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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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.

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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.

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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.

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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.

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

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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.

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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.

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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.

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

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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.

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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 ...

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).

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?

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?

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[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.)

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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

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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]

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.)

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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?

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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.

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.

Comments will be blocked for 24 hours.

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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.

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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.

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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.)

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Gene Genie #44

 
The 44th edition of Gene Genie has been posted at Mary Meets Dolly [Gene Genie #44].

My first Gene Genie! For my Catholic readers, Gene Genie is the "blog carnival of genes and genetic conditions." (No rubbing of ancient oil lamp necessary.) I hope I shall do it justice.

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
33. Neurophilosophy
34. ScienceRoll
35. Microbiology Bytes
36. Human Genetic Disordrs
37. The Genetic Genealogist
38. ScienceRoll
39. Genetics & Health
40. Human Genetics Disorders
41. ScienceRoll
42. Genetic Future
43. Pharmamotion
44. Mary Meets Dolly

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SEED Reviews The 10,000 Year Explosion

The latest issue of SEED praises US President Obama's emphasis on science and offers a list of ideas "for revising the role of science in America." The number one recommendation is "Make Scientific Literacy a National Priority."

What's needed is better ways of fostering critical thinking and imagination not only in the nation's schools but among its citizenry.

Scientific literacy is not just about being able to weigh in on scientific debates of the day by parsing climate change or understanding the difference between a theory and a guess. The ability to empirically test one's ideas about the world and discard beliefs in light of new evidence is fundamental to the ideals of a just and democratic society; it brings people to the table to debate issues reasonably and with minimum rhetoric.

Good advice, although I wish they'd mentioned the importance of skepticism along with critical thinking. Scientifically literate citizens should not blindly accept every new breakthrough that appears in the scientific literature.

We must rely on good science journalism to inform the general public. Good science journalists will analyze and distill the latest scientific information and help put it in context. They will explain things that are controversial, but exciting, and avoid being swept up by the inevitable rhetoric that accompanies every new discovery.

T.J. Kelleher is a senior editor at SEED. In this same issue, Kelleher reviews The 10,000 Year Explosion a book by Gregory Cochran and Henry Harpending. Let's see whether the review is an example of critical thinking.

This is a trade book, not a scientific publication. The main thesis of the book is that humans are evolving rapidly. This thesis is supported by several lines of evidence.

1. A number of just-so stories from anthropology [see Examples of Accelerated Human Evolution]. Some of them are reasonable, many aren't.
2. A paper published in Dec. 2007 claiming there are thousands of human genes being selected in various populations (Hawks et al. 2007). To the best of my knowledge this analysis has not been independently replicated in the scientific literature and the technology is not without critics.
3. A paper by Hawks et al. (2008) claiming that human adaptive evolution has recently accelerated by acquiring genes from Neanderthals.
4. A claim that within the past 1,000 years the IQ of Ashkanazi Jews has increased relative to the general European population because medieval Ashkanazi Jews engaged in occupations that required high intelligence (Cochran et al. 2006). [See Race and Intelligence, Evolution in the Ashkenazi Jewish Population.]

All this makes for a very interesting book and an idea that's worth serious consideration. It will be interesting to discover, over the next few years, whether there are thousands of genes under positive selection, whether there are only hundreds and the rest are being influenced by random genetic drift, or whether the genetic analysis is subject to artifacts.

Let's see what T.J. Kelleher thinks of all this. Here's the first two paragraphs of the review.

"The 10,000 Year Explosion" would be important even if it were only about population genetics and evolutionary biology, but Gregory Cochran and Henry Harpending, a physicist turned biologist and a biological anthropologist, respectively, at the University of Utah, have written something more. This book is a manifesto for and an example of a new kind of history, a biological history and not just of the prehistoric era. Covering broad ground over human history and prehistory, the authors argue for the singular importance of genes in human history, not just as markers but also as makers.

The first four of the book's seven chapters serve as something of a preamble to the final three. Cochran and Harpending first present the evidence for recent, accelerated human evolution after the invention of agriculture. In its own right that argument is a fairly revolutionary proposition, bit one with clear data, both skeletal and genetic, to back it up: investigations of the human genome undertaken as part of the International Hap Map Project and elsewhere have clearly demonstrated that selection has been ongoing and has accelerated over time. This has been a landmark finding in human biology, and Cochran and Harpending, building on their own work and that of others, including John Hawks of the University of Wisconsin-Madison, convincingly tie the advent of architecture—and the stresses resulting from the new diets. new modes of habitation, new animal neighbors, and new modes of living that agriculture made possible—to this accelerated evolution. It is work destined to launch a thousand careers.[My emphasis-LAM]

Is this an example of critical thinking? Is this the best way to enhance scientific literacy?

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Cochran, G., Hardy, J., and Harpending, H. (2006) Natural history of Ashkenazi intelligence. J. Biosoc. Sci. 38:659-93.

Hawks, J., Cochran, G., Harpending, H.C., and Lahn, B.T. (2008) A genetic legacy from archaic Homo. Trends Genet. 24:19-23. Epub 2007 Dec 3. [PubMed] [DOI: 10.1016/j.tig.2007.10.003 ]

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]

New Scientist Sheds its Last Ounce of Credibility

Many of us were upset last month when New Scientists published some old news about the early tree of life and sensationalized it on their cover [Darwin Was Wrong?]. They claimed that "Darwin Was Wrong" when, in fact, Charles Darwin didn't even know about molecular evolution or the relationships of bacterial species.

The New Scientist editors admitted that the cover was designed to sell magazines and they seemed to be aware of the problem [Explaining the New Scientist Cover].

They even published a critical letter from Daniel Dennett, Richard Dawkins, Jerry Coyne, and PZ Myers [Blunt Talk from Four Evolutionists].

New Scientists has now begun an ad campaign to attract new subscribers and guess which cover they choose? Jerry Coyne and PZ Myers are advocating a scientific (Coyne) or personal (PZ) boycott of New Scientist. I'm conflicted about that. In spite of its recent errors, New Scientist is far superior to SEED and Discover as a science magazine. If we really want to punish the worst of the popular science magazines then SEED is a much better target.¹

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1. The monthly column by PZ Myers in SEED is the exception, not the rule.

Here's What Fox News Thinks of Canada's Military

 
The ignorance in this segment makes me very angry. Can anyone tell me what the US military is protecting Canada from? The Iraqis? Cubans? The people of Granada or Panama? Kosovo? Afghanistan? Lebanon? Maybe the Somalis, or the Vietnamese?

Canada has only been invaded once in its history (1812) and it wasn't by any of those countries.

Does this embarrass any of my American friends, especially those who like to defend the American media?

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[Hat Tip: Canadian Cynic]

What Is This?

 
This is cool (and refreshing). To find out what it is, visit Mentha ×piperita.

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Canada Has Been Saved from George Galloway

 
George Galloway is a Scottish MP who speaks out on behalf of Palestinians and expresses support for Hamas. He was recently invited to Canada to give a speech in Toronto but Canada's Immigration Minister, Jason Kenney, immediately recognized that Canada can't tolerate that. Kenney determined that a member of the British parliament is a threat to our national security and Galloway was banned from entering Canada.

Jennifer Smith is embarrassed by her country's behavior [Jason Kenney's Personal War on Terror]. So am I.

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"Science journalists? Don't make me laugh"

 
"Science journalists? Don't make me laugh" is the title of an article by Ben Goldacre appearing in The Guardian. Goldacre discusses how British health and science journalists covered the recent papers on testing for prostate cancer.

The bottom line is ...

Journalists insist that we need professionals to mediate and explain science. From today's story, their self-belief seems truly laughable.

Note to science journalists; people are beginning to catch on to your scam. Matt Nisbet helped a lot by making it obvious.

I want science journalists to start policing themselves. It's time to take off the blinders and recognize that many science journalists are not very good at accurately reporting about science. The good ones need to speak out instead of issuing motherhood statements about how good they all are.

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Get a Job in Newfoundland

 

Memorial University of Newfoundland
Tenure-track Positions in Gene Expression and Metabolic Biochemistry
The Department of Biochemistry at Memorial University invites applications for two tenure-track positions at the level of Assistant Professor, one in each of the targeted areas listed below. Applicants should have a PhD or equivalent degree with a minimum of two years post-doctoral research experience and should possess a strong research record with significant future promise. The successful applicants will be expected to develop externally funded research programmes with relevance to one of the research foci of the department: 1) Development and health, and 2) Membranes and molecular interactions. They will also be expected to show a commitment to effective teaching at the undergraduate and graduate levels. The new faculty members will be encouraged to collaborate with the faculty in the department and elsewhere in the university.

1) Gene Expression (ref # VPA-BIOC-2008-001). The successful applicant for this position will be expected to develop a research programme focused on some area of gene regulation such as, but not limited to, transcriptional regulation by DNA-protein interactions, chromatin structure/remodeling, or gene expression profiling.

2) Metabolic Biochemistry (ref # VPA-BIOC-2008-002). The successful applicant will be expected to develop a research programme focused on some area of metabolic biochemistry such as, but not limited to, metabolomics, gene-nutrient interactions, or metabolic regulation including signaling pathways.

Applicants should submit a curriculum vitae, a summary of past research, a statement of proposed research and reprints of 3 publications. The application must be accompanied by the names, affiliations and contact information of three referees.

Memorial University is the largest university in Atlantic Canada offering diverse undergraduate, graduate and medical school programmes to almost 18,000 students. As the Province’s only university, Memorial plays an integral role in the educational and cultural life of the Province of Newfoundland and Labrador. The Biochemistry Department consists of 18 faculty with expertise in a wide range of biochemical areas. For information about the Department of Biochemistry please see the departmental webpage. St. John’s is a safe, friendly city with great historic charm, a vibrant cultural life, affordable housing and easy access to a wide range of outdoor activities. For more information about St. John’s please see the municipal website.

Memorial University is committed to employment equity and encourages applications from qualified women and men, visible minorities, aboriginal people and persons with disabilities. All qualified candidates are encouraged to apply; however, Canadian Citizens and Permanent Residents will be given priority. Partners of candidates for positions are invited to include their resumes for possible matching with other job opportunities.

Applications should be received by the Department of Biochemistry by May 15, 2009.

Applications should be addressed to: Dr. Martin Mulligan, Head, Department of Biochemistry, Memorial University, St. John’s, NL, Canada, A1B 3X9. Applications may also be submitted electronically to biochead@mun.ca or by fax: (709) 737-2422. Please quote the appropriate job reference number on all correspondence.

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Happy Vernal Equinox!

 
Today at 11:44 UT (= 7:44 AM Eastern Time) the sun appeared to cross the celestial equator in its northward movement. (See Movement of Our Star for the real explanation.)

Most people in the Northern Hemisphere think of this as the first day of Spring. I prefer to think of it as the end of Winter. Springlike days are still a few weeks off in Toronto.

Here's a brief explanation from Wikipedia.

An equinox in astronomy is the moment in time (not a whole day) when the centre of the Sun can be observed to be directly above the Earth's equator, occurring around March 20 and September 23 each year.

More technically, at an equinox, the Sun is at one of two opposite points on the celestial sphere where the celestial equator (i.e., declination 0) and ecliptic intersect. These points of intersection are called equinoctial points—the vernal point and the autumnal point. By extension, the term equinox may be used to denote an equinoctial point.

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[Photo Credit: The photograph shows the position of the sun at various times throughout the year at 12h (UT) over the Temple of Aphaia (490-480 BC), Athens (Anthony AYIOMAMITIS). The image is called the solar analemma. See here for an explanation. The celestial equator is perpendicular to the long axis of the image and half way between the top and bottom. The crossover point of the figure eight depends on your distance from the equator. I'd love to see one taken on the equator or in the southern hemisphere.]

[Image Credit: eSky]

"Science is my job - faith is my rock"

 
"Science is my job - faith is my rock" is the title of an article in today's Globe and Mail. Zosia Bielski is a journalist who writes on a wide range of topics with an emphasis on social issues. She was prompted to write about the conflict between science and religion because of the controversy surrounding Canada's Science Minister, Gary Goodyear.

As usual, there's no mention of the fact that most active scientists are non-religious. The proportion of atheist scientists is much higher than the proportion of atheists in the general public. Apparently this fact has little to do with a conflict between science and religion.

Zosia Bielski takes the standard approach to this issue. She interviews three religious scientists and discovers that they can reconcile their faith and science. What a surprise!

She does not interview anyone who thinks there's a serious conflict between science and religion. If she had written an article about the lack of faith among scientists and had only interviewed atheist scientists, she would have been accused (rightly) of biased journalism. The lack of balance would have been recognized by any competent editor and she would have been told to go out and get statements from religious scientists. It seems like "balance" only works one way.

What's interesting about the article is that she interview Rev. Ambury Stuart, a climatologist who is also a United Church minister. What Stuart has to say about the conflict between science and religion is very interesting.

"I struggled with this all my life. I grew up in the United Church, I always attended. You say, 'Well, can you believe in God if you believe in Newton's laws?' And the short answer is yes, you can, but it takes a while," Mr. Stuart said.

"You have to think through a lot of stuff. It's not simplistic. You try and divide your brain into two bits: One bit you'll use on Sunday and the rest of it you'll use the rest of the week, and it doesn't work. It doesn't have to."

Evolutionary evangelist Michael Dowd's book "Thank God For Evolution" helped Mr. Stuart smooth out his own message at Glebe Road United Church in Toronto. He weaves his scientific passions into his sermons.

"You can look at scripture and say this means a whole lot more than we ever thought it meant before, because it applies to everything," Mr. Stuart said. "The idea that we are related, that we are kin with the rest of life, is essential for Christianity to do anything constructive in the ecological crisis."

This is about as honest as you get. Stuart is telling us that the conflict between religion and science is real and challenging. You have to work really hard at reconciling science and religion. Many religious beliefs don't survive the challenge.

That's an important lesson for people like Gary Goodyear. Any religion that denies evolution is incompatible with science. You have to choose one or the other. You can't be a Young Earth Creationist without being anti-science. If that kind of faith is your "rock" then science can't be your job.

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Nobel Laureate: Willard Libby

 

The Nobel Prize in Chemistry 1960.

"for his method to use carbon-14 for age determination in archaeology, geology, geophysics, and other branches of science"


Willard Frank Libby (1908 - 1980) won the Nobel Prize in Chemistry for using ¹⁴C decay to date organic material. Libby set out to study cosmic rays. He, and others, determined that one of the effects of cosmic ray is to produce carbon-14 atoms from nitrogen-14 atoms in the upper atmosphere.

He determined that the rate of production of carbon-14 and its rate of disintegration (half-life ~5600 years¹) has reached an equilibrium. No matter where you find carbon, in the ocean, the atmosphere, or the biosphere, its radioactivity corresponds to about 14 disintegrations per minute per gram.

Living things incorporate this equilibrium mixture of ¹⁴C and ¹²C. Thus, we, like all other living things, are radioactive and this level of radioactivity can be measured using techniques that Willard Libby developed. When living things die, they stop incorporating carbon and the existing ¹⁴C continues to decay. As time goes on, the level of radioactivity declines with a half-life of ~5600 years. The age of organic material can be determined directly by measuring the remaining radioactivity of extracted carbon.

That's the basis of radiocarbon dating. Libby confirmed the feasibility of the technique by dating Egyptian artifacts, tree rings of known age, and the dead sea scrolls (labeled "Bible" in the figure). The results confirmed that radiocarbon dating works.


The results were published in the late 1940's. Since then, the technology has improved considerably. Today, scientists measure ¹⁴C directly using mass spectrometry so they don't have to wait for it to decay. Detailed calibration curves have been worked out to take account of the fact that cosmic ray intensity has varied somewhat over the past few thousand years.

With current technology, reliable dates back as far as 60,000 years can be obtained. This is about the limit of radiocarbon dating because the half-life of Carbon-14 is so short compared to more long-lived isotopes.

The presentation speech highlights the importance of radiocarbon dating in a number of disciplines.
THEME:
Nobel Laureates

Libby's dating method soon attracted attention from the scientific world, and it was not long before carbon-14 laboratories were set up in many countries. Today, some forty institutions carry on investigations in this field, nearly half of them in America. Also here, in Sweden, we have such institutions, and their investigations have given results of great value. All age determinations - nowadays several thousand every year - are published in a general review, and thus made rapidly available throughout the world. The literature in this field has grown from year to year, and at present covers an impressive area.

One of the scientists who suggested Libby as a candidate for the Nobel Prize has characterized his work in the following way: "Seldom has a single discovery in chemistry had such an impact on the thinking in so many fields of human endeavour. Seldom has a single discovery generated such wide public interest".

Professor Libby. The idea you had 13 years ago of trying to determine the age of biological materials by measuring their carbon-14 activity was a brilliant impulse. Thanks to your great experimental skill, acquired during many years devoted to the study of weakly radioactive substances, you have succeeded in developing a method that is indispensible for research work in many fields and in many institutes throughout the world. Archaeologists, geologists, geophysicists, and other scientists are greatly indebted to you for the valuable support you have given them in their work. The Swedish Academy of Sciences desires to join those who offer you grateful thanks for what you have done for the benefit of so many sciences, and has decided to award you this year's Nobel Prize for Chemistry. May I congratulate you on behalf of the Academy, and ask you to receive the prize from the hands of His Majesty the King.

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1. The modern value is 5730±40 years.

[Photo Credit: University of California History Digital Archives, Copyright © 2006 The Regents of the University of California.]

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.

Science Journalism in Decline

 
There's an editorial in Nature this week on science journalism [Filling the Void]. It's not very interesting.

There's an article by Geoff Brumfiel that's much more interesting [Science journalism: Supplanting the old media?]. Since I'm mentioned in that article, and since I can't comment on their site, I thought I'd make a few comments here.

First, I posted a comment on Chris Mooney's blog where I said, "Most of what passes for science journalism is so bad we will be better of without it." What I meant to say was, "Most of what passes for science journalism is so bad we will be better off without it". I just want there to be a correct version that everyone can quote.

The article correctly points to a trend ...

Traditional journalists are increasingly looking to such sites to find story ideas (see 'Rise of the blogs'). At the same time, they rely heavily on the public-relations departments of scientific organizations. As newspapers employ fewer people with science-writing backgrounds, these press offices are employing more. Whether directly or indirectly, scientists and the institutions at which they work are having more influence than ever over what the public reads about their work.

Over the past decade it has been the "professional" science journalists themselves who were the gullible victims of scientific hype and PR. The scientific accuracy of press releases leaves a great deal to be desired. They are, after all, intended to promote the researcher and the institution. They are heavily biased.

It is not a good thing that individual scientists and their institutions are managing the science news. It's a disaster.

The amount of material being made available to the public by scientists and their institutions means that "from the pure standpoint of communicating science to the general public, we're in a kind of golden age", says Robert Lee Hotz, a science journalist for The Wall Street Journal. But that pure standpoint is not, or should not be, all that there is to media coverage of science. Hotz doubts that blogs can fulfil the additional roles of watchdog and critic that the traditional media at their best aim to fulfil. That sort of work seems to be on its way out. "Independent science coverage is not just endangered, it's dying," he says.

I hear this a lot. Science journalists seem to think that they have served as watchdogs and science critics by tempering the hype and propaganda spewed out by institutional PR departments.

I wish it were true. If science journalists really did their job of separating the wheat from the chaff then I would be their biggest cheerleader. Instead, for the most part they have been completely seduced by the lure of scientific breakthroughs and revolutions promoted by self-serving scientists and their institutions. There are notable exceptions, but the majority of science journalists have failed at the one job they are supposed to do better than non-science journalists.

That's why we would be better off without them.

Coincidentally, Ryan Gregory has just posted an article about Scitable, "A Collaborative Learning Space for Science" hosted by Nature magazine. I'm pretty sure that Nature is proud of this site. They think the articles are good examples of science writing.

Ryan highlights an article by Leslie Pray, a free-lance science writer. The title is: Transposons, or Jumping Genes: Not Junk DNA?. Read what Ryan Gregory has to say at Scitable Again. He thinks the article is "total nonsense." I agree with him.

If this is an indication of the ability of science journalists to cut to the chase and give us the straight dope, then it's no wonder that scientists are skeptical.

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Regulatin' Genes

 
Some of us old fuddy-duddies have been learning about the regulation of transcription for over forty years. When you've been teaching about regulatory proteins, like HOX proteins, for twenty-five years, the novelty sort of wears off.

It's fun to see the enthusiasm of students who have just recently been "turned on" by gene regulation, especially when one of them is also a Toronto Blue Jays fan! Strange that the university looks a lot more like Stanford than the University of Toronto [HumBio instructor, students rap about science on YouTube].

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Time to Change the Channel

 
My local Liberal candidate is Omar Alghabra, who lost the last election to one of Harper's Conservatives. Omar sent me a link to this video. He though I might get a kick out of it.

I did.

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