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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Exposing Undergraduates to the Scientific Literature

 
In most biochemistry and molecular biology departments it has become almost an article of faith that part of a good undergraduate education involves exposing senior students to the latest papers in the scientific literature. These departments will mount several advanced undergraduate courses that focus on reading and discussing the latest papers in a field. The idea is to go beyond the textbooks and show students how science really works.

Nobody seems to ask the obvious question. How do experienced scientists go about reading the latest papers and how do they distinguish the wheat from the chaff? Given that much of the current literature is wrong or misleading, what is the value of getting undergraduates to read it without giving them the tools to read critically?

And where are the experts who can teach them how to interpret the literature? Has the average graduate student mastered the task? From my observations, I'd say probably not. Where do we get the idea that typical undergraduates can do it productively?

There's another problem. You need to have a solid foundation in basic concepts in order to appreciate and understand the latest technologies and the latest scientific advances. Often these foundations are sacrificed in order to expose undergraduates to the cutting edge research. This is because students can only take so many courses and in complex disciplines like biochemistry, cell, and molecular biology there are so many fundamental concepts that we barely have enough time to cover them all.

In an ideal world we would cover all the basic concepts and also give students an opportunity to do a research project where they gain experience in reading the latest results in a specific field under the guidance of an experienced mentor.

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Junk DNA and the Scientific Literature

 
A discussion about junk DNA has broken out in the comments to Monday's Molecule #128: Winners.

Charlie Wagner, an old talk.origins fan, wonders why junk DNA advocates are still around given that there have been several recent papers questioning the idea that most of our genome is junk.

Charlie asks ...

So why are Larry and many others still clinging to the myth of "junk DNA"? Do they not read the literature?

Of course we read the literature, Charlie, but unlike you we read all of the literature. You can't just pick out the papers that support your position and assume that the question has been settled.

The skill in reading the scientific literature is to put things into perspective and maintain a certain degree of skepticism. It's just not true that everything published in scientific journals is correct. An important part of science is challenging the consensus and many scientists try to make their reputation by coming up with interpretations that break new ground. The success of science depends on the few that are correct but let's not forget that most of them turn out to be wrong.

THEME

Genomes & Junk DNA
The trick is to recognize the new ideas that may be on to something and ignore those that aren't. This isn't easy but experienced scientists have a pretty good track record. Inexperienced scientists may not be able to distinguish between legitimate challenges to dogma and ones that are frivolous. The problem is even more severe for non-scientists and journalists. They are much more likely to be sucked in by the claims in the latest paper—especially if it's published in a high profile journal.

Lots of scientists don't like the idea of junk DNA because it doesn't fit into their view of how evolution works. They gleefully announce the demise of junk DNA whenever another little bit of noncoding DNA is discovered to have a function. They also attach undue significance to recent studies showing that a large part of mammalian genomes are transcribed at one time or another in spite of the fact that this phenomenon has been known for decades and is perfectly consistent with what we know about spurious transcription.

I've addressed many of the specific papers in previous postings. You can review my previous postings by clicking on the Theme Box URL. The bottom line is "don't trust everything you read in the recent scientific literature."

Another good rule of thumb is never trust any paper that doesn't give you a fair and accurate summary of the "dogma" they are opposing. When you challenge the concept of junk DNA, for example, it's not good enough to just present a piece of new evidence that may not fit the current "dogma." You also have to deal with all the evidence that was used to create the consensus view in the first place and show how it can be better explained by your new model. A good place to start is The Onion Test.

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The figure is from Mattick (2007), an excellent example of what I'm talking about. This is a paper attacking the current consensus on junk DNA but in doing so it uses a figure that reveals an astonishing lack of understanding of genomes. This makes everything else in paper suspect. The figure was chosen by Ryan Gregory to be the classic example of a Dog's Ass Plot.

Mattick, J.S. (2004) The hidden genetic program of complex organisms. Sci Am. 291:60-67.

04:05:06 07/08/09

 
Shortly after 4 AM this morning you could write the exact time and date as 04:05:06 07/08/09.

But only in America—and a few other countries [Date and time notation by country].

In Europe you'll have to wait until August 7th and if your country is unlucky enough to have adopted the international standard notation then you've missed the big day by two years.

In Canada we use all three notations and this leads to a great deal of confusion. The good news is that we get to celebrate the sequential date three times. Tonight there will be a huge celebration in downtown Toronto with parades and fireworks and speeches by famous people.

How many more sequential time/dates will we celebrate in Canada this millennium?

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Monday's Molecule #128: Winners

 
The molecule was progesterone and the official complete IUPAC name is 8S,9S,10R,13S,14S,17S)-17-acetyl-10,13-dimethyl-1,7,8,9,10,11,12,13,14,15,16,17-dodecahydro-2H-cyclopenta[a]phenanthren-3(6H)-one. Progesterone is a female sex hormone that controls the maintenance of the endometrial lining during pregnancy.

The Nobel Laureate who worked out the structure of progesterone was Johann Butenandt.

Dara Gilbert of the University of Waterloo was the first person to get the correct answers using the abbreviated IUPAC name. This week there's a special award to Anne Johnson of Ryerson University for supplying the complete IUPAC name as well as the most complete description of the function of progesterone and additional information on the Nobel Laureate.

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Name this molecule. Include the IUPAC name and a brief description of its function.

One Nobel Laureate got the prize for contributions to organic chemistry, including working out the structure of this molecule.

The first person to identify the molecule and the Nobel Laureate, 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: 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, Bill Chaney of the University of Nebraska, Ian Clarke of New England Biolabs Canada in Pickering ON, Canada and Dima Klenchin of the University of Wisconsin at Madison.

Dima 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 open.

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Canadian Institutes of Health Research (CIHR) Strategic Plan

 
The Canadian Institutes of Health Research (CIHR) provides most of the funding for health-related research, including most of the basic research that goes on in Canadian Medical Schools. CIHR has recently issued a draft strategic plan that will guide its priorities in the future. The strategic plan is based on the Government of Canada's Science & Technology Strategy: Mobilizing Science and Technology to Canada's Advantage. This is a plan developed by the current Conservative government. It is based on the premise that research should be directed toward specific goals; namely, the health of Canadian citizens and the profitability of Canadian companies.

Clearly, the governing body of CIHR feels obligated to carry out the wishes of the current government in developing a long-range plan. On the surface it seems logical that a government agency should be doing what the government orders. However, there are two problems with this logic: (1) the strategy goes against the wishes of most Canadian scientists, and (2) governments change but strategic decisions are difficult to reverse.

This is the biggest problem. Government funding agencies should be advising the government, not vice versa. Government funding agencies should have an "arms length" relationship to the government of the day. Scientists should have more input.

My colleague, Tania Watts, is the current President of the Canadian Society for Immunology. She has written a letter to Alain Beaudet. the President of CIHR in which she defends basic research [see CSI Response to CIHR Stategic Plan]. Tania's letter makes a lot of sense.

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Monday's Molecule #128

 
Name this molecule. Include the IUPAC name and a brief description of its function.

One Nobel Laureate got the prize for contributions to organic chemistry, including working out the structure of this molecule.

The first person to identify the molecule and the Nobel Laureate, 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: 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, Bill Chaney of the University of Nebraska, Ian Clarke of New England Biolabs Canada in Pickering ON, Canada and Dima Klenchin of the University of Wisconsin at Madison.

Dima 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.

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Are Creationists Rational?

 
I don't think that creationism is a rational choice, especially Young Earth Creationism. John Wilkins isn't so sure [Are Creationists Rational?].

I highly recommend his article. It addresses the reasons why creationists think the way they do. I disagree with John's conclusion that you can't change the minds of most committed creationists and I disagree somewhat with John's definition of science. John seems to imply that science is what scientists do whereas I see science as a way of knowing that permeates all aspects of knowledge discovery. I would even argue that John is using the scientific way of knowing in his philosophy papers.

If you disagree, John, can you identify the other way of knowing that you are using?

I think that science as a way of knowing&mdashbased on evidence and rationality—should not only be taught in science classes. It should also be part of the core concepts in history, geography, English, civics, and social studies.

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IDiot Contest Question

 
Denyse O'Leary continues to look for ways to give away a few copies of the Expelled DVD. In order to win you have to write a 400 word essay on a particular topic and Denyse will pick the one that best conforms to her personal criteria.

This time Denyse is worried about Rob Day (aka Canadian Cynic) so she asks ... [Uncommon Descent: Contest Question 7: Foul anonymous Darwinist blogger exposed. Why so foul?]

Why do so many of Darwinists spout so much filth, hostility, and aimless detraction?

Realizing that she might get the wrong answers she adds another rule to the contest.

Note: Entries that merely claim it isn’t happening will not be judged. Too many people here know otherwise.

On a completely urelated topic, here are some interesting quotations from Conservapedia ...

Dr. Josef Mengele's evolutionary thinking was in accordance with social Darwinist theories that Adolph Hitler and a number of German academics found appealing.[15] Dr. Joseph Mengele studied under the leading proponents the "unworthy life" branch of evolutionary thought.[16] Dr. Mengele was one of the most notorious individuals associated with Nazi death camps and the Holocaust.[17] Mengele obtained a infamous reputation due to his experiments on twins while at Auschwitz-Birkenau.[18]

Prominent evolutionist and atheist Richard Dawkins stated the following regarding Adolf Hitler in an interview: “What’s to prevent us from saying Hitler wasn’t right? I mean, that is a genuinely difficult question."[19] The interviewer of Richard Dawkins wrote the following regarding the Richard Dawkins comment about Hitler: "I was stupefied. He had readily conceded that his own philosophical position did not offer a rational basis for moral judgments. His intellectual honesty was refreshing, if somewhat disturbing on this point."[20]

In addition to greatly influencing Hitler's Nazism, evolutionary ideas influenced the thinking of the Communists, including Marx, Engels, Vladimir Lenin, and Joseph Stalin.[21] Marx wrote, "Darwin's book is very important and serves me as a basis in natural science for the class struggle in history."

...

As noted earlier, evolutionary ideas contributed to the scourge of racism. [25][26] Charles Darwin and Thomas Huxley contributed greatly to the theory of evolution broadly being accepted in the 1900s. [27] Darwin, Huxley, and the 19th century evolutionists were racist in sentiment and believed the white race was superior.

And here's an interesting posting from Denyse O'Leary herself: If you accept the argument in Descent of Man, you accept a racist argument . Now don't get me wrong, I'm not saying that the creationists are being mean and hostile by accusing evolutionists of racism and genocide. No siree, not me. I'm sure they wouldn't do that.

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Quacks in the ER

 
Here's what the emergency room would look like if homeopathy and naturopathy became real medicine instead of alternative medicine.

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[Hat Tip: Pharyngula]

Nobel Laureate: Leopold Ruzicka

 

The Nobel Prize in Chemistry 1939.

"for his work on polymethylenes and higher terpenes"




Leopold Ruzicka (1887 - 1976) won the Nobel Prize in Chemistry for his contributions to organic chemistry—especially the structures of polymethylenes and higher terpenes.

One of the structures that Ruzicka solved was that of muscone, the molecule responsible for the smell of musk. The perfume industry required large supplies of this molecule which could only be prepared from the musk gland of musk deer. The preparation of synthetic muscone probably saved the musk deer from extinction.

Ruzika was born in Austria-Hungary but he spent most of his career in Switzerland. Do to political circumstances in 1939, the prize was awarded at a special ceremony in Switzerland in January 1940. Ruzika attended another ceremony in Sweden at the end of the war. He shared the 1939 Nobel Prize with Adolf Friedrich Johann Butenandt.


The special award presentation describes the work on sex hormones.
THEME:
Nobel Laureates

When studying the natural odorants occurring in musk and civet, muscone and civetone, little known until then, Ruzicka obtained fundamentally new and surprising results during the years 1924-1926. He discovered that the molecule of muscone as well as that of civetone contains one single ring of carbon atoms, the number of which was considerably larger than that in all hitherto known cyclic molecules, larger even than had been considered possible. During his investigations of these odora he synthesized many kindred macrocyclic compounds, and drew attention to the plant-physiologically remarkable fact that these could be prepared from natural fatty acids.

Many interesting relationships exist between the polyterpenes studied by Ruzicka and a series of physiologically and medicinally important groups of compounds, viz. the bile acids, the sterols and the sex hormones. Among the many interesting results obtained by Ruzicka and his collaborators with sex hormones, the preparation of compounds with the same action as male sex hormones is of signal importance. It is his merit that by establishing preparative methods for androsterone and testosterone the technical synthesis of these two hormones has been made possible.

Moreover, the numerous new related compounds prepared by Ruzicka have contributed fundamentally to our knowledge of the physiologically so very important sex hormones, thus creating a sound basis for future investigations.

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[Photo Credit (bottom): ETH-Bibliothek Zürich, Bildarchiv: Creative Commons License]

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.

Nobel Laureate: Hans Spemann

 

The Nobel Prize in Physiology or Medicine 1935

"for his discovery of the organizer effect in embryonic development"

Hans Spemann (1869 - 1941) won the Noble Prize in 1935 for his contributions to developmental biology. He worked mostly with the eggs of newts and frogs and through careful observation of the developing embryo he was able to work out the fate of many cells in the early embryo.

Spemann reasoned that some cells in the early embryo were able to direct the fate of other cells. By transplanting parts of one embryo to specific locations in another embryo he determined which cells acted as organizing centers, presumably by secreting regulatory molecules [see Monday's Molecule #126 and The Spemann–Mangold organizer experiment in 1924].

Here's an excerpt from the Presentation Speech.
THEME:
Nobel Laureates

Much thought has been given to the nature of the forces and causality regulating this development. It is at this point that Spemann's researches begin. He used eggs of various animal species which differ in colour, and with his simple instruments transplanted small pieces of tissue in different stages of development. By this means he was able to establish that, for example, a cell mass normally destined to become ventral epidermis - Spemann calls it presumptive ventral epidermis -could develop into nerve tissue if it were put in the place where the spinal cord was to develop. Hence, the course of development of these cells was not laid down in advance or it could - if such was the case - be altered by transplantation; so that the transplanted portion adjusted itself to its new environment. When Spemann then transplanted the anterior lip of the blastopore of an embryo into the ventral side of another embryo it grew a new brain and spinal cord. This brain and spinal cord did not arise from the transplanted cell material, but from the presumptive ventral epidermis whose course of development was thus altered by the presence of the blastopore. From this Spemann could ascertain that the blastopore had an organizing influence on its environment. The cell material which was grafted into the ventral epidermis and caused the development of the new spinal cord was actually of the kind that, developing normally, would have given rise to the notochord. Further experiments showed that it is the notochord primordia which organize the development of the primordial spinal cord, while, on the other hand, the mesoderm in the head causes the development of a primordial brain. Near this arise the so-called optic vesicles which are the origin of the retina of the eye. Where these approach the ectoderm of the head they organize the development of the lens of the eye. Or, to take another example: the anterior end of the primordial gut (the oesophagus) organizes the development of a primordial mouth and primordial teeth inside it. Thus, we now see how cell masses originally undifferentiated have the course of their development laid down by the influence of rudiments of organs formed earlier. Thereafter, a cell mass such as this can assume the role of organizer in relation to its environment.

In this way we begin to understand how the laws of development work. We begin to perceive why a primordial head arises at the anterior end of the embryo, why a brain always arises in the head and never anywhere else, or why the mouth always has its place below the primordial brain and never elsewhere.

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

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.

Canadian Cynic Is Coming to Town

 
Don't forget that Canadian Cynic is giving a talk tomorrow night at CFI Toronto [Creationism, ID and the Douchebaggery of Really Bad Arguments: An Evening with the Canadian Cynic].

This is your big chance to meet the man behind the blog.

We'll be getting together for food and beverages before his talk. Email me if you'd like to join us.

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Monday's Molecule #127: Winner

 
The molecule is muscone or [R]-3-methyl-cyclopenta-decanone. This is one of the main ingredients in the musk odor used in perfumes. The original chemical is the R-enantiomer shown below. It was extracted from the musk glands of musk deer (right). Modern perfumes are made from synthetic muscone, which is a mixture of the R- and S-enantionmers.

The Nobel Laureate is Leopold Ruzicka, who worked out the structure of muscone.

This week's winner is Dima Klenchin of the University of Wisconsin.

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Today's molecule stinks.¹ You have to identify it by giving me the common name and the IUPAC name.

There's only one Nobel Laureate whose name is linked to this molecule. The Laureate was responsible for determining its structure.

The first person to identify the molecule and the Nobel Laureate, 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: 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, Bill Chaney of the University of Nebraska and Ian Clarke of New England Biolabs Canada in Pickering ON, Canada.

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 open.

---

1. Opinions may vary.

Genes, Phylogeny, and Orangutans: A Correction

 
In a recent posting I described how New Scientist devoted several pages to the idea that orangutans could be our closest relatives [Genes, Phylogeny, and Orangutans. Here are my exact words,

It's a lesson that New Scientist should have learned. They devote several pages to the Grahan and Schwartz paper thereby giving it much more publicity than it deserves [Could the orang-utan be our closest relative?]. The article is written by Graham Lawton who you might remember from the "Tree of Life" episode [see: Explaining the New Scientist Cover]. The editors of New Scientist knew full well that their decision would be controversial so they took a proactive position by writing a short editorial [In praise of scientific heresy ]. [my emphasis - LAM]

I've received an email message from Graham Lawton, Deputy editor of New Scientist and the author of the article. He points out correctly that the article was exactly two pages long and the editorial was 400 words. He thinks that this is significantly less than "several pages" and asks me to correct my "mistake."

So, for those who think that two pages and a short editorial don't qualify as "several pages," I apologize for my "mistake." I only wanted to make it clear that the coverage was not just a few lines in their weekly survey of press releases.

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Does Teaching Science Lead to Atheism?

 
Does science lead to atheism? My short answer is "no" just like the answer given by John Wilkins and Matt Young. Their emphasis is on whether scientists are always atheists and whether those who are atheists became atheists because of science or whether they picked science as a profession because they were nonbelievers. Not all scientists are atheists, therefore science doesn't inevitably lead to atheism. That's their position.

Let's ask a different question. Would good science education in the public schools convert religious students to atheism? No, it is not true that exposing students to good science teaching will inevitably make them abandon their religion.

Is that all there is? No, the question can't be answered in such a simple manner. I think that a good science education will threaten most religious beliefs and in some cases will cause students to abandon those beliefs.

Let's imagine what a good science education would look like. The teachers would explain how science works. They would teach that scientific explanations require evidence and logic and that everyone should learn to be skeptical of all claims. Teachers would use examples like evolution, plate tectonics and cosmology to describe good science and how new ideas are incorporated into our understanding of the way things work. They would use astrology, homeopathy, and the deluge as examples of how some explanations do not conform to the expectations of science. The goal is to stimulate students to think and teach them how to do it in a scientific manner.

Imagine that there are religious students in the class. There seem to be three possible ways they could incorporate their knowledge about science into their religious worldview.

1. It will have no effect on their beliefs.
2. It will cause them to question and possibly abandon some of their beliefs.
3. It will reinforce and strengthen their beliefs.

I strongly suspect that more students will start questioning their beliefs when they are exposed to good science education but I admit I have no data to support that suspicion. Does anyone think that the net effect would be to strengthen beliefs or leave them unaffected?

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Genes, Phylogeny, and Orangutans

Jeffrey H. Schwartz is well known to talk.origins veterans because we discussed his book (Sudden Origins: Fossils, Genes, and the Emergence of Species) back in 1999. Schwartz tried to make the case for a "groundbreaking and radical new theory of evolution." This "theory" was based on the idea that new species spring into existence very quickly when a mutation in a homeobox (HOZ) gene arises in a population. It's a "theory" of saltation but it's based on such a flawed understanding of genetics that you really have to read to book to see just how bad it is. Sudden Origins is a leading candidate for the worst science book ever published.

In case you want to see a shorter version, the basic idea is explained in Schwartz (1999).

Over the years, Schwartz has published many other ideas that are controversial. Lately he has been pushing the concept that molecular phylogenies are unreliable. In part this is because he is opposed to gradual change as documented in the record of the genes. He thinks that real evolution takes place when alterations of regulatory genes result in major new phenotypes. Thus, the best way to discover the history of life is to examine anatomical homologies and differences.

But part of the problem lies in Jeffrey Schwartz's idiosyncratic understanding of genetics and molecular biology. When you put these together, this is what you get in Schwartz (2009).

This having been said, systematics and evolutionary biology need not remain estranged. Developmental biology increasingly makes clear that organismal change (and by extension, evolution), is not how it was imagined when the synthesis emerged (see reviews in Schwartz 1999, 2009b; Maresca and Schwartz 2006). Further, because of the interrelation between, e.g., the physical properties of cells, signaling pathways, epigenetic effects and development and consequently the origination of form, the false dichotomy of ‘‘molecules versus morphology’’ that resulted in the 1980s from the dethroning of morphology by the hegemony of molecular analyses is no longer tenable (Schwartz 2009a). Indeed, the undeniable hierarchical continuum from the molecular through the morphological, firmly centralizes morphology (as understood via development) in systematic endeavors (Schwartz 2009a).

Grahan and Schwartz (2009) have just published a paper in which they claim that orangutans are more closely related to humans that are chimpanzees. According to them, the molecular data is not reliable. They claim that detailed morphological comparisons show that orangutans are our closest ancestor.

John Hawks asks the question "Are orangutans our closest living relatives?" and he comes up with the best possible answer to scientists with a well-known history of promoting "unusual" positions on evolution.

It's a lesson that New Scientist should have learned. They devote several pages to the Grahan and Schwartz paper thereby giving it much more publicity than it deserves [Could the orang-utan be our closest relative?].¹ The article is written by Graham Lawton who you might remember from the "Tree of Life" episode [see: Explaining the New Scientist Cover]. The editors of New Scientist knew full well that their decision would be controversial so they took a proactive position by writing a short editorial [In praise of scientific heresy ].

If its claims are so outlandish, should the research even have been published? Some scientists would clearly have preferred it if the paper had never seen the light of day, and question the judgement of the journal.

That is territory we should tread with care. Ideas that mainstream opinion "knows" to be wrong occasionally turn out to be right. The insights of Galileo, Stan Prusiner - who discovered prions - and many others were once denounced as heresy. And even those that are wrong can be valuable.

Science proceeds by questioning its own assumptions and regarding every "fact" as provisional, so alternative hypotheses should be given an airing, if only to reaffirm the strength of the orthodoxy. Science that pulls up the drawbridge on new ideas risks becoming sterile. The journal recognised that and should be applauded for its decision to disseminate this challenging paper.

There's some truth here, but only some. You can't use Stanley Prusiner as an excuse to publish every crazy idea that comes along. Some ideas really are crazy—they are not revolutions in disguise. The plain fact is that Jeffrey H. Schwartz has already had his chance to make his case and he has not been successful. How many chances does he get before we draw the obvious conclusion?

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1. The article was two pages long and the editorial was much less than one page. This may not qualify as "several" pages by some definitions.

[Photo Credit: Daily Mail]

Grehan, J.R. and Schwartz, J.H. (2009) Evolution of the second orangutan: phylogeny and biogeography of hominid origins. Journal of Biogeography, published online June 22. 2009. [doi:10.1111/j.1365-2699.2009.02141.x]

Schwartz, J.H. (1999) Homeobox genes, fossils, and the origin of species. Anat Rec. 15:15-31. [PubMed]

Schwartz, J.H. (2009) Reflections on Systematics and Phylogenetic
Reconstruction. Acta Biotheor 57:295–305 [doi: 10.1007/s10441-009-9078-9]

What Can Scientists Do to Help Science Journalism?

 
This week's issue of Nature has a number of articles devoted to science journalism. Their publication coincides with the 6th World Conference of Science Journalists in London, UK.

One of the articles is an editorial, Cheerleader or watchdog?, about what scientists can do to help science journalism.

Scientists can do little to stem this bloodletting. But whatever they can do to engage with those caught up in it, and ensure that questioning and informed science journalism persists, will be worthwhile. If there is to be a transition to new — perhaps philanthropic — business models for in-depth reporting or new types of analytical media, science journalism will integrate into them all the better if scientists are taking an active interest in its health. And if the future of the media truly is a dire landscape of top-100 lists, shouting heads and minimal attention span, then such efforts might at least defer the grim end.

Even amid the turmoil, however, scientists can help ensure that reporting about science continues to be both informed and accurate.

I agree that scientists should work on trying to make science reporting more accurate. So far, we haven't been too successful.

But there's another important contribution we can make. We can help clean up our own act so that less bad science is published. This will not only make science better, it will have the spin-off effect of making life easier for science journalists. At the very least, we should make sure that press releases coming from our institutions are accurate. Every scientists should have to stand behind and endorse the press releases from their supporting institution. Let's take responsibility.

Also, wouldn't it be nice if most of the papers published in the scientific literature were careful to put their work in the proper perspective? Wouldn't it be nice if scientists themselves stopped exaggerating their contributions and stopped making outrageous claims? Science journalists have not done a good job of sifting the wheat from the chaff, in spite of what they think. They are far from blameless but scientists carry a bigger share of the blame for the sorry state of science literacy.

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Campus Excitement

 
There's usually something exciting happening on the University of Toronto campus during the summer.

It's a popular location for shooting movies and TV shows and you never know what you'll find on any given day. This is the scene that greeted me today when I emerged from the subway station. It took a few seconds to realize that I wasn't in the middle of a real emergency.

Last week the front campus was the scene of a bank truck robbery in Germany, just in front of a sidewalk café. I wish they'd left the outdoor tables and umbrellas and kept serving the wine and food.

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Monday's Molecule #127

 

Today's molecule stinks.¹ You have to identify it by giving me the common name and the IUPAC name.

There's only one Nobel Laureate whose name is linked to this molecule. The Laureate was responsible for determining its structure.

The first person to identify the molecule and the Nobel Laureate, 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: 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, Bill Chaney of the University of Nebraska and Ian Clarke of New England Biolabs Canada in Pickering ON, Canada.

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.

---

1. Opinions may vary.