Monday's Molecule #122: Winner?

 
UPDATE: The molecule is epinephrine or adrenaline. IUPAC name = (R)-4- (1-hydroxy-2- (methylamino)ethyl)benzene-1,2-diol.

The Nobel Laureate is Charles Robert Richet who discovered and described anaphylaxis or anaphylactic shock. Epinephrine, in the form of an EpiPen, is used to treat anaphylactic shock.

Ten people got the molecule but Dima Klenchin was the only person to guess the correct Nobel Laureate. He isn't eligible so there is no winner this week.

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Today's molecule is a drug as well as a biological molecule that's found in some species. You need to supply the common name and the correct IUPAC name for this molecule. The stereochemistry isn't shown in the figure but you have to specify it in your answer.

As a drug, this molecule is used to treat a common but life-threatening condition. Identify that condition and name the Nobel Laureate who first described and characterized it.

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: Mike Fraser of Toronto, Alex Ling of the University of Toronto, Laura Gerth of the University of Notre Dame, Stefan Tarnawsky of the University of Toronto, Dima Klenchin of the University of Wisconsin, Madison, Adam Santoro of the University of Toronto., and Michael Clarkson of Waltham MA (USA).

The Canadians are still ahead in the competition between Canadians the rest of the world but their recent dominance is coming to an end. I want to thank all those smart Canadians who have been holding back in order to give the rest of the world a chance.

I still have one extra free lunch donated by a previous winner (Michael Clarkson) 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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Science for Humanity

 
Today's issue of The Toronto Star has an article on Andras Nagy, a colleague who works at one of the hospital research institutes here in Toronto. Apparently Nagy made a list of "Top 10 awards for work in science-related endeavours" in a magazine called Scientific Magazine [Scientist honoured for stem-cell coup].

I tried to find this magazine and the names of the other winners but nothing seemed to work. Google was not my friend today.

Later on, after lunch, I noticed a press release from "Scientific American." That magazine was naming "Ten researchers, politicians, business executives and philanthropists who have recently demonstrated outstanding commitment to assuring that the benefits of new technologies and knowledge will accrue to humanity" [Scientific American 10: Guiding Science for Humanity].

Sure enough, Andras Nagy was on that list. Here's the complete list. Congratulations to Genie Scott.

1. Todd Brady
   Corporate environmental manager
   Intel, Santa Clara, Calif.
   A chip company makes expansion of its environmental footprint a priority


2. Shai Agassi
   Founder and chief executive
   Better Place, Palo Alto, Calif.
   A wonderfully simple recharging scheme may ensure a future for electric vehicles


3. Wafaa El-Sadr
   Chief
   Infectious Disease Division, Harlem Hospital Center, New York City
   The physician leads a multipronged public health campaign to fight the scourge of HIV


4. Robert J. Lin­hardt
   Professor of Biocatalysis and Metabolic Engineering
   Rensselaer Polytechnic Institute
   A chemical sleuth unravels the cause of deaths from a tainted drug


5. Eugenie Scott
   Executive director
   National Center for Science Education, Oakland, Calif.
   A champion for the teaching of evolution steps up her advocacy


6. Bill Gates/Michael Bloomberg
   Co-chair
   Bill and Melinda Gates Foundation
   Mayor of New York City
   Celebrity heft propels a campaign to limit smoking


7. Bryan Willson
   Professor of mechanical engineering
   Colorado State University
   An engineer facilitates clean energy technology for the developing world


8. Kristian Olson
   Program Leader
   Center for Integration of Medicine and Innovative Technology, Boston
   Simple, low-cost resuscitators and incubators can save newborns in the developing world


9. Andras Nagy
   Senior investigator
   Mount Sinai Hospital, Toronto
   A biologist discovers a practical method of making stem cells from mature cells


10. Barack Obama
    President of the U.S.
    The new chief executive begins his term by initiating a radical shift in science policy

It would be fun to see the top ten scientists—men and women who have contributed the most to our understanding of the natural world.

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Monday's Molecule #122

 
Today's molecule is a drug as well as a biological molecule that's found in some species. You need to supply the common name and the correct IUPAC name for this molecule. The stereochemistry isn't shown in the figure but you have to specify it in your answer.

As a drug, this molecule is used to treat a common but life-threatening condition. Identify that condition and name the Nobel Laureate who first described and characterized it.

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: Mike Fraser of Toronto, Alex Ling of the University of Toronto, Laura Gerth of the University of Notre Dame, Stefan Tarnawsky of the University of Toronto, Dima Klenchin of the University of Wisconsin, Madison, Adam Santoro of the University of Toronto., and Michael Clarkson of Waltham MA (USA).

The Canadians are still ahead in the competition between Canadians the rest of the world but their recent dominance is coming to an end. I want to thank all those smart Canadians who have been holding back in order to give the rest of the world a chance.

I still have one extra free lunch donated by a previous winner (Michael Clarkson) 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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Who Knew?

 
The misreporting of the evolution issue is one key reason for this site. Unfortunately, much of the news coverage has been sloppy, inaccurate, and in some cases, overtly biased. Evolution News & Views presents analysis of that coverage, as well as original reporting that accurately delivers information about the current state of the debate over Darwinian evolution.

Evolution News & ViewsJonathan Wells has a Ph.D. He can explain why "Darwinism" is false in only two paragraphs [Persisting in Spite of the Evidence: Why Darwinism Is False].

Darwin called The Origin of Species “one long argument” for his theory, but Jerry Coyne has given us one long bluff. Why Evolution Is True tries to defend Darwinian evolution by rearranging the fossil record; by misrepresenting the development of vertebrate embryos; by ignoring evidence for the functionality of allegedly vestigial organs and non-coding DNA, then propping up Darwinism with theological arguments about “bad design;” by attributing some biogeographical patterns to convergence due to the supposedly “well-known” processes of natural selection and speciation; and then exaggerating the evidence for selection and speciation to make it seem as though they could accomplish what Darwinism requires of them.

The actual evidence shows that major features of the fossil record are an embarrassment to Darwinian evolution; that early development in vertebrate embryos is more consistent with separate origins than with common ancestry; that non-coding DNA is fully functional, contrary to neo-Darwinian predictions;¹ and that natural selection can accomplish nothing more than artificial selection — which is to say, minor changes within existing species.

Amazing.

When it comes to evaluating Creationist arguments, we are often faced with a difficult decision. Is the Creationist just ignorant or is he lying? I think it's much easier to answer that question in Wells' case. He has a Ph.D. in biology from a reputable university. It's not possible for him to be that ingnorant about the basic facts of biology.

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1. It's a lie that non-coding DNA is fully functional and it's a lie that "neo-Darwinism" predicts the presence of large amounts of junk DNA in some species.

One Angry Christian

 
Charlotte Allen doesn't like atheists very much. She writes in Los Angeles Times [Atheists: No God, no reason, just whining].

I can't stand atheists -- but it's not because they don't believe in God. It's because they're crashing bores.

She then proceeds to describe all the "boring" things that upset her.

I'd like to comment on one of the points that she makes.

The problem with atheists -- and what makes them such excruciating snoozes -- is that few of them are interested in making serious metaphysical or epistemological arguments against God's existence, or in taking on the serious arguments that theologians have made attempting to reconcile, say, God's omniscience with free will or God's goodness with human suffering.

This is becoming a mantra for Christian apologists and it's about time we put an end to it.

The reason why atheists aren't interested in making serious arguments against God's existence is that it's impossible to prove the non-existence of something. On the other hand, we can easily show that the arguments in favor of supernatural beings are nonsensical. There are no "serious mtaphysical or epistemological arguments" for God and that's what we point out to anyone who takes the time to listen.

I suppose that makes us boring.

Furthermore, atheists are not interested in "taking on" the "serious" (sic) arguments of theologians when they attempt to reconcile their God with free will and evil. Why should we be interested in such arguments? The premise behind these arguments is that God exists. Atheists reject the premise. If they want to be taken seriously, "serious" theologians have to first prove that God exists before they begin their apologetics.

Christians like Charlotte Allen make me angry. It's not because they're Christians, it's because they are so irrational.

What atheists don't seem to realize is that even for believers, faith is never easy in this world of injustice, pain and delusion. Even for believers, God exists just beyond the scrim of the senses. So, atheists, how about losing the tired sarcasm and boring self-pity and engaging believers seriously?

OK. Here's an attempt to engage believers seriously.

If believing is so hard in the face of the real world, and if your belief is "just beyond the ... senses," then why do you continue to believe?

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[Hat Tip: RichardDawkins.net]

Happy Victoria Day!

 
Today's the day we celebrate Queen Victoria's birthday (Victoria Day) in most Canadian provinces. Queen Victoria was actually born on May 24th but the modern holiday is the first Monday before or on May 24th.

Since the death of Queen Victoria, the holiday does double duty as a celebration of the birthday of the current monarch. Queen Elizabeth II was actually born on April 21st—it must be nice to have two birthday parties every year!

Although Queen Elizabeth II is officially Canada's head of state, the duties are actually carried out by her representative, the Governor General. Governors General are appointed every few years and their duties are largely ceremonial. I really like a system where the head of state is not the same person as the head of government. It avoids a lot of problems.

Officially, Canada's form of government is called a Constitutional Monarchy with a Parliamentary System of government.

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[The painting of Queen Victoria's Family in 1846 is by Franz Xaver Winterhalter.]

Michael Bliss - Anti-Science Conservative

 
Michael Bliss is a Professor Emeritus at the University of Toronto. He has written some excellent books on the history of science, notably a book about the discovery of insulin.

Bliss has always been a small-c conservative and many of his opinion pieces have supported conservative policies.

On Thursday, May 14th, Michael Bliss entered the debate on Canadian science funding [Michael Bliss: Anti-Harper campaign politicizes research to the detriment of science]. His main point is that Canadian scientists are whiners and complainers who should keep their mouths shut because they are damaging the reputation of science in Canada.

It’s time that responsible leaders of the Canadian science and research communities began thinking of ways to cool down their more hot-headed colleagues. The strategy of declaring war on a government because some of its policies are temporarily inconvenient and vexatious can generate cheap short-term applause and support in some quarters, but in the long run tags its adherents as unreliable and unworthy, or worse. Eventually doors get shut in their faces, and/or they’re left to wither on the vine.

It’s a sad way to tarnish what often has been and still could be one of the success stories of Canadian public policy.

I've never been a fan of Michael Bliss but this diatribe goes way over the line. Scientists are justifiably criticizing a science policy that they feel is doing great damage to Canada's ability to be competitive in the 21st century. Michael Bliss is saying that scientists should not speak out when they disagree with government policy. That's a strange position for someone who has made a reputation of speaking out on controversial topics.

But it's at least consistent with conservative thinking.

Michael Bliss thinks it's OK for governments to direct scientific research. He thinks the only important kind of research is that which directly benefits business and consumers. Applied research and technology is "accountable."

By and large, Canadian researchers have not had a bad inning in recent years. Some observers think that the research community has actually had an easy ride, never having been forced to show exactly what benefits are being generated for the Canadian people by the money given researchers. If the government of Canada ever decided, for example, that this country should lead the world in demanding hard accountability from researchers who live off taxpayers’ largesse, today’s discontents would seem like extremely small beer.

I suppose that's why Bliss admires Banting and Best and the others who discovered and produced insulin. I suppose he hates those scientists who discovered recombinant DNA technology to help with their curiosity motivated research even though it led directly to the production of human insulin—a far more effective form than the old insulin from pigs.

The main product of research is knowledge and knowledge is always of more benefit to the Canadian people than ignorance. During his many decades at the University of Toronto, Michael Bliss and his students contributed to that knowledge base in many ways. Some of the work in history that he published was paid for by research grants. I wonder if he can meet the demand of "hard accountability" that he demands of others? With respect to his own scholarly work, I wonder if he can explain "exactly what benefits are being generated for the Canadian people"?

(Read Commentary strives to politicize science funding debate on Researcher Forum for a similar perspective on Michael Bliss.)

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Stephen Harper: Just Leaving

 

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Godless Radio

 
Yesterday I was interviewed on Godless Radio by Godless Dave and Godless Rob. It was a fun time. We spent an hour talking about the conflict between science and religion. I think we pretty much solved all the problems.

There will be a podcast version for those of who missed the live broadcast.

Godless is an internet radio show designed to give atheists at the University of Toronto, Scarborough Campus, a voice. We aim to reach out to non-believers, whether they call themselves atheists, agnostics, secular humanists or anything else, and provide a platform for the promotion of reality-based thinking.

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Metabolism First and the Origin of Life

There are several competing hypotheses about the origin of life. Most people know about the Primordial Soup scenario; that's the one where complex organic molecules are created by spontaneous chemical reactions. Over time these complex molecules, such as amino acids and nucleotides, accumulate in a warm little pond and eventually they come together to form proteins and nucleic acids.

The RNA World scenario is similar except that nucleic acids (RNA) are thought to form before proteins. For a while, RNA molecules are the main catalysts in the primordial soup. Later on, proteins take over some of the catalytic roles. One of the problems with the RNA world hypothesis is that you have to have a reasonable concentration of nucleotides before the process can begin.

The third hypothesis is called Metabolism First. In this scheme, the first reactions involve spontaneous formation of simple molecules such as acetate, a two-carbon compound formed from carbon dioxide and water. Pathways leading to the synthesis of simple organic molecules might be promoted by natural catalysts such as minerals and porous surfaces in rocks. The point is that the origin of life is triggered by the accumulation of very simple organic molecules in thermodynamically favorable circumstances.

Simple organic molecules can then be combined in various ways that result in simple amino acids, lipids, etc. These, in turn, could act as catalysts for the formation of more organic molecules. This is the beginning of metabolism.

Eventually simple peptides will be formed and this could lead to better catalysts. Nucleic acids and complex amino acids will only form near the end of this process.

One of the advantages of the metabolism first scenario is that it offers a simple "solution" to the chirality/racemization problem by explaining why all naturally occurring amino acids are left-handed [see Can watery asteroids explain why life is 'left-handed'?]. Another advantage is that it doesn't require spontaneous formation of nucleotides—a major limitation of the RNA world scenario since spontaneous formation of such molecules is very improbable.¹

James Trefil, Harold Morowitz, and Eric Smith have written up a very nice summary of the Metabolism First hypothesis for American Scientist: The Origin of Life. The subtitle, "A case is made for the descent of electrons," is a clever play on words. It illustrates the point that synthesis of simple organic molecules such as acetate are thermodynamically favorable. This is science writing at its best.²

The authors have reconstructed the simplest, most fundamental, biochemical pathways concluding that a reductive citric acid cycle is probably the best example of the first metabolic pathway. In this pathway, the two-carbon acetate molecule is made from carbon dioxide and water in the reverse of the common citric acid pathway found in eukaryotes.

In fact, the reductive pathway occurs in many bacteria. They can still use it to fix carbon. The authors use the figure on the left to illustrate the basic pathway.

Almost all of the common molecules of life are synthesized from acetate or the molecules of the citric acid cycle. The simple amino acids, for example, are formed in one step. More complex amino acids are derived from the simple amino acids, etc. Similarly, simple fatty acids can be formed from acetate and more complex ones come later; once the simple ones accumulate.

The central role of citric acid cycle metabolism in biochemistry has been known for decades. It's involvement in biosynthesis pathways is often ignored in introductory biochemistry courses because they are heavily focused on fuel metabolism in mammals and biosynthetic pathways get short shrift in such courses.



The essence of Metabolism First is that the various complex molecules of life came after the spontaneous formation of very simple molecules. Pathways leading to the complex molecules evolved and their evolution was assisted by the evolution of various catalysts, some of which were biological in nature.

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1. In spite of the claims surrounding a recent paper in Nature: RNA world easier to make.

2. Probably good science editing as well. My friend Morgan Ryan is managing editor and he is very good.

[Photo Credit: American Scientist, courtesy of Scripps Institution of Oceanography, University of California, San Diego.]

Get a Job in Waterloo

 

Biology - Assistant Professor (Invertebrate Developmental Biology)

University of Waterloo
Location: Ontario
Date posted: 2009-04-06

Invertebrate Developmental Biologist.

The Department of Biology of the University of Waterloo invites applications for a tenure track position at the assistant professor level in invertebrate developmental biology. Applicants must have a PhD and be prepared to establish an active research program; evidence of the ability to attract independent research funding and/or teaching experience would be an asset. We are particularly interested in applicants using genetic approaches to model invertebrate systems in conjunction with modern imaging techniques. Duties include research, management of departmental imaging facility, teaching at the undergraduate and graduate levels, as well as graduate student supervision.

Applicants should send their curriculum vitae, the names of three references and an outline (one to two pages) of their proposed research program, by electronic means if possible, to: D.R. Rose, Chair, Department of Biology, University of Waterloo, Waterloo, Ontario, N2L 3G1 Canada, or via email to givan@sciborg.uwaterloo.ca.

The closing date for applications is May 15, 2009 with a start date no later than September 1, 2009.

All qualified candidates are encouraged to apply; however Canadian and permanent residents will be given priority. The University of Waterloo encourages applications from all qualified individuals, including women, members of visible minorities, native peoples, and persons with disabilities. This appointment is subject to availability of funds. Additional information on the Department is available at http://www.biology.uwaterloo.ca/.

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The Problems with Research Funding in Canada

 
Jim Turk is Executive Director of the Canadian Association of University Teachers (CAUT). He is a staunch defender of university research, especially curiosity motivated research.

In Tuesday's Globe and Mail, Turk explains why current government policy is wrong. It puts too much emphasis on research that directly helps business and not enough on fundamental research [Get the state out of the labs of the nation].

He also makes a point that needs emphasis. The Presidents of Canada's granting agencies are getting into bed with the government. They increasingly see themselves as obedient pawns of the government and not as independent agents who will stand up for what they believe in regardless of the consequences.

Our federal government has acknowledged that politicians should not try to pick winners and losers in the economic marketplace, but persists in trying to do so in the marketplace of ideas. In the 2007 and 2008 budgets, the federal government dictated where new money for granting councils could be spent - ruling out the vast majority of researchers' work. In the 2009 budget, it restricted new social science humanities graduate scholarships to students "focused on business-related degrees."

That research funding has become politicized was also evident when the presidents of the three granting councils - the Natural Sciences and Engineering Research Council, the Social Sciences and Humanities Research Council and the Canadian Institutes of Health Research - failed to object when their budgets were cut, and when Genome Canada's president expressed concerns, then quickly retracted them. Canada's research funding agencies should be made arms' length from government.

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[Hat Tip: T. Ryan Gregory: Genomicron]

Is Your Irony Meter Working?

 
Back in the days of newsgroups (last century) the howlers in talk.origins developed a running joke about irony meters. They were always being fried by outrageous comments from the anti-science creationists. New, more powerful, irony meters were needed every few months.

Here's a chance to calibrate your new irony meter.

The National Center for Science Education (NCSE) has just published a brief they submitted to the US Federal Government on the issue of scientific integrity [NCSE encourages federal scientific integrity].

Part of it reads ...

There is a long-running conflict over a creationist book being sold in the science section of bookstores at Grand Canyon National Park, creating a conflict between the scientifically-oriented presentations of Park Service staff and an implied Park Service endorsement of erroneous scientific views. The federal government should not lend its credibility to material which falsely claims scientific support for a 6000 year-old Earth or other attempts to masquerade religious apologetics as science. It is appropriate to discuss religious views in publications, presentations, and other educational settings, but the integrity of the scientific process is compromised when descriptions of religious views are not clearly distinguished from empirically tested scientific results.

Re-read that last sentence; "the integrity of the scientific process is compromised when descriptions of religious views are not clearly distinguished from empirically tested scientific results." I agree 100%; "The federal government should not lend its credibility to ... attempts to masquerade religious apologetics as science."

So how does that rule about integrity play out when leading scientific organizations like AAAS and NAS promote the compatibility of science and religion by endorsing and publicizing religious scientists in their official publications? Or how about the evolution display at the American Museum of Natural History?

What value registered on your irony meter?

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[Image Credit: Wikipedia: Irony Meter]

Denyse O'Leary and Harun Yahya

 
Adnan Oktar is a Turkish creationist whose anti-evolution diatribes are usually published under the name Harun Yahya. Denyse O'Leary is a Canadian creationist who publishes anti-evolution diatribes under her own name.

I suppose it was only a matter of time before those two were attracted to one another. Denyse interviews Adnan Oktar on Uncommon Descent [Interview with Turkish Darwin doubter Adnan Oktar].

O’LEARY: How did you become interested in the evolution controversies? The conventional wisdom offered by many media sources in North America is that doubts about Darwin are a product of American evangelical Christianity in the deep rural South, and can only be understood with reference to that culture. Unless I have lost the plot, your doubts could not stem from that culture. From what, then, did they stem?

ADNAN OKTAR: I realized while I was still in high school that there was something odd about World War I, World War II and revolutions. Because people do not suddenly wake up one day and decide to start slaughtering their neighbors or ruining and devastating a country. I did some investigation and saw that the Darwinist materialist mindset lies behind all wars, revolutions and anarchy. I was terribly distressed by the way people were suffering so much, by the oppression and injustice they were being subjected to, and decided to wage an intellectual campaign against Darwinism to the utmost of my powers.

Amazing. It's really hard to decide which one is more wrong, although I must say I'm tilting toward Adnan Oktar. The idea that all wars were due to Darwinism—especially those fought during the expansion of the Ottoman Empire— is mind-boggling.

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[Image Credit: Guide Martine]

Canadian Invasion

 
The Canadian invasion is proceeding as planned.

Most of the rest stops along the New York State Thruway have a Timmy's and you can find lots of them in the bigger cities. It won't be long before Starbucks is in trouble.

Note to my American friends ... be afraid ... be very afraid. Civilization is coming to America. You will be assimilated.

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