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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The Ascent of Darwinism

 
The latest issue of Discover has several articles on Darwin and evolution. They are introduced in an editorial by Corey S. Powell, Discover editor-in-chief.

Today it is difficult to read the news without invoking Darwinian thinking. It shows up not just in the obvious places, such as stories about drug-resistant bacteria in hospitals. In dispatches from the Middle East, it is hard not to see the way that kin selection can organize people into tight-knit, warring clans. In financial news, it is difficult not to notice an evolutionary battle between self-preservation and altruistic group impulses. If anything, it is too easy to perceive the hand of natural selection everywhere and to lapse into just-so stories. On the pages that follow, we strip away the embellishments and show how the true, unvarnished Darwin remains one of the most powerful, controversial, and influential figures in science.

Hmmmm ... this doesn't sound very encouraging. Let's see how Discover gets to the "true, unvarnished Darwin."

The very first article is titled "The Ascent of Darwin: 'Survival of the fittest' is helping us understand not only the origin of species but also love, politics, and even the cosmos." The author is Karen Wright who lists herself as a science writer living in New Hampshire. The website version of the article is We All Live in Darwin's World.

It begins ....

You could call Helen Fisher a Darwinian matchmaker. The acclaimed anthropologist from Rutgers University is also a best-selling author of books on love and the chief scientific adviser to an online dating service called Chemistry.com. This service utilizes a questionnaire that Fisher developed after years of research on the science of romantic attraction. It reveals which of four broad, biologically based personality types an applicant displays and helps identify partners with compatible brain chemistry. In designing the questionnaire, Fisher relied on the principles of evolutionary psychology, a field inspired by Charles Darwin’s insights. She has even used those principles to size up Darwin himself. (He is a “negotiator,” “imaginative and theoretical,” “unassuming, agreeable, and intuitive”—but also married, alas, and dead.)

Fisher’s work is just one of the innumerable offshoots of Darwin’s grand theory of life. In the 150 years since the publication of On the Origin of Species, it seems no sphere of human thought or activity has been left untouched by Darwinian analysis. Evolutionary theory has infiltrated the social sciences, where it has been used to explain human politics and spending habits. It has transformed computer science, inspiring problem-solving algorithms that adapt and change like living things. It is cited by a leading theoretical physicist who proposes that evolution helped shape the laws governing the cosmos. A renowned neuroscientist sees ideas of selection as describing the honing of connections among brain cells. Literary critics analyze the plots, themes, and characters of novels according to Darwinian precepts. Even religion, the sector most famously at odds with Darwin, now claims an evolutionary evangelist.

I don't think this is helpful. When it comes to understanding science, one of the problems most people have is appreciating that scientific knowledge helps us understand the universe and how it works. Biological sciences help us understand life.

The average person is all too willing to take any bit of science and apply it to their daily concerns. "What's in it for me?" is the usual question. This year we have a wonderful opportunity to explain the science of evolution and why nothing in biology makes sense except in the light of evolution. Instead, the lead article in Discover begins with an example of how Darwin's ideas helps you find a partner on an online dating service.

The article goes on to mention some real science but the emphasis comes perilously close to praising social Darwinism. Evolutionary biologists agree that biological evolution does not provide any justification for human behavior and many of them are skeptical of evolutionary psychology.

According to Helen Fisher and other proponents of evolutionary psychology, the theory of evolution helps them address questions like “What is love?” and “Why do we vote the way we do?” Many evolution­ary psychologists believe that the cognitive and emotional makeup of human beings represents an adaptation to our ancestral environment. Biologist Edward O. Wilson of Harvard University launched the discipline in 1975 with one slim chapter in his book Sociobiology: The New Synthesis, suggesting that insights into animal behavior afforded by evolutionary theory could apply to human animals, too.

Today the evolutionary worldview has expanded into analyses of economics and politics as well as of human mating behavior. It has enriched the “rational choice” model long espoused by economists to explain human behavior in the marketplace. Traditional economic models assume that people act exclusively in their self-interest, just as traditional evolutionary theory describes competition among individuals. But cooperation and altruistic tendencies also show up routinely in studies of economic behavior. People who stand to lose from progressive taxation, for example, may still vote for it. “You can’t predict how people will vote on the issue of income redistribution based on their income,” says economist Herbert Gintis of the Santa Fe Institute in New Mexico.

Last week I was involved in a discussion with Chris Mooney. He was lamenting the fact that science writers were losing their jobs and I suggested that we might be better off if most of them stopped writing. I said, "Seriously, most of what passes for science journalism is so bad we will be better of without it." [The Future of Science Journalism]

This is an example. I honestly believe that this article does more to degrade and demean science than to enhance it. I think it misrepresents Darwin and his contribution to biology. I think it seriously distorts the modern field of evolutionary biology. We would have been better off if Discover had published nothing at all in celebration of Darwin's birthday.

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Ray Comfort Teaches Us about Evolution and Atheism

 
Ray Comfort wrote a book. He's not very happy because the book isn't doing so good. This is because of an atheist conspiracy [Atheists strategize against book on God].

Ray knows there must be a conspiracy because the case for God is overwhelming.

Comfort said the strong opposition easily is explained.

"I simply expose atheistic evolution for the unscientific fairy tale that it is, and I do it with common logic. I ask questions about where the female came from for each species. Every male dog, cat, horse, elephant, giraffe, fish and bird had to have coincidentally evolved with a female alongside it (over billions of years) with fully evolved compatible reproductive parts and a desire to mate, otherwise the species couldn't keep going. Evolution has no explanation for the female for every species in creation," he said.

When I read something like this I'm (temporarily) speechless. PZ Myers has a short explanation of how evolution really works for those of you who might be confused [It's a conspiracy!].

Meanwhile, just for fun, let's think about how many females were around when Cain and Abel got the urge to reproduce ...

"I also show that the 'God' issue is moral rather than intellectual."

Truer words were never spoken. Ray Comfort has, indeed, proven that his arguments aren't intellectual.

"No one needs to prove that God exists. Creation is clear evidence for any sane person that there's a Creator. But if I can convince myself that there is no God, it means I am not morally accountable, and evolution opens the door to a whole lot of sinful delicacies such as pornography, fornication, lying, theft, and of course writing bad reviews for a book I haven't read," he continued.

Thinking of Cain and Abel reminds me that we shouldn't forget about delicacies like incest and murder.

And you wonder why we call them IDiots?

There's a serious point here. There must be some semi-intelligent Intelligent Design Creationists out there somewhere. Why aren't they speaking out against the idiotic rantings of Ray Comfort and his ilk?

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Nobel Laureates: Frederick Banting and J.J.R. Macleod

 

The Nobel Prize in Physiology or Medicine 1923

"for the discovery of insulin"

Frederick Grant Banting (1891 - 1941) and John James Richard Macleod (1876 - 1935) won the Noble Prize in 1923 for discovering insulin and using it to relieve the symptoms of diabetes.

Frederick Banting was a physician who convinced J.J.R. Macleod to lend him space and funds to work in Macleod's lab during the summer of 1921. Macleod assigned a young medical student, Charles Best, to work with Banting. Over the summer Banting and Best worked out a purification scheme for insulin and they had some success in treating dogs whose pancreas had been removed.

When Macleod returned to Canada in the Fall he helped improve the protocols, provided more funds and more dogs, and started paying Banting a salary. Macleod brought James Collip, a visiting biochemistry Professor from Alberta, into the project to help improve the purification. The experiments were a success and the first patients were treated in January 1922.

Frederick Banting thought that Charles Best, and not Macleod, should have shared the Nobel Prize with him. This is one of the most famous Nobel Prize controversies. Banting shared his prize money with Best and Macleod shared his money with Collip.

The original building where the work was done no longer exists. It was torn down and replaced by a larger building where my office is currently located. The plaque commemorating the discovery of insulin is attached to the side of the J.J.R. Macleod Auditorium. Across the street is the C.H. Best Institute. The Banting & Best Department of Medical Research is a research department in the Faculty of Medicine. Busts of Banting and Best are prominently displayed in the lobby of my building.

Here's an excerpt from the Presentation Speech. It hints at another controversy; namely, whether the work of Banting and Macleod was truly original.

THEME:
Nobel Laureates

We must not imagine that insulin is able to cure diabetes. How could that be possible if the cause of diabetes is to be found in the fact that the cells within our organism that produce the hormone necessary for the combustion of sugar are definitively destroyed? But insulin gives us the possibility of transforming the severe form to a milder one and thereby of restoring his capacity for work and a comparative state of health to the hopeless invalid who, despite the most trying and rigorous restrictions in diet, is constantly threatened by a fatal state of poisoning. Most striking is the effect of insulin in the cases in which the state of poisoning has already passed into that of diabetic coma, against which we have hitherto been helpless and which, before the days of insulin, inevitably led to death.

It could be prophesied with a very great degree of probability that such a substance as insulin some day would be produced from the pancreatic gland, and much of the work had been done beforehand by previous investigations, several of whom very nearly reached the goal. Consequently it also has been said that its discoverer was in a preeminent degree favoured by lucky circumstances. Even if this be so, yet there would seem to be cause to remember Pasteur's words: «La chance ne favorise que l'intelligence préparée.»¹

The Professorial Staff of the Caroline Institute has considered the work of Banting and Macleod to be of such importance, theoretically and practically, that it has resolved to award them the great distinction of the Nobel Prize. Doctor Banting and Professor Macleod not having the opportunity of being present today, I have the honour of asking the British Minister to accept from His Majesty the King the prize, and to transfer it to the Laureates, together with the congratulations of the Professorial Staff of the Royal Caroline Institute.

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1. Chance favors the prepared mind.

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.

Canadian Parliament Rejects Theory of Evolution?

 
The Canadian Press is reporting that the House of Common rejected a motion to recognize Darwin's theory of evolution as the only scientific explanation for the origin of the human species [Ottawa rejects motion to favour Darwin theory over other scientific explanations].

Here's what happened. Yesterday, Pierre Paquette, the Bloc Québécois member for Joliette, rose in the House to make the following request as recorded in Hansard.

Mr. Speaker, I seek the unanimous consent of the House to adopt the following motion: That the House acknowledge the 200th anniversary of the birth of Charles Darwin and the 150th anniversary of the publication On the Origin of Species by Natural Selection or the Preservation of Favoured Races in the Struggle for Life, which launched the theory of evolution, the only proven and recognized scientific explanation for the origin of man. I believe you will find unanimous consent for adoption of this motion.

Some honourable members shouted "yes" and some shouted "no." The speaker ruled that there was no unanimous consent.

According to the Canadian Press report, most of the naysayers were on the Conservative benches and most MP's answered "yes."

I'm a little bit uneasy about the scientific accuracy of the statement but that's not my main objection. My main objection is that the House of Commons should not be voting on motions concerning the accuracy of scientific theories. That's none of their business.

The motion should have read ...

That the House acknowledge the 200th anniversary of the birth of Charles Darwin and the 150th anniversary of the publication of "On the Origin of Species."

That motion would have stood a much better chance of getting unanimous consent.

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I Hate Cilantro/Coriander!

 
I'm one of those people who hate the taste of coriander (called cilantro in most of North America). It's mostly Chinese parsley (Coriandrum sativum L.) but there are similar American plants that taste just as bad. Coriander/cilantro completely ruins any food that it touches.

From time to time I encounter others with the same reaction. I was told that about 5% of the population doesn't like the taste. As a general rule, they seem to be far more intelligent than cilantro lovers, but there are exceptions. :-)

Today I discovered that we're not alone. There's an entire website devoted to eliminating coriander/cilantro from human food [IHateCilantro.com].

Supporting the Fight Against Cilantro!

Cilantro. The most offensive food known to man.

Welcome! You are visiting the web site of a growing community of cilantro haters. We are, however, rational people. In fact, we are the most rational people on earth. No normally functioning human being would ever in a lifetime consider cilantro edible.

It's the reason you are here. Please browse the site in support of your anti-cilantro confederates and help spread the word any way you can:

I wonder if hating cilantro is genetic? Is there an allele that affects a particular taste receptor? If so, I wonder about the adaptive significance of the hate cilantro allele. There must be one .....

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[Hat Tip: Josh Rosenau]

Monday's Molecule #110:Winners

 
UPDATE: The three molecules are preproinsulin, proinsulin, and insulin. The pathway depicts the processing of the newly synthesized prepro- form. The first step is removal of the signal sequence in the endoplasmic reticulum. The signal sequence helps target the molecule for secretion. The second step is cleavage of proinsulin to remove an internal segment of the polypeptide chain. The completed molecule has several disulfide bridges. Such bonds are characteristic of secreted proteins. They help maintain the structure in the harsher environments found outside of the cell.

The Nobel Laureates are Frederick Banting and J.R.R. Macleod. Banting, Best, Macleod and Collip, who all ended up with a share of the prize money, worked in a lab that's on the same site as my office, where Sandwalk is mostly produced.

This week's winner is Maria Altshuler of the University of Toronto.

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Identify all three molecules shown here. Be as specific as possible.

There's are several possible Noble Laureates associated with these molecules. I'm looking for the one(s) who got the first prize. There's a special connection to Sandwalk, can you guess what it is?

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 seven ineligible candidates for this week's reward: David Schuller of Cornell University, Nova Syed of the University of Toronto, Dima Klenchin of the University of Wisconsin and undergraduate Alex Ling of the University of Toronto, and James Fraser of the University of California, Berkeley, Guy Plunket III from the University of Wisconsin, and Deb McKay of Toronto.

David, and Dima have offered to donate their 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 a free lunch. Please indicate in your email message whether you are an undergraduate and whether you came make it for your free lunch (with a friend).

THEME:

Nobel Laureates
Send your guess to Sandwalk (sandwalk (at) bioinfo.med.utoronto.ca) and I'll pick the first email message that correctly identifies the molecule and names the Nobel Laureate(s). Note that I'm not going to repeat Nobel Laureate(s) so you might want to check the list of previous Sandwalk postings by clicking on the link in the theme box.

Correct responses will be posted tomorrow. I 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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Octo-mom: could it happen in Canada?

 
The short answer is .... no.

The University of Toronto Bulletin publishes an interview with fertility expert Robert Casper [Octo-mom: could it happen here?"

Q. The woman in California who gave birth to octuplets was single. Is this common?

Yes. While couples (both heterosexual and same-sex) comprise the majority of IVF patients, we see many single women using donated sperm as well. We don’t discriminate.

Q. The California woman was implanted with six embryos using in-vitro fertilization. Could something like this happen in Canada?

In Canada no reproductive infertility specialist would be putting back that many embryos.
There’s no law in Canada—it’s up to the doctor and the patient to decide. Our guidelines are to transfer up to two embryos in women under 35, up to three for women between 35 and 39 and up to five for women 40 and older. The reason that the number of embryos goes up as you get older is that there are more and more chromosomal abnormalities that accumulate in the eggs as a woman ages. By the time a woman is 40, for example, 90 per cent or more of her eggs have a chromosomal abnormality that would be incompatible with a live birth. So the idea of putting more embryos in an older patient is to try and ensure that there’s one healthy normal embryo that will actually implant.

Q. So, in a nutshell, this is pretty much unheard of?

To put six embryos in someone who is 33 is way, way outside what it is considered to be normal standard of care.

Q. Any thoughts on what the doctor was thinking?

I have no idea what was happening in that clinic. It sounded like they didn’t have much experience. They put a lot of embryos in to increase her chances—I don’t think they were counting on the fact that she was so fertile or thinking about the fact that she had six previous children.

Q. Are women counseled psychologically before receiving IVF? This woman had six other kids – should her doctor have discouraged her from trying to have more?

Psychological counseling is mandatory—a standard of care in Canada—for women using donor sperm. However, we wouldn’t turn away a woman who has six children and wants another—it’s her decision if she wants to have another child. But at 33, we would encourage that she have only one embryo put back, especially, as with the case with this woman, she has proven very high fertility.

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Monday's Molecule #110

 
Identify all three molecules shown here. Be as specific as possible.

There's are several possible Noble Laureates associated with these molecules. I'm looking for the one(s) who got the first prize. There's a special connection to Sandwalk, can you guess what it is?

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 seven ineligible candidates for this week's reward: David Schuller of Cornell University, Nova Syed of the University of Toronto, Dima Klenchin of the University of Wisconsin and undergraduate Alex Ling of the University of Toronto, and James Fraser of the University of California, Berkeley, Guy Plunket III from the University of Wisconsin, and Deb McKay of Toronto.

David, and Dima have offered to donate their 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 a free lunch. Please indicate in your email message whether you are an undergraduate and whether you came make it for your free lunch (with a friend).

THEME:

Nobel Laureates
Send your guess to Sandwalk (sandwalk (at) bioinfo.med.utoronto.ca) and I'll pick the first email message that correctly identifies the molecule and names the Nobel Laureate(s). Note that I'm not going to repeat Nobel Laureate(s) so you might want to check the list of previous Sandwalk postings by clicking on the link in the theme box.

Correct responses will be posted tomorrow. I reserve the right to select multiple winners if several people get it right.

Comments will be blocked for 24 hours.

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Bacteria in Your Mouth

 
A paper examining the diverstiy of human salivary bacteria has recently appeared in the journal Genome Research (Nasidze et al. 2009).

The authors looked at 120 individuals from different locations all over the world. They extracted DNA from their saliva and isolated small fragments of DNA copied from a highly variable region of 16S ribosomal RNA. On average, they sequenced 120 different DNA fragments from each individual. After eliminating artifacts they were left with 14,115 fragments.

The DNA sequences were compared with a large database of bacterial sequences in order to identify the bacterial species present in the mouths of each person. In most cases it was possible to positively identify the genus although they did find 196 sequences that were not in the database. These are probably unknown species of bacteria.

There were 101 different types of bacteria (genera). Each person has between six and thirty different species of bacteria in their mouth. There are about 45 different genera in each location (e.g. Bolivia, Congo, China, California, Germany, etc.).

Some genera were seen only once while others are quite common. The most common ones are listed below.

Actinomyces: Actinomyces are rod-shaped, gram positive bacteria that can survive under both aerobic (oxygen) and anaerobic conditions. Such bacteria are called facultative anaerobes. A. naeslundii forms dental placque by adhering to the surface of your teeth.

Enterobacter: Enterobacter species belong to the γ-proteobacteria group of gram negative bacteria. They are facultative anaerobes. Enterobacter are related to Escherichia coli—no examples of E. coli were found in this study.

Fusobacterium: These are gram negative, anaerobic, bacteria that are normal inhabitants of the oral cavity. They cause periodontal disease under some (unknown?) circumstances .

Granulicatella: The Granulicatella species belong to the phylum Firmicutes. They are gram positive bacteria related to Streptococcus.

Haemophilus: These species belong to the γ-proteobacteria as well. They are rod-shaped, gram negative bacteria related to E. coli.

Leptotrichia: The Leptotrichia species are long, filamentous, gram negative, anaerobic, bacteria in the Bacteroides group.

Neisseria: Neissria is a genus in the β-proteobacteria group. They are usually small, aerobic, bacteria. N. gonorrhoeae causes gonorrhea and N. meningitidis causes meningitis but most of the species in your mouth are harmless.

Porphyromonas: These are gram negative, anaerobic, members of the Bacteriodes group. P. gingivalis is normally harmless but it can cause periodontal disease.

Prevotella: Prevotella species are gram negative, rod-shaped, anaerobic, bacteria closely related to Bacteriodes. They are among the most common bacteria in the intestines of sheep and cattle where they aid digestion.

Rothia: These gram negative bacteria belong to the phylum Actinobacteria. They are related to micrococcus.

Serratia: These are motile, rod-shaped, gram negative bacteria. S. marcescens grows in bathrooms where it is often found on tile grout. The bacteria produce a characteristic red pigment and that's why contaminated areas appear pink.

Streptococcus: Streptococcus species are small, gram negative, nonmotile, and round. They are mostly facultative anaerobes. Individual bacteria associate in long chains. It is the most common genus in mouth cultures.

Vellionella: These common species are gram negative, anaerobic cocci.

There are problems with bacterial phylogeny, especially with a classification that relies exclusively on the sequences of ribosomal RNA [Bacteria Phylogeny: Facing Up to the Problems]. Reliable trees can be constructed using concatenated sequences and these trees (see below) reveal that the main groups of bacteria diverged from each other billions of years ago.



(You can see a high resolution image here.)

Note that the Firmicutes (red) are on the same branch as Actinobacteria (olive green) but these two groups are still as distantly related as dogs and dandelions. The α-proteobacteria (orange) are also very distantly related. The diversity of bacterial species in your mouth is truly remarkable.

Stoneking's group was interested in the differences between humans and especially between groups living in different parts of the world. Stoneking was one of the original authors on the Mitochondrial Eve paper so I suspect he was looking for bacterial markers that he could use to trace human ancestry.

Unfortunately, there isn't much difference between individuals or between groups from different parts of the world. The most significant geographical variation is between the samples from the Congo and everyone else. People in the Congo have a higher percentage of Enterobacteria. The only other significant difference is that there tend to be fewer Prevotella in people from Louisiana.

The somewhat surprising conclusion is that diet, culture, and environment don't seem to play much of a role in the diversity of the human salivary microbiome.

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Nasidze, I., Li, J., Quinque, D., Tang, K., and Stoneking, M. (200() Global diversity in the human salivary microbiome. Genome Res. Published in Advance February 27, 2009, [doi:10.1101/gr.084616.108] [Genome Research]

I. Nasidze, J. Li, D. Quinque, K. Tang, M. Stoneking (2009). Global diversity in the human salivary microbiome Genome Research DOI: 10.1101/gr.084616.108

When Chiropractors Get Angry ....

 
Gary Goodyear is Canada's Minister of State (Science and Technology). He's also a chiropractor.

Last week he met with two representatives of the Canadian Association of University Teachers (CAUT). CAUT has a long history of lobbying in favor of increased funding for university research. Apparently the meeting didn't go well [Researchers fear 'stagnation' under Tories].

The screaming erupted last Wednesday afternoon, just down the street from Parliament Hill, in the offices of a Conservative cabinet minister.

Two officials with Canadian Association of University Teachers sat on one side of a boardroom table and on the other sat Gary Goodyear, Minister of Science and Technology, his policy adviser Wesley Moore and a civil servant ready to take notes.

CAUT, a lobby group that represents 65,000 staff at 121 colleges and universities, had planned to raise concerns over the government's handling of research funding. But within moments, it became clear they wouldn't get very far.

“The minister was very angry,” said David Robinson, associate executive director of CAUT. “He was raising his voice and pointing his finger … He said everyone loves their [federal budget] and we said, ‘A lot of our members don't love it'… and he said, ‘That's because you're lying to them, misleading them.'”

The talks, Mr. Robinson said, went from bad to worse. In 15 years on the job, he “never had a meeting like that.”

Mr. Goodyear agrees. “I, too, have never had a meeting like that. It was a unique experience and one I don't care to repeat.”

I don't know what could possibly have gone wrong. Perhaps it was something that Mr. Goodyear said?

Mr. Goodyear said he has met university presidents, deans of research, and researchers themselves and believes government critics are few. “You're going to see that one person who didn't get what they wanted,” he said. But “eight out of 10 folks I talk to get it … they are very positive.”

Mr. Goodyear, a chiropractor from Cambridge, Ont., said the government has been steadily investing in science and technology since 2006, with a new emphasis on commercialization and that it has designed an overall strategy to ensure Canada remains a world leader in research.

“We have done everything right,” he said.

Or maybe it had something to with the change in science policy since the Conservatives took over in 2006?

After years of double-digit budget increases in the early 2000s, government contributions in recent years to NSERC, SSHRC and CIHR have barely kept pace with inflation – and last year they underwent a government-mandated strategic review to reduce their spending.

So while the Barack Obama administration in Washington has added $10-billion (U.S.) to finance basic research in the United States, the three agencies that back basic research in Canada must cut spending by $148-million over the next three years.

CIHR, for example, Canada's main funding body for medical research, has to find about $35-million in savings by 2012, and $28-million of that is by eliminating a program that provided grants to research teams.

In any case, it ended badly ...

CAUT, however, is less confident. It was the position of researchers fretting for the future the lobby group hoped to represent at last week's meeting with Mr. Goodyear.

They had barely begun to state their case, Mr. Robinson said, when the minister accused them of twisting facts.

When CAUT staff said the Conservatives have a spotty record on science and noted they abolished the office of the national science adviser, Mr. Robinson said, the minister's assistant screamed at them to shut up.

“Then the minister said, ‘You've burned all your bridges with us!' and they stormed out.

“In all the meetings I've been in like this, I've never been shouted at and told to shut up,” Mr. Robinson said. The civil servant who escorted them to the elevator suggested it would not even be a good idea to return to the minister's office to collect their coats, he said. Instead, she retrieved them.

This meeting is more extreme than most but it confirms an impression I had when I used to go up to Ottawa for those lobbying weeks in March. When dealing with the Conservatives, the only workable strategy is to vote them out of office as quickly as possible.

Trying to reason with them doesn't work.

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Liberal Party Policy Development Workshop

 
Here's where I'll be this evening.

WHEN:
Monday, March 2, 2009
7:30 - 10:00 PM

WHERE:
Mississauga Central Library
Meeting Room #3, second floor

PRICE:
Cost: $5 (to recover room and refreshment costs)

CONTACT:
For more information, please contact
Sharon McCarthy 905 828 5786
Omar Alghabra 416 564 5468

NOTES:
The Mississauga-Erindale Federal Liberal Riding Association is organizing an informative and engaging workshop on policy development and promotion. The workshop will be facilitated and presented by Maryanne Kampouris, Vice President, Policy, Liberal Party of Canada (Ontario)

The session will discuss policy development process touching upon different components, including Party structure, Policy Structure, role of the riding association, role of the policy committee with practical ideas on how to engage constituents in 'ideas' or policy discussions.

The session will include practical discussion on how riding associations can proceed in engaging their members and their constituents in this process.

The purpose of this workshop is to empower Liberals and educate them on how to convert their policy ideas into real resolutions that can make a difference, and how to promote and advocate for their policy ideas.

Does anyone have any suggestions? How can the Liberal riding associations engage voters and make them care about defeating Stephen Harper and the Conservatives?

We should probably start with hiring a proofreader for press releases but is there anything else?

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Can We Win in Afghanistan?

 
It's seems like only a few years ago (March 6, 2006) when Prime Minister Stephen Harper said this ...

A debate on whether Canadian troops should be in Afghanistan would put the troops in danger, and any attempt to pull them back would be a betrayal, says Prime Minister Stephen Harper.

Harper, speaking after a cabinet meeting on Tuesday, stressed that the previous Liberal government committed the troops to their Afghan mission, which has proved deadly in recent weeks, and that the Conservatives will honour the commitment.

"I'm saying that Canadians don't cut and run at the first sign of trouble," he told reporters. "That's the nature of this country, and when we send troops into the field, I expect Canadians to support those troops." He repeatedly rejected the idea of a debate and said his government will not make decisions based on opinion polls.

"I understand the frustrations," he said. "Perhaps the previous government should have had a vote on the deployment, but that was not their decision. The decision was taken and we can't change our opinion when the troops are in danger."

He did not say why a debate in Canada would put soldiers at risk in Afghanistan, but he stressed it is "a very dangerous mission. "It's not the intention of this government to question the particular commitment when our troops are in danger," he said. "Such a debate or such a lack of strength by any of the political parties in Canada will merely weaken the resolve of our troops and will even put our troops in even more danger."

At the time, the issue was all about "supporting the troops." The danger, according to Harper, was in raising the possibility that our soldiers might have died in vain. That's unacceptable to many Canadians. Unacceptable, perhaps, but is it true?

Here's what Prime Minister Stephen Harper said yesterday, according to The Canadian Press [Western forces alone can't beat Afghan insurgents: Harper].

Western forces alone can never defeat the Taliban insurgency in Afghanistan and President Barack Obama better realize that in shaping his strategy there, says Prime Minister Stephen Harper.

In an interview aired Sunday on the U.S. cable news network CNN, Harper said he's "delighted" the president is sending more troops to the country in the short term.

Many of them will be deployed in the Kandahar region, where more than 2,000 Canadian soldiers already on the ground can use the help.

But in the longer run, said Harper, it's the government in Kabul that will have to run its own country and be responsible for its own security.

"We're not going to win this war just by staying," he told interviewer Fareed Zakaria.

"Quite frankly, we are not going to ever defeat the insurgency. Afghanistan has probably had - my reading of Afghanistan history (is) it's probably had an insurgency forever of some kind."

"What has to happen in Afghanistan is we have to have an Afghan government that is capable of managing that insurgency."

Asked if the current administration of President Hamid Karzai has the legitimacy to do that, Harper replied: "There is no doubt that governance in Afghanistan has to improve, and has to improve, and has to improve, much more quickly than we've seen."

Harper has repeatedly stated he's sticking to a commitment to pull Canadian combat forces out of Afghanistan by the end of 2011, although Canada would likely maintain a more limited presence focusing on development and reconstruction.

Obama said on his recent visit to Ottawa he didn't press the prime minister to change his mind. But if the U.S. leader did ask him to stay, Harper said Sunday, he'd want to know more about the long-term goals and the ultimate end date for the mission.

"Over the long haul, if President Obama wants anybody to do more, I would ask very hard questions about what is your strategy for success and for an eventual departure."

The comments are not a radical departure from Harper's past observations but he has rarely been so blunt in assessing the situation.

It's true that right now Canada is committed to withdrawal in 2011, so, in that sense, these comments don't represent a shift in policy.

However, Harper's current "bluntness" does make some of his earlier comments look hypocritical. If he really knew his history, as he now claims, then he has known all along that foreign troops can't impose an unpopular government on the people of Afghanistan. In other words, he knew that Canadian troops would die in a hopeless cause.

And why is Harper "delighted" that more US soldiers are about to die in Afghanistan in the same hopeless cause?

Now we need to hear from Michael Ignatieff, the leader of the Liberal Party. Can he be as honest with the Canadian people as Harper was yesterday? I hope he can.

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[Thanks to The Galloping Beaver and Canadian Cynic]