Thursday, March 26, 2009
Wednesday, March 25, 2009
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.
THEME:
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?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.
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.
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]
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.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.
....
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.
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.
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 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.
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.Sounds good to me. It can't possibly be any worse.
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.
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??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?
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.
M.D.O.D. is a group blog. Another American doctor, 911doc, has added this update ...
EDITOR'S NOTE: OLDFART POSTED BELOW A FEW HOURS AGO AND SITTING HERE IN BED WITH THE WIFE I LEARNED, IN THAT REPUTABLE MEDICAL JOURNAL 'PEOPLE MAGAZINE', THAT MRS. RICHARDSON HAD INDEED REFUSED TRANSPORT AND MEDICAL CARE AFTER WHAT WAS A MINOR FALL ON A 'BUNNY SLOPE' (ON WHICH SHE WAS NOT WEARING A HELMET).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?
THOUGH I TOO WONDERED IF THE 'QUEUE UP' PROBLEM WAS AT PLAY HERE IT EVIDENTLY WAS NOT, AND SO WHILE WE WILL NO DOUBT HAVE OTHER OPPORTUNITY TO COMPARE THE ACCESS TO EMERGENCY CARE IN SOCIALIZED COUNTRIES TO THE ACCESS TO EMERGENCY CARE HERE, THIS IS NOT THE CASE TO DO IT WITH.
I WILL ASK THIS QUESTION OF ANY CANADIAN PHYSICIANS WHO HAPPEN BY HOWEVER. HOW QUICKLY CAN ONE GET A CT OF THE BRAIN IN A CASE SUCH AS THIS WHERE THERE APPARENTLY WAS NO OBVIOUS TRAUMA AND THE ONLY COMPLAINT ONE HOUR AFTER THE FACT WAS A WORSENING HEADACHE? HOW ABOUT FOR A INTERNATIONAL CELEBRITY?
And what does Hussein have to do with medical care in Canada?
[Hat Tip: Pure Pedantry]
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
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."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?
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."
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