A few months ago I began a series of postings on the top science questions as posed by SCIENCE magazine back in 2005. The idea was to discuss the questions and also to examine how they were chosen. Are the editors of Science able to recognize the important questions in the biological sciences? So far, the results are not encouraging.
This survey was also a survey of science journalism since each of the article has been written by a different science writer. Read the postings below to get a sense of the results. There seems to be a lot of room for improvement.
"in recognition of his work on catalysis and for his investigations into the fundamental principles governing chemical equilibria and rates of reaction"
Wilhelm Ostwald (1853-1932) won the Nobel Prize in Chemistry for his work on reaction rates and catalysis. His Nobel Lecture On Catalysis is one of the most fascinating and most bizarre Nobel Lectures that I have read. It's worth a look. My impression on Ostwald is that he had lost his edge and was very much aware of it. (There are references in the speech.) Does anyone know the story behind that lecture and the mysterious references?
The presentation speech provides insight into the ways scientists though about biology in those days. The idea that enzymes were catalysts was just coming into favor and it was hoped that their reactions could be followed in the same way chemical reactions were measured.
Your Majesty, Your Royal Highnesses, Ladies and Gentlemen.
The Royal Academy of Sciences has resolved to award the former professor at Leipzig University and Geheimrat, Wilhelm Ostwald, the Nobel Prize for Chemistry 1909 in recognition of his work on catalysis and associated fundamental studies on chemical equilibria and rates of reaction.
As early as the first half of last century it had in certain cases been observed that chemical reactions could be induced by substances which did not appear to participate in the reaction themselves and which at all events were not altered in any way. This led Berzelius in his famous annual reports on the progress of chemistry for 1835 to make one of his not infrequent brilliant conclusions whereby scattered observations were collated in accordance with a common criterion and new concepts were introduced in science. He termed the phenomenon catalysis. However, the catalysis concept soon came up against opposition from another eminent quarter as allegedly unfruitful and gradually fell utterly into discredit.
Some 50 years later Wilhelm Ostwald carried out a number of studies to determine the relative strength of acids and bases. He sought to solve this extraordinarily important matter for chemistry in a variety of ways which all yielded consistent results. Amongst other things he found that the rate at which different processes take place under the action of acids and bases can be used to determine the relative strengths of the latter. He performed extensive measurements along these lines, and in so doing laid the foundations for the entire procedure for studying rates of reaction, all the more essential typical cases of which he examined. From that time onwards the theory of the rate of reaction has become increasingly important for theoretical chemistry; these tests, however, were also able to throw new light on the nature of catalytic processes.
After Arrhenius had formulated his well-known theory that acids and bases in aqueous solution are separated into ions and that their strength depends on their electrical conductivity, or more accurately, on their degree of dissociation, Ostwald tested the correctness of this view by measuring the conductivity and hence the concentration of the hydrogen and hydroxyl ions with the acids and bases which he had used in his previous experiments. He found Arrhenius' theory corroborated in all of the many cases which he himself investigated. His explanation why he consistently found the same values for the relative strength of the acids and bases whichever method he used was that in all these cases the hydrogen ions of the acids and the hydroxyl ions of the bases acted catalytically and that the relative strength of the acids and bases was determined solely by their ion concentration.
Ostwald was hence led to undertake a more thorough study of catalytic phenomena and he extended its scope to other catalysts, as they were called, as well. After consistent, continuous research he successfully formulated a principle to describe the nature of catalysis which is satisfactory for the present state of knowledge, namely that catalytic action consists in the modification, by the acting substance, the catalyst, of the rate at which a chemical reaction occurs, without that substance itself being part of the end-products formed. The modification can be an increase, but also a decrease of the reaction rate. A reaction which otherwise proceeds at a slow rate, taking perhaps years before equilibrium is attained, can be accelerated by catalysts to such an extent that it is complete in a comparatively short time, in certain cases within one or a few minutes, or even in fractions of a minute, and conversely.
The rate of a reaction is a measurable parameter and hence all parameters affecting it are measurable as well. Catalysis, which formerly appeared to be a hidden secret, has thus become what is known as a kinetic problem and accessible to exact scientific study.
Ostwald's discovery has been profusely exploited. Besides Ostwald himself a large number of eminent workers have recently taken up his field of study and the work is advancing with increasing enthusiasm. The results have been truly admirable.
The significance of this new idea is best revealed by the immensely important role - first pointed out by Ostwald - of catalytic processes in all sectors of chemistry. Catalytic processes are a commonplace occurrence, especially in organic synthesis. Key sections of industry such as e.g. sulphuric acid manufacture, the basis of practically the whole chemical industry, and the manufacture of indigo which has flourished so during the last ten years, are based on the action of catalysts. A factor of perhaps even greater weight, however, is the growing realization that the enzymes, so-called, which are extremely important for the chemical processes within living organisms, act as catalysts and hence the theory of plant and animal metabolism falls essentially in the field of catalyst chemistry. As an illustration, the chemical processes involved in digestion are catalytic and can be simulated step by step using purely inorganic catalysts. Furthermore the ability of various organs to transform nutrients from the blood in such a way that they are suitable for the specific tasks of each organ can indubitably be explained by the occurrence of various kinds of enzymes within the organ capable of catalytic actions adapted to their particular purpose. That apart, it is strange that such substances as hydrocyanic acid, mercuric chloride, hydrogen sulphide and others which act as extremely potent poisons on the organism have also been observed to neutralize or "poison"even pure inorganic catalysts such as e.g. finely dispersed platinum. Even from these brief references it should be clear that a new approach to the difficult problems of physiological processes has been possible with the aid of Ostwald's theory of catalysis. Because they are related to the actions of enzymes in the living organism, the new field of research is of an importance for mankind that cannot as yet be fully gauged.
Although the Nobel Prize for Chemistry is now being awarded to Professor Ostwald in recognition of his work on catalysis, he is a man to whom the chemical world is indebted also in other ways. By the spoken and the written word he, perhaps more than any other, has carried modern theories to a rapid victory and for several decennia he played a leading part in the field of general chemistry. In other ways too he has furthered chemistry by his versatile activity with numerous discoveries and refinements in both the experimental and the theoretical spheres.
[Photo Credit: The photograph of Ostwald's lab is from Ostwald]
Monday's Molecule #46 was the chemical reaction shown above. This is an historically important reaction that contributed to our understanding of catalysis.
The reaction shows the hydrolysis of sucrose to glucose and fructose in an acid solution. The reason why this was such an important reaction 100 years ago is because it is accompanied by a change in the direction of rotation of polarized light. Sucrose is an optically active compound, which means that it causes polarized light to rotate when you shine it through a solution of sucrose. The rotation is measured in a polarimeter. In the case of sucrose, light is rotated to the right. We call this dextrorotatory or "d" (lower case) from the latin prefix for "turning to the right". In modern chemical terminology it would be (+)-sucrose.
In the presence of acid, sucrose breaks down into D-glucose D-fructose. Both of the sugars are optically active. The "D" forms (Upper case "D" or small caps) are identified by the orientation of the CH2OH group (red oval) in the ring structures shown above. In both cases the group is above the plane of the sugar so these are the "D" forms of the molecule. In L-glucose and L-fructose those groups would be below the plane of the sugar ring and all the -OH groups would be flipped as well.
Now here's the tricky part. The original determination of the "D" and "L" structures was related to the optical rotation properties. It was thought that all carbohydrates with the "D" configuration were dextrorotary ("d") and that's why they were named "D". The "L" forms were thought to be laevorotary (Latin: "turning to the left). However, it turns out that this assumption isn't correct and D-glucose and D-fructose are good examples. They both have the "D" configuration but D-glucose rotates the plane of polarized light slightly to the right and D-fructose rotates it strongly to the left. The way to identify this property in modern terms is D(+)-glucose and D(-)-fructose. There's a good description of these properties on the Biochemical Howlers website.
That's all very interesting but why was it important back in 1900? It was important because if you treated a solution of sucrose with acid it "inverted" polarized light from rotating to the right to rotating to the left because D-fructose affected rotation more strongly than D-glucose. This meant that you could follow the reaction in real time by carrying it out in a test tube placed in a polarimeter. This was one of the few reactions of this sort that were amenable to kinetic studies back then.
Many workers discovered that the rate of the reaction was increased by increasing acid concentrations and it led to detailed studies of reaction kinetics with large molecules. (There were plenty of inorganic reactions that could be followed by watching changes in color.) An modern example is shown in the accompanying figure from Shalaev et al. (2000).
As you can see, the kinetics of the reaction are easy to follow and the results lead to simple mathematical interpretations of the rate and extent of the reaction. It was experiments like this that led to a theory of catalysis in the early 1900's and the awarding of a Nobel Prize to Wilhelm Ostwald in 1909.
Shalaev, E.Y., Lu, Q., Shalaeva, M. and Zografi, G. (2000) Acid-catalyzed inversion of sucrose in the amorphous state at very low levels of residual water. Pharm. Res. 17:366-70.
I'm very proud of the Ontario Citizen's Assembly on Electoral Reform. That's the group who examined many electoral systems and selected the mixed member proportional (MMP) system for Ontario. We will vote on it in a referendum tomorrow. It won't win this time around.
I think the Citizen's Assembly should be a model for many decision making processes in a democracy. In fact, I think it could be a model for grappling with complex problems in other situations as well.
Today I went to hear the President of the University brief us on long term strategic planning for the University of Toronto. I pointed out that the process was doomed from the beginning because the five major task forces were filled with appointed members of the Board of Governors and senior administrators (and former administrators). No ordinary faculty members, no students, no ordinary staff members. Nobody is going to listen to a group like that telling us what a university should be like in 20 years.
The response was that we need experienced people on these committees and that means people who have served in administrative positions in the university. I disagree. Watch this video to see another way of doing things.
What in the world are they afraid of? Last week the editors of the Toronto Star came out against the mixed member proportional (MMP) system that voters will decide on in tomorrow's referendum [Electoral reform a backward step].
The editors were widely criticized for misinformation and fearmongering in that Sept. 30th editorial (e.g. The Toronto Star Endorses First-Pass-the-Post and links therein). They attacked the MMP system for giving more power to party bosses when the experience in other countries indicates that this is not a valid concern in the MMP system. Furthermore, all party leaders in Ontario are committed to a fair an open system for selecting list members. It turns out that the list will almost certainly contain only candidates who have been nominated in individual ridings.1. Indeed, the parties have little choice but to commit to a fair and democratic process if they hope to attract voters. Read the statements of the party leaders on the Vote for MMP website [Party Leaders Quote].
Today, the editorial in the Toronto Star attacks MMP once again [Electoral reform fraught with risk]. The editors seemed to have heard part of the criticism because in this latest attack they avoid any mention of party lists. However, they return to another of the fears they raised earlier; namely, the fear of unstable government.
While some see this as a "fairer" system that produces a Legislature more closely aligned with the popular vote, it has one major drawback.
Countries that have gone this route, including Israel, Italy, Germany, and Belgium, have become notorious for chaotic, horse-trading minority governments and legislative gridlock.
Now let's think about this logically for a minute. The editors would have us believe that the Ontario Citizen's Assembly of 103 Ontario voters simply overlooked this major "problem" when they did all their research. The editors would have us believe that all 80 countries that use a proportional system have chaotic governments. Does that make sense? Of course not.
Germany, Belguim, Italy and Israel are hardly examples of failed governments in spite of what the fearmongers would have you believe. The MMP campaign refuted most of the points raised by the first Toronto Star editorial including the claim that Germany, Italy, Israel, and Belgium are in chaos because of MMP. (Belgium and Israel don't even use the MMP system.)
So why do the Toronto Star editors repeat the same false claims that were refuted 10 days ago? Why do they say the following even though they've been told that it misrepresents the experience in other countries?
Granted, some minority or coalition governments do manage to deliver solid, progressive government. But they are rarities. More commonly, governments in proportional systems are divisive, unstable, short-lived and paralyzed by conflict. Too often, the leading party is forced to align with small, sometimes radical, special-interest parties. That can badly skew the policy-making process.
Is that the kind of government that Ontario voters really want? Will it be good for Ontario? We don't think so.
Wouldn't you expect the editors to do their homework and look at the stability of comparable governments with proportional systems? Countries such as Finland, Denmark, Sweden, Norway, Switzerland, Spain, South Africa, and Austria. Is is fair to say that all these countries have governments that are "divisive, unstable, short-lived and paralyzed by conflict"? Of course not. It's a stupid thing to say. (Incidentally, all those countries use a full proportional system that's even more likely to produce "chaos" than the MMP system according to the reasoning of the fearmongers.)
In light of their previous attempts at misinformation wouldn't you expect the editors to be embarrassed? After all the Toronto Star like all newspapers prides itself on accuracy. Right?
Wrong! It's almost as though the editors have been completely oblivious to the serious attempts by the Ontario Citizen's Alliance to educate them and correct their misinformation. They repeat the same flawed argument they made ten days ago.
When people spread misinformation and fear for the first time you can put it down to ignorance. When they do it a second time there's something more serious going on. Why do the Toronto Star editors fear MMP so much that they have to publish an editorial the day before the vote? This is really strange given that all the polls show that MMP will be soundly defeated tomorrow.
It's a difficult question. As far as I can tell, the main problem is the fear of minority viewpoints—or "fringe" parties as the editors prefer. The editors are comfortable with the present first-past-the-post (FPTP) system because they know that minorities in our society have no chance of being represented in the legislature under that system.
Take the Green Party for example. Under FPTP their chances of electing a member to parliament are close to zero. Under MMP they will get four seats (out 0f 129) if 3% of the population votes for them. (The Green Party is the only "small, sometimes radical, special-interest" party that has a decent chance of electing members.)
This could lead to chaos if you believe the editors because parties with less than a majority of seats would have to negotiate with the other parties in order to get legislation passed—just like the current federal government under Harper and the previous one under Martin. Is that the "chaos" that the Toronto Star fears?
I don't think the editors and their allies are afraid of minority governments so much as they're afraid of giving minority citizens a voice in parliament. In other words, what they really want is a system that blocks out the views of minority groups. That's exactly the flaw that MMP is designed to overcome. It would be more honest if the opponents of MMP would simply come right out and what they're really afraid of instead of making up stories about unstable governments in countries with proportional voting.
Perhaps we could reach a compromise? We could have a mixed member proportional system but then ban all those parties we don't like? The editors and other concerned citizens could draw up a list of minority groups who would be specifically excluded from parliament, like the environmentalist extremists. The sitting members of Parliament would then pass a law preventing these undesirable parties from running candidates in the next election. That way we could have the best of both worlds, a proportional system that excludes all those undesirable minorities who might cause chaos if we let them have a voice in Parliament. That's how democracy is supposed to work, isn't it?
Do you think the fearmongers would go for this? I doubt it, it makes their motive a little too obvious. It's so much better to hide behind the unfair FPTP system on the grounds that it produces "stable" government. Those of you who laughed at this video should watch it again now that the anti-MMP side has triumphed. It pretty much sums up the logic of their arguments.
1. The reason why the list will contain candidates who have been nominated in ridings—and who will run in those ridings—is because if a party wins an election they will not have any members chosen from the list. Thus, a party who hopes to win would be foolish to put candidates on the list who they want to be in parliament but who don't seek election in a constituency. Since no party will want to be seen to anticipate losing it will probably be standard practice to put people on the list who are running for election in a riding. Thus, the MMP system will end up being similar to FPTP and fears about party bosses choosing favorites are unfounded.
According to several sources, this add is being shown on television in the USA and it's sponsored by the US government. I hope this is an elaborate leg-pulling. Surely there are no rational adults who think that telling kids not to have sex is going to work? I'm even surprised that there might be adults who think it's a good idea. Haven't they heard? Sex is fun and healthy.
Shalini at Scientia Natura has tagged me with the evolution meme [ I've been tagged!]. The idea is to pick five postings that show the evolution of Sandwalk from the time it first started until now.
This is going to be hard since my blog is less than one year old. Starting in the very first week I published an article on the sea urchin genome [Sea Urchin Genome Sequenced and I've continued to post science articles all along. The biggest change occurred in January when I started combining Monday's Molecule with Wednesday's Nobel Laureates to develop themes for the week. Gradually these themes spread over into following weeks (e.g. Blood Clotting). They began to take over my life!
My postings about atheism and religion haven't changed very much over the past year so there doesn't seem to be any evolution there. Many people will be upset by that since they would very much like to have changed my opinion! My interest in the influence of atheism and the confrontation with the "appeasers" was there from the very first weeks. The thing that's changed is that I now avoid the word "appeasers" and "Neville Chamberlain" whenever possible [The Neville Chamberlain Atheists].
When I started Sandwalk I blogged about Canada and local politics but not very often [I'm Voting for Hurricane Hazel!]. I thought I should avoid being seen as too Canadian because it would scare off readers, especially Americans. Now I'm posting more on Canadian issues because there's a large Canadian audience out there and because non-Canadians don't seem to mind—some even find it interesting [MMP: Debunking the Myths, Chastising the Fearmongers].
The biggest change has been the number of people who comment on Sandwalk. In my opinion, some of the most interesting things on this blog are taking place in the debates and discussions that occur after an initial posting [Plants, not Fungi, Are Most Closely Related to Animals?]. This was one of the things I wanted to happen since I'm coming from a newsgroup background but it didn't happen for the first six months. I realize now that you need a critical mass of readers in order to get a discussion going.
Today's molecule is actually three molecules. You have to identify each one precisely by giving the complete IUPAC names.
There's an indirect direct connection between the reaction shown above and Wednesday's Nobel Laureate(s). See if you can guess the Nobel Laureate. This one is not easy.
The reward goes to the person who correctly identifies the molecules and the Nobel Laureate(s). Previous free lunch winners are ineligible for one month from the time they first collected the prize. There are two ineligible candidates for this Wednesday's reward. The prize is a free lunch at the Faculty Club.
Send your guess to Sandwalk (sandwalk(at)bioinfo.med.utoronto.ca) and I'll pick the first email message that correctly identifies the molecule and the Nobel Laureate(s). Correct responses will be posted tomorrow along with the time that the message was received on my server. This way I may select multiple winners if several people get it right.
Comments will be blocked for 24 hours. Comments are now open.
Note: The reaction shown above may not be entirely accurate. If you can identify a way to improve it you can double your prize to two free lunches anywhere within two blocks of the downtown campus!
The winners of the 2007 Nobel Prize in Physiology or Medicine were just announced this morning. This year's prize goes to Mario R. Capecchi, Martin J. Evans and Oliver Smithies for their work on "principles for introducing specific gene modifications in mice by the use of embryonic stem cells."
This is a bit of a surprise. These were not names that came up regularly in Nobel Prize Gossip. Many people, including me, thought that there would be a specific award for stem cells before anyone got the prize for exploiting stem cells. This doesn't mean that todays winners aren't worthy. I doubt that anyone will question the award to Oliver Smithies, for example. I don't know as much about Capecchi and Evans.
See Press release for a complete description of the work of Capecchi, Evans, and Smithies. Here's the summary ...
This year's Nobel Laureates have made a series of ground-breaking discoveries concerning embryonic stem cells and DNA recombination in mammals. Their discoveries led to the creation of an immensely powerful technology referred to as gene targeting in mice. It is now being applied to virtually all areas of biomedicine – from basic research to the development of new therapies.
Gene targeting is often used to inactivate single genes. Such gene "knockout" experiments have elucidated the roles of numerous genes in embryonic development, adult physiology, aging and disease. To date, more than ten thousand mouse genes (approximately half of the genes in the mammalian genome) have been knocked out. Ongoing international efforts will make "knockout mice" for all genes available within the near future.
With gene targeting it is now possible to produce almost any type of DNA modification in the mouse genome, allowing scientists to establish the roles of individual genes in health and disease. Gene targeting has already produced more than five hundred different mouse models of human disorders, including cardiovascular and neuro-degenerative diseases, diabetes and cancer.
Scientists first began to get a glimpse of the organization of mammalian genomes about 40 years ago when they looked at the overall complexity using hydridization technology. It soon became apparent that most of the genome was made up of short stretches of DNA that were repeated thousands of times. One major component of this repetitive DNA was about 6000 bp in length. These sequences were called Long Interspersed Elements or LINEs. The other component was much shorter, about 300 bp. These were called Short Interspersed Elements or SINEs.
We now know that LINEs are a form of retrotransposon. The major human LINE is called L1 and it has two open reading frames (ORF's) that are similar to the gag and pol genes of typical retrotransposons [Retrotransposons].
The LINE sequence (blue, above) is organized like a typical gene with a 5′ untranslated region (5′ UTR) and a 3′ untranslated region (3′ UTR). There are two open reading frames (ORF) encoding an RNA binding protein, a reverse transcriptase, and an endonuclease similar to the retrovirus integrase. Like most transposons, L1 is flanked by a short repeated section of genomic DNA.
The role of the RNA binding protein has not been fully worked out but the roles of the reverse transcriptase and endonuclease proteins are known. When the L1 sequences is transcribed, it can be copied into double-stranded DNA and this copy can be integrated into the genome at a site cleaved by the endonuclease.
The net effect of this mechanism is to spread a copy of L1 to another part of the genome. Thus, L1 is a typical selfish DNA transposon.
The human genome contains about 500,000 copies of L1 but the vast majority are fragments of various sizes. Most of the fragments are missing the 5′ end and they presumably arose when the copying mechanism failed to completely copy the L1 mRNA from the 3′ end. About 10,000 copies are full length (6000 bp) and of these 80-100 are known to be "active." Active L1s have intact ORFs and they are regularly transcribed.
About 17% of your genome is composed of L1 LINEs and fragments. It is one of the major sources of junk DNA in your genome.
The important point to remember is that the active L1 LINEs are constantly producing reverse transcriptase in human cells. This enzyme can copy any available RNA into double-stranded DNA. It is responsible for most of the pseudogenes that litter our genome contributing to the mass of functionless DNA known as junk.
On Friday evening there was a 20 minute segment about atheism on CBC's The National. The National is the main evening news program on CBC. The segment is broken up into three YouTube videos (below).
I think it's a pretty good introduction to atheism and I can't imagine that it would have made the evening news a few years ago. No matter what anyone says, the evidence that Dawkins, Harris, et al. have moved this debate into the public realm seems overwhelming. I just don't understand those who think that the "militant" atheists are hurting the cause.
Look for Justin Trottier of the Centre for Inquiry. He's at the beginning of the third video. If you live in Toronto you should come out to our meetings at the centre [Standing Room Only]. It's just a block south of the campus. If you're a student you should join the University of Toronto Secular Alliance. We have many exciting events planned for this year. Watch for "Café Inquiry" coming this winter.
Here's an example of bad science journalism from the latest edition of New Scientist [Tea might pose fluoride risk].
Tea might pose fluoride risk
Tea drinkers beware. Too much of the wrong kind can add significantly to the amount of fluoride you consume, with the tea in just four cups supplying up to one-third of the maximum safe daily amount.
You have to read further in the article to see that it refers to a study done in Sri Lanka where the drinking water contains high levels of fluoride.
In some parts of Sri Lanka drinking water contains up to five times the maximum fluoride recommended by the World Health Organization, and some 98 per cent of people are affected by fluorosis.
The study shows that local tea grown in Sri Lanka contains fluoride so when you make tea with the water containing excess fluoride you get an increased dose of fluoride. Even if you make the local tea with distilled water you still get excessive doses of fluoride with just four cups of this tea.
All this is explained in the article but the headline and the opening paragraph are very misleading. It's only certain kinds of tea that might cause a problem and it's not at all clear whether people in other countries can even buy this tea. It almost seems as though the person who wrote this article was deliberately trying to to scare people in order to attract readers. That's not acceptable science journalism.
A psychic who defrauded someone of $220,000 US ($218,000 CDN) was recently arrested in Calgary. I'm not going to give you the details. You'll have to hop on over to Mike's Weekly Skeptic Rant to find out.
Fortunately, Mike makes it a bit easy to guess the right answer when he proposes this multiple choice question.
So there's this "psychic" who reads palms, gives advice, sees the future; she is on the run from police. The cops are hot on her trail. Does she:
a) use her psychic powers to see where the cops are and how they'll approach?
b) influence the "universe" by putting her desires out there to be realized?
c) go downstairs and sit at the kitchen table with a delicious Hot Pocket and a pistol to await her bullet-ridden showdown with Johnny Lawdog? or
d) realize that her "powers" are non-existent and hide in the closet under some blankets?
Mike also has a useful suggestion for what to do with all the money, assuming it's recovered. Should it all be returned to the "victim"?
A few months ago I began a series of postings on the top science questions as posed by SCIENCE magazine back in 2005. The idea was to discuss the questions and also to examine how they were chosen. Are the editors of Science able to recognize the important questions in the biological sciences? So far, the results are not encouraging.
