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Tuesday, March 31, 2009

Advice for Women: What to Do When You Discover He's an Atheist

Friendly Atheist found the answer on YouTube.

Sean Eddy on "Open Education"

I've been thinking a lot lately about how to get my textbook online without asking everyone involved to work for free. It's not an easy problem.

There's a myth out there that some places like MIT are putting up all kinds of useful information for free. The Open Courseware project sounds really exciting until you realize that they can't publish any of the slides they use in their powerpoint presentations because they're all copyrighted. It also doesn't take much perusal to realize that many MIT professors don't know as much about their subjects as you might imagine.

There's a new book advocating the concept of "Open Education" ("Opening Up Education" T. IIyoshi and M.S.V. Kumar eds. MIT Press). The book is reviewed by Sean Eddy on PLoS Biology [Open Revolution].

Sean Eddy used to be an active participant on the newsgroup back when he was a graduate student so I eagerly followed the link to his review. I wasn't disappointed. It's the same Sean Eddy that I knew 12 years ago. He can still recognize bullshit when he sees it.
So, while I like storming the establishment with pitchforks and torches as much as anyone, when I picked up Opening Up Education (or rather, when I downloaded the PDF to my Kindle), I was looking for pragmatism, not utopianism. After 500 pages of “the silos we all know about in higher education are under assault in the new world,” the “hated textbook publishers,” the “epistemological hegemony of higher education,” and the “noble philosophy” of making everything free—“traitors” and “patriots” and “communists,” oh my!—my hopes were beaten down. Many of the 30 essays in this collection are more manifesto than explanation, and many of the 38 authors are writing more for their fellow revolutionary comrades than for us.
Life is never as simple as the Web 2.0 fans make out. Somebody is going to have to do a lot of work before the quality of a website matches what's in the best introductory textbooks. And it's extremely naive to think that all that work is just going to be given away for free.

I'm not just talking about authors. There's a whole team of people involved in publishing my textbooks. This includes editors who correct my spelling and grammar—an onerous task in my case. It includes artists who make the figures and editors who obtain permissions and copyrights for photographs. Then there's the staff at the publishers who receive and mail out manuscripts for review and editing and who handle all the paperwork/electrons associated with a major project.

Are we going to ask all of them to work for free by putting everything on the web? Of course not.

Sean does an excellent job of bursting the bubble.
“Remix,” “collective wisdom,” “Web 2.0”—many of these essays ride a bubble of popular digital punditry enthusiastically but too uncritically. Many technologists today are infected with an idea that “community is king,” that high-quality content will rain down freely merely because we connect digital communities openly. This confuses ways of sharing ideas with ways of creating ideas. It is a kind of magical thinking that has much in common with the cargo cults that cut landing strips in the jungle and carved radios from sticks in hope that more sophisticated beings would parachute technological artifacts down upon them. With all respect to the passionate and pioneering initiatives described in this collection, building landing strips to receive open educational content will not be enough. More attention must be paid to the fact that someone still needs to spend time painstakingly developing artful ways to make difficult concepts understandable—to teach!—and that it will take even more time (thus money) to render these hard-won ideas using multimedia web technology compared with writing textbooks. Success hinges on the adoption of open licensing by the professionals who make digital educational resources, and on finding ways to finance their work.
I have some ideas. I'd like to put my book on the web so that everyone can read it but nobody can download it or print out the figures and text. If you need a printed version you can sign on to the server and print out a chapter for $3. The pages would come with your name and email address printed in the header and footer—or perhaps as a watermark. The idea is to make the material available at minimal cost to an individual user while inhibiting the distribution of photocopies.

No matter how easy it is to read something online, I think there's still a market for a printed version of the material. I know from personal experience that highlighting and scribbling in the margins on my computer monitor doesn't work.

Online textbooks have several advantages such as hyperlinks, frequent revisions and updates, and interactive learning. But we need to find a way to pay for it. If you think the work is going to be given away for free then you are living in a dream world. Check out the MIT Open Courseware site under Biology to see what the cargo cult version of Web 2.0 gets you.

[Photo Credit: Nature]

[Hat Tip: Jonathan Eisen at The Tree of Life]

Religion and Child Abuse

I don't think that religious indoctrination is always an example of child abuse. However, there are other ways that count as clear examples of abuse [Taliban blocks UN polio treatment in Pakistan].
Militants had reportedly agreed to allow the [polio] vaccination program to take place as part of the peace agreements.

However, the militants had reneged on their word and despite assiduous efforts made by the increasingly irrelevant local administration, no vaccinations have taken place.

“It’s a US tool to cut the population of the Muslims. It is against Islam that you take a medicine before the disease”, said, Muslim Khan, Swat’s Taliban spokesman, speaking by telephone.

[Photo Credit: daylife/Reuters: "A man holds his twins as he waits for them to receive polio vaccines in the southern province of Kandahar September 21, 2007. Afghan health officials said on Friday they had brokered a deal with Taliban leaders to allow the immunization of children against polio in rebel-held areas in a rare sign of cooperation between the warring sides."]

[Hat Tip:]

Way too Sensitive?

The techniques for detecting DNA and RNA are extremely sensitive. This sensitivity often leads to misinterpretations because it become difficult to separate signal from noise. The idea that 90% of our genome may be transcribed into functional RNA, for example, may be due to the sensitivity of an assay that can easily detect tiny amounts of accidental transcription.

Similarly, the often proclaimed ubiquity of alternative splicing may be due to the easy detection of splicing mistakes. Other examples of problems with noise might be the presumed abundance of small regulatory RNAs and the frequency of transcription factor binding sites.

The problem is acute when it comes to analyzing DNA from fossils. There, tiny amounts of contamination can really screw things up. That's why John Hawks is also interested in this problem of over-sensitive DNA assays.

Just how sensitive is the technology? Hawks has found a very interesting and informative example [The trouble with contamination]. This example is about contamination but keep in mind that it also applies to the detection of noise in transcription, DNA binding, and splicing.

Here's the original report from the BBC ['DNA bungle' haunts German police]. Over the past few years German police have been on the lookout for a mysterious woman who was linked to several murders. Her DNA was found at over 40 different crime scenes. This woman became one of the most wanted people in Europe but nothing was known about her aside from her DNA.

Finally someone became suspicious and started to look closely at the way they were collecting and analyzing DNA. To make a long story short, the alleged murderer is a factory worker in Bavaria who works in a factory that manufactures cotton swabs. The same swabs that are used to collect samples at a crime scene. Those swabs were contaminated with her DNA.

There's a lesson here. Any technology that can detect the DNA from a factory worker on a cotton swap is quite capable of detecting tiny insignificant amounts of nucleic acids inside a cell.

1,2,3 ... What Are We Fighting for?

President Obama wants to sacrifice more American in Afghanistan and Canada's Prime Minister, Stephen Harper, is suggesting that this might be something that Canada should support. This is in spite of the fact that there are times when he seems to know the right answer to the question; Can We Win in Afghanistan?.

Let's make sure everyone knows what we're fighting for: 'Worse than the Taliban' - new law rolls back rights for Afghan women.
Hamid Karzai has been accused of trying to win votes in Afghanistan's presidential election by backing a law the UN says legalises rape within marriage and bans wives from stepping outside their homes without their husbands' permission.

The Afghan president signed the law earlier this month, despite condemnation by human rights activists and some MPs that it flouts the constitution's equal rights provisions.

The final document has not been published, but the law is believed to contain articles that rule women cannot leave the house without their husbands' permission, that they can only seek work, education or visit the doctor with their husbands' permission, and that they cannot refuse their husband sex.

Glass Knives

One of the best labs I ever took as an undergraduate was an advanced cytology lab where we learned to use the electron microscope.1 Part of the process was preparing thin sectioned material and that involved making our own glass knife that would cut very thin slices from wax-embedded tissue.

Here's a video from Leica showing how it's done today.2

I was reminded of this recently when I had occasion to refer to an electron micrograph taken by Harrison Latta. Latta invented the glass knife back in 1949. You can read about his discovery in this tribute to him on the University of California, Los Angeles, website.

This is one of those simple technological innovations that made a huge difference but would never have been recognized by the Nobel Prize committee.

1. Yes, they had electron microscopes back in those days!
2. You can also buy diamond knives but that's a lot less fun.

Monday, March 30, 2009

YouTube Suspends the Account of the James Randi Education Foundation

If you have a YouTube account, follow these instructions.

To complain to youtube follow this link;

Scroll to the very bottom and click on "new issue"

Select "suspended account" from the options and express your opinion.

The mediafire link is;

UPDATE: I was astonished to learn that some readers don't know who James Randi is or what the James Randi educational foundation is all about.

Randi is a former magician ("The Amazing Randi") from Toronto, Ontario (Canada). He is best known for investigating claims of the paranormal and for his one million dollar challenge. He has appeared on television many times and often writes columns and article debunking paranormal claims.

The goal of the James Randi Educational Foundation is ...
The James Randi Educational Foundation is a not-for-profit organization founded in 1996. Its aim is to promote critical thinking by reaching out to the public and media with reliable information about paranormal and supernatural ideas so widespread in our society today.

The Foundation's goals include:

* Creating a new generation of critical thinkers through lively classroom demonstrations and by reaching out to the next generation in the form of scholarships and awards.
* Demonstrating to the public and the media, through educational seminars, the consequences of accepting paranormal and supernatural claims without questioning.
* Supporting and conducting research into paranormal claims through well-designed experiments utilizing "the scientific method" and by publishing the findings in the JREF official newsletter, Swift, and other periodicals. Also providing reliable information on paranormal and pseudoscientific claims by maintaining a comprehensive library of books, videos, journals, and archival resources open to the public.
* Assisting those who are being attacked as a result of their investigations and criticism of people who make paranormal claims, by maintaining a legal defense fund available to assist these individuals.

To raise public awareness of these issues, the Foundation offers a $1,000,000 prize to any person or persons who can demonstrate any psychic, supernatural or paranormal ability of any kind under mutually agreed upon scientific conditions. This prize money is held in a special account which cannot be accessed for any purpose other than the awarding of the prize.

Located in Fort Lauderdale, Florida, the Foundation is funded through member contributions, grants, sales of books and videos, seminars, and conferences.
The current President of the foundation is Phil Plait of Bad Astronomy.

Monday's Molecule #115

Identify this molecule and explain why it is useful. You must supply the common name and the formal IUPAC name.

I'm looking for the Nobel Laureate whose name is associated with this molecule.

The first person to identify the molecule and the Nobel Laureate wins a free lunch at the Faculty Club. Previous winners are ineligible for one month from the time they first won the prize.

There are seven ineligible candidates for this week's reward: Maria Altshuler of the University of Toronto, David Schuller of Cornell University, Adam Santoro of the University of Toronto, Dima Klenchin from the university of Wisconsin, Alex Ling from the University of Toronto, Bill Chaney of the University of Nebraska, and Elvis Cela from the University of Toronto.

Dima and Bill have donated their free lunch to a deserving undergraduate so I'm going to continue to award an additional free lunch to the first undergraduate student who can accept it. Please indicate in your email message whether you are an undergraduate and whether you can make it for lunch.


Nobel Laureates
Send your guess to Sandwalk (sandwalk (at) 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 Prizes 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 reserve the right to select multiple winners if several people get it right.

Comments will be blocked for 24 hours.

Ethical Framing

The bad news is that Matt Nisbet has published some guidelines for proper framing. You won't be surprised to learn that Richard Dawkins and PZ Myers are engaging in "unethical" framing [The Ethics of Framing Science: Four Guiding Principles]. You will be surprised to learn that fellow framer Chris Mooney is also unethical.

Although Matt doesn't mention it, I assume that scientists like Ken Miller and Francis Collins are "ethical" framers.

The good news is in the comments section of Nisbet's blog. Hardly anyone agrees with him any more. It looks like his 15 minutes of fame are just about over, proving that Andy Warhol knew more about framing than Matt Nisbet.

[Photo Credit: Andy Warhol, DeVorzon Gallery]

God Won't Allow Climate Catastrophe

You'll be pleased to know that global climate change isn't going to end in catastrophe. Rep. John Shimkus from Illinois says as much during a hearing of the U.S. House Subcommittee on Energy and Environment in Washington.

He quotes directly from the Bible concluding, "The Earth will end only when God declares it’s time to be over. Man will not destroy this Earth. This Earth will not be destroyed by a flood."

It's comforting to know that church and state are separated in America and free speech is sacrosanct.

In Canada we just had a major kerfuffle in the press over a science minister who hinted that he might not believe in evolution. I wonder if Rep. John Shimkus is going to get into trouble for not believing in global warming because it conflicts with the Bible?

[Hat Tip: Friendly Atheist]

Scientific Breakthroughs for March 30, 2009

I was reading the list of press releases on ScienceDaily Headlines and I thought you might be interested to learn about some of the most important discoveries in the past 24 hours. For the most part, these are press releases from universities and research institutes.

None of them are real breakthroughs. Some of them are interesting, incremental advances in our understanding of the natural world. Some of them are trivial results that have been elevated to importance by a press release and a headline. Some of them are silly. Some of them are probably wrong.

Free Speech in Oklahoma

The Oklahoma legislature is trying to intimidate the University of Oklahoma for inviting Richard Dawkins to speak last month. The Tulsa World publishes an article today that covers both sides of the controversy. After reading that article, the only logical conclusion is that free speech in Oklahoma is being threatened by elected politicians [Dispute evolves on OU speech by scientist].

This is outrageous. How can you have State Representatives advocating laws that violate the American Constitution and the Bill of Rights? Isn't that treasonous?

Oklahoma is one of those states that still has the death penalty and it still carries out executions. According to US Federal Law, the penalty for treason can be death [Capital punishment in the United States]. That raises an interesting possibility when it comes to dealing with creationists.

[Hat Tip:]

Sunday, March 29, 2009

Don McLeroy, Creationist Dentist

This has already been posted on Panda's Thumb and elsewhere but it deserves to be seen by everyone. It's Don McLeroy, the creationist dentist who is chair of the Texas Board of Education. He has somehow gotten the idea that he knows more about evolution than the experts.

That makes him very dangerous.

Friday, March 27, 2009

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There's a prize for this one!!

Media distortion damages both science and journalism

New Scientist has just published an article on the dangers of bad science journalism. Irony noted.

Simon Baron-Cohen explains how Media distortion damages both science and journalism .
WHEN media reports state that scientist X of Y university has discovered that A is linked to B, we ought to be able to trust them. Sadly, as many researchers know, we can't.

This has three serious consequences. For starters, every time the media misreports science, it chips away at the credibility of both enterprises. Misreporting can also engender panic, as people start to fear the adverse consequences of the supposed new link between A and B. Lastly, there can be a damaging effect on researchers' behaviour. Funding agencies and science institutions rightly encourage scientists to communicate with the media, to keep the public informed about their research and so foster trust. If their work is misrepresented, they may withdraw into the lab rather than risk having to spend hours setting the record straight.

I work in one of those sensitive areas of research, autism, in which the facts are liable to be misreported or - sometimes worse - misinterpreted.

[Photo Credit: Simon Baron-Cohen: by Brian Harris (GNU Free Documentation License).]

Thursday, March 26, 2009

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Carl Zimmer on Science Journalism

Carl Zimmer has written a lengthy blog posting about the troubles with science journalism [Visions of the Crash]. You should read all of it but I want to comment on one small part.
The rise of blogs about science has brought me many pleasures. I’ve particularly liked the astringent criticism of bad science journalism. As soon as a piece is published, scientists who know the lot about the subject can, if necessary, rip a journalist a new one. I personally have been very influenced by Mark Liberman, a linguist at Penn, who has time and again shown how important it is for reporters to pay attention to the statistics in science. What seems at first like stark results–like the difference between the male and female brain–can melt away if you look at the actual data.

But some bloggers go a step further. They claim that these individual cases of journalistic misconduct add up to an indictment of the whole business. Hence, as Moran declares, we can live without science journalists.

It’s odd that many of the people making these pronouncements are scientists themselves–people, in other words, who know that you don’t do science by anecdote. If a blogger sits down in the morning and reads ten stories in a newspaper’s science section and notices that one that makes a howler of a mistake, you know what that blogger will be writing about. Blogs are an outlet for righteous fury. Bloggers are much less likely to write a post that begins, “I read nine articles this morning about science that were fairly accurate and pretty well written.” Ho hum.
I'm not an expert in everything. Most of the science articles I read are explaining things that are way outside my area of expertise. They may be good articles or they may not be. I'm usually skeptical.

However, the majority of articles I read that fall within my areas of expertise—biochemistry, molecular biology, genomes, evolution—do not impress me. It's not just a case of picking out the worst article out of ten to criticize. It's more like every second article has a problem.

When I talk to people in other fields there report the same statistics. It's looks like the average quality of science journalism, even in popular science magazines like SEED, Discovery, New Scientist, and National Georgraphic, leaves a lot to be desired.

I'm not very happy with most scientific papers either.

Darwin's two-for-one deal

Three cheers for Ryan Gregory! He has published an article in todays Globe and Mail explaining why evolution is both a fact and a theory: Darwin's two-for-one deal.

Go to his blog [Evolution Commentary] and congratulate him.

How Does Streptomycin Work?

Streptomycin is a powerful antibiotic that inhibits growth of bacteria while having very little effect on eukaryotes. It blocks protein synthesis by binding to the bacterial ribosome.

Let's review the steps of protein synthesis. The three steps are initiation, where the ribosome and factors are assembled at the start codon on the messenger RNA (mRNA); elongation, where the polypeptide chain elongates as the translation machinery moves along the mRNA; and termination, where the assembly falls apart and the completed polypeptide chain is release.

During the elongation phase there are three sites at the interface between the ribosome and the mRNA where transfer RNAs (tRNAs) can bind. The P site holds the peptidyl-tRNA molecule. The growing polypeptide chain is bound to the tRNA molecule that contributed the last amino acid. The A site binds the incoming aminoacylated tRNA molecule. The anticodon of this aa-tRNA is complementary to the mRNA codon located in the A site. Insertion of the correct aa-tRNA is mediated by elongation factor Tu (in bacteria)..

Formation of the peptide bond then occurs in a reaction catalyzed by peptidyl transferase—an enzymatic activity of the ribosomal RNA in the ribosome. When this happens the growing peptide chain (grey balls) is transferred to the tRNA that was in the A site.

The next step is to shift the ribosome relative to the mRNA bringing the peptidyl-tRNA molecule into position in the P site and freeing up the A site for a new amimoacyl tRNA to bind. This step is called translocation and it is mediated by elongation factor G (EF-G). During the translocation the uncharged tRNA is temporarily moved to the exit site (E site) before being released.

Streptomycin inhibits the translocation step by binding to the small subunit ribosomal RNA and blocking the activity of EF-G.

Here's a picture (below) of what the bacterial ribosome looks like. Most of it is RNA (yellow chain) folded into a complex conformation. The three dimensional structure is stabilized by a number of small proteins (orange + blue) bound to the outer surface of the RNA. One of these proteins is S12, located in the grove where mRNA binds to the ribosome. S12 stabilizes the RNA three-dimensional structure to which streptomycin binds.

Bacteria rapidly develop resistance to streptomycin, which explains why it isn't as effective today as it was when it was first introduced in the 1940s. One of the common resistance mutations affects ribosomal protein S12. The mutant protein is able to maintain the proper RNA conformation in the presence of streptomycin and this allow translocation to proceed.

Thesis Defense - 35th Anniversary

Today is the 35th anniversary of my Ph.D. oral defense. The event took place in the Department of Biochemical Sciences at Princeton University back in 1974.

It began with a departmental seminar. When the seminar was over I retired with my committee to a small classroom for the oral exam.

I don't remember everyone who was on my committee. My Ph.D. supervisor (Bruce Alberts) was there, as was my second reader, Abe Worcel. I know Uli Laemmli was there and so was Arnie Levine. I'm pretty sure the external member of the committee was Nancy Nossal from NIH in Bethesda, MD (USA). It's a bit of a blur after all these years.

I remember being fairly confident about the exam. After five and a half years I was pretty sure that everyone on my committee wanted to get rid of me and the easiest way to do that was to let me pass. Bruce stood to gain $3000 per year of research money and Uli was going to get back the basement of his house where Ms. Sandwalk and I had been living for the past month.

The toughest questions were from Uli Laemmli, which should not come as a surprise to anyone who knows him. He has this annoying habit of expecting people to understand the basic physics and chemistry behind the biochemical sciences. Fortunately, my inability to answer most of his questions didn't deter him from voting to pass me.

This photograph was taken at a party that evening. I look pretty calm at that point but this may have had a lot to do with the various refreshments that were being served.

The amazing thing about the photograph—as I'm sure you all agree—is how little I've changed since then—apart from a haircut.

Back in those days we didn't spend a lot of time writing a thesis. I started in the middle of January and the entire process of writing and defending took nine weeks. My thesis was bound and delivered to the library about one week after the Ph.D. oral.

The second page of my thesis has only three words on it. It says, "To Leslie Jane." This is Ms. Sandwalk. She really should have her name on the cover 'cause I couldn't have graduated without her. Typing my thesis was only one of her many contributions. There are 257 pages in my thesis and she typed every one. As a matter of fact, she typed them twice, one draft and then the final version.

The figures in my thesis were all hand drawn. I've included one (below) to illustrate what I was doing during those five and a half years.

The Alberts lab was interested in DNA replication during bacteriophage T4 infections of E. coli. We knew that replication was carried out by a complex protein machine that assembled at a replication fork but we didn't know all the players or what they did.

The T4 proteins required for DNA replication were known from genetic studies. The most important genes were genes 30 (ligase), 32 (single-stand DNA binding protein), 41, 43 (DNA polymerase), 44, 45, and 62. The products of the unknown genes were called 41P, 44P, 45P and 62P.

We wanted to purify and characterize those proteins; my target was the product of gene 41, or 41P.

We had a cool assay, developed mostly by a postdoc in the lab named Jack Berry. What we did was to prepare a cell lysate from cells that had been infected by bacteriophage carrying an amber mutation in one of the genes. This lysate could not support DNA synthesis, as measured by incorporation of 32P nucleotides, unless we added back the missing component. This is the basis of an in vitro complementation assay that worked for each of the unknown proteins.

In my case, I used traditional protein purification methods to isolate fractions of proteins and them tested them for activity in the complementation assay. The figure below shows the elution profile of proteins bound to a hydroxylapatite column. The peak centered on fraction 61 is the activity of the complementation assay. It indicates that 41P elutes early as a sharp peak in the elution profile.

The complementation assay doesn't tell us anything about the function of 41-protein, only that it complements an extract that's deficient in 41P. Strictly speaking, it doesn't even tell us that the activity is due to the product of gene 41 since it could be something else that complements in vitro.

Fortunately we had another way of identifying 41P. I started my purification with extracts from 17 liters of infected cells. To this I added extracts from cells that had been labeled with radiaoctive amino acids. One batch was from a wild-type infection where all T4 proteins are labeled with 14C amino acids. The other batch is from an infection with an amber mutation in gene 41. In this case every protein except 41P is labeled with 3H amino acids.

You can adjust the settings on a scintillation counter so they distinguish between 14C and 3H but there's some overlap. The equations for calculating the contribution of each isotope in each window are relatively simple. All you need are good standards to get the distribution. One of the most fun things I did as a graduate student was to write a computer program (in Fortran) that did these calculations automatically and plotted them on a plotter. This was back in the time when computers were housed in large separate buildings and required dozens of people to look after them.

If you look of the elution profile in the figure you'll see there's an excess of 14C over 3H in the same fractions where the complementation activity is located. What this means is that the wild-type extract has a protein at that position that's not found in the am41 extract. It's another way of identifying the product of gene 41.

The double label technique was useful 35 years ago but nobody does it anymore. It was fun while it lasted.

(I never did figure out what 41P did during DNA replication but a few years after I left a postdoc identified 41P as a helicase—an enzyme that unwinds DNA ahead of the replication fork. The enzyme is now called gp41 for "gene product.")

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Wednesday, March 25, 2009

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What's the best way to describe a graduate student?

The controversy over the 1952 Nobel Prize reminds me that we haven't had a poll in a long time. Check out the poll in the left-hand sidebar. How would you describe a graduate student?

You must answer by April Fool's Day.

Nobel Laureate: Selman Waksman


The Nobel Prize in Physiology or Medicine 1952

"for his discovery of streptomycin, the first antibiotic effective against tuberculosis"

Selman Abraham Waksman (1888 - 1973) won the Noble Prize in 1952. The award was for discovering streptomycin.

Waksman was a soil microbiologist at Rutgers University in New Jersey (USA). In the 1930s, after the success of penicillin, he decided to change the focus of his research and look for more antibiotics. He reasoned that soil microorganisms should be a good source of novel anti-bacterial drugs.

Streptomycin was the most famous of the many antibiotics discovered in Waksman's lab. It was largely due to the dedicated work of a graduate student, Albert Schatz, who first identified streptomycin's potent effect on gram negative bacteria in October 1943. Over the next few years, Waksman became famous for discovering streptomycin and Schatz was all but forgotten.

In 1950, Schatz sued his former supervisor for recognition, and a share of the royalties. The case was settled out of court with Rutgers agreeing that Schatz and Waksman would be identified as co-discoverers of streptomycin. Schatz received a share of the royalties.

In spite of this settlement, the Nobel Prize committee awarded the prize to Wakesman and not to Waksman and Schatz. This was mildly controversial at the time but didn't qualify as a major scandal. It seems more egregious today.

The issue is part of a continuing controversy about how to attribute recognition when graduate students are working under the direction of their supervisors. There's no better way to start a fight than to bring this up with a group of graduate students. Are they apprentices, slaves, or collaborators?

I am indebted to Philip Johnson of York University (Toronto, Canada) for alerting me to the controversy and for sending along this excellent article about Albert Schatz.

Waksman does not specifically mention Schatz's contribution in his Nobel lecture but he is mentioned in the presentation speech (see below) in an obvious attempt to minimize his contribution. Knowing what we know now, should the Nobel Prize website be modified to include a discussion of the controversy? I think it should.

Nobel Laureates
In 1940 Dr.Waksman and his collaborator had succeeded in isolating the first antibiotic, which was called «actinomycin» and it was very toxic. In 1942 another antibiotic was detected and studied, called «streptothricin». This had a high degree of activity against many bacteria and also against the tubercle bacillus. Further studies revealed that streptothricin was too toxic. During the streptothricin studies Dr. Waksman and his collaborators developed a series of test-methods, which turned out to be very useful in the isolation of streptomycin in 1943.

Encouraged by the discovery of streptothricin and stimulated by the triumphal development of penicillin treatment, the research team headed by Dr.Waksman continued their untiring search for new antibiotic-producing microbes. Before the discovery of streptomycin no less than 10,000 different soil microbes had been studied for their antibiotic activity. Dr. Waksman directed this work and distributed the various lines of research among his young assistants. One of these was Albert Schatz, who had previously worked with Dr. Waksman for 2 months and in June 1943 returned to the laboratory. Dr. Waksman gave him the task of isolating new species of Actinomyces. After a few months he isolated two strains of Actinomyces which were shown to be identical with Streptomyces griseus, discovered by Dr. Waksman in 1915. In contrast to the previous one the rediscovered microbe was shown to have antibiotic activity. To this antibiotic Dr. Waksman gave the name «streptomycin». He studied the antibiotic effect of streptomycin with Schatz and Bugie and found that it was active against several bacteria including the tubercle bacillus. These preliminary studies were completed in a relatively short time, thanks to the clear principles which had been set out previously by Dr. Waksman for the study of streptothricin.

The images of the Nobel Prize medals are registered trademarks of the Nobel Foundation (© The Nobel Foundation). They are used here, with permission, for educational purposes only.

Making Tracks

Look at the photo on the right. Do you know why this is an important discovery? Did you know you could win a case of beer for discoveries like this?

Find the answer on Catalogue of Organisms: More Crunchy Scleritome Goodness. Find out more about the little "problematic" animal in the photo.

Stasis Is Data, says Don McLeroy

Don McLeroy is a creationist dentist from Texas. His claim to fame is that he is the current chair of Texas State Board of Education. That board is trying to insert creationist-friendly standards into the state curriculum.

Today, the Austin American Statesman published an op-ed piece by McLeroy in which he defends creationism: Enlisting in the culture war.

It makes for amusing reading. I want to address one particular issue that illustrates how creationists misunderstand the science they criticize. It vividly points out what we are up against. The opponents of science don't even take the time to understand what they oppose.

Let's start by looking at the chart (right). It illustrates the now-famous pattern of punctuated equilibria as detected in the fossil record. What it shows is that speciation by cladogenesis (splitting) is associated with morphological change. When a new species evolves from a parent species it does so quite rapidly. After the speciation event (horizontal lines on the chart) the two species exist side-by-side in the same environment for millions of years without significant morphological change. Eventually they becomes extinct as shown by the termination of the vertical lines.

Species exist for 5-10 million years. During most of that time they do not change very much. This is what Eldredge and Gould called "stasis." The entire pattern is one of stasis interrupted by short periods of evolution at the time of speciation, or "punctuated equilibria."

The patterns in the fossil record raise interesting questions. One of the most important is whether it represents the normal pattern of evolution or whether it is confined to a minority of clades. What causes stasis? Why is change associated with cladogenesis? Why do species go extinct? All of these are widely discussed in the scientific literature.

None of the questions is a challenge to evolution. Punctuated equilibria is a pattern that might lead to an extension of evolutionary theory.

Now let's look at what McLeroy writes in his op-ed piece.
It is absolutely safe to say that if you meet somebody who claims not to believe in evolution, that person is ignorant, stupid or insane (or wicked, but I’d rather not consider that).

Richard Dawkins
The next step in resolving this controversy is simply to use the scientific method to weigh in on the issue of evolution. Consider the fossil record. What do we actually observe? What are the data?

Stephen Jay Gould stated: "The great majority of species do not show any appreciable evolutionary change at all. [This is called 'stasis.'] These species appear ... without obvious ancestors in the underlying beds, are stable once established and disappear higher up without leaving any descendants."

"...but stasis is data..."

Once we have our observations, we can make a hypothesis. The controversial evolution hypothesis is that all life is descended from a common ancestor by unguided natural processes. How well does this hypothesis explain the data? A new curriculum standard asks Texas students to look into this question. It states: "The student is expected to analyze and evaluate the sufficiency or insufficiency of common ancestry to explain the sudden appearance, stasis, and sequential nature of groups in the fossil record." It should not raise any objections from those who say evolution has no weaknesses; they claim it is unquestionably true.
I don't see a problem with explaining punctuated equilibria to high school students, assuming, of course, that Texas has competent science teachers. It would teach students about critical thinking and reinforce some of the fundamental concepts of evolution.

This isn't what McLeroy has in mind. I think it's very clear what he thinks about punctuated equilibria. He thinks it supports some (unstated) version of creationism. The point of his op-ed piece is to convince his supporters that scientists are trying to hide important evidence for creationism.

I'm assuming that McLeroy simply doesn't understand the science behind punctuated equlibria, or evolution, and that's why he misrepresents it in his article. This means that McLeroy is ignorant, stupid, or insane. There's another possibility but we won't consider that.

Here's something I found on the Wikipedia website for Don McLeroy.
In 2009, McLeroy spoke at a board meeting with several quotes from scientists in an attempt to discredit evolution. The quotes were later revealed by a biology teacher to be incomplete, out of context, or incorrect taken from a creationist website.[10][11] McLeroy said that while "some of the material was taken from the creationist site, he added: “A lot of the quotes I did get on my own.”
You may be wondering if these out-of-context quotations include anything on punctuated equilibria or stasis. It would be embarrassing to find out that McLeroy repeated those misleading quotations only a few weeks after learning that they were wrong. Here's the list: Collapse of a Texas Quote Mine.

Pray for Texas. The decision on education standards will be made any day now.

[Image Credit: Punctuated Equilibrium and Patterns from the Fossil Record]

Old Tools


Tuesday, March 24, 2009

I'm Beginning to Really Like Jerry Coyne

That's because he writes things like Must we always cater to the faithful when teaching science?.
As long as I have been a scientist, I have lived with my colleagues’ view that one cannot promote the acceptance of evolution in this country without catering to the faithful. This comes from the idea that many religious people who would otherwise accept evolution won’t do so if they think it undermines their faith, promoting atheism or immoral behavior. Thus various organizations promoting the teaching of evolution, including the National Academy of Sciences and the National Center for Science Education, have published booklets or websites that explicitly say that faith and science are compatible. In other words, that is their official position. The view of many other scientists that faith and science (or reason) are incompatible is ignored or disparaged. As evidence for the compatibility, the most frequent reason cited is that many scientists are religious and many of the faithful accept evolution. While this proves compatibility in the trivial sense, it doesn’t show, as I’ve pointed out elsewhere, that the two views are philosophically compatible.


Because of this, I think that organizations promoting the teaching of evolution should do that, and do that alone. Leave religion and its compatibility with faith to the theologians. That’s not our job. Our job is to show that evolution is true and creationism and ID aren’t. End of story.
I agree. Organizations like NCSE, AAAS, and the National Academies should just talk about science. As soon as they start to say that science and religion are compatible they are misrepresenting a huge number of scientists and stepping outside their mandates.

Monday's Molecule #114: Winners

UPDATE: The molecule is streptomycin, 5-(2,4-diguanidino-3,5,6-trihydroxy-cyclohexoxy)- 4-[4,5-dihydroxy-6-(hydroxymethyl) -3-methylamino-tetrahydropyran-2-yl] oxy-3-hydroxy-2-methyl-tetrahydrofuran-3-carbaldehyde. Streptomycin inhibits protein synthesis in bacteria. The Nobel Laureate is Selman Waxman.

This week's winners are Bill Chaney of the University of Nebraska and Elvis Cela of the University of Toronto.

Identify this molecule and briefly describe its function. You must supply the common name and one of the the formal IUPAC names.

I'm looking for the Nobel Laureate who discovered this molecule.

The first person to identify the molecule and the Nobel Laureate wins a free lunch at the Faculty Club. Previous winners are ineligible for one month from the time they first won the prize.

There are seven ineligible candidates for this week's reward: Guy Plunket III from the University of Wisconsin, Deb McKay of Toronto, Maria Altshuler of the University of Toronto, David Schuller of Cornell University, Adam Santoro of the University of Toronto, Dima Klenchin from the university of Wisconsin, and Alex Ling from the University of Toronto.

Dima has offered to donate a free lunch to a deserving undergraduate so I'm going to continue to award an additional free lunch to the first undergraduate student who can accept it. Please indicate in your email message whether you are an undergraduate and whether you can make it for lunch.


Nobel Laureates
Send your guess to Sandwalk (sandwalk (at) 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 Prizes 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 reserve the right to select multiple winners if several people get it right.

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

Let the Physicists Fix the Economy.

Chad Orzel at Uncertain Principles has an interesting idea on how to fix the current economic crisis. He thinks all traders and financial wizards should be fired because Physics Can Fix This.
And, seriously, do you really think that these transactions are too complicated for physicists to figure out? We're talking about people who have spent the last several years thinking about folding and twisting strings in eleven dimensions. Unless the transaction records are all encrypted in some private cipher, they'll have no trouble figuring it out. And even if they are encrypted, that will only slow things down a little-- given what we know about the rocket scientists on Wall Street, the cipher key is probably written on a Post-It stuck to the computer. With a magnet.

Better yet, they'll be cheap. We're talking about theoretical physics grad students and post-docs-- most of them are currently working for less than Vikram Pandit spends on shoes. The pre-bonus salary given to a typical financial executive is more money than they can reasonably expect to make in their current line of work. It'll be a major blow to the over-priced restaurant industry in lower Manhattan, but they'll rebound once they learn to mark up Ramen noodles a thousand percent.

And best of all, we don't have to worry about them getting greedy and wrecking the entire global economy in order to make some short-term gains. We're talking about people who, to this point, have completely sacrificed their financial well-being in pursuit of higher mathematical truth. They're used to working toward the long-term success of abstract goods.
Sounds good to me. It can't possibly be any worse.

Medical Care? - Canada Bad, America Great

OldFart is an American doctor who sometimes posts on M.D.O.D.. Here's what (s)he wrote last Friday [Natasha Richardson R.I.P.].
How do you think Natasha Richardson's family likes that socialized medicine in Canada??

Any 3rd year med student or an EMT worth his salt would know she was a set-up for an epidural hematoma. It is an incredibly classic story for it. And so easy to diagnose with an 8 second CT of the brain.

But in Canada I bet she was "put in queue" for a CT scan next week and had to fly to the US in order to get one in a real hospital's ED. But by then she was brain dead.

Still want Hussein's version of medicine here you fuckin' brain dead liberals?? Could save a lot of tax payor's dollars, huh? Everybody could get the "same access" to health care huh?

Just not when it's your family..

My prayers to Ms Richardson's family.
Every civilized country has socialized medicine because they think it's a fundamental right to get medical care without having to worry about how to pay for it. What is it about American doctors that they are so opposed to this concept?

M.D.O.D. is a group blog. Another American doctor, 911doc, has added this update ...


I'm also curious. How easy is it to get a CT scan in the first aid station at the bottom of a ski slope in either country? How often are CT scans performed in the small town local hospitals? In the USA does it matter whether you have insurance or would everyone be given a CT scan after banging their head? Do celebrity actresses get treated differently than single mothers earning $35,000 per year with no health insurance?

And what does Hussein have to do with medical care in Canada?

[Hat Tip: Pure Pedantry]

Old Tools

Eva has posted some photos of old lab equipment and tools [Old Tools]. Check them out to see if you recognize anything.

Here's another contribution. This one is pretty easy but starting tomorrow they're going to get much harder. (Click to embiggen.)

Signals of Positive Selection in Humans?

Signals of recent positive selection in a worldwide sample of human populations is the title of a paper that has just been published in Genome Research (Pickrell et al. 2009).

These workers looked for signs of positive selection using techniques similar to those employed by Hawks et al. in their 2007 paper. That 2007 paper serves as one of the important bits of evidence in the recently published book, The 10,000 Year Explosion.

The idea is to pick out regions of the genome that have linked clusters of polymorphisms (SNPs = single nucleotide polymorphisms). These cluster are called haplotypes and they indicate that a region of the genome has not undergone much recombination in the recent past, because recombination tends to shuffle polymorphisms. One way this linkage could be preserved is when a part of the genome is under positive selection so its increase in frequency is rapid. This is called a selective sweep.

Pickrell et al. (2009) examined a database of 657,143 SNPs called the Human Genome Diversity-CEPH Panel (HGDP). These polymorphisms come from a global sample of 53 populations. The Hawks et al. (2007) paper examined the HapMap database of 3.1 million SNPs from three populations.

Pickrell et al. (2009) also detect a large number of regions that are candidates for positive selection. Their sites overlap those of the earlier study—about half of their sites were also identified by Hawks et al. (2007).

A number of candidates for positive selection are discussed in the paper but the authors note that many of the potential sites are not near any genes that have been well-characterized. It's important to look at individual cases in order to get a feel for the data, especially since the possibility of false positives is a concern.

Specific Examples

Here are a few of the single genes that were identified in one or more groups (e.g. Bantu, Europeans, native American etc.) They are from the top ten strongest signals so they presumably represent some of the best cases for selection.

Heat Shock Transcription Factor 2 (HSF2): This is one of two genes for the major heat shock transcription factor. The heat shock genes are highly conserved and so is their regulation. It's very unlikely that a mutation in the native North American population would be beneficial relative to the allele in all other populations.

succinate-CoA ligase, GDP-forming, β-subunit (SUCLG2) This is the gene for succinyl-CoA synthetase, one of the enzymes of the Krebbs cycle. The data suggest that an allele of this gene was positively selected in the population of Oceania (Pacific Ocean). This doesn't seem very likely.

oxoacyl-ACP synthase, mitochondrial (OXSM) This is the mitochondrial version of a β-ketoacyl synthetase, a standard enzyme required for fatty acid synthesis. An allele shows signs of positive selection in Eurasian populations but not in any other population. It doesn't seem likely that there's an allele conferring a beneficial effect that hasn't already become fixed in mammals over 100 million years ago.

mannosidase, alpha, class 2A, member 1 (MAN2A1) This is a mannosidase located in the Golgi. It's required for one of the last stages in the oligosaccharide maturation pathway—a pathway that's found in all eukaryotes. Pickrell et al. (2009) suggest that an allele of this gene has been selected in the pygmy and Bantu populations. Again, it isn't likely that a standard metabolic gene would be selected in this way.

False Positives?

The patterns of potential selective sweeps strongly suggest local and/or regional sweeps. Since this is the pattern you might expect from random genetic drift, it raises a question about false positives. The authors of the 2009 paper say, ...
Further exploration of the geographic patterns in these data and their implications is warranted, but from the point of view of identifying candidate loci for functional verification, the fact that putatively selected loci often conform to the geographic patterns characteristic of neutral loci is somewhat worrying. This suggests that distinguishing true cases of selection from the tails of the neutral distribution may be more difficult than sometimes assumed, and raises the possibility that many loci identified as being under selection in genome scans of this kind may be false positives. Reports of ubiquitous strong (s = 1-5%) positive selection in the human genome (Hawks et al. 2007) may be considerably overstated. [My emphasis-LAM]
It should come as no surprise that John Hawks disagrees. He has posted a rebuttal on his blog at: Overstating the obvious.

It's an interesting debate but let's not lose sight of the most important point—it is a scientific debate. The case for massive amounts of accelerated human evolution has not been proven in spite of what you might read in The 10,000 Year Explosion and in articles in the popular press.

UPDATE: See Razib's posting: Signals of recent positive selection in a worldwide sample of human populations...maybe

Hawks, J., Wang, E.T., Cochran, G.M., Harpending, H.C., and Moyzis, R.K. (2007) Recent acceleration of human adaptive evolution. Proc. Natl. Acad. Sci. (USA) 104:20753-20758. Epub 2007 [PubMed] [DOI:10.1073/pnas.0707650104]

Pickrell, J.K., Coop, G., Novembre, J., Kudaravalli, S., Li, J.Z., Absher, D., Srinivasan, B.S., Barsh, G.S., Myers, R.M., Feldman, M.W., and Pritchard, J.K. (2009) Signals of recent positive selection in a worldwide sample of human populations. Genome Research 23 published in advance March 23, 2009 [DOI: 10.1101/gr.087577.108]

Monday, March 23, 2009

Old Tools

Eva has posted some photos of old lab equipment and tools [Old Tools]. Check them out to see if you recognize anything.

Here's another contribution. How many readers know what this is and what it was used for in prehistoric times? (Click to embiggen.)

Fox News host apologizes

From the CTV website: Fox News host apologizes in face of Canadian outrage. [See the video at: Here's What Fox News Thinks of Canada's Military.]
The host of a Fox News program has apologized for a segment on the Canadian military that Defence Minister Peter MacKay called "disgusting" and "crass."

A group of pundits on "Red Eye with Greg Gutfeld," which airs weekdays at 3 a.m. on Fox News, each took turns trashing Canada and its military during an episode that aired on March 17.


Gutfeld issued an apology Monday afternoon saying, "I realize that my words may have been misunderstood. It was not my intent to disrespect the brave men, women and families of the Canadian military, and for that I apologize."

But the host also seemed to defend his program, adding "Red Eye is a satirical take on the news, in which all topics are addressed in a lighthearted, humorous and ridiculous manner."
I wonder if they've ever treated 9/11 in a "lighthearted, humorous and ridiculous" manner? What about the USA? Have they ever mocked their own country on this show?

Monday's Molecule #113

Identify this molecule and briefly describe its function. You must supply the common name and one of the the formal IUPAC names.

I'm looking for the Nobel Laureate who discovered this molecule.

The first person to identify the molecule and the Nobel Laureate wins a free lunch at the Faculty Club. Previous winners are ineligible for one month from the time they first won the prize.

There are seven ineligible candidates for this week's reward: Guy Plunket III from the University of Wisconsin, Deb McKay of Toronto, Maria Altshuler of the University of Toronto, David Schuller of Cornell University, Adam Santoro of the University of Toronto, Dima Klenchin from the university of Wisconsin, and Alex Ling from the University of Toronto.

Dima has offered to donate a free lunch to a deserving undergraduate so I'm going to continue to award an additional free lunch to the first undergraduate student who can accept it. Please indicate in your email message whether you are an undergraduate and whether you can make it for lunch.


Nobel Laureates
Send your guess to Sandwalk (sandwalk (at) 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 Prizes 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 reserve the right to select multiple winners if several people get it right.

Comments will be blocked for 24 hours.

Dropping Courses

Chad Orzel of Uncertain Principles has started a discussion about when students should be allowed to drop courses [Academic Poll: Drop It Like It's Hot?].

Why not visit his blog and share your thoughts? I think this is an important issue. Universities may need to make changes.

Astrology in The Toronto Star

I read The Toronto Star every day but I missed this article published last Friday [The vernal equinox: Science and mysticism].

Staff reporter Nick Aveling thought it would be fun to contrast the words of a scientist (Astronomer Randy Attwood) and an astrologer (Michael Barwick). The title of the article implies that this might be an attempt at humor but I'm not sure.
What are the implications of today's equinox?

Attwood: As the earth goes around the sun it appears that the overhead sun seems to be creeping towards the north. For the next three months it will continue to creep north until the first day of summer, when it's at its farthest point north. As the sun gets higher that means it's able to concentrate more heat on the ground.

Barwick: Somebody who's born at 0 degrees Aries – that's a particularly strong Aries person ... William Shatner, Captain Kirk, has kind of the ultimate Aries energy in a way: going forth, boldly going where no one has gone before, pioneering, being in command, leading intuitively. This is Aries.
Phil Plait of Bad Astronomy didn't think it was funny: Canada slips further into goofiness. Neither did any of the people who posted comments on the newspaper's website.

Old Tools

Eva has posted some photos of old lab equipment and tools [Old Tools]. Check them out to see if you recognize anything.

Here's my contribution. How many readers know what this is and what it was used for in prehistoric times? (Click to embiggen.)