Mitotic Recombination

 
It is widely believed that recombination, or crossing over, only occurs at meiosis in diploid eukaryotes. Most textbooks reinforce this belief by associating crossovers with chiasmata, which are only seen at meiosis.

In spite of the textbook claims, most people are well aware of the fact that recombination takes place in somatic cells. After all, it's the basis of most recombinant DNA technology and underlies many of the mechanisms that cause cancer. Furthermore, some developmental processes, such as immunoglobulin gene rearrangements require recombination in somatic cells.

Mitotic recombination has been known to occur since the 1930s when it was used for fate mapping in Drosophila so it's somewhat surprising that crossing over is so intimately connected with meiosis in the textbooks. The frequency of mitotic crossing over may be lower than that seen during meiosis, although the differences may not be great in most species.

In yeast, the frequency of recombination during meiosis can be 10,000 times greater than the frequency of crossing over in somatic cells but that's partly because meiotic recombination is very high in yeast cells. Perhaps they have been selected in vitro for high rates of recombination.

Why does recombination occur in mitotic cells? Probably for the same reason it occurs during meiosis—it's a form of DNA repair.

There's a short review of mitotic recombination in the lastest issue of PLoS Genetics [Mitotic Recombination: Why? When? How? Where?]. Let's try and put an end to the false idea that recombination and crossing over only takes place during meiosis.

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Levels of Selection

 
There's an interesting article in the latest issue of New Scientist. Bob Holmes writes about The selfless gene: Rethinking Dawkins's doctrine.

Evolutionary success is all about looking out for number one - or so most biologists would tell you. The genes that do the best job of passing themselves along to the next generation, whether by brute selfishness or canny cooperation, are the ones that flourish - a view most memorably championed by Richard Dawkins more than 30 years ago in his bestselling book The Selfish Gene.

This relentless focus on the gene may not tell the whole story, however. A small but growing coterie of evolutionary biologists argue that it leaves us blind to crucial evolutionary processes at higher scales - among groups, species and even whole ecosystem. If they are right, the popular view of evolution and the biological world needs a radical shake-up.

Almost everyone agrees that the gene's-eye view works perfectly well most of the time. "It's dominated the field, and dominated for a long time," says Michael Ruse, a philosopher of science at Florida State University in Tallahassee. Indeed, many biologists think the selfish-gene concept can explain all the intricacies thrown up by evolution, and not just the obviously selfish ones.

The article is better than most. It gives an adequate overview of group selection and species selection (sorting).

However, before reading on you should be aware of two false notions that are being perpetuated. First, there's more to evolution than adaptation and selfish genes. Not all genes are selfish and even at higher levels species sorting may occur in the absence of species selection.

Second, the concept of the selfish gene has been very important in evolutionary theory. Far more important, I think, than most people realize. But it is not correct to say that it has dominated the field, or that it's the current dogma. If you consult any evolutionary biology textbook you'll find that "selfish gene" barely gets mentioned. Almost everything is explained by considering the individual organism as the unit of selection. Dawkins has failed to convince any but a handful of evolutionary biologists that the gene perspective is a better way of looking at evolution.

The article closes with ....

It is still too early to know whether group, species and ecosystem-level selection are major evolutionary forces or merely minor curiosities - baroque ornaments on the central edifice of individual or gene-level selection. But the dominance of the "selfish gene" in evolutionary thought is facing its strongest challenge in many years.

This is a good way of putting it. Hierarchical theory is an interesting development and it is making some headway but it's fair to say that most evolutionary biologists don't think of group selection and species selection as major players.

However, the dominant thinking is that it's the individual and not the gene that forms the proper unit of selection. And the greatest challenge to the dominance of selection at the level of the either the gene or the individual is neither group selection or species selection, it's random genetic drift.

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Note: People get confused about the meaning of The Selfish Gene. Just because we talk about population genetics and changing frequencies of alleles does not mean that we are adopting Dawkins' perspective. He explains what he means by "selfish gene" in the opening chapter of The Extended Phenotype.

The thesis that I shall support is this. It is legitimate to speak of adaptations as being "for the benefit of" something, but that something is best not seen as the individual organism. It is a smaller unit which I call the active germ-line replicator. The most important kind of replicator is the "gene" or small genetic fragment. Replicators are not, of course, selected directly, but by proxy; they are judged by their phenotypic effects. Although for some purposes it is convenient to think of those phenotypic effects as being packaged together in discrete "vehicles" such as individual organisms, this is not fundamentally necessary. Rather, the replicator should be thought of as having extended phenotypic effects, consisting of all its effects on the world at large, not just its effects on the individual body in which it happens to be sitting.

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Examples of Accelerated Human Evolution

Gregory Cochran and Henry Harpending claim that human evolution has accelerated in the last 10,000 years. In one sense this has to be correct since the number of humans is increasing exponentially and that means far more mutations are occurring every generation. Many of those new mutations are contributing to a significant increase in variation.

But that's not what they mean. They claim that adaptations have increased. When they talk about accelerated human evolution they are mostly talking about an increase in natural selection.

For those of you who have not read the book, I thought I'd give you some of the examples that feature prominently in the opening chapter.

... when humans hunted big game 100,000 years ago, they relied on close-in attacks with thrusting spears. Such attacks were highly dangerous and physically taxing, so in those days, hunters had to be heavily muscled and have thick bones. That kind of body had its disadvantages—if nothing else, it required more food—but on the whole, it was the best solution in that situation. But new weapons like the atlatl (a spearthrower) and the bow effectively stored muscle-generated energy, which meant that hunters could kill big game without big biceps and robust skeletons. Once that happened, lightly built people, who were better runners and did not need as much food, became competitively superior. A heavy build was yesterday's solution: expensive, but no longer necessary. (p. 3)

With the invention of nets and harpoons, fish became a more important part of the diet in many parts of the world., and metabolic changes that better suited humans to that diet were favored. (p. 4)

Close-fitting clothing provided better protection against cold, allowing people to venture farther north. In cool areas, people needed fewer physiological defenses against low temperatures, while in the newly settled colder regions they needed more such defenses, such as shorter arms and legs, higher basal metabolism, and smaller noses. (p. 4)

With the advent of new methods of food preparation, such as the use of fire for cooking, teeth began to shrink, and they continued to do so over many generations. Pottery, which allowed storage of liquid foods, accelerated that shrinkage. (p. 4)

As the complexity of human speech approached modern levels, there must have been selection for changes in hearing (both changes in the ear and in how the brain processes sounds) that allowed better discrimination of speech sounds. Think of the potential advantages in being just a bit better at deciphering a hard-to-understand verbal message than other people: Eavesdropping can be a life-or-death affair. (p. 4)

... we believe that the obvious difference between racial groups are linked to gene variants that have recently increased in fitness and had major fitness effects. Blue eyes, found only in Europeans and their near neighbors, are a result of a new version of the DNA that controls the expression of OCA2 that has undergone strong selection, at least in Europe. (p. 18)

Dry earwax is common in China and Korea, rare in Europe, unknown in Africa: The gene variant underlying dry earwax is the product of strong recent selection. (p. 18)

We can confidently predict that many (perhaps most) as yet unexplained racial differences are also the product of recent selection. For example, we argue that the epicanthic eyelid found in the populations of northern Asia is most likely the product of strong and recent selection. (p. 18)

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Atheist Buses Will Run in Ottawa

 
Ottawa city council voted last month to ban the atheist ads from OC Transpo buses.¹ Last night they voted 13-7 to allow the ads after city solicitor Rick O'Connor told them the ban is an unreasonable infringement of free speech [City blesses atheist ads].

Transit officials made the decision after receiving four complaints from the public, but O'Connor said in the end the city's argument may not hold up in court.

"Based on the information available at this time, it appears that the city may not be able to justify its refusal of the proposed advertising on the basis that it is offensive, and consequently, it may be found to be an unreasonable infringement of the association's freedom of expression under Section 2(b) of the Charter," the memo says.

"If the decision to refuse the ads was based solely on the four complaints received from the public, it is likely that this decision will be found to be unreasonable and lacking in proportionality, and therefore not justifiable under Section 1 of the Charter."

Thanks to the Humanist Association of Ottawa for standing up for freedom of expression.

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1. Technically, they did not ban the ads. Instead, they failed, in a tie vote, to overturn the decision of OC Transpo. That decision has now been overturned in a second vote and the ads will run.

Teach Your Children Well

 
Chelsea Juman is one of the Intel Baby Nobelist Finalists on the Scientific American website.

According to her study, if you drank underage as a teenager you should never tell your children 'cause, if you do, they'll think it's OK.

Well, it's too late for me but all you young people out there better pay attention. You need to start lying to your children from a very young age. Whatever you do, pretend you never touched a glass of wine or a bottle of beer before you were 21 years old.¹ Don't even think about drugs. Lie through your teeth. That'll make 'em respect you.

As soon as they turn 21 you can take them out to a bar and have a long talk about responsible drinking.

Better not tell them about sex either. Abstinence is the only answer.

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1. If you're an American. If you live in any other country you can tell them you drank when you were much younger—16 in Italy, Germany, or France, for example.

In the Quality of Heatlh Care Journalism

 
A survey of members of the Association of Health Care Journalists (AHCJ) reaches the following conclusions [U of Minnesota professor authors report the state of health care journalism] ....

• Ninety-four percent of survey respondents say the bottom line pressure in media organizations is seriously hurting the quality of news coverage of health care issues
• Forty percent of staff reporters in the survey say the number of health reporters at their organization has gone down since they've been there, and 11 percent say they personally have been laid off over the past few years due to downsizing.
• Thirty-nine percent of respondents who are still in the business believe it is at least somewhat likely that their position will be eliminated in the next few years
• Nearly nine in ten (88 percent) survey respondents think health care coverage leans too much toward short "quick hit" stories, and two-thirds (64 percent) say the trend toward shorter stories has gotten worse in the past few years
• A majority of respondents (52 percent) say there is too much coverage of consumer or lifestyle health, and too little of health policy (70 percent), health care quality (70 percent) and health disparities (69 percent)

So, the quality of health care journalism has declined. This isn't earth shattering news.

I bet that 100% of health care journalists will say that it's not their fault.¹

"Real" science journalists are different. Most of them say they are doing a terrific job and the bad science reporting is all due to other journalists writing about science.

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1. Of course it's not all their fault but when a bad health care article gets published you can't blame it all on the editors.

On the Demise of Religion

 
Michael Spencer writes about The coming evangelical collapse in The Christian Science Monitor.

We are on the verge – within 10 years – of a major collapse of evangelical Christianity. This breakdown will follow the deterioration of the mainline Protestant world and it will fundamentally alter the religious and cultural environment in the West.

Within two generations, evangelicalism will be a house deserted of half its occupants. (Between 25 and 35 percent of Americans today are Evangelicals.) In the "Protestant" 20th century, Evangelicals flourished. But they will soon be living in a very secular and religiously antagonistic 21st century.

This collapse will herald the arrival of an anti-Christian chapter of the post-Christian West. Intolerance of Christianity will rise to levels many of us have not believed possible in our lifetimes, and public policy will become hostile toward evangelical Christianity, seeing it as the opponent of the common good.

Millions of Evangelicals will quit. Thousands of ministries will end. Christian media will be reduced, if not eliminated. Many Christian schools will go into rapid decline. I'm convinced the grace and mission of God will reach to the ends of the earth. But the end of evangelicalism as we know it is close.

I agree with him but I think he's mistaken if he thinks that belief in God will survive the collapse of the evangelical right.

Evangelical Christianity is in trouble because its very core is being challenged, not because of its association with old-fashioned morality.

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[Hat Tip: RichardDawkins.net]

Darwin First Day Cover

 
Heather sent me a package of stuff from the Royal Mail, including a complete set of Darwin stamps and various brochures. She included a magazine on Darwin and a first day cover (see below).

I bet there aren't any other bloggers who have a first day cover. Eat your hearts out.

Thanks Heather, I owe you one.

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Nobel Laureate: Fred Sanger

 

The Nobel Prize in Chemistry 1958.

"for his work on the structure of proteins, especially that of insulin"


Frederick Sanger (1918 - ) won the Nobel Prize in Chemistry for developing techniques to sequence proteins and for determining the amino acid sequence of insulin. This was Sanger's first Nobel Prize. The second was for developing the chain termination method of DNA sequencing.

From today's perspective it's difficult to appreciate the importance of Sanger's work on protein sequencing. His work confirmed that the functions of proteins depended on the sequence of amino acid residues in a polypeptide chain and it confirmed that every molecule of a protein had the same amino acid sequence. Recall that in 1958 the relationship between the nucleotide sequence of a gene and the amino acid sequence of a protein was still being worked out and the genetic code had not been discovered.

Sanger's work led to the widespread use of sequencing technology which, in turn, led to the discovery of differences between species. It wasn't long before phylogenetic trees based on amino acid sequences were being published.

Some Nobel Prizes are given for quick discoveries but this isn't one of those. Sanger worked on his project for ten years making only small advances each year. The presentation speech specifically mentions this.
THEME:
Nobel Laureates

Doctor Frederick Sanger. It sometimes happens that an important scientific discovery is made so to say "overnight" - if the time is ripe and the necessary background is there. Yours is not of that kind. The first successful determination of the structure of a protein is the result of many years of persistent and zealous work, in which the final solution of the problem has been approached step by step. You knew when you began to look into the structure of the insulin molecule 15 years ago that the problem was a formidable one. So did the whole scientific world. Those who knew you, were confident, however, that you would ultimately succeed, and each successive publication from your laboratory strengthened our confidence. Intelligence, knowledge and skill in the mastering of the methods required - we know you have them all - but in such a venture these are not enough. Without your wholehearted devotion to the task you had set before you, many obstacles on your way would have appeared insurmountable. Now that many years of work have been crowned with success you may look back and rejoice. You can also enjoy the satisfaction of seeing the roads you have broken and paved being used by many in their search for the building principles of the key substances of Life. However, very likely you are more apt to look ahead. It was Alfred Nobel's intention that his prizes should not only be considered as awards for achievements done but that they should also serve as encouragement for future work. We are confident that you are a worthy recipient of the Nobel award also in this sense.

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The images of the Nobel Prize medals are registered trademarks of the Nobel Foundation (© The Nobel Foundation). They are used here, with permission, for educational purposes only.

Why Is Science Important?

 
The short answer is that science is important because knowledge is always better than ignorance and science teaches you how to distinguish between them.

The long answer is ... [Why Is Science Important?]


Why is Science Important? from Alom Shaha on Vimeo

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[Hat Tip: Bad Astronomy]

Putting the Atheist Bus Campaign in Context

 
You can skip to the two minute mark after watching for one minute.

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[Hat Tip: Friendly Atheist]

Shopping Is a Throwback to the Days of Cavewomen

 
David Holmes is a Fellow in the Division of Psychology and Social Change at Manchester Metropolitan University in Manchester (UK). His latest "research" results were reported in the Telegraph: Shopping is 'throwback to days of cavewomen'.

Shoppers are using instincts they learnt from their Neanderthal ancestors, researchers have found.¹

Dr David Holmes, of Manchester Metropolitan University, said skills that were learnt as cavemen and women were now being used in shops.

He said: "Gatherers sifted the useful from things that offered them no sustenance, warmth or comfort with a skill that would eventually lead to comfortable shopping malls and credit cards.

"In our evolutionary past, we gathered in caves with fires at the entrance.

"We repeat this in warm shopping centres where we can flit from store to store without braving the icy winds."

The study was commissioned by Manchester Arndale shopping centre in response to a rise in January visitors, according to the Daily Express.

Now, assuming that women did all the gathering (they probably didn't), and assuming everyone lived in caves (they didn't), it still seems improbable that you could gather much food by strolling around the inside of a cave.

Amanda Marcotte at Pandagon hits the nail on the head [The next evolutionary step for evo psych].

I’m curious to know what kind of study they commissioned with what kind of data collection, because right now it appears that they just paid someone with a PhD to make shit up. Of course, evo psych has been on about that for forever, so it was just a matter of time before marketers saw the potential---if you can make something up and call it science because of the sexist content and the thin veneer of authority granted by doctorate degrees, why not go whole hog?

Making shit up is NOT science. It's closer to stand-up comedy.

Here's an example of comedy/satire by MissPrism.

When cave-ladies ground up roots and seeds to make pies for their cave-husbands, a white colour indicated the food was free of toxic contaminants. Cave-ladies accordingly evolved to value white above all other colours, which is why women today all long for a white wedding dress!

However, cave-ladies also needed to be able to tell when their cave-pie was cooked to a delicious golden brown. Women's visual systems therefore make a far more acute distinction between white and brown than those of men, who in our evolutionary past only saw the pies in their cooked state. For this reason, men can't see dirt and should never do laundry.

In spite of the fact that I like the conclusion, this isn't science. MissPrism's story is just as credible as the stories made up by evolutionary psychologists and that's a damning conclusion. It suggests that the entire field of evolutionary psychology is practically worthless as a science—maybe when we kick all the the evolutionary psychologists out of the universities, they can make a living by writing comedy.

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1. All available scientific evidence indicates that Neanderthals were not our ancestors.

[Hat Tip: Hopeful Monster at Chance and Necessity: Malls, caves, and evolutionary psychology]

Salmon with Peas on Toast

 
When my kids were growing up I used to make them one of my favorite meals—Mom's Creamed Salmon on Toast. We usually enjoyed it when Ms. Sandwalk was away from home.

Now that they are adults, my children never lose an opportunity to make fun of Dad's cooking and how they were forced to eat salmon when Mom was away.

Now the joke's on them ... or at least on my son, because ...

Teenage boys who eat fish at least once a week achieve higher intelligence scores. Looks like boys get smart by eating salmon. It explains why my son is so smart. It also explains why my daughter never appreciated salmon and peas on toast. It doesn't work on girls.¹

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1. I don't believe the study. It's ridiculous to think that eating fish is all it takes to make you smarter. If that were true then Newfoundlanders would be smarter than cowboys or vegetarians ... hmmmmm, come to think of it ....

P.S. Just in case there is someone out there who doesn't get my sense of humor, here's a link to a posting about my daughter [Another Dr. Moran]. And just so he doesn't feel left out, here's a link to my son's website [Gordon Moran].

Richard Dawkins on "Purpose"

One of the most astonishing discoveries of modern science is that the universe does not exhibit any signs of "purpose" or "goals." This single conclusion is probably more responsible for the profound conflict between science and religion than any other. The attractiveness of religion was that it seemed to answer the "why" questions that science, presumably, could not answer. Now, modern science tells us that the question was meaningless.

That evolution is a blind, purposeless process is difficult to grasp, yet it is a fundamental part of understanding biology. The concept is explicitly mentioned in college level textbooks, although some introductory biology textbooks place less emphasis on it than you will find in more advanced courses.

Here's how Douglas Futuyma describes purpose in Evolution (2005) (p. 12).

Above all, Darwin's theory of random, purposeless variation acted on by blind, purposeless natural selection provided a revolutionary new kind of answer to almost all questions that begin with "Why?" Before Darwin, both philosophers and people in general answered "Why?" questions by citing purpose. Since only an intelligent mind, with the capacity for forethought, can have purpose, questions such as "Why do plants have flowers?" or "Why are there apple trees?"—or diseases, or earthquakes—were answered by imagining the possible purpose that God could have had in creating them. This kind of explanation was made completely superfluous by Darwin's theory of natural selection. The adaptations of organisms—long cited as the most conspicuous evidence of intelligent design in the universe—could be explained by purely mechanistic causes. For evolutionary biologists, the flower of the magnolia has a function but not a purpose. It was not designed in order to propagate the species, much less to delight us with its beauty, but instead came into existence because magnolias with brightly colored flowers reproduced more prolifically than magnolias with less brightly colored flowers. The unsettling implication of this purely material explanation is that, except in the case of human behavior, we need not invoke, nor can we find any evidence for, any design, goal, or purpose anywhere in the natural world.

It must be emphasized that all of science has come to adopt the way of thought that Darwin applied to biology. Astronomers do not seek the purpose of comets or supernovas, not chemists the purpose of hydrogen bonds. The concept of purpose plays no part in scientific explanations.

Richard Dawkins made the same point in his book River Out of Eden (1995) (pp. 96-98). Here he is reading those pages.


The concept of purposeless, or accidental, evolution comes naturally to those evolutionary biologists who are used to thinking about random genetic drift. Those biologists tend to be comfortable with the idea that the tape of life will never be replayed.

But, as Richard Dawkins notes at the end of his reading, there are other biologists for whom "the illusion of purpose is so powerful that [they] use the assumption of good design as a working tool." Many of these biologists are not completely comfortable with the idea that the tape of life may not play out the same. They tend to see convergence, and other things, as evidence of some sort of inevitable purpose (design) in the history of life. This is, of course, materialistic design, not supernatural design.

This point of view crops up in terms such as "the evolution of evolvability," "facilitated variation," and even "self-organization."

In addition to this subtle form of "purpose" we see clear evidence of true purpose in animals with sophisticated brains. Those animals clearly develop goal-oriented behaviors.

Dawkins addresses these points in his current lecture tour by making a distinction between different definitions of purpose.

The Purpose of Purpose

"We humans are obsessed with purpose. The question, “What is it for?” comes naturally to a species surrounded by tools, utensils and machines. For such artifacts it is appropriate, but then we go too far. We apply the “What is it for?” question to rocks, mountains, stars or the universe, where it has no place.

How about living things? Unlike rocks and mountains, animals and plants, wings and eyes, webbed feet and leaves, all present a powerful illusion of design. Since Darwin, we have understood that this, too, is an illusion. Nevertheless, it is such a powerful illusion that the language of purpose is almost irresistible. Huge numbers of people are seriously misled by it, and biologists in practice use it as a shorthand.I shall develop two meanings of “purpose”. Archi-purpose is the ancient illusion of purpose, a pseudo-purpose fashioned by natural selection over billions of years. Neo-purpose is true, deliberate, intentional purpose, which is a product of brains. My thesis is that neo-purpose, or the capacity to set up deliberate purposes or goals, is itself a Darwinian adaptation with an archi-purpose.

Neo-purpose really comes into its own in the human brain, but brains capable of neo-purposes have been evolving for a long time. Rudiments of neo-purpose can even be seen in insects. In humans, the capacity to set up neo-purposes has evolved to such an extent that the original archi-purpose can be eclipsed and even reversed. The subversion of purpose can be a curse, but there is some reason to hope that it might become a blessing."

Wesley Elsberry was at the Dawkins lecture in Michigan on March 2nd and he has posted a lengthy summary on The Panda's Thumb: Richard Dawkins and “The Purpose of Purpose”. It's very helpful for those of us who couldn't attend one of these lectures.

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Monday's Molecule #111: Winners

 
UPDATE: I guess the hint was too much of a giveaway. The molecule is insulin from pig (Sus scrofa). Pig pancreas was the major source of insulin for diabetics before recombinant DNA. It is very similar to human insulin.

The Nobel Laureate is Fred Sanger who won in 1958 for determining the sequence of insulin. It was his first of two Noble Prizes.

The winners are David Schuller of Cornell University by one minute over Dima Klenchin, and Adam Santoro of the University of Toronto.

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Identify this molecule. Be as specific as possible, including the species. Explain why that species was chosen.

Here's a hint: 1b17.

There's are several possible Noble Prizes associated with this molecule. I'm looking for the prize that was awarded for determining the primary structure.

The first person to identify the molecule and the Nobel Laureate wins a free lunch at the Faculty Club. Previous winners are ineligible for one month from the time they first won the prize.

There are six ineligible candidates for this week's reward: Dima Klenchin of the University of Wisconsin. Alex Ling of the University of Toronto, James Fraser of the University of California, Berkeley, Guy Plunket III from the University of Wisconsin, Deb McKay of Toronto and Maria Altshuler of the University of Toronto.

Dima has offered to donate a free lunch to a deserving undergraduate so I'm going to continue to award an additional free lunch to the first undergraduate student who can accept it. Please indicate in your email message whether you are an undergraduate and whether you can make it for lunch.

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 Prizes 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 reserve the right to select multiple winners if several people get it right.

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

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