Taxonomic Inflation

 
The number of new species discovered is growing every year, although we often hear more about threatened extinctions. In many cases this is because of new observations leading to the identification of new species. For the most part, these are not entirely new organisms—they are species that are closely related to existing species.

Given the ongoing battles between lumpers and splitters in the taxonomic community, one wonders whether the discovery of new species isn't just due to the elevation of varieties to the level of species. For example, there are many varieties of giraffe and some people propose that the current species, Giraffa camelopardalis, should be split into several species. This depends on your definition of species.

Christopher Taylor of Catalogue of Organisms reviews a recent paper that addresses the problem [Keeping an Eye on Inflation]. Turns out that the recent redefinition of species doesn't correlate with the increase in splitting so that doesn't seem to explain taxonomic inflation.

Unfortunately Chris doesn't answer the most important questions.

• Is it true that God has an inordinate fondness for beetles or is it just overzealous insect taxonomists?


• If you split G. camelopardalis then why not split Homo sapiens as well?

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Signature in the Cell

 
Denyse O'Leary can hardly contain herself 'cause Stephen Meyer's book is about to go on sale.

In case you can't wait, there's a Signature in the Cell website that explains the significance of this momentous event.

The foundations of scientific materialism are in the process of crumbling. In Signature in the Cell, philosopher of science Stephen C. Meyer shows how the digital code in DNA points powerfully to a designing intelligence behind the origin of life. The book will be published on June 23 by HarperOne.

Unlike previous arguments for intelligent design, Signature in the Cell presents a radical and comprehensive new case, revealing the evidence not merely of individual features of biological complexity but rather of a fundamental constituent of the universe: information. That evidence has been mounting exponentially in recent years, known to scientists in specialized fields but largely hidden from public view. A Cambridge University-trained theorist and researcher, director of the Discovery Institute’s Center for Science and Culture, Dr. Meyer is the first to bring the relevant data together into a powerful demonstration of the intelligence that stands outside nature and directs the path life has taken.

...

As a philosopher and a scientist himself, having worked in the field of geophysics for Atlantic Richfield, Meyer is able to step back from the fray of competing views about Darwinian theory and offer a searching, compelling investigation of life’s beginning.

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Education and Science vs. Religion

 
As far as I'm concerned, the proper teaching of science involves explaining that it is a legitimate and powerful way of knowing based on evidence and rationalism. The scientific way of knowing conflicts with the vast majority of religious beliefs. In other words, the proper teaching of science is a threat to almost all religions and, in that sense, it encourages skepticism at least, and non-belief at best.

In most countries that fact isn't a problem but in the USA there's a problem. If the proper teaching of science promotes a "religious" point of view, namely atheism, then science can't be taught in public schools. It's fun to watch the contortions that many atheists have to go through in order to escape the obvious conclusion.

Andrew Brown (not an American, I might add) points out the problem [on being told by PZ ...]. I agree with him just as I agreed that Michael Ruse was making a valid point at the recent Center for Inquiry conference [Wherein Michael Ruse Avoids My Questions].

Jerry Coyne tries to get around the problem by concentrating on the teaching of evolution (just the scientific truth) and not "science" [Andrew Brown makes another dumb argument for accommodationism]. I think this is disengenuous but I do agree with Coyne that Andrew makes a silly case for accommodationism.

Coyne says,

Actually, we teach evolution because it’s a wonderful subject, explains a lot about the world, and happens to be true. And yes, it’s likely that teaching evolution probably promotes a critical examination of religious beliefs that may lead to rejecting faith. But teaching geology, physics, or astronomy does that, too.

This seems to contradict his main argument since it implies that teaching science does, indeed, lead to rejecting religious beliefs. But, wait a minute, he goes on to say that ..

In fact, education in general leads to the rejection of faith. (Statistics show that the more education one has, the less likely one is to be religious.) Should we then worry about teaching physics, astronomy, or indeed, allowing people access to higher education, because those “promote” atheism?

No, we shouldn't "worry" about that but it would be foolish to deny it. The essence of the scientific way of knowing is evidence, rationalism, and also one-mindedness and skepticism. We need to teach that to our children. To deny that this is inimical to faith-based ways of knowing is to deny the obvious.

Should we constantly be looking over our shoulders because the courts may catch onto this?

Maybe you should, if you live in America. The evolutionist side in America has put a high value on winning court cases based on rather arcane legal arguments—who, besides lawyers, cares about the Lemon test? If the bad guys decide to fight back in the courts by challenging the teaching of proper science then watch out. I've heard there are a lot of lawyers in America.

Speaking of lawyers, John Pieret has an opinion on this subject [Science, Philosophy and Law].

Teach only the science and the "problem" evaporates. Any tendency to reject faith because of the teaching of the science is what church and state scholar Kent Greenawalt has called "spillover effects," which do not render the teaching unconstitutional because they are not a "primary effect" of it.

If I understand him correctly, the teaching of Intelligent Design Creationism is unconstitutional because its "primary effect" is to promote religion. The teaching of evidence based rationalism (i.e. scientific reasoning) has as its primary purpose the destruction of superstitious beliefs but the fact that this includes religion is just a "spillover effect."

Wouldn't it be ironic if American courts ruled that it is unconstitutional to teach children how to think?

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Common Sense, Rationalism, and other Points of Views

 
Steven Pinker is an evolutionary psychologist. In this debate he defends that point of view. The other participants in the debate don't agree and I think they make a lot of sense.

You can also listen to Steve Jones defend the idea that human evolution has stopped. In that discussion you'll probably notice that random genetic drift isn't mentioned. I get the impression that most of the time none of the participants think about anything other than natural selection when they're discussing evolution. (But see part 5, where "random variation" is briefly mentioned.) However, I'm sure they'll deny that they are adaptationists when challenged. I'm sure they'll swear up and down that they know all about the other mechanisms of evolution.

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Bora Zivkovic Writes About Journalism

 
Bora Zivkovic of A Blog Around the Clock has long been interested in the role of journalists—especially science journalists—in our society. He writes about the legitimacy of quotations in The Ethics of the Quote.

At the risk of incurring his wrath for quote mining, I give you one of the most important and controversial ideas in his posting.

Even when asked, journalists openly state that their role is not to find the truth, but to register the spectrum of opinions out there. That is stenography at best (not even that, as some opinions are never registered, including some very valid opinions), not journalism.

But that is absolutely NOT what the audience expects. Audience is already aware of the spectrum of opinions out there. They look for you to tell them exactly which one of those opinions is correct, and which ones are bunk. But you never deliver. Which is why people are mad, and the press has an extremely low ranking in popular opinion on trustworthiness.

If you disagree with the above paragraph, think why that is so? Did you hear it from your editors and colleagues? If so, they are dead wrong. If you learned it in J-school, your professors were dead wrong. Wrong, wrong, wrong, wrong, wrong, wrong!!!

Now think again.

Is everything you ever learned in a professional setting about the role of journalism wrong? Could be. Time for deep introspection.

I agree with Boris when he says that journalists don't deliver, however I disagree with him slightly about what they think they are doing. Many journalists think their role is just what Boris says it should be. They believe that journalists should be able to explain which ideas are wrong and which ones are correct. Many science journalists claim to be able to do this. They claim that they don't just report the opinions of scientists who disagree but provide "value added" by figuring out which ones are correct.

If that's what they're trying to do then they don't do a very good job in the fields that I'm familiar with.

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Would You Get a Baccalauréat if You Were a Student in France?

 
French high school students must obtain the baccalauréat if they are to have any chance of getting into university. Almost all teenagers have to write the nationwide standardized tests at the same time. About half of them pass.

Everyone has to write the philosophy exam, which was held yesterday. Charles Bremner tells us what questions were on the exam [Stress test for France's young philosophers]. You have four hours to answer one of the questions. How would you do?

If you were in the economics and social science stream, the questions were ....

1. What is gained by exchange?
2. Does technological development transform mankind?

If you were one of the science students the questions were ....

1. Is it absurd to desire the impossible?
2. Are there questions which no science can answer?

If you were in the literature stream the questions were ....

1. Does objectivity in history suppose impartiality in the historian?
2. Does language betray thought?

To me the questions indicate that France expects more of its potential university students than we do in Canada. We used to have standardized province-wide exams in Ontario but they were abolished 40 years ago. As far as I know we never had a test that everyone in the entire country had to write.

I don't think such a test has ever been popular in the USA.

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[Hat Tip: Uncertain Principles: Answers Matter More than Questions]

Deciphering Michael Ruse

 
To put it mildly, I'm not a big fan of Michael Ruse. I don't think he understands evolution very well in spite of the fact that he gives talks about it all over the world. I've been at some of those talks and they make me very angry [Michael Ruse: 90% 0f Scientists Are Selectionists, Evolution at Chautauqua, Darwinism at the ROM].

Ruse frequently argues the accommodationist position and he's gotten himself in trouble recently by taking on Jerry Coyne [Brown + Ruse vs. Myers: Are atheists responsible for creationism?]. Jason Rosenhouse has weighed in to defend the atheist position, pointing out that Ruse is very confusing [Ruse News]. Sometimes Ruse seems to be aiding and abetting creationism by allying himself with people like Bill Dembski.

Jason is particularly upset by the book Debating Design co-edited by Michael Ruse and Bill Dembski. I'm not bothered so much by this book. In fact, it's a very useful collection of essays by proponents of both sides. That includes people like Francisco Ayala, Ken Miller, Elliott Sober, and Robert T. Pennock.¹

In that book, Michael Ruse has an essay on the history of the argument from design. In order to illustrate how inconsistent and frustrating Ruse can be, I've selected a passage from the conclusion to that essay. Here, Ruse seems to be saying that the accommodationists are wrong. I think Ruse has it right, for once.

I draw to the end of my survey of twenty-five hundred years of the argument from design. Deliberately, I have tried to be nonjudgmental, merely telling the story of the ideas as they appear in history. But, as I conclude, I cannot resist drawing an obvious inference from my history. Intelligent Design theorists and atheistical Darwinians cannot both be right, but they are both surely right in thinking that they are more in tune with modern evolutionary biology than are the mainstream reconcilers of science and religion.

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1. I agree with Jason when he says, "Making matters worse was the fact that the four essays Ruse chose to represent “Darwinism” added up to a very weak case for the good guys. If all I knew about this issue came from that book, I would be an ID proponent."

The Logic (and Intelligence) of Believers

 
PZ Myers discovered a wonderful website that proves, once again, that the correlation between believers and idiots is very strong and the fight really is between superstition and rationalism.

Have fun at Proof That God Exists.

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On Faith and Science

 
Peter Hess is Faith Project Director at National Center for Science Education (NCSE). (I don't know if they have another director for people who don't rely on faith. Is there an Rationalism Project Director?) Hess was written an article in The Washington Post [On Faith].

It's a typical accommodationist article—full of unsubstantiated statements with no attempt whatsoever to come to grips with the main problem. The article maintains that science and religion are compatible without explaining what kind of religion you have to believe in to avoid conflict with science. Can you believe in miracles, the power of prayer, the existence of a soul, the importance of the Bible, the divinity of Jesus, and life after death without coming into conflict with science?

Joshua Rosenau likes the article by Hess. Josh has posted excerpts on his blog Thoughts from Kansas [NCSE's Peter Hess takes down Disco.'s John West]. Here's one of the excerpts that Josh posted.

Too often, debates over the public perception of evolution are dominated by the fringes, by fundamentalist Christians and others who reject basic science due to their literal reading of the Bible and by ardent atheists who reject religion because they've embraced metaphysical naturalism ― that nature is all that exists. But the silent majority ― that spans the spectrum from theism to atheism ― have no problem reconciling their religious beliefs with established sciences such as evolution, or with new sciences such as stem cell research. My work at the National Center for Science Education brings me into contact with voices across that spectrum and I've found that honest, open, and inclusive dialog is not only possible, but vital for our children's education, for the credibility of religious traditions, and for the continued role of the United States as a scientific and moral leader in our increasingly interconnected world.

There are several problems with the logic expressed here. I'm always suspicious of those who claim to represent the "silent majority" but in this case the claim makes no sense because I'm not convinced that this so-called "silent majority" in the USA actually exists. Is it true that a majority of Americans have "no problem reconciling their religious beliefs with established sciences"?

Now let's imagine a hypothetical situation where Peter Hess is writing an article for a Swedish newspaper, where a majority of citizens are non-religious and atheists could not be labeled a "fringe" group. Would his argument be any weaker because he can no longer claim to represent the "silent majority"? If the answer is "yes" then the argument has no meaning. It's just empty rhetoric. I hate arguments based on the appeal to popularity even if the appeal is merely implicit.

Like Peter Hess, I also value "honest, open and inclusive dialog." That's why I think it's important to debate the conflict between science and religion. If one is being open and honest than one will address the potential sources of conflict such as the existence of a personal god and whether humans have a purpose. It would be dishonest to avoid those issues—and the ones listed above—in order to try and makes religious people more comfortable. It would not be "inclusive" to dismiss atheists as a "fringe" group whose opinions don't count because they're not part of the "silent majority.".

If we really value the education of our children then lets talk about the existence of supernatural beings and let's hear a defense of their existence and not just rhetoric about how belief is the majority position in the USA. Let's hear about those religious traditions that are compatible with science and let's, at least, get rid of the ones that are clearly incompatible.

Finally, who appointed the USA as the "moral leader" of the world? Did I miss the vote?

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Preparing for Professor Palazzo

 
Alex Palazzo (The Daily Transcript) is coming to Toronto. In two weeks he will be joining my Department as a Professor (Assistant variety) and colleague.

There's been a flurry of activity in the lab that's been assigned to him. It's just around the corner from my office so I've been able to keep track of the clean-out and the renovations. So far it looks like it will be ready just in time.

It will be exciting to have another blogger in the department. (We already have several.) I'm really looking forward to Alex's arrival so I can teach him a few things about science—things he seems to have missed while doing his post-doc in one of the lesser schools south of the border.

I'm not looking forward to paying off my bet with him. I'd explain why I lost but it's a long story.

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Nicholas Wade on the Origin of Life

Nicholas Wade is a science journalist who writes for the New York Times. His particular area of expertise is evolution and molecular biology and he is often mentioned as one of the best science writers in America.

That's not an opinion that I share, although it's true that he writes very well.

Wade's latest article is New Glimpses of Life’s Puzzling Origins. The focus of this article is on recent discoveries in chemistry and biology relating to the origin of life. These all support a scenario where complex molecules in a warm little pond give rise to replicating nucleic acids enclosed in a membrane vesicle. Not much attention is paid to the competing scenarios—especially the one I favor: Metabolism First and the Origin of Life.

Now don't get me wrong. There's no reason why Nicholas Wade can't prefer one particular scenario for the origin of life. After all, many scientists agree with him. The problem I have is that when it comes to informing those who read newspapers, they won't be getting the full story.

One of the "problems" in origin of life studies is the "chirality" problem. The idea is to explain why life prefers left-handed amino acids instead of right-handed amino acids. The "problem" arises when you postulate that life arose in a soup consisting of equal amounts of both types of amino acid.

Sandwalk readers will know my opinion on the "problem." I think it's a "non-problem" since life probably didn't arise from a pool of 20 different concentrated amino acids. I prefer a scenario where a few simple amino acids contributed to the first catalysts and expansion of the repertoire of amino acids resulted from synthesis of more complex ones from simple ones. Since this was "biological" synthesis, the complex amino acids were all left-handed forms from the beginning because the precursors were already left-handed [Can watery asteroids explain why life is 'left-handed'?].

Let's see how Nicholas Wade describes recent results.

Another striking advance has come from new studies of the handedness of molecules. Some chemicals, like the amino acids of which proteins are made, exist in two mirror-image forms, much like the left and right hand. In most naturally occurring conditions they are found in roughly equal mixtures of the two forms. But in a living cell all amino acids are left-handed, and all sugars and nucleotides are right-handed.

Prebiotic chemists have long been at a loss to explain how the first living systems could have extracted just one kind of the handed chemicals from the mixtures on the early Earth. Left-handed nucleotides are a poison because they prevent right-handed nucleotides linking up in a chain to form nucleic acids like RNA or DNA. Dr. Joyce refers to the problem as “original syn,” referring to the chemist’s terms syn and anti for the structures in the handed forms.

The chemists have now been granted an unexpected absolution from their original syn problem. Researchers like Donna Blackmond of Imperial College London have discovered that a mixture of left-handed and right-handed molecules can be converted to just one form by cycles of freezing and melting.

Hmmm ... I see two problems here. First, I'm not aware of any experiments by Donna Blackmond or anyone else that solves the chirality problem. Does anyone have a reference?

The second problem with Wade's description concerns the "handedness" of nucleotides. It's true that the sugar component of nucleotides is exclusively D-ribose (or D-deoxyribose) and not L-ribose. The nucleic acids that we know today (DNA and RNA) could not be made with L-ribose or L-deoxyribose. This is a "problem" that's similar to the one with amino acids; how do you get a pool of sugars that are all D- configurations? (Do you get them by synthesizing them all from D-glyceraldehyde?)

The terms syn and anti refer to different conformations of nucleotides and not different stereoisomers. Conformations are different three-dimensional shapes that a molecule can adopt in solution. They don't require the breaking of any chemical bonds. See Nucleotides Can Adopt Many Different Conformations for a discussion of these different shapes.

Here's a figure showing the anti and syn conformations of deoxyguanylate. (Click to embiggen.)


Free nucleotides can easily switch back and forth between the two forms since all it requires is rotation around the β-N-glycosidic bond—the one with the circular arrow around it. This has nothing to do with stereochemistry or the chirality problem.

In fact, nucleotides like deoxyguanylate can switch between the two conformations even while they are part of DNA. The anti conformation is found in normal B-DNA but the double helix can adopt a Z-DNA conformation under some circumstances and in that conformation the deoxyguanylate residues are in the syn conformation.

Mistakes like this are what makes science journalism difficult. I don't expect Nicholas Wade to be an expert in biochemistry—although if he'd had a copy of my textbook he could have avoided the error. What I do expect is a bit of fact-checking with other experts. Wade could have asked any biochemist to check this out.

Furthermore, Wade should probably have been suspicious when he realized that the syn and anti conformations of nucleotides don't come up in any other discussions about chirality. Indeed, nucleotides are rarely mentioned in such discussions.

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[Figure is from Moran/Scrimgeour et al. Biochemistry 2nd ed. (1994) ©Neil Patterson Publishers/Prentice Hall.

Nobel Laureate: Robert Koch

 

The Nobel Prize in Physiology or Medicine 1905

"for his investigations and discoveries in relation to tuberculosis"

Robert Koch (1843 - 1910) won the Noble Prize in 1905 for demonstrating that specific bacteria can cause common diseases. Tuberculosis was the specific disease mentioned in the citation.

At the time of the award, Koch was already a very famous scientist. Part of his reputation was based on The Most Famous Speech in Medical History but he was also widely respected for identifying the bacteria causes of other diseases.

The most important part of the Presentation Speech is the part that emphasizes the general contribution of Koch to the study of bacteriology (see below). Koch is recognized as one of the founders of the modern field of microbiology. One of his co-workers, Paul Ehrlich, won the Nobel Prize three years after Koch [Nobel Laureate: Paul Ehrlich].
THEME:
Nobel Laureates

To start with, developing a general methodology is as valuable as finding the correct technique for every special case. Koch's genius has blazed new trails in this respect and has given present-day research its form. To give a detailed description of this is beyond the scope of this account. I only want to mention that he had moreover already given a significant development to techniques in staining and microscopic investigation as well as in the field of experiment in his earliest work. Shortly after this he produced the important method, which is still generally the usual one, of spreading the material under investigation in a solid nutrient medium to allow each individual among the micro-organisms present to develop into a fixed colony, from which it is possible, in further research, to go on to obtain what is known as a pure culture.

Shortly after the publication of his investigations into diseases from wound infections Koch was appointed to the new Institution, the «Gesundheitsamt» (Department of Health), in Berlin. There he started work on some of the most important human diseases, namely, tuberculosis, diphtheria and typhus. He worked on the former one himself. The two latter investigations he left to his first two pupils and assistants, Loeffler and Gaffky. For all three diseases the specific bacteria were discovered and studied in detail.

To give an account of the work which Koch carried out, or accomplished through his pupils, and also to mention the work which derives more indirectly from Koch, would nearly be the same as describing the development of bacteriology over the last few decades. I will content myself with naming some of the most important discoveries and items of research which, in addition to those already named, are more directly linked with Koch's name. At the head of the German Cholera Commission Koch investigated the parasitic aetiology of cholera in Egypt and India, and discovered the cholera bacillus and the conditions necessary for its life. Experience thus gained found practical application in the development of measures taken to prevent and combat this devastating disease. In addition Koch made important investigations concerning plague in humans, malaria, tropical dysentery, and the Egyptian eye disease (trachoma) among others, and now finally concerning typhus recurrens in tropical Africa. He has also carried out work of exceptional importance, concerning a host of destructive tropical cattle diseases, such as rinderpest, Surra disease, Texas fever, and finally concerning coast fever in cattle and the trypanosome disease carried by the tsetse fly.

Through the perfection he gave to methods of culturing and identifying micro-organisms, he has been able to carry out his work with regard to disinfectants and methods of disinfection so important for practical hygiene, and advice concerning the early detection and combating of certain epidemic diseases such as cholera, typhus and malaria.

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[Image Credits: photograph:zgapa.pl/drawing: Wolsztyn - Wollstein/statue: Wikipedia/movie poster: Journal of Medicine and Movies]

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.

Monday's Molecule #126: Winner

 
The molecules are: BMPR = Bone morphogenic bone receptor; BMP4 = Bone morphogenetic protein 4, CHD = Chordin, TGS = twisted gastrulation. These molecules play an important role in regulating development in the embryos of the amphibian (frog) Xenopus laevis.

BMP binds to its receptor (BMPR) on certain cells and acts as a signal leading to induction of a number of developmental genes. Most of them are involved in establishing dorsal-ventral polarity (the back and belly of the the tadpole). Chordin is an antagonist of BMP4 and it is secreted by another group of cells in the early embryo to inhibit the action of BMP4.

The discovery of specific cells that secreted morhogenic factors is mostly due to the pioneering work of Hans Spemann, who was awarded a Nobel Prize in 1935. This marked a turning point in the history of developmental biology because it signaled the transition from a descriptive science to an experimental/molecular/genetic science.

We have a single winner this week. It's Ian Clarke of New England Biolabs Canada in Pickering ON, Canada.

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Today's molecule is actually four molecules. Your task is to identify the four molecules shown in the cartoon. Explain what they are doing in the figure. Be sure to name the species or you won't get credit for a correct answer.

These molecules are directly connected to one of the most significant Nobel Prizes in the 20th century. The Nobel Laureate didn't know the names of these molecules but that doesn't diminish the achievement. Identify the Nobel Laureate and the connection between Monday's Molecules and the work for which the prize was awarded.

The first person to identify all four molecules and the Nobel Laureate, wins a free lunch at the Faculty Club. Previous winners are ineligible for six weeks from the time they first won the prize. Please note the change in the length of time you are ineligible. The idea is to give more more people a chance to win.

There are eight ineligible candidates for this week's reward: Dima Klenchin of the University of Wisconsin, Madison, Adam Santoro of the University of Toronto., Michael Clarkson of Waltham MA (USA), Òscar Reig of Barcelona, Maria Altshuler of the University of Toronto, Mike Fraser of the University of Toronto, Jaseon Oakley of the University of Toronto, and Bill Chaney of the University of Nebraska.

Bill Chaney has donated his free lunch to a deserving undergraduate so I'm going to continue to award an additional free lunch to the first undergraduate student who can accept it. Please indicate in your email message whether you are an undergraduate and whether you can make it for lunch.

THEME:

Nobel Laureates
Send your guess to Sandwalk (sandwalk (at) bioinfo.med.utoronto.ca) and I'll pick the first email message that correctly identifies the molecule(s) 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 allowed.

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[Image Credit: De Robertis, E.M. and Kuroda, H. (2004)]

Creationism, ID and the Douchebaggery of Really Bad Arguments: An Evening with the Canadian Cynic

 
Join us at the Centre for Inquiry (Toronto) for Creationism, ID and the Douchebaggery of Really Bad Arguments: An Evening with the Canadian Cynic.

Sandwalk readers will be able to withstand the suspense since you already know who Canadian Cynic is.

Starts: Friday, July 3rd 2009 at 7:00 pm
Ends: Friday, July 3rd 2009 at 9:00 pm
Location: Centre for Inquiry Ontario, 216 Beverley St., Toronto

Creation Science, Intelligent Design and the Douchebaggery of Really, Really Bad Arguments

A polemic by the Canadian Cynic, aka ???

For over five years, the blogger "Canadian Cynic" has railed against the appalling idiocy of the right-wing wankersphere. Along with his carefully-acquired co-bloggers "LuLu" and "Pretty Shaved Ape", "CC" (as he is known to his readers) has struck fear into the hearts of Canada's wanks from coast to coast, using a combination of awesome intellect, devastating logic and, sometimes, just calling people "douchebags" when the situation calls for it.

And for the first time, he comes out publicly ... at the Centre for Inquiry.

The evening's presentation will consist of some war stories from many years back during CC's anti-creation science years, plus some updates on how, depressingly, nothing seems to have changed.

There will be a subsequent Q/A session, during which outraged audience members will be allowed to vent until told to put a sock in it, after which we will adjourn to a convenient pub that serves real beer, and you're buying.

Event admission: $5 regular, $4 student, FREE for Centre for Inquiry Friends of the Centre

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Gene Evolution Process Discovered

 
This press release heralds a major breakthrough in evolution: Gene Evolution Process Discovered.

One of the mechanisms governing how our physical features and behavioural traits have evolved over centuries has been discovered by researchers at the University of Leeds.

Darwin proposed that such traits are passed from a parent to their offspring, with natural selection favouring those that give the greatest advantage for survival, but did not have a scientific explanation for this process.

In research published this week, the Leeds team reports that a protein known as REST plays a central role in switching specific genes on and off, thereby determining how specific traits develop in offspring.

The article is by Johnson et al. (2009). Here's the abstract.

Specific wiring of gene-regulatory networks is likely to underlie much of the phenotypic difference between species, but the extent of lineage-specific regulatory architecture remains poorly understood. The essential vertebrate transcriptional repressor REST (RE1-Silencing Transcription Factor) targets many neural genes during development of the preimplantation embryo and the central nervous system, through its cognate DNA motif, the RE1 (Repressor Element 1). Here we present a comparative genomic analysis of REST recruitment in multiple species by integrating both sequence and experimental data. We use an accurate, experimentally validated Position-Specific Scoring Matrix method to identify REST binding sites in multiply aligned vertebrate genomes, allowing us to infer the evolutionary origin of each of 1,298 human RE1 elements. We validate these findings using experimental data of REST binding across the whole genomes of human and mouse. We show that one-third of human RE1s are unique to primates: These sites recruit REST in vivo, target neural genes, and are under purifying evolutionary selection. We observe a consistent and significant trend for more ancient RE1s to have higher affinity for REST than lineage-specific sites and to be more proximal to target genes. Our results lead us to propose a model where new transcription factor binding sites are constantly generated throughout the genome; thereafter, refinement of their sequence and location consolidates this remodeling of networks governing neural gene regulation.

Correct me if I'm wrong, but haven't there been occasional rumors about other regulatory proteins (repressors and activators) that might play a role in regulating development? Haven't they sometimes been implicated in causing the differences between species? I seem to remember hearing something about "evo-devo"—does that ring any bells?

Do scientists have any responsibility to make sure their work is accurately reported by university press offices? I think they do.

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Johnson, R., Samuel, J., Ng, C.K., Jauch, R., Stanton, L.W., and Wood, I.C. (2009) Evolution of the Vertebrate Gene Regulatory Network Controlled by the Transcriptional Repressor REST. Molecular Biology and Evolution 26:1491-1507. [doi:10.1093/molbev/msp058]