Saturday, May 31, 2008

Godless Canadians

 
According to a recent poll, 23% of Canadians do not believe in God [Quarter of Canadians don't believe in any god, poll says].

Here's a summary of the findings ...
The Harris-Decima poll also indicated:
  • Women (76 per cent) were more likely than men (67 per cent) to say they believed in a god.
  • Canadians over the age of 50 (82 per cent) were far more likely than those under the age of 25 (60 per cent) to say they believed in a god. More than one in three (36 per cent) of those under the age of 25 said they did not believe in any god.
  • English Canadians (73 per cent) were more likely than French Canadians (67 per cent) to say they believed in a god.
  • Belief in a god is higher in rural Canada (76 per cent) than in urban Canada (69 percent).

[Hat Tip: The Unexamined Life]

Best College Atheist Groups

 
The Guelph Skeptics at the University of Guelph won $300 from the Student Secular Alliance for Best Media Appearance.
They were in the campus newspaper once, then twice. They were in their local city paper, and most impressively, they are hosting their own radio show in Canada. They’re working on getting the show syndicated so they can play is across North America (it already airs in Guelph, in Victoria, BC and Winnipeg, MB).

Katie Kish of the group says: “With our own radio show we’ve had interviews with each of us on it, interviews with our speaker, coverage of our events. Hopefully it’ll all be podcasted soon.”
Cool.

One of the newspaper articles was about me! [How do you solve a problem like Moran?] It seems like a pretty fair representation of my talk at Guelph.


[Hat Tip: Friendly Atheist]

Friday, May 30, 2008

Are Science and Religion Compatible? AAAS Says Yes.

 
This is a short video produced by the American Association for the Advancement of Science (AAAS). This is the organization that publishes Science.

The video features Francis Collins and others who promote the idea that religion and science are compatible.

Here's the question; why is the AAAS taking a position on this issue? Why aren't they also producing a video to present the other side; namely that science and religion are not compatible? I'm especially interested in hearing from John Pieret because he is highly critical of scientists who venture opinions about religion. John, does your criticism extend to an organization of scientists like AAAS who are taking sides in a controversial non-scientific debate? You wouldn't be happy if they came down on the side of incompatibility, is this any better?

It seems to me that organizations like AAAS should remain neutral in the debate about whether science and religions are compatible. It's okay for them to point out that intelligent design isn't science and it's okay to criticize astrology and quack medicine, but I don't think it's okay to say that the beliefs of Francis Collins (and others) are compatible with science. I don't think it's okay to promote the evangelical Christian views of Collins and not the atheist views of Richard Dawkins.

Does this meant that it will be difficult to publish an incompatibility article in Science because it contradicts official AAAS policy?




[Hat Tip: Framing Science, because Nisbet thinks this is a good frame.]

How Many Biochemists Does It Take ....

 

... to fix a projector?

At one point during yesterday's talk the projector and Lewis Kay's powerpoint presentation failed to communicate with each other. That's Lewis behind the podium shortly after the problem was fixed. Helping him were, from left to right, David Isenman, Jacque Segall, Charlie Deber, and Peter Lewis.

They are all Mac users so they're used to this kind of tag team effort to solve computer problems. They do it quite often.

There were no glitches with the Windows operating systems.


Biochemistry's 100th Birthday: Day 2

 
Day 2 of the Department of Biochemistry 100th Anniversary Symposium began with a series of lectures by former graduates of the department; Shelagh Ferguson-Miller (Michigan State University), Natalie Goto (University of Ottawa), and Mark Glover (University of Alberta).

This was followed by a talk on the early history of the department by Professor Marian Packham. Marian was a student in the department from 1946-1949 and then she did her Ph.D. in the department. After a postdoc and a few years working for the government and the Red Cross, she joined the department as a faculty member in 1966 and rose to become a University Professor in 1989 (our highest title). Professor Packham gave an entertaining summary of the early years complete with humorous anecdotes that I won't repeat here.

Following Marian's talk we heard from two current members of the department: Lewis Kay and Lynn Howell.

The early afternoon was devoted to the poster session, featuring posters from students and postdocs. More than half the graduate students presented posters. One of my colleagues suggested that the high participation rate was due to the prize money being given out. Students have a 12.5% chance of winning at least $250. I'd like to think that they were motivated by a desire to communicate good science and just as many would have turned out if the prizes were just a handshake from our Chair.

I took a picture of Professor Packham at the poster session.

The speaker in the afternoon session (Theo Hoffman Lecture) was Greg Petsko from Brandies University in Boston (USA). Petsko is one of the gurus of structural biology. He has many connections to our department through his former students, postdocs and colleagues. He spoke on the structure of enzymes involved in Parkinson's disease.

Greg Petsko is as proud of his teaching as he is of his research accomplishments—and that's saying a lot. He is a very entertaining speaker. At the end of his talk everyone wanted to rush back to the lab to solve neurodegenerative diseases since many of us are going to get them. That was the main point.

The day ended with a gala banquet at Hart House that lasted until midnight. A very, very good time was had by all. There was plenty of opportunity to experience the products of anaerobic metabolism in yeast.

The person in the photo is John Challice, a former graduate student in our department and currently Vice President and Publisher Higher Education for the U.S. division of Oxford University Press.


Thursday, May 29, 2008

Telomeres

 
Telomeres are sequences at the ends of linear chromosomes that protect the essential part of the chromosome from damage following repeated rounds of DNA replication.

Because of the way DNA replication works, it is impossible to replicate both stands of parental DNA right to the very end. Consequently, after each round of DNA replication the chromosome loses a little bit of DNA and the ends get shorter and shorter.

The telomere consists of multiple copies of repetitive DNA. In the case of humans, the repeat is (TTAGGG)n where "n" is usually between 1500-2000 in germ line cells. Thus, the average telomere is about 10 kb (10,000 base pairs) in length (Riethman 2008).

THEME

Genomes & Junk DNA

Total Junk so far

    54%
After every cell division the telomere gets a little shorter so that in old individuals the average length is reduced to about 2-3 kb in most somatic cells. The original length is preserved in germ line cells.

There are 23 chromosomes in humans. If the average telomere length is about 10 kb then the total amount of TTAGGG repeats is 230 kb, or far less than 1% of the genome. Even if the total amount of essential sequence at chromosome ends is increased to include adjacent regions, it won't even come close to a significant percentage. Thus, while telomeric DNA is essential non-coding DNA—and not junk— it doesn't change our calculation.


[Image Credit: The image shows human chromosomes labelled with a telomere probe (yellow), from Christoher Counter at Duke University.]

Riethman, H. (2008) Human Telomere Structure and Biology. Annual Review of Genomics and Human Genetics 9: epub ahead of print [doi:10.1146/annurev.genom.8.021506.172017]

Biochemistry's 100th Birthday: Day 1

 
Yesterday was the first day of our department's 100th birthday party celebrations [Department of Biochemistry 100th Anniversary Symposium].

About 250 people showed up. It was fun to meet former students and retired faculty members, some of whom I hadn't seen for 10 or 20 years.

The first Connell Centennial Lecture was given by James Rothman of Columbia University (soon to be Yale University). His title was The biochemical basis of vesicle transport in the cell.

No matter how many times you hear him talk you can't fail to be impressed by Rothman's style and his ability to present complex material in a manner that can be understood by everyone in the audience. It was a wonderful way to begin our celebrations.


Tangled Bank #106

 
The latest issue of Tangled Bank is #106. It's hosted at ars technica [Welcome to the 106th Tangled Bank].
Greetings, and welcome to Nobel Intent, the corner of Ars Technica devoted to science. For those Tangled Bank readers who have never stumbled across Ars before, it's a large, tech-focused site that takes its science seriously. We have six science writers here, with backgrounds in planetary science, physics, chemistry, materials science, and biology, and we set them free daily on whatever bit of science catches their fancy. Check things out once you've feasted on the content of this edition of the Tangled Bank, a carnival of science blogging content.

If you want to submit an article to Tangled Bank send an email message to host@tangledbank.net. Be sure to include the words "Tangled Bank" in the subject line. Remember that this carnival only accepts one submission per week from each blogger. For some of you that's going to be a serious problem. You have to pick your best article on biology.

Science Fiction and Intelligent Design

 
Peter Kazmaier (photo, left) is a research scientist for some private company. He is also an Adjunct Professor of Chemistry at Queen’s University in Kingston, ON (Canada). Kazmaier is the author of a science fiction novel called The Halcyon Dislocation.

Peter Kazmaier has a blog. He recently posted some comments that were picked up by Denyse O'Leary. Here's what Kazmaier says on Who is ‘Galileo’ in 2008? Limitations of Science II.
Recently a film has been released Expelled! No Intelligence Allowed. In it Ben Stein and the producers argue that this very process of suppression is operating in the area of investigation into Intelligent Design. An excellent interview of Ben Stein and others can be found on the website for ListenUp tv.

I have listed the way in which 2008 science is even more susceptible to suppression than science in Galileo’s time. Are there any advantages on the side of those who believe they are being blocked? Yes there are. Through the democratization of knowledge, it is much easier to disseminate ideas today than in Galileo’s time. One can circumvent the journal refereeing process and publish the information directly through books, movies, or the internet.

So what are the personal messages for me to take away from this? First of all I need to understand and follow up the claims made by Expelled. Secondly, as I referee articles, I need to be aware of my own prejudices and biases and not allow them to influence my comments. Finally, at every turn I need to oppose suppression of free discussion of scientific ideas, whatever their source.
I really hope he will follow up on the claims made by Ben Stein in the movie Expelled. I look forward to seeing another post in the next few days where Kazmaier admits that he has been duped by the IDiots. That's what I expect from a Professor at Queen's.

It's true that we need to avoid suppression of good scientific ideas. That's always a given in science. On the other hand, the importance of free expression and skepticism is only manifest if we are able to freely speak out against bad science and bad ideas. There's no rule that says we have to praise every idea just because it claims to be science.

The mark of a good scientist is to be able to separate the potentially good ideas from those that are just plain silly. Offering tacit support to Ben Stein is not a good beginning.

In addition to being a scientist and a writer of science fiction, Peter Kazmaier is also a member of The Word Guild. Here's their mission statement.
Our goal is to impact the Canadian culture through the words of Canadian writers and editors with a Christian worldview. We will do this by connecting, developing and promoting Canadian writers and editors who are Christian.
Hmm ... I see why Kazmaier is so worried about bais when he says, "I need to be aware of my own prejudices and biases and not allow them to influence my comments."

Denyse O'Leary is on the Board of Directors of The Word Guild. Now I see why she promotes Kazmaier on her blog(s). I bet it has something to do with prejudices and biases.


Wednesday, May 28, 2008

Nobel Laureate: Wendell Stanley

 

The Nobel Prize in Chemistry 1946.

"for their preparation of enzymes and virus proteins in a pure form"


Wendell Meredith Stanley (1904 - 1971) was awarded the 1946 Nobel Prize in Chemistry for purifying and crystallizing tobacco mosaic virus (TMV). Stanley shared the Nobel Prize with James Sumner and John Northrop who purified and crystallized the enzymes urease and pepsin, respectively.

Stanley's work seemed to indicate that the infectious agent in TMV was a protein, in spite of the fact that TMV was known to contain RNA. You can see from the presentation speech below that back in 1946 the prevailing consensus favored protein as the genetic material. We now know that in 1946 there was a small group of scientists who were thinking that nucleic acid was the genetic material and not protein.

The presentation speech was delivered by Professor A. Tiselius, member of the Nobel Committee for Chemistry of the Royal Swedish Academy of Science.THEME: Nobel Laureates
Your Majesty, Royal Highnesses, Ladies and Gentlemen.

In 1897 Eduard Buchner, the German research worker, discovered that sugar can be made to ferment, not only with ordinary yeast, but also with the help of the expressed juices of yeast which contain none of the cells of the Saccharomyces. The discovery was considered so important that in 1907 Buchner was awarded the Nobel Prize for Chemistry.

Why was this apparently somewhat trivial experiment considered to be of such significance? The answer to this question is self-evident, if the development within the research work directed on the elucidation of the chemical nature of the vital processes is followed. Here, as in other fields of research, progress has taken place step by step, and the conquest of new fields has often been very laborious. But there, more than in most fields, a tendency has showed itself to consider the unexplained as inexplicable - which is actually not strange where problems of life and the vital processes are concerned. Thus ordinary yeast consists of living cells, and fermentation was considered by the majority of research workers - among them Pasteur - to be a manifestation of life, i.e. to be inextricably associated with the vital processes in these cells. Buchner's discovery showed that this was not the case. It may be said that thereby, at a blow, an important class of vital processes was removed from the cells into the chemists' laboratories, to be studied there by the chemists' methods. It proved, too, that, apart from fermentation, combustion and respiration, the splitting up of protein substances, fats and carbohydrates, and many other similar reactions which characterise the living cell, could be imitated in the test tube without any cooperation at all from the cells, and that on the whole the same laws held for these reactions as for ordinary chemical processes. But - and this is a very important reservation - this was only possible if extracts or expressed juices of such cells were added to the solution in the test tube. It was then natural to assume that these cell juices or cell extracts contained some substance which had the capacity of initiating and maintaining the reactions and guiding them into the paths they follow in the cell. These unknown active substances were called enzymes or ferments, and the investigation of their effects became one of the principal problems of chemistry during the first decades of this century, which for the rest it still is.

The important question of the nature of the enzymes remained unsolved, however, in spite of the energetic efforts of the research workers. It is manifestly a question of substances of complicated structures, which are present in such extremely small amounts that they, so to speak, slip through the fingers when one tries to grasp them. It is really remarkable to see how far it was possible to get in the study of the effects of the enzymes and the course of the enzymatic reactions, without knowing anything definite about the nature of these very active substances, nay, even without even being quite clear that they were substances which could be isolated in the pure form at all.

In 1926, however, in connection with his studies of a special enzyme "urease", James B. Sumner of Cornell University, Ithaca, U.S.A. succeeded in producing crystals which exhibited strikingly great activity. The basic material was the bean of a South American plant, Canavalia ensiformis, in America called the "jack bean", and the crystals had an activity that was about 700 times as great as that of bean flour. What was still more important was that it was possible to dissolve the substance and re-crystallize it several times without its activity being affected. The crystals proved to consist of a protein substance. Sumner expressed the opinion that in reality this protein substance was the pure enzyme.

As is so often the case with important discoveries, this result will probably to a certain degree have "been in the air", in that at the time it had been assumed in many quarters that the enzymes were protein substances of quite a special nature. On the other hand, Willstätter, the German chemist and Nobel Prize winner, had carried out far-reaching purifying experiments with enzymes and had arrived at results which caused him to doubt whether it was a question of protein substances or carbohydrates at all. We know now that this was due to the fact that Willstätter's purifying methods yielded solutions which were all too weak for it to be possible for chemical reactions to give a definite result.

For the chemist crystallization is the final goal in the preparation of a substance in pure form. Even though crystallizability is not such a reliable criterion of purity in the case of protein substances as in that of simpler substances, nevertheless Sumner's results have now been accepted as verified and thus also accepted as the pioneer work which first convinced research workers that the enzymes are substances which can be purified and isolated in tangible quantities. Thereby the foundation was laid for a more detailed penetration of the chemical nature of these substances, on which an understanding of the reactions taking place in living cells must finally depend.

Sumner's pioneer work was not immediately followed by similar work in other quarters, which might perhaps have been expected. About three years after Sumner's work had been published, however, Dr John Northrop of the Rockefeller Institute at Princeton began to work on the purification of the protein-splitting enzymes met with in the digestive apparatus and gradually succeeded in obtaining a number of them in crystallized form, e.g. the pepsin met with in the gastric juice and the trypsin and chymotrypsin in the pancreas. Northrop and his collaborators, among whom should be mentioned in the first place Kunitz, also made extremely comprehensive studies of the homogeneity and purity of these purified enzymes, and in that connection gave further proof of their nature as protein substances. Exceedingly interesting results were attained also in the isolation of some protein substances which appeared to be the mother substances of these enzymes. On the whole Northrop used his purified material for detailed chemical studies to a greater extent than did Sumner, and his contributions in the matter of working out the most satisfactory conditions for the crystallization of enzymes have been of the greatest importance for subsequent research workers.

This year's third Nobel Prize winner in Chemistry, Dr Wendell Stanley, first worked at the Rockefeller Institute in New York but moved in 1932 to the department of that Institute at Princeton. The problem which attracted his attention, namely the chemical nature of the viruses, was to a certain degree analogous to the problem of the enzyme just mentioned. As is well known, viruses are contagia which give rise to a large number of the best known illnesses in man, animals and plants, e.g. smallpox, infantile paralysis, influenza, foot-and-mouth disease, mosaic disease (on tobacco plants), etc. The virus particles are invisible in the microscope, and when Stanley began his work, they could only be identified by the symptoms of disease which they occasioned. Thus the problem was more difficult, inasmuch as the effect of the virus could not be as easily measured as that of an enzyme, where an exactly known chemical reaction can be employed. Stanley first tried to show the protein nature of viruses by studying how the virus of the tobacco mosaic disease was attacked by protein-splitting enzymes, but in 1934 he passed on to attempting to purify that virus by methods similar to those which Sumner and Northrop had employed so successfully for enzymes. In 1945, by using large quantities of infected tobacco leaves, he did succeed in producing small amounts of crystals which were extremely active, and which, after detailed investigation, proved to be the bearers of the virus's activity. Here, too, it was a matter of active protein substances. Subsequently it has been proved that nucleic acid also forms an important constituent of the latter.

It seems as though Stanley's discovery may take us another long step forward along the road towards a closer understanding of the chemical nature of the vital processes, for apart from the fact that in extremely small quantities they can give rise to diseases, the virus substances, like the bacteria, have the capacity to reproduce themselves. It was remarkable enough when Buchner found that certain of the functions of the living cell can be separated out from it and are to be found in the expressed juice, but it appears still more remarkable that the capacity to reproduce - this unique characteristic of life - can also be exhibited by certain molecules, thus by dead substances. It must be borne in mind, however, that, as far as we know now, this capacity is only possessed by the virus molecule when it is in contact with the living cell, and that probably the latter is materially responsible for the reproduction of the virus substance.

Investigations both by Stanley and by other research workers show that many kinds of viruses, e.g. the smallpox virus, are considerably more complicated in structure. It is conceivable that the "molecular virus" which Stanley isolated represents the simplest type in a long series of different kinds of viruses which gradually approach the living bacteria. An extraordinarily fascinating field is hereby opened up to research workers, and it is not improbable that development will lead to a closer scrutiny of the border-line between living and dead matter.

Even among scientists we sometimes hear the assumption expressed that the innermost secrets of the vital processes will always be hidden from us, that there is a wall through which we cannot penetrate. Today we do not know whether that be correct, but we know that this wall - if there is one - is considerably farther away than one had dared to believe earlier. That this is so is to an appreciable degree the result of the discoveries which have been rewarded with the 1946 Nobel Prize for Chemistry.

...

Doctor Wendell Stanley. We owe to you one of the most striking discoveries in modern chemistry and biology. The demonstration of the fact that a virus can be crystallized in the same way as many proteins and enzymes, and that it actually is a protein, at once opened up an almost unlimited field of research with fascinating possibilities. You have not only thrown open the portals to this domain, but you are yourself successfully exploring its possibilities, and rich fruits have already been harvested, thanks to your own work and that of your school.

Gentlemen. The fundamental problems which you have attacked and solved with such remarkable success are closely related, and the methods used have much in common. The more recent achievements have added to the significance of the earlier advances in this field. Your work and your discoveries deserve the gratitude of mankind. The award to you of the Nobel Prize in Chemistry for 1946 is an expression of this gratitude.

Doctor James Sumner, Doctor John Northrop, Doctor Wendell Stanley. With the warmest congratulations of the Academy I now ask you to receive your awards from the hands of His Majesty the King.


Browser Wars: What Browser Do You Use?

 
I started using Netscape about 15 years ago when it first evolved from Mosaic. I kept using the latest versions until just a few years ago when I switched to Firefox—the offspring of Netscape (they use similar Mozilla engines). I never liked Microsoft's Internet Explorer (IE) because it didn't work well on some of the scientific websites. Safari is okay but not as easy to use as Firefox, in my opinion. I'm not that familiar with Opera. (Most bloggers have to have several different browsers in order to make sure their blogs look good for all readers.)

Firefox is about to release a new version and this event is covered on the Scientific American website [The latest version of the Firefox Web browser: Fast and secure]. It's interesting that Scientific American would consider this a newsworthy event. I assume it's because so many scientists are using Firefox?

Anyway, that's not what I want to talk about today. Here's part of the SciAm article.
Where would we be without the ubiquitous Web browser? More than a decade ago, Netscape, AOL and its ilk helped transform the Internet from simply a network of networks to the backbone of modern society by giving users access to anything and everything that was searchable. In typical fashion, Microsoft soon took hold of the Web browser market with Internet Explorer, which chased its competitors down to single-digit market share and borderline irrelevance.

That's the way it was until 1998, when Netscape (battered by Microsoft in the browser wars) decided to share its Mozilla browser software with the public for free. To make a long story short, the public tweaked and improved the software over time until, in 2003, the Firefox Web browser was born. Today, there are about 180 million people using Firefox to navigate the Web, according to Mozilla Corp., formed three years ago to oversee a number of public software projects.

With the Firefox version 3.0 (the latest) only a few weeks away from launching, the Web browser poses a serious threat to Internet Explorer's dominance. As of April, about 40 percent of Web surfers were using Firefox compared with 55 percent relying on Internet Explorer to navigate the Web, according to W3Schools, a Web site that tracks browser usage. Not bad, considering Microsoft held nearly 69 percent of the market at the end of 2005, the first year Firefox started its rise to prominence. (Firefox, which runs on the Windows, Linux and Mac operating systems, was used by about 24 percent of Web surfers at that time.)
One of the advantages of Firefox is that there are many second party add-ons because of the open source nature of the browser engine. Some of these widgets are pretty useful.

I'm not too excited about the upcoming changes in the new version of Firefox but it looks like other people might be more impressed. The trend is clear. Firefox is on the verge of displacing IE from it's dominant position.

Here's the question. What browser do you use? You can answer in the poll found at the top of the left sidebar. Why do you like your browser?


What's the Difference Between Female DNA and Male DNA?

 
Answer: The "female" DNA sequence is incomplete because it lack DNA from the Y chromosome.

A recent press release from the Leiden University (Netherlands) proclaims Leiden scientists sequence first female DNA.

This is a well-deserved winner of Jonathan Eisen's second Genomics by Press Release Award [Genomics By Press Release Award #2: Lieden University and the First "Female" Genome]. Read the award persentation speech on his blog The Tree of Life.

Congratulations to Leiden University1 for showing us how science should not be done and how science journalism is taking over from peer review publication.2.


1. "Leiden University is the oldest university in the Netherlands. It was founded in February 1575, as a gift from William of Orange to the citizens of Leiden who had withstood a long siege by the Spaniards."

2. We look forward to more press releases when the data is actually published in the peer reviewed literature.

The Blue Watermelon Theory

 
A reader sent me the link to this video with the following comment ...
I came across this movie. It's amazing!!
Please make time to watch it. It'll blow your mind.
We can turn it into a contest.

Question 1: What is the IQ of Shawn? and where did he learn to talk so fast?

Question 2: How many times are the words "false," "falisfiy" and "falsification" used in the video?

Question 3: How come nobody ever told me that evolution has been falsified?


Question 4: Why do we call them IDiots?


Apologies to those who have seen this video before.

Tuesday, May 27, 2008

An Amazing Photograph

 
This is an amazing photograph. Phil Plait of Bad Astronomy explains why [Phoenix Descending].

Phil is an excitable guy but you've rarely seen him this excited in a video.

He has good reason ...


Tobacco Mosaic Virus

 

Monday's Molecule #73 is tobacco mosaic virus (TMV). As its name implies, TMV is a plant virus that infects tobacco and related species. It was one of the first viruses to be identified and one of the first to be purified.

A large number of studies have been done with TMV because it is so easy to purify and because of its simple structure. The virus is composed of 2130 copies of a small coat protein (158 amino acids) wrapped around a single-stranded RNA molecule of 6000 nucleotides.

Stanley won the Nobel Prize in 1946 for crystallizing TMV—a result that was widely interpreted as evidence that proteins were the genetic material (the RNA component wasn't recognized). Watson studied TMV crystals in order to learn about helices. Later on Rosalind Franklin worked on the structure of TMA with Stanley. Aaron Klug worked out the mechanism of assembly based on the demonstration by Fraenkel-Conrat and Williams (1955) that purified coat protein and purified RNA could be mixed and spontaneously reassembled to form active virus particles [See Citation Classic from Oct. 26, 2007].

Later, Fraenkel-Conrat mixed and matched coat protein and RNA from different viruses and used the hybrids to infect plant cells. He showed that the new viruses always had the properties of the RNA and not the coat protein, demonstrating that the genetic material was the RNA and not the protein.

Early workers on in vitro translation uses TMV RNA as a template since it was one of the few examples of pure mRNA.


[Image Credits: The figures are from Alberts et al. (2002) Figure 3-33.]

Alberts, B., Johnson, A., Lewis, J., Raff, M., Roberts, K. and Walter, P. (2002) The Molecular Biology of the Cell 4th ed., Garland Science, New York (USA)

Making Rudyard Kipling Proud

 
We wish to question a deeply engrained habit of thinking among students of evolution. We call it the adaptationist programme, or the Panglossian paradigm.
S.J. Gould & R.C. Lewontin (1979) p. 584
A typical just-so story has two components. First, it postulates the existence of an allele "for" some trait in the absence of evidence that the gene(s) actually exist (or even that such genes are possible). Second, it postulates that the allele "for" the trait was selected in the past so that now it has become fixed in the population. The attractiveness of most just-so stories lies in the creation of an elaborate, but plausible, adaptive advantage for the postulated allele.

The field of evolutionary psychology seems to have been largely taken over by those who can create the most elaborate just-so stories to "explain" modern society. For example, the avoidance of incest in most (but not all) societies is due to fixation of an anti-incest gene in our ancestors [Another Boring Just-so Story]. As with most just-so stories, there is no evidence for the existence of multiple alleles of a gene where one allele confers incest avoidance while the other allele confers acceptance of incestuous relationships. (The problem becomes even more difficult if it's a trait due to multiple alleles at different loci.)

There's a trendy extension of just-so storytelling that looks superficially like evidence. It's the creation of a computer program to simulate one's just-so story. Naturally, these programs always work as expected since that's the nature of a just-so story. You have a postulated beneficial allele with a postulated selective advantage and, presto!, the allele becomes fixed in your simulated population. It doesn't prove a thing. If your program doesn't work as expected, then all you have to do is fiddle with the selective advantage (s) until it does.

This year's fad in just-so stories is the religion gene. Here's one of the latest from NewScientist, which should know better [Religion is a product of evolution, software suggests]. The article reviews the speculations of James Dow, an Emeritus Professor of evolutionary anthropology at Oakland University in Michigan.
To simplify matters, Dow picked a defining trait of religion: the desire to proclaim religious information to others, such as a belief in the afterlife. He assumed that this trait was genetic.

The model assumes, in other words, that a small number of people have a genetic predisposition to communicate unverifiable information to others. They passed on that trait to their children, but they also interacted with people who didn't spread unreal information.

The model looks at the reproductive success of the two sorts of people – those who pass on real information, and those who pass on unreal information.

Under most scenarios, "believers in the unreal" went extinct. But when Dow included the assumption that non-believers would be attracted to religious people because of some clear, but arbitrary, signal, religion flourished.

"Somehow the communicators of unreal information are attracting others to communicate real information to them," Dow says, speculating that perhaps the non-believers are touched by the faith of the religious.
Make no mistake. This is bad science. It does not meet any of the criteria of good science.

From time to time we challenge the veracity of press releases so it's always wise to check the source to see if the views of the author have been misrepresented. In this case, the original paper is online at The Jounral of Artificial Societies and Social Simulation website [Is Religion an Evolutionary Adaptation?]. Here's the abstract. You can read the article and decide for yourself whether you think this is a worthwhile contribution to the literature on evolution.
Religious people talk about things that cannot be seen, stories that cannot be verified, and beings and forces beyond the ordinary. Perhaps their gods are truly at work, or perhaps in human nature there is an impulse to proclaim religious knowledge. If so, it would have to have arisen by natural selection. It is hard to imagine how natural selection could have produced such an impulse. There is a debate among evolutionary scientists about whether or not there is any adaptive advantage to religion at all (Bulbulia 2004a; Atran and Norenzayan 2004). Some believe that it has no adaptive value itself and that it is just a hodge podge of of behaviors that have evolved because they are adaptive in other non-religious contexts. The agent-based simulation described in this article shows that a central unifying feature of religion, a belief in an unverifiable world, could have evolved along side of verifiable knowledge. The simulation makes use of an agent-based communication model with two types of information: verifiable information (real information) about a real world and unverifiable information (unreal information) about about an imaginary world. It examines the conditions necessary for the communication of unreal information to have evolved along side the communication of real information. It offers support for the theory that religion is an adaptive complex and it disputes the theory that religion is a byproduct of unrelated adaptive processes.
How many of you think that this work supports the just-so story and refutes other possibilities?


Monday, May 26, 2008

Centromere DNA

 
During mitosis in eukaryotic cells the chromosomes are duplicated and the two sister chromosomes separate and move to opposite ends of the dividing cell. This segregation is controlled by spindle microtubules that attach to specific regions of the chromsomes called centromeres.

Centromeres are easily seen in the light microscope following chromosome condensation. They appear as a constricted region where the daughter chromosomes remain attached to each other. In non-dividing cells the centromere region is heterochromatic, which means that it remains relatively condensed compared to the rest of the chromatin that contains active genes (euchromatin).

Yeast centromeres are very simple but mammalian centromere DNA has not been extensively characterized because it consists largely of multiple repeats of simple sequence DNA. Because of the repetitive nature of centromeric DNA these region are difficult to clone. They are missing from the human genome database.

THEME

Genomes & Junk DNA

Total Junk so far

    54%
Nevertheless, we have a pretty good idea of the organization of centromere DNA from the few centromeres that have been sequenced. In humans the dominant repeat is α satellite DNA, a 171 bp sequence that is repeated about 18,000 times at an average centromere. Kinetochore proteins bind to the central region of the centrosome and the spindle microtubules attach to the kinetochore (Cheeseman and Desai, 2008).

Fluorescent hybridization studies with α satellite DNA light up all centromeres on human chromosome indicating an abundance of α satellite DNA at all centromeres. We don't know how much of this DNA is essential for chromosome segregation. There are rare examples of neocentromeres (newly formed centromeres) that have very little α satellite DNA suggesting that much of it is non-essential. Artificial human chromosomes segregate at mitosis with only a few copies of α satellite DNA at their centromeres.

Not all α satellite DNA is associated with functional centromeres since the presence of inactive, nonfunctional centromere sequences in the human genome is well known. (Such as one of the ancestral centromeres associated with the formation of human chromosome 2 from a fusion of two separate primate chromosomes. See Stanyon et al. (2008) for a review of the evolution of primate chromosomes with an emphasis on the formation of new centromeres and the loss of ancient ones.)

There are also at least 68,214 monomeric α satellite sequences in the human genome (Alkan et al. 2007).

Human centromeres range from 0.3Mb to 5Mb in size (Cleveland et al. 2003). If the average centromeric region is 3Mb (3,000 kb) in size then 23 centromeres represents 2% of the entire genome sequence. Not all of this DNA is essential because, among other reasons, there is considerable variation between individuals in the length of a given centromere. Nevertheless, lets assume for the sake of our junk DNA calculation that all of it is essential.

Monomeric α satellite sequences make up about 0.3% of the genome (Alkan et al. 2007). These bits of DNA are almost certainly non-essential "escapees" from centromeric regions or fossil centromeres. The total amount of α satellite DNA in the human genome is between 2% and 5%. The vast majority of these sequences are not in the databases. If we add in the fossil centromeres we can estimate that the total amount of junk α satellite DNA comes to about 1% of the genome.


[Image Credits: The drawing of a centromere is from Alberts et al. (2002) Figure 4-50. The photograph of chromosomes is from Hunt Willard (Schueler et al. (2001)]

Alberts, B., Johnson, A., Lewis, J., Raff, M., Roberts, K. and Walter, P. (2002) The Molecular Biology of the Cell 4th ed., Garland Science, New York (USA)

Alkan, C., Ventura, M., Archidiacono, N., Rocchi, M., Sahinalp, S.C., et al. (2007) Organization and Evolution of Primate Centromeric DNA from Whole-Genome Shotgun Sequence Data. PLoS Comput Biol 3: e181. [doi:10.1371/journal.pcbi.0030181]

Cheeseman, I.M. and Desai, A. (2008) Molecular architecture of the kinetochore–microtubule interface. Nature Reviews Molecular Cell Biology 9:33-46. [doi:10.1038/nrm2310]

Cleveland, D.W., Mao, Y., and Sullivan, K.S. (2003) Centromeres and Kinetochores From Epigenetics to Mitotic Checkpoint Signaling. Cell 112:407-421. [doi:10.1016/S0092-8674(03)00115-6 ]

Schueler, M.G., Higgins, A.W., Rudd, M.K., Gustashaw, K. & Willard, H.F. (2001) Genomic and genetic definition of a functional human centromere. Science 294:109-115.

Stanyon, R., Rocchi, M., Capozzi, O., Roberto, R., Misceo, D., Ventura, M., Cardone, M.F., Bigoni, F., and Archidiacono, N. (2008) Primate chromosome evolution: Ancestral karyotypes, marker order and neocentromeres. Chromosome Research 16:17-39. [doi: 10:1007/s10577-007-1209-z]

An inordinate fondness for systematics

 
The title of this posting is from the blog Catalogue of Organisms. Some of you may think it's a bit weird to be interested in taxonomy in the 21st century. If you think that way then you haven't been paying attention to what's going on in biology these days.

Christopher Taylor, the blogger at Catalogue of Organisms, has just posted an article about why it's important to pay attention to systematics [Poor Taxonomic Practice takes some F****ing Liberties!]. Read what he has to say.1 You can tell from the title of his posting that he feels strongly about the subject.


1. Especially the part about the botched attempt to save a native American species, Spartina foliosa.

Monday's Molecule #73

 
Today's molecule is rather large but it's made up of only two different macromolecules. It has been a favorite molecule of many famous scientists. Several fundamental advances in our understanding of biochemistry and molecular biology have come from studies of this molecules and its components.

You need to identify the molecule and give its correct common name. We don't need the formal IUPAC name in this case, because there isn't one!. Pay attention to the correct common name—you may not be able to guess it just by looking at the molecule but you should be able to deduce it knowing that it is connected to a Nobel Prize.

There's an direct connection between today's molecule and a Nobel Prize. The prize was awarded for purifying the molecule and determining its composition. The first person to correctly identify the molecule and name the Nobel Laureate(s) wins a free lunch at the Faculty Club. Previous winners are ineligible for one month from the time they first collected the prize. There are four ineligible candidates for this week's reward.

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 and names the Nobel Laureate(s). Note that I'm not going to repeat Nobel Laureate(s) 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. I may select multiple winners if several people get it right.

Comments will be blocked for 24 hours. Comments are now open.

UPDATE: The molecule is tobacco mosaic virus (TMV). The Noble Laureate is Wendell Meredith Stanley (Chemistry 1946). There were quite a few readers who got it right but the first one was John Dennehy of CUNY New York (USA). Congratulations John! He has already declined my offer of lunch on Thursday and taken a rain check to be cashed the next time he's in Toronto.


Sunday, May 25, 2008

A Canadian Biochemist

 
This week's citation classic on The Evilutionary Biologist is really a classic. It's the Journal of Biological Chemistry paper on site-directed mutagenesis from Michael Smith's lab at the University of British Columbia.

Michael Smith, who died in 2000, won the Nobel Prize in 1993 for his work on site-directed mutagenesis.

A couple of weeks ago I pooked fun at John Dennehy's selection of a Richard Dawkins paper for his citation classic series [It Happens to All of Us Eventually]. This week John writes,
Any connection between a recent Sandwalk post, the fact that Smith is Canadian and that this article is biochemical in bent is purely coincidental.
I think we can all appreciate that this is just a coincidence. We expect you to recognize all outstanding Canadian biochemists on the grounds that they are truly excellent scientists and not just because you are pandering to your neighbors up north.1

I'll assume that the last citation classic was just a temporary moment of insanity.



1. Although a little pandering never hurt anyone. You never know when you might have to emigrate.

Gene Genie #32

 
The 32nd edition of Gene Genie has been posted at Highlight Health [Gene Genie #32 - Googling the Genie].
Welcome to the 32nd edition of Gene Genie, a blog carnival devoted to genes and genetic conditions. This edition includes some excellent articles on genes and gene-related diseases, genetics, genomics and personalized genetics.

Google Health launched publicly this week and to recognize the event, the last section of the carnival is devoted to articles specifically about the service. Google, financial backer of 23andMe, also funds the Personal Genome Project, which plans to unlock the secrets of common diseases by decoding the DNA of 100,000 people in the world’s biggest gene sequencing project [1]. With the vast number of genetic data points collected for each genome sequenced, a digital system for the movement and storage of personal health information is critical for the widespread use of individualized healthcare. Google’s entrance into the online personal health records market may thus help to accelerate the era of personalized medicine.

With these thoughts in mind, let’s get to to this month’s edition of the Genie.
The beautiful logo was created by Ricardo at My Biotech Life.

The purpose of this carnival is to highlight the genetics of one particular species, Homo sapiens.

Here are all the previous editions .....
  1. Scienceroll
  2. Sciencesque
  3. Genetics and Health
  4. Sandwalk
  5. Neurophilosophy
  6. Scienceroll
  7. Gene Sherpa
  8. Eye on DNA
  9. DNA Direct Talk
  10. Genomicron
  11. Med Journal Watch
  12. My Biotech Life
  13. The Genetic Genealogist
  14. MicrobiologyBytes
  15. Cancer Genetics
  16. Neurophilosophy
  17. The Gene Sherpa
  18. Eye on DNA
  19. Scienceroll
  20. Bitesize Bio
  21. BabyLab
  22. Sandwalk
  23. Scienceroll
  24. biomarker-driven mental health 2.0
  25. The Gene Sherpa
  26. Sciencebase
  27. DNA Direct Talk
  28. Greg Laden’s Blog
  29. My Biotech Life
  30. Gene Expression
  31. Adaptive Complexity
  32. Highlight Health



Saturday, May 24, 2008

Good Science Writing

 
In case you haven't noticed, there's a debate going on about the quality of science writing. Many scientists—I am one—think that the quality of science journalism is not as good as it could be.

I maintain that the top three criteria for good science writing are: 1) accuracy, 2) accuracy, and 3) accuracy. Everything else is much less important. Scientists tend to score high in accuracy when they write about science, especially if it's their field. (There are many exceptions.)

Professional science journalists tend to score high in other categories such as readability and style. These are very important features of good science writing and no scientist can be considered a good science writer without being a good writer as well as a good scientist.

What about the non-professional who writes a good story that is not scientifically accurate? Can such a person be awarded kudos for good science writing? If the awards are handed out by other journalists, and not by scientists, is accuracy of information going to count for very much?

All these questions come up in a posting on Thomas Levensen's Blog The Inverse Square Blog [More on Richard Dawkins’ Peculiar View of Science Writing]. Levensen is upset about the fact that Dawkins only selected articles by scientists in his recently published anthology The Oxford Book of Modern Science Writing.

Read Levensen's posting to see the point of view that I dispute. Note that Levinsen refers to some very popular books by science writers who were not scientists. Some of these books may be popular but they do not score high in the category of scientific accuracy. How would Levensen know this? He's turned on by a good read and not by whether or not the information is correct. Other books by science writers are excellent. They are well written and scientifically accurate. Nobody disputes that. The question we're addressing is the general quality of science writing and not the obvious counter-examples.

As a general rule, do you think that science journalists are doing a good job of presenting accurate scientific information in their books and articles? Do you think that professional scientists do a better job?


[Hat Tip: John Wilkins]

Rating Science Blogs

 
I received the following message this morning from Amy Liu of Blogged,com.
Dear Larry Moran,

Our editors recently reviewed your blog and have given it an 8.0 score out of (10) in the Education/Science category of Blogged.com.

This is quite an achievement!

Blogged.com: Science

We evaluated your blog based on the following criteria: Frequency of Updates, Relevance of Content, Site Design, and Writing Style.

After carefully reviewing each of these criteria, your site was given its 8.0 score.

... Please accept my congratulations on a blog well-done!!
Sandwalk ranks 190th out of 822 science blogs. The top blog is Centauri Dreams an astronomy blog with a 9.8 rating. Bad Astronomy ranks 94th with an 8.9 rating.

I only recognized two blogs in the top 20: Science Blog (2nd 9.8), and Cosmic Variance (5th 9.8). In my opinion, Cosmic Variance deserves a high ranking, but so does Bad Astronomy for slightly different reasons. Science Blog is a joke, it just copies press releases.

Pharyngula (36th 9.1), The Genetic Geneologist (38th 9.0) and Aetiology (39th 9.0) make the top 40. Molecule of the Day (42nd 9.0), Discovering biology in a digital world (46th 9.0), Biocurious (47th 9.0), The Evilutionary Biologist (48th 9.0), and Sex, Genes & Evolution (49th 9.0) are in the next 20 top science blogs.

There are other ways of ranking science blogs. For example, they could be ranked by popularity as on Wilko [The Top 100 Science Blogs]. The problem with that ranking is that some of the best science blogs aren't even listed as science blogs (e.g. Bad Astrononmy).

I'm not under any illusions about the rankings of science blogs. They don't count for much in my book and I can't imagine that anyone is going to make a decision based on what Blogged.com reviewers say about a blog. But it does raise an important point. The world wide web is a mess. There's lots of inaccurate information out there and lots of blogs and web sites with hidden agendas that are not obvious. (See OpenCourseWare for one aspect of this bigger problem.)

The question is whether anything can be done about it. Is there any way to provide web users with a reliable way of determining what is accurate scientific information and what isn't? In the case of blogs, I suppose that forming clusters of blogs such as ScienceBlogsTM or Nature Network is one way.

Both of those groups are run by for-profit science magazines. It seems a shame that we have to rely on the private sector to put their stamp of approval on good science blogs. Besides, that's only going to work if the quality of blogs on such sites is maintained at a high level so that outsiders can trust them as authorities. So far, it seems to work reasonably well although there are a few mistakes now and then (cough, Framing Science, cough).


Friday, May 23, 2008

Fugu, Pharyngula, and Junk

 
PZ Myers writes about Random Acts of Evolution in the latest issue of Seed magazine. The subtitle says it all.
The idea of humankind as a paragon of design is called into question by the puffer fish genome—the smallest, tidiest vertebrate genome of all.
The genome of the puffer fish (Takifugu rubripes or Fugu rubripes) has about the same number of genes as other vertebrates (20,000) but its genome is only 400 Mb in size [Fugu Genome Project]. This is about 12.5% of the size of mammalian genomes.

THEME

Genomes & Junk DNA

Total Junk so far

    53%
The Fugu Genome Project was initiated by workers who wanted to sequence a vertebrate genome with as little junk DNA as possible in order to determine which sequences are essential in vertebrate genomes. The small size of the fugu genome suggests that more than 80% of our genome is non-essential junk.

Many of you might recall the results of my Junk DNA Poll from last January. In case you've forgotten the results, I'll post them again. The question was: "How much of our genome could be deleted without having any significant effect on our species?" The question was designed to find out whether Sandwalk readers believed in junk DNA or whether they were being persuaded by some scientists to think that most of our genome was essential. (Modern creationists are also promoting the death of junk DNA.) There was some dispute about the interpretation of the question but most readers took it to be a question about the amount of junk DNA.




Astonishingly, almost half of Sandwalk readers think that we need more than half of our genome to survive. This would be a surprise to a puffer fish.

I began a series of postings in order to explain what our genome actually looks like. So far we've determined that about 2.5% is essential and 53% is junk. Now it's time to finish off this particular theme and have another vote.

PZ points out that most of what we call junk DNA is not controversial. It consists of LINEs and SINES, which are (mostly) defective transposons. The pufferfish genome has a lot less of this kind of junk DNA than we do. This accounts for a good deal of the reduction n genome size that we see in modern pufferfish.

PZ also points out that we need to think differently about evolution ...
In the world of genomic housekeeping, the puffer fish is a neatnik who keeps the trash under control, while the rest of us are pack rats hoarding junk DNA.

There's a lot of thought these days going into trying to figure out some adaptive reason for such a sorry state of affairs. None of it is particularly convincing. We'd be better off reconciling ourselves to the notion that much of evolution is random, and that nothing prevents nonfunctional complexity from simply accumulating.
Well said PZ!!1

Watch for a few more postings on the remaining 45% of our genome then get ready to vote again. I'm hoping for a better result next time!


1. I used to know someone named Paul Myers who would never had said such a thing on talk.origins. Any relation?

[Image Credit: The junk DNA icon is from the creationist website Evolution News & Views.]

Congratulations Janet Stemwedel

 
Janet Stemwedel has just been promoted to Associate Professor with tenure at San Jose State University [The letter].

Congratulations Janet.


Here's a picture of me congratulating her in advance. Wait 'till she learns what it's really like to be a tenured Professor. She won't be smiling for long!


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.