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]

Gasoline Temperature Maps

 
I recently posted about problems with the Alberta oil sands and the impact on carbon emissions and the environment [The Problem with the Alberta Oil Sands].

I noted that Alberta had received lots of money from the oil companies and suggested that the provincial government was well-positioned to take the lead in developing cleaner methods of extracting oil. I specifically said that the province had "plenty of room to manoeuvre."

One commenter noted that the provincial government doesn't have as much money as we think. But that wasn't the entire point. I was also referring to the fact that provincial income taxes are lower in Alberta and the province does not have a sales tax.

I was thinking about gasoline prices as well. Here's a map of current gas prices across Canada from GasBuddy.com. Most of the differences are due to taxes. Notice anything peculiar about Alberta—the province that's being accused of so much pollution? I think there's room to manoeuvre if it's serious about climate change.


Here's the USA map for comparison.



A typical US price is $2 per (US) gallon. The current Canadian dollar is equivalent to about 0.8 US dollars and there are 3.79 litres per US gallon. This means that a typical US gas price of $2.00/gal is equivalent to 53¢(US)/liter or 66¢(CDN)/liter.

A typical price for Canadian gas is about 86¢(CDN)/liter so the USA is selling gasoline for 20% less than Canada. I think this is mostly due to lower taxes.

I don't know what the current price of gasoline is in Europe but I suspect it's much more.

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