1972) was Prime Minister of Canada from 1963 until 1968. He lead the Liberal Party to two minority victories in the elections of 1963 and 1965.

Pearson won the Nobel Peace Prize in 1957 for his work on forming the United Nations peacekeeping forces following the Suez crisis.

Pearson is responsible for some of the most important legislation passed by Parliament in the 20th century. His government brought in universal health care, and the Canada pension plan. It also adopted the new Canadian flag. Most of these reforms were supported in the House by the New Democratic Party under Tommy Douglas.¹

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1. Tommy Douglas was recently voted the The Greatest Canadian. Lester Pearson is #6 and his Minister of Justice, Pierre Trudeau, is #3.

The Tree of Life

 
From RNA to Humans: A Symposium on Evolution is the title of a meeting held at Rockefeller University on May 1st and 2nd.¹ The entire series of lectures is available online at Evolution.



There are several interesting talks but the one that you need to listen to, in my humble opinion, is the talk by Ford Doolittle on Barking up the Wrong Tree: The Dangers of Reification in Molecular Phylogenetics and Systematics. Ford Doolittle challenges the common belief in The Three Domain Hypothesis and Norm Pace's idea that the term "prokaryote" is no longer useful. (Norm Pace is Carl Woese's bulldog.)

Furthermore, Ford Doolittle challenges the very way we think about phylogeny and the tree of life. If you want to keep on top of the current controversies in the field of molecular evolution then this is an excellent way to begin. Ford allies himself with Stephen Jay Gould and against Richard Dawkins. You may not agree with him but it is extremely important that all evolution supporters become aware of the controversy.

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1. An unfortunate choice of title. Why not "from RNA to E. coli" or, better yet, "from RNA to modern organisms"?

[Hat Tip: Panda's Thumb]

Breaking News: Denyse O'Leary Has a New Blog!

 
Denyse "Buy My Book" O'Leary has started a new blog. That makes four altogether. What's the new one all about? It's about a new book she's going to write on the multiverse [Today at Colliding Universes].

Oh well, look on the bright side. Now she'll be posting the same IDiot article four times so your chances of accidentally missing it are very slim.

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Nobel Laureate: Luis Leloir

 

The Nobel Prize in Chemistry 1970.

"for his discovery of sugar nucleotides and their role in the biosynthesis of carbohydrates"


Luis F. Leloir (1906 - 1987) was awarded the 1970 Nobel Prize in Chemistry for his work on the metabolism of carbohydrates, specifically glycogen [Glycogen Synthesis]. He discovered a key intermediate in that pathway; namely UDP-glucose. His discovery led to the realization that sugar nucleotides play an important role in many different metabolic pathways.

Luis Leloir was an Argentinian. For most of his career he was a faculty member of the University of Buenos Aires. Leloir began his scientific career working with Bernardo Houssay and in 1944 he worked briefly with Carl Cori in St. Louis (USA).

The presentation speech was written by Professor Karl Myrbäck, member of the Nobel Committee for Chemistry of the Royal Swedish Academy of Sciences and delivered by Professor Arne Tiselius.THEME: Nobel Laureates

Your Majesty, Your Royal Highnesses, Ladies and Gentlemen.

The 1970 Nobel Prize for chemistry has been awarded to Dr. Luis Leloir for work of fundamental importance for biochemistry. Dr. Leloir receives the prize for his discovery of the sugar nucleotides and their function in the biosynthesis of carbohydrates.

Carbohydrates, as everybody knows, form a comprehensive group of naturally occurring substances, which include innumerable sugars and sugar derivatives, as well as high-molecular carbohydrates (polysaccharides) like starch and cellulose in plants and glycogen in animals. A polysaccharide molecule is composed of a large number of sugar or sugar-like units.

Carbohydrates are of great importance in biology. The unique reaction, which makes life possible on Earth, namely the assimilation of the green plants, produces sugar, from which originate, not only all carbohydrates but, indirectly, also all other components of living organisms.

The important role of carbohydrates, especially sugars and starch, in human food and, generally, in the metabolism of living organisms, is well known. The biological break-down of carbohydrates (often spoken of as "combustion") supplies the principal part of the energy that every organism needs for various vital processes. It is not surprising, therefore, that the carbohydrates and their metabolism have been the subject of comprehensive and in many respects successful biochemical and medical research for a long time. While working on these problems, Leloir made the discoveries for which he has now been awarded the Nobel Prize.

Before these discoveries were made, our knowledge of carbohydrate biochemistry was rather one-sided. The biological processes which break down carbohydrates, including the so-called combustion, have been well known for several decades. Over the years many Nobel Prizes have been awarded for chemistry and still more for physiology or medicine for discoveries about the reactions and catalysts involved. However, our knowledge about the innumerable corresponding synthetic reactions which occur in all organisms, was fragmentary. We had to resort to doubtful hypotheses; it was usually assumed that the syntheses were a direct reversal of the well-known breakdown reactions. The work of Leloir has indeed revolutionized our thinking about these problems.

In 1949 Leloir published the discovery which became the foundation for a remarkable development. He found that in a certain reaction, which results in the transformation of one sugar to another sugar, the participation of a so far unidentified substance was essential. He isolated the substance and determined its chemical nature. It turned out to be a compound of an unknown type, containing a sugar moiety bound to a nucleotide. Compounds of this type are now called sugar nucleotides. Leloir established that the transformation reaction does not occur in the sugars as such, but in the corresponding sugar nucleotides. To put it simply, one may say, that the linking with the nucleotide occasions an activation of the sugar moiety which makes the reaction possible.

The remarkable aspect of the discovery was not the explanation of a single reaction, but Leloir's quick comprehension that he had found the key which would enable us to unravel an immense number of metabolic reactions. He ingeniously realized that a path had been opened to a field of research containing an accumulation of unsolved problems. In the twenty years that have elapsed since his initial discovery he has carried on his research in this field in an admirable manner.

Other scientists were quick to grasp the fundamental importance of Leloir's discovery; they realized that a vast field was now accessible to worth-while scientific investigation and started research along the path which he had opened. There can be no doubt that few discoveries have made such an impact on biochemical research as those of Leloir. All over the world, his discoveries initiated research work, the volume of which has grown over since. Leloir has been the forerunner and guide throughout; he made all the primary discoveries which determined the path and the objectives of the ensueing research work.

Leloir soon found that besides the sugar nucleotide first isolated, several others of the same type occur in Nature, and many have also been found by other research workers. Today more than one hundred sugar nucleotides which are essential participants in various reactions are known and well characterized. Some of them have an action similar to that of the first isolated, namely in the transformations of simple sugars to other simple sugars or sugar derivatives.

Still more important was Leloir's discovery that other sugar nucleotides have another action which occurs in the biological synthesis of compounds which are composed of or contain simple sugars or sugar derivatives. Leloir showed that all these syntheses are essentially transfer reactions. Sugar moieties from sugar nucleotides are transferred to accepting molecules which thereby increase in size. Probably the most sensational discovery made by Leloir was that the synthesis of the high-molecular polysaccharides also functions in this manner. The first example of the fundamental role of the sugar nucleotides in polysaccharide biosynthesis was found by Leloir in 1959 in the case of glycogen. It became clear that the polysaccharide biosynthesis is not a reversal of the biological breakdown, as had doubtfully been assumed earlier. On the contrary, Nature uses different and quite independent processes for synthesis and breakdown. Later on the same extremely important principle was also shown to be valid with other groups of substances, for instance with proteins and nucleic acids.

Through Leloir's work and the work of others, who were inspired by his discoveries, knowledge of great significance has been gained in wide and important sections of biochemistry, which were previously obscure. It can be readily appreciated that Leloir's work has also had far-reaching consequences in physiology and medicine.

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