More Recent Comments

Wednesday, July 08, 2009

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.


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.



Saturday, July 04, 2009

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.


Quacks in the ER

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




[Hat Tip: Pharyngula]

Friday, July 03, 2009

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.


[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.


[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.

Thursday, July 02, 2009

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.


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.




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.



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?