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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A Letter from the President of CIHR

 

There's a crisis in science funding in Canada. The budgets of the main granting councils are being cut by $148 million over the next three years.

Laura Frost is the President of the Canadian Society of Biochemistry, Molecular & Cellular Biology (CSBMCB). She recently wrote to Prime Minister Harper to draw his attention to the seriousness of this decision.

Dear Mr. Harper;

On behalf of the Canadian Society of Biochemistry, Molecular & Cellular Biology (CSBMCB), I would like to congratulate the Government of Canada for a number of measures in the 2009 Budget, including the more than $1.5 billion investment in science and technology. The CSBMCB is pleased to see in the budget $750 million for the Canada Foundation for Innovation (CFI) in support of research infrastructure and $87.5 million for the temporary expansion of the Canada Graduate Scholarship Program as well as continued funding for Genome Canada.

However, the lack of additional new investment in Canada’s granting agencies Canadian Institutes of Health Research (CIHR), NSERC and SSHRC is of great concern. Without increased investments in operating funds to support doing research, Canada could lose the competitive edge that previous investments in students, scientists and infrastructure have achieved. Operating monies are the funds that allow our gifted students and other trainees to become competitive at an international level and leaders in the next generation of scientists. Without these crucial increases, fewer labs will be funded and fewer students, scholarships notwithstanding, will be trained in the diverse areas of science that define “interdisciplinary research”. Targeted research is one essential component of the funding process, but as a country, we need a strong background in basic research that feeds into technological development and planning for crises ranging from SARS to mountain pine beetles to environmental concerns in the oil sands.

Over the past several years, many leaders and national and provincial partners dedicated to advancing research in Canada have advocated for increased investments in discovery research through the granting councils to match the growth in infrastructure and research capacity through the CFI and the Canada Research Chairs Program respectively. Failure to align these funding streams at the federal level has created a serious imbalance in the supply and demand in health research and research generally, which will, in turn, increasingly affect our capacity to retain and recruit the best scientists.

The biotechnology sector is also suffering from a lack of investment capital. This industry serves as a primary receptor for much of Canadian research related to health, agriculture, manufacturing, environmental and resource-based emerging technologies. Fifty percent of Canadian companies indicate they will be closing or selling off their operations to international partners by the end of this year. Canada cannot afford to ignore the competitive environment other nationals will be adopting to help grow and stimulate their knowledge-based industries.

The economic impact of Canadian health research is significant. On an annual basis our industry generates $12 billion in economic activity and provides employment and training for over 10,000 people across Canada. The sector also supports more than 20,000 scientists, clinical investigators and other researchers and staff.

Canada has many of the right ingredients to succeed in the knowledge-based economy including a highly skilled workforce and some of the best research facilities in the world. The CSBMCB looks forward to working with the Government of Canada in laying the foundation for a stronger and more sustainable economy of the future in which research and development in the health and life sciences are a top national priority.

Sincerely,



Laura Frost, Ph.D.
President, CSBMCB

CSBMCB has also published a letter from the President of the Canadian Institutes of Health Research (CIHR). Read this letter ... comments below.

MESSAGE FROM THE PRESIDENT OF CIHR

Following the January 26, 2009 Speech from the Throne, the Government of Canada tabled its 2009 Budget, Canada’s Economic Action Plan in the House of Commons on January 27. The Budget outlined the Government’s economic stimulus package designed to bolster the Canadian economy and provide support for Canadians as the world’s economies work through the current economic crisis. The Budget 2009 speech and documents can be found on the Finance Canada website at: http://www.fin.gc.ca.

Research plays a key role in improving the health of Canadians. That’s why, over the past three years, the Government has increased the annual base budget of the Canadian Institutes of Health Research (CIHR) by over $142 million. This year CIHR plans to spend approximately $917 million on peer-reviewed health research projects conducted at universities, hospitals and research centres across Canada.

I have summarized below the details of Budget 2009 as it relates to CIHR.

First, CIHR will receive $35M over the next three years for Canada Graduate Scholarships (CGS) to fund an additional 200 doctoral scholarships, valued at $35, 000 each per year for three years beginning in 2009-10, and an additional 400 master’s scholarships, valued at $17, 500 each for one year, in both 2009-10 and 2010-11.

Second, Budget 2009 also provided the results of the Government’s Strategic Review process. CIHR was one of the 21 Government Departments and Agencies that undertook a Strategic Review of its programs and services. The objective of the process was to assess whether programs:

• are effective and efficient;

• meet the priorities of Canadians; and

• are aligned with federal responsibilities.

The results of the process are as follows:

• CIHR funding of the Open Team Grant program will be discontinued. To respect current commitments, reductions will be phased in over the next three years with $1.5M in 2009-10, $5.5M in 2010-11, and $27.6M in 2011-12 and thereafter; and

• Funding for the Intellectual Property Mobilization (IPM) program will be discontinued. To respect CIHR’s current commitments, the annual reductions of $2M will commence in 2010-11 and end in 2011-12.

In addition, funding under the Indirect Costs Program will be reduced in proportion to reductions in the above direct cost programs. The relative ratio of funding for the direct and indirect costs will therefore remain essentially the same as prior to the Strategic Review.

In summary, taking into account the new investments for the Canada Graduate Scholarships and the strategic reallocations, CIHR’s budget for 2009-10 will increase by $12.5M, bringing our total budget to $978.8M.


Sincerely,



Alain Beaudet, MD, PhD
President
Canadian Institutes of Health Research

This is unacceptable. It sounds like a letter from a political lackey and not from someone who is really concerned about scientific research in Canada. Why can't Alain Beaudet mention that he is fighting on behalf of all Canadian scientists to increase CIHR funding in order to better support basic research? Is it because he isn't fighting?

We need someone who will stand up and oppose government underfunding, not someone who will make excuses for it. If the current President does not have the confidence of the scientists who are supported by CIHR then perhaps we should find a new CIHR President who does have their confidence.

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Happy Birthday PZ!

 
Today is PZ Meirirz birthday.

So far he's not having a good one [No More Birthday] so don't bother to send him an email message.

Wait until tomorrow.

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Monday's Molecule #111

 
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.

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Good Quality Journalism Sells Newspapers

 
On Saturday night we celebrated my nephew's birthday at Pic Nic on Queen St. East. I won't tell you how many years we were celebrating ... let's just say that I remember babysitting Mark when I was 18 years old. He's old enough to fend for himself (on most days).

We got to discussing science journalism—he reads my blog. Mark was defending (poorly ) the idea that newspapers, TV, etc. are profit-making companies and, consequently, it is unreasonable to expect them to be truthful and accurate. Sensationalism sells. I was defending the idea that telling the truth about science isn't necessarily going to hurt profits. Accurate science can be just as exciting as gross distortions of the truth. Maybe even more exciting.

We had a really fun time discussing the topic, aided, perhaps, by the excellent wine list at the restaurant. I wish I could remember all the points I made. I think some of them were brilliant.

Along comes André Picard of The Globe and Mail to back up my case better than I was able to do on Saturday night. (You lose again, Mark! ) Here's his bio.

André Picard is the public health reporter at The Globe and Mail, where he has been a staff writer since 1987.

He has received much acclaim for his writing, including the Michener Award for Meritorious Public Service Journalism, the Canadian Policy Research Award, the Atkinson Fellowship for Public Policy Research and the Award for Excellence in Women’s Health Reporting. In 2002, he received the Centennial Prize of the Pan-American Health Organization as the top public health reporter in the Americas.

I think we can assume he's an expert on health journalism in the same way that we have experts in science writing.

Does André Picard try and sell papers by sensationalizing topics like vaccination, prescription drugs, complementary medicines and "health" foods?

Let's check out his article in last Thursday's paper: The Internet has changed the nature of scientific debate.

If you read scientific literature and health research with an open mind and still conclude that vaccines are not poisons, that chelation therapy will not cure heart disease, that realigning someone's chakra is not going to clear up a bladder infection, or that strange concoctions of vitamins and minerals cannot cure bipolar disorder - all theories that have pretty broad followings on the Web - then you are dismissed as an agent of an evil empire.

Those who promote these bogus therapies - and often profit from them - will, paradoxically, dismiss you as a paid shill for Big Pharma, oppressive government or some other branch of the devilish military-industrial complex.

Doctors, nurses, pharmacists, pharmacologists, biochemists, immunologists, geneticists and journalists are not to be trusted. They are all on the take.

Medical journals that publish peer-reviews research: They are nothing but promotional tools for Big Pharma and researchers are their puppets and profiteers.

So who do you trust?

Well, you depend on chiropractors and Hollywood stars to give you advice about vaccinating your baby; you trust the guy at the health-food store to offer up a sure-fire cure for arthritis; and you take as gospel the e-mail that warns ominously that if new food safety rules are adopted by government, storm troopers will soon be busting down your front door to seize the chamomile tea.

In the world of cyberspace science, the best evidence is anecdote and the more fantastical the claims, the larger the following they seem to garner.

This is an example of honest, skeptical reporting and I think the general public will be just as interested in reading about the exposure of quacks as in reading articles that promote their claims.

In other words, accuracy and the truth can sell newspapers. And the public benefits.

Let's have more of it in the science section.

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[Photo Credit: Dr. Louise Nadeau and Mr. André Picard as masters of ceremonies at the 2006 Fifth Annual Canadian Health Research Awards celebration.]

[Hat Tip: Propter hoc: The most sensible thing I’ve read in months and RichardDawkins.net]

Did biologists really think that human evolution stopped?

John Hawks has responded to my posting on the Discover article. In that posting [Are Humans Still Evolving?] I criticized Hawks and his colleagues for claiming that the consensus view among scientists is that human evolution is over.

Recall that the opening sentence of the article is ...

For decades the consensus view—among the public as well as the world’s preeminent biologists—has been that human evolution is over.

John replies with: Did biologists really think that human evolution stopped?.

Yet despite the abundant evidence that human biologists have opposed the idea of recent human evolution, I still think that McAuliffe's opening sentence does construct a "straw man" argument. Many prominent examples don't prove that there has been a decades-long consensus that human evolution stopped. And our research is not about human evolution merely continuing -- we think it actually accelerated. Evidence that some biologists thought that human evolution stopped is interesting. But the reality is that almost no one has thought that human evolution accelerated.

So, John and I agree that McAuliffe's article was misleading when she suggested that the consensus view was that human evolution had stopped. It was misleading in spite of the fact that one can find quotations from some prominent scientists who might have held this view.

My position is that the consensus view is often that found in the leading textbooks. The textbooks on evolution always discuss recent examples of human evolution; such as lactose tolerance, skin color, and shifts in the frequency of blood type alleles. Most of them spend time discussing races and diversity—usually with the goal of dispelling false concepts of race, but always with the assumption that humans have, and are, evolving.

Take Evolution by Barton et al. (2007), for example. They have sections on the evolution of humans by random genetic drift and natural selection. One section on page 775 is headed: Natural Selection Has Shaped, and Is Shaping, Human Evolution. The standard examples are explained.

Barton et al. discuss what happens when negative selection is relaxed due to medical advances and they point out, correctly, that this will lead to the accumulation of formerly deleterious alleles by drift. They even address the very issue that Hawks writes about (p. 775).

It is unclear how effective natural selection has been in our recent history. On the one hand, our relatively low effective population size (N_e ~ 10⁴) makes it impossible for us to avoid accumulating mildly deleterious mutations, and there is evidence that more such mutations have accumulated along our lineage than along that of our sister species, the chimpanzee. However, it could be that our low effective population size actually reflects the effects of a large number of selective sweeps, and therefore the success of natural selection. (Recall that N_e is really a measure of the inverse rate of genetic drift. It can be reduced by both low population size and selective sweeps.) When a favorable mutation is swept to fixation, it may carry with it more weakly deleterious alleles that happen to be tightly linked to the original mutation. Thus, we can make two radically different interpretations of the observed low genetic diversity within our species: on the one hand, that it reflects a low population size in the past, implying inefficient selection, or on the other, that it is a side effect of intense adaptive selection.

Since this is what evolutionary biologists are teaching undergraduates, I think it's fair to say that the consensus among evolutionary biologists is that humans are evolving. Indeed, most evolutionary biologists know that it is impossible to stop evolution.

I guess we can conclude that the author of the Discover article didn't get her straw man version of human evolution from John Hawks. Where, then, did she get it? Maybe it was from Henry Harpending, John's former postdoc advisor and collaborator.

Harpending has just published a book with Gregory Cochran, another collaborator on the "acceleration" paper. The opening chapter of The 10,000 Year Explosion is Overview: Conventional Wisdom.

Scientists have long believed that the "great leap forward," some 40,000 t0 50,000 years ago in Europe, marked the advent of cultural evolution and the end of significant biological evolution in humans. At this time, the theory goes, humans developed culture, as shown by the sophisticated new tools, art, and forms of personal decoration that emerged in the Upper Paleolithic. Culture then freed the human race from the pressures of natural selection: We made clothes rather than growing fur and built better weapons rather than becoming stronger.

The argument that the advent of behavioral modernity somehow froze human evolution is dependent on the notion of a static environment. In other words, if a population—of humans, wolves, crabgrass, you name it—experiences a stable environment for a long time, it will eventually become genetically well matched to that environment. Simple genetic changes then do little to improve individual fitness, because the species is close to an optimum.

I assume John Hawks will agree that this "conventional wisdom" is a straw man. Perhaps Gregory Cochran and Henry Harpending are referring to a subset of scientists when they talk about arrested human evolution. Perhaps they are only referring to adaptationists, or maybe just adaptationist anthropologists?

My own view is that humans are evolving (duh!) and that the evidence for accelerated evolution is unconvincing at this time, but intriguing. I think this is the consensus view among evolutionary biologists. If I were trying to educate the general public that's what I would tell them.

I would not tell them that a revolution in our thinking about human evolution is in progress.

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Epigenetics, Lamarck, and Darwin.

 
Ryan Gregory at Genomicron educates us about Jean-Baptiste Pierre Antoine de Monet, Chevalier de la Marck and Charles Darwin [Lamarck didn't say it, Darwin did.

What people insist on dubbing "Lamarckian inheritance" in the context of epigenetics is actually closer to the view held by Darwin than by Lamarck....

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International Women's Day

 
Yesterday (Sunday) was International Women's Day.

Ms. Sandwalk and I celebrated by buying a new monitor for her computer. The monitor was designed and marketed by an American company and assembled in Asia (probably by women) using parts that were produced in five or six other countries.

Hey, don't knock it! What did you do to celebrate international women yesterday?

Apparently men in Russia celebrate a little differently.

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The Value of Science in Canada

 
Canadian Girl Postdoc in America writes about The Value of Science in Canada. Here's a teaser ... read it all.

Stephen Harper (the Prime Minister of Canada) is, as far as I'm concerned, has an underlying ideology that he weasels into every policy. While I may be a granola eating birkie-wearing tree hugger, Harper is a neo-con who lives and dies by the market. He won't listen to hard-done-by stories of the 'little people' and his natural inclination is toward rigid conservative policies. Stephen Harper's closest advisor (Tom Flanagan) believes in the teachings of Leo Strauss, a man who taught that people "are too stupid to make informed decisions about their political affairs. Elite philosophers must decide on affairs of state for us." Strauss also believed that the ruling elite should hide the truth from the public -- Strauss's "noble lie" -- in order to protect the citizens from themselves.

The comparison between Harper and Bush is stark and explains why Canadian scientists are fearful about the future of science.

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[Hat Tip: Canadian Cynic: Chicks with brains]

The Streetcar We Desire

 
Last night we rode the atheist streetcar for about an hour and a half through downtown Toronto. Nobody reacted to the sign. That's probably a good thing.

Thanks to Chris, the Freethought Association of Canada, and The Centre for Inquiry for organizing the event and the bus campaign.

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The Untenability of Theistic Evolution

 
A reader has alerted me to an essay by Bart Klink, a Dutch atheist [The Untenability of Theistic Evolution].

I think that from all the arguments mentioned above, the believer, and especially the Christian, is on the horns of a dilemma. The one horn is that he takes his religion, including its holy book, seriously, which leads to scientific conflicts. The other horn is that he avoids all conflict with science, which reduces his creation story to myth and leads to deism or atheism. Conservative Christians often choose the first horn, with scientific untenability as consequence. Proponents of theistic evolution are forced to choose the latter horn, with philosophical and theological untenability as consequence. Besides this, the theistic conception of an omnipotent, omniscient, and perfectly good God is hardly compatible with the process of evolution.

I agree with the main points of the article. Most versions of theistic evolution still conflict with science in one way or another and the only way to avoid conflict entirely is to adopt some form of deism.

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Are Humans Still Evolving?

This is a follow-up to my earlier posting about the latest issue of Discover magazine [Ascent of Darwinism]. I want to discuss another article in that issue: "Are We Still Evolving" by Kathleen McAuliffe. The title of the web version is: They Don't Make Homo Sapiens Like They Used To.

In a minute we'll look at the quality of science journalism in this article, but first a little background.

The point of the article is that human evolution may have accelerated enormously in the past 40,000 years. The idea is based almost entirely on a few papers by John Hawks and his colleagues. What they did was to look at various polymorphisms in the human genome. The most common variants are single nucleotide mutations (single nucleotide polymorphism = SNP = "Snips"). Some people will have one tpe of variant while other people will have another. Almost all of these variants are neutral—they have no visible or functional effect—but some of them will affect fitness.

Some SNPs can linked to variants (alleles) that are under selection. If you assay for enough SNPs, you'll find several that just happen to be located near variants that are being selected. If selection is rapid then the nearby SNPs will be swept up along with the actual variant that improves fitness. A block of SNPs that forms a cluster found in many individuals is called a "haplotype." The presence of these haplotypes is evidence of a selective sweep (rapid increase in frequency due to selection).

As time goes on these clusters are broken up by recombination so using this technique you only see examples of recent adaptations.

Hawks and his colleagues claim to have found more than 11,000 examples of genes that are being selected in the human population. (Humans have about 20,000 genes.) They conclude that human evolution has accelerated in the past 40,000 years because our hunter-gatherer ancestors settled down to become farmers and this created a new environment. We have been adapting to that new environment ever since.

The important paper is Hawks et al. (2007). For more information read: Is Evolution Linked to Environmental Change?, Accelerated Human Evolution, Are Humans Evolving Faster? and Human Evolution Has Accelerated

The work is controversial. Many people are skeptical of both the result and the explanation. The general consensus among evolutionary biologists is "wait and see." They treat this as a preliminary result because they are well aware of the technical problems and how easy it is to score false positives. The technology is not foolproof.

Evolutionary biologists are not surprised by the claim that humans are evolving. The textbooks are full of examples of recent human evolution by both natural selection and random genetic drift. Besides, the evidence is all around us—you only have to look at the different appearance of people in Africa, Asia, and Europe to see the obvious. We also have the well-studied examples of human migration out of Africa and of coalescence to identify Mitochondria Eve. This is more evidence of recent human evolution.

So, evolutionary biologists aren't the least bit surprised by evidence of human evolution but they're skeptical of this particular study because it claims recent accelerated human evolution. The paper isn't that exciting to most people who know about evolution.

The popular press had a fit, aided and abetted by the PR departments at several universities and, more recently, by a newly published book: The 10,000 Year Explosion: How Civilization Accelerated Human Evolution.

This brings us to the article in Discover. The author, Kathleen McAuliffe, is a freelance writer who specializes in science and medicine. She has an M.A. in natural science. She just won an Alicia Patterson Journalism Fellowship "to continue her research into human evolution from the Stone Age to the present."

Here's how the article begins ....

For decades the consensus view—among the public as well as the world’s preeminent biologists—has been that human evolution is over. Since modern Homo sapiens emerged 50,000 years ago, “natural selection has almost become irrelevant” to us, the influential Harvard paleontologist Stephen Jay Gould proclaimed. “There have been no biological changes. Everything we’ve called culture and civilization we’ve built with the same body and brain.” This view has become so entrenched that it is practically doctrine. Even the founders of evolutionary psychology, Leda Cosmides and John Tooby, signed on to the notion that our brains were mostly sculpted during the long period when we were hunter-gatherers and have changed little since. “Our modern skulls house a Stone Age mind,” they wrote in a background piece on the Center for Evolutionary Psychology at the University of California at Santa Barbara.

I think this is wrong. I do not believe that the consensus among the world's preeminent evolutionary biologists¹ is that human evolution is over.

I'm not familiar with the Gould quotation. It seems to have been uncovered by Cochran and Harpending, two of the authors on the Hawks et al. paper. They use it on the first page of their book The 10,000 Year Explosion: How Civilization Accelerated Human Evolution. Even if it's accurate, it does not represent the mainstream view of most evolutionary biologists.

So to suggest that humans have undergone an evolutionary makeover from Stone Age times to the present is nothing short of blasphemous. Yet a team of researchers has done just that. They find an abundance of recent adaptive mutations etched in the human genome; even more shocking, these mutations seem to be piling up faster and ever faster, like an avalanche. Over the past 10,000 years, their data show, human evolution has occurred a hundred times more quickly than in any other period in our species’ history.

There are two things wrong with this. First, the hype about blasphemy is a serious distortion of the truth. The scientific literature is full of examples of recent human evolution. Haven't you heard of the sickle cell gene, lactose intolerance, and blood types?

Second, while the Hawks et al. paper is interesting, it is extremely misleading to imply that their evidence is unchallenged. That's not good science journalism. (Incidentally, the peer-reviewed paper says that human evolution accelerated in the past 40,000 years, not 10,000.)

It's not until you get to the sixth paragraph that you find any sort of balance.

Not surprisingly, the new findings have raised hackles. Some scientists are alarmed by claims of ethnic differences in temperament and intelligence, fearing that they will inflame racial sensitivities. Other researchers point to limitations in the data. Yet even skeptics now admit that some human traits, at least, are evolving rapidly, challenging yesterday’s hallowed beliefs.

What kind of balance is that? Where's the sober description of the consensus view; namely, that humans are always evolving and the evidence of Hawks and his colleagues isn't convincing?

John Hawks is featured prominently in this article.

These overriding trends are similar in many parts of the world, but other changes, especially over the past 10,000 years, are distinct to specific ethnic groups. “These variations are well known to forensic anthropologists,” Hawks says as he points them out: In Europeans, the cheekbones slant backward, the eye sockets are shaped like aviator glasses, and the nose bridge is high. Asians have cheekbones facing more forward, very round orbits, and a very low nose bridge. Australians have thicker skulls and the biggest teeth, on average, of any population today. “It beats me how leading biologists could look at the fossil record and conclude that human evolution came to a standstill 50,000 years ago,” Hawks says.

Beats me how John could possibly think that "leading biologists" have ignored the data.

McAuliffe also interviews Henry Harpending and Robert Moyzis, two other authors on the original paper. Not surprisingly, she gets a similar story from them about how their revolutionary ideas are overthrowing entrenched dogma.

McKauliffe is now on a role and she includes a number of just-so stories.

Paralleling the constant war against pathogens, human sperm may also be evolving at high speed, driven by the race to get to the egg before another man’s sperm. “It could be that cities create more sexual partners, which means fiercer competition among males,” Hawks says. Because sperm can fertilize an egg up to 24 hours after being ejaculated in the vagina, a woman who copulates with two or more partners in close succession is setting up the very conditions that pit one man’s sperm against another’s. Hawks infers that “sperm today is very different from sperm even 5,000 years ago.” Newly selected mutations in genes controlling sperm production show up in every ethnic group he and his team have studied; those genes may affect characteristics including abundance, motility, and viability. The selection for “super sperm,” Hawks says, provides further corroboration that our species is not particularly monogamous—a view widely shared by other anthropologists.

As agriculture became established and started creating a reliable food supply, Hawks says, more men and women would have begun living into their forties and beyond—jump-starting the selection pressure for increased life span. In support of that claim, Moyzis is currently performing a genetic analysis of men and women in their nineties who are of European ancestry. He has traced many early-onset forms of cancer, heart disease, and Alzheimer’s to older human gene variants. “The idea is that people with more modern variants tend to have greater resistance to these chronic illnesses of old age and should be overrepresented in the age 90-plus population,” Moyzis says.

Harpending and Cochran had previously—and controversially—marshaled similar evidence to explain why Ashkenazi Jews (those of northern European descent) are overrepresented among world chess masters, Nobel laureates, and those who score above 140 on IQ tests. In a 2005 article in the Journal of Biosocial Science, the scientists attributed Ashkenazis’ intellectual distinction to a religious and cultural environment that blocked them from working as farm laborers in central and northern Europe for almost a millennium, starting around A.D. 800. As a result, these Jews took jobs as moneylenders and financial administrators of estates. To make a profit, Harpending says, “they had to be good at evaluating properties and market risks, all the while dodging persecution.” Those who prospered in these mentally demanding and hostile environments, the researchers posit, would have left behind the most offspring.

The last one is accompanied by a passing reference to reality, "Critics note that the association between wealth and intelligence in this interpretation is circumstantial, however."

Six pages into the article we come to this ...

NOT SO FAST
Despite all these clues that human evolution has continued and accelerated into modern times, many evolutionary biologists remain deeply skeptical of the claims. Their resistance comes from several directions.

Some independent experts caution that the tools for studying the human genome remain in their infancy, and reliably detecting genomic regions that have been actively selected is a challenging problem. The hypothesis that human evolution is accelerating “all rests on being able to identify recent areas of the genome under natural selection fairly accurately,” says human geneticist Jonathan Pritchard of the University of Chicago. And that, he warns, is tricky, involving many different assumptions (about population sizes on different continents, for instance) in the poorly documented period before recorded history.

Given such uncertainties, researchers are more likely to be persuaded that a mutation has been recently selected if they understand its function and if its rise in prevalence meshes well with known human migratory routes. Genetic variants fitting that description include those coding for lighter skin coloring, resistance to diseases such as malaria, and metabolic changes related to the digestion of novel foods. There is broad consensus that these represent genuine examples of recent adaptations.

Hmmm ... there is "broad consensus" that humans have evolved recently.

How is that consistent with the outrageous claims in the opening paragraphs?

Do we blame science writer Kathleen McAuliffe or John Hawks and his colleagues for this misleading article?

Does the article contribute positively to educating the general public about human evolution or would we be better off if it had never been published?

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1. I realize that McAuliffe said "biologist," not "evolutionary biologists" but surely the only biologists who count are the experts in the field? After all, you wouldn't ask ecologists their opinion about biochemistry, would you?

Hawks, J., Wang, J.T., Cochran, G., Harpending, H.C. and Moyzis, R.K. (2007) Recent acceleration of human adaptive evolution. Proc. Natl. Acad. Sci. (USA) 104:20753-20758 [doi: 10.1073/pnas.0707650104]

[Photo Credit: MSNBC]

Ribonucleic Acid (RNA)

 
There was a time in the not-to-distant past when RNA didn't get no respect. Most biochemists worked with proteins or DNA and RNA was relegated to minor status as just an intermediate in the information flow pathway.

We all knew that there were five main types of RNA:

1. Messenger RNA (mRNA) and its precursors: The primary RNA transcripts are produced by copying the DNA of a protein-encoding gene.¹ Subsequent processing steps include addition, removal, and modification of nucleotides as well as splicing events that excise internal segments.² The mature mRNA is translated to produce a protein whose amino acid sequence is determined by the sequence of the coding region in the gene. The messenger RNA, as the name implies, is the molecule that carries the message from the gene to the protein synthesis machinery. (And from the nucleus to the cytoplam in eukaryotic cells.)


2. Ribosomal RNA (rRNA): The ribosomes are the most important part of the translation machinery and it has long been known that much of the mass of ribosomes is due to the presence several types of ribosomal RNA. These are noncoding RNAs produced by transcription of ribosomal RNA genes.³ One of the key steps in translation—formation of the peptide bond—is catalyzed by the rRNA component of the ribosome. It is the major catalytic RNA in cells.


3. Transfer RNA (tRNA): tRNAs are intermediates in protein synthesis. There are many different tRNA molecules in every cell and each one binds a specific amino acid, yielding an aminoacylated-tRNA (aa-tRNA). Each different aminoacylated tRNA interacts with a particular codon in mRNA thus delivering the correct amino acid to to the site of protein synthesis.⁴


4. Small RNAs: The small RNAs represent a heterogeneous category of RNAs covering a wide ranges of functions. Some of them have catalytic functions—RNAse P is the classic example.⁴ Some of them are structural components of ribonucleoprotein complexes (e.g. signal recognition particle).⁵ Some of them are guide RNAs involved in various processing events. The best known examples of guide RNAs are the small RNAs of the spliceosome complexes that mediate the splicing of mRNA precursors.² Other small RNAs were known to be involved in the regulation of gene expression.


5. Genomic RNA: Some viruses, notably retroviruses, have an RNA genome instead of a DNA genome. In addition, the mobility of various transposons is due to an intermediate RNA copy of the transposon sequence (retrotransposons).

This was the state of knowledge 25 years ago. Since then, the study of RNA has made remarkable progress. Our knowledge of all the fundamental processes—transcription, processing, and catalysis—has expanded enormously.

The biggest change is in the area of small RNAs. Today there are several categories of small RNAs—siRNA, microRNA, piRNA—that were only discovered in the past 10-15 years. The functions of these small RNA molecules are still being worked out. There's little doubt that some of them have important biological roles but there's considerable controversy over what percentage might be artifacts of one sort or another.

This month's issue of Cell is devoted to RNA [Cell]. There are important reviews and essays on everything from micro RNAs to spliceosomes and transcriptional scaffolds. This is your chance to catch up on the latest work in the RNA field.

The Centrality of RNA
Phillip A. Sharp

RNA-Based Therapeutics: Ready for Delivery?
Laura Bonetta

MicroRNAs and Cancer: Short RNAs Go a Long Way
Andrea Ventura, Tyler Jacks

Viral RNAs: Lessons from the Enemy
Bryan R. Cullen

Crawling Out of the RNA World
Thomas R. Cech

The Dynamic Landscapes of RNA Architecture
José Almeida Cruz, Eric Westhof

Transcriptional Scaffolds for Heterochromatin Assembly
Hugh P. Cam, Ee Sin Chen, Shiv I.S. Grewal

Regulatory RNAs in Bacteria
Lauren S. Waters, Gisela Storz

Evolution and Functions of Long Noncoding RNAs
Chris P. Ponting, Peter L. Oliver, Wolf Reik

Origins and Mechanisms of miRNAs and siRNAs
Richard W. Carthew, Erik J. Sontheimer

Small RNAs as Guardians of the Genome
Colin D. Malone, Gregory J. Hannon

Origin, Biogenesis, and Activity of Plant MicroRNAs
Olivier Voinnet

Pre-mRNA Processing Reaches Back to Transcription and Ahead to Translation
Melissa J. Moore, Nick J. Proudfoot

The Spliceosome: Design Principles of a Dynamic RNP Machine
Markus C. Wahl, Cindy L. Will, Reinhard Lührmann

mRNA Localization: Gene Expression in the Spatial Dimension
Kelsey C. Martin, Anne Ephrussi

Regulation of Translation Initiation in Eukaryotes: Mechanisms and Biological Targets
Nahum Sonenberg, Alan G. Hinnebusch

Fidelity at the Molecular Level: Lessons from Protein Synthesis
Hani S. Zaher, Rachel Green

The Many Pathways of RNA Degradation
Jonathan Houseley, David Tollervey

RNA and Disease
Thomas A. Cooper, Lili Wan, Gideon Dreyfuss

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1. Theme: Transcription.


2. RNA Splicing: Introns and Exons.


3. Human Ribosomal RNA genes; Ribosomal RNA Genes in Eukaryotes; Ribosomal RNA Genes in Bacteria; The Composition of Ribosomes


4. Transfer RNA: Structure; Transfer RNA: Synthesis; Transfer RNA Processing: RNase P.


5. The Signal hypothesis; Signal Recognition Particle
   

[Hat Tip: Bayblab - CELL Website Gets Massive RNA Contamination]

Depth vs Breadth

 
A University of Virginia press release announces ...

A recent study reports that high school students who study fewer science topics, but study them in greater depth, have an advantage in college science classes over their peers who study more topics and spend less time on each.

I have no idea if the results are reliable but it does highlight an issue that needs to be addressed. Is it better to learn a single subject in some depth than several subjects at a more superficial level? One can make a good case for both sides.

This is an important question here at the University of Toronto because we are in the middle of a huge shift away from in-depth studies to more breadth. For example, there were 50 students who enrolled in our enhanced biochemistry program a few years ago but last year that number dropped to 17. There's no indication that we have bottomed out.

Instead of taking an honors biochemistry program with advanced labs, research projects, and 4th year honors courses, our students are opting for a lighter biochemistry program that whey can combine with other programs, like economics, psychology, or physiology. This breadth can only be achieved by taking a higher percentage of lower level introductory courses.

Is this a good idea? Our students seem to think it is, and so far the university is doing everything to encourage them to abandon the rigorous honors programs. (Part of the problem is that all our students graduate with "honors" no matter what program they take and what grades they achieve.)

Is this happening at other universities? Is it better to have a broad general education in science than a specialized one? Personally, I think that specialization in one subject is essential for critical thinking and for understanding scholarship. I don't care which subject a student chooses but they should pick one and take the most advanced undergraduate courses.

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