Matt Tries Framing for the Umpteenth Time

 
Matt Nisbet promotes two of his essays that have just been published. He summarizes them in Two Essays on Expelled, Dawkins, and PZ by saying ...

In both essays, I draw attention to the confusing messages that scientist pundits such as Richard Dawkins and PZ Myers continue to send to the wider American public. By combining their attacks on religion with their defense of evolution, they blur the lines between science, religion, and atheism, providing fodder to creationists who claim that evolution is part of a larger atheist agenda. These confusing messages are only likely to be amplified next year during the anniversary celebration of Charles Darwin, as Dawkins goes on a publicity tour for his new book and Myers is reported to also have a book in the works.

Poor old Matt. He just doesn't get it. There's no confusion. Dawkins and PZ (and me) are on the side of rationalism in the war between rationalism and superstition. Evolution is part and parcel of the rationalism perspective while religion and creationism are on the other side.

The only person who is confused is Matt Nisbett because he wants to spin frame the debate differently. It isn't working for him 'cause Dawkins and PZ aren't playing his game.

At the end of the second essay Matt Nisbet comes very close to saying that Dawkins and Myers should shut up because they are interfering with the Nisbett spin frame.

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Everything Is There for a Reason?

 
Nils Reinton of The Sciphu Weblog has just posted an article entitled Junk, DNA, RNA, Brain, Biology and Possible Solutions.

Nils makes the point that biology is very complex and we may only have scratched the surface. He then writes,

New ideas, approaches and tools are needed to explain how this seemingly chaotic system works. Dismissing reasons for the obvious complexity using terms like “junk-DNA” is not going to get us anywhere.

Instead, let’s start by acknowledging that we know very little. All we know is that function comes out of an apparent chaotic mixture of DNA protein and RNA. Let’s assume that everything is there for a reason. Without reason you loose hope and visions and those are qualities that science is vitally dependent upon.

This statement combines two of my pet peeves. First, our use of the term "junk" DNA is not based on ignorance in spite of what Nils implies. We know, for example, that 50% of our genome consists of defective transposons. That looks like junk to me [Genomes & Junk DNA]. It makes me really, really annoyed when fellow scientists assume that junk DNA supporters are basing their entire argument on lack of knowledge about biology. Instead, it appears that the other side is the guilty party.

Second, by explicitly stating that one should assume that everything is there for a reason, Nils is making the case for adaptationism. It's a weak case. Why should we assume, without evidence, that everything is an adaptation? Why not consider the possibility that it may have no function and proceed to investigate while keeping an open mind? [Adaptationomics] If becoming a pluralist makes you lose hope and visions then maybe you're in the wrong business.

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We Need to Soften the Modern Synthesis

Lately there's been a lot of talk about updating evolutionary theory. Much of the hype has been generated by journalist Susan Mazur who has been drawing attention to a meeting that took place in July. At that meeting there were 16 people interested in evolution. They met at the Konrad Lorenz Institute for Evolution and Cognition Research in Altenberg, Austria. Their goal was to reach a consensus on what needs to be added to evolutionary theory in order to bring it up to date. They've been dubbed the "Altenberg 16."

The current version of evolutionary theory is often referred to as the Modern Synthesis—a term coined by Julian Huxley to describe the consensus reached by evolutionary biologists in the late 1940's. That version of evolutionary theory was appropriately pluralistic, giving prominence to random genetic drift as an important mechanism of evolution.

By the time of the Darwinian centennial celebrations in 1959, the Modern Synthesis had hardened to the point where random genetic drift was barely mentioned. Most prominent evolutionary biologists were confirmed adaptationists—including those who had been more open-minded a decade earlier.

The Altenberg 16 have some interesting ideas but unfortunately, they are also lending their reputations to some ideas that are just plain crazy. Let's see how a prominent science journalist, Elizabeth Pennisi, handles the issue in an article for Science magazine [Modernizing the Modern Synthesis].

That hyperbole has reverberated throughout the evolutionary biology community, putting Pigliucci and the 15 other participants at the forefront of a debate over whether ideas about evolution need updating. The mere mention of the "Altenberg 16," as Mazur dubbed the group, causes some evolutionary biologists to roll their eyes. It's a joke, says Jerry Coyne of the University of Chicago in Illinois. "I don't think there's anything that needs fixing." Mazur's attention, Pigliucci admits, "frankly caused me embarrassment."

That's a pretty accurate commentary on how the Alternberg 16 are viewed by most evolutionary biologists. They don't think the Modern Synthesis needs fixing. But—and this is a big "but"—they are referring to the hardened version of the Modern Synthesis; the version that can be described as ultra-Darwinian. The version that Stephen Jay Gould and others have been trying to change since 1970.

Elizabeth Pennisi seems completely unaware of this controversy in evolution. Here's how she describes modern evolutionary theory ...

Modern tradition

The modern synthesis essentially represents a marriage of the 19th century concept of evolution with Mendelian genetics, which was rediscovered at the beginning of the 20th century; the birth of population genetics in the 1920s added to the intellectual mix. By the 1940s, biologists had worked out a set of ideas that put natural selection and adaptation at evolution's core. Julian Huxley's 1942 book, Evolution: The modern synthesis, brought together this work for a broad audience.

Simply put, the modern synthesis holds that organisms have a repertoire of traits that are passed down through the generations. Mutations in genes alter those traits bit by bit, and if conditions are such that those alterations make an individual more fit, then the altered trait becomes more common over time. This process is called natural selection. In some cases, the new feature can replace an old one; in other instances, natural selection also leads to speciation.

This is definitely not the pluralism promoted by Gould and others and it's not even the original version of the Modern Synthesis published in the 1940's. Two of the key principles of the original Modern Synthesis were ...

5. Evolutionary change is a populational process: it entails, in its most basic form, a change in the relative abundances (proportions or frequencies) or individual organisms with different genotypes (hence, often with different phenotypes) within a population. One genotype may gradually replace other genotypes over the course of generations. Replacement may occur within only certain populations, or in all the populations that make up a species.

6. The rate of mutation is too low for mutation by itself to shift a population from one genotype to another. Instead, the change in genotype proportions within a population can occur by either of two principle processes; random fluctuations in proportions (genetic drift), or nonrandom changes due to the superior survival and/or reproduction of some genotypes with others (i.e., natural selection). Natural selection and random genetic drift can operate simultaneously. (Futuyma, 2005)

The hardened version of the Modern Synthesis only talks about natural selection and random genetic drift barely gets mentioned. It's too bad that Pennisi only interviewed adaptationists and it's too bad that she didn't bother to read an evolution textbook.

The current, most popular view of evolutionary theory needs to be changed. Random genetic drift needs to be restored to its rightful place. At the same time, other points of view should be considered. The problem with the current debate is that the emphasis is on the wrong problem. It's not that we need to incorporate evo-devo; instead. we need to re-incorporate well-established ideas (random genetic drift) that have been known for fifty years!

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Futuyma, D. (2005) Evolution, Sinauer Associates, Inc. Sunderland, MA, USA (p. 10)

Should Science Speak to Faith?

 

The Scientifi American website has articles on the Evolution vs. Creationism debate. My students might be interested in a debate over how to present science to people of faith [Should Science Speak to Faith?]. The debate is between Lawrence M. Krauss and Richard Dawkins. Here's a teaser ...

Krauss: Both you and I have devoted a substantial fraction of our time to trying to get people excited about science, while also attempting to explain the bases of our current respective scientific understandings of the universe. So it seems appropriate to ask what the primary goals of a scientist should be when talking or writing about religion. I wonder which is more important: using the contrast between science and religion to teach about science or trying to put religion in its place? I suspect that I want to concentrate more on the first issue, and you want to concentrate more on the second.

I say this because if one is looking to teach people, then it seems clear to me that one needs to reach out to them, to understand where they are coming from, if one is going to seduce them into thinking about science. I often tell teachers, for example, that the biggest mistake any of them can make is to assume that their students are interested in what they are about to say. Teaching is seduction. Telling people, on the other hand, that their deepest beliefs are simply silly—even if they are—and that they should therefore listen to us to learn the truth ultimately defeats subsequent pedagogy. Having said that, if instead the primary purpose in discussing this subject is to put religion in its proper context, then perhaps it is useful to shock people into questioning their beliefs.

Dawkins: The fact that I think religion is bad science, whereas you think it is ancillary to science, is bound to bias us in at least slightly different directions. I agree with you that teaching is seduction, and it could well be bad strategy to alienate your audience before you even start. Maybe I could improve my seduction technique. But nobody admires a dishonest seducer, and I wonder how far you are prepared to go in “reaching out.” Presumably you wouldn’t reach out to a Flat Earther. Nor, perhaps, to a Young Earth Creationist who thinks the entire universe began after the Middle Stone Age. But perhaps you would reach out to an Old Earth Creationist who thinks God started the whole thing off and then intervened from time to time to help evolution over the difficult jumps. The difference between us is quantitative, only. You are prepared to reach out a little further than I am, but I suspect not all that much further.

...

Dawkins: I like your clarification of what you mean by reaching out. But let me warn you of how easy it is to be misunderstood. I once wrote in a New York Times book review, “It is absolutely safe to say that if you meet somebody who claims not to believe in evolution, that person is ignorant, stupid or insane (or wicked, but I’d rather not consider that).” That sentence has been quoted again and again in support of the view that I am a bigoted, intolerant, closed-minded, intemperate ranter. But just look at my sentence. It may not be crafted to seduce, but you, Lawrence, know in your heart that it is a simple and sober statement of fact.

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15 Answers to Creationist Nonsense

 
The Scientific American website has several articles on Creationism Vs. Evolution.

One of the articles is 15 Answers to Creationist Nonsense from their June 2002 issue. The answers suffer from the same confusion about evolution that I've been addressing for years. It does not distinguish between evolution and natural selection and it fails to mention random genetic drift as a dominant mechanism of evolution. This is most obvious in the response to a question about speciation.

11. Natural selection might explain microevolution, but it cannot explain the origin of new species and higher orders of life.

Evolutionary biologists have written extensively about how natural selection could produce new species. For instance, in the model called allopatry, developed by Ernst Mayr of Harvard University, if a population of organisms were isolated from the rest of its species by geographical boundaries, it might be subjected to different selective pressures. Changes would accumulate in the isolated population. If those changes became so significant that the splinter group could not or routinely would not breed with the original stock, then the splinter group would be reproductively isolated and on its way toward becoming a new species.

Natural selection is the best studied of the evolutionary mechanisms, but biologists are open to other possibilities as well. Biologists are constantly assessing the potential of unusual genetic mechanisms for causing speciation or for producing complex features in organisms. Lynn Margulis of the University of Massachusetts at Amherst and others have persuasively argued that some cellular organelles, such as the energy-generating mitochondria, evolved through the symbiotic merger of ancient organisms. Thus, science welcomes the possibility of evolution resulting from forces beyond natural selection. Yet those forces must be natural; they cannot be attributed to the actions of mysterious creative intelligences whose existence, in scientific terms, is unproved.

One can easily imagine cases where speciation is driven entirely by natural selection but most of the textbooks are more pluralistic. The standard models have two populations diverging in phenotype due to either natural selection or random genetic drift or a combination of the two mechanisms.

The standard models postulate that divergence is initiated when two populations become geographically isolated as described above. If the two locales are different then the population that occupies the new environment might undergo adaptive selection, causing the divergence in morphology. However, if the two locales are similar the populations might just diverge by chance when they become geographically isolated.

Speciation occurs when the two populations have diverged to the point where they can no longer interbreed. At this point they become not only geographically isolated but also reproductively isolated.

There's no obvious way that the evolution of reproductive isolation could be due to natural selection. This would require that one population keep testing itself against the other with lack of cross-fertility providing some benefit to individuals in one of the populations. Instead, it's extremely likely that reproductive isolation is due to chance mutations that become fixed by random genetic drift. John Wilkins, our blogger expert on speciation, described this in a 2006 article that introduces sympatric speciation. Here are the relevant parts concerning the much more common mode of allopatric speciation.

Nobody denies, not even the most ardent antiadaptationist [that's me!], that aspects of organisms are strongly subject to selection, whether during speciation or after it. The critical issue is whether selection is a cause of speciation itself.

The allopatric consensus view allows for local adaptation, of course, when isolated from the parent metapopulation. What it denies is that selection for RI [reproductive isolation] occurs - how could it when speciation is occurring without contact with the reproductively isolated populations? There is selection of RI, of course, since RI on that account is a byproduct of changes in the population that are selectively favoured for ecological reasons. But not selection for RI itself [the selection of and selection for distinction is due to Elliot Sober]. So, argue allopatrists such as Jerry Coyne and Allan Orr, selection is not a cause of speciation in allopatry. And this seems right.

... If we think of speciation as "what makes a species" then we get ecological and other selective processes. If we think of speciation as "what makes it not the same species", then the explanatory focus shifts, and here the answer is, in cases when divergent selection is not going on, populations simply drift away from the reproductive reach of the ancestral population.

The bottom line here is that much of what we call speciation—especially the crucial reproductive isolation—is probably not due to natural selection. Instead, random genetic drift is the culprit. What this meams is that the answer to the question above is somewhat misleading. As it turns out, natural selection cannot account entirely, or even mostly, for all speciation events.

Some of you might recall a discussion I had in July with my colleague Spencer Barrett on this issue. He acted very annoyed when I suggested that random genetic drift might play an important role in speciation [see Species Diversity, Darwinism at the ROM]. This disagreement was made obvious to me today when I took a poll of my students in our class on Scientific Misconceptions. I asked them what they had learned from Professor Barrett in their first year class on evolution and more than 70% of them defined evolution as adaptation and were unable to identify random genetic drift as a mechanism of evolution. This means I'm going to have to explain evolution before we can discuss the evolution vs creationism controversy.

Go back and look at the second paragraph of the Scientific American answer (above). Isn't it strange that they don't even mention random genetic drift when listing other mechanisms of evolution? What's going on here? Do the science writers¹ at scientific American not know about random genetic drift or do they not think that it's a valid mechanism of evolution according to their definition of evolution. I suspect both.

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1. The article was written by John Rennie, a science writer who currently serves as editor in chief of Scientific American.

[Image Credits: The top image comes from webpages on evolution at CUNY Brooklynn (New York). The accompanying text reads, ""In small populations, other forces are at work. When a population is small, the presence or absence of a single individual can have a profound effect on the population gene pool. A sudden reduction in population size can also alter the remaining gene pool. This is the bottleneck effect.

A change in the gene pool brought about by chance is a genetic drift.

An extreme form of genetic drift, combined with the bottleneck effect is called the founder effect, which depends on a small group becoming isolated from the larger group, and can rapidly lead to the creation of a new species."

The bottom image comes from another article by John Wilkins, Explanation, that discusses, among other things, the role of stochastic events, such as random genetic drift, in speciation.]

Six Different Kinds of Slime Moulds

 
Which one doesn't belong on the list?

1. Myxogastrea
2. Dictyostelia
3. Protostelia
4. Buddenbrockia
5. Myxococcales
6. Labyrinthulea
7. Acrasea

Check out Catalogue of Organisms, The Diversity of Slime Moulds for the correct answer.

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The Nature of Science: Is Science the only Way of Knowing?

In my course today I described science as a way of knowing based on evidence and rational thinking. The key point is that science is a process, or a way of thinking. Science—the process—is not confined to the "natural" sciences. It can be used in any type of investigation that's designed to seek factual knowledge about the universe we inhabit (see Sokal, 2008).

Are there any other ways of knowing? Well, that depends on what kind of knowledge you seek. If you're interested in "truth", which I loosely define as factually correct information, then my answer is no. The application of evidence and rationality is the only way to go.

Lots of people disagree. For the sake of discussion, I've selected some examples from an article on The Nature of Science and Scientific Theories published by the Arkansas Science Teachers Association 2006. They propose four different ways of knowing.

People have several ways that they know about their world.  The chart below lists some of the ways of knowing.  One way of knowing is no more valid that another to most people.  However, as you read the chart please note that science is a way of knowing that requires the use of certain rules and methods that differs from the other means of knowing.  Scientific knowledge limited to the natural world. Scientific knowledge and religious knowledge do not have to be contradictory.  It is important to know these differences, so that they can be complementary.

Religious Knowledge

• Seeks answers to any question that can be posed including answers to the ultimate questions (What is my purpose? What is the meaning of life? Is there a supreme being? etc.).
• Explanations can include supernatural forces.
• Is a belief system and seeks truths.

Philosophic Knowledge

• Seeks answers to any question that can be posed including answers to the ultimate (What is my purpose? What is the meaning of life? Is there a supreme being? etc.).
• Explanations can include supernatural forces and viewpoints
• Is a point of view and seeks truths.

Cultural Knowledge

• Seeks answers to any question that can be posed including answers to the ultimate questions (What is my purpose? What is the meaning of life? etc.), but generally relates to how people treat one another.
• Explanations can include supernatural forces and other historical viewpoints.
• May be a belief system rooted in historical views and seeks truths.

Science Knowledge

• Can only seek answers about the natural world but cannot answer ultimate questions (Is there a god? What is the meaning of life?).
• Explanations cannot include supernatural forces.
• Is not a belief system nor seeks truths.

Why can't the science way of knowing address questions like "Is there any evidence of purpose in evolution?" "Does life have any meaning?" and "Is there any evidence of Gods?" Why are these questions arbitrarily ruled out of bounds? Does it mean that we can't apply evidence and rationality to questions about the possibility of purpose?

If religious, philosophical and cultural knowledge can be "beliefs" or "points of view" then what kind of knowledge is that? These may be some sort of "ways of knowing" but knowing about what? Surely not factual knowledge of the sort that would be convincing to an impartial observer?

Finally, why are the other three "ways of knowing" referred to as ways of "seeking truths" but science is the only one that does NOT "seek truth"? What does the scientific way of knowing seek ... lies?

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Sokal, Alan (2008) What is science and why should we care?, Third Annual Sense About Science lecture February 27, 2008, University College London (UK)

Nobel Laureate: Kurt Wüthrich

 

The Nobel Prize in Chemistry 2002.

"for his development of nuclear magnetic resonance spectroscopy for determining the three-dimensional structure of biological macromolecules in solution"



Kurt Wüthrich (1938 - ) received the 2002 Nobel Prize in Chemistry for his contribution to solving complex three-dimensional structures using nuclear magnetic resonance (NMR) spectroscopy. He made significant advances in the technique of using NMR to solve the structures of proteins. Here's the description in the press release.

At the beginning of the 1980s, Kurt Wüthrich developed an idea about how NMR could be extended to cover biological molecules such as proteins. He invented a systematic method of pairing each NMR signal with the right hydrogen nucleus (proton) in the macromolecule (see fig. 4). The method is called sequential assignment and is today a cornerstone of all NMR structural investigations. He also showed how it was subsequently possible to determine pairwise distances between a large number of hydrogen nuclei and use this information with a mathematical method based on distance-geometry to calculate a three-dimensional structure for the molecule.

The first complete determination of a protein structure with Wüthrich's method came in 1985. At present 15-20% of all the thousands of known protein structures have been determined with NMR. The structures of the others have been determined chiefly with X-ray crystallography; a few with other methods such as electron diffraction or neutron diffraction.

Wüthrich shared the 2002 Nobel Prize with John B. Fenn and Koichi Tanaka.

THEME:
Nobel LaureatesThe presentation speech was delivered in Swedish on December 10, 2002 by Professor Astrid Gräslund of the Royal Swedish Academy of Sciences,

Your Majesty, Your Royal Highnesses, Ladies and Gentlemen.

What would life be without proteins! Proteins are large molecules that do almost all the work in our cells. Every living organism, including a human being, has a large array of various kinds of proteins. Like diligent worker bees, they take care of what needs to be done. In principle, it works the same in this flower as in me or you.

To learn more about the diligent workers inside of cells, we want to know how they look, in order to understand what they do. This year's Nobel Laureates in Chemistry have developed methods that enable us to weigh and create pictures of giant molecules like proteins in new ways that we could hardly believe were possible. I am convinced that biochemistry is now standing on the threshold of a new era – we are beginning to become acquainted with the complete genetic code of many organisms. Soon we will be able to survey all the thousands of protein varieties that work simultaneously in a given cell. It is in this new era that the discoveries of the 2002 Nobel Laureates are so important.
Mass spectrometry has been part of the chemist's toolkit for identifying small molecules since the beginning of the 20th century. But for many years, being able to make accurate measurements of the molecular masses of large proteins was a dream for chemists. For this reason, it caused a minor revolution in the field when John Fenn and Koichi Tanaka, each in his own way, succeeded to making intact proteins fly through the mass spectrometer.

Fenn discovered that it was possible to spray a water solution of the protein, in the presence of an electrical field, in order to obtain hovering electrically charged drops. The water evaporates and the drops are scattered by their electrical charge, becoming smaller and smaller. Finally only pure protein molecules are left. Then their mass is determined by measuring the time it takes them to accelerate across a given distance – the principle being that the heavier the molecule is, the more slowly it moves.

Tanaka's special method was to fire a laser pulse toward the sample. With the right wavelength in the laser, he could make the proteins be released from their surroundings without falling apart, so that they hovered freely as charged particles. Their mass could then also be determined by measuring their time of flight.

This was one half of the year's Chemistry Prize – now I will move to the second half. This time it is not a matter of flying proteins, but swimming proteins. Using nuclear magnetic resonance, or NMR, a method that Kurt Wüthrich has further refined, it is now possible to determine the three-dimensional structure of protein molecules in a water solution. NMR is one of the chemist's best methods for examining molecules, and it has been used extensively for small molecules since the mid-20th century. But large molecules like proteins involve special problems. One of the fine points of NMR is that it enables us to see individual signals, for example, from each hydrogen nucleus in a molecule. But because a protein can contain thousands of hydrogen nuclei, how do you know which signal belongs to which nucleus?

Wüthrich devised a way of systematically determining how each signal fits together with its special hydrogen nucleus. In the bargain, he was also able to determine a large number of pairwise distances between hydrogen nuclei. This enabled him to calculate a three-dimensional structure for the protein molecule. It is something like drawing a picture of a house if you know a large number of distances in the house. So thanks to Wüthrich's discovery, we can now use NMR to examine and depict proteins in their natural environment, surrounded by water like in a cell.

So, what would life be without proteins? Since I view the world through the eyes of a biochemist, my answer is: nothing at all! Next question: How would life be as a biochemistry researcher without the tools that this year's Nobel Laureates have given us? My answer to this question is: much more difficult, and also more dull! So I would like to conclude by saying to the 2002 Nobel Laureates in Chemistry: Thank you for your fantastic contributions, which help us to better understand the chemical miracles that constantly occur in our cells – what we call life.

Dr. Fenn, Mr. Tanaka and Dr. Wüthrich,

You have made pioneering contributions to the development of methods for identification and structure analyses of biological macromolecules. Your work to make mass spectrometry and NMR applicable for detailed studies of large molecules like proteins has given us new tools for investigations of the processes that constitute life. In recognition of your services to chemistry, the Royal Swedish Academy of Sciences has decided to confer upon you this year's Nobel Prize in Chemistry.

On behalf of the Academy, I convey to you our warmest congratulations and I now ask you to receive the Prize from the hands of His Majesty the King.

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Monday's Molecule #87

 
This could be difficult so I'll give you a few clues. This molecule is secreted and it's function is to degrade nucleic acid. I want the name of the molecule and also a brief description of the image you see on the left. What is it showing?

There's a indirect connection between the image of today's molecule and a Nobel Prize. We are looking for the single person most responsible for the particular kind of image you see here.

The first person to correctly identify the molecule and name the Nobel Laureate, wins a free lunch at the Faculty Club. Previous winners are ineligible for one month from the time they first collected the prize. There are four ineligible candidates for this week's reward. You know who you are.

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 Laureate(s) so you might want to check the list of previous Sandwalk postings by clicking on the link in the theme box.

Correct responses will be posted tomorrow. I reserve the right to select multiple winners if several people get it right.

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

UPDATE: This week's winner is Dima Klenchin of the University of Wisconsin. The molecule is bovine ribonuclease and the image depicts the different conformations of the molecle in solution as solved by NMR. The Nobel Laureate is Kurt Wüthrich. Congratulations Dima!

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Denyse O'Leary Is a "Top-flight Science Journalist"

 
Now that I've got your attention, let me explain.

Deborah Gyapong—that's her on the right—has a blog called Deborah Gyapong (of course). According to her profile ...

Deborah Waters Gyapong’s journalism career spans more than 20 years in television, print and radio, including 12 years as a producer for the Canadian Broadcasting Corporation’s television news and current affairs programming. Deborah now covers religion and politics primarily for Roman Catholic and Evangelical newspapers.

In a recent posting, Denyse O'Leary takes Rob Breakenridge to task, she comments on the op-ed article that Denyse published in the Calgary Herald (See Intelligent Design Creationism Is Just Anti-Evolutionism). Here are two quotations about Denyse O'Leary written by Deborah Gyapong.

Denyse, who is an expert on the various theories of evolution and intelligent design and a top-flight science journalist, ...

Denyse is the EZ [Ezra Levant] of intelligent design, i.e. she is well-informed, rational, and will eat you for breakfast if you don't have a logical, well-presented, well-researched factual argument.

No comment is necessary except to note that science journalism is in even worse shape that I imagined.

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[Hat Tip: Eamon Knight in the comments section of The Big Tent Springs a Leak.]

Teaching Both Sides of the Controversy

 
I found this on Sneer Review [Teach Both Sides Of The Controversy - part 2]. It's an accurate portrayal of the weight of evidence for evolution and for Intelligent Design Creationism. So, what are we afraid of?


What we're afraid of is that the controversy won't be taught properly. I think we need to make this clear. Scientists aren't the least bit afraid of going head-to-head with any form of creationism. Teaching critical thinking and analyzing controversies is a valid part of science education and, if done properly, it can be a wonderful way to learn.

But that's not what's going to happen when creationist teachers cover evolution. They are not going to teach the controversy. They are going to teach lies about science. Teaching the controversy only applies to qualified teachers who are knowledgeable about their subject.

Let's not get trapped into opposing critical thinking and controversy. Let's focus on making sure that teachers are qualified to teach the curriculum.

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The Big Tent Springs a Leak

 
It doesn't happen very often but every now and then some of the Intelligent Design Creationists slip up by not keeping on message. Here's an example of Denyse O'Leary revealing that there's a wee bit of difference between "Evolutionary Creation" and "Intelligent Design Creation" [ Evolutionary Creationism? I am supposed to promote THAT?].

She refuses to promote a book called Evolutionary Creation: A Christian Approach to Evolution by Denis Lamoureux because he had the audacity to criticize Michael Behe.

I have had several conversations with Lamoureux, and he has struck me as a typical fatuous sellout of the decaying “evangelical Christian” culture that currently helps to deform Canada.

Earth to Lamoureux: Darwin is not the answer to any problem we now have. There is NO need to figure out how to incorporate him into our life together.

Just forget him and start figuring out what really happened in the history of life. Stop attacking people who know that Darwinism - and all its works - is false.

Hmmm ... many the wedge strategy is working after all.

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Science Writers Need Science History

 
Carl Zimmer does it again! This time he shows why he's the best science writer by getting three things right in the same article: (1) junk DNA, (2) the existence of regulatory sequences isn't news, and (3) history is important [Science Writers Need Science History].

I bet he reads the blogs [What's Wrong wiht Modern Science?] [Junk in Your Genome: Protein-Encoding Genes] [Stop the Press!!! ... Genes Have Regulatory Sequences!].

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Into the Textbooks It Goes

 
This week's issue of Science contains an important paper.

Maier, T,, Leibundgut, M. and B. Nenad (2008) The Crystal Structure of a Mammalian Fatty Acid Synthase. Science 321:1315-1322.

We've known for a long time that this is a very important enzyme and that it's a classic example of a little protein machine combining the activities of may different enzymes in order to carry out the complex reactions of fatty acid synthesis. Here's how I described it in the last edition of my book ...

In bacteria, each reaction in fatty acid synthesis is catalyzed by a discrete monofunctional enzyme. This type of pathway is known as a type II fatty acid synthesis system (FAS II). In animals, the various enzymatic activities are localized to individual domains in a large multifunctional enzyme and the complex is described as a type I fatty acid synthesis system (FAS I). The large animal polypeptide contains the activities of malonyl/acetyl transferase, 3-ketoacyl-ACP synthase, 3-ketoacyl–ACP reductase, 3-hydroxyacyl–ACP dehydratase, enoyl–ACP reductase, and thioesterase. It also contains a phosphopantetheine prosthetic group (ACP) to which the fatty acid chain is attached. Note that the malonyl CoA:ACP transacylase enzyme shown in Figure 16.3 is replaced by a transferase activity in the FAS I complex. This transferase catalyzes a substrate loading reaction where malonyl CoA is covalently attached to the ACP-like domain on the multienzyme polypeptide chain. The eukaryotic enzyme is called fatty acid synthase.

The structure (shown below) will be going right into the textbooks.

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Citation Classic: Recombinant DNA

 
Read John Dennehy's citation classic for this week at This Week's Citation Classic: Genetic Engineering. The paper is one of the first examples of genetic engineering and recombinant DNA technology. Before you go, try and guess when the paper was published. Was it before you were born or after?

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[Photo Credit: Protesters at the National Academy of Sciences Forum on Recombinant DNA from The Maxine Singer Papers]