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]

Science Scouts

 
Join Science Scouts and win cool badges! In case you don't know, the complete offical name of Science Scouts is "Order of the Science Scouts of Exemplary Repute and Above Average Physique." (They're lenient about the physique.)

This is one of my favorite badges. All you have to do is Science with no conceivable application (known among friends as the "useless" badge). I've done lots of that kind of science. I'm also eligible for the next level badge— for science that not only has no conceivable application but also isn't even interesting to fellow scientists.

This one's quite ordinary. It's the cloner badge. You can earn it just by cloning something. An advanced version is coming out next year. It's for people who have cloned something that terrorized a small village.

I'm really proud of this one. It's the "somewhat confused as to what scientific field I actually belong to" badge. When you put it on your CV you can refer to it by its more formal name: the transdiscplinary, interdiscplinary, multidisciplinary, or intradisciplinary (TIMI) badge.

Here are some of my other badges ...

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[Hat Tip: Eva Amsen]

Who Is Canadian Cynic?

 
Blogger Canadian Cynic chose to remain anonymous. As most of you know, I prefer bloggers who are not anonymous but I respect the decision of my friends who disagree.

Some of Canadian Cynic's enemies don't respect his decision so they did some digging and outed him. Tsk, tsk, typical behavior for right-wing idiots.

Canadian Cynic is my old friend Rob Day from talk.origins. I'm secretly delighted that he can now be identified even though I deplore the behavior of his enemies.

He's probably going to be giving a talk in Toronto very soon so you can all come out and meet Canadian Cynic [You might want to keep Friday, July 3, open]. I have stories, and lots of photos! So do my daughter Jane and her husband Michael—they rented his house! We'll have a real "outing" party.

BTW, Rob doesn't want anyone to retaliate by outing the right-wing idiots who choose to remain anonymous [On outing].

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Canada's Secret Plan for World Domination

 
The secret is out [Donuts To Dollars].

Our Friendly Neighbors In Canada Are About To Wage An International Food Fight Over Your Morning Coffee

(CBS) Americans are about to be dragged into an international food fight … and it's our friendly neighbors in Canada who are throwing down the gauntlet. Jeff Glor reports our Cover Story:

There was some chance that the story would be ignored since it only appeared on CBS News but that turned out to be a forlorn hope. John Pieret of Thoughts in a Haystack has taken on the role of a modern Paul Revere [Rally 'Round the Flag].

Now the whole world knows the secret.

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Monday's Molecule #126

 
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 now allowed.

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

I can't wait to see this ...

 
This looks really good, judging from the trailer. Like PZ Myers I'm a little nervous about how it will turn out but I'll certainly be watching it as soon as it's available.

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Amway sells genetic tests?

 
Many blogs have been shamelessly promoting genetic testing and giving free advertising to the for-profit companies that have been exploiting the technology. Some of the bloggers are indirectly or directly associated with those companies.

Of course we all know where this is going. It's only a matter of time before a rash of private companies catch on to this get-rich scheme and decide to reap the profits.

Daniel MacArthur of Genetic Future has identified one of these companies: Amway sells genetic tests?. Read his posting and read the response from the company (Interleukin Genetics) in the comments.

This is just the tip of the iceberg. It's going to get much worse. I wonder if the cheerleader bloggers are going to take the lead in calling for government controls?

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