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Thursday, July 09, 2009

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.




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?


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!


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


Wednesday, July 08, 2009

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.


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.


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.


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.


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?


Tuesday, July 07, 2009

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.



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.


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.


Monday, July 06, 2009

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.