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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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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