Monday's Molecule #116: Winners

 
UPDATE:The photographs of the mouse embryos are from a paper by Kothary et al. (1989). This was a study where a lacZ (β-galactosidase) gene under the control of a strong, ubiquitously competent promoter was introduced into mouse zygotes. When the gene was induced (right) the presence of β-galactosidase was detected by a blue color assay. The foreign gene is induced in almost every tissue.

These sorts of experiments in construction of transgenic mice were later extended by the work of Nobel Lauteates Mario Capecchi, Martin Evans, and Oliver Smithies who developed techniques for using embryonic stem cells.

Several people guessed the Nobel Laureates but only two people provided an explanation of the "molecule." Dima Klenchin, who is ineligible, was the only one to pick up on the hint and find the 1989 paper.

The winner is Shumona De of Dalhousie University.

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If you look closely you'll realize that these mouse embryos aren't really "molecules" in any meaningful sense of the word "molecule." That doesn't matter 'cause I still want you to identify what's going on here. This is the first time that I've resorted to using photographs from my previous life—shows you how desperate I'm getting!

The images are supposed to remind you of the work of some Nobel Laureates. See if you can guess who they are.

The first person to identify the photographs and the Nobel Laureates 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 eight ineligible candidates for this week's reward: David Schuller of Cornell University, Adam Santoro of the University of Toronto, Dima Klenchin from the university of Wisconsin, Alex Ling from the University of Toronto, Bill Chaney of the University of Nebraska, Elvis Cela from the University of Toronto, Peter Horwich from Dalhousie University, and Devin Trudeau from the University of Toronto.

Dima and Bill have donated 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 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.

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

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Kothary, R., Clapoff, S., Darling, S., Perry, M.D., Moran, L.A., Rossant, J. (1989) Inducible expression of an hsp68-lacZ hybrid gene in transgenic mice. Development. 105:707-14. [PDF]

Applying to NSERC? Everyone gets a grant!

 
According to a study done by Richard Gordon and Bryan J. Poulin, Cost of the NSERC Science Grant Peer Review System Exceeds the Cost of Giving Every Qualified Researcher a Baseline Grant. (NSERC is Canada's funding agency for non-medical science research.)

Using Natural Science and Engineering Research Council Canada (NSERC) statistics, we show that the $40,000 (Canadian) cost of preparation for a grant application and rejection by peer review in 2007 exceeded that of giving every qualified investigator a direct baseline discovery grant of $30,000 (average grant). This means the Canadian Federal Government could institute direct grants for 100% of qualified applicants for the same money. We anticipate that the net result would be more and better research since more research would be conducted at the critical idea or discovery stage. Control of quality is assured through university hiring, promotion and tenure proceedings, journal reviews of submitted work, and the patent process, whose collective scrutiny far exceeds that of grant peer review. The greater efficiency in use of grant funds and increased innovation with baseline funding would provide a means of achieving the goals of the recent Canadian Value for Money and Accountability Review. We suggest that developing countries could leapfrog ahead by adopting from the start science grant systems that encourage innovation.

This sounds like a good idea to me. Thanks to Bora Zivkovic of A Blog Around the Clock for finding the paper.

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Royal Protocol

 
Ever country has a protocol officer and part of their job is to specify how one is supposed to treat the Head of State. In America, for example, you must always refer to the President as Mr. President and unelected cabinet ministers are addressed as Mr./Madam Secretary [Office of the Chief of Protocol].

Visiting Heads of State are expected to conform to American protocol and when the President visits another country he is expected to conform to their rules of protocol. That's how international diplomacy works. It's a system that has evolved over several centuries to try and makes things easier when two different countries communicate. The idea is for countries to respect each other.

Postdiluvian at The Unexamined Life doesn't think that Americans need to respect the protocols and traditions of a foreign country [Is it OK to hug the Queen?]. Now, as it turns out, Michelle's hug was a breach of protocol but not that big a deal, even in England. It would be comparable to someone forgetting to say "Mr. President" when addressing Barack Obama.

That doesn't justify this kind of response ....

Now here’s the bottom line: you can have your “Queen” as a powerless (and utterly pointless) figurehead if you like. She can even keep her massive wealth that somehow came into her family’s possession over the centuries. But if you ever start this bullshit about “Royal Protocol” again, or whether or not it’s okay for people to touch her, you will be removing yourself from the realm of the Serious and joining the realm of Laughingstock, much like the concept of Monarchy did ages ago.

Americans often wonder why they have so much trouble making friends in "foreign" countries. I can't imagine why.

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Five Against One

 
It's sounds so unfair. Four Christians against one lone atheist. If you add in the moderator it's five against one.

But the atheist is Christopher Hitchens so they didn't have a chance.¹

Next time they should try half a dozen Christians—and they should look for ones that are smart.²

Christian Book Expo 2009

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1. Actually, if you watch the "debate" you'll realize that Hitchens didn't need to do or say anything. Every single one of their arguments for the existence of God has been refuted dozens of times. It's like a kindergarten class in Christian apologetics. Most of the time I wish Hitchens had kept his mouth shut.

2. Assuming that ....

[Hat Tip: Friendly Atheist]

What Is Epigenetics?

 
Berger et al. (2009) attempt to define epigenetics.

"An epigenetic trait is a stably heritable phenotype resulting from changes in a chromosome without alterations in the DNA sequence."

Sounds good to me. Just about anything wold be better than the kitchem sink definition proposed by Eva Jablonka [Epigenetics at SEED].

The main examples are "DNA methylation, histone modifications, histone variants, and nucleosome positioning." These are chromosomal alterations that are passed on to daughter cells following cell division by mitosis or meiosis.

Although the Berger et al. don't mention it, these epigenetic signals are all reversible. I still don't find the term useful. It's far more accurate to refer to each of the individual examples by name and the field is "regulation of gene expression."

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Berger, S.L., Kouzarides, T., Shiekhattar, R., and Shilatifard, A. (2009) An operational definition of epigenetics. Genes & Dev. 23:781-783. [DOI: 10.1101/gad.1787609]

[Hat Tip: Hopeful Monster]

Monday's Molecule #116

 
If you look closely you'll realize that these mouse embryos aren't really "molecules" in any meaningful sense of the word "molecule." That doesn't matter 'cause I still want you to identify what's going on here. This is the first time that I've resorted to using photographs from my previous life—shows you how desperate I'm getting!

The images are supposed to remind you of the work of some Nobel Laureates. See if you can guess who they are.

The first person to identify the photographs and the Nobel Laureates 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 eight ineligible candidates for this week's reward: David Schuller of Cornell University, Adam Santoro of the University of Toronto, Dima Klenchin from the university of Wisconsin, Alex Ling from the University of Toronto, Bill Chaney of the University of Nebraska, Elvis Cela from the University of Toronto, Paul Horwich from Dalhousie University, and Devin Trudeau from the University of Toronto.

Dima and Bill have donated 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 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.

Comments will be blocked for 24 hours.

---

Religion Wars: Linux and Mac vs. Rationalism

 
Greg Linux is disappointed that the Confliker virus didn't do more damage on April 1st [Did Conflicker Flop? Yes. Why? Nobody knows].

I wasn't worried because I checked all five of my computers and not one them were infected. If they had been, it was very easy to get rid of the worm. My Linux machine didn't have the worm either.

That doesn't stop Greg from offering this advice ...

Experts expect that the worm is going to re-awaken at some time in the future and possibly actually do something. In the mean time, you may want to get rid of it if is on your system.

If you run Windows, the best way to get rid of the computer is to get a Mac or a Linux computer. There are probably other ways to do this but I don't really care. If you are running Linux, this worm can't directly affect you.

Sheesh, those religious nuts sure can be silly.

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The End of Christian America?

 
The number of Americans who don't identify with a religion has increased from 8% in 1990 to 15% today. This is encouraging but it doesn't quite mean that the battle between rationalism and superstition has been won.

Nevertheless, the fact that a national magazine could publish an article like "The End of Christian America" is an indication that the debate is on.

If North American societies become much less religious—like those in Europe—then most of the major problems with creationism will go away. Maybe then we can concentrate on promoting good science education. That's why some of us would rather put our efforts into promoting rationalism over superstition rather than defending specific creationist attacks on schools.

Both approaches are needed but those who advocate the compatibility of science and superstition are not helping.

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[Hat Tip: Hemant Mehta who has some interesting comment.]

Last Week's Scientific Breakthroughs

 
This are stories from the past week that would make good topics for discussion. I don't have time so I'll leave it up to you.

Scientists Find 'Baffling' Link between Autism and Vinyl Flooring

Masturbation could bring hay fever relief for men

New research shows lower educational outcomes for survivors of childhood cancer

6 out of every 10 university students present mathematical anxiety or fear of this subject

Humanoid Robot Helps Scientists To Understand Intelligence

Omega-3 kills cancer cells

How probiotics can prevent disease

UBC study first to show evolution's impact on ecosystems

UT Southwestern researchers reveal how the brain processes important information

Your oral health is connected to your overall health

Penn researchers demonstrate a new model for drug discovery with a fluorescent anesthetic

Humans May Be Losers If Technological Nature Replaces The Real Thing, Psychologists Warn

Milkshakes Are Medicine For Anorexic Teens In Family-based Outpatient Therapy

Hermit Arthropods 500 Million Years Ago?

Alzheimer's Disease Linked To Mitochondrial Damage

Robot Scientist Becomes First Machine To Discover New Scientific Knowledge

Virus-built Battery Could Power Cars, Electronic Devices

Athletic Ability May Lie in a Single Gene

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Washington D.C.

 
In a few days I'll be on my way to Washington (Bethesda, actually) to attend the Center for Inquiry World Congress 2009. Let me know if you'll be there and we can meet up.

Here are the main events ....

Thursday April 9, evening: Panel: The Influence of Darwin

Friday April 10, afternoon: Science and Public Policy

Friday April 10, 5:45pm: James Randi: Search for the Chimera

Saturday April 11, morning: Skepticism and Science

Saturday April 11, 5pm: Special Feature: Separation of Church and State

Sunday April 12, morning: Secularism Around the World

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Darwin Rocks

 
Watch this video about evolution and see if you can figure out what's going on. You can check your answer here.

In the fight to increase scientific literacy, I'm not sure if this contribution is useful, useless, or counter-productive but I'm leaning toward counter-productive.

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[Hat Tip: John Dennehy, who leans toward the "useful" point of view.]

Will Universities Survive?

 
Believe it or not, there are supposedly intelligent people out there who think the internet will replace universities.¹ It didn't take Sean Caroll very long to come up with some excelent reasons why this ain't gonna happen [Will the Internet Replace Universities?].

Let me add one more—research experience. You can't learn what it's like to work in a research lab if you're sitting at your desk in the suburbs.

Why do I get the feeling that most people don't understand what a university is supposed to be like? Is it true that most people think of universities just as places where you come and listen to lectures and then go home?

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1. Back in 1970 their parents were convinced that television would mean the end of universities as we know them.

Electronic Textbooks

 
There's an article in this week's issue of Nature on The textbook of the future.

Most of the article is about a Kindle version of science textbooks.

Another drawback of current e-readers is that they have small black-and-white displays, just a little larger than 9 by 12 centimetres. This makes them unsuited to most science textbooks, which typically have large pages and colourful graphics. "The market is not likely to expand until the e-readers improve," says Hegarty.

Publishers are experimenting with ways of delivering their textbooks electronically (e.g. CourseSmart) but there are still problems to be solved.

Competing ideas, such as Wiki's that replace textbooks, have a long way to go before they become a threat to the textbook market [Wikibooks: Biochemistry]. Besides, there are other problems that need to be solved.

For now these free textbooks remain a cottage industry, says Esposito. Wikipedia-like volunteer efforts are much better suited to self-contained modules that are small enough for an individual to see through from A to Z. But a textbook demands a coherent overall structure and coordination between sections. That is why creating one has always been a major undertaking, demanding long-term commitments by publishers — who need to make a profit — and by authors who usually want to be paid for their effort.

Still, perhaps 'free' and 'profitable' need not be a contradiction in terms. One group of veteran textbook publishing executives is trying to put open textbooks on a solid commercial footing. In 2007 they created Flat World Knowledge, based in Nyack, New York, and in January 2009 rolled out the first of the 21 textbooks they have in development so far. The texts are written by some 40 domain experts who will be paid 20% of royalties. The company also plans to make its content available via Kindle and other e-readers. All its content will be free to reuse for non-commercial purposes under a creative commons licence.

Eric Frank, Flat World's co-founder, says that the strategy is to attract greater use by giving the e-textbooks away — the initial targets are the high-volume texts for first-year students — and then look for profit from students' purchase of print-on-demand versions at $29.95 for black and white, and $59.95 for colour. Students can copy and use the electronic content in any way they wish, says Frank. "Cheap prices are the most effective digital-rights management," he says. "We want to avoid a digital-rights war with students." The company also hopes to make money by licensing its content to commercial companies, such as distance-learning outfits and course-management software firms.

I think there's going to be a way to make cheaper electronic versions of textbooks and still compensate the people who do all the work. I'm not sure how it's going to work but I'd love to put my book on a website where I can make changes quickly and get instant feedback from the users.

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James Lunney: Creationist, Chiropractor, Conservative

 
Meet Dr. James Lunney a chiropractor and a Conservative Party Member of Parliament for Nanaimo-Alberni in British Columbia.

"Dr." Lunney recently made a fool of himself by making the following statement in the House of Commons as reported in Maclean's magazine [James Lunney v. Evolution].

Mr. Speaker, recently we saw an attempt to ridicule the presumed beliefs of a member of this House and the belief of millions of Canadians in a creator. Certain individuals in the media and the scientific community have exposed their own arrogance and intolerance of beliefs contrary to their own. Any scientist who declares that the theory of evolution is a fact has already abandoned the foundations of science. For science establishes fact through the study of things observable and reproducible. Since origins can neither be reproduced nor observed, they remain the realm of hypothesis.

In science, it is perfectly acceptable to make assumptions when we do not have all the facts, but it is never acceptable to forget our assumptions. Given the modern evidence unavailable to Darwin, advanced models of plate techtonics, polonium radiohalos, polystratic fossils, I am prepared to believe that Darwin would be willing to re-examine his assumptions.

The evolutionists may disagree, but neither can produce Darwin as a witness to prove his point. The evolutionists may genuinely see his ancestor in a monkey, but many modern scientists interpret the same evidence in favour of creation and a creator.

PZ Myers is making fun of Canada by posting Lunney's remarks on Pharyngula. He's right. We deserve it. Lunney is a genuine kook who quite obviously wouldn't know real science if it bit him on the backbone.

Listen up, all you people who live on Vancouver Island! Don't send this guy back to Ottawa after the next election or you're going to look very silly.

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March on Sandwalk

 
Bora's doing it and Greg Laden is doing it. They're revisiting their posts from last month.

Now I'm doing it too.

Last month Sandwalk attracted 107,747 page views and 75,156 visits from all over the world. That's a new record. I posted 123 times.



The month began with an account of my streetcar ride and the atheist sign campaign in Toronto [The Streetcar We Desire]. I also celebrated the 35th anniversary of my thesis defense.

There were three debates that took up a lot of posting time.

One of them was about positive selection in humans, especially the idea that human evolution might have accelerated in the past 10,000 years. I tried to explain why some of the data looks suspicious in Signals of Positive Selection in Humans?.

We also talked a lot about the quality of science journalism. The two topics were combined when I reviewed SEED magazine's coverage of a recent book on accelerated human evolution [SEED Reviews The 10,000 Year Explosion].

The third debate was about Canada's science minister, Gary Goodyear, and the fact that he is a creationist [Gary Goodyear "Clarifies" His Stance on Evolution].

I'm pretty proud of this posting: Casey Luskin on Junk DNA and Junk RNA. It generated some comments and got a mention on several blogs.

Speaking of comments, one other posting caught the attention of Sandwalk readers and stimulated comments. You were interested to know why I Hate Cilantro/Coriander!.

In terms of most popular postings there was nothing in March that's going to make the top 20 postings. I still get a lot of traffic from people who want to learn about The Genetics of Eye Color from a posting in February 2007. Another popular posting is The Genetics of ABO Blood Types, also from February 2007.

As usual, there were lots of people who tried to guess Monday's molecule. There are a small number of regulars who get most of the prizes, The rest of you are going to have to be faster. I think I'll try and post much earlier in the day to give my European readers a better chance. We don't need to worry about giving the Australians a chance 'cause they probably wouldn't win anyway! :-)

We had an interesting group of Nobel Laureates. These postings always get looked at but nobody leaves comments. I guess there isn't much to say. The most interesting Nobel Laureates from my perspective were Frederick Banting and J.J.R. Macleod because they're from the University of Toronto. Several of the recent prize winners were controvesial, especially Selman Waksman.

Does anyone have suggestions for future postings?

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A field guide to misunderstandings about open access

 
Want to find out what Open Access is really all about? Read A field guide to misunderstandings about open access.

Do you think that articles in open access journals aren't peer reviewed? Think again.

Do you think that all open access journals charge huge publication fees? Wrong.

Do you think that open access journals are lower quality? Nope.

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[Hat Tip: Bora Zivkovic: A Blog Around the Clock]

Dynamic Genomes

There may have been a time in the past when scientists imagined a static genome that only changed slowly over millions of years. However, beginning in the 1960's we began to see the genome as a much more dynamic entity. The first evidence of this kind of genome came with the discovery of huge amounts of variation between individuals in a species.

This was followed by the discovery of transposons and junk DNA. We began to see genomes as rather sloppy DNA molecules with lots of pieces hopping in and out on a timescales of generations. We began to realize that many genomes were full of pseudogenes.

Chromosomal rearrangements such as inversions, duplications, and translocations were documented. In mammals, many of them were associated with cancer, thalassemias, and other diseases but the general impression was that these rearrangements of genetic material were quite common. Indeed, some non-disease examples began to accumulate in the literature. Clear evidence of normal rearrangements associated with regulation and development—including mating type switching in yeast, immunoglobulin rearrangements in mammals, chorion gene amplification in Drosophila, and antigenic variation in trypanosomes—reinforced the idea that the genome was not static.

Most of this information was incorporated into the textbooks. For example, by the early 1980's Benjamin Lewin' textbook Genes had an entire group of chapters under the heading "The Dynamic Genome: DNA in Flux."

We soon learned about the expansion and contraction of repetitive sequences in the human genome. These observations eventually gave rise to DNA fingerprinting whereby every individual could be uniquely identified by variations in the genome.

By the early 1990's the concept of the dynamic genome had become so widely entrenched among molecular biologists that when Singer and Berg published "Genes and Genomes" they felt obliged to inject a note of caution. While genomes are dynamic at the scale of species evolution, the typical genome of an individual is not subject to significant rearrangements.

Outside of molecular biology, the idea that genomes were flexible never seemed to catch on. Most people thought of genomes as relatively static entities that didn't change much over millions of years. In part, they adopted this position because they still placed a great deal of emphasis on the power of natural selection. If genomes were well-adapted then why would they change? Part of the skepticism about junk DNA stems from the belief that selection will eliminate useless DNA.

Recent developments have stirred many people to re-think their concept of genomes. For example, Sandra Porter of Discovering Biology in a Digital World recently asked, "What if everything you thought you knew about the genome was wrong?."

To the extent that such questions acquaint people with the concept of a dynamic genome, they are good. On the other hand, if such questions lead to the unthinking acceptance of alternative splicing, superabundant transcription, and a plethora ot RNAs, they are bad.

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Handel's Messiah

 
One year Ms. Sandwalk took the entire family to see a full performance of Handel's Messiah. It was agony, except for one brief part of the performance where we all got to stand up. Ms. Sandwalk thought it was wonderful but, remember, she also likes some country music.

My children still talk about it. I guess it's one of those "experiences" that contribute to character building, or something.

Now there's an explanation in New Scientist: How misery inspired Handel's Messiah. I knew there had to be a reason.

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Monday's Molecule #115: Winners

 
UPDATE: The molecule is indigotin or indigo dye [2,2’-Bis(2,3-dihydro-3- oxoindolyliden)]. The Nobel Laureate is Johann Friedrich Wilhelm Adolf von Baeyer.

This week's only winner is Alex Ling from the University of Toronto.

The winners this week are Pete Horwich from Dalhousie University and Devin Trudeau from the University of Toronto.

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Identify this molecule and explain why it is useful. You must supply the common name and the formal IUPAC name.

I'm looking for the Nobel Laureate whose name is associated with this molecule.

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: Maria Altshuler of the University of Toronto, David Schuller of Cornell University, Adam Santoro of the University of Toronto, Dima Klenchin from the university of Wisconsin, Alex Ling from the University of Toronto, Bill Chaney of the University of Nebraska, and Elvis Cela from the University of Toronto.

Dima and Bill have donated 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 it. Please indicate in your email message whether you are an undergraduate and whether you can make it for lunch.

THEME:

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

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

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

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Nobel Laureate: Adolf von Baeyer

 

The Nobel Prize in Chemistry 1905.

"in recognition of his services in the advancement of organic chemistry and the chemical industry, through his work on organic dyes and hydroaromatic compounds"


Johann Friedrich Wilhelm Adolf von Baeyer (1835 - 1917) won the Nobel Prize in Chemistry for his work on the preparation of organic dyes from coal tar.

His most notable achievement was the synthesis of indigo dye and determination of its structure. A cheap industrial synthesis of indigo was soon developed, freeing Europe from its dependence on indigo from India.

He was also the first person to synthesize phenolphthalein, the well-known acid or base indicator.

The presentation speech highlights the importance of the relationship between basic science and industry.
THEME:
Nobel Laureates

The complex and unique composition of indigo, however, made this also one of the hardest of tasks. Here there could be no question of one of those casual discoveries, which by happy accident seem to achieve half the work. Years of work were required for even von Baeyer's acumen and experimental skill to achieve the necessary insight into the pigment's chemical composition and to be able to manufacture it from simpler constituents. Even after the purely scientific part of the work had been completed it still took a number of years to make the results obtained from research applicable to technology.

Von Baeyer succeeded in producing indigo synthetically in three principal ways, namely from ortho-nitrophenylacetic acid, from ortho-nitrocinnamic acid and from ortho-nitrobenzaldehyde and acetone. This paved the way for the reproduction of indigo from raw material obtainable without much difficulty from coal tar. And if the problem of producing indigo industrially has now been solved from the technical as well as the economic point of view, this is entirely due to von Baeyer's basic work in the fields in question.

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

2,296,911 visits?

 
It's April 1st and PZ Myers tells us that Pharyngula had 2,296,911 visits last month [What are all you people doing here?].

Problem is, I don't think this is an April Fool's joke.¹

There are already 225 comments to that posting, which is probably what PZ means when he asks what everyone is doing there. Now he knows—they're posting comments!

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Sandwalk had 107,747 visits or less than 5% of the number that visited Pharyngula.

Nobel Laureate: Michael Behe

 

The Nobel Prize in Biochemistry 2009.

"for his contributions to understanding complex biological systems"


Michael Behe (1952 - ) wins the Nobel Prize in Biochemistry for his amazing work on complex biological systems, especially the concept of irreducible complexity.

Beginning with the publication of his first book, Darwin's Black Box, Behe has written numerous articles on the organization of molecular machines such as the snare complex of Mus musculus and the bacterial flagellum. He has shown that these systems exhibit a fundamental property that previous biochemists overlooked—they are so well integrated that their origin cannot be explained by the older naturalistic theory of natural selection.

His later work, The Edge of Evolution, is a seminal contribution to modern evolutionary theory. In that book he explains how previous versions of evolution are incapable of explaining the origin of protein-protein interaction sites.

The presentation speech highlights the importance of this work.
THEME:
Nobel Laureates

The development of protein features, such as protein-protein binding sites, that require the participation of multiple amino acid residues is a profound, fundamental problem that has stumped the evolutionary biology community until the present day (and continues to do so, as I explain below). It is a fundamental problem because all proteins exert their effects by physically binding to something else, such as a small metabolite or DNA or other protein, and require multiple residues to do so. The problem is especially acute for protein-protein interactions, since most proteins in the cell are now known to act as teams of a half-dozen or more, rather than individually. Yet if one can’t explain how specific protein-protein interactions developed, then it is delusional to claim that we can explain how anything that depends on them developed, such as the molecular machinery of the cell. It’s like saying “we understand perfectly well how a car could evolve; we just don’t know how the pieces could get fit together.” If such a basic requirement for putting together complex systems is not understood, nothing is understood. Keep this in mind the next time you hear a blithe Darwinian tale about the undirected evolution of the cilium or bacterial flagellum.

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Posted on April 1st, 2009.

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.

Advice for Women: What to Do When You Discover He's an Atheist

 
Friendly Atheist found the answer on YouTube.

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Sean Eddy on "Open Education"

 
I've been thinking a lot lately about how to get my textbook online without asking everyone involved to work for free. It's not an easy problem.

There's a myth out there that some places like MIT are putting up all kinds of useful information for free. The Open Courseware project sounds really exciting until you realize that they can't publish any of the slides they use in their powerpoint presentations because they're all copyrighted. It also doesn't take much perusal to realize that many MIT professors don't know as much about their subjects as you might imagine.

There's a new book advocating the concept of "Open Education" ("Opening Up Education" T. IIyoshi and M.S.V. Kumar eds. MIT Press). The book is reviewed by Sean Eddy on PLoS Biology [Open Revolution].

Sean Eddy used to be an active participant on the talk.origins newsgroup back when he was a graduate student so I eagerly followed the link to his review. I wasn't disappointed. It's the same Sean Eddy that I knew 12 years ago. He can still recognize bullshit when he sees it.

So, while I like storming the establishment with pitchforks and torches as much as anyone, when I picked up Opening Up Education (or rather, when I downloaded the PDF to my Kindle), I was looking for pragmatism, not utopianism. After 500 pages of “the silos we all know about in higher education are under assault in the new world,” the “hated textbook publishers,” the “epistemological hegemony of higher education,” and the “noble philosophy” of making everything free—“traitors” and “patriots” and “communists,” oh my!—my hopes were beaten down. Many of the 30 essays in this collection are more manifesto than explanation, and many of the 38 authors are writing more for their fellow revolutionary comrades than for us.

Life is never as simple as the Web 2.0 fans make out. Somebody is going to have to do a lot of work before the quality of a website matches what's in the best introductory textbooks. And it's extremely naive to think that all that work is just going to be given away for free.

I'm not just talking about authors. There's a whole team of people involved in publishing my textbooks. This includes editors who correct my spelling and grammar—an onerous task in my case. It includes artists who make the figures and editors who obtain permissions and copyrights for photographs. Then there's the staff at the publishers who receive and mail out manuscripts for review and editing and who handle all the paperwork/electrons associated with a major project.

Are we going to ask all of them to work for free by putting everything on the web? Of course not.

Sean does an excellent job of bursting the bubble.

“Remix,” “collective wisdom,” “Web 2.0”—many of these essays ride a bubble of popular digital punditry enthusiastically but too uncritically. Many technologists today are infected with an idea that “community is king,” that high-quality content will rain down freely merely because we connect digital communities openly. This confuses ways of sharing ideas with ways of creating ideas. It is a kind of magical thinking that has much in common with the cargo cults that cut landing strips in the jungle and carved radios from sticks in hope that more sophisticated beings would parachute technological artifacts down upon them. With all respect to the passionate and pioneering initiatives described in this collection, building landing strips to receive open educational content will not be enough. More attention must be paid to the fact that someone still needs to spend time painstakingly developing artful ways to make difficult concepts understandable—to teach!—and that it will take even more time (thus money) to render these hard-won ideas using multimedia web technology compared with writing textbooks. Success hinges on the adoption of open licensing by the professionals who make digital educational resources, and on finding ways to finance their work.

I have some ideas. I'd like to put my book on the web so that everyone can read it but nobody can download it or print out the figures and text. If you need a printed version you can sign on to the server and print out a chapter for $3. The pages would come with your name and email address printed in the header and footer—or perhaps as a watermark. The idea is to make the material available at minimal cost to an individual user while inhibiting the distribution of photocopies.

No matter how easy it is to read something online, I think there's still a market for a printed version of the material. I know from personal experience that highlighting and scribbling in the margins on my computer monitor doesn't work.

Online textbooks have several advantages such as hyperlinks, frequent revisions and updates, and interactive learning. But we need to find a way to pay for it. If you think the work is going to be given away for free then you are living in a dream world. Check out the MIT Open Courseware site under Biology to see what the cargo cult version of Web 2.0 gets you.

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[Photo Credit: Nature]

[Hat Tip: Jonathan Eisen at The Tree of Life]

Religion and Child Abuse

 
I don't think that religious indoctrination is always an example of child abuse. However, there are other ways that count as clear examples of abuse [Taliban blocks UN polio treatment in Pakistan].

Militants had reportedly agreed to allow the [polio] vaccination program to take place as part of the peace agreements.

However, the militants had reneged on their word and despite assiduous efforts made by the increasingly irrelevant local administration, no vaccinations have taken place.

“It’s a US tool to cut the population of the Muslims. It is against Islam that you take a medicine before the disease”, said, Muslim Khan, Swat’s Taliban spokesman, speaking by telephone.

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[Photo Credit: daylife/Reuters: "A man holds his twins as he waits for them to receive polio vaccines in the southern province of Kandahar September 21, 2007. Afghan health officials said on Friday they had brokered a deal with Taliban leaders to allow the immunization of children against polio in rebel-held areas in a rare sign of cooperation between the warring sides."]

[Hat Tip: RichardDawkins.net]

Way too Sensitive?

 
The techniques for detecting DNA and RNA are extremely sensitive. This sensitivity often leads to misinterpretations because it become difficult to separate signal from noise. The idea that 90% of our genome may be transcribed into functional RNA, for example, may be due to the sensitivity of an assay that can easily detect tiny amounts of accidental transcription.

Similarly, the often proclaimed ubiquity of alternative splicing may be due to the easy detection of splicing mistakes. Other examples of problems with noise might be the presumed abundance of small regulatory RNAs and the frequency of transcription factor binding sites.

The problem is acute when it comes to analyzing DNA from fossils. There, tiny amounts of contamination can really screw things up. That's why John Hawks is also interested in this problem of over-sensitive DNA assays.

Just how sensitive is the technology? Hawks has found a very interesting and informative example [The trouble with contamination]. This example is about contamination but keep in mind that it also applies to the detection of noise in transcription, DNA binding, and splicing.

Here's the original report from the BBC ['DNA bungle' haunts German police]. Over the past few years German police have been on the lookout for a mysterious woman who was linked to several murders. Her DNA was found at over 40 different crime scenes. This woman became one of the most wanted people in Europe but nothing was known about her aside from her DNA.

Finally someone became suspicious and started to look closely at the way they were collecting and analyzing DNA. To make a long story short, the alleged murderer is a factory worker in Bavaria who works in a factory that manufactures cotton swabs. The same swabs that are used to collect samples at a crime scene. Those swabs were contaminated with her DNA.

There's a lesson here. Any technology that can detect the DNA from a factory worker on a cotton swap is quite capable of detecting tiny insignificant amounts of nucleic acids inside a cell.

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1,2,3 ... What Are We Fighting for?

 
President Obama wants to sacrifice more American in Afghanistan and Canada's Prime Minister, Stephen Harper, is suggesting that this might be something that Canada should support. This is in spite of the fact that there are times when he seems to know the right answer to the question; Can We Win in Afghanistan?.

Let's make sure everyone knows what we're fighting for: 'Worse than the Taliban' - new law rolls back rights for Afghan women.

Hamid Karzai has been accused of trying to win votes in Afghanistan's presidential election by backing a law the UN says legalises rape within marriage and bans wives from stepping outside their homes without their husbands' permission.

The Afghan president signed the law earlier this month, despite condemnation by human rights activists and some MPs that it flouts the constitution's equal rights provisions.

The final document has not been published, but the law is believed to contain articles that rule women cannot leave the house without their husbands' permission, that they can only seek work, education or visit the doctor with their husbands' permission, and that they cannot refuse their husband sex.

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Glass Knives

 
One of the best labs I ever took as an undergraduate was an advanced cytology lab where we learned to use the electron microscope.¹ Part of the process was preparing thin sectioned material and that involved making our own glass knife that would cut very thin slices from wax-embedded tissue.

Here's a video from Leica showing how it's done today.²



I was reminded of this recently when I had occasion to refer to an electron micrograph taken by Harrison Latta. Latta invented the glass knife back in 1949. You can read about his discovery in this tribute to him on the University of California, Los Angeles, website.

This is one of those simple technological innovations that made a huge difference but would never have been recognized by the Nobel Prize committee.

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1. Yes, they had electron microscopes back in those days!
2. You can also buy diamond knives but that's a lot less fun.

YouTube Suspends the Account of the James Randi Education Foundation

 

If you have a YouTube account, follow these instructions.

To complain to youtube follow this link;
http://www.google.com/support/youtube...

Scroll to the very bottom and click on "new issue"

Select "suspended account" from the options and express your opinion.

The mediafire link is;
http://www.mediafire.com/?sharekey=4d...

UPDATE: I was astonished to learn that some readers don't know who James Randi is or what the James Randi educational foundation is all about.

Randi is a former magician ("The Amazing Randi") from Toronto, Ontario (Canada). He is best known for investigating claims of the paranormal and for his one million dollar challenge. He has appeared on television many times and often writes columns and article debunking paranormal claims.

The goal of the James Randi Educational Foundation is ...

The James Randi Educational Foundation is a not-for-profit organization founded in 1996. Its aim is to promote critical thinking by reaching out to the public and media with reliable information about paranormal and supernatural ideas so widespread in our society today.

The Foundation's goals include:

* Creating a new generation of critical thinkers through lively classroom demonstrations and by reaching out to the next generation in the form of scholarships and awards.
* Demonstrating to the public and the media, through educational seminars, the consequences of accepting paranormal and supernatural claims without questioning.
* Supporting and conducting research into paranormal claims through well-designed experiments utilizing "the scientific method" and by publishing the findings in the JREF official newsletter, Swift, and other periodicals. Also providing reliable information on paranormal and pseudoscientific claims by maintaining a comprehensive library of books, videos, journals, and archival resources open to the public.
* Assisting those who are being attacked as a result of their investigations and criticism of people who make paranormal claims, by maintaining a legal defense fund available to assist these individuals.

To raise public awareness of these issues, the Foundation offers a $1,000,000 prize to any person or persons who can demonstrate any psychic, supernatural or paranormal ability of any kind under mutually agreed upon scientific conditions. This prize money is held in a special account which cannot be accessed for any purpose other than the awarding of the prize.

Located in Fort Lauderdale, Florida, the Foundation is funded through member contributions, grants, sales of books and videos, seminars, and conferences.

The current President of the foundation is Phil Plait of Bad Astronomy.

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Monday's Molecule #115

 
Identify this molecule and explain why it is useful. You must supply the common name and the formal IUPAC name.

I'm looking for the Nobel Laureate whose name is associated with this molecule.

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: Maria Altshuler of the University of Toronto, David Schuller of Cornell University, Adam Santoro of the University of Toronto, Dima Klenchin from the university of Wisconsin, Alex Ling from the University of Toronto, Bill Chaney of the University of Nebraska, and Elvis Cela from the University of Toronto.

Dima and Bill have donated 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 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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Ethical Framing

The bad news is that Matt Nisbet has published some guidelines for proper framing. You won't be surprised to learn that Richard Dawkins and PZ Myers are engaging in "unethical" framing [The Ethics of Framing Science: Four Guiding Principles]. You will be surprised to learn that fellow framer Chris Mooney is also unethical.

Although Matt doesn't mention it, I assume that scientists like Ken Miller and Francis Collins are "ethical" framers.

The good news is in the comments section of Nisbet's blog. Hardly anyone agrees with him any more. It looks like his 15 minutes of fame are just about over, proving that Andy Warhol knew more about framing than Matt Nisbet.

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[Photo Credit: Andy Warhol, DeVorzon Gallery]

God Won't Allow Climate Catastrophe

 
You'll be pleased to know that global climate change isn't going to end in catastrophe. Rep. John Shimkus from Illinois says as much during a hearing of the U.S. House Subcommittee on Energy and Environment in Washington.

He quotes directly from the Bible concluding, "The Earth will end only when God declares it’s time to be over. Man will not destroy this Earth. This Earth will not be destroyed by a flood."

It's comforting to know that church and state are separated in America and free speech is sacrosanct.


In Canada we just had a major kerfuffle in the press over a science minister who hinted that he might not believe in evolution. I wonder if Rep. John Shimkus is going to get into trouble for not believing in global warming because it conflicts with the Bible?

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[Hat Tip: Friendly Atheist]

Scientific Breakthroughs for March 30, 2009

 
I was reading the list of press releases on ScienceDaily Headlines and I thought you might be interested to learn about some of the most important discoveries in the past 24 hours. For the most part, these are press releases from universities and research institutes.

None of them are real breakthroughs. Some of them are interesting, incremental advances in our understanding of the natural world. Some of them are trivial results that have been elevated to importance by a press release and a headline. Some of them are silly. Some of them are probably wrong.

• New Breakthrough In Global Warming Plant Production


• Optimal Running Speed Associated With Evolution Of Early Human Hunting Strategies


• Fish Oils Reduce Greenhouse Gas Emissions From Flatulent Cows


• Food Choices Evolve Through Information Overload


• Psychiatric Disorders Are Common In Adults Who Have Had Anorexia


• Genetic Changes Outside Nuclear DNA Suspected To Trigger More Than Half Of All Cancers


• Why Parachutists Die


• Brain Building: Brain Growth Tied To Cell Division In Mouse Embryos


• New Theory On Largest Known Mass Extinction In Earth's History


• Team Approach Appears To Work Best For Insect Colonies

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Free Speech in Oklahoma

 
The Oklahoma legislature is trying to intimidate the University of Oklahoma for inviting Richard Dawkins to speak last month. The Tulsa World publishes an article today that covers both sides of the controversy. After reading that article, the only logical conclusion is that free speech in Oklahoma is being threatened by elected politicians [Dispute evolves on OU speech by scientist].

This is outrageous. How can you have State Representatives advocating laws that violate the American Constitution and the Bill of Rights? Isn't that treasonous?

Oklahoma is one of those states that still has the death penalty and it still carries out executions. According to US Federal Law, the penalty for treason can be death [Capital punishment in the United States]. That raises an interesting possibility when it comes to dealing with creationists.

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[Hat Tip: RichardDawkins.net]

Don McLeroy, Creationist Dentist

 
This has already been posted on Panda's Thumb and elsewhere but it deserves to be seen by everyone. It's Don McLeroy, the creationist dentist who is chair of the Texas Board of Education. He has somehow gotten the idea that he knows more about evolution than the experts.

That makes him very dangerous.

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Old Tools

 
There's a prize for this one!!

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Media distortion damages both science and journalism

 
New Scientist has just published an article on the dangers of bad science journalism. Irony noted.

Simon Baron-Cohen explains how Media distortion damages both science and journalism .

WHEN media reports state that scientist X of Y university has discovered that A is linked to B, we ought to be able to trust them. Sadly, as many researchers know, we can't.

This has three serious consequences. For starters, every time the media misreports science, it chips away at the credibility of both enterprises. Misreporting can also engender panic, as people start to fear the adverse consequences of the supposed new link between A and B. Lastly, there can be a damaging effect on researchers' behaviour. Funding agencies and science institutions rightly encourage scientists to communicate with the media, to keep the public informed about their research and so foster trust. If their work is misrepresented, they may withdraw into the lab rather than risk having to spend hours setting the record straight.

I work in one of those sensitive areas of research, autism, in which the facts are liable to be misreported or - sometimes worse - misinterpreted.

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[Photo Credit: Simon Baron-Cohen: by Brian Harris (GNU Free Documentation License).]

Old Tools

 

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Carl Zimmer on Science Journalism

 
Carl Zimmer has written a lengthy blog posting about the troubles with science journalism [Visions of the Crash]. You should read all of it but I want to comment on one small part.

The rise of blogs about science has brought me many pleasures. I’ve particularly liked the astringent criticism of bad science journalism. As soon as a piece is published, scientists who know the lot about the subject can, if necessary, rip a journalist a new one. I personally have been very influenced by Mark Liberman, a linguist at Penn, who has time and again shown how important it is for reporters to pay attention to the statistics in science. What seems at first like stark results–like the difference between the male and female brain–can melt away if you look at the actual data.

But some bloggers go a step further. They claim that these individual cases of journalistic misconduct add up to an indictment of the whole business. Hence, as Moran declares, we can live without science journalists.

It’s odd that many of the people making these pronouncements are scientists themselves–people, in other words, who know that you don’t do science by anecdote. If a blogger sits down in the morning and reads ten stories in a newspaper’s science section and notices that one that makes a howler of a mistake, you know what that blogger will be writing about. Blogs are an outlet for righteous fury. Bloggers are much less likely to write a post that begins, “I read nine articles this morning about science that were fairly accurate and pretty well written.” Ho hum.

I'm not an expert in everything. Most of the science articles I read are explaining things that are way outside my area of expertise. They may be good articles or they may not be. I'm usually skeptical.

However, the majority of articles I read that fall within my areas of expertise—biochemistry, molecular biology, genomes, evolution—do not impress me. It's not just a case of picking out the worst article out of ten to criticize. It's more like every second article has a problem.

When I talk to people in other fields there report the same statistics. It's looks like the average quality of science journalism, even in popular science magazines like SEED, Discovery, New Scientist, and National Georgraphic, leaves a lot to be desired.

I'm not very happy with most scientific papers either.

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Darwin's two-for-one deal

 
Three cheers for Ryan Gregory! He has published an article in todays Globe and Mail explaining why evolution is both a fact and a theory: Darwin's two-for-one deal.

Go to his blog [Evolution Commentary] and congratulate him.

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How Does Streptomycin Work?

Streptomycin is a powerful antibiotic that inhibits growth of bacteria while having very little effect on eukaryotes. It blocks protein synthesis by binding to the bacterial ribosome.

Let's review the steps of protein synthesis. The three steps are initiation, where the ribosome and factors are assembled at the start codon on the messenger RNA (mRNA); elongation, where the polypeptide chain elongates as the translation machinery moves along the mRNA; and termination, where the assembly falls apart and the completed polypeptide chain is release.

During the elongation phase there are three sites at the interface between the ribosome and the mRNA where transfer RNAs (tRNAs) can bind. The P site holds the peptidyl-tRNA molecule. The growing polypeptide chain is bound to the tRNA molecule that contributed the last amino acid. The A site binds the incoming aminoacylated tRNA molecule. The anticodon of this aa-tRNA is complementary to the mRNA codon located in the A site. Insertion of the correct aa-tRNA is mediated by elongation factor Tu (in bacteria)..

Formation of the peptide bond then occurs in a reaction catalyzed by peptidyl transferase—an enzymatic activity of the ribosomal RNA in the ribosome. When this happens the growing peptide chain (grey balls) is transferred to the tRNA that was in the A site.

The next step is to shift the ribosome relative to the mRNA bringing the peptidyl-tRNA molecule into position in the P site and freeing up the A site for a new amimoacyl tRNA to bind. This step is called translocation and it is mediated by elongation factor G (EF-G). During the translocation the uncharged tRNA is temporarily moved to the exit site (E site) before being released.

Streptomycin inhibits the translocation step by binding to the small subunit ribosomal RNA and blocking the activity of EF-G.

Here's a picture (below) of what the bacterial ribosome looks like. Most of it is RNA (yellow chain) folded into a complex conformation. The three dimensional structure is stabilized by a number of small proteins (orange + blue) bound to the outer surface of the RNA. One of these proteins is S12, located in the grove where mRNA binds to the ribosome. S12 stabilizes the RNA three-dimensional structure to which streptomycin binds.


Bacteria rapidly develop resistance to streptomycin, which explains why it isn't as effective today as it was when it was first introduced in the 1940s. One of the common resistance mutations affects ribosomal protein S12. The mutant protein is able to maintain the proper RNA conformation in the presence of streptomycin and this allow translocation to proceed.

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