Monday's Molecule #63

 
Today's molecule is a cartoon depicting a particular conformation of molecules. Your task is to identify the structure. Be as specific as possible.

There's an indirect connection between this molecule and Wednesday's Nobel Laureate(s). Your task is to figure out the significance of today's structure and identify the Nobel Laureate(s) who is associated with discovering it. (Be sure to check previous Laureates.)

The reward goes to the person who correctly identifies the structure and the Nobel Laureate(s). Previous winners are ineligible for one month from the time they first collected the prize. There are three ineligible candidates for this week's reward. The prize is a free lunch at the Faculty Club.

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 structure and the Nobel Laureate(s). Note that I'm not going to repeat Nobel Laureates so you might want to check the list of previous Sandwalk postings.

Correct responses will be posted tomorrow along with the time that the message was received on my server. I may select multiple winners if several people get it right.

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

UPDATE: We have a winner. The molecule is a depiction of a (right-handed) α helix, one of the most common examples of secondary structure in proteins. Linus Pauling proposed it in 1948 and he won the Nobel Prize in 1954 for his work on chemical bonds.

The winner is David J. Schuller of Cornell University.

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Jane Harris Zsovan Doesn't Understand Speciation

 
Jane Harris Zsovan posts on a blog called Design of Life. I don't read her blog on a regular basis but Denyse O'Leary recently linked to a post on how speciation doesn't agree with evolutionary theory [Hybridization One Key to Survival].

Jane Harris Zsovan is intrigued by hybrids that appear to be more fit than either of their parents. She thinks this conflicts with Darwinian Theory. Here's an example of how she thinks evolution should work.

Hybrids With Genetic Advantages A Problem for Darwinian Theory

Darwin's theory of natural selection requires offspring to diverge from a common ancestor to create new species. It requires genetic differences to increase as descendants adapt to their environmental niches.

It is this 'natural selection' and 'adaptation' that creates species. And, as the newly created species continue to adapt, they should become more different over time. Following this line of thought, hybrids should be less viable than their parents.

There are many different ways for two isolated populations to evolve into separate species. In many (most?) cases the two lineages diverge by random genetic drift and not just natural selection. The exact mutations leading to genetic incompatibility are most likely to arise by accident and become fixed in one of the lineages by drift.

Evolutionary theory does not require that two separated lineages diverge by natural selection. Speciation does not depend on adaptation. This hasn't been a requirement of speciation for over thirty years [Speciation].

Typically a new population will be founded by a small number of individuals. As the new isolated population grows it will lack much of the genetic variation of the parent population and, consequently, it may be far less fit in it's new environment than a random selection of individuals from the parent population might be. An infusion of new alleles from the parent population by hybridization might lead to individuals that are more fit.

There is nothing in evolutionary theory that says hybrids can't be more fit than either parent. The flaw in Jane Harris Zsovan's logic is entirely due to the obsession creationist have with Darwin and natural selection. They have convinced themselves that everything in evolution must be explained by "Darwinism." This fits with their political agenda. That's why they try so hard to associate evolution with a man who died over one hundred years ago.

The irony comes when they start believing their own false caricature of evolution. That's what happened here, and Denyse O'Leary falls for it hook line and sinker [ More evidence that Darwin's theory of natural selection as the origin of new species is wrong]. The title of Denyse's post is very revealing. Of course, it's wrong to attribute everything to natural selection. Denyse has been told this time and time again and so, I presume, has Jane Harris Zsovan. They are very slow learners. They look like IDiots.

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Gene Genie #26

 
The 26th edition of Gene Genie has been posted at sciencebase [Rubbing Up the Gene Genie].

Sciencebase is this week proud to play host to the Gene Genie Blog Carnival thanks to an offer from Bertalan “Berci” Meskó over on the excellent ScienceRoll. For those who don’t already know, a Blog Carnival doesn’t usually involve a lot of be-costumed revellers dancing through the streets to the sound of the samba band, but is a gathering of like-minded bloggers brought together through the power of the tubular Interwebs to share their latest posts on a given subject.

The beautiful logo was created by Ricardo at My Biotech Life.

The purpose of this carnival is to highlight the genetics of one particular species, Homo sapiens.

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Erudite critic takes on new atheists

 
A column in yesterday's Toronto Star criticized the position of the so-called "New Atheists" [Erudite critic takes on new atheists]. The column was written by Stephen Scharper who frequently writes columns about religion. Scharper was formerly at St. Michael's College (Roman Catholic) in the University of Toronto where he was a Professor in the Department and Centre for the Study of Religion. He is currently a Professor in the Dept. of Anthropology at the University of Toronto Mississauga Campus but he maintains a cross-appointment to the Department and Centre for the Study of Religion.

Scharper's opinion piece begins with what, by now, is becoming a familiar complaint.

A couple of years ago, I was on a televised panel with a man who claimed that religions were to blame for most of the death and destruction throughout history, and that, by extension, religious people were more inherently violent than secular folks.

The implication of his claim was that discrimination against religious adherents would not only be acceptable, but advisable in such matters as job hiring, policy formation, and policing.

Prejudice against people of faith was subtly being proclaimed as an inherent good.

That panelist's view, extreme as it appears, may have some powerful mainstream resonance in a spate of recent publications from the so-called "new atheists."

I don't agree with the extreme view pictured by Stephen Scharper and neither do most atheists. It is simply not true that religious people are inherently more violent than atheists. On the other hand, it is simply not true that believers are more moral than non-believers.

People who believe in supernatural beings are fond of making the association between their belief and superior moral behavior. They often imply—or even state overtly—that atheists must be immoral because they don't believe in God. Many of the "New Atheists" (Scharper mentions Dawkins, Harris, and Hitchens) have pointed out that those claims are not supported by evidence. That's the main point. The "New Atheist" stance is a response to centuries of false propaganda and hypocrisy on the part of believers.

Religious apologists need to stop whining about this counter-offensive and start recognizing that their claims of moral superiority just don't measure up. While it would be wrong to deny someone a job just because they falsely claim to be morally superior, it would also be wrong to give them a job just because they say they are morally superior.

Scharper goes on to praise a recent book by John Haught (God and the New Atheism: A Critical Response To Dawkins, Harris And Hitchens). I haven't read this book but from what Scharper says it sounds like the same-old, same-old that we've heard dozens of time before [e.g. Alister McGrath's Defense of Religion, Propaganda Techniques: Shift the Burden of Proof, Alister McGrath].

Here's how Scharper describes it.

Haught, a senior fellow at the Woodstock Theological Center at Georgetown University, adroitly distills the common themes from this troika [Dawkins, Harris, Hitchens], which suggests that outside of nature, "there is no God, no soul, and no life beyond death," that the universe has no overarching purpose, that all life developments can be explained by science, and that faith in God is the source of countless evils and should thus be jettisoned on moral grounds.

What Haught finds ironic is that the new atheists have little interest in atheism at all, and don't engage in the main philosophical debates raised by atheistic giants such as Karl Marx, Friedrich Nietzsche, Jean-Paul Sartre and Albert Camus. Instead, they base their notion of religion on the creationism of a select band of fundamentalists. In short, they adopt a theologically bereft caricature of religion.

Now, let's be absolutely clear about this argument. It is completely bogus. This is not a debate about religion, it's a debate about the existence of supernatural beings. Atheists are simply not interested in debating how many angels can dance on the head of a pin. They want to debate the evidence for angels. Atheists don't want to debate why God and evil can coexist. They want to debate whether God exists at all. We don't care about the extensive literature on the interpretation of Chapters 1 & 2 of Genesis. It's irrelevant.

We don't need to read up on transubstantiation because we're challenging the divinity of Jesus and not whether wine and bread can turn into blood and flesh. We atheists don't care about the "sophistication" of religious apologetics. (Just as Roman Catholics don't care about ancient Greek texts on how to interpret the Oracle at Delphi or Roman treatises on the entrails of chickens.)

We know that every large religion has tons of literature justifying their particular beliefs. This was as true of the ancient Greek and Roman religions as it is of the modern religions such as Hinduism, Islam, and Taoism. You do not need to be an expert in all the sophisticated delusions in order to question the fundamental issue—do supernatural beings exist?

The form of argument that Haught advances, and Scharper supports, has been called The Courtier's Reply by PZ Myers [see The Emperor's New Clothes and the Courtier's Reply for an explanation]. This needs to be widely known so I'm going to quote PZ once again in case some of the Sandwalk readers are unfamiliar with his response. Here's how PZ describes the Courtier's Reply to the revelation that the Emperor has no clothes.

I have considered the impudent accusations of Mr Dawkins with exasperation at his lack of serious scholarship. He has apparently not read the detailed discourses of Count Roderigo of Seville on the exquisite and exotic leathers of the Emperor's boots, nor does he give a moment's consideration to Bellini's masterwork, On the Luminescence of the Emperor's Feathered Hat. We have entire schools dedicated to writing learned treatises on the beauty of the Emperor's raiment, and every major newspaper runs a section dedicated to imperial fashion; Dawkins cavalierly dismisses them all. He even laughs at the highly popular and most persuasive arguments of his fellow countryman, Lord D. T. Mawkscribbler, who famously pointed out that the Emperor would not wear common cotton, nor uncomfortable polyester, but must, I say must, wear undergarments of the finest silk.

Dawkins arrogantly ignores all these deep philosophical ponderings to crudely accuse the Emperor of nudity.

Personally, I suspect that perhaps the Emperor might not be fully clothed — how else to explain the apparent sloth of the staff at the palace laundry — but, well, everyone else does seem to go on about his clothes, and this Dawkins fellow is such a rude upstart who lacks the wit of my elegant circumlocutions, that, while unable to deal with the substance of his accusations, I should at least chide him for his very bad form.

Until Dawkins has trained in the shops of Paris and Milan, until he has learned to tell the difference between a ruffled flounce and a puffy pantaloon, we should all pretend he has not spoken out against the Emperor's taste. His training in biology may give him the ability to recognize dangling genitalia when he sees it, but it has not taught him the proper appreciation of Imaginary Fabrics.

Here's my challenge to Stephen Scharper: if you know of a sophisticated argument for the existence of God that hasn't already been addressed, and refuted, by atheists, then here's your chance to present it. I notice that you didn't mention it in your column and none of your colleagues have actually presented one of those secret theological debating points that you claim exist in the corridors of seminaries and departments of philosophy or religion.

I'm sick and tied of hearing apologists make false claims about the existence of some sort of deal-breaking point that the "New Atheists" have overlooked because they are addressing a kindergarten version of religion. As far as I'm concerned the rationality behind belief in supernatural beings is kindergarten philosophy. If Professor Scharper disagrees, then lets hear about the killer evidence for God that atheists don't know about because we haven't studied theology.

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[Photo Credit: The photograph of Professor Stephen Scharper is from the University of Toronto News]

Brussels

 
My daughter Jane and her husband Michael live in Brussels. Last weekend we visited them and they took us on a walking tour of downtown Brussels.

Many of the streets are closed to vehicle traffic and even on a chilly Friday (about 7°C) there were plenty of shoppers and quite a few tourists. My goal was to sample the food of Brussels—other members of our party were more interested in the shops and we visited a fair number of those on our tour.

The very first stop was a place that sold Belgian waffles. There are dozens of these shops with windows open to the street. It's the Brussels equivalent of Tim Horton's. The waffles were delicious and I would have eaten several except that I was saving up for even better things later on.

Brussels was officially founded in 979 by Charlemagne's grandson Lothar, although there had been a settlement on the site for several hundred years before Lothar build a fortress. The city prospered as a trading center in medieval times and much of the central part of the modern city dates from that era. The name of the city comes from an Old Flemish word Broekzele, which means marshland. The city was originally built on an island in the river Senne [History of Brussels].

Belgium is a relatively young country although it is named after the ancient Celtic tribe of the Belgae, one of the tribes defeated by Julius Caesar in his Gaul campaign (about 55 B.C.). Over the years the region has been controlled by German, French, Dutch, Austrian, Spanish, and British forces. It is still disputed territory although in the modern age the conflict is between the French speaking Walloons and the Flemish population that speaks Dutch. (The French are losing.)

Eventually we reached a delightful part of the city with narrow medieval streets filled with restaurants. Our goal was a fascinating restaurant called Chez Leon. The specialty is mussels and frites (French fries), a meal that can't be found anywhere else in the world as far as I know.

There are several varieties on mussels on the menu. Our party ordered mussels au gratin, mussels and curry, and mussels à la crème. Of course any meal of mussels and frites has to be accompanied by beer and there were many brands to choose from. The mussels were delicious, the frites were excellent, and the beer was wonderful.

Some of you may be curious about the price of such a meal. The mussels and frites were 22.50 € and that works out to about $33 in Canadian or American currency. This seems expensive but it's not out of line with many other prices in the local restaurants. I really don't know how the French and Belgians can afford to eat out so much. Their salaries don't seem to be higher than what we are used to in North America. I guess they just have different priorities.

There are very few McDonald's restaurants in Brussels (or Paris) and it's rare to see any of the other fast-food places we're used to in North America. The local population prefers a longer sit-down meal even if it's more expensive. It's a major cultural difference and one that I could easily adjust to. In fact, I did adjust to it when we lived in Europe from 1974-1978.

You can't walk very far in Brussels without encountering a chocolate shop. (We visited several.) Everyone has their favorite but I'm told that Neuhaus chocolate is widely believed to be the best Belgian chocolate. The Belgians are very proud of their chocolate. They think it's superior to Swiss chocolate. I'm not going to take sides on that one since I lived in Switzerland for many years and still have many friends there.

The shops are very popular. I was surprised to see so many Belgians buying chocolates since they are not cheap. This is another example of differing priorities. I guess they prefer a small amount of excellent chocolate to a cheaper Mars bar or M&M's.

I'm used to seeing chocolate shops but the really surprising shops were the ones that sell beer. We saw a dozen stores that specialized in beers with a huge emphasis on Belgian beers. These stores look like wine stores except that it's bottles of beer that are lined up on the shelves.

In many cases, the stores advertise 250 or 300 different brands of beer. We didn't have time to taste all of them but the ones I had were excellent. Thanks to all those Sandwalk readers, and Michael, who made recommendations. I won't reveal my current favorite because I don't want to hurt anyone's feelings. And also because there are still several hundred beers that I haven't (yet) tried. This is definitely a place where bloggers and talk.origins readers should get together for a Howlerfest.

After a long day we stopped at one of the Häagen-Dazs Cafés for chocolate fondue. We were served a plate full of small balls of ice cream of various flavors. These can be dipped in a creamy pot of rich chocolate. The ice cream was accompanied by a plate of fresh fruit and pieces of muffin that also went well with the hot chocolate. All in all it was an excellent way to end our delicious tour of Brussels.

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The Ladies' Privilege

 
Friday's Urban Legend: TRUE

According to legend, girls can propose to their boyfriends on February 29th. Snopes.com says this is a true custom known as The Ladies Privilege [The Privilege of Ladies]. Back in the thirteenth century a man had to accept a proposal on February 29th or pay a fine. This probably explains why so many men were off fighting wars at the end of February during a leap year.

It's based on the idea that February 29th is an unusual day and unusual things are permitted on that day only. One of the unusual things that is allowed is for women to propose marriage. Nowadays this is much more common on all the other days but apparently there was a time when only the man could propose marriage. I wonder what those times were like when men were in control?

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The State of Science Blogging

 
There's an interesting discussion going on over at Bayblab on The State of Science Blogging. The commenters are responding to some provocation by Anonymous Coward^[1] who took a look at the top five science blogs and said,

Of those only Cognitive daily is consistantly talking about peer-reviewed research. Why is that? Perhaps there is less appeal in discussing recent papers than bashing creationists. But bashing creationists is almost too easy, and not very constructive. It's been said before, you can't reason somebody out of a position in which they didn't reason themselves into. And it worries me because to the lay audience listening to PZ Myers (the 800lb gorilla), it would seem that science's purpose is to attack religion. In fact I suspect the blog gets most of its traffic from creationists. According to technorati, his top tags are "Creationism, godlessness, humor, kooks, politics, religion, weblog, weirdness", so should it really count as a science blog?

If you examine the elephant in the room, ScienceBlogs, the trend is maintained: politics, religion books, technology, education and music are tagged more often than biology or genetics. This suggests that their primary motives are entertainment rather than discussing science. Why? Because it pays. Seed Magazine and the bloggers themselves profit from the traffic. That's right, Seed actually pays these bloggers for their posts. And the whole ScienceBlogs thing is a little incestuous, they really like linking to each other, but not so much to the little blogs. I'm afraid gone is the amateur blogger, and in is the professional gonzo science journalist. Might as well read Seed magazine.

One of the most interesting comments comes from Dave Munger of Cognitive Daily ....

So... the most popular science blogs cover the most popular topics related to science?

You also seem to be saying that you wish these bloggers would write about less popular topics. But that would make them... less popular. And then other science blogs would become the most popular. Then you could complain about those blogs.

At least you'd have something to write about.

This is a very important point. Many of us are interested in blogging about science and in teaching science. But you can't be an effective advocate for science if you don't have an audience. One way to get an audience is to blog about science related issues that are controversial and then sneak in some good science blogs when people come to visit.

In my case, that's not the only motive for blogging about rationalism and superstition. I happen to have (at least) two interests in life and I like to blog about everything that interests me. As it turns out, there are more people interested in the conflict between science and religion—or the war in the Middle East—than in hard-core science. I posted a whole series of articles on The Three Domain Hypothesis and got only a handful of comments. The series on junk DNA is bringing in just a trickle of interested readers. On the other hand, when I post about religion or politics there are dozens of comments and a lively discussion ensues.

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1. I don't like linking to anonymous bloggers. In the future I'm going to make it a policy to only link to bloggers who identify themselves, except under rare circumstances.

Tangled Bank #99

 
The latest issue of Tangled Bank is #99. It's hosted by Greg Laden at GregLaden's Blog [The Tangled Bank].

This is the February 20, 2008 edition of The Tangled Bank web carnival. The next edition will be hosted at Archaeoporn.

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If you want to submit an article to Tangled Bank send an email message to host@tangledbank.net. Be sure to include the words "Tangled Bank" in the subject line. Remember that this carnival only accepts one submission per week from each blogger. For some of you that's going to be a serious problem. You have to pick your best article on biology.

In the Cafeteria

 
Yesterday we were at the Musée d'Orsay. We sat down to have a coffee in the museum cafeteria. As you can see, some cafeterias in France are a little more fancy than the average museum cafeteria in North America.

My wife's weird sense of humor produced this picture of me admiring the statues.

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Les Invalides

 
This is my fourth visit to Paris but it's the first time I've been to Les Invalides. The tomb of Napoleon Bonaparte is much more impressive than I ever expected.

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Pictures of Paris

 


The church is St. Germain des Prés. It's just a few blocks from where we're staying.

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Are Brussel Sprouts Bad for You?

 

Probably not, and that's a good thing because I like Brussel sprouts. They may be OK for humans but they're bad for aphids [Eat up all of your Brussels sprouts -- unless you're an aphid].

I'm going to be in Brussels today. I'm looking forward to a nice meal of Brussel sprouts with beer and chocolate.

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An IDiot Software Developer Opines About Junk DNA

 
Randy "I want to believe" Stimpson is a software developer who thinks he understands biology. He has written a post where he claims Most DNA is not Junk. Doppelganger has already pointed out the most obvious faults with Randy's point of view [Software developer PROVES that there is no junkDNA*... and other stuff].I just want to comment on one small paragraph in order to clear up any confusion.

A bacterial genome has 4 million base pairs of DNA and according to Professor Larry Morgan, a bacterial genome doesn’t have junk. So I think it is safe to say that there is at least 1MB of information in the human genome.

I'm pretty sure he's referring to me. I'd like to point out for the record that bacterial genomes range in size from about 10⁶ bp up to 10⁷ bp.

All bacterial genomes have junk DNA consisting mostly of defective transposons and defective prophage. In most cases the amount of junk DNA is only a few percent of the genome.

The views expressed by Randy Stimpson are typical of those who desperately want to believe in intelligent design creationism. Junk DNA is not compatible with intelligent design creationism no matter how you cut it.

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La Tour Eiffel

 
These are my pictures of the Eiffel Tower.

It's much easier to take pictures like this from the second level 'cause you don't have to hang out near the outer railing where the risk of falling off is very high. I found that it's much better to say far away from the edge. My knees were much more stable when I did that.

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Rue du Cherche Midi

 
This is a picture of Rue du Cherche Midi right outside our apartment in Paris. The street is full of nice shops (expensive), bakeries, and small restaurants. It's perfectly situated in the middle of the 6th (6^e) arrondissement [Map].

There are lots of interesting places to see right in our neighborhood. One of the nearby cafés is shown below along with a close-up of a plaque hanging on the wall of a building in on the next street. It says that John Paul Jones died in that building in July 1792. (It seems as though the prominent men and women of the Revolutionary War were very fond of France.) Incidentally, I took a quick poll of several people in the vicinity and none of them knew who John Paul Jones was.

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