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.

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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]

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.

Matt Nisbet Is Puzzled

 
The results of the Pew Science Survey tell us that American love science and they love scientists. Here's what the Pew researchers say in the summary ...

Americans like science. Overwhelming majorities say that science has had a positive effect on society and that science has made life easier for most people. Most also say that government investments in science, as well as engineering and technology, pay off in the long run.

And scientists are very highly rated compared with members of other professions: Only members of the military and teachers are more likely to be viewed as contributing a lot to society's well-being.

Matt Nisbet believes every word. He points out that the "experts" (e.g. he and his buddies) have been saying this for years. As he puts it in his most recent posting [On the Pew Science Survey, Beware the Fall from Grace Narrative].

I shared a similar observation in a post yesterday, detailing the Pew results that indicate an almost unrivaled amount of cultural respect, admiration, authority, and deference to science and scientists.

Matt can't understand why some of us are a bit skeptical. He doesn't seem to be the least bit concerned about a public who have "an almost unrivaled amount of cultural respect, admiration, authority, and deference to science and scientists" and yet reject evolution, the role of humans in global warming, and the importance of vaccinating your children. Matt never bothers to ask why a public that admires science so much would flock to homeopaths, buy Q-ray bracelets, and read the astrology column in the daily newspaper.

That's because Matt Nisbet isn't a scientist. He isn't skeptical and he never questions his own assumptions. Matt thinks that when people say they admire and respect science and scientists then that's the gospel truth. It never occurs to him to wonder what they mean by "science" and "scientists" and it never occurs to him to wonder about the obvious conflict between what people say in one question and what they say in another. How does he account for the fact that the general public does not support high quality science education for their children in spite of the fact they have a great respect for science?

One of the consequences of Matt's belief is that he proposes solutions to the science literacy problem based on the "fact" that the public has a great deal of confidence in scientists. For example, he quotes from an article he is about to publish in a science journal.

The implication is that relative to authority, deference, and respect, scientists have earned a rich bounty of perceptual capital. When controversies occur, the challenge is to understand how to use this capital to sponsor dialogue, invite differing perspectives, facilitate public participation, reach consensus when appropriate, learn from disagreement, and avoid common communication mistakes that undermine these goals.

I disagree with the premise. I think that real public respect for science is much lower than the Pew summary indicates. To me the survey results suggests a general public that doesn't understand science very well and doesn't trust scientists.

I think that scientists, and everyone else, have to concentrate on educating the general public about the differences between science and superstition. I think that scientists have to work on gaining true respect and authority and that it's a huge mistake to assume they already have it. I'm not sure they ever had it in North America.

Part of gaining more respect involves cleaning our own house and educating the media. We also need to stop listening to the so-called expects on science communication.

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The Good News ....

 
The good news is that FOX is doing its proper job of informing America about religious beliefs in other countries. The bad news is that many FOX news viewers probably had a heart attack when they saw this ...

I know lots of people—mostly accommodationists—who think that religion is here to stay and it's a waste of time trying to fight it. I wonder if they've ever been to Western Europe?

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[Hat Tip: Pharyngula]

The PEW Poll on Science in America

 
There is much to digest in the recent poll by the Pew Research Center for the People & the Press in collaboration with the American Association for the Advancement of Science [Public Praises Science; Scientists Fault Public, Media: Overview].

One of the most remarkable findings isn't new: the American public claims to have a great deal of respect for scientists while, at the same time, a substantial percentage rejects evolution and the scientific conclusions on climate change and vaccinations.

It's hard to reconcile these findings. If most people respect scientists then why do they disagree with the science?

Everyone is going to focus on different aspects of this poll. Matt Nisbet has already weighed in with his interpretation [Pew Survey of Scientists & the Public: Implications for Public Engagement and Communication]. His first conclusion is something that he has claimed many times.

1. In the U.S., scientists and their organizations enjoy almost unrivaled respect, admiration, and cultural authority. Americans overwhelmingly trust scientists, support scientific funding, and believe in the promise of research and technology. Among institutions, only the military enjoys greater admiration and deference.

It's a strange kind of "authority" that we scientists enjoy when only 32% of the general public believe that humans evolved due to natural processes. Among scientists, 87% hold this view. If that's what you call "trust" then I'd hate to see what "distrust" looks like!

Here are some highlights from the report [Public Praises Science; Scientists Fault Public, Media].

More than half of the public (55%) says that science and religion are “often in conflict.” Close to four-in-ten (38%) take the opposite view that science and religion are “mostly compatible.” Yet the balance is reversed when people are asked about science’s compatibility with their own religious beliefs. Only 36% say science sometimes conflicts with their own religious beliefs and six-in-ten (61%) say it does not.

Highly observant Americans are among the most likely to see conflicts between science and their own religious beliefs. But less religiously observant people are more likely to see broader conflicts between science and religion in general. Among those who attend religious services at least weekly, 46% say they see a conflict between science and their religious beliefs (52% do not). Among those who seldom or never attend services, just 21% see a conflict. Yet 60% of those who seldom or never attend services believe science and religion are “often in conflict,” compared with 48% of Americans who attend religious services weekly or more often.

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Religious belief among scientists varies somewhat by sex, age and scientific specialty. Younger scientists are substantially more likely than their older counterparts to say they believe in God. In addition, more chemists than those in other specialties say they believe in God. More men (44%) than women (36%) say they believe neither in God nor a higher power; belief in God is comparable for men and women scientists, but more women than men profess belief in a different supreme being or higher power.

This result confirms some other studies showing that younger scientists are more religious than older scientists. Some people see this as the beginning of a trend leading to scientists becoming more religious.

I suppose that's possible in America but it's also possible that the longer you are a scientist, the more likely you are to abandon your religious beliefs.

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When asked about the importance of various factors that motivated them to pursue careers in science, an overwhelming share of scientists (86%) say an interest in solving intellectually challenging problems was very important. This view is widely shared across scientific specialties.

Substantially smaller percentages of scientists say the desire to work for the public good (41%) and the desire to make an important discovery (30%) were very important reasons for choosing science as a career. However, large majorities do cite these factors as at least somewhat important (81% work for public good, 74% make important discovery).

....

Few scientists say that the desire for a financially rewarding career was a very important part of their decision to become a scientist (4%). However, a third (33%) say this was at least somewhat important in their choice of career.

As might be expected, far more scientists working in industry than those working in other sectors view a desire for a financially rewarding career as very or somewhat important. About half of industry scientists (51%) say this, compared with only about three-in-ten of those working for government (31%), academia (29%) and for non-profits (29%).

More generally, a far larger share of those in the applied sciences (43%) attribute their career choice at least in part to a desire for a financially rewarding career, compared with 25% of those in basic sciences. Among scientific specialties, those in chemistry (40%) are more likely than those in other fields to say financial rewards were a consideration in their career choice.

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Take the Science Knowledge Quiz

 
The Science Knowledge Quiz is on the PEW website. It's associated with their recent poll on science and attitudes about science.

I don't think this is an accurate quiz about scientific knowledge. Many of the questions concern simple facts about science and technology and not principles or concepts.

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Student Attitudes: 60s vs 90s

 
Old fogies who grew up in the 1960s are constantly complaining that today's university students are different. Modern students are much more materialistic and much less concerned about the important things in life—or so they (we) think.

I was reading The Happy Planet Index when I came across an interesting chart.

The chart shows the results of a survey of college students in the USA. They were asked to rate the importance of several goals including whether they wanted to become "very well-off financially" or whether they wanted to "develop a meaningful philosophy of life." Students who rated either (or both) of these choices as "very important" or "essential" were plotted by the year of the survey. The chart is shown below.


I can think of several problems with the data. The 60s were a special time, especially on college campuses. Everyone was an idealist and anti-materialism was very much in vogue. There really were students who wanted to spend the rest of their lives on communes in the countryside. Some of my friends are still there.

Those times are long gone and it's not reasonable to expect today's students to have the same attitudes because the culture is very different.

Another difference is that in the 60s most students didn't have to worry too much about money. As a general rule, they came from families who were well-off and when they graduated from college they were almost certain to get a good paying job if they wanted it.

As the participation rate increased and the economy went through ups and downs, more and more students came to college from a less financially secure background. They are rightly more concerned about having the minimum amount of wealth to be secure and happy.

But in one sense it doesn't really matter why today's students are more materialistic. It's a fact that professors have to cope with when teaching and designing courses. When you look at the chart it's not surprising that fewer students are interested in science careers or getting a Ph.D. in philosophy. It's not surprising that most of our biochemistry students want to be physicians, or dentists, or pharmacists.

One question remains. Should the old fogies continue to butt heads against the wall in order to try and change student aspirations? Should we just forget about our own values from the 60s and give up trying to explain why we thought they were worth pursuing back then, and are still worth pursuing today?

The whole point of the Happy Planet Index and the new economics foundation is to change attitudes and expectations. Their goal is to create a more sustainable lifestyle by convincing people to abandon the pursuit of wealth and material items.

In an age of uncertainty, society globally needs a new compass to set it on a path of real progress. The Happy Planet Index (HPI) provides that compass by measuring what truly matters to us - our well-being in terms of long, happy and meaningful lives - and what matters to the planet - our rate of resource consumption. The HPI brings them together in a unique form which captures the ecological efficiency with which we are achieving good lives.

This report presents results from the second global HPI. It shows that we are still far from achieving sustainable well-being, and puts forward a vision of what we need to do to get there.

The current economic and ecological crises have discredited the dogmas of the last 30 years. The unwavering pursuit of economic growth - embodied in the overwhelming focus on Gross Domestic Product (GDP) - has left over a billion people in poverty, and has not notably improved the well-being of those who were already rich, nor even provided us with economic stability. Instead it has brought us straight to the cliff edge of rapidly diminishing natural resources and unpredictable climate change. We need to see this current crisis as an opportunity. Now is the time for societies around the world to speak out for a happier planet, to identify a new vision of progress, and to demand new tools to help us work towards it. The HPI is one of these tools. We also hope that it will inspire people to act.

That sounds like something right out of the 60s. Those of us who were there have to recognize that we didn't succeed in changing society for the better in spite of our idealism. Are today's students going to do any better when they've even lost the idealism?

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How Many People Have a Tape Worm Named After Them?

 

How many people have a tape worm named after them? Quite a few, as it turns out.

Do you know any of these people? Yes [A Tapeworm To Call My Own].

Ugh!

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Who Do Canadians Trust?

 
Harris/Decima conducted a poll of almost 1200 English-speaking Canadian adults on behalf of Reader's Digest [The Canadians You Trust. Each respondent was given a list of 100 names and photos of prominent Canadians and they were asked to choose the person they trusted the most.

Here's the top ten. The number one most trusted Canadian is a scientist! The rest of the list is pretty impressive. I would probably have picked some of them myself, especially Rick Hillier and Stephen Lewis. I would not have picked #8.

I had to look up #9—she's the Auditor General of Canada.

1. David Suzuki
2. The Queen, Elizabeth II
3. Gen. Rick Hillier (Ret'd)
4. Stephen Lewis
5. Michael J. Fox
6. Lloyd Robertson
7. Peter Mansbridge
8. Stehpen Harper
9. Sheila Fraser
10. Rick Mercer

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Francis Collins: Director of NIH

 
Bad news from The White House.

President Obama Announces Intent to Nominate Francis Collins as NIH Director

WASHINGTON – Today, President Barack Obama announced his intent to nominate Francis S. Collins as Director of the National Institutes of Health at the Department of Health and Human Services.

President Obama said, "The National Institutes of Health stands as a model when it comes to science and research. My administration is committed to promoting scientific integrity and pioneering scientific research and I am confident that Dr. Francis Collins will lead the NIH to achieve these goals. Dr. Collins is one of the top scientists in the world, and his groundbreaking work has changed the very ways we consider our health and examine disease. I look forward to working with him in the months and years ahead."

Francis S. Collins, Nominee for Director, National Institutes of Health, Health and Human Services
Francis S. Collins, M.D., Ph.D., a physician-geneticist noted for his landmark discoveries of disease genes and his leadership of the Human Genome Project, served as Director of the National Human Genome Research Institute (NHGRI) at the National Institutes of Health from 1993-2008. With Dr. Collins at the helm, the Human Genome Project consistently met projected milestones ahead of schedule and under budget. This remarkable international project culminated in April 2003 with the completion of a finished sequence of the human DNA instruction book. In addition to his achievements as the NHGRI Director, Dr. Collins’ own research laboratory has discovered a number of important genes, including those responsible for cystic fibrosis, neurofibromatosis, Huntington's disease, a familial endocrine cancer syndrome, and most recently, genes for adult onset (type 2) diabetes and the gene that causes Hutchinson-Gilford progeria syndrome. Dr. Collins has a longstanding interest in the interface between science and faith, and has written about this in The Language of God: A Scientist Presents Evidence for Belief (Free Press, 2006), which spent many weeks on the New York Times bestseller list. He has just completed a new book on personalized medicine, The Language of Life: DNA and the Revolution in Personalized Medicine (HarperCollins, to be published in early 2010). Collins received a B.S. in Chemistry from the University of Virginia, a Ph.D. in Physical Chemistry from Yale University, and an M.D. with Honors from the University of North Carolina. Prior to coming to NIH in 1993, he spent nine years on the faculty of the University of Michigan, where he was an investigator of the Howard Hughes Medical Institute. He has been elected to the Institute of Medicine and the National Academy of Sciences, and was awarded the Presidential Medal of Freedom in November 2007.

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It's Just a Cracker

 
From the Telegraph-Journal in New Brunswick [It's a scandal!].

A senior New Brunswick Roman Catholic priest is demanding the Prime Minister's Office explain what happened to the sacramental communion wafer Stephen Harper was given at Roméo LeBlanc's funeral mass.

During communion at the solemn and dignified service held last Friday in Memramcook for the former governor general, the prime minister slipped the thin wafer that Catholics call "the host" into his jacket pocket.

In Catholic understanding, the host - once consecrated by a priest for the Eucharist - becomes the body and blood of Jesus Christ. It is crucial that the small wafer be consumed when it is received.

Monsignor Brian Henneberry, vicar general and chancellor in the Diocese of Saint John, wants to know whether the prime minister consumed the host and, if not, what happened to it.

If Harper accepted the host but did not consume it, "it's worse than a faux pas, it's a scandal from the Catholic point of view," he said.

I am not a fan of Steven Harper but I don't see anything wrong with what he did. I probably would have done the same thing under the circumstances. Friendly Atheist agrees and PZ Myers offers to help Harper dispose of his wafer.

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