Web Site Story

 
I have a confession to make. I've always been a fan of West Side Story. I never saw the Broadway production but I saw the movie and even bought the soundtrack album back in 1961.

Some of the songs are true classics that are still being played on the radio today (Especially if you have satellite radio and listen to the 60s channel or the showtime channel. )

I bet every one of you can since a few bars of "Maria", "Tonight", "America", "I Feel Pretty", or "Somewhere" and probably most of you know a line or two from "Gee, Officer Krupke" and "Something's Coming".

Here's a very clever and funny, updated, version that was posted on A Blog Around the Clock.

See more funny videos and funny pictures at CollegeHumor.

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Sometimes Violence Is Excusable

 
Here's Buzz Aldrin reacting to being called a coward and a liar. This is one of those times when I can't blame someone for throwing a punch.

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[Hat Tip: Canadain Cynic]

Neutral pH

 

I'm working on the next edition of my textbook. From time to time I'm going to use you (readers) as guinea pigs to try out some new ideas. This is one of those times.

The concept of pH is difficult for students. It's easy for them to memorize the definition—the negative log of the hydrogen ion concentration—but that's not the same thing as understanding what it means.

Textbooks usually tell students that the equilibrium constant (K_eq) for the ionization of water is 1.8 × 10^-16. They can then calculate the ion product for water (K_w) at 25°C knowing the concentration of pure water (55.5 M). This value (1.0 × 10^-14) happens to be a convenient round number, giving rise to the standard pH scale from 1 to 14.

The square root of the ion product for water is the concentration of hydrogen ions ([H⁺]) and the concentration of hydroxide ions ([OH^-]). This concentration is 1.0 × 10^-7 or pH = 7.0, which corresponds to neutral pH at 25°C.

It occurs to me that students would have a better understanding of the concept if they were asked to do some calculations on their own rather than just reading the derivations in the textbooks. I propose to add the following problem. How many Sandwalk readers know the answer?

Neutral pH is the pH at which the concentrations of H⁺ and OH^- are equal in aqueous solvent. This pH is 7.0 for pure water at 25°C.

What is the neutral pH in your blood? What is the neutral pH in extremeophiles growing at 0°C or 100°C? (You may have to look up the values of some parameters in the Handbook of Chemistry & Physics).

Post your answers in the comments. You can post anonymously if you want but all the best biochemists will be signing their names.

Don't look at the comments until you come up with your own answer.

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Monday's Molecule #129: Winner

 
The molecule is the Src protein tyrosine kinase from chicken (Gallus gallus). The scr gene is a proto-oncogene, meaning that is the normal version of an oncogene, or a cancer-causing gene. Mutant alleles of proto-oncogenes are responsible for many types of cancer.

A highly derived version of the normal src gene (v-src) is present in strains of the chicken Rous sarcoma virus discovered by Payton Rous in 1911. RSV causes cancer in chickens and it was the first cancer-causing virus to be identified.

It wasn't until the 1970's that the gene responsible for the cancer was identified and recognized as a derivative of a normal cellular gene involved in signal transduction and regulation of cell growth. Michael Bishop and Harold Varmus received the Nobel Prize for identifying the src gene as a proto-oncogene. They are this week's Nobel Laureates.

Many people got the right answer but the first one was Cody Cobb, soon to be a graduate student at Rutgers University in New Jersey. He will be joining me for lunch in a week or two.

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Today's molecule is very famous so you aren't going to get any hints other than the fact it's from the species Gallus gallus

You need to name the molecule, identify its function, and explain why it is so famous. That will lead you to one or more Nobel Laureates whose Nobel Prize was directly related to this protein and, more importantly, its gene.

The first person to identify the molecule and the Nobel Laureate(s), wins a free lunch. Previous winners are ineligible for six weeks from the time they first won the prize.

There are seven ineligible candidates for this week's reward: Mike Fraser of the University of Toronto, Jason Oakley of the University of Toronto, Bill Chaney of the University of Nebraska, Ian Clarke of New England Biolabs Canada in Pickering ON, Canada. Dima Klenchin of the University of Wisconsin at Madison, Dara Gilbert of the University of Waterloo, and Anne Johnson of Ryerson University.

I have an extra free lunch for a deserving undergraduate so I'm going to continue to award an additional prize 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 open.

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The figure is from Williams et al. (1997).

Williams, J.C., Weijland, A., Gonfloni, S., Thompson, A., Courtneidge, S.A., Superti-Furga, G., Wierenga, R.K. (1997) The 2.35 A crystal structure of the inactivated form of chicken Src: a dynamic molecule with multiple regulatory interactions. J. Mol. Biol. 274:757-75. [PubMed] [doi:10.1006/jmbi.1997.1426]

Chris Mooney and Sheril Kirshenbaum in Newsweek

 
Chris Mooney and Sheril Kirshenbaum have published an article in Newsweek [Defenders of the Faith: Scientists who blast religion are hurting their own cause].

The subtitle reveals that Mooney and Kirshenbaum just don't get it. I am a scientist who "blasts" religion. My "cause" is to demonstrate that religion is superstitious nonsense and should be abandoned. There are many people who share my opinion and they aren't all scientists. The fact that I am a scientist isn't really relevant.

The position that Mooney and Kirshenbaum adopt would be equivalent to saying that Christopher Hitchens should back off because he's hurting the "cause" of journalism, or that Rickey Gervais is hurting the "cause" of comedy, or Bill Gates is hurting the "cause" of making tons of money. They make the assumption that atheist scientists are only interested in promoting science (to the American public) and everything else is secondary.

This point has been explained to them hundreds of times. I don't know whether they are deliberately ignoring the facts order to frame the argument in their own terms or whether they are incapable of grasping the distinction we are tying to make.

There are times when Mooney and Kirshenbaum seem to be on the verge of understanding. The Newsweek article contains such an example. After the typical rant about how great Francis Collins is and how evil PZ Myers is, they go on to say ....

The public's willingness to reject science for religious reasons is certainly lamentable. But by arguing that science contradicts religion and makes it untenable, many atheists reinforce the very concerns that are keeping people from accepting science to begin with. Someone like Collins, by contrast, can convince those who think science conflicts with their beliefs that this needn't be the case.

This is the same old story we've heard before. Yes, it's true that someone like Francis Collins, who claims that science and religion are compatible, can be a great comfort to people who long to hear this. But that's not the point. The point is whether science and religion really are compatible. That's the question that certain atheists are asking and it won't be settled by pointing to Francis Collins. That's about as absurd as claiming that incompatibility is proven by pointing to Neil deGrasse Tyson or Jerry Coyne.

But wait. Here's where Mooney and Kirshenbaum offer us a glimmer of hope. They come very close to recognizing that the real question is whether science and religion are compatible and not just whether Collins thinks they are. They recognize that there's an "intellectual" question that might be important.

And Collins's approach isn't just good as a strategy to get the public to better appreciate science. The idea that science and religion can be compatible is strong on the intellectual merits as well. Granted, it depends how you define your terms: if your religion holds that Genesis must be read literally, then you are in direct conflict with scientific findings about the age of the Earth, the diversity of life on the planet, and so on. Yet if we consider religion more broadly—in its own considerable diversity—we find many sophisticated believers who've made a peace between their belief and the findings of modern science. It's not just Collins; consider the words of the Dalai Lama: "If science proves some belief of Buddhism wrong, then Buddhism will have to change."

Oh dear. Close but no cigar. They're still relying on the argument from authority—in this case the Dalai Lama—and their "evidence" still depends on the fallacy of The Doctrine of Joint Belief. And there's those mysterious "sophisticated believers" that we hear so much about but never actually encounter. Where are they hidden?

Still, there's a glimmer of hope. Keep trying, Chris and Sheril. One of these days you may see a frozen waterfall and everything will become clear.

UPDATE: James Hrynyshyn draws your attention to the same passage from the Newsweek article but he puts a different spin on it [Science v. Atheism: the Dalai Lama gambit]. Imagine that Francis Collins makes the same kind of statement that that Dalai Lama made. Collins would say, "If science proves some belief of Christianity wrong, then Christianity will have to change."

How many Christians want to hear that their religion might be wrong and might have to change?

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[Hat Tip: RichardDawkins.net]

The Calling

 
I'm deeply suspicious of people who think they're doing God's will. But I'm positively frightened by people who believe they have been given responsible government positions (elected or appointed) because it is God's will.

Today I stumbled upon this passage from The Language of God by Francis Collins. He's discussing his appointment to head the Human Genome Project (pp. 118-119).

An intense national search ensued to find a new director. No one was more surprised than I to find the selection process converging on me. Being quite happy at the time leading a genome Center at the University of Michigan, and never having imagined myself as a federal employee, I initially indicated no interest. But the decision haunted me. There was only one Human Genome Project. This was going to be done only once in human history. If it succeeded, the consequences for medicine would be unprecedented. As a believer in God, was this one of those moments where I was somehow being called to take on a larger role in a project that would have profound consequences for our understanding of ourselves? Here was a chance to read the language of God, to determine the intimate details of how humans have come to be. Could I walk away? I have always been suspicious of those who claim to perceive God's will in moments such as this, but the awesome significance of this adventure, and the potential consequences for humankind's relationship with the Creator, could hardly be ignored.

Visiting my daughter in North Carolina in November 1992, I spent a long afternoon praying in a little chapel, seeking guidance about this decision. I did not "hear" God speak—in fact, I have never had that experience. But during those hours, ending in an evensong service that I had not expected, a peace settled over me. A few days later, I accepted the offer.

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Rationalism vs Superstition: More than just Evolution vs Creationism

 
The Texas Board of Education is doing all of us a great favor by showing that the real fight isn't just evolution vs creationism or science vs religion. The real fight is religion vs everything. In other words, the problem isn't just creationists—it's people with a religious agenda.

We can see this now that the Texas Board of Education has turned its attention to modifying the social studies curriculum. They've appointed a panel of "experts" to recommend changes in the curriculum. There were three "experts" appointed by the conservative camp within the Board and three appointed by other side. The result is reported in The Wall Street Jounral [The Culture Wars' New Front: U.S. History Classes in Texas].

The three reviewers appointed by the moderate and liberal board members are all professors of history or education at Texas universities, including Mr. de la Teja, a former state historian. The reviewers appointed by conservatives include two who run conservative Christian organizations: David Barton, founder of WallBuilders, a group that promotes America's Christian heritage; and Rev. Marshall, who preaches that Watergate, the Vietnam War and Hurricane Katrina were God's judgments on the nation's sexual immorality. The third is Daniel Dreisbach, a professor of public affairs at American University.

The conservative reviewers say they believe that children must learn that America's founding principles are biblical. For instance, they say the separation of powers set forth in the Constitution stems from a scriptural understanding of man's fall and inherent sinfulness, or "radical depravity," which means he can be governed only by an intricate system of checks and balances.

The curriculum, they say, should clearly present Christianity as an overall force for good -- and a key reason for American exceptionalism, the notion that the country stands above and apart.

"America is a special place and we need to be sure we communicate that to our children," said Don McLeroy, a leading conservative on the board. "The foundational principles of our country are very biblical.... That needs to come out in the textbooks."

But the emphasis on Christianity as a driving force is disputed by some historians, who focus on the economic motivation of many colonists and the fractured views of religion among the Founding Fathers. "There appears to me too much politics in some of this," said Lybeth Hodges, a professor of history at Texas Woman's University and another of the curriculum reviewers.

Let's imagine for a moment that the conservative reviewers on the panel are theistic evolutionists. (This is a thought experiment, take it as a given.) How would my accommodationist friends deal with their recommendations? Is it okay to teach Christianity in history classes as long as it's kept out of science classes?

I wonder if the accommodationists see the potential problem with their position? They are happy to ally with theists as long as those theists accept science—or at least claim to accept science. But that's not all there is to the conflict between the religious and the non-religious.

What do we teach our children in the public schools? Do we teach them that morality comes from God or do we teach them that people can be moral without God? Or do we avoid the problem altogether and teach them nothing at all about the origins of morality?

In American schools do you teach that America is a Christian nation or do you teach that this is a myth that needs to be abandoned? Or is this another topic that has to be avoided in order to avoid conflicts with the Constitution?

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Andrew Coyne on Conservative Values

We don't really have a (small "c") conservative party in Canada. The closest thing we have is the (large "C") Conservative Party but their policies include socialized medicine, government support of private industry, and a taxation scheme where the wealthy pay more.

I like Andrew Coyne even though we don't agree on anything. He's a smart guy and he knows what real (small "c") conservative values should look like. Running up huge deficits by increasing government spending is not part of the game. Neither is "corporate welfare."

Here's Andrew Coyne explaining why he disagrees with the current Canadian government. Apparently it has something to do with "principles," whatever they are.¹

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1. No Canadian political party seems to have them.

[Hat Tip: Canadian Cynic]

Bastille Day

Today is the Fête Nationale in France known also as "le quatorze juillet" or Bastille Day.

This is the day in 1789 when French citizens stormed and captured the Bastille—a Royalist fortress in Paris. It marks the symbolic beginning of the French revolution although the real beginning is when the Third Estate transformed itself into the National Assembly on June 17, 1789 [Tennis Court Oath].

Ms. Sandwalk and I visited the site of the Bastille (Place de la Bastille) when we were in Paris last year. There's nothing left of the former castle but the site still resonates with meaning and history.

One of Ms Sandwalk's ancestors, William Playfair participated in the storming of the Bastille.

In honor of the French national day I invite you to sing the French national anthem, La Marseillaise. An English translation is provided so you can see that La Marseillaise is truly a revolutionary call to arms. (A much better translation can be found here.)

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Check out Uncertain Principles for another version of La Marseillaise—this is the famous scene in Casablanca.

Monday's Molecule #129

 
Today's molecule is very famous so you aren't going to get any hints other than the fact it's from the species Gallus gallus

You need to name the molecule, identify its function, and explain why it is so famous. That will lead you to one or more Nobel Laureates whose Nobel Prize was directly related to this protein and, more importantly, its gene.

The first person to identify the molecule and the Nobel Laureate(s), wins a free lunch. Previous winners are ineligible for six weeks from the time they first won the prize.

There are seven ineligible candidates for this week's reward: Mike Fraser of the University of Toronto, Jason Oakley of the University of Toronto, Bill Chaney of the University of Nebraska, Ian Clarke of New England Biolabs Canada in Pickering ON, Canada. Dima Klenchin of the University of Wisconsin at Madison, Dara Gilbert of the University of Waterloo, and Anne Johnson of Ryerson University.

I have an extra free lunch for a deserving undergraduate so I'm going to continue to award an additional prize 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.

---

The figure is from Williams et al. (1997).
Williams, J.C., Weijland, A., Gonfloni, S., Thompson, A., Courtneidge, S.A., Superti-Furga, G., Wierenga, R.K. (1997) The 2.35 A crystal structure of the inactivated form of chicken Src: a dynamic molecule with multiple regulatory interactions. J. Mol. Biol. 274:757-75. [PubMed] [doi:10.1006/jmbi.1997.1426]

Timmy's Takes Manhattan

 
Tim Hortons is opening 13 stores in Manhattan and several more in Brooklyn. The first nine stores started serving coffee and donuts yesterday. Click here for a photo of New Yorkers lining up at the Penn Station store. The story even made the New York Times.

This is all part of a secret plot by Canadians to take over the best parts of the USA. (There are no plans to open stores in Texas.) Once we succeed we will impose universal health care¹ and ban Starbucks.

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1. Also known as socialized medicine.

Sequencing Koreans

 
There are several complete¹ sequences of human genomes. The standard reference sequence is the one published at NCBI as a result of the human genome project It is a composite sequence from several individuals.

There are four personal genomes available. Craig Ventor, Jim Watson, an African (Yoruban), and an individual from China. Last May the sequence of a Korean was published in Genome Research.

Ahn, S.M., Kim, T.H., Lee, S., Kim, D., Ghang, H., Kim, D.S., Kim, B.C., Kim, S.Y., Kim, W.Y., Kim, C., Park, D., Lee, Y.S., Kim, S., Reja, R., Jho, S., Kim, C.G., Cha, J.Y., Kim, K.H., Lee, B., Bhak, J., Kim, S.J. (2009) The first Korean genome sequence and analysis: Full genome sequencing for a socio-ethnic group. Genome Res. 2009 Jun 24. [Epub ahead of print] [PubMed] [doi: 10.1101/gr.092197.109],

Pay attention to the dates ... it's going to be important.

This paper was received by the journal on Feb. 3, 2009. It was accepted on May 22, 2009 and published online on May 26, 2009. The sequence was posted on a Korean website in December 2008 and it has been freely available since then.

Another Korean group published a paper In Nature last week.

Kim, J.I., Ju, Y.S., Park, H., Kim, S., Leek S., Yi, J.H., Mudge, J., Miller, N.A., Hong, D., Bell, C.J., Kim, H.S., Chung, I.S., Lee, W.C., Lee, J.S., Seo, S.H., Yun, J.Y., Woo, H.N., Lee, H., Suh, D., Lee, S., Kim, H.J., Yavartanoo, M., Kwak, M., Zheng, Y., Lee, M.K., Park, H., Kim, J.Y., Gokcumen, O., Mills, R.E., Zaranek, A.W., Thakuria, J., Wu, X., Kim, R.W., Huntley, J.J., Luo, S., Schroth, G.P., Wu, T.D., Kim, H., Yang, K.S., Park, W.Y., Kim, H., Church, G.M., Lee, C., Kingsmore, S.F., Seo, J.S. (2009) A highly annotated whole-genome sequence of a Korean individual. Nature July 8 [epub ahead of print] [PubMed] [doi: 10.1038/nature08211]

This paper was received by the journal on March 6, 2009. It was accepted on June 18, 2009 and published online on July 8, 2009.

Neither paper mentions the other. There is nothing in the Nature paper that acknowledges the prior publication of the complete genome of a Korean. (Normally in circumstances like this you would expect a note at the end of the paper.)

Were the authors of the Nature paper completely unaware of the other work and the availability of the sequence data? Probably not, since it's mentioned in the press release.

The announcement, however, is likely to fuel a dispute over who was the first to have completed a genome map in Korea. Professor Kim Seong-jin, director of the Lee Gil-ya Cancer and Diabetes Research Institute at Gachon University of Medicine and Science in Incheon, completed a genome map in December last year and published it in the international journal Genome Research.

Seo said, “Since the accuracy is inadequate, (Kim’s) map cannot be considered Korea’s first.”

Gachon professor Ahn Seong-min refuted Seo’s claim, however, saying, “Professor Kim’s genomes were analyzed 29 times and the map is no less accurate than Professor Seo’s.”

It's going to be very difficult for the authors of the second paper to defend their actions. It looks like they behaved unethically by completely ignoring their competitors in their publication and then making a feeble excuse in the press release.

I also think the authors of the first paper should have mentioned that another Korean genome was about to be published although they probably did not have access to the data.

It will be interesting to see how this plays out. My first thoughts are that Nature ought to take a stand and retract the paper. My second thoughts are that Korean science seems to be very competitive and the scientific standars in that country seem to be more "flexible" than elsewhere.

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1. Published sequences don't include centromeric regions and other regions with large blocks of repetitive DNA.

Dennis Kucinich on Canadian Health Care Statistics

 
If I were an American I would have voted for Dennis Kucinich during the Democratic primaries. Here's why ...


David Gratzer is a Canadian psychiatrist and a senior fellow at the Manhatten Institute. He has a practice in Toronto. His latest book is The Cure: How Capitalism Can Save American Health Care.

The Wikipedia article on David Gratzer has a section titled Allegations regarding the misuse of statistics.

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[Hat Tip: Canadian Cynic]

The Doctrine of Joint Belief

The Doctrine of Joint Belief is the idea that just because a single person holds two different worldviews (e.g. science and religion, Christianity and racism, free market capitalism and universal health care) it follows logically that those two views are compatible. Clay Shirky has written a nice summary of the logical fallacy behind the doctrine [Religion and Science]. His article is effective because he used to believe in The Doctrine of Joint Belief.

Lately, Chris Mooney has been arguing in books and blogs that the so-called "new atheists" are hurting his cause by arguing that science and religion are incompatible. Mostly it's a political argument, and that makes sense because Chris Mooney is interested in policy and politics and not science or philosophy.

On Friday, however, Chris shifted gears and tried to defend accommodationism on logical grounds. This is not his forte [Eugenie Scott Powerfully Makes the Case for Science-Religion Compatibility]. It's the classic defense according to The Doctrine of Joint Belief, explained in this case by Eugenie Scott.



Jerry Coyne exhibits a great deal of patience when he explains, for about the millionth time, why the doctrine is logically absurd [Eugenie Scott and Chris Mooney dissemble about accommodationism].

Isn't it about time for one of the accommodationists to speak up and admit that this argument makes no sense? It's about as logical as saying science and Intelligent Design Creationism are compatible because of Michael Behe.

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Nobel Laureate: Adolf Butenandt

 

The Nobel Prize in Chemistry 1939.

"for his work on sex hormones"




Adolf Friedrich Johann Butenandt (1903 - 1995) won the Nobel Prize in Chemistry for his work on the structure and function of sex hormones, particularly estradiol, progesterone, and testosterone.

He was not allowed to accept the Nobel Prize in 1939. After the war, in 1949, he was given the medal at a special ceremony.

He shared the 1939 Nobel Prize with Leopold Ruzicka.

The original (1939) award presentation describes Butenandt's isolation and identification of estradiol.
THEME:
Nobel Laureates

As recently as twelve years ago, very little was known about the nature of the sex hormones. As regards the oestrogenic, or follicle, hormone it was established that extracts from certain organs, e.g. the ovaries and placenta, bring about the characteristic oestrus phenomena in castrated female rats. Only a few observations were available concerning the stability and solubility of their active principles. Further development in the chemistry of the oestrogenic hormones could not take place until the purely biological discoveries by Allen and Doisy in 1923 and by Aschheim and Zondek in 1927 had been made.

Butenandt made the first big step forward in clarifying the chemistry of the follicle hormone in 1929 in Göttingen, simultaneously with Doisy in the United States. Both workers succeeded in isolating from the urine of pregnant women a substance in crystalline form having oestrogenic effects. Butenandt named this substance folliculine, a designation which was later changed to oestrone. He established that its empirical formula was C18H22O2, and that it was an oxyketone.

Shortly after the discovery of oestrone, Marrian in London (1930) isolated from the urine of pregnant women a new hormone which he called oestriol. Butenandt confirmed Marrian's discovery and explained the relationship between the new substance and oestrone. The relation between sterols and oestrogenic substances which had been assumed on crystallographical grounds became probable from the chemical point of view only after Butenandt and Marrian had shown, independently of one another, that only three benzoide double bonds enter into the ring system of these substances.

In 1932, Butenandt was able, from observations made in spectral analysis, and especially on the basis of the then established correct formula of cholesterol to draw up the formulae of the chemical structure of oestrone and oestriol. But there remained the important task of proving the chemical structure of the ring system as assumed by Butenandt. By breaking down the oestriol molecule stage by stage Butenandt proved that both œstrogenic hormones contained a phenanthrene core. At the same time he was able to obtain the same dimethyl phenanthrene from etiobilianic acid, a transformation product of cholic acid. He had thus confirmed the close relationship existing between the follicle hormones on the one hand and the bile acids and sterols on the other.

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[Photo Credit: ULLSTEIN BILD from Nature]

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.