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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New York: Central Park

 

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Nobel Laureate: Richard Ernst

 

The Nobel Prize in Chemistry 1991.

"for his contributions to the development of the methodology of high resolution nuclear magnetic resonance (NMR) spectroscopy"




Richard R. Ernst (1933 - ) won the Nobel Prize in Chemistry for important contributions to the technology of nuclear magnetic resonance (NMR) as a tool to understanding the three-dimensional structure of molecules.

The press release describes his work in some detail.
THEME:
Nobel Laureates

Revolutionary developments make a spectroscopic technique indispensable for chemistry

The 1991 Nobel Prize in Chemistry has been awarded to Professor Richard R. Ernst of the ETH, Zurich, for important methodological developments within nuclear magnetic resonance (NMR) spectroscopy. NMR spectroscopy has during the last twenty years developed into perhaps the most important instrumental measuring technique within chemistry. This has occurred because of a dramatic increase in both the sensitivity and the resolution of the instruments, two areas in which Ernst has contributed more than anybody else.

NMR spectroscopy is today used within practically all branches of chemistry, at universities as well as industrial laboratories. The method has its most important applications as a tool for the determination of molecular structure in solution. It can today be applied to a wide variety of chemical systems, from small molecules (e.g. drugs) to proteins and nucleic acids. Further, chemists use NMR to study interactions between different molecules (e.g. enzyme - substrate, soap - water), to investigate molecular motion, to get information on the rate of chemical reactions and for many other problems. The NMR technique is today also important in related sciences, such as physics, biology and medicine.

Background

The first successful NMR experiments were reported in 1945, by two independent groups in the USA (Bloch and co-workers at Stanford and Purcell with his group at Harvard). Their discovery was awarded a Nobel Prize in Physics in 1952. The NMR phenomenon can be explained in the following way. When matter is placed in a magnetic field, some of the atomic nuclei (e.g. nuclei of hydrogen atoms, called protons) behave like microscopic compass needles. These tiny compass needles (called nuclear spins) can, according to the laws of quantum mechanics, orient themselves with respect to the magnetic field in only a few ways. These orientations are characterized by different energy levels. The nuclear spins can be forced to jump between levels if the sample is exposed to radio waves of exactly specified frequency. The frequency is varied during the course of the experiment and, when it exactly matches the characteristic frequency of the nuclei (the resonance frequency), an electric signal is induced in the detector. The strength of the signal is plotted as a function of frequency in a diagram called the NMR spectrum. Around 1950, it was discovered that nuclear resonance frequencies depended not only on the nature of the atomic nuclei, but also on their chemical environment. The possibility of using NMR as a tool for chemical analysis soon became obvious and was mentioned by, among others, Professor Purcell in his 1952 Nobel lecture. A fundamental difficulty in the early days was the relatively low sensitivity of the NMR method.

A major breakthrough occurred in 1966 when Ernst (together with Weston A. Anderson, USA) discovered that the sensitivity of NMR spectra could be increased dramatically if the slow radiofrequency sweep that the sample was exposed to was replaced by short and intense radiofrequency pulses. The signal was then measured as a function of time after the pulse. The next pulse and signal acquisition were started after a few seconds, and the signals after each pulse were summed in a computer. The NMR signal measured as a function of time is not amenable to a simple interpretation (see Figure la). It is however possible to analyze what resonance frequencies are present in such a signal - and to convert it to an NMR spectrum - by a mathematical operation (Fourier transformation, FT) performed rapidly in the computer. The result of the Fourier transformation of Figure la is shown in Figure lb.

This discovery is the basis of modern NMR spectroscopy. The ten-fold, and sometimes hundred-fold, increase in sensitivity has made it possible to study small amounts of material as well as chemically interesting isotopes of low natural occurrence, e.g. carbon- 13. The enormous potential of the new technique - called FT NMR - quickly became obvious to NMR spectroscopists. The chemical research community got access to it in the early seventies through commercial FT NMR instruments. Nowadays, practically no other types of NMR spectrometer are manufactured.

By the end of the sixties, NMR spectroscopists had begun to use new magnet designs, based on superconducting materials, and the quality of spectra - expressed both in terms of sensitivity and resolution - improved quickly during the seventies. Consequently, more complex systems could be studied and more sophishcated questions answered. To move to very large molecules, macromolecules, another breakthrough was necessary, and this again carried the signature of Ernst. Inspired by a lecture of Jean Jeener, Belgium, at a summer school at the beginning of the seventies, Ernst and co-workers showed in 1975-76 how "two-dimensional" (2D) NMR experiments could be performed and demonstrated that 2D FT NMR opened entirely new possibilities for chemical research.

This 2D methods functions in the following way. Nuclear spins in a magnetic field are now subjected to sequences of radio-frequency pulses rather than to single pulses. The time course of the experiment is divided into four intervals. During the "preparation period", the equilibrium of the nuclear spin system is distorted by one or several pulses. This non-equilibrium is allowed to evolve for a certain time (the "evolution period"), after which the next series of pulses (the "mixing period") leads to the "detection period". Here the NMR signal is detected as a function of time in the same way as in ordinary, one-dimensional FT NMR. After this, one moves to the next preparation period and repeats the experiment with different evolution period. The change in the evolution period causes the signal measured during the detection period to change. One might say that the history of spins during the evolution period becomes encoded in the variation of the signal measured during the detection period. This gives a two-dimensional table with signal intensity as a function of both the point in time during the detection period and the length of the evolution period. Finally, the Fourier transformation is performed twice - with respect to both these time parameters - to obtain a two-dimensional frequency spectrum in the form of a map of the dependence of the signal intensity on two frequency parameters (denoted f1 and f2 in Figure 2).

Introduction of the second frequency dimension allows the spectral information to attain much higher resolution - like looking at the skyline of a mountain range and then looking at the whole range from an aircraft above. Depending on the design of the preparation and the mixing periods, one obtains a variety of 2D NMR experiments. Some are used to spread the information over two dimensions rather than one (separation of interactions) while others are designed to find which nuclei have some form of contact with each other (correlation of signals).

In the mid-seventies, Ernst also proposed a method of obtaining NMR-tomographic images which became one of the most common (the NMR tomography method as such was earlier realized by Lauterbur in the USA, Mansfield in England and others).

Since the mid-seventies, Ernst and co-workers have continuously and decisively contributed to the development of NMR spectroscopy, and in particular its two-, and more recently three- and multi-dimensional varieties. Applications of his methods were soon to come. For example, it has become possible over the past ten years to use NMR to determine the three-dimensional structure of organic and inorganic compounds as well as proteins and other biological macromolecules in solution with an accuracy comparable to what can be attained in crystals using X-ray diffraction. Interactions between biological molecules and other substances (metal ions, water, drugs) have also been studied in detail. Other important chemical applications are identification of chemical species (where NMR spectra act as the fingerprint of a molecule), studies of rates of certain chemical reactions and of molecular motions in the liquid state. In the border area between chemistry and biology, NMR is being used to study how metabolic processes are influenced by drugs, ischaemia etc. Ernst's own work often falls in the border area between chemistry and physics and can, if one so wishes, be treated as extremely elegant experimental verification of the correctness of quantum mechanics.

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[Photo Credit: Science Festival]

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.

Nobel Laureate: Harald zur Hausen

 

The Nobel Prize in Physiology or Medicine 2008

"for his discovery of human papilloma viruses causing cervical cancer"

Harald zur Hausen (1936 - ) won the Noble Prize in 2008 for discovering that a virus, human papilloma virus, causes cervical cancer. He also won a Gairdner Award in 2008.

Zur Hausen's discovery led eventually to the development of an HPV vaccine. Gardasil is the best known of the two vaccines on the market. Most doctors recommend that young girls be vaccinated.

Here's the 2008 press release on Zur Hausen.
THEME:
Nobel Laureates

Discovery of human papilloma virus causing cervical cancer

Against the prevailing view during the 1970s, Harald zur Hausen postulated a role for human papilloma virus (HPV) in cervical cancer. He assumed that the tumour cells, if they contained an oncogenic virus, should harbour viral DNA integrated into their genomes. The HPV genes promoting cell proliferation should therefore be detectable by specifically searching tumour cells for such viral DNA. Harald zur Hausen pursued this idea for over 10 years by searching for different HPV types, a search made difficult by the fact that only parts of the viral DNA were integrated into the host genome. He found novel HPV-DNA in cervix cancer biopsies, and thus discovered the new, tumourigenic HPV16 type in 1983. In 1984, he cloned HPV16 and 18 from patients with cervical cancer. The HPV types 16 and 18 were consistently found in about 70% of cervical cancer biopsies throughout the world.

Importance of the HPV discovery

The global public health burden attributable to human papilloma viruses is considerable. More than 5% of all cancers worldwide are caused by persistent infection with this virus. Infection by the human papilloma virus is the most common sexually transmitted agent, afflicting 50-80% of the population. Of the more than 100 HPV types known, about 40 infect the genital tract, and 15 of these put women at high risk for cervical cancer. In addition, HPV is found in some vulval, penile, oral and other cancers. Human papilloma virus can be detected in 99.7% of women with histologically confirmed cervical cancer, affecting some 500,000 women per year.

Harald zur Hausen demonstrated novel properties of HPV that have led to an understanding of mechanisms for papilloma virus-induced carcinogenesis and the predisposing factors for viral persistence and cellular transformation. He made HPV16 and 18 available to the scientific community. Vaccines were ultimately developed that provide ≥95 % protection from infection by the high risk HPV16 and 18 types. The vaccines may also reduce the need for surgery and the global burden of cervical cancer.

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[Photo Credit: IBMLive]

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.

New York City

 

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New York: American Museum of Natural History

 
Guess who I saw in the American Museum of Natural History in New York?

No, I'm not thinking of a family of stuffed elephants or a giant blue whale. I'm not even thinking of the butterflies in the butterfly conservatory. The people who I'm thinking about are much more exciting.

My friend and I visited the evolution display. It was really excellent. The dioramas and descriptions described a no-holds-barred version of evolution complete with supporting evidence from fossils, DNA sequences, and biogeography. The statements were factual (mostly) and scientific. No dumbing down and no pulling punches.

I remarked to my friend that this was unusual and I would be surprised if there weren't some "disclaimers" at the end of the display.

Sure enough, just before reaching the end we saw some familiar faces. There were Ken Miller, Francis Collins, and Genie Scott in full length videos explaining why evolution and religion are compatible. I waited to see if PZ Myers or Richard Dawkins would put in an appearance—no such luck.

We didn't even see Neil deGrasee Tyson in the video in spite of the fact he's the director of the Hayden Planetarium at the museum. Niles Eldredge famous evolutionary biologist and curator of paleontology at the museum wasn't there either. I wonder why?

Add the American Museum of Natural History to the list of accommodationists. There was no compelling reason to interrupt an otherwise excellent scientific display with a sop to religion.

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Britich Columbia Rejects Electoral Reform

 
In yesterday's election the people of British Columbia were asked to choose between the old first-past-the post electoral system and a new single transferable vote system. The referendum question was ...

Which electoral system should British Columbia use to elect members to the provincial Legislative Assembly? The existing electoral system (First-Past-the-Post) or the single transferable vote electoral system (BC-STV) proposed by the Citizen's Assembly on Electoral Reform.

Up until the beginning of May, it was widely anticipated that more than 60% would vote for STV, thus ensuring that a fair electoral system would become law in British Columbia.

The actual result was a disaster for electoral reform. Only 39% of the voters favored STV while 61% voted to retain the old unfair first-past-the-post system [Elections BC].

This is a major defeat. It will make it much more difficult to get electoral reform passed in Ontario or any other province. As usual, North Americans are much more conservative than the civilized world.

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