Dynamics and Sloppiness in Protein Synthesis

 

Protein synthesis can be divided into three stages.

First, there's the initiation stage when a ribosome binds to the initiation codon in messenger RNA (mRNA) and the translation initiation complex forms by recruiting additional components.

Second, there's the elongation stage when the elongation complex moves along the mRNA translating the coding region and producing a polypeptide chain. The elongation rate is relatively constant but from time to time the elongation complex pauses at particular sites that are difficult to translate.

Finally, the elongation complex encounters a termination site where it disassembles and the ribosome with its various factors is released from the mRNA.

We Are All Apes

 
Richard Dawkins created a bit of a stir among the theists by claiming that he is an African ape.

Someone named Vasko Kohlmayer was partularly upset so he wrote up a "rebuttal" for the Moonie newspaper The Washington Times: Is Richard Dawkins an Ape?.

I don't much care about the opinions of theists like Vasko Kohlmayer because they have an obvious agenda. Scientific arguments are meaningless to them.

But I do care about the opinions of other scientists and philosophers. Jerry Coyne explains why we are apes and why it's not a good idea to say that people living in Oxford or Chicago are African apes [Washington Times denies that Richard Dawkins is an ape]. I agree with Jerry.

John Hawks disagrees [Humans aren't monkeys. We aren't apes, either.]. He claims that the term "ape" is not a legitimate phylogenetic term and therefore is doesn't have to refer to a monophyletic group.

Chimpanzees are apes. Gorillas are apes, as are bonobos, orangutans, and gibbons. We routinely differentiate the "great apes" from the "lesser apes", where the latter are gibbons and siamangs. Humans are not apes. Humans are hominoids, and all hominoids are anthropoids. So are Old World monkeys like baboons and New World monkeys like marmosets. All of us anthropoids. But humans aren't monkeys.

I don't agree with this distinction. There's nothing to be gained by saying that our closest relatives are apes but we aren't.

John Wilkins thinks we are apes [Are humans, apes, monkeys, primates, or hominoids?]. John argues like a philosopher but, in this case, he's right.

It is not possible to stem the tide of linguistic change, as the Académie Française has found out repeatedly. If experts can redefine terms influentially, then there is nothing wrong with that so long as it doesn’t confuse the experts. Using paraphyletic terms (that is, group names that denote what is left of the group once a subset has been removed) is a Very Bad Idea that hangs on in science, but it need not hang on in folk usage. And there’s nothing wrong with saying “humans are apes”, because, on the best construal of what those terms denote, they are.

Neil Shubin’s excellent book Your Inner Fish makes a similar point. Where once a “fish” was anything that lived in water (including swans, geese, alligators and crocodiles, whales, and water snakes), it came to mean a vertebrate that had gills and fins and scales. Shubin shows how the Gnathostomes (jawed fishes) includes land vertebrates, including mammals and ultimately us, as well. Language can change…

UPDATE: Brian Switek of Laepaps weighs in with: I’m an Ape, and I’m Also a Fish.

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Monday's Molecule #162

 

The last few challenges have been too easy so I'm going to make this week's molecule a bit more difficult. Not only do you have to identify the molecule but you also have to identify each of the four residues that are sugar derivatives. What is the molecule in blue and what are the other three sugary-looking residues?

Be sure to give a complete unambiguous name—that means getting the stereochemistry correct.

Post your answer in the comments. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post correct answers to avoid embarrassment. The winner will be treated to a free lunch. I'll be setting up a lunch for this Thursday so expect an email message. If I owe you a lunch, it wouldn't hurt to remind me in case I forget you.

There could be two winners. If the first correct answer isn't from an undergraduate student then I'll select a second winner from those undergraduates who post the correct answer. You will need to identify yourself as an undergraduate in order to win. (Put "undergraduate" at the bottom of your comment.)

Some past winners are from distant lands so their chances of taking up my offer of a free lunch are slim. (That's why I can afford to do this!)

In order to win you must post your correct name. Anonymous and pseudoanonymous commenters can't win the free lunch.

Winners will have to contact me by email to arrange a lunch date.

Comments are invisible for 24 hours. Comments are now open.

UPDATE: The molecule is ganglioside G_M2. The residues are N-acetyl-α-neuraminic acid (blue), N-acetyl-β-D-galactosamide, β-D-galactose, and β-D-glucose (left to right). You were asked to be specific in naming the sugar residues. Several people got the molecule correct but nobody named the sugar residues in a completely unambiguous manner, although the correct names are implied in the formal name of the molecule. There is no winner this week.

Winners
Nov. 2009: Jason Oakley, Alex Ling
Oct. 17: Bill Chaney, Roger Fan
Oct. 24: DK
Oct. 31: Joseph C. Somody
Nov. 7: Jason Oakley
Nov. 15: Thomas Ferraro, Vipulan Vigneswaran
Nov. 21: Vipulan Vigneswaran (honorary mention to Raul A. Félix de Sousa)
Nov. 28: Philip Rodger
Dec. 5: 凌嘉誠 (Alex Ling)
Dec. 12: Bill Chaney
Dec. 19: Joseph C. Somody
Jan. 9: Dima Klenchin
Jan. 23: David Schuller
Jan. 30: Peter Monaghan
Feb. 7: Thomas Ferraro, Charles Motraghi
Feb. 13: Joseph C. Somody
March 5: Albi Celaj
March 12: Bill Chaney, Raul A. Félix de Sousa
March 19: no winner

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The "Reason Rally" Will Have Everything But Reason.

 

A lot of people are going to Washington next Saturday to stand¹ near the reflecting pool for eight hours listening to short speeches and videos during the Reason Rally.

One of the speakers will be PZ Myers and he is rightly upset about some of the other speakers who don't exactly fit the criterion of "reason." Read what he has to say about Senator Tom Harkin and Bill Maher [The Reason Rally ought to have some standards].

Was Deepak Chopra busy on 24 March? Did Oprah have a hair appointment? Maybe it’s not too late to sign up John Edward — he could channel Ingersoll and Russell and Sagan for us, although of course we’d have to be content with him guessing at their words one letter at a time.

So what's the point of having a "Reason Rally" if you schedule talks from known kooks who oppose reason?

I suspect that a lot of people will be wandering off to look at the cherry blossoms behind the Jefferson Memorial. I hope the size of the crowd isn't an embarrassment.

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You can buy a ticket for the seating area in front of the stage if you're willing to pay $500, $1000, or $5000 [VIP Seating].

John Mattick Wins Chen Award for Distinguished Academic Achievement in Human Genetic and Genomic Research

Shame on the Human Genome Organization (HUGO). It has awarded a prestigious prize (US $10,000) to John Mattick, director of the Centre for Molecular Biology and Biotechnology at the University of Queensland in Brisbane, Australia. Here's the report from the Sydney Morning Herald.

Making something of junk earns geneticist top award

WHEN Sydney geneticist John Mattick suggested junk DNA was anything but rubbish he was challenging an assumption that had underpinned genetics for 50 years.

''The ideas I put forward 10 years ago were quite radical but I thought I was right,'' Professor Mattick said.

He was. And tomorrow he will become the first Australian honoured with the Chen Award for distinguished academic achievement in human genetic and genomic research, awarded by the Human Genome Organisation.

For decades after James Watson and Francis Crick discovered DNA was a double helix, scientists believed most genes were the written instructions for proteins, the building blocks of all body processes. The assumption was true for bacteria but not complex organisms like humans, said Professor Mattick, the new executive director of the Garvan Institute.

In humans, more than 95 per cent of the genome contains billions of letters that do not make proteins, called non-coding DNA. ''When people bumped into all this DNA that didn't make proteins they thought it must be junk,'' he said. But Professor Mattick felt it was unlikely that useless material would survive hundreds of millions of years of evolution.

He found that the non-protein-coding sections of DNA had a function, to produce RNA.

"The obvious and very exciting possibility was that there is another layer of information being expressed by the genome - that the non-coding RNAs form a massive and previously unrecognised regulatory network that controls human development.''

Many scientists now believe this RNA is the basis of the brain's plasticity and learning, and may hold the secret to understanding many complex diseases.

Happy Ides!

 

Today is the Ides of March a famous day in European history because of Brutus, Cassius and a bunch of other Roman dudes.

Did you ever wonder what an "ide" was. Here's the explanation from Wikipedia [Ides of March].

The word Ides comes from the Latin word "Idus" and means "half division" especially in relation to a month. It is a word that was used widely in the Roman calendar indicating the approximate day that was the middle of the month. The term was used for the 15th day of the months of March, May, July, and October, and the 13th day of the other months.

I think you have to be more than 50 years old to appreciate this skit. You might have to be Canadian.¹

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1. Wayne & Shuster are graduates of the University of Toronto.

What Does a Eukaryotic Ribosome Look Like?

 

There's a picture of a yeast (Saccharomyces cerevisiae) ribosome on the cover of the Dec. 16, 2011 issue of Science. The paper inside by Ben-Sham et al. (2011) describes the structure at 3Å resolution.

There's nothing revolutionary here but I thought I would show you the structure just to emphasize a particular point. You can see the same image below without the distracting orange background.

Most of the ribosome is composed of RNA (silver-gray strands). You can see that a lot of this single-stranded RNA forms short double-helical regions when the RNA folds back on itself. Small ribosomal proteins (various colors) decorate the surface of the ribosome by binding to specific regions of the ribosomal RNA.

The overall impression is that the ribosome is a big ball of RNA with a small amount of protein. The actual site of translation, where messenger RNA is translated into a polypeptide, takes place in the middle of the ribosome near the hole you see in this structure. Translation is catalzyed by the RNA component of the ribosome, not by the ribosomal proteins.

I don't know about the rest of you but I grew up with an electron-micrographic image of a ribosome in my head and I just assumed that what I was seeing was a large glob of protein. If course I realized that there was a huge amount or RNA in there somewhere but I didn't think it contributed very much to the dark blobs in the cell.

When the first crystal structures of ribosomes were published I had to stare at them for quite some time in order to purge the old images from my mind and adopt a new perspective.

Eukaryotes have 79 ribosomal proteins and prokaryotic ribosomes have only 52 proteins. There are prokaryotic ribosomal proteins that have no homoogues in eukaryotes and 33 of the eukaryotic ribosomal proteins have no homologues in bacteria—they are eukaryotic specific. Furthermore, many of the eukaryotic proteins differ considerably from their bacterial homologues. (Mostly by extensions of the poly peptide chain.)

The protein components of ribosomes are not highly conserved. One gets the impression that they don't contribute much to the function of a ribosome—an impression confirmed by the fact that the RNA by itself can catalyze polypeptide synthesis. They may help stabilize the three-dimensional structure of the ribosome.

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[Image credit: The bottom image is "courtesy of Prof Marat Yusupov (IGBMC, Strasbourg)" from The 9th international Conference on Ribosome Synthesis that takes place this summer in Banff, Alberta, Canada.]

Ben-Shem A, Garreau de Loubresse N, Melnikov S, Jenner L, Yusupova G, Yusupov M. (2011) The structure of the eukaryotic ribosome at 3.0 Å resolution. Science 334:1524-1529. (Epub 2011 Nov 17). [doi: 10.1126/science.1212642]

Monday's Molecule #161

 

Some species make this molecule for a very special reason. Identify the molecule using the common name and the IUPAC name. You must also say why it's important for some species.

Post your answer in the comments. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post correct answers to avoid embarrassment. The winner will be treated to a free lunch with a famous Nobel Laureate, or with me if the Nobel Laureate isn't available.

There could be two winners. If the first correct answer isn't from an undergraduate student then I'll select a second winner from those undergraduates who post the correct answer. You will need to identify yourself as an undergraduate in order to win. (Put "undergraduate" at the bottom of your comment.)

Some past winners are from distant lands so their chances of taking up my offer of a free lunch are slim. (That's why I can afford to do this!)

In order to win you must post your correct name. Anonymous and pseudoanonymous commenters can't win the free lunch.

Winners will have to contact me by email to arrange a lunch date.

Comments are invisible for 24 hours. Comments are now open.

UPDATE: The molecule is taurocholate (2-{[(3α,5β,7α,12α)-3,7,12-trihydroxy-24-oxocholan-24-yl]amino}ethanesulfonate). Taurocholate is a bile salt in mammals. This week's winners are Bill Chaney and Raul A. Félix de Sousa.

Winners
Nov. 2009: Jason Oakley, Alex Ling
Oct. 17: Bill Chaney, Roger Fan
Oct. 24: DK
Oct. 31: Joseph C. Somody
Nov. 7: Jason Oakley
Nov. 15: Thomas Ferraro, Vipulan Vigneswaran
Nov. 21: Vipulan Vigneswaran (honorary mention to Raul A. Félix de Sousa)
Nov. 28: Philip Rodger
Dec. 5: 凌嘉誠 (Alex Ling)
Dec. 12: Bill Chaney
Dec. 19: Joseph C. Somody
Jan. 9: Dima Klenchin
Jan. 23: David Schuller
Jan. 30: Peter Monaghan
Feb. 7: Thomas Ferraro, Charles Motraghi
Feb. 13: Joseph C. Somody
March 5: Albi Celaj

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On the Sandwalk

 
Here's a panoramic view of what it's like to be on the Sandwalk behind Down House (Darwin's Home). This is the stretch along the very back of the property at the top of the image in the header for this blog.

360 Panoramic - Sandwalk

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[Hat Tip: Michael Fisher]

How to Control Pesky Scientists

 
This is from Rick Mercer, a Canadian comedian [The Rick Mercer Report].

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[Hat Tip: Craig Smibert]

Should We Challenge the Beliefs of Our Students?

 

Is it part of our role as university educators to challenge the beliefs of our students? You're damn right it is! That's what university is all about.

Here's what Peter Boghossian says in Should We Challenge Student Beliefs?.

Until two weeks ago, I had been laboring under the naïve assumption that one of the primary goals of every academic was to change students’ beliefs when they were based on inaccurate information. I was awakened from this dogmatic slumber at an interdisciplinary faculty meeting by colleagues who reacted with dismay to my confession that I had tried and failed to disabuse one of my students of Creationist beliefs.

The conversation became more heated when I read to the group what the student had written on her final exam: "I wrote what I had to ‘agree’ with what was said in class, but in truth I believe ABSOLUTELY that there is an amazing, savior GOD, who created the universe, lives among us, and loves us more than anything. That is my ABSOLUTE, and no amount of ‘philosophy’ will change that."

Two of my colleagues, one in the language arts and one in psychology, argued that it was an inappropriate use of my authority to attempt to change this student’s belief; rather, my role should have been to provide her with data so that she could make better decisions.

I countered that both the process that allows one to arrive at Creationist conclusions, and the conclusions themselves, are completely divorced from reality, and that my role was not simply to provide evidence and counterexamples and hope for the best, but to help her overcome a false belief and supplant it with a true one.

Their unanimous reaction to this declaration temporarily made me question one of my basic assumptions about the responsibilities of college educators: Should professors attempt to change students’ beliefs by consistently challenging false beliefs with facts?

I share his frustration. There are far too many university professors who think that the "beliefs" of a student are off limits as long as they have something to do with religion. Those same professors would not hesitate to challenge belief in the superiority of whites over blacks or the efficacy of homeopathy or the validity of supply-side economics.

But it's a different story if a student says that God created the universe 6000 years ago. That belief mustn't be directly challenged because the foolishness of religious beliefs is off limits.

Isn't that strange?

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[Hat Tip: RichardDawkins.net]

Is Science Restricted to Methodologial Naturalism?

Maarten Boudry, Stefaan Blancke, and Johan Braeckman have an article coming out in Science & Education on "Grist to the Mill of Anti-evolutionism: The Failed Strategy of Ruling the Supernatural out of Science by Philosophical Fiat."

It relates to the idea that science is limited by its insistence on adhering to methodological naturalism. According to this view, science cannot investigate the supernatural. The view is popular among some who oppose creationism since it means that creationism can't be scientific, by fiat. It's also important for accommodationists because it allows science and religion to co-exist in separate magisteria.

I oppose such a definition of science but, up until a few years ago, I was always told that my opinion is irrelevant since all philosophers, and many scientists, agree that science is limited by methodological naturalism. That's why I was so delighted to meet the philosophers from Gent. Finally there was another point of view opposed to the methodological naturalism limitation. Now those who promote this limitation on science have to honestly admit that it's just their opinion and not a universally accepted definition of science.¹

Good News from Gent
Methodological Naturalism
Methodological Naturalism - How Not to Attack Intelligent Design Creationism
Here Be Dragons
An Interview with Maarten Boudry

Here's the abstract of the Science & Education paper.

According to a widespread philosophical opinion, science is strictly limited to investigating natural causes and putting forth natural explanations. Lacking the tools to evaluate supernatural claims, science must remain studiously neutral on questions of metaphysics. This (self-imposed) stricture, which goes under the name of ‘methodological naturalism’, allows science to be divorced from metaphysical naturalism or atheism, which many people tend to associate with it. However, ruling the supernatural out of science by fiat is not only philosophically untenable, it actually provides grist to the mill of anti-evolutionism. The philosophical flaws in this conception of methodological naturalism have been gratefully exploited by advocates of intelligent design creationism to bolster their false accusations of naturalistic bias and dogmatism on the part of modern science. We argue that it promotes a misleading view of the scientific endeavor and is at odds with the foremost arguments for evolution by natural selection. Reconciling science and religion on the basis of such methodological strictures is therefore misguided.

And here's a brief summary of their position ...

A widespread philosophical opinion conceives of methodological naturalism as an intrinsic and self-imposed limitation of science, as part and parcel of the scientific enterprise by definition. According to this view (Intrinsic Methodological Naturalism or IMN) – which is the official position of both the National Center for Science Education and the National Academy of Sciences and has been adopted in the ruling of Judge John E. Jones III in the Kitzmiller vs. Dover case – science is simply not equipped to deal with the supernatural and hence has no authority on the issue.3

In our view, however, methodological naturalism is a provisory and empirically anchored commitment to naturalistic causes and explanations, which is in principle revocable in light of extraordinary evidence (Provisory or Pragmatic Methodological Naturalism – PMN). Methodological naturalism thus conceived derives its rationale from the impressive dividends of naturalistic explanations and the consistent failure of supernatural explanations throughout the history of science.4

The distinction between Intrinsic Methodological naturalism (IMN) and Pragmatic Methodological Naturalism (PMN) is important. PMN is a conclusion based on centuries of scientific evidence strongly suggesting that natural explanations are sufficient to explain all phenomena. Those investigations include looking onto possible supernatural explanations.

Scientists have actually investigated possible miracles and found no evidence for them. Scientist have actually investigated the supernatural explanation for a world-wide deluge and refuted it. And if someone says that God made bacterial flagella, real scientists will try and find out whether that's true instead of just throwing up their hands and claiming that such an explanation is outside of science.

The implications of PMN are profound. It means that science and religion really are in conflict.

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1. Of course the accommodationists will admit no such thing as I'm sure you are about to see in the comments. Such an admission would require them to say that they mislead Judge Jones in the Dover trial.

Pikaia is most primitive vertebrate known

 

Yesterday I was talking to one of my colleagues and she asked me if I'd heard the latest news about the Burgess Shale. I confessed ignorance so she told me that scientists had just discovered a primitive vertebrate fossil in the Burgess Shale.

Hmmm ... I was aware of possible primitive vertebrates ("Craniates" is a better term) in the deposits from China (e.g. Myllokunmingia) but I'd never heard of a vertebrate fossil in the Burgess Shale so I thought I'd check out the press release.

It's from my university!!! [Pikaia is most primitive vertebrate known]

Researchers from the University of Toronto, the Royal Ontario Museum (ROM) and the University of Cambridge have confirmed that a 505 million-year-old creature, found only in the Burgess Shale fossil beds in Canada’s Yoho National Park, is the most primitive known vertebrate and therefore the ancestor of all descendant vertebrates, including humans.

The research team’s analysis proves the extinct Pikaia gracilens is the most primitive member of the chordate family, the group of animals that today includes fish, amphibians, birds, reptiles and mammals. Their study is based on the analysis of 114 specimens and is published in the British scientific journal Biological Reviews.

The headline is wrong. Pikaia is a chordate but not a vertebrate as the quotations from the researchers make clear. The press release from Cambridge is only a bit better [Humans' ancient ancestor revealed - as a 505 million-year-old 'eel']

“The discovery of myomeres is the smoking gun that we have long been seeking,” said the study’s lead author, Professor Simon Conway Morris of the University of Cambridge. “Now with myomeres, a nerve chord, a notochord and a vascular system all identified, this study clearly places Pikaia as the planet’s most primitive chordate. So, next time we put the family photograph on the mantle-piece, there in the background will be Pikaia."

Furthermore, this really isn't news. Pikaia was featured in Stephen Jay Gould's book Wonderful Life published in 1989. Even then, Pikaia gracilens was thought to be a chordate similar in broad features to the cephalochordate (non-vertebrate chordate) Amphioxus. This classification was attributed to Simon Conway Morris in 1979. The Wikipedia article [Pikaia] points out that this classification was not universally accepted.

The important points are: (1) that Pikaia is a primitive chordate but not a primitive vertebrate and the press release is just dead wrong about that and, (2) this is old news.

BTW, is Conway-Morris right about Pikaia being the oldest chordate? I thought the fossils from China were older and some of those might even be vertebrates. If that's true then Pikaia lived after the divergence of cephalochordates and vertebrates and it's not even remotely possible that it's our ancestor.

There ought to be a new rule about press releases. Each one should have a statement at the end saying the the press release has been read by the authors of the study and they approve its content.

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Conway Morris, S. and Caron, J-B (2012) Pikaia gracilens Walcott, a stem-group chordate from the Middle Cambrian of British Columbia. Biological Reviews. Article first published online: 4 MAR 2012 [doi: 10.1111/j.1469-185X.2012.00220.x]

Redshirting: Holding kids back from kindergarten

 
Until a few minutes ago I had never heard of "redshirting" although I was familiar with the concept. Some parents want to hold their children back from kindergarten (or have them repeat kindergarten) so they will be older and more mature than the other students in their class. A school teacher advised us to do that for one of our children but we adamantly refused. Best decision we ever made concerning the education of our children.

When I was growing up the best and brightest students were allowed to skip a grade if they were doing well. (I took grades three and four in a single year.) It was a mark of achievement to be among the youngest in your class, especially if you were doing as well, or better, than the other students. On the other hand, if you were the oldest in the class then your achievements were discounted because you had an intrinsic advantage.

When I was growing up it would have been psychologically devastating to be the oldest student in the class and not be at the top of the class academically. (That's partly because the oldest students were usually the ones who had flunked a grade.) I wonder if parents who hold their children back have ever thought about the potential negative consequences? What happens if your child is just average and redshirting doesn't work?

Here's a 60 Minutes segment on redshirting. It features two people from the University of Toronto: writer Malcolm Gladwell (B.A. 1984, Trinity College) and economist Elizabeth Dhuey a professor in the Department of Management.

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Carnival of Evolution #45

 

This month's Carnival of Evolution (45th version) is hosted by Adrian, a Canadian from Edmonton, Alberta who blogs at Splendor Awaits: Carnival of Evolution #45.

Here at last is the Carnival of Evolution. Because there were so few bug-based submissions, I had to change my plans and think of a new approach. I decided this would be a good time to try the new Google Presentation. This plays for me in the latest edition of Firefox, let me know how it works on your browser.

On with the Carnival! It’s awkward, a bit goofy and tongue-in-cheeky, but it does have bugs.

The next Carnival of Evolution (April) needs a host. Contact Bjørn Østman at Carnival of Evolution if you want to volunteer. Meanwhile, you can submit your articles for next month's carnival at Carnival of Evolution.

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