Monday's Molecule #117: Winners

 
UPDATE: The molecule is yellow fever virus.

The Nobel Laureate is Max Theiler.

This week's winner is Maria Altshuler of the University of Toronto.

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Today's "molecule" is fairly complex for a "molecule" but not quite as complex as a living cell. You have to identify the particular type of "molecule" that's shown here but it will be too hard to do that without some clues. One of the clues is the connection to a Nobel Laureate. The other one is cleverly hidden in the bottom part of this posting.

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: Dima Klenchin from the university of Wisconsin, Alex Ling from the University of Toronto, Bill Chaney of the University of Nebraska, Elvis Cela from the University of Toronto, Peter Horwich from Dalhousie University, Devin Trudeau from the University of Toronto, and Shumona De of Dalhousie University

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.

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.

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

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Child Abuse and the Anti-Vaccination Movement

 
I was attending the Center for Inquiry 12th World Congress in Washington last weekend and I happened to catch a re-broadcast of a Larry King show on the "dangers" of vaccinating children. It was an appropriate reminder of the lack of rationalism in our society.



Normally I'm fairly tolerant of people who reject standard medicine. In fact, society might actually benefit when these stupid people are eliminated by succumbing to various diseases. That's what the Darwin awards are for.

But this case is different. These adults are not putting themselves at risk—they are endangering their children.

If you stop vaccinating your children you are putting them at risk for many deadly diseases. Some of your children will die. If everyone stops vaccinating children then millions of children will die. How can anyone in their right mind think that vaccinations are so dangerous that the risk is worth it?

I'm not surprised that movie actors and average citizens are kooks. I am surprised that normally responsible TV networks like CNN contribute to potential child abuse. But I'm absolutely shocked that there are physicians who go along with the kooks.

One of those physicians is Dr. Bernadine Healy who appears in this CNN clip. I was astonished to hear her advocate more studies, lending credibility to the claims that vaccinations cause autism and other diseases. Bernadine Healy is a Republican who was the head of the National Institutes of Health under George H.W. Bush. She was removed when Clinton took over the Presidency in 1993.

Healy's defense of the anti-vaccination movement did not ring true. Her "statistics" didn't sound reasonable to me but I was in no position to refute them directly. Fortunately Orac has taken up the task at Bernadine Healy: Flirting with the anti-vaccine movement. Thanks Orac.

You know we're in trouble when the media and former NIH directors can't tell the difference between science and superstition.

This reminds me of the debate over the fluoridation of water back in the 1950's. There were kooks who warned us that fluoridation was dangerous and that it was a communist plot.

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Dying for Love in Afghanistan

 
It's been eight years since coalition forces "liberated" Afghanistan. Here's the result: Taleban 'kill love affair couple'.

Mr Azad said: "An unmarried young boy and an unmarried girl who loved each other and wanted to get married had eloped because their families would not approve the marriage."

Officials said the couple were traced by militants after they tried to go to Iran. They were made to return to their village in Khash Rod district. [Nimroz province, south-west Afghanistan - see map]

"Three Taleban mullahs brought them to the local mosque and they passed a fatwa (religious decree) that they must be killed. They were shot and killed in front of the mosque in public," the governor said. ...

Extrajudicial "honour killings" have been widely carried out in Afghanistan since then by conservative families angered by a relative who has brought them shame - usually by refusing to marry a chosen partner.

The Taleban have widened their influence over the past three years and now control many remote districts where there are not enough coalition forces to establish a permanent presence.

The people of Afghanistan should make up their own minds about whether this sort of behavior is tolerable. We cannot do it for them. As long as the country is semi-united in repulsing foreign invaders it will put off the social reforms that could bring it into the 21st century.

It's time to leave and let them face up to, and solve, their own internal problems. No people in the world would tolerate a foreign army from a different culture coming in and telling them how to behave—even if they suspected that their behavior was immoral.

Imagine that the USA was invaded and conquered by a European army who insisted that gays be allowed to marry, socialized medicine is begun, the metric system is imposed, proportional representation becomes the law, and capital punishment is abolished. Would those changes be welcomed by Americans who all of a sudden recognize that the foreigners are correct? Or would the changes be resisted even more fiercely because advocating change means siding with the enemy?

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[Hat Tip: Pharyngula]

Wild chimpanzees exchange meat for sex

 
I don't know if it's true that Wild chimpanzees exchange meat for sex but I know some vegetarians who may find it interesting.

Wild female chimpanzees copulate more frequently with males who share meat with them over long periods of time, according to a study led by researchers from the Max Planck Institute for Evolutionary Anthropology in Germany, published in the open-access, peer-reviewed journal PLoS ONE April 8.

It probably works for humans as well.

I'm going out to buy some steaks for dinner.

The original paper is Gomes and Boesch (2009)

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Gomes, C.M. and Boesch, C. (2009) Wild Chimpanzees Exchange Meat for Sex on a Long-Term Basis. PLoS ONE 4(4): e5116. DOI:10.1371/journal.pone.0005116

Which Gas Is Cheapest?

 
Here's three photographs of gas station signs. The one on the left was taken in Mississauga, Ontario, Canada and the two on the right were taken in Bethesda, Maryland, USA. The Bethesda gas stations are one block apart.

Assuming that the photos were taken on the same day (Wednesday, April 8, 2009), which station has the cheapest gas if you pay by credit card?

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A Breakthrough in Gene Expression?

When we teach protein synthesis in undergraduate molecule biology classes we cover the main mechanisms regulating the rate of translation.

One of them is the influence of codon bias among synonymous codons. We've known for 35 years that rare codons are translated more slowly that the common codons. Highly expressed genes have a pronounced codon bias in favor of the most common codons. As a result of this phenomenon, it is not true that every codon for leucine, for example, is equal. Some are better than others in some genes. Synonymous codons are not always neutral in their effect. (For a complete description of this phenomenon see: Silent Mutations and Neutral Theory.)

We also teach about the influence of messenger RNA secondary stucture. The classic examples in the E. coli ribosomal protein genes are in all the textbooks, as are the examples of attentuation—especially in the Trp operon. Again, this stuff was standard fair in textbooks and courses beginning in the 1970's.

A press release caught my eye: Penn biologists discover how 'silent' mutations influence protein production. "Cool," I thought, "maybe this is something that I'll have to put into the next edition of my textbook."

Here's the breakthrough.

For biologists, these results fundamentally change the understanding of the role of synonymous mutations, which were previously considered evolutionarily neutral. ....

The silent mutations changed the amount of fluorescent protein by as much as 250-fold, without changing the properties of the protein. Codon bias, the probability that one codon of three adjacent nucleotides will code for one amino acid over another, was previously thought to be the cause for protein expression variance, but it did not correlate with gene expression in these experiments.

"At first we were stumped," Plotkin said. "How were the silent mutations influencing protein levels? Eventually, we looked at mRNA structure and discovered that this was the underlying mechanism."

Imagine that. They've rediscovered what most of my students have been taught for 35 years!

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[Image Credit: The figure is from page 706 of my textbook. Similar figures are in all biochemistry and molecular biology textbooks. The figure shows the secondary mRNA structure around the initiation codon of the S7 ribosomal protein gene in E. coli. The secondary structure inhibits translation initiation. Although in this case the actual codons are not involved in the formation of double-stranded regions, in other cases they are.]

Monday's Molecule #117

 
Today's "molecule" is fairly complex for a "molecule" but not quite as complex as a living cell. You have to identify the particular type of "molecule" that's shown here but it will be too hard to do that without some clues. One of the clues is the connection to a Nobel Laureate. The other one is cleverly hidden in the bottom part of this posting.

The first person to identify the "molecle" 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: Dima Klenchin from the university of Wisconsin, Alex Ling from the University of Toronto, Bill Chaney of the University of Nebraska, Elvis Cela from the University of Toronto, Peter Horwich from Dalhousie University, Devin Trudeau from the University of Toronto, and Shumona De of Dalhousie University

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.

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.

Comments will be blocked for 24 hours.

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Down with Darwinism!

 
I've been fuming ever since hearing Michael Ruse speak on Friday night. It's a crying shame that the skeptics at the 12th World Congress had to get their information about evolution from him.

One of the things I detest about Michael Ruse is his insistence on using the word "Darwinism" to describe evolutionary biology. As most of you know I am not a Darwinist.

Adam M. Goldstein at Evolution:Education and Outreach reminds us that we should all stop using the word "Darwinism" when we are trying to educate people about evolutionary biology [Give the old man a break, and let’s stop it with “Darwinism”].

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[Hat Tip: Stranger Fruit]

The New Skeptics

 
The next generation of skeptics/atheists is well represented at the CFI World Congress in Washington.

Meet Derek Rodgers (left), a computer science student at Dalhousie University in Halifax, Nova Scotia (Canada) and Jason Ball (right), a political science/history and philosophy of science student at Melborne University (Australia). Jason might be taking a course from John Wilkins next term. I expressed my sympathy. :-)

Visit the Dalhousie Atheists and Young Australian Skeptics to see what these leaders of the future are doing today.

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A Night at the Newseum

 
Okay, so technically it wasn't a "night" at the Newseum—it was most of a day. Ms. Sandwalk and I had a wonderful time at the Newseum. It's on Pensylvania, just one block from the Mall and right next door to the Canadian embassy.

If you're in Washington you must go to the Newseum.

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Michael Ruse: 90% 0f Scientists Are Selectionists

 
I'm at the Center for Inquiry 12th World Congress in Washington D.C.

Last night I attended a session on "The Influence of Darwin." The four panelists were: Michael Ruse, a philosopher, Barbara Forrest, a philosopher, David Contosta, a historian, and Edward Tabash, a lawyer.

Ruse presented his usual distorted view of evolutionary biology only this time he added a comment in his defense. He said, "90% of scientists are selectionists, and the other 10% are selectionists 90% of the time." This was obviously a response to people who have criticized Ruse for being too much of an adaptationist.

Incidentally, Ruse made it clear that he is an atheist, even though he is strongly opposed to the idea that science/evolution leads to a loss of faith. I mention this because I've seen numerous references to Ruse implying that he is religious.

I asked the panel why there was no scientist on the panel and whether they thought that they could represent science accurately. I added, provocatively, that in my opinion three of the four panelists did not do a good job of describing science

The panel didn't think this was problem. I assume Darwin had a great influence on law, philosophy, and history but not much of an influence on science.

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Twisted Tree of Life Award #3

 
Jonathan Eisen at The Tree of Life has just awarded his third Twisted Tree of Life Award. And well-deserved it is.

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New Breakthrough in Evolution Theory

 
Imagine a culture of yeast cells growing in a medium where sucrose is the only carbon source. Sucrose isn't the preferred carbon source for yeast but yeast can handle it if need be. Cells secrete an enzyme called invertase that breaks down sucrose to glucose and fructose


The products of the reaction, glucose and fructose, can be taken up by the cell or they may diffuse away before being taken up. Molecules produced by the invertase from one cell can be absorbed by a neighboring cell.

As the concentration of free glucose and fructose rises in the medium, cells that lack the ability to synthesize and secrete invertase may survive. Thus invertase negative mutants may accumulate because they don't need to make their own invertase in order to have a source of carbon. In game theory, such mutants are called "cheaters."

Hands up, all you people who think that the existence of a stable equilibrium of cheaters and cooperators is a new discovery in evolutionary theory.

Right, it's not.

The editors of Nature think it is, so they published the paper from the Dept. of Physics at MIT (Gore et al., 2009).

The MIT PR department thought it was revolutionary enough to warrant a press release that was picked up by ScienceDaily [Cooperative Behavior Meshes With Evolutionary Theory].

One of the perplexing questions raised by evolutionary theory is how cooperative behavior, which benefits other members of a species at a cost to the individual, came to exist.

Cooperative behavior has puzzled biologists because if only the fittest survive, genes for a behavior that benefits everybody in a population should not last and cooperative behavior should die out, says Jeff Gore, a Pappalardo postdoctoral fellow in MIT's Department of Physics.

Gore is part of a team of MIT researchers that has used game theory to understand one solution yeast use to get around this problem. The team's findings, published in the April 6 online edition of Nature, indicate that if an individual can benefit even slightly by cooperating, it can survive even when surrounded by individuals that don't cooperate.

In short, the study offers a concrete example of how cooperative behaviors can be compatible with evolutionary theory.

I agree that this is an interesting example but I don't think the public is well served by presenting it as a new contribution to evolutionary theory. The public is entitled to think that evolutionary biologists must be really stupid if they've never thought of this before.

They (the public) would be really confused if they happened to read the Wikipedia entry on John Maynard Smith (1920 - 2004).

There are no references to Maynard Smith's work in the citations at the end of the Nature paper, although there is a reference to "Smith, J.M." who wrote the book Evolution and the Theory of Games.

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Gore, J., Youk, H., and van Oudenaarden A. (2009) Snowdrift game dynamics and facultative cheating in yeast. Nature advance online publication 6 April 2009. [DOI: doi:10.1038/nature07921]

What Stephen Harper Said in 1997

 
I don't know where Canadian Cynic gets all this stuff but he has just posted a link to a speech by Stephen Harper in 1997 [CTV.ca].

It's worth reading the entire speech if you can stomach it. If you can't, then try this little excerpt.

OTTAWA -- The text from a speech made by Stephen Harper, then vice-president of the National Citizens Coalition, to a June 1997 Montreal meeting of the Council for National Policy, a right-wing U.S. think tank, and taken from the council's website:

Ladies and gentlemen, let me begin by giving you a big welcome to Canada. Let's start up with a compliment. You're here from the second greatest nation on earth. But seriously, your country, and particularly your conservative movement, is a light and an inspiration to people in this country and across the world.

Now, having given you a compliment, let me also give you an insult. I was asked to speak about Canadian politics. It may not be true, but it's legendary that if you're like all Americans, you know almost nothing except for your own country. Which makes you probably knowledgeable about one more country than most Canadians.

But in any case, my speech will make that assumption. I'll talk fairly basic stuff. If it seems pedestrian to some of you who do know a lot about Canada, I apologize.

I'm going to look at three things. First of all, just some basic facts about Canada that are relevant to my talk, facts about the country and its political system, its civics. Second, I want to take a look at the party system that's developed in Canada from a conventional left/right, or liberal/conservative perspective. The third thing I'm going to do is look at the political system again, because it can't be looked at in this country simply from the conventional perspective.

First, facts about Canada. Canada is a Northern European welfare state in the worst sense of the term, and very proud of it. Canadians make no connection between the fact that they are a Northern European welfare state and the fact that we have very low economic growth, a standard of living substantially lower than yours, a massive brain drain of young professionals to your country, and double the unemployment rate of the United States.

In terms of the unemployed, of which we have over a million-and-a-half, don't feel particularly bad for many of these people. They don't feel bad about it themselves, as long as they're receiving generous social assistance and unemployment insurance.

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2009 Canada Gairdner Awards

 
The 2009 Canada Gairdner Award recipients were announced last week. Each awardee gets $100,000 (CDN). The winners are ...

Richard Losick: "for the discovery of mechanisms that define cell polarity and asymmetric cell division, processes key in cell differentiation and in the generation of cell diversity"

Kazutoshi Mori: "for the dissection and elucidation of a key pathway in the unfolded protein response which regulates protein folding in the cell"

Nubia Muñoz: "for her epidemiological studies that defined the essential role of the human papilloma virus in the etiology of cervical cancer on a global level which led to the development of successful prophylactic vaccines"

David Sackett: "for his leadership in the fields of clinical epidemiology and evidence-based medicine, which have had major impacts internationally in applied clinical research and in the practice of medicine"

Lucy Shapiro: "for the discovery of mechanisms that define cell polarity and asymmetric cell division, processes key in cell differentiation and in the generation of cell diversity"

Peter Walter: "for the dissection and elucidation of a key pathway in the unfolded protein response which regulates protein folding in the cell"

Shinya Yamanaka: "for his demonstration that the key transcription factors which specify pluripotency may become reprogrammed somatic cells to pluripotent stem cells"

The awards will be presented next October at the University of Toronto. Since this is the 50th anniversary of the Gairdner Awards there will be quite a gathering. You should plan on being here.

This year The Gairdner Foundation is celebrating its 50th Anniversary in spectacular fashion.

Between March and November we will hold 7 major international symposia across the country, in Vancouver, Edmonton, Ottawa, Toronto (York), Sherbrooke, Montreal and Halifax (see under Events). The finale will occur in Toronto, where we will host 50 past Gairdner recipients, including 22 Nobel Laureates, from Oct 28-30. This will be by far the largest gathering of the world's top scientists ever held in Canada. We will also introduce the 2009 Canada Gairdner Award recipients.

Canada Gairdner Laureates will participate in lectures, panel discussions, public forums, interviews and informal talks with academics, researchers, biotech and pharma companies, government leaders, graduate and postgraduate students, high school students, the media and interested members of the general public. With the exception of the social events, all the programs will be free and open to anyone who wants to share in the excitement of leading edge biomedical science.

The 50th Anniversary will be a spectacular culmination of everything The Gairdner Foundation has achieved in becoming Canada's premier international prize, and one of the top three biomedical prizes in the world. It will be a vehicle to raise awareness of the fascinating world of biomedical science and its importance to lives.

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