This is green green ixia or Ixia viridiflora. Go to Botany Photo of the Day to find out where it grows.
Friday, May 23, 2008
Botany Photo of the Day
This is green green ixia or Ixia viridiflora. Go to Botany Photo of the Day to find out where it grows.
A Chip Bus in Ottawa
Chip buses in Ottawa and Quebec are almost as common as Tim Horton's. You haven't really tasted poutine until you've bought it at a chip bus.
OpenCourseWare
Eva Amsen has an article in this week's issue of The Bulletin—the newspaper published by the University of Toronto (not a student newspaper). You can read her description of how this article came to be published by checking out her Nature network blog [Teaching course and article on OpenCourseWare]. The article is online at The Bulletin. Scroll to the last page.The article is about OpenCourseWare in general, and the MIT experiment in particular. MIT, and a few other schools, have made a commitment to put course material on a website and make if freely available to anyone who wants to use it. All one has to do is follow the guidelines of the Creative Commons License. MIT retains the rights to the material even though students and other lecturers are free to use it. MIT strips out all material that is copyrighted by third parties; this includes textbook figures and photographs and images taken from other websites. According to the MIT OpenCourseWare Website, it costs between $10,000 and $15,000 to publish each course. The costs will be twice as high if videos of the lectures are posted online.
Eva's article mentions some of the benefits of OpenCourseWare. Not all of them are believable; for example, one third of freshman students claim to have chosen MIT because they were influenced by OpenCourseWare. This probably doesn't mean what one might think.
Eva is a graduate student in our department so she asks, "Why is the the University of Toronto, one of Canada's leading universities, not part of the OpenCourseWare Consortium?" I'd like to address that question, making particular reference to biochemistry courses.
Let's begin by looking at the OpenCourseWare site for the Department of Biology (MIT doesn't have a Biochemistry Department) [Biology].
The first thing you notice is that most of the material is quite old. Some of the courses are from 2004, only one is 2007, and none are 2008. Let's check out the Spring 2006 course in Introductory Biology to see what OpenCourseWare is really like. Two clicks take you to complete audio lectures. You can listen to the lectures or read a transcript of the lecture. There is no supplemental material to speak of and no figures to see. I don't find this very helpful.
Contrast the MIT website with a typical university website like ours at the University of Toronto. We have more than 2000 course websites but the vast majority are restricted to University of Toronto students [Course Catalog]. If you could access the introductory biology course you would find complete powerpoint lectures with all figures and plenty of additional course material. All of it is up to date.
In some department the course material is not password protected [Dept. of Biochemistry] but it is not advertised and outsiders are not encouraged to visit the site. Complete lecture notes with figures are made available to the students. In my opinion, these notes are much more valuable to students taking our courses than the MIT OpenCourseWare lecture notes because we can post the figures without having to be wary of copyright infringement (especially if access is restricted).
Thus, one of the biggest downsides of OpenCourseWare is that the notes have to be stripped of figures. Why should our department go to great effort and expense to create a parallel site for external viewing when we know full well that the stripped down notes are practically useless? There has to be a compensating gain, right?
Eva argues that the gain is significant.
While the implementation of OpenCourseWare asks for extra work from its faculty in preparing high-quality, legally distributable course materials, this works as an incentive to produce better teaching materials. As a result, making course materials available online can not only raise an institution's visibility but also its quality.I don't believe this for a minute. The quality of lecture material on the web is highly variable and the fact that it's freely available does not to seem to have much effect on quality. If the argument holds, we would expect the biochemistry lectures at MIT to be outstanding examples of high quality lectures.
Let's check it out. The introductory biology course from 2006 (the latest one on the web) has ten lectures on "foundations." Three of them are on biochemistry. The first one [Biochemistry 1] is all about cancer cells. The material is present at a high school level, at best. The second lecture (Biochemistry 2) is not available on the website. The third one [Biochemistry 3] is on enzymes. Here's how it begins ...
OK. So we’re going to continue with the discussion about biochemistry, and specifically focus on enzymes today. Professor Sive introduced those to you briefly in her last lecture. I’m actually covering for her today. This is one of her lectures but she has given me her material, so hopefully it will go fine. She wanted me to remind you a little bit about energetics, specifically that a negative Delta G in a reaction implies that the reaction can occur spontaneously, that is if the products have lower energy than the reactants. And so given enough time this will happen in that direction.It's pretty much downhill from then on.
I checked out a lot of lectures on the MIT biology OpenCourseWare site and I don't see much evidence that the faculty has taken the time to prepare high quality lectures. Furthermore, if I had to evaluate the quality of teaching at MIT based on the OpenCourseWare, I don't think it would enhance the reputation of the university.
One of the main arguments for OpenCoureWare has been altruistic. The idea is that a really good university should make its lectures available to the world so that lecturers at "lesser" universities can copy it and use it in their classrooms (an argument that is also condescending). In my experience, the lecturers at smaller schools often give much better lectures in biochemistry than those at the big research intensive universities. If I'm looking for a really good textbook reviewer, for example, I'm much more likely to find one at the University of Maine or the University of Nebraska than at Harvard or Berkeley.
If every school puts up their stripped down versions of lectures, you can be assured that there will be some real gems out there. On the other hand, you can be certain there will be lots of garbage as well. OpenCourseWare may end up being just another way of cluttering up the web with useless information, or worse. If every school participates in the consortium, for example, you would probably find 100 incorrect definitions of a gene, or the Central Dogma, and 100 false conception of free energy at the top of your Goggle search. What's the point of promoting that?
Do you want to learn about enzymes on the web? Here's where you go to get free and accurate information from people who know what teaching is all about [Enzymes] [Enzymes] [Enzymes] .
Detect Alien DNA
Friday's Urban Legend: TRUE!You can buy this device from TokyoFlash. Here's what it does ...
With the threat of Alien Invasion growing ever closer & the distinct possibility that "they" are already here, it's about time we had a device to detect the humans from the human-oids. The Biohazard wrist scanner probes the immediate vicinity for Alien DNA & displays the results so that you may assess the threat level.You will have to read the rest of the description on their website but the bottom line is that the alien detection device does exactly what it's advertised to do!
[Hat Tip: Eye on DNA]
Thursday, May 22, 2008
Lester B. Pearson
Lester Bowles ("Mike") Pearson (1897-1972) was Prime Minister of Canada from 1963 until 1968. He lead the Liberal Party to two minority victories in the elections of 1963 and 1965. Pearson won the Nobel Peace Prize in 1957 for his work on forming the United Nations peacekeeping forces following the Suez crisis.
Pearson is responsible for some of the most important legislation passed by Parliament in the 20th century. His government brought in universal health care, and the Canada pension plan. It also adopted the new Canadian flag. Most of these reforms were supported in the House by the New Democratic Party under Tommy Douglas.1
1. Tommy Douglas was recently voted the The Greatest Canadian. Lester Pearson is #6 and his Minister of Justice, Pierre Trudeau, is #3.
The Tree of Life
From RNA to Humans: A Symposium on Evolution is the title of a meeting held at Rockefeller University on May 1st and 2nd.1 The entire series of lectures is available online at Evolution.
There are several interesting talks but the one that you need to listen to, in my humble opinion, is the talk by Ford Doolittle on Barking up the Wrong Tree: The Dangers of Reification in Molecular Phylogenetics and Systematics. Ford Doolittle challenges the common belief in The Three Domain Hypothesis and Norm Pace's idea that the term "prokaryote" is no longer useful. (Norm Pace is Carl Woese's bulldog.)
Furthermore, Ford Doolittle challenges the very way we think about phylogeny and the tree of life. If you want to keep on top of the current controversies in the field of molecular evolution then this is an excellent way to begin. Ford allies himself with Stephen Jay Gould and against Richard Dawkins. You may not agree with him but it is extremely important that all evolution supporters become aware of the controversy.
1. An unfortunate choice of title. Why not "from RNA to E. coli" or, better yet, "from RNA to modern organisms"?
[Hat Tip: Panda's Thumb]
Wednesday, May 21, 2008
Breaking News: Denyse O'Leary Has a New Blog!
Denyse "Buy My Book" O'Leary has started a new blog. That makes four altogether. What's the new one all about? It's about a new book she's going to write on the multiverse [Today at Colliding Universes].
Oh well, look on the bright side. Now she'll be posting the same IDiot article four times so your chances of accidentally missing it are very slim.
Nobel Laureate: Luis Leloir
The Nobel Prize in Chemistry 1970.
"for his discovery of sugar nucleotides and their role in the biosynthesis of carbohydrates"
Luis F. Leloir (1906 - 1987) was awarded the 1970 Nobel Prize in Chemistry for his work on the metabolism of carbohydrates, specifically glycogen [Glycogen Synthesis]. He discovered a key intermediate in that pathway; namely UDP-glucose. His discovery led to the realization that sugar nucleotides play an important role in many different metabolic pathways. Luis Leloir was an Argentinian. For most of his career he was a faculty member of the University of Buenos Aires. Leloir began his scientific career working with Bernardo Houssay and in 1944 he worked briefly with Carl Cori in St. Louis (USA).
The presentation speech was written by Professor Karl Myrbäck, member of the Nobel Committee for Chemistry of the Royal Swedish Academy of Sciences and delivered by Professor Arne Tiselius.THEME: Nobel Laureates
Your Majesty, Your Royal Highnesses, Ladies and Gentlemen.
The 1970 Nobel Prize for chemistry has been awarded to Dr. Luis Leloir for work of fundamental importance for biochemistry. Dr. Leloir receives the prize for his discovery of the sugar nucleotides and their function in the biosynthesis of carbohydrates.
Carbohydrates, as everybody knows, form a comprehensive group of naturally occurring substances, which include innumerable sugars and sugar derivatives, as well as high-molecular carbohydrates (polysaccharides) like starch and cellulose in plants and glycogen in animals. A polysaccharide molecule is composed of a large number of sugar or sugar-like units.Carbohydrates are of great importance in biology. The unique reaction, which makes life possible on Earth, namely the assimilation of the green plants, produces sugar, from which originate, not only all carbohydrates but, indirectly, also all other components of living organisms.
The important role of carbohydrates, especially sugars and starch, in human food and, generally, in the metabolism of living organisms, is well known. The biological break-down of carbohydrates (often spoken of as "combustion") supplies the principal part of the energy that every organism needs for various vital processes. It is not surprising, therefore, that the carbohydrates and their metabolism have been the subject of comprehensive and in many respects successful biochemical and medical research for a long time. While working on these problems, Leloir made the discoveries for which he has now been awarded the Nobel Prize.
Before these discoveries were made, our knowledge of carbohydrate biochemistry was rather one-sided. The biological processes which break down carbohydrates, including the so-called combustion, have been well known for several decades. Over the years many Nobel Prizes have been awarded for chemistry and still more for physiology or medicine for discoveries about the reactions and catalysts involved. However, our knowledge about the innumerable corresponding synthetic reactions which occur in all organisms, was fragmentary. We had to resort to doubtful hypotheses; it was usually assumed that the syntheses were a direct reversal of the well-known breakdown reactions. The work of Leloir has indeed revolutionized our thinking about these problems.In 1949 Leloir published the discovery which became the foundation for a remarkable development. He found that in a certain reaction, which results in the transformation of one sugar to another sugar, the participation of a so far unidentified substance was essential. He isolated the substance and determined its chemical nature. It turned out to be a compound of an unknown type, containing a sugar moiety bound to a nucleotide. Compounds of this type are now called sugar nucleotides. Leloir established that the transformation reaction does not occur in the sugars as such, but in the corresponding sugar nucleotides. To put it simply, one may say, that the linking with the nucleotide occasions an activation of the sugar moiety which makes the reaction possible.
The remarkable aspect of the discovery was not the explanation of a single reaction, but Leloir's quick comprehension that he had found the key which would enable us to unravel an immense number of metabolic reactions. He ingeniously realized that a path had been opened to a field of research containing an accumulation of unsolved problems. In the twenty years that have elapsed since his initial discovery he has carried on his research in this field in an admirable manner.
Other scientists were quick to grasp the fundamental importance of Leloir's discovery; they realized that a vast field was now accessible to worth-while scientific investigation and started research along the path which he had opened. There can be no doubt that few discoveries have made such an impact on biochemical research as those of Leloir. All over the world, his discoveries initiated research work, the volume of which has grown over since. Leloir has been the forerunner and guide throughout; he made all the primary discoveries which determined the path and the objectives of the ensueing research work.
Leloir soon found that besides the sugar nucleotide first isolated, several others of the same type occur in Nature, and many have also been found by other research workers. Today more than one hundred sugar nucleotides which are essential participants in various reactions are known and well characterized. Some of them have an action similar to that of the first isolated, namely in the transformations of simple sugars to other simple sugars or sugar derivatives.
Still more important was Leloir's discovery that other sugar nucleotides have another action which occurs in the biological synthesis of compounds which are composed of or contain simple sugars or sugar derivatives. Leloir showed that all these syntheses are essentially transfer reactions. Sugar moieties from sugar nucleotides are transferred to accepting molecules which thereby increase in size. Probably the most sensational discovery made by Leloir was that the synthesis of the high-molecular polysaccharides also functions in this manner. The first example of the fundamental role of the sugar nucleotides in polysaccharide biosynthesis was found by Leloir in 1959 in the case of glycogen. It became clear that the polysaccharide biosynthesis is not a reversal of the biological breakdown, as had doubtfully been assumed earlier. On the contrary, Nature uses different and quite independent processes for synthesis and breakdown. Later on the same extremely important principle was also shown to be valid with other groups of substances, for instance with proteins and nucleic acids.
Through Leloir's work and the work of others, who were inspired by his discoveries, knowledge of great significance has been gained in wide and important sections of biochemistry, which were previously obscure. It can be readily appreciated that Leloir's work has also had far-reaching consequences in physiology and medicine.
Baldwin and Lafontaine
The statues of Robert Baldwin and Louis Hippolyte LaFontaine on Parliament Hill in Ottawa commemorate two of the most important reformers in Canada. They played a major role in establishing parliamentary government following the union of Upper Canada (Ontario) and Lower Canada (Quebec) in 1841.
The Historical Foundation of Canada has produced a number of short videos about Canada's history. There's one on Baldwin and LaFontaine. Watch it and read more about their historical alliance at Building Democracy: Baldwin and LaFontaine.
Tuesday, May 20, 2008
Toronto Rising
Last week's issue of Nature has an interesting article on biomedical research in Toronto [Toronto Rising].The area around my building contains one of the densest populations of researchers in the world. The problem is that hardly anyone knows about it. Toronto isn't on everyone's radar in spite of the fact that there's a lot of high quality work being done.
Most of this basic research is concentrated in Toronto's city centre. Within two kilometres of the intersection of University Avenue and College Street, on the University of Toronto campus, there are nine research hospitals, roughly 5,000 principal investigators, and research budgets totalling about Can$1 billion (US$990 million) a year. Since 2005, 93,000 square metres of research space have been added in this zone, with twice as much more planned.There are problems with having so many labs—too many seminars! There's also a lot of internal competition for the best young scientists. (5000 P.I.s is a bit of an exaggeration. I think it's more like 1000.)
The main research engine is the University of Toronto, along with its affiliated research hospitals, including the Hospital for Sick Children, St Michael's, Sunnybrook and Mt Sinai. Also downtown is the Centre for Addiction and Mental Health, which employs 100 research scientists and is building an 110,000-square-metre site at the cost of Can$380 million.
Where Toronto has had less success so far is in commercializing its academic research. Ontario has more biotechnology companies than any US state with the exception of Massachusetts and California. But judged against the amount spent on basic research in Toronto, the region generates only about half the commercialization opportunities it should, compared with successful biotech clusters such as Boston, says David Shindler, executive director of Biodiscovery Toronto, an organization that commercializes research.Since when did putting more emphasis on basic research become a bad thing?
"When you look at University Avenue and the billion dollars spent there annually, you're sort of saying, why aren't we the size of San Diego? Where are all the companies?" says Grant Tipler, chair of the Biotechnology Initiative, a non-profit organization committed to promoting the growth of biotechnology in Toronto and the surrounding region. He says there are a number of reasons Toronto has lagged — a research culture that values basic research more than entrepreneurship; lack of government funding for applied research; and a shortage of venture capital for early stage companies.
The Ottawa River
Two views of the Ottawa River from Parliament Hill. That's the City of Gatineau (Quebec) on the other side of the river. It used to be called Hull when I was growing up in Ottawa.
High School Science Fair Winners
The Intel International Science and Engineering Fair bills itself as "the World's Largest Pre-College Science Competition."
The Intel International Science and Engineering Fair (Intel ISEF), a program of Society for Science & the Public, is the world's largest pre-college science competition, bringing together more than 1,500 young scientists from over 51 countries, regions and territories in 2008.The title of the competition includes technology (engineering) but the descriptions are a bit confusing. It's not always clear that the "science" fair will also reward technology projects.
Every year, talented students share ideas, showcase cutting-edge science, and compete for more than USD 4 million in awards and scholarships.
Here are the 2008 winners.
Sana Raoof, left, 17, of Muttontown, N.Y., Yi-Han Su, 17, center, of Chinese Taipei and Natalie Saranga Omattage, right, 17, of Cleveland, Miss., pose after receiving top honors at the 2008 Intel International Science and Engineering Fair in Atlanta, Friday, May 16, 2008. The young women each received a $50,000 scholarship from the Intel Foundation as part of their award. The 2008 Intel International Science and Engineering Fair brought together more than 1500 students from 51 countries, regions and territories to compete for more than $4 million in awards and scholarships.Here's a description of the winning projects.
Omattage developed a more efficient and less expensive way to screen for food additive contaminants, including those responsible for the recent deaths of many pets. By developing biosensors based on quartz crystal microbalance (QCM), Omattage’s research provides a new way for ports and warehouses to more thoroughly screen for food additives and other contaminants that could be found in food imported into the United States.Congratulations to the winners. They should be proud ot their achievements.
Raoof’s research provided new insight into how a better understanding of mathematical knot theory could help resolve classic biochemical problems. Specifically, her work focused on the Alexander-Conway polynomial invariant for chord diagrams to help prove how to classify molecules on a structural basis.
Su focused her efforts on identifying a high-activity catalyst that could improve methanol reforming reactions in order to generate hydrogen more efficiently. In doing so, Su has developed a method that can be used to improve the homogeneity of metal mixing and increase the surface area of catalysts which can also be used for the synthesis of other multi-composition materials with high homogeneity.
Am I the only one who finds it a bit sad that there is so much emphasis on the applications of science and so little on discovering new things about the natural world? This is not meant to detract from the efforts of the competition winners since they were following the rules. But I'd like to change the rules. Why couldn't we have separate competitions for science and applications of science?
The event was held in Atlanta, Georgia. This is one of the states that removed the word "evolution" from the school curriculum. Kathy Cox is Georgia's superintendent of schools and she explained it like this ... [ Georgia Takes On 'Evolution' As 'Monkeys to Man' Idea].
Georgia's schools superintendent, Kathy Cox, held a news conference near the Capitol on Thursday, a day after The Atlanta Journal-Constitution published an article about the proposed changes.Kathy Cox was one of the speakers at the Intel Science and Engineering Fair awards ceremony. Her favorite science fair project was one were a student was trying to discover whether kudzu would be a good source of biofuel.
A handful of states already omit the word ''evolution'' from their teaching guidelines, and Ms. Cox called it ''a buzz word that causes a lot of negative reaction.'' She added that people often associate it with ''that monkeys-to-man sort of thing.''
Still, Ms. Cox, who was elected to the post in 2002, said the concept would be taught, as well as ''emerging models of change'' that challenge Darwin's theories. ''Galileo was not considered reputable when he came out with his theory,'' she said.
...
In the past, Ms. Cox, has not masked her feelings on the matter of creationism versus evolution. During her run for office, Ms. Cox congratulated parents who wanted Christian notions of Earth and human creation to be taught in schools.
''I'd leave the state out of it and would make sure teachers were well prepared to deal with competing theories,'' she said at a public debate.
What Is Science For?
What Is Science For? is the title of a debate between Sir John Sulston and John Harris. Those of us who are scientists will recognize John Sulston as the Nobel Laureate who won the prize in 2002 with Sidney Brenner and John Horvitz. John Harris is a professor of ethics. The debate is sponsored by The James Martin 21st Century School at Oxford University.
The debate is introduced by Richard Dawkins who expresses his own opinion of what science is. (Be sure to listen to the questions & answers with Dawkins.)
John Sulston argues the case for curiosity motivated research and for science as a quest for knowledge. John Harris argues the case that science must do good and it must benefit humanity. The second half of the "debate" degenerates, in my opinion, into a discussion about the value of biotechnology. That is not the topic that should have been debated. Science is not technology. Sulston tries to make this point about science not being technology during the question period but Dawkins seems to dismiss it as "obvious." It's not at all obvious.
The issue was raised in the comments to Should Universities Help Students Become Good Citizens?. This is good, since it is exactly the problem that I wanted to debate.
[Hat Tip: RichardDawkins.net]
Should Universities Help Students Become Good Citizens?
Academic Matters is an educational journal published by the the Ontarion Confederation of University Faculty Associations (OCUFA). Last Fall's issue was devoted to "The Engaged University" and one of the lead articles is by Professor Janice Stein of the University of Toronto. Stein is often seen on local television discussing foreign affairs since she holds an appointment at the Munk Centre for International Studies. I'm a fan of hers because she often seems to make a lot of sense when discussing the Middle East and international politics.
Her article is titled The University as Citizen. In it she says,
I argue that universities have two fundamental civic obligations, obligations that flow directly from what universities are. The first is to help their students to become good citizens. The second is a broader obligation to the public: to share knowledge, explore issues, and create safe space for debate and discussion of public issues.I don't have a problem with the second obligation, although I wouldn't have made it so specific. I would have left off the last three words on the grounds that a university should also be a place where science can be explored. Investigations of cosmology, for example, aren't necessarily "public issues."
I want to question Janet Stein's first obligation. Is it true that universities have a direct obligation to teach students how to become good citizens? And what exactly is a "good citizen?" Who decides?
Notice that I added the word "direct" here because I think that is Prof. Stein's intent. Later on in her article she gives examples of what a university should be doing.
Educating students to be better citizens is the easier of the two challenges, though by no means easy. In the last decade, universities across North America have broadened and deepened their commitment to the civic education of their own students and to students in the broader community. My own university, the University of Toronto, runs special programs for students in some of the most challenged neighbourhoods in the city. It works closely with high schools across the city to provide opportunities for students that have special interests, special needs, and special gifts.Now don't get me wrong. I don't object to students doing these things if they're so inclined. I also wouldn't object to students who would oppose some of these things on the grounds that they are not the most effective use of our resources. There's nothing wrong with social activism. It's a perfectly legitimate way for university students to behave. I just don't want it to become a goal of the university that every students should do this.
My university also asks its students to do more, to consider actively how they can become better citizens. It encourages students to volunteer and provide assistance to people in neighbourhoods without shelter. Students work with university leaders to provide environmentally-friendly and healthy food in its cafeterias across campus. Those in classes on democratic theory go out into neighbouring communities to work with neighbourhood associations. Students studying global politics look at successful examples of social innovation and then go to their local communities to see how the global translates into the local. Students in the Faculty of Law work in neighbourhood legal clinics and with Legal Aid. Students and faculty increasingly understand that education is not only a classroom activity, that what happens outside the classroom is important. Learning and active citizenship are increasingly intertwined.
And I certainly don't want my university to be taking a position on what kinds of activities are example of "good" citizenship and which ones might be bad. Do all members of the university community agree, for example, on the right kind of food that should be served in our cafeteria? Not in my experience. Some of the students who want to dictate what I can or can't eat in the cafeteria don't necessarily qualify as "good citizens" in my book.
The main problem is whether this form of activity should be valued higher than all other activities in the university. Should community involvement of students really be an important obligation of a university?
I believe that education is an important goal of a university. I like to think that what we're trying to do is to teach students how to think critically. If that makes them better citizens then I count that as a beneficial spin-off but not a primary goal. For all I know, teaching students to think for themselves might lead to severe disruptions in our current society and I'm not certain that would qualify as teaching students how to be "good citizens." Universities are often centers of social change as we saw during the civil rights movement and opposition to the war in Viet Nam.
Another reason for being suspicious of Prof. Stein's view is that she seems to be coming from a humanities/social science perspective. She's only thinking of students who are at university to study human culture in one way of another. It makes some sense that such students might direct their energies toward improving the human condition by direct engagement.
What about science students? We have more than 10,000 science students on campus. One could argue that their primary focus is on learning about the natural world. Should the university be directing resources toward training these students to become "good citizens" according to the criteria established by Janice Stein? Or, is the acquisition of knowledge for it's own sake going to lead in the long run to good citizens in a knowledge based economy?
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