The Ladies' Privilege

 
Friday's Urban Legend: TRUE

According to legend, girls can propose to their boyfriends on February 29th. Snopes.com says this is a true custom known as The Ladies Privilege [The Privilege of Ladies]. Back in the thirteenth century a man had to accept a proposal on February 29th or pay a fine. This probably explains why so many men were off fighting wars at the end of February during a leap year.

It's based on the idea that February 29th is an unusual day and unusual things are permitted on that day only. One of the unusual things that is allowed is for women to propose marriage. Nowadays this is much more common on all the other days but apparently there was a time when only the man could propose marriage. I wonder what those times were like when men were in control?

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The State of Science Blogging

 
There's an interesting discussion going on over at Bayblab on The State of Science Blogging. The commenters are responding to some provocation by Anonymous Coward^[1] who took a look at the top five science blogs and said,

Of those only Cognitive daily is consistantly talking about peer-reviewed research. Why is that? Perhaps there is less appeal in discussing recent papers than bashing creationists. But bashing creationists is almost too easy, and not very constructive. It's been said before, you can't reason somebody out of a position in which they didn't reason themselves into. And it worries me because to the lay audience listening to PZ Myers (the 800lb gorilla), it would seem that science's purpose is to attack religion. In fact I suspect the blog gets most of its traffic from creationists. According to technorati, his top tags are "Creationism, godlessness, humor, kooks, politics, religion, weblog, weirdness", so should it really count as a science blog?

If you examine the elephant in the room, ScienceBlogs, the trend is maintained: politics, religion books, technology, education and music are tagged more often than biology or genetics. This suggests that their primary motives are entertainment rather than discussing science. Why? Because it pays. Seed Magazine and the bloggers themselves profit from the traffic. That's right, Seed actually pays these bloggers for their posts. And the whole ScienceBlogs thing is a little incestuous, they really like linking to each other, but not so much to the little blogs. I'm afraid gone is the amateur blogger, and in is the professional gonzo science journalist. Might as well read Seed magazine.

One of the most interesting comments comes from Dave Munger of Cognitive Daily ....

So... the most popular science blogs cover the most popular topics related to science?

You also seem to be saying that you wish these bloggers would write about less popular topics. But that would make them... less popular. And then other science blogs would become the most popular. Then you could complain about those blogs.

At least you'd have something to write about.

This is a very important point. Many of us are interested in blogging about science and in teaching science. But you can't be an effective advocate for science if you don't have an audience. One way to get an audience is to blog about science related issues that are controversial and then sneak in some good science blogs when people come to visit.

In my case, that's not the only motive for blogging about rationalism and superstition. I happen to have (at least) two interests in life and I like to blog about everything that interests me. As it turns out, there are more people interested in the conflict between science and religion—or the war in the Middle East—than in hard-core science. I posted a whole series of articles on The Three Domain Hypothesis and got only a handful of comments. The series on junk DNA is bringing in just a trickle of interested readers. On the other hand, when I post about religion or politics there are dozens of comments and a lively discussion ensues.

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1. I don't like linking to anonymous bloggers. In the future I'm going to make it a policy to only link to bloggers who identify themselves, except under rare circumstances.

Tangled Bank #99

 
The latest issue of Tangled Bank is #99. It's hosted by Greg Laden at GregLaden's Blog [The Tangled Bank].

This is the February 20, 2008 edition of The Tangled Bank web carnival. The next edition will be hosted at Archaeoporn.

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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.

In the Cafeteria

 
Yesterday we were at the Musée d'Orsay. We sat down to have a coffee in the museum cafeteria. As you can see, some cafeterias in France are a little more fancy than the average museum cafeteria in North America.

My wife's weird sense of humor produced this picture of me admiring the statues.

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Les Invalides

 
This is my fourth visit to Paris but it's the first time I've been to Les Invalides. The tomb of Napoleon Bonaparte is much more impressive than I ever expected.

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Pictures of Paris

 


The church is St. Germain des Prés. It's just a few blocks from where we're staying.

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Are Brussel Sprouts Bad for You?

 

Probably not, and that's a good thing because I like Brussel sprouts. They may be OK for humans but they're bad for aphids [Eat up all of your Brussels sprouts -- unless you're an aphid].

I'm going to be in Brussels today. I'm looking forward to a nice meal of Brussel sprouts with beer and chocolate.

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An IDiot Software Developer Opines About Junk DNA

 
Randy "I want to believe" Stimpson is a software developer who thinks he understands biology. He has written a post where he claims Most DNA is not Junk. Doppelganger has already pointed out the most obvious faults with Randy's point of view [Software developer PROVES that there is no junkDNA*... and other stuff].I just want to comment on one small paragraph in order to clear up any confusion.

A bacterial genome has 4 million base pairs of DNA and according to Professor Larry Morgan, a bacterial genome doesn’t have junk. So I think it is safe to say that there is at least 1MB of information in the human genome.

I'm pretty sure he's referring to me. I'd like to point out for the record that bacterial genomes range in size from about 10⁶ bp up to 10⁷ bp.

All bacterial genomes have junk DNA consisting mostly of defective transposons and defective prophage. In most cases the amount of junk DNA is only a few percent of the genome.

The views expressed by Randy Stimpson are typical of those who desperately want to believe in intelligent design creationism. Junk DNA is not compatible with intelligent design creationism no matter how you cut it.

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La Tour Eiffel

 
These are my pictures of the Eiffel Tower.

It's much easier to take pictures like this from the second level 'cause you don't have to hang out near the outer railing where the risk of falling off is very high. I found that it's much better to say far away from the edge. My knees were much more stable when I did that.

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Rue du Cherche Midi

 
This is a picture of Rue du Cherche Midi right outside our apartment in Paris. The street is full of nice shops (expensive), bakeries, and small restaurants. It's perfectly situated in the middle of the 6th (6^e) arrondissement [Map].

There are lots of interesting places to see right in our neighborhood. One of the nearby cafés is shown below along with a close-up of a plaque hanging on the wall of a building in on the next street. It says that John Paul Jones died in that building in July 1792. (It seems as though the prominent men and women of the Revolutionary War were very fond of France.) Incidentally, I took a quick poll of several people in the vicinity and none of them knew who John Paul Jones was.

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Gene Genie #25

 
The 25th edition of Gene Genie has been posted at Gene Sherpas [Gene Genie is Back at The Sherpa!].

There are many posts that were submitted. I have to say, we are doing a good job of covering these genes, but probably won't get through them all. I am excited about a ton of this content. But when we move through genetic discovery, talk always falls back to personalized medicine.

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.

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How Matt Nisbet Conned AAAS

 
Some of you might recall an earlier posting where I criticize Matt Nisbet for the way he organized a panel at the AAAS meeting without allowing anyone to give the other side of the issue [AAAS Panel: Communicating Science in a Religious America].I sent an email message to Professor Goldston, the panel moderator. Here's part of what I said.

I don't object to Nisbet presenting his point of view at a AAAS meeting but my respect for AAAS and your panel would be greatly diminished if the other side did not get a chance to make its case. Surely you do not want to give the impression that AAAS will only support scientists who agree with Nisbet? Surely you do not want to have a panel where the so-called "New Atheist" perspective is excluded and only religious scientists, or their close allies, are allowed to speak? Is that fair?

Please make sure that you have appropriate balance on your panel. Please make sure you don't give the impression that AAAS endorses Nisbet and his ideas about framing. The other side needs to be heard.

Mike Dunford has followed up with a posting from several days ago [Yeah, could have seen that one coming].

It's about time we realized that Matt Nisbet is not a friend of science. He needs to be strongly opposed before he succeeds in fooling any more naive scientists who might fall for his silly nonsense.

This "framing" thing has gone too far.

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Nobel Laureate: André Lwoff

 

The Nobel Prize in Physiology or Medicine 1965.

"for their discoveries concerning genetic control of enzyme and virus synthesis"

André Lwoff (1902 - 1994) received the Nobel Prize in Physiology or Medicine for his work on gene expression in bacteriophage λ. He shared the prize with François Jacob and Jacques Monod. The three men worked together at the Institut Pasteur in Paris, France, at a time when it was one of the leading centers of research in this field.

Jacob and Monod were recognize for their pioneering work on The lac Operon. Lwoff worked on the regulation of gene expression in λ. He was responsible for discovering that bacteriophage λ could enter a dormant (lysogenic) state by integrating into the E. coli genome and repressing transcription of all the genes required in the lytic stage of development.

THEME:

Nobel Laureates
The presentation speech was given by Professor Sven Gard, member of the Nobel Committee for Physiology or Medicine of the Royal Caroline Institute.

Your Majesties, Royal Highnesses, Ladies and Gentlemen.

The 1965 Nobel Prize in Physiology or Medicine is shared by Professors Jacob, Lwoff and Monod for «discoveries concerning the genetic regulation of enzyme and virus synthesis».

This particular sphere of research is by no means easy. I heard one of the prize winners, Professor Jacob, forewarn an audience of specialists more or less as follows: «In describing genetic mechanisms, there is a choice between being inexact and incomprehensible». In making this presentation, I shall try to be as inexact as conscience permits.

It has become progressively more apparent that the answer to what has hitherto been romantically termed the secret of life must be sought in the mechanism of action and in the structure of the hereditary material, the genes. This central field of research has naturally been approached from the periphery and in stages. Only in recent years has it been possible to make a serious attack on these fundamental problems.

Several previous Nobel Prize holders: Beadle, Tatum, Crick, Watson, Wilkins, Kornberg and Ochoa have worked in this sphere of research and have formulated certain basic proposals which have enabled the French scholars to continue their efforts. It has been established that one of the principal functions of genes must be to determine the nature and number of enzymes within the cell, the chemical apparatus which controls all the reactions by which the cellular material is formed and the energy necessary for various life processes is released. There is thus a particular gene for each specific enzyme.

In addition, some light has been thrown on the chemical structure of genes. In principle, they have the form of a long double chain consisting of four different components, which can be designated by the letters a, c, g, and t, and with the property of forming pairs with each other. An «a» in one of the chains has to be matched by a «t» in the other, a «g» only by a «c». However, they can be linked along the length of the chain in any order whatsoever, so that the number of possible combinations is virtually unlimited. A chain of genes contains from several hundreds to many thousands of units; such structures can easily carry the specific patterns for the million or more genes which it is estimated that a cell may have.

This model of the genes represents a coded message containing two types of information. If the double chain of a gene is split lengthwise and each half acquires a new partner, then the final result is two double chains identical to the original gene. The model thus contains information relative to the actual structure of the gene, which permits multiplication, in its turn a condition of heredity. When a cell divides, each daughter cell receives an exact copy of the parent gene. The structure of the double chain ensures the stability and permanence required by hereditary material.

But the model can also be read in another way. Along the length of the chain, the letters are grouped in threes in coded words. An alphabet of four letters allows the formation of more than 30 different words and the sequence in the gene of such words provides the structural information for an enzyme or some other protein. Proteins are also chain molecules built up from twenty or so different types of building blocks. To each of these building blocks there corresponds a chemical code word of three letters. The gene thus contains information on the number, nature, and order of the building blocks in a particular protein.

Thus it was already clear that the hereditary blueprint contained the collective structural information for all substances necessary for the functions of the living cell. It was not known how the genetic information was put into effect or transformed into chemical activity. As to the function of the genes, it was thought that they participated in a sort of procreative act when the new cell came into being, producing new substances necessary for the life of the cell, but subsequently lying dormant until the next cell division. It was presumed that the structure and formation of the chemical apparatus determined in this way defined all the regulatory mechanisms necessary for the cell's ability to adapt to changes in the environment and to respond in an adequate manner to stimuli of different types.

To begin with, the group of French workers were able to demonstrate how the structural information of the genes was used chemically. During a process resembling gene multiplication an exact copy of the genetic code is produced, termed a messenger. The latter is then incorporated into the chemical «workshop» of the cell and wound like magnetic tape onto a spool. For each word arriving on the spool, a constructional unit is attracted, which carries a complement to this word and attaches itself there just like a piece of jigsaw puzzle. The building blocks of a protein are selected in this way one by one, aligned, and joined together to form a protein with the appropriate structure.

The messenger substance is, however, short-lived. The tape lasts only for a few recordings. The enzymes are also used up in a similar way. For the cell to maintain its activity, it is thus necessary to have an uninterrupted production of the messenger material, that is to say continuous activity of the corresponding gene.

However, cells can adapt themselves to different external conditions. Thus there must exist some mechanisms controlling the activity of the genes. The research into the nature of these mechanisms is a remarkable achievement which has opened the way for the possible explanation of a series of hitherto mysterious biological phenomena. The discovery of a previously unknown class, the operator genes, which control the structural genes, marks a major breakthrough.

There are two types of operator genes. One type releases chemical signals, which are perceived by a second, receptor, type. The latter controls in its turn one or more structural genes. As long as the signals are being received the receptor remains blocked and the structural genes are inactive. Certain substances coming from outside or formed within the cell can, however, influence the chemical signals in a specific manner, changing their character so that they can no longer influence the receptor. The latter is unblocked and activates the structural genes; messenger material is produced and the synthesis of enzymes or another protein commences.

Control of gene activity is thus of a negative nature; the structural genes are only active if the repressor signals do not arrive. One can speak here of chemical control circuits similar in many ways to electrical circuits, for example in a television set. In the same way, they can be interconnected or arranged in a series to form complicated systems.

With the aid of such control circuits, the free living monocellular organism can produce enzymes when required, or interrupt chemical reactions if they are likely to cause damage; an excitatory stimulus can provoke movement, flight or attack, depending on the nature of the excitation. With such mechanisms it is possible to direct the development of cells into more complicated structures. It is particularly interesting to note that the activity of viruses is controlled, in principle, in the same manner.

Bacteriophages contain a genetic control circuit complete with emitter, receptor, and structural genes. While chemical signals are being sent and received, the virus remains inactive. When incorporated into a cell, it behaves like a normal component of the cell, and can confer on it new properties which may improve its chances of survival in the struggle for existence. However, if the signals are interrupted, the virus is activated, starts to grow rapidly and soon kills the host cell. There is considerable evidence for the view that certain types of tumor virus are incorporated into a normal cell in the same way, thus transforming it into a tumour cell.

We are easily inclined to hold an exaggerated opinion of ourselves in this era of advanced technology. Thus, we are justified in having a great admiration for the achievements in electronics, where, for example, the attempts at miniaturization to reduce component size, to lower the weight, and reduce the volume of apparatus have enabled a rapid development of space science. However, we should bear in mind that, millions of years ago, nature perfected systems far surpassing all that the inventive genius of man has been able to conceive hitherto. A single living cell, measuring several thousandths of a millimetre, contains hundreds of thousands of chemical control circuits, exactly harmonized and functioning infallibly. It is hardly possible to improve on miniaturization further; we are dealing here with a level where the components are single molecules. The group of French workers has opened up a field of research which in the truest sense of the word can be described as molecular biology.

Lwoff represents microbiology, Monod biochemistry, and Jacob cellular genetics. Their decisive discovery would not have been possible without competence and technical knowledge in all these fields, nor without intimate cooperation between the three researchers. But the mystery of life is not resolved simply with knowledge and technical skill. One must also have a gift for observation, a logical intellect, a faculty for the synthesis of ideas, a degree of imagination, and scientific intuition, qualities with which the three workers are liberally endowed.

Research in this field has not yet yielded results that can be used in practice. However, the discoveries have given a strong impetus to research in all domains of biology with far-reaching effects spreading out like ripples in the water. Now that we know the nature of such mechanisms, we have the possibility of learning to master them, with all the consequences which that will surely entail for practical medicine.

François Jacob, André Lwoff, Jacques Monod. Thanks to your technically unimpeachable experiments and your ingenious and logical deductions, you have gained a more intimate familiarity with the nature of vital functions than anyone before you has done. Action, coordination, adaptation, variation - these are the most striking manifestations of living matter. By placing more emphasis on dynamic activity and mechanisms than on structure, you have laid the foundations for the science of molecular biology in the true sense of the term. In the name of the Caroline Institute, I ask you to accept our admiration and our most sincere congratulations. Finally, I invite you to come down from the platform to receive the prize from His Majesty the King.

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A Canadian in Paris

This is where I'll be for the next few weeks. I know, it's really tough being a biochemist, but somebody has to do it.

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Goodbye Timmy's

 

Thank God, there's a Tim Hortons at the airport.

Extra large coffee and a honey cruller. Hmmmmm....

I won't be seeing any Timmy's for a very long time.

I wonder if they have bake goods and beverages where I'm going?

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