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Wednesday, February 06, 2008

Nobel Laureate: François Jacob

 

The Nobel Prize in Physiology or Medicine 1965.
"for their discoveries concerning genetic control of enzyme and virus synthesis"


François Jacob (1920 - ) received the Nobel Prize in Physiology or Medicine for his work on gene expression. He shared the prize with André Lwoff 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 made major contributions to the discovery of messenger RNA and the regulation of transcription when these processes were just beginning to be understood. His name, and Monod's, are mostly associated with the lac operon in E. coli but the prize was also given for work with bacteriophage. The concepts of operons, operators, and repressors all come from the work of Jacob and Monod.

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. As you read it, note how much they knew in 1965 after only a few years of intense work in deciphering the genetic code and working out how genes are transcribed. This is only 12 years after Watson & Crick's paper on the structure of DNA. That's the same amount of time that has elapsed between 1996, when Dolly the sheep was cloned, and today.
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.



Gods Behaving Badly

 
Gods Behaving Badly is a new book by Marie Phillips. It was just reviewed in the New York Times [The House of Myth]. Here's a teaser,
Americans have long delighted in movies like ''It's a Wonderful Life,'' ''Heaven Can Wait'' (both the 1943 and 1978 versions) and ''Bruce Almighty'' -- ''divine comedies,'' to borrow the marketing shtick of the day, in which a benevolent male Judeo-Christian God and sometimes his demonic counterpart are represented by stock imagery like billowing clouds, bolts of lightning, bumbling plainclothes angels and horned creatures thumping pitchforks. The humor may be irreverent, but it's always delivered with a basic attitude of respect.

Such deference, a holdover perhaps from the days of the Hays Code, is entirely lacking in Marie Phillips's first novel, ''Gods Behaving Badly,'' in which the 12 major deities of ancient Greece uneasily cohabit in a dilapidated town house in 21st-century London, dwelling just above the city's ''greasy tide'' of human flesh. It's like Hesiod's ''Theogony'' meets MTV's ''Real World.''

In the author's affectionate telling, Zeus, the fading patriarch, is squirreled away on the top floor; Apollo is a horny and malcontented television psychic; and Aphrodite is a phone-sex worker whose buttocks, when she mounts a staircase, resemble ''two hard-boiled eggs dancing a tango'' -- maybe the most original description of the female posterior since Jerry approvingly deemed Sugar Kane's ''Jell-O on springs'' in ''Some Like It Hot.'' Apollo's virginal, pragmatic twin sister, Artemis, walks dogs for a living and jogs compulsively in her spare time. Dionysus owns a nightclub called Bacchanalia and is constantly plugged in to a music player. Meanwhile, Athena has been cast as an efficient boardroom type who distributes handouts to her bored family as she subjects them to streams of corporate gobbledygook.
This sounds like a terrific book. I don't normally read fiction—other than creationist books—but this will be an exception. Has anyone read it?


What Happened to the "Peers" on this Paper?

 

Quite a few science bloggers were shocked at a paper that appeared recently in the journal Proteomics—a respectable journal up 'till now.

PZ Myers had the stomach to blog about this train wreck of a paper. Read his article at A baffling failure of peer review.


[Photo Credit: Train Wreck at Gare Montparnasse, Paris, France, 1895 from Answers.com]

Joshua Lederberg

 

Joshua Lederberg died last Saturday (Feb. 2, 2008). In his honor, John Dennehy has selected one of Lederberg's famous papers as This Week's Citation Classic: Joshua Lederberg.

I think it's too bad that our current generation of students is growing up without being sufficiently aware of the fundamental principles of biochemistry and molecular biology that were worked out in bacteria and bacteriophage.

UPDATE: [Loss of a giant: Joshua Lederberg]


Tangled Bank #98

 
The latest issue of Tangled Bank is #98. It's hosted by Steve Matheson at Quintessence of Dust [Tangled Bank #98].
Hey! Welcome to Tangled Bank #98, and thanks for stopping by. If you've never been to Quintessence of Dust, the lobby is below and to the right. I hope you'll poke around a little.

PZ didn't give me a budget for refreshments, but if you come to the house I'll make sure we at least have plenty of guacamole. Chips are here, and beer is over there. Our city was once used by Anne Lamott as a metaphor for plainness, but it's much cooler than most people think. You can get to our house on a nice bus system, and after the carnival we can pick one of two Ethiopian restaurants. My day job is at Calvin College, but right now I'm on sabbatical in the lab of a friend and collaborator at the Van Andel Institute in downtown Grand Rapids.


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.

Tuesday, February 05, 2008

Evolution as Tinkering

François Jacob won the Nobel Prize in 1965 for his work on the lac operon. He is also known for his thoughts on evolution, especially the concept of a tinkerer. The idea deserves to be better known so I present a long quotation from his little book The possible and the Actual published in 1994. The book contains a lecture that was based on an article he published in Science back in 1977 (Jacob, 1977).

I'm a big fan of this view of evolution [Evolution by Accident].
The action of natural selection has often been compared to that of an engineer. This comparison, however, does not seem suitable. First, in contrast to what occurs during evolution, the engineer works according to a preconceived plan. Second, an engineer who prepares a new structure does not necessarily work from older ones. he electric bulb does not derive from the candle, nor does the jet engine descend from the internal combustion engine. To produce something new, the engineer has at his disposal original blueprints drawn for that particular occasion, materials and machines specially prepared for that task. Finally, the objects thus produced de novo by the engineer, at least by a good engineer, reach the level of perfection made possible by the technology of the time.

In contrast, evolution is far from perfection, as was repeatedly stressed by Darwin, who had to fight against the argument from perfect creation. In the Origin of Species, Darwin emphasizes over and over again the structural and functional imperfections in the world. He always points out the oddities, the strange solutions that a reasonable God would never have used.

In contrast to the engineer, evolution does not produce innovations from scratch. It works on what already exists, either transforming a system to give it a new function or combining several systems to produce a more complex one. Natural selection has no analogy with any aspect of human behavior. If one wanted to use a comparison, however, one would have to say that this process resembles not engineering but tinkering, bricolage we say in French.

While the engineer's work relies on his having the raw materials and the tools that exactly fit his project, the tinkerer manages with odds and ends. Often without even knowing what he is going to produce, he uses whatever he finds around him, old cardboards, pieces of string, fragments of wood or metal, to make some kind of workable object. As pointed out by Claude Levi-Strauss, none of the materials at the tinkerer's disposal has a precise and definite function. Each can be used in several different ways. What the tinkerer ultimately produces is often related to no special project. It merely results from a series of contingent events, from all the opportunities he has to enrich his stock with leftovers. In contrast with the engineer's tools, those of the tinkerer cannot be defined by a a project. What can be said about an of these objects is that "it could be of some use." For what? That depends on the circumstances.

In some respects, the evolutionary derivation of living organisms resembles this mode of operation. In many instances, and without any well-defined long-term project, the tinkerer picks up an object which happens to be in his stock and gives it an unexpected function. Out of an old car wheel, he will make a fan; from a broken table, a parasol. This process is not very different from what evolution performs when it turns a leg into a wing, or a part of a jaw into pieces of ear.

...

When different engineers tackle the same problem, they are likely to end up with very nearly the same solution: all cars look alike, as do all cameras and all fountain pens. In contrast, different tinkerers interested in the same problem will reach different solutions, depending on the opportunities available to each of them. This variety of solutions also applies to the products of evolution, as is shown, for instance, by the diversity of eyes found throughout the living world. The possession of light receptors confers a great advantage under a variety of conditions. During evolution, many types of eyes appeared, based on at least three different principles: the lens, the pinhole, and multiple holes. The most sophisticated ones, like ours, are lens-based eyes, which provide information not only on the intensity of incoming light but also on the objects that light comes from, on their shape, color, position, motion, speed, distance, and so forth. Such sophisticated structures are necessarily complex.

One might suppose, therefore, that there is just one way of producing such a structure. But this is not the case. Eyes with lenses have appeared in molluscs and in vertebrates. Nothing looks so much like our eye as the octopus eye. Yet it did not evolve the same way. In vertebrates, the photoreceptor cells of the retina point away from the light while in molluscs they point toward the light. Among the many solutions found to the problem of photoreceptors, these two are similar but not identical. In each case, natural selection did what it could with the materials at its disposal.
For a more up-to-date view of the evolution of eyes see PZ Myers' article in the current (January/February 2008) issue of SEED magazine.


Jacob, F. (1977) Evolution and Tinkering. Science 196:1161-1166. ]JSTOR]

Jacob, F. (1994) from The Possible and the Actual, reprinted in Evolution Extended, Connie Barlow ed. MIT Press, Cambridge, MA (USA) 1994.

The Streisand effect

 
This is a new term to me. It was used over on simra.net in reference to the attempt by students at Wilfred Laurier University to dictate to the Laurier Freethought Alliance [Follow-up on the WLU controversy]. I had to look up the term on Wikipedia.

Just in case there are any other old people out there, here's the definition.
The "Streisand effect" is a term used to describe a phenomenon on the Internet where an attempt to censor or remove (in particular, by the means of cease-and-desist letters) a certain piece of information (for example, a photograph, a file, or even a whole website) backfires. Instead of being suppressed, the information receives extensive publicity, often being widely mirrored across the Internet, or distributed on file-sharing networks in a short period of time.[1][2] Mike Masnick said he jokingly coined the term in January 2005, “to describe [this] increasingly common phenomenon.”[3] The effect is related to John Gilmore's observation that, "The Net interprets censorship as damage and routes around it."

The term Streisand effect originally referred to a 2003 incident in which Barbra Streisand sued photographer Kenneth Adelman and Pictopia.com for US$50 million in an attempt to have the aerial photo of her house removed from the publicly available collection of twelve thousand California coastline photographs, citing privacy concerns.[4][5][1] Adelman claims he was photographing beachfront property to document coastal erosion as part of the California Coastal Records Project.[6] Paul Rogers of the San Jose Mercury News later noted that the picture of Streisand’s house was popular on the Internet.


The Quacks Fight Back

 
Last week David Colquhuon gave a talk sponsored by the Centre for Inquiry and the University of Toronto Secular Alliance [Quackery in Academia] [Science in an Age of Endarkenment].

During his visit to Toronto he was interviewed by Michael Enright of the CBC Radio show The Sunday Edition. The interview was broadcast on Sunday, January 27th. As you might imagine, there were lots of comments and emails and a second show was required in order to restore some "balance." The second show was broadcast on Sunday, February 3rd [The Sunday Edition].
A stirred-up hornet's nest is a mild disturbance compared to the firestorm we unleashed last week over my conversation with Dr. David Colquhoun. Dr. Colquhuon is a gangly, pipe-puffing British pharmacologist who thinks all alternative medicine, all of it, is a fraud perpetrated by quacks. But he went further, somehow suggesting that those who believe in it probably supported Margaret Thatcher, Ronald Reagan and the Ayatollah Khomeini. He pooh-poohed acupuncture, chiropractic, homeopathy, even vitamins.

Well, his remarks opened the floodgates of listener mail, screaming for Dr. Colquhoun's head on a pike. In a few moments, alternative or complimentary medicine strikes back. With the help of two experts, we will try to give the other side of contentious Colquhounism.
Two quacks were required to restore the rift in the space-time continuum caused by too much rationality: Dugald Seely of the Canadian College of Natrupathic Medicine and Dr. Kien Trinh of the DeGroote School of medicine at McMaster University in Hamilton. It's shocking that one of them is from a genuine medical school: he's in a Ph.D. program.

You can listen to the podcast on the CBC website but I can assure you that you won't learn anything new. There's some important issues here. Here's one of the letters that was read on the show ...
Most proponents of alternative medicine do not deny the place of Western medicine. It is too bad that for some the respect is not reciprocal.
                                 Dale Jack
The logic here is that just because some quacks are able to recognize the value of evidence-based medicine then it follows that scientists should extend the same respect to quacks who promote non-evidence-based medicine.

It's a mark of how silly our society has become that such an argument even merits a response. It would be like saying that the most outlandish ideas deserve equal time as long as their proponents are respectful to the proponents of reality.

Here's a similar comment ...
He [Colquhoun] is the very representative of the darkness of the scientific method. He is one of the very ilk that would have driven the new hand-washing surgeons to suicide. As a past-President of the Complementary and Integrative Physicians of B.C., I do hope you will spend the next few weeks in contrition—to re-establish your usually balanced and worthwhile reputation.
                                 Steven Faulkner
Coming from a quack, I guess we shouldn't be surprised at the "logic" exhibited here. The first example is the old saw about truly brilliant innovators who were originally scoffed at. The idea is that because one person took on the scientific establishment and won, it follows logically that all renegades must be right. Conversely, scientists who scoff at quacks must be wrong.

No, this does not compute. As they say, people laughed at Galileo but they also laughed at Bozo the clown.

The second example of silly logic is the concept of "fairness" and "balance" that is used time and time again by quacks and IDiots. Apparently it doesn't matter how stupid your ideas are, society demands that you be given a hearing if you are attacked. Well I've got news for all you quacks out there. You don't get to promote your crazy ideas just because you have them. There's no rule that says you have to be given a platform on public radio just because you've been criticized.

If you want to be heard go the Hyde Park on a Sunday morning. Take a soapbox.


SciBarCamp

 
I'm blatantly copying this from the SciBarCamp Website. I'll be there. There are still places available and scientists are especially encouraged to register.
SciBarCamp is a gathering of scientists, artists, and technologists for a weekend of talks and discussions. It will take place at Hart House at the University of Toronto on the weekend of March 15-16, with an opening reception on the evening of March 14. The goal is to create connections between science, entrepreneurs and local businesses, and arts and culture. The themes are:
  • The edge of science (eg, synthetic biology, quantum gravity, cognitive science)
  • The edge of technology (eg, mobile web, ambient computing, nanotechnology, web 2.0)
  • Science 2.0 (open access, changing models of publication and collaboration, scientific software)
  • Scientific literacy and public engagement (eg, one laptop per child project, policy and science, technology as legislation, enfranchising the poor, the young, the old)
  • The interactions of science, art and culture: Scientists and artists as partners in the continuing evolution of the culture.
In the tradition of BarCamps, otherwise known as "unconferences", (see BarCamp.org for more information), the program is decided by the participants at the beginning of the meeting, in the opening reception. Presentations and discussion topics can be proposed here or on the opening night. SciBarCamp will require active participation; while not everybody will present or lead a discussion, everybody will be expected to contribute substantially - this will help make it a really creative event.

The talks will be informal and interactive; to encourage this, speakers who wish to give PowerPoint presentations will have ten minutes to present, while those without will have twenty minutes. Around half of the time will be dedicated to small group discussions on topics suggested by the participants. The social events and meals will make it easy to meet people from different fields and industries. Our venue, Hart House, is a congenial space with plenty of informal areas to work or talk, and there will be free wireless access throughout.

Our goals are:
  • Igniting new projects, collaborations, business opportunities, and further events.
  • Intellectual stimulation and good conversation.
  • Integrating science into Toronto's cultural, entrepreneurial, and intellectual activities.
  • Prototyping a model that can be easily duplicated elsewhere.
Attendance is free, but there is only space for around 100 people, so please register by sending an email to Jen Dodd (dodd.jen@gmail.com) with your name and contact details. Please include a link to your blog or your organization's webpage that we can display with your name on the participants list at www.SciBarCamp.org.
Eva Amsen is one of the organizers. Read what she has to say on easternblot [SciBarCamp].


Stuart Kauffman: Reinventing the Sacred

 
The Centre for Inquiry in Toronto is sponsoring a talk by Stuart Kauffman this Friday evening.
REINVENTING THE SACRED:
How the Paradigm of Emergence Offers New Scientific Views on the Origin of Life and Biodiversity, Economics, Ethics, and Spirituality


Stuart Kauffman, Institute for Biocomplexity and Informatics, University of Calgary

Thurs, Feb 8, 7:30pm, Centre for Inquiry Ontario, 216 Beverley St, downtown Toronto.

Part of our ongoing Voices of Reason lecture series - Centre for Inquiry.

The event is open to the public.
Cost: $7 general, $4 students, FREE for Friends of the Centre

A catered reception at 6pm at the Centre for Inquiry Ontario will be held with Dr. Kauffman exclusively for Friends of the Centre so join today by contacting us at ontario@centerforinquiry.net!
Check out Kauffman's bio on The Edge [Stuart Kauffman].

Kauffman's ideas are difficult to understand; although, in fairness, I haven't tried very hard. To me they seem fuzzy and ill-defined with more than a hint of spiritualism in spite of the fact that Kauffman is a non-believer.

Here's an example from an interview with the University of Calgary campus newspaper.
It turns out that the behaviour of genetic networks depends critically on the level at which the genes are connected. If they are heavily connected the system is chaotic, and if they are only lightly connected the system is ordered. An attractive hypothesis is that biological systems, like genetic networks, flourish in a “transition zone” between the ordered and chaotic regimes. I call this transitional phase the complex regime. So biocomplexity refers to biological systems that thrive in this balance between order and chaos. Other examples include the immune and neural systems.
The essence of Kauffman's idea, as I understand it, is that life has a built-in tendency for self-organization. He argues that if you replay the tape of life, very similar sorts of organisms will arise because the ones we see are highly constrained by the basic laws of chemistry and physics operating on our planet. In other words, evolving life doesn't have as many choices or options as we imagine.

Daniel Dennett explains it well in Darwin's Dangerous Idea (p. 225).
It is the non-optionality of these "choices" that Kauffman wants to stress, and so he and his colleague Brian Goodwin (e.g., 1986) are particularly eager to discredit the powerful image, first made popular by the great French biologists Jacques Monod and François Jacob, of Mother Nature as a "tinker," engaging in the sort of tinkering the French call bricolage. The term was first made salient by the anthropologist Claude Lévi Struss (1966). A tinker or bricoleur is an opportunistic maker of gadgets, a "satisficer" (Simon 1957) who is always ready to settle for mediocrity if it is cheap enough. A tinker is not a deep thinker. The two elements of classical Darwinism that Monod and Jacob concentrate on are chance on the one hand and, on the other, the utter directionlessness and myopia (or indeed blindness) of the watchmaker. But, says Kauffman, "Evolution is not just 'chance caught on the wing.' It is not just a tinkering of the ad hoc, of bricolage, of contraption. It is emergent order honored and honed by selection." (Kauffman 1993, p. 644).

[Photo Credit: University of Calgary: OnCampus Weekly]

Things Get Complicated at Wilfred Laurier University

 
Some of you will recall the issue. The Laurier Freethought Alliance applied for club status at Wilfred Laurier University but they were turned down by the Campus Clubs Office [Bigots at Wilfrid Laurier University]. In case you've forgotten the reason, here's what the Campus Clubs Office said in rejecting the application.
While the Campus Clubs department understands the goals and visions of your organization, they are not compatible with the guidelines of what may be approved and incorporated into our department. While the promotion of reason, science and freedom of inquiry are perfectly legitimate goals, what is most in question in regards to your club's vision is the promotion of "a fulfilling life without religion and superstition". While this university is indeed technically a secular institution, secular does not denote taking an active stance in opposition to the principles and status of religious beliefs and practices. To be clear, this is not meant to say that the promotion of science and reason are illegitimate goals. But due to the need to respect and tolerate the views of others, the Campus Clubs department is unable to approve a club of this nature at this time. If you wish to adjust and rethink your club's application and vision, you may resubmit a revised proposal at any time.
This is political correctness taken to absurd lengths. I very much doubt that the same criteria are applied to religious clubs at Wilfred University.

Can you imagine a Christian club being denied status because they promote, "a fulfilling life by following the teachings of Jesus Christ"? The Laurier Freethought Alliance is promoting the idea that you have have a fulfulling life without Jesus of any other God. What's wrong with that?

Anyway, the response of the atheist community took the Campus Clubs Office by surprise and they are now stuggling to cover their asses rear ends. You can read the response on Anatoly Venovcev's blog [Eye of the Hurricane].

Anatoly wants everyone to calm down and stop pointing out the obvious to the powers that be at Wilfred Laurier. The Laurier Freethought Alliance wants to negotiate a way out of this problem and the publicity isn't helping right now.

That's a bit naive. The cat is out of the bag. Now is the time for the Laurier Freethought Alliance to stand firm and not bow to pressure from the Campus Clubs to change their true mission.


[Hat Tip: The Frame Problem]

Monday, February 04, 2008

Monday's Molecule #61

 
Today's molecule is three molecules. You have to identify the purple molecule on the left and the blue one near the top. You also have to identify the multicolored double-stranded helically thing that's holding them all together. (Hint: it's DNA.) The electron micrographs at the top serve as additional hints.

You have to give me the common names of these molecules and explain what's going on in the figure. You'll be pleased to know that I don't need the systematic IUPAC name for this one. This should be as easy as falling off a log for every biochemistry and molecular biology student but I fear that it may fall into the category of things that have been forgotten in modern courses.

There's an indirect connection between this molecule and Wednesday's Nobel Laureate(s). Your task is to figure out the significance of today's molecule and identify the Nobel Laureate(s) who worked with it. Here's an additional hint for this week only; I'm looking for a single name and if you can't decide between two or more possibilities, choose the earliest winner. (Be sure to check previous Laureates.)

The reward goes to the person who correctly identifies the molecule and the Nobel Laureate(s). Previous winners are ineligible for one month from the time they first collected the prize. There are three ineligible candidates for this week's reward. The prize is a free lunch at the Faculty Club.

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 the Nobel Laureate(s). Note that I'm not going to repeat Nobel Laureates so you might want to check the list of previous Sandwalk postings.

Correct responses will be posted tomorrow along with the time that the message was received on my server. I may select multiple winners if several people get it right.

Comments will be blocked for 24 hours. Comments are no open.

UPDATE: No winner this week. There were (only) three people who got the molecule correct. Only one of them was close to getting the Nobel Laureate (singular). That person named him correctly (François Jacob) but he threw in a second Nobel Laureate who had already been featured on Sandwalk.

The molecule is lac repressor bound to two sites on DNA forming a loop. The loop contains the binding site for cyclic AMP regulatory (receptor) protein or CRP, also known as catabolite activator protein (CAP). That's the other protein in the figure. The figure is from Lac Repressor and Operator.


Protest for Improving Science Education

 
John Pieret makes a very good point on his blog Thoughts in a Haystack. He points out that many American high school teachers avoid teaching evolution in their classes because it's too controversial. They'll skip that section of the curriculum even if it's required by the school board. "Who needs the hassle from parents," they say.

This fact needs to be widely known. It means the IDiots are winning in spite of the court cases that go against them. (John will probably disagree with this point.) If evolution is being removed from classrooms—and all the evidence suggests that it is—then we're fooling ourselves if we think the good guys are winning.

Stand up and protest if you think this is happening in your school district [Sounds of Silence]. Even better, encourage our students to take to the streets. You'd be surprised at how many of them want a decent education.


[Photo Credit: "Joining nationwide demonstrations, high-school students in Valparaíso [Chile] take to the streets on May 30 [2006] to protest [for] proposed changes in Chile's public education system." Eliseo Fernandez—Reuters /Landov (Encyclopedia Britanica Online)]

Ann Coulter Praises Canada for Sending Toops to Vietnam

 
That's right. You read the title correctly. Watch the video where she's challenged about her lack of truthiness. It's hilarious.




[Hat Tip: Canadian Cynic]

Sunday, February 03, 2008

How to Think About Science

 
One of my colleagues send me a link to a CBC (Canadian Broadcasting Corporation) radio series about How to Think About Science. You can download podcasts of all 10 episodes.
If science is neither cookery, nor angelic virtuosity, then what is it?

Modern societies have tended to take science for granted as a way of knowing, ordering and controlling the world. Everything was subject to science, but science itself largely escaped scrutiny. This situation has changed dramatically in recent years. Historians, sociologists, philosophers and sometimes scientists themselves have begun to ask fundamental questions about how the institution of science is structured and how it knows what it knows. David Cayley talks to some of the leading lights of this new field of study.
A "new field of study"? I didn't know that.

I recognize the names of some of the people who were interviewed and I'm more than a little skeptical. What do you think? Are these the leading lights of a new way of looking at epistemology? Or, is this just a subtle version of new-age psychobabble?

Episode 1 - November 14 - Simon Schaffer
Episode 2 - November 21 - Lorraine Daston
Episode 3 - November 28 - Margaret Lock
Episode 4 - December 5 - Ian Hacking and Andrew Pickering
Episode 5 - December 12 - Ulrich Beck and Bruno Latour
Episode 6 - January 2 - James Lovelock
Episode 7 - January 9 - Arthur Zajonc
Episode 8 - January 16 - Wendell Berry
Episode 9 - January 23 - Rupert Sheldrake
Episode 10 - January 30 - Brian Wynne