The View from Siberia

 
Total eclipse of the sun, in the Altai region of Siberia on Friday, August 1, 2008.

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[Photo Credit: SciAm.com]

The Night Chicago Died

 
Last weekend we watched Donnie Brasco, a 1997 film with Al Pacino and Johnny Depp. The plot is based on the true story of an FBI agent, played by Johnny Depp, who infiltrates the New York mob and befriends a petty criminal, played by Al Pacino. The acting is great. It's hard to understand why Al Pacino wasn't nominated for a major acting award. Perhaps it's because we had been nominated many times in the past and won best actor in 1992. The last scene in the movie is a classic.

The movie reminded me of a song by the British group Paper Lace. They wrote a song about a fictional² night of warfare between Al Capone and the Chicago police. The song, The Night Chicago Died, reached #1 for a brief time in 1974.² I think it's one of the best songs of the 70's but very few people agree with me.

If you haven't heard it you should click on the video and listen at least once. I love songs that tell a story and in order to appreciate the story you need to listen to the words as well as the music. I've included the lyrics. Read the opening lines in order to get the context. The song is about the family of a Chicago cop.

Daddy was a cop
On the East Side of Chicago
Back in the USA
Back in the bad old days

In the heat of a summer night
In the land of the dollar bill
When the town of Chicago died
And they talk about it still

When a man named Al Capone
Tried to make that town his own
And he called his gang to war
Against the forces of the law

I heard my momma cry
I heard her pray the night Chicago died
Brother, what a night it really was
Brother, what a fight it really was
Glory be

I heard my momma cry
I heard her pray the night Chicago died
Brother, what a night the people saw
Brother, what a fight the people saw
Yes, indeed

And the sound of the battle rang
Through the streets of the old East Side
'Til the last of the hoodlum gang
Had surrendered up or died

There was shouting in the street
And the sound of running feet
And I asked someone who said
'Bout a hundred cops are dead

I heard my momma cry
I heard her pray the night Chicago died
Brother, what a night it really was
Brother, what a fight it really was
Glory be

I heard my momma cry
I heard her pray the night Chicago died
Brother, what a night the people saw
Brother, what a fight the people saw
Yes, indeed

Then there was no sound at all
But the clock up on the wall
Then the door burst open wide
And my daddy stepped inside
And he kissed my momma's face
Then brushed her tears away

I heard my momma cry
I heard her pray the night Chicago died
Brother, what a night it really was
Brother, what a fight it really was
Glory be

I heard my momma cry
I heard her pray the night Chicago died
Brother, what a night the people saw
Brother, what a fight the people saw
Yes, indeed

The night Chicago died
The night Chicago died
Brother, what a night it really was
Brother, what a fight it really was
Glory be

The night Chicago died
The night Chicago died

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1. There never was such a night in Chicago. Most of the killing took place when rival gangs fought it out, not between police and gang members. The British songwriters had never been to Chicago and knew very little of the history. It's one of those stories that you would like to be true but sometimes real history sucks.

2. It is often thought to be a backhanded reference to the Chicago riots of 1968 but there's no evidence to support that theory and by 1974 the memory had faded.

Soccer Team Wins by Scoring on Itself

 
Friday's Urban Legend: TRUE

This sounds so much like an urban legend that it's astonishing to learn it really happened. The story is covered on snopes.com [Football Follies].

It was a match between Barbados and Grenada in 1994. In order to advance to the finals, Barbados had to win by at least two goals. Near the end of the game Barbados was ahead 2-0 when an error resulted in an own goal by Barbados. With the score now 2-1 the Barbados team was threatened with elimination.

Here comes the funny part. The tournament rules state that in the event of a tie the game will be decided by sudden death overtime and, for the purposes of calculating points, the winner will be rewarded as though they had won by a score of 2-0. In the 87th minute, the Barbados team deliberately scored on themselves in order to tie the game and send it into overtime.

The Granada team realized what was going on and tried to score on themselves to avoid overtime and advance to the finals. (Winning 3-2 would not allow the Barbados team to advance.) Thus you have this bizarre scene where a team is trying to score in its own net while the opposition is defending their opponent's goal.

Here's a video of some of the action. Listen to the commentators. It sounds like a scene written by Monty Python.

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Species Diversity

 
Some of you might recall my series of postings last year on the top Science questions. One of them was What Causes Species Diversity?. This is an important unanswered question in evolutionary biology even if it's conflated with speciation. We don't really have a good handle on what causes speciation.

That doesn't mean that we are completely ignorant. There are several candidates that, singly or in combination, account for much of what we understand about speciation and diversity. I'd like to quote Richard Dawkins from Unweaving the Rainbow since, as an admitted adaptationist, his view carries much more weight than that of a pluralist. (The reason will become apparent.) Here's how Dawkins describes the problem ...

The standard neo-Darwinian view of the evolution of diversity is that a species splits into two when two populations become sufficiently unalike that they can no longer interbreed. Often the populations begin diverging when they chance to be geographically separated. The separation means that they no longer mix their genes sexually and this permits them to evolve in different directions. The divergent evolution might be driven by natural selection (which is likely to push in different direction because of different conditions in the two geographical areas). Or it might consist of random evolutionary drift (since the two populations are not genetically held together by sexual mixing, there is nothing to stop them drifting apart). In either case, when they have evolved sufficiently far apart that they no longer interbreed even if they were geographically united again, they are defined as belonging to separate species.

Either, or both, of the two main mechanisms of evolution—natural selection and random genetic drift—can lead to speciation and diversity.

One could also argue that diversity depends ultimately on mutation. In this case, the main role of natural selection and random genetic drift is to reduce diversity by eliminating unfit and neutral alleles.

This has always been similar to my understanding of speciation and diversity. I was surprised, therefore to learn that one of my colleagues at the University of Toronto, Spencer Barrett, doesn't think random genetic drift plays a role in speciation [see Darwinism at the ROM]. Barrett is one of the featured presenters in a video at the Darwin exhibit at the Royal Ontario Museum.

In a display on the evolution/creation controversy, I copied down the following statement ...

Darwin's Theory of Evolution by Natural Selection is the only scientific explanation for the spectacular diversity of life on Earth.

So, here's the question of the day. Do you agree with that statement? Do you agree that natural selection is the only scientific explanation of diversity? Spencer Barrett seems to agree. Richard Dawkins would not agree. What do you think?¹

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1. If you disagree with the statement then please try and explain why it is featured so prominently in the Darwin exhibit. Is this an example of framing, or ignorance?

Darwin: The Evolution Revolution

 


My how time flies. It was almost four months ago that the The Evolution Revolution opened at the Royal Ontario Museum (ROM) here in Toronto. The ROM is only ten minutes from my office so I wasn't in any particular rush to see the exhibit. After all, it wasn't going to close until August 4th.

Now August 4th is almost here and I still hadn't made the effort—until yesterday, that is. Ms. Sandwalk and I went and got a delightful dose of Charles Darwin.

For me, the most exciting exhibit was Darwin's red notebooks, especially the page with the tree and "I think" at the top of the page. It was awesome just realizing that Charles Darwin himself wrote those words 170 years ago. Ms. Sandwalk was not nearly as impressed (those messy things?). She liked the Wedgewood china representing the better side of the Darwin family.

There were lots of examples of Darwin's original collection. Mostly plants and birds and some fossils. Seeing an old photograph of the Sandwalk was another highlight.

I've heard two main criticisms of the exhibit. The first is that there's too much to read. I agree that there's a lot to read but it's mostly well written and informative. The majority of people at the exhibit were being appropriately selective in their reading. It wasn't a serious problem. The second criticism is the American slant in some of the exhibits; notably those that address the evolution/creation controversy. It was noticeable but most of the people there just took it as quaint to learn that some states want to put stickers in textbooks.

The biggest pain for me was having to watch and listen to theistic evolutionists explain—in three separate video presentations—why there's no conflict between evolution and religion. Ken Miller did an okay job but Francis Collins looks and talks like a used car salesman, in my humble opinion.

There was one other problem but I'm saving that for another posting.

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I'm Your Man

 
Here's a reason why you should be my friend and invite me to all those parties that I never seem to hear about until they're over. In case of trouble, I make an excellent human shield!

65%

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[Hat Tip: GrrlScientist, My Body Makes a Really Crappy Human Shield]

I'm so glad I took Latin

 
It means I can understand Christopher Taylor at Catalogue of Organisms when he writes about The Gender of a Table.

Eat your hearts out, all you speakers of living languages!

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[Photo Credit: AP Photo]

Nobel Laureate: Joshua Lederberg

 
 

The Nobel Prize in Physiology or Medicine 1958.

"for his discoveries concerning genetic recombination and the organization of the genetic material of bacteria"

Joshua Lederberg (1925 - 2008) received the Nobel Prize in Physiology or Medicine for discovering that not only do bacteria have genes, they also have sex and recombination. Bacterial sex consists of passing genes from one individual to another by a method known as conjugation. The bacteria are joined by a long hollow tube [Monday's Molecule #82].

In 1958 Lederberg was only 33 years old, making him one of the youngest Nobel Laureates. He died only a few months ago, prompting comments on several blogs (e.g. Joshua Lederberg) and a special citation tribute from John Dennehy [Joshua Lederberg].

The New York Times called him one of the 2oth century's greatest scientists—an honor that would only be contested by those who don't know him. The New York Times obituary goes on to say,

Dr. Lederberg’s discovery that bacteria engage in sex created new understandings of how bacteria evolve and acquire new traits, including resistance to antibiotic drugs. A founder of the field of molecular biology, he helped lay the foundations for many biological revolutions, including biotechnology.

Dr. Lederberg moved in diverse worlds. A brilliant analyst and visionary, he led early inquiries into the possibility of computer intelligence, theorized about alien life in distant galaxies and advised American presidents for a half century. He also wrote a weekly newspaper column, “Science and Man.” His ideas were often decades ahead of the conventional wisdom.

Lederberg shared the 1958 prize with George Beadle and Edward Tatum [Nobel Laureates: George Beadle and Edward Tatum].

The presentation speech was delivered by Professor T. Caspersson, member of the Staff of Professors of the Royal Caroline Institute.

THEME:
Nobel Laureates

Your Majesties, Your Royal Highnesses, Ladies and Gentlemen.

One of the most striking features in the development of science during the past two decades is the rapid advance in the diverse fields of biology. Here the tempo of progress continues to quicken. The research contains a vast and complex material whose major portion remains the business of specialists. The observations they make in the laboratories of basic research are apparently distant from the needs of the everyday world. But again and again we discover how short the step is from these basic findings to advances in medical therapy or diagnosis that are of importance to all of us in our daily lives.

For an example we need turn only to the previous Nobel Prize in Genetics, awarded to H.J. Muller for his discovery that X-ray irradiation can change the genetic material in living organisms. The discovery was made, and the detailed analysis carried out, in a type of small fruit fly, and at the time that the prize was awarded, perhaps gave the impression that its greatest interest was in its contribution to basic principles. Now, with the era of atomic energy upon us, we all know that the genetic risks from the high-energy radiation threatening man, belong to the things I just mentioned, of vital and immediate importance to us all.

Experimental genetics is a branch of modern biology in which progress has been especially rapid. The methods and points of view of this and its allied disciplines are indispensable for many fields of medicine today. This rapidly increasing importance of experimental genetics and cell research is easily understood. The research is now reaching towards the very elements of heredity, the structures within each cell that control its life and its behavior, and thus ultimately determine the development of the whole organism. Now we begin to see what the fundamental biological processes may be. That discoveries in this field have consequences in many others is surely no surprise to any of us.

The work of all three winners of the prize lies on this plane. Their studies are concerned with the very basis of heredity and the manner in which the genes function. That hereditary characters are transmitted from parents to offspring via special elements in the ovum and spermatozoon, the so-called genes, has long been known. The organism that develops from the fertilized ovum receives certain of the parents' characters through these genes, and the genetic material in the fertilized egg, that is to say, all these genes combined, determines the development of the organism.

The cells that together constitute an organism as a rule contain a complete set of genes characteristic of the species. In ordinary cell division these are divided and subsequently distributed equally between the two daughter cells. At fertilization, the different genetic materials from two individuals unite in the fusion of the egg and the sperm. The result of the sexual reproduction is to provide offspring with genes from both of their parents. In this way, individuals with differing combinations of characters originate. And just herein lies the biologic value of the sexual process, which can be traced throughout practically the entire animal and plant kingdoms. Without the renewal such a constant recombination of characters involves, an animal or plant species would not be able to survive the struggle for existence.

The characters, which are transmitted by the genes from generation to generation, present a picture of bewildering multiplicity. This very multiplicity of the genes' effects made it difficult to attack experimentally the problem of their structure and manner of functioning; it was impossible to trace straightforward lines that could serve as a background for an experimental study.

The situation was radically changed by Beadle and Tatum, who, through a daring and astute selection of experimental material, created a possibility for a chemical attack upon the field. Circumstantial evidence pointed to a similarity of the genetic mechanisms throughout the entire plant and animal kingdoms. Beadle and Tatum selected as object for their investigations an organism with very simple structure, a bread mold, Neurospora crassa, which is far easier to work with, in many respects, than the objects usually studied in genetics. It is able to synthesize its body substances from a very simple culture medium: sugar, salts, and a growth factor. When cultures of the mold are exposed to X-ray irradiation, mutations - that is, changes in individual genes - result as they do in other organisms. By producing a large number of such mutations and by means of an analysis of the material, which should serve as a model for analytic research, Beadle and Tatum succeeded in demonstrating that the body substances are synthesized in the individual cell step by step in long chains of chemical reactions, and that genes control these processes by individually regulating definite steps in the synthesis chain. This regulation takes place through formation by the gene of special enzymes. If a gene is damaged, for example through irradiation-induced mutation, the chain is broken, the cell becomes defective - and may possibly be unable to survive. Even in the formation of comparatively simple substances the steps in the synthetic chain are many, and consequently the number of collaborating genes large. This explains simply why gene function appeared to be so impossibly complex. The discovery provides our best means of penetrating into the manner in which the genes work and has now become one of the foundations of modern genetics. Its importance extends over other fields as well, however.

Especially valuable is the possibility it affords for detailed study of the processes of chemical synthesis in the living organism. In Neurospora material it is easy by means of X-ray irradiation to produce quickly a large number of strains in which the function of different individual genes has been disturbed. By comparing these strains we are able to determine in detail how the different stages of synthesis succeed one another when the cell's substances are formed. Beadle and Tatum's technique has become one of our most important tools for the study of cell metabolism and has already yielded results of significance to various problems in the fields of medicine and general biology.

The successful results with Neurospora also provided an incentive to continued efforts to probe the basic processes further with the aid of even simpler organisms. The bacteria are even more primitive than Neurospora. The bacterial genetic mechanism was little known; many even doubted that they had one comparable with that of the higher forms of life. Tatum extended the approaches worked out in Neurospora to the bacteria. When Lederberg came to Tatum's laboratory as a young student, they discovered that different bacterial strains could be crossed to produce an offspring containing a new combination of genetic factors. This is the counterpart of the normal sexual fertilization in higher organism; it is usually considered preferable here, however, to speak of «genetic recombination». Bacterial genetics has been developed, primarily through the efforts of Lederberg and his coworkers, into an extensive research field in recent years. He also contributed further evidence that the genetic mechanism of the bacteria corresponds to that of the higher organisms. Moreover, thanks to their simple structure and extraordinarily rapid growth, bacteria provided new and excellent possibilities for a more profound study of the genetic mechanisms. Lederberg has made many contributions in this field. Particularly important is his discovery that sexual fertilization is not the only process leading to recombination of characters in bacteria. Bits of genetic material can, if they are introduced into the bacterial body, become part of the genetic material of the bacterial cell and thus change its constitution. This is usually termed «transduction», and it is the first example demonstrating that it is possible experimentally to manipulate an organism's genetic material and to introduce new genes into it and, the organism new characters. Studies in this are now being carried out in many laboratories in different parts of the world.

The transduction process and certain other related phenomena have greatly improved our means of penetrating experimentally into the basic processes of cell function and cell growth. In all probability they will also prove to have great significance in the study of the function of the higher organisms under normal and pathologic conditions. Work in this field, carried out in laboratories throughout the world, has already greatly expanded our knowledge of the basic processes in bacteriophage infection and of the mechanism of virus infection. The observations also have opened the way to a more profound understanding of certain growth problems. Certainly cancer research will be increasingly influenced by the evolution of our knowledge of the organization of the genetic material and its manner of functioning, that has been made possible by the discoveries of this year's three winners of the Nobel Prize in Physiology or Medicine.

Doctor Beadle and Doctor Tatum. In consequence of an exemplary collaboration in which each has complemented the other to unusual advantage, it has been given to you to make discoveries of fundamental importance to our understanding of the mechanism of Life's processes.

Doctor Lederberg. At first in collaboration with your co-winners of this year's Nobel Prize, and subsequently, along ever-broadening independent lines, you have made possible the advance of research to the structure of the actual genetic material.

Gentlemen. In recognition of your outstanding contributions to science the Karolinska Institute has awarded you this year's Nobel Prize in Physiology or Medicine. On behalf of the Institute I wish to extend the warmest congratulations from your colleagues on your brilliant achievements.

It is my honoured privilege now to invite you to receive your awards from the hands of His Majesty the King.

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Talk.origins Is Back

 
The newsgroup talkorigins is back online. It's been down since last Friday but I wasn't aware of the problem until Sunday. I couldn't fix it myself so I had to get in touch with our esteemed king and moderator, DIG, and that took some time.

He has now fixed the problem so post away! Fortunately, there were no serious injuries except for John Wilkins, who was forced to drink scotch [Email hiatus].

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Ohmygod! Not that "Framing" Thing again?

Yes, it's the old framing argument rearing its ugly head. I know, I know, we've probably said just about everything that could be said and we should just agree to disagree. Nisbet and Mooney want us to "spin" science in the interests of promoting their favorite policies. Scientists resist because that's not what science does.

Now we have a posting by Philip H. on The Intersection that makes the issue clearer than ever before. I'm sure Nisbet and Mooney are happy.

Philip H. is discussing a Washington Post article about American voters [The American Voter]. Here's what he says about the scientific aspects of the study ...

Equally interesting to me as a scientist and framer of scientific messages, is how the writer talked about the academic work she reported on. She talks about academic conclusions from a multi-year study "couched in academic understatement." My guess is the social scientists here were doing the usual, scientifically correct thing and describing their data and conclusions within the statistically appropriate confidence intervals. Probably something along the lines of: "our results appear to apply, statistically to the American population within a 95% probability. Alternately, bootstrapped ANCOVA without regression might have yielded..." That may be correct in a talk to the National Academy of Public Administration, but somehow it always leads newspaper reporters.... to wonder what the academics area really saying, and try to get "other sides" of the story. In other words - this is bad framing for an general audience. Thankfully, in this particular case, the "fairness in reporting" stchick works - and it contributes to the reporting. In the case of Creationism/Intelligent Design vs. Evolution, it doesn't.

This is a very important point, one that the "framers" have never made explicitly. The scientific reporting of information may be okay for scientists but when you're talking to non-scientists you've got to be non-scientific. The "scientifically correct" approach just won't do for the hoi-polloi.

I know, I know, scientists hate to make firm conclusions when the data do contain the possibility of error or omission. They even hate to make black and white statements when there is a really LOW probability of error. I took those courses too.

I'm so glad he took the courses. Now he knows how scientists are supposed to behave.

But this is a public policy debate. It is about how to get American voters more engaged, or if they can be more engaged. And if the truth is Americans are one or two issue voters who inherit their political allegiances like a house or a trust fund, those facts tells us something. And no one will fault the scientists for saying so directly, and with out describing the confidence interval.

It's not true that "no one will fault the scientists." I will fault the scientists for lying or distorting the scientific truth by omitting the qualifications. And I'm not alone. Many other scientists think the same way and that's why scientists are not jumping on the spin framing bandwagon (see Going Public with the Scientific Process for a better approach).

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[Photo Credit: Blick Art Materials]

We're Really, Really Sorry

 
This is an old video from This Hour Has 22 Minutes. I'm sorry to be posting it now but GrrlScientist put it up on her blog and I just couldn't resist. Again, my sincere apologies to all my American friends for what Canada has done to you.

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Epigenetics in New Scientist

 
As a general rule, the magazine New Scientist does an acceptable job of covering the issues that I'm familiar with. Sure, from time to time they screw up big time, but the good articles outweigh the bad.

The July 12-18 issue has one of the big time screw-ups. There is it on the cover, "Forget Genes: The strange inheritance from your parents." The article inside is by Emma Young, an Australian writer for New Scientist who has mostly specialized in stories about space. The title of the article in the magazine is "Strange Inheritance" and the title on the website is Rewriting Darwin: The new non-genetic inheritance

HALF a century before Charles Darwin published On the Origin of Species, the French naturalist Jean-Baptiste Lamarck outlined his own theory of evolution. A cornerstone of this was the idea that characteristics acquired during an individual's lifetime can be passed on to their offspring. In its day, Lamarck's theory was generally ignored or lampooned. Then came Darwin, and Gregor Mendel's discovery of genetics. In recent years, ideas along the lines of Richard Dawkins's concept of the "selfish gene" have come to dominate discussions about heritability, and with the exception of a brief surge of interest in the late 19th and early 20th centuries, "Lamarckism" has long been consigned to the theory junkyard.

Now all that is changing. No one is arguing that Lamarck got everything right, but over the past decade it has become increasingly clear that environmental factors, such as diet or stress, can have biological consequences that are transmitted to offspring without a single change to gene sequences taking place. In fact, some biologists are already starting to consider this process as routine. However, fully accepting the idea, provocatively dubbed the "new Lamarckism", would mean a radical rewrite of modern evolutionary theory. Not surprisingly, there are some who see that as heresy. "It means the demise of the selfish-gene theory," says Eva Jablonka at Tel Aviv University, Israel. "The whole discourse about heredity and evolution will change" (see "Rewriting Darwin and Dawkins?").

Ugh.

This is, of course, nonsense. The article is all about epigenetics but it's a very broad definition of epigenetics. One that makes you cringe when you read ...

Epigenetics deals with how gene activity is regulated within a cell - which genes are switched on or off, which are dimmed and how, and when all this happens. For instance, while the cells in the liver and skin of an individual contain exactly the same DNA, their specific epigenetic settings mean the tissues look very different and do a totally different job. Likewise, different genes may be expressed in the same tissue at different stages of development and throughout life. Researchers are a long way from knowing exactly what mechanisms control all this, but they have made some headway.

Some headway? That's quite an understatement isn't it? Emma Young then goes on to describe some of that mysterious headway. Turns out that methylation of DNA, histone modification, and RNAi are the prime suspects in the upcoming paradigm shift. Who woulda guessed?

According to the New Scientist article, there are a host of scientists who are ready to abandon the gene as the unit of evolution. These include Eva Jablonka from Tel Aviv University, Israel and Russell Bonduriansky, at the University of New South Wales in Sydney, Australia. But wait. What does Richard Dawkins have to say about this?

For Bonduriansky the accumulating evidence calls for a radical rethink of how evolution works. Jablonka, too, believes that "Lamarckian" mechanisms should now be integrated into evolutionary theory, which should focus on mechanisms, rather than units, of inheritance. "This would be very significant," she says. "It would reintroduce development, in a very direct and strong sense, into heredity and hence evolution. It would mean the pre-synthesis view of evolution, which was very diverse and very rich, can return, but with molecular mechanisms attached."

That needn't necessarily mean an end to the idea of the gene as the basic unit of inheritance, or Richard Dawkins's selfish gene, according to some. "I don't think it violates the basic concept that Dawkins articulated," says Eric Richards, at Washington University in St Louis, Missouri. "Epigenetic marks can also be viewed as part of that basic unit in a more inclusive definition of a gene," he says.

What does Dawkins himself think? "The 'transgenerational' effects now being described are mildly interesting, but they cast no doubt whatsoever on the theory of the selfish gene," he says. He suggests, though, that the word "gene" should be replaced with "replicator". This selfish replicator, acting as the unit of selection, does not have to be a gene, but it does have to be replicated accurately, the occasional mutation aside. "Whether [epigenetic marks] will eventually be deemed to qualify as 'selfish replicators' will depend upon whether they are genuinely high-fidelity replicators with the capacity to go on for ever. This is important because otherwise there will be no interesting differences between those that are successful in natural selection and those that are not." If all the effects fade out within the first few generations, they cannot be said to be positively selected, Dawkins points out.

That's a relief. All epigenetic phenomena are unstable and/or reversible and Dawkins isn't buying any of this pseudoscientific nonsense about its effect on evolution. Now if we could only convince the science writers to pay more attention to the skeptics and less attention to the self-serving "revolutionaries."

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Epigenetics Revisited

I'm still struggling with the concept of epigenetics [see Epigenetics]. Most of the modern definitions are so broad that they become meaningless. It's impossible to distinguish between epigenetics and plain old regulation of gene expression.

One of my colleagues, Craig Smibert, was so annoyed by my questions about epigenetics that he pointed me to a series of articles in Nature in the hopes it would shut me up. The relevant article is Perception of Epigenetics by Adrian Bird (Bird 2007).

It's not going to help. After describing several examples like methylation and histone modifications, Bird then points out that these modifications are not necessarily stable ...

So how accurately transmitted should an epigenetic mark be? Variation due to faulty copying is compounded by current evidence that all histone modifications, as well as DNA methylation itself, can be abruptly removed during development, thereby preventing the persistence of these modifications in a heritable epigenetic sense.

In other words, an epigenetic phenomenon doesn't really need to be heritable in order to qualify as epigenetic.

Furthermore, an epigenetic phenomenon doesn't even have to be passed on to progeny to qualify.

The restrictiveness of the heritable view of epigenetics is perhaps best illustrated by considering the brain. A growing idea is that functional states of neurons, which can be stable for many years, involve epigenetic phenomena, but these states will not be transmitted to daughter cells because almost all neurons never divide.

That's not very helpful. It's beginning to look like any activation or repression of eukaryotic genes will count as epigenetics. (According to some, it doesn't have to be eukaryotes. There is epigenetic regulation in bacteria as well, Casadesús and Low (2006).)

Here's the definition ...

Given that there are several existing definitions of epigenetics, it might be felt that another is the last thing we need. Conversely, there might be a place for a view of epigenetics that keeps the sense of the prevailing usages but avoids the constraints imposed by stringently requiring heritability. The following could be a unifying definition of epigenetic events: the structural adaptation of chromosomal regions so as to register, signal or perpetuate altered activity states.

Does this include simple activation and repression of genes during development in the manner of control of lac operon expression? You betcha.

Bird may be thinking mostly of histone modifications and DNA methylation but he's well aware of the fact that these are often consequences, not causes, of activation and repression. He says,

For example, transcriptional activation through sequence-specific DNA-binding proteins brings in histone acetyltransferases, which then epigenetically adapt the promoter region for transcription (for histone acetyl groups, although ephemeral, would now be epigenetic).

So we're right back where we started, Craig will not be happy. Just about anything that modifies or regulates gene expression in eukaryotes (multicellular?) counts as epigenetics.

One could ask, what's the point? Why create a special word to describe regulation of gene expression in eukaryotes (and prokarotes) using mechanisms that we've known about for thirty years?

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Bird, A. (2007) Perceptions of epigenetics. Nature 447:396-398. [doi:10.1038/nature05913]

Casadesús, J. and Low, D. (2006) Epigenetic Gene Regulation in the Bacterial World. Microbiology and Molecular Biology Reviews 70:830-856. [doi:10.1128/MMBR.00016-06

What Breed of Liberal Are You?

 

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[Hat Tip: Mike Dunford (Social Justice Crusader)]

Monday's Molecule #82

 
Today's molecule isn't exactly a molecule. Your task is to figure out what's going on in the photograph. Be as specific as possible using proper terminology—remember, this is a family blog.

There's a connection between today's molecule and a Nobel Prize. Sometimes I just can't identify a molecule that points to a Nobel Laureate so I have to use something else. This is going to get harder and harder as I run out of "easy" Nobel Prizes.

The first person to correctly identify what's happening in the photo 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 three ineligible candidates for this week's reward. You know who you are.

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 winner is Steve Matheson who knew that the photograph represented conjugating bacteria (group sex) and the Nobel Laureate is Joshua Lederberg (1958). Congratulations Steve!

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[Photo Credit: Researchers Trade Insights About Gene Swapping by Elizabeth Pennasi Science 305:334 - 335. DOI: 10.1126/science.305.5682.334]