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Wednesday, May 13, 2009

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.

[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.




[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

 







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.


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.


Is Acupuncture Better than Toothpicks?

 
Orac is at it again. He describes a pretty good study of the possible effects of acupuncture on lower back pain [Another acupuncture study misinterpreted]. The study showed that patients who got a sham procedure using toothpicks instead of needles reported the same "cure" as those who got two different versions of acupuncture.

In other words, acupuncture doesn't work. The scientific evidence is conclusive. Acupuncture is associated with a potent placebo effect but that's all. Patients can't tell the difference between needles and toothpicks. As long as they think they're getting the full-blown acupuncture treatment they'll report an improvement in lower back pain.

Here's the description of the toothpick technique that "cures" back pain.
Simulated acupuncture. We developed a simulated acupuncture technique using a toothpick in a needle guide tube, which was found to be a credible acupuncture treatment by acupuncture-naïve patients with back pain.Simulating insertion involved holding the skin taut around each acupuncture point and placing a standard acupuncture needle guide tube containing a toothpick against the skin. The acupuncturist tapped the toothpick gently, twisting it slightly to simulate an acupuncture needle grabbing the skin, and then quickly withdrew the toothpick and guide tube while keeping his or her fingers against the skin for a few additional seconds to imitate the process of inserting the needle to the proper depth. All acupuncture points were stimulated with toothpicks at 10 minutes (ie, the acupuncturist touched each acupuncture point with the tip of a toothpick without the guide tube and rotated the toothpick clockwise and then counterclockwise less than 30°) and again at 20 minutes just before they were "removed." To simulate withdrawal of the needle, the acupuncturist tightly stretched the skin around each acupuncture point, pressed a cotton ball firmly on the stretched skin, then momentarily touched the skin with a toothpick (without the guide tube) and quickly pulled the toothpick away using the same hand movements as in regular needle withdrawal. The acupuncturists simulated insertion and removal of needles at the 8 acupuncture points used in the standardized treatment.
Just about anyone could be trained to do this. Think of how much unnecessary back pain could be eliminated if spouses and friends would just poke each other with toothpicks!

I think I'll ask Ms. Sandwalk to try it next time my back hurts.


Monday's Molecule #121: Winner

 
UPDATE:The image is a 2D Nuclear magnetic resonance spectrum of cane sugar from the Nobel website. This kid of image can only be produced by mathematically transforming the primary data to create a multidimensional representation. Richard Ernst discovered the Fourier transform method that led to solving three dimensional structures by NMR. He won a Nobel Prize in 1991.

This week's winner is Michael Clarkson of Waltham MA (USA). The dominance of Canadians is coming to an end.




This is a true representation of the structure of a biological molecule but I don't expect you you to guess the molecule. Instead, you have to explain what this image is depicting and how it relates to a Nobel Laureate.

There is one Nobel Laureate who is most closely identified with this particular type of image. You have to identify the Nobel Laureate and what the prize was for. Be careful, because I'm looking for the pioneer in this field and not for other Nobel Prize winners who may have come later. Be sure to check the list of previous Nobel Laureates on Sandwalk.

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: Maria Altshuler of the University of Toronto, 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 and Adam Santoro of the University of Toronto.

The Canadians are still ahead in the competition between Canadians the rest of the world but Dima and Laura are at least keeping it from being a total rout.

I still have one extra free lunch donated by a previous winner 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.





Tuesday, May 12, 2009

Monday's Molecule #121

 
This is a true representation of the structure of a biological molecule but I don't expect you you to guess the molecule. Instead, you have to explain what this image is depicting and how it relates to a Nobel Laureate.

There is one Nobel Laureate who is most closely identified with this particular type of image. You have to identify the Nobel Laureate and what the prize was for. Be careful, because I'm looking for the pioneer in this field and not for other Nobel Prize winners who may have come later. Be sure to check the list of previous Nobel Laureates on Sandwalk.

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: Maria Altshuler of the University of Toronto, 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 and Adam Santoro of the University of Toronto.

The Canadians are still ahead in the competition between Canadians the rest of the world but Dima and Laura are at least keeping it from being a total rout.

I still have one extra free lunch donated by a previous winner 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.


E.O. Wilson in New York

It was Saturday morning and I was in the offices of the New York Academy of Sciences on the 40th floor of 7 World Trade Center. The view to the East was spectacular. We could see the Brooklyn bridge and the 59th Street bridge with Brooklyn and Queen's in the background.

I love cities, I love the tall buildings and the hustle and bustle of the street life.

E.O. Wilson was about to kick off the opening session of The Two Cultures in the 21st Century. I had never heard him in person so I grabbed a good seat and settled down.

Most of his talk was about imaging the brain, behaviorial psychology, and evolutionary psychology. His main point was that scientists are learning a lot about how the brain works and this brings together the humanities and science. E.O. Wilson favors consilience.

Let me give you one example from his talk to illustrate the concept. Wilson talked about a study that was done to determine the ideal environment for humans. People were asked to identify their favorite scenes and the results were used to derive a composite view of what the ideal human environment would look like.

Wilson illustrated it with a slide taken from the third or fourth floor of the John Deere headquarters in Illinois. The view showed extensive grasslands with some water in the foreground. The trees had large branches that were almost parallel to the ground. Massive abstract sculptures evoked an image of large animals.

According to Wilson, this idealized environment is an ancient memory of the environment where we evolved. Our ancestors lived in caves on a cliff side overlooking a savanna full of large animals. The trees of the savanna have branches that are almost parallel to the ground. We like to have water nearby. This is why the typical modern human prefers that type of environment. Science and beauty come together.

Here's how Wilson describes it in The Creation: An Appeal to Save Life on Earth pp. 66-67.

…Researchers have found that when people of different cultures, including those of North America, Europe, Asia and Africa, are given freedom to select the setting of their homes and work places, they prefer an environment that combines three features. They wish to live on a height looking down and out, to scan a parkland with scattered trees and copses spread before them, closer in appearance to a savanna than either a grassland or a closed forest, and to be near a body of water, such as a lake, river, or sea. Even if all these elements are purely aesthetic and not functional, as in vacation homes, people who have the means will pay a very high price to obtain them.

There is more. Subjects in choice tests prefer their habitation to be a retreat, with a wall, cliff, or something else solid to the rear. They want a view of fruitful terrain in front of the retreat. They like large animals scattered thereabout, either wild or domestic. Finally, they favour trees with low horizontal branches and divided leaves. It is probably not a coincidence that some people, I among them, consider the Japanese Maple the world’s most beautiful tree.

These quirks of human nature do not prove but are at least consistent with the savanna hypothesis of human evolution. Supported by considerable evidence from fossil record, this interpretation holds that human beings today still choose the habitats resembling those in which our species evolved in Africa during millions of years of prehistory.

I realized then and there that I was a strange sort of human. My love of cities must be some kind of aberration. I also realized in an instant that all of my mother's ancestors from the past 2000 years must have been desperately unhappy. They all come from Northern Europe where they lived in clusters of small farms in rolling hills covered in dense forest. The only thing they had going for them was the presence of large animals in the barns. How sad.


[Photo Credit: ©John Deere (John Deere Attractions)]

New York City: Theater and Dinner

 





The Human Genome Sequence Is not Complete

 
The latest version of the human genome sequence is called Build 36 or GRCh37. Here's an overview from the Genome Reference Consortium.


The large red triangles represent regions where there is a lot of variability so that no single representation of the genome sequence will describe a majority of humans.

The black regions represent parts of the chromosomes that have not been sequenced and assembled into long stretches (contigs) of reliable sequence. Most of the unsequenced regions are at centromeres, or telomeres, or on the Y chromosome. These regions consist of thousands of copies of highly repetitive DNA. It is impossible to assemble these repetitive sequences.

Scientists are urging that more attention be focused on completing the chimpanzee and macaque genome sequences. We have been waiting a long time for the draft sequences of those genomes to be finished. The explosion of data on the human genome can only be realistically evaluated by comparing it to our closest relatives. (For example, are human non-coding RNAs conserved in primates?)

The fact that the human genome is not complete is not a problem. We know what's in the repetitive sequence regions even though we don't know exactly how it is arranged. The effort required to finish of the last bit is probably not as important as getting a final draft of other sequences.

Sandra Porter wonders Why don't we finish the human genome first?.


Jason Rosenhouse Doesn't Understand Pluralists

 
Jason Rosenhouse has posted some comments on a recent book review by Richard Lewontin. In that book review, Lewontin—who along with Gould is the co-author of the spandrels paper—questions the emphasis on natural selection and the use pf "Darwinism" as a synonym for evolution. Read Lewontin on Darwin to see what Jason thinks of the book review.

I want to focus on a specific question that Jason Rosenhouse asks.
I've never really understood what it is exactly that anti-selectionists are complaining about. If they agree that complex adapations arise as the result of gradual accretion mediated by natural selection, then I fail to see how they are really so different from people like Richard Dawkins or Daniel Dennett (two people often described as being beknighted uber-selectionists). If they do not agree then I would like to hear their proposed alternative mechanism.
The original paper by Gould and Lewontin, The Spandrels of San Marco and the Panglossian Paradigm: A Critique of the Adaptationist Programme, explains the problem very well. The authors begin their criticism with ...
We wish to question a deeply engrained habit of thinking among students of evolution. We call it the adaptationist programme, or the Panglossian paradigm. It is rooted in a notion popularized by A.R. Wallace and A. Weismann, (but not, as we shall see, by Darwin) toward the end of the nineteenth century: the near omnipotence of natural selection in forging organic design and fashioning the best among possible worlds. This programme regards natural selection as so powerful and the constraints upon it so few that direct production of adaptation through its operation becomes the primary cause of nearly all organic form, function, and behavior. Constraints upon the pervasive power of natural selection are recognized of course (phyletic inertia primarily among them, although immediate architectural constraints, as discussed in the last section, are rarely acknowledged). But they are usually dismissed as unimportant or else, and more frustratingly, simply acknowledged and then not taken to heart and invoked.
The anti-selectionists—I am one—do not question the fact that adaptations are produced by natural selection. What we question is whether everything in evolution is an adaptation. We question those who think that "evolution" and "natural selection" are synonyms. And since "Darwinism" is equivalent to evolution by natural selection we question whether evolution is the same as Darwinism.

We pluralists like to point out that much of evolution is due to random genetic drift. Since Darwin's name is not associated with the theory of evolution by random genetic drift, it is inappropriate to say that all of evolution is Darwinist.

It's not that complicated. It was all explained in the classic spandrels paper published 30 years ago. Complex biological structures may be due entirely to adaptation, or they may be mostly an accident that's arisen by random genetic drift, or they may be due to combinations of drift and selection.


Friday, May 08, 2009

What do protein crystallographers dream of?

 
"What do protein crystallographers dream of?" is the question asked by Ananyo Bhattacharya in an article published in Nature [Protein structures: Structures of desire].

The structures of many protein complexes have been determined but crystallographers have a list of holy grails that, so far, have eluded them. It's an interesting list and one that I mostly agree with. Can you identify the structure shown here in cartoon form?

One glaring omission is pyruvate dehydrogenase. Lot's of people want to see that structure. Other notable omissions include complex I of the membrane-associated electron transport chain and the protein import complex of the endoplasmic reticulum. Don't protein crystallographers dream of those?


The Biology Textbooks Are Wrong?

 
The other day I suggested that Casey Luskin was probably just ignorant. Unlike other creationists, he problably isn't a liar. Today I'm not so sure.



What is it with FOX news?


Thursday, May 07, 2009

Win Free Prizes from Denyse O'Leary

 
Every week there are dozens of people who try to guess Monday's Molecule and win a free lunch with me. Now, that's a valuable prize—it's no wonder that so many people are trying to win.

Now you've got another chance to win valuable prizes. Denyse O'Leary is giving out prizes for people who comment on Uncommon Descent [Earn free stuff!: The Uncommon Descent Contest].

What are the prizes?
  • 10 DVDs of Expelled,courtesy the producers.
  • 10 DVDs of Privileged Planet, courtesy the producers.
  • 5 subscriptions, including back issues, to the excellent Christian/theistic science and culture mag, Salvo, complete with recent back issues, courtesy the editor-in-chief.
Looks like I've got serious competition!

Here's the first contest question: Does the multiverse help science make sense - or simply destroy science?. Hmmm ... I wonder what the right answer is?



Casey Luskin Writes About the Universal Common Ancestor

 
Casey Luskin is writing about the tree of life and the universal common ancestor. The second installment in a series of five posting is here.
When speaking to the public, evolutionists are infamous for overstating the evidence for universal common ancestry. For example, when speaking before the Texas State Board of Education in January, 2009, University of Texas evolutionist biologist David Hillis cited himself as one of the “world’s leading experts on the tree of life” and later told the Board that there is “overwhelming agreement correspondence as you go from protein to protein, DNA sequence to DNA sequence” when reconstructing evolutionary history using biological molecules. But this is not accurate. Indeed, in the technical scientific literature, one finds a vast swath of scientific papers that have found contradictions, inconsistencies, and flat out failures of the molecular data to provide a clear picture of phylogenetic history and common descent.

Indeed, the cover story of the journal New Scientist, published on the very day that Dr. Hillis testified, was titled, “Why Darwin was wrong about the tree of life.” Directly contradicting Hillis’ gross oversimplification of molecular systematics, the article reported that “The problem was that different genes told contradictory evolutionary stories.” The article observed that with the sequencing of the genes and proteins of various living organisms, the tree of life fell apart:
It's true that things are very confusing at the base of the tree of life. The evidence indicates that genes were frequently exchanged between primitive prokaryotic species and this means there is no single tree that represents all of life.

But this doesn't negate the idea of a universal common ancestor. The origin of life could still be a unique event that gave rise over millions of years to many different descendants that subsequently exchanged genes. Or, there may have been a few independent origins of life.

The available evidence shows that most fundamental properties of life are shared by all living things (e.g. basic metabolic pathways, genetic code). This is consistent with a unique origin of life but it's also consistent with multiple origins as long as only one version of each process has survived. The odds favor a single origin and a universal common ancestor.

What's interesting about Luskin's article is that he is hopelessly confused about the difference between a phylogenetic tree and the origin or life. He seems to think that a bushy tree with many interconnecting branches rules out a universal common ancestor. I don't know what he postulates in its place unless the idea of God creating three or four different primitive prokaryotes is what appeals to him more than God just doing it once.

Intelligent Design Creationists come in many different flavors. Often it's hard to decide whether they are being deceptive (lying) or just ignorant. I think that Casey Luskin is just ignorant. He finds it difficult to make a coherent argument and he doesn't take the time to learn more about his subject. In that sense, he's much less dangerous than Jonathan Wells.


Call a Canadian!!

 
Dear Americans,

Have you ever thought about asking an average Canadian what they think of their health care system? Read Call a Canadian on Effect Measure.


Oops! Did New Scientist Goof Again?

 
New Scientist published an article on Science and art: Still two cultures divided?.

The journal invited six people to comment on the two cultures. Here's the list ....
  • Stefan Collini is a professor of literature and intellectual history at the University of Cambridge. He edited The Two Cultures (1993, CUP)
  • Susan Haack is a professor of philosophy and a professor of law at the University of Miami, Florida
  • Harry Collins is professor of sociology at Cardiff University in the UK
  • Mary Midgley is a philosopher and writer
  • Sandra Harding is a philosopher and professor of education at the University of California, Los Angeles
  • A. C. Grayling is a professor of philosophy at Birkbeck, University of London
A perceptive commenter (Khoo) asks, "Why was an entire article written about the divide between the arts and the sciences, and not a single physical scientist or mathematician interviewed? Does the author believe these scientists have nothing to say about the arts?"

Good point. A classic demonstration of the two cultures in action.


Wednesday, May 06, 2009

Atheists Serve the Devil!

 

Who knew? I wonder what the Devil eats for lunch? If I'm going to serve him I'd better find out.

Is he a big tipper?

This is Pat Robertson responding to a question. A caller wants to know how she, a Christian, can get along with her boyfriend, an atheist. Can you guess how the good Christian responds? Think about it, then watch.




[Hat Tip: Friendly Atheist]

How to Frame a Null Hypothesis

A reader has alerted me to an article by Michael White at Adaptive Complexity: Genomic Junk and Transcriptional Noise.
With hot, new technologies, biologists are taking higher-resolution snapshots of what's going on inside the cell, but the results are stirring up controversy. One of the most interesting recent discoveries is that transcription is everywhere: DNA is transcribed into RNA all over the genome, even DNA that has long been thought to have a non-functional role. What is all of this transcription for? Does the 'dark matter' of the genome have some cryptic, undiscovered function?

Unfortunately, in all of the excitement over possible new functions, many biologists have forgotten how to frame a null hypothesis - the default scenario that you expect to see if there is no function to this transcribed DNA. As a result, the literature is teeming with wild, implausible speculation about how our excess DNA might be beneficial to us.

So here, let's step back and look at what we expect from DNA when it's playing absolutely no functional role; in other words, let's look at the null hypothesis of genomic junk and transcriptional noise. We can then take our null hypothesis and use it to look at a fascinating new study of how genomic parasites sculpt transcription in our cells.
If you are interested in what's wrong with science these days then you must read his article.

The point is not whether you believe that all transcription is adaptive and functional, or whether you believe that most of it is noise. The real point is that it is very bad science to ignore the null hypothesis and publish naive speculation as if it were the only possible explanation.

Whenever you see a paper that fails to address the null hypothesis you can be sure that you are reading bad science. Everything else in the paper is suspect.

The key fact that most scientists are overlooking is that RNA polymerase and the various transcription factors must bind non-specifically at thousands of sites in a random sequence of junk DNA. This is just basic biochemistry of the sort that should be taught in undergraduate classes. Transcription will be initiated by accident at some of these sites even though they are not functional promoters. Again, this is basic biochemistry.


[Image Credit: Horton et al. Principles of Biochemistry 4/e p.657]

Two Cultures in New York City

 
Tomorrow is the 50th anniversary of a lecture by C.P. Snow on The Two Cultures.

He said,
A good many times I have been present at gatherings of people who, by the standards of the traditional culture, are thought highly educated and who have with considerable gusto been expressing their incredulity at the illiteracy of scientists. Once or twice I have been provoked and have asked the company how many of them could describe the Second Law of Thermodynamics, the law of entropy. The response was cold: it was also negative. Yet I was asking something which is about the scientific equivalent of: 'Have you read a work of Shakespeare's?'

I now believe that if I had asked an even simpler question — such as, What do you mean by mass, or acceleration, which is the scientific equivalent of saying, 'Can you read?' — not more than one in ten of the highly educated would have felt that I was speaking the same language. So the great edifice of modern physics goes up, and the majority of the cleverest people in the western world have about as much insight into it as their Neolithic ancestors would have had.
Not much has changed in fifty years. We still live in a society that is at best scientifically illiterate and, at worst, anti-science.

Tomorrow I'll be on my way to New York City to attend a conference on The Two Cultures in the 21st Century. The meeting was organized (in part) by Chris Mooney and Sheril Kirshenbaum. It begins with a keynote address by E.O. Wilson followed by four symposia on ...
  • The Two Cultures in Historical Perspective: From Aristotle to "Science Wars" and the "Third Culture"
  • How to More Effectively Communicate Science Issues to the Public
  • Restoring Science to Its Rightful Place in Politics
  • A Better Future through Science Citizenship
Carl, (I Got Your Two Cultures Right Here), Zimmer will be there.

We all have our stories and our examples of the problem. The one I like to tell is the story about a group of knowledgeable adults at a cocktail party when something mathematical comes up in the conversation. Chances are someone is going to brag about how much they feared math in schools and how little they know about the subject. This will undoubtedly get murmurs of sympathy from many people.

Now imagine that the group was discussing modern literature and I said something similar; "I hated literature in school, I never 'got' the point of these modern writers and why they are so famous. Literature was way too hard for me so I stopped taking literature courses as soon as I could." Do you think there would be murmurs of sympathy and understanding? I doubt it. The group would probably think I'm stupid.

The two cultures problem will only be solved when the proper response to someone who claims to be an idiot in mathematics is the same as to someone who claims to be an idiot about art and literature.

The other problem is when people claim to be knowledgeable about science when they aren't. Chris Matthews of MSNBC has the right idea when he attacks Rep. Mike Pence (Indiana-R) ["You Want to Educate Americans About Science; Do You Believe In Evolution?"]. We can't allow people to pretend they know about science when they reject the core principles of science. If you are ignorant about science then you are ignorant, period.

Today's issue of New Scientist has an article on Science and art: Still two cultures divided? .


On the Origin of Chloroplasts

 
We know that many species contain chloroplasts. In most cases, these species descend directly from a common ancestor that acquired the chloroplast through an endosymbiotic relationship with a cyanobacterium. The endosymbiotic origin of chloroplasts from cyanobacteria is not in doubt.

What is in doubt is whether the original endosymbiosis happened just once or whether there are multiple independent origins of chloroplasts. We also know that some species acquired chloroplasts by fusing with another chloroplast-containing eukaryotic species. How many examples of secondary acquisition are required to explain the phylogeny of species that contain chloroplasts? Are there tertiary and quaternary acquisitions?

Christopher Taylor of Catalogue of Organisms has posted a nice summary of the problems in this field at Crossing the Algal Divide. If you want to keep up with one of the important problems in evolution then this is an excellent place to start.


[Photo Credit: micro*scope]

Tuesday, May 05, 2009

Monday's Molecule #120: Winners

 
UPDATE: The image depicts the genome of a human papillomavirus. The Nobel Laureate is Harald zur Hausen.

This week's winners are Dima Klenchin of the University of Wisconsin and Adam Santoro of the University of Toronto. They were the first of many who got the right answer. This surprises me 'cause I thought it would be harder. I didn't realize how easy it was to get the molecule by searching for "E6" or "E7."




This is a cartoon showing the genes present in a particular DNA molecule. Your task is to identify the kind of DNA molecule being depicted.

There is one Nobel Laureate who is most closely identified with this particular type of molecule. You have to identify the Nobel Laureate and what the prize was for.

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 six ineligible candidates for this week's reward: Shumona De of Dalhousie University, Maria Altshuler of the University of Toronto, Mike Fraser of Toronto, Alex Ling of the University of Toronto, Laura Gerth of the University of Notre Dame, and Stefan Tarnawsky of the University of Toronto.

The Canadians continue their total dominance of the rest of the world. That's as it should be.

I still have one extra free lunch donated by a previous winner 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.


How to Teach Evolution?

 
You're not going to believe this. The National Institute of General Medical Sciences (NIGMS), the Office of Science Education (OSE), and the National Academy of Sciences (NAS) sponsored Matt Nisbet to give a lecture on Communicating About Evolution.

Who knew that Matt was an expert on evolution? Here's what Matt says about the lecture on his website [Video for NAS Lecture: Communicating about Evolution].
For readers of this blog and followers of the "Framing Science" thesis, the National Academies presentation is the most detailed lecture I have given on how to effectively engage with the public on the relationship between science and religion and the specific topic of evolution. The lecture follows closely articles and book chapters that I have previously published or that are forthcoming.
Near the end of his lecture Matt defends the "frame" of emphasizing that religion and science are not in conflict (~50 minutes). In this context, frame is not much different than spin and spin is not much different than lie. The truth is that science and religion are often in conflict. Any statement to the contrary is not the truth.

Matt's views about framing have been so thoroughly rejected by scientists that The National Institute of General Medical Sciences (NIGMS), the Office of Science Education (OSE), and the National Academy of Sciences (NAS) should be ashamed of themselves.


See Matt Nisbet Endorses Francis Collins for Presidential Science Advisor - The Kiss of Death for an example of how Nisbet wants to frame the debate.

Do High School Student Want to Become Scientists?

 
Do High School Student Want to Become Scientists? the answer is, no [Is Canada losing the lab-rat race?].
"Look up 'scientist' on Google," the 16-year-old says, "and you will see someone in a lab coat." At the moment, she is considering something with more immediate results, such as physiotherapy.

Ask her biology classmates at Colonel By Secondary School in Ottawa if any of them want to be scientists and only a few tentative hands flicker up. What's worrying is that this is no average high-school science class. It is part of the International Baccalaureate program, chosen from a large pool of applicants. These are students who spend half of their time in labs, working through experiments, not dozing off during lectures - the kind of education most scientists wish they had had. If any group should be producing lab-coat keeners, it should be this one.

Julia Dutaud, 16, sitting in the back in her school-rugby T-shirt, would like to study environmental science - a field growing as rapidly as any - but she wonders if she could make a good living at it: "Going into science would be a nice thing to do," she says. "But we aren't sure how much opportunity we would get after university."

Half the students are planning to be doctors instead, a profession they and their parents consider more stable.
I don't think this is a new problem. Back in the olden days, there also weren't a huge number of high school students who wanted to be scientists. Why should there be a significant number in a typical high school class? At my university there are about 8,000 students entering first year and about 400 or so want to pursue a career in science. That's about right—half of them (200) will be able to enter graduate school when they graduate and that's also about right. It means that a typical high school science class of 25 students will likely have only two or three who want to be scientists.

It would be a disaster if half of every high school science class wanted to become scientists because the vast majority would be disappointed.

There's another problem not covered in the Globe and Mail article. In my experience, many students don't begin to understand what a scientist is until they get to university and start seeing them in their natural environment. A surprising number of high school students think you have to be a physician in order to do the cool research on genes and diseases. It's only after they get to university that they learn the difference between a physician and a scientist.

When did you, dear reader, first develop a serious interest in science? Was it in high school or university? Is it a problem that there aren't more high school students who want to become scientists?


Science Education in Alberta

 
The Alberta legislature is considering a law that allows parents to pull their children out of certain classes if those classes conflict with the family's religion. Many people interpreted this to mean that parents could take their children out of biology classes when evolution is being taught [see Don't Like Evolution in Alberta?].

According to an article in The Globe and Mail this may have been an over-reaction [Alberta law imperils teaching of 'religious' topics like evolution, critics fear]. While the opposition parties are incensed and the school teachers are angry, it appears that there is at least one senior government official who knows the difference between science and religion.
Frank Bruseker, head of the Alberta Teachers' Association, said he is also concerned about what the new rules could mean.

He is worried that some parents might think mentioning different classes of worms would constitute a reference to evolution.

And he said no discussion of ancient geologic formations can be had without mentioning the world is billions of years old, much more than a literal reading of the Bible would suggest.

Meanwhile, history and literature from around the world are full of references to religious upheaval.

"Religion is kind of a fuzzy thing, in a sense, in that what some people see as religion others might not," Mr. Bruseker said.

Opposition parties have hammered the government on the issue, saying the province is headed back to the time of the 1925 Scopes trial, in which a high school biology teacher in Tennessee was tried for teaching Darwin's theory of evolution.

Premier Ed Stelmach conceded to reporters last week that the provision could be used to pull students out of classes dealing with evolution if parents preferred their kids be taught what's in the Bible instead.

"The parents would have the opportunity to make that choice," he told a news conference.

But Lindsay Blackett, the minister responsible for human rights, said in an interview that the intention of the law is to allow parents to pull children out only when the curriculum specifically covers religion, something that happens for a few hours each school year.

"It's talking about religion [such as] Hindu, or Muslim, or that type of religion, not ... the curriculum with respect to, for instance, evolution," he said.

"That's science and we're not arguing science."
I hope he (Blackett) is right and not the premier. I hope the new legislation will contain an amendment making it clear that students cannot be taken out of science classes when evolution is covered. It's nice to see so many teachers and politicians in Alberta standing up for science.


[Photo Credit: Minister of Culture and Community Spirit]

Politics and the Judicial Branch in America

 
Since America is a "nation of laws" it becomes very important to pass the "right" laws and to make sure that the American Supreme Court upholds them. To this end, each side of an issue wants to stack the Supreme Court with their sympathizers. Now that one of the members of the Supreme Court has retired, the lobbying to replace him has begun.

Eddie Tabash is very interested in the separation of church and state issue and he wants the next Supreme Court justice to be sympathetic to his point of view on the law. Apparently, there are well-qualified judges who would not be sympathetic, so the nomination process becomes highly politicized. Apparently, the Democrats want a judge who will agree with Tabash while the Republicans want a judge who might favor different laws.

Tabash has written a special article on RichardDawkins.net explaining how the process works [ It happened. There is now a Supreme Court vacancy]. It's very helpful for those of us in other countries. The politicization of the Judicial Branch of government seems very bizarre.


[Photo Credit: Tim Dillon, USA TODAY]

Monday, May 04, 2009

Monday's Molecule #120

 
This is a cartoon showing the genes present in a particular DNA molecule. Your task is to identify the kind of DNA molecule being depicted.

There is one Nobel Laureate who is most closely identified with this particular type of molecule. You have to identify the Nobel Laureate and what the prize was for.

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 six ineligible candidates for this week's reward: Shumona De of Dalhousie University, Maria Altshuler of the University of Toronto, Mike Fraser of Toronto, Alex Ling of the University of Toronto, Laura Gerth of the University of Notre Dame, and Stefan Tarnawsky of the University of Toronto.

The Canadians continue their total dominance of the rest of the world. That's as it should be.

I still have one extra free lunch donated by a previous winner 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.


Sunday, May 03, 2009

Theistic Evolution: How Does God Do It?

Theistic Evolution is a form of creationism that limits God's involvement in the creation event. The chief limitation is that most of God's activity have to be consistent with the facts of evolution.

Francis Collins has created a website devoted to his concept of BioLogos, which, it turn out, is just another word for Theistic Evolution. The website is funded by a grant from the John Templeton Foundation.

Many of us have difficulty understanding how a personal God can be involved in guiding evolution without violating the laws of physics and chemistry. In other words, how is Theistic Evolution/BioLogos compatible with science? This is a key question since we know that major scientific organizations (AAAS, NAS, NCSE) support the notion that science and religion are compatible. In fact, they explicitly support Francis Collins and Theistic Evolution.

Let's see how science and religion are compatible by looking at Question 14 on the BioLogos website [What role could God have in evolution?].
Divine Action is defined as God’s interaction with creation. Due to the understanding that evolution accounts for the diversity of present life forms, it might appear God played no role in the process of evolution. (See Question 26 about The Complexity of Life.) Clearly this contradicts the central doctrine of creation for many faiths. Christianity, for example, professes a God actively involved in creation. Many faiths share the concept of an interactive God, or theism. The opposing belief — the belief in an uninvolved, disinterested God — is deism.
Collins sees this a a major problem. According to him, Christians believe in creation and a strictly scientific explanation of evolution seems incompatible with this belief.

Elsewhere on the website, Collins makes it clear that theism is not deism and his view of Theistic Evolution/BioLogos is not deistic. So how does he solve the problem?

Any God worthy of the name has to be capable of miracles, and each of the great Western religions attributes a number of very special miracles to their conception of God. What can science say about a miracle? Nothing. By definition, the miraculous is beyond explanation, beyond our understanding, beyond science.

Ken Miller in "Finding Darwin's God" p. 239
Well, it's not very clear to me. There is some hand-waving and some backhanded suggestions but nothing specific is described. In this sense, the Francis Collins version of Theistic Evolution is similar to that of Ken Miller in Finding Darwin's God. Here's the BioLogos version..
Even before Darwin’s contribution to biology, the scientific revolution in physics marked a tremendous advance in our understanding of the world. Scientists discovered that the world’s behavior could be explained and predicted with great accuracy on the basis of physical laws. Nature, as understood at the time, appeared to reliably follow a set of fundamental rules. For example, the motion of planets could be explained as a necessary result of their obedience to the force of gravity. This understanding of the world lent itself to the belief in a rational, consistent creator.

But, as Polkinghorne puts it, these laws might also come across as “a gift from the Greeks.”5 Given a second look, they challenge basic theism. For as much as these laws signify a rational creator, their trustworthiness could also imply God’s absence. After all, if the laws of nature can explain almost any phenomenon, how is God involved? In order to understand how God could take an active role, or how the world could have any inherent freedom, the laws of nature must be somehow open or flexible. The world’s future cannot be entirely determined or predictable from any given moment.
This is the potential area of conflict. If science says that evolution obeys the laws of physics and chemistry then there's no room for an interventionist God without violating those rules. And if your God does that then there's a conflict between science and religion. They are not compatible.

What to do? Miller and Collins, and many other theists, opt for a solution where God can intervene at the quantum level without ever being detected. Thus, nature only appears to obey the fundamental laws of physics and chemistry because God is clever enough to disguise his interventions.
The mechanical worldview of the scientific revolution is now a relic. Modern physics has replaced it with a very different picture of the world. With quantum mechanical uncertainty and the chaotic unpredictability of complex systems, the world is now understood to have a certain freedom in its future development. Of course, the question remains whether this openness is a result of nature’s true intrinsic chanciness or the inevitable limit to humans’ understanding. Either way, one thing is clear: a complete and detailed explanation or prediction for nature’s behavior cannot be provided. This was already a problem for Newtonian mechanics; however, it was assumed that in principle, science might eventually provide a complete explanation of any natural event. Now, though, we see that the laws of nature are such that scientific prediction and explanation are ultimately limited.

It is thus perfectly possible that God might influence the creation in subtle ways that are unrecognizable to scientific observation. In this way, modern science opens the door to divine action without the need for law breaking miracles. Given the impossibility of absolute prediction or explanation, the laws of nature no longer preclude God’s action in the world. Our perception of the world opens once again to the possibility of divine interaction.

Despite the uncertainty and unpredictability of the world, we are not forced to reject the earlier understanding of God’s creation as consistent and reliable. After all, the world still exhibits the same orderly behavior that inspired so many faithful scientists of earlier centuries. Regardless of the irregularity of tiny,quantum mechanical, or complex, chaos theoretical, systems, the sun stills rises and sets, the tides ebb and flow, and objects fall to the ground. Nature is reliable enough to reflect God’s faithfulness yet flexible enough to permit God’s involvement.
So this is how to make science and religion compatible. Let's restate it so that everyone can grasp the argument,
"... modern science opens the door to divine action without the need for law breaking miracles. Given the impossibility of absolute prediction or explanation, the laws of nature no longer preclude God’s action in the world.."
On the surface it seems to work since, by definition, all of God's interventions and guidance are undetectable. Therefore, there can't be any obvious conflict between the purely modern scientific view of evolution and creationism.

Personally, I don't think you can have your cake and eat it too. Once you start attributing events to God's intervention you are conflicting with a strictly materialistic interpretation of those same events. It doesn't matter whether your God is extremely careful to fool scientists into thinking that evolution is natural. The very act of postulating divine intervention in the natural world is not compatible with the scientific way of knowing.

Here's the bottom line, according to Francis Collins.
Our modern understanding of physical laws combined with a proper understanding of God’s relationship to time can be synthesized into a robust theistic worldview. Darrel Falk provides the following perspective:
“The Bible tells us that God created, but it does not tell us how, and we need to be careful that we do not force the God of the Universe into one of our human molds. […] What do we learn about the nature of God’s activity from studying the Bible? One thing we learn is that God builds freedom into His creation. […] Just as God builds freedom into our lives today, so freedom may well be a central component of God’s biological world as well. This is not to say that God is not playing a supervisory role in creation in a manner resembling the role God plays in my life and yours. But there is no a priori scriptural reason to assume that the biological world was created one species at a time by the God of the Universe “pushing creation buttons” each time he wanted a new species. […] God’s spirit guides the progression of life. His presence is never far from creation, just as it is never far from the events of my life. Nonetheless God respects my freedom and (I suspect) values freedom in the rest of creation as well.”
This is how evolution and creationism are compatible. This idea that "God’s spirit guides the progression of life" is the view that major scientific organizations and the NCSE endorse as being compatible with science.


[Photo Credit: Francis Collins discusses “The Language of God”]

Saturday, May 02, 2009

What American Science Teachers Can't Say

 
John Pieret is a pain in the lawyer. He has something to say about a recent court case [Accommodating the Law].
The latest ruling on the religion-science front is by a Federal judge in California holding that a public school teacher who called creationism "religious, superstitious nonsense," violated a creationist student's First Amendment rights.
Since John has been following the debate on the blogs, he realizes the implications.
The lesson is not restricted to such blatant cases, however. It is clear that a government teacher could not teach that philosophical naturalism is true, as that would clearly render most religions false. And it is more than doubtful that a public school teacher could teach that science was true while, at the same time maintaining that it was in conflict with most religions, since that which is in conflict with the truth is, necessarily, false.
This is pretty much what I thought. High school science teachers cannot say that the deluge never happened and they cannot say that the idea of a 10,000 year-old Earth is wrong.1 That would violate the American Constitution.

God Bless America.


1. I don't understand how they can get away with saying that evolution is true, since that statement is logically equivalent to saying that many forms of creationism are superstitious nonsense.

The Accommodationist Postion in Academic Matters

 
Margaret Somerville has written an essay on Facing up to the dangers of the intolerant university: Bird on an ethics wire. It is published in Academic Matters, the publication of the Ontario Confederation of University Faculty Associations (OCUFA).

Here's her brief biography as published in the journal.
Margaret Somerville is Samuel Gale Professor in the Faculty of Law and a professor in the Faculty of Medicine at McGill University and is the founding director of the McGill Centre for Medicine, Ethics and Law. In 2004, she received the UNESCO Avicenna Prize for Ethics in Science and in 2006 delivered the prestigious Massey Lectures.
I agree with a lot of what Somerville has to say about rampant political correctness in the universities.
That is where political correctness enters the picture. It excludes politically incorrect values from the “all values are equal” stable. The intense moral relativists will tolerate all values except those they deem to be politically incorrect—which just happen to be the ones that conflict with their values.

Political correctness operates by shutting down non-politically correct people’s freedom of speech. Anyone who challenges the politically correct stance is, thereby, automatically labeled as intolerant, a bigot, or hatemonger. The substance of their arguments against a politically correct stance is not addressed; rather people labeled as politically incorrect are, themselves, attacked as being intolerant and hateful simply for making those arguments. This derogatorily -label-the-person-and-dismiss-them-on-the-basis-of-that-label approach is intentionally used as a strategy to suppress strong arguments against any politically correct stance and, also, to avoid dealing with the substance of these arguments.
However, I also agree with Jeffrey Shallit that she applies her own standards inconsistently, such as when she insists that physicians are being "forced" to act against their conscience when treating certain patients [Margaret Somerville in "Academic Matters"].

Shallit is an expert on the difference between real free speech and its imposters.

I'd like to focus on another part of Somerville's essay.
Sixth, not only can we, but we must, cross the secular/religious divide, the science/religion divide and the divide between religions, if we are to find a shared ethics. This is where I believe both the fundamentalist religious people and the fundamentalist neo-atheists are wrong because they demand that we choose between religion and science. We must accommodate both.

Some would like to reduce religion to being seen as nothing more than a personal fantasy or superstition. But that’s not realistic. At best it will fail; at worst it will do serious harm because it will exacerbate the acrimony of the values conflicts and make it more likely, not less likely, that religion will become a focus of serious conflict. Also, because culture and religion are linked, even within democratic, multicultural, pluralistic Western societies, it will increase the number and intensity of the current values clashes and may contribute to culture wars.
I'm not sure what this means. I believe that religion is a superstition and I advocate a non-religious society. According to Somerville the "best" thing that could happen is that I will fail to convince people. The worst thing that will happen is that I will succeed but the result will make religion the focus of serious conflict. What a strange choice. The second option is exactly my goal.

I suppose the politically correct thing to do is to accommodate because we certainly can't have a situation where religion is challenged, can we?

Somerville says that religion and culture are linked. That's correct. It's an attitude that I want to change and there's lots of evidence that it is changing in other countries. Did this lead to "culture wars"? Yes, it did in some places—notably the Canadian province of Quebec in the 1960's. What Somerville fails to address is whether the culture wars are a good thing or a bad thing. She seems to be implying that we should not criticize religion because religious people might be upset. Don't we have a word for that kind of thinking?


[Photo Credit: The Catholic Registrar]

Vanier Canada Graduate Scholarships

 
There are 166 winners of Vanier Canada Graduate Scholarships. Of these, 34 are from the University of Toronto and several will be in the labs of my close colleagues. Congratulations to all the winners.

The scholarships will be administered by the three granting councils and each one is worth an astonishing $50,000 per year. That means that these scholarships amount to twice the level of funding of a typical graduate student at my university.

There's no sound logic behind awarding such a sum. T. Ryan Gregory points out that if the scholarships had been for $25,000 per year, the excess could have funded 73 research grants at an average of $34,000 per year. I agree that this money could have been better spent.