Last week's molecule (above) [Monday's Molecule #240] is a derivative of 2′-deoxythymidine triphosphate that's used in DNA sequencing reactions. The derivative has a 3′-O-azidomethyl group so that when this nucleotide is incorporated into a growing chain it cannot be extended because the 3′ -OH group is blocked. This is a chain-termination derivative. The large group attached to the methyl group at the C5 position on the thymine base is a color compound (a fluor). When this nucleotide is incorporated it stops chain growth, makes the DNA visible, and indicates that there's a T in the last position. The winner is James Wagstaff.
Almost all of you are familiar with today's molecule (right) although I suspect that many of you don't recognize it right away. Name the molecule—the common name will do—and briefly describe its biochemical function.
Email your answer to me at: Monday's Molecule #241. The first one with the correct answer wins. I will only post the names of winners to avoid embarrassment. The winner will be treated to a free lunch.
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 email message.)
The decision to fire Robert Buckingham gets more and more interesting every day. On Wednesday, the Provost fired Buckingham and told him that ...
You are to receive your final pay on May 30, 2014, as per the normal payroll cycle. You are to leave campus immediately and are not to return to your office, the School of Public Health or the university. All benefits and pension cease as of today.
Please contact ... Human Resources ... to make arrangements for the return of university equipment and your office keys, as well as to arrange a time that is appropriate to collect any remaining personal effects.
(see the letter below)
I don't care how you spin this, the Provost made a very serious error and there's no way he should continue in his job. You can help him make the honorable decision to resign by signing the petition organized by University of Saskatchewan faculty at: University of Saskatchewan: Have Brett Fairbairn, Provost of the University of Saskatchewan, Resign.
The more serious question is whether the President, Ilene Busch-Vishniac, should resign. Watch this video of her apologizing for making a mistake and taking responsibility for it: "That should never have happened.". It seems to me that this is more than just a bureaucratic slip-up.
Here's a radio interview with Robert Buckingham and Ilene Busch-Vishniac on CBC's As It Happens: University of Saskatchewan President apologizes & admits school's reputation damaged. The President says that a mistake was made but she's not worried about her job. Apparently the university will launch an investigation to see what went wrong and who is responsible. (These things usually take several months.)
It really shouldn't take more than a few seconds to see that the Provost, at least, screwed up.
Meanwhile, there seems to be a bit of confusions about what kind of an offer is being made to Buckingham. He resolutely (and correctly) defends the idea that Dean's should speak out against university policies that they disagree with.
The Saskatoon newspaper, The StarPhoenix reports that ...
(Busch-Vishniac says), ""We, frankly, blundered. That should never have happened. Tenure is certainly one of the values that every university in the world holds dear. That's as true here as is it is anywhere else and I have no excuse for what happened."
She promised that "people will be held accountable" for the decision, but did not say whether her own job is on the line. "That's for the board to decide," she said."
It's difficult to see how someone who truly believes that academic freedom is important could have made such a mistake. It sounds an awful lot like someone who didn't really believe in academic freedom but is backpedaling furiously in order to avoid being fired.
I think she should be fired because she has done enormous damage to the reputation of the University of Saskatchewan and she has lost the confidence of the faculty. She can't continue to govern under those circumstances.
Apparently, some sane person at the University of Saskatchewan had a talk with the President and informed her that she was in very deep doo-doo [see Ilene Busch-Vishniac should resign immediately as President of the University of Saskatchewan].
According to CBC News: Robert Buckingham offered tenured role at Saskatchewan university after firing.
The University of Saskatchewan said today it will offer Prof. Robert Buckingham a tenured faculty position but he won't be returning to his old job after he was fired for speaking out against the school's cuts and restructuring plans.
In a news release, the university says Buckingham won't be given back his job as head of the university's School of Public Health.
“Academic freedom and tenure are sacrosanct at the University of Saskatchewan. This case, however, is not about academic freedom," U of S president Ilene Busch-Vishniac said in the release. "Dr. Buckingham was removed from his executive director position for acting contrary to the expectations of his leadership role.”
Buckingham was fired Wednesday morning for criticizing the institution's budget cuts as part of the TransformUS restructuring plan.
“The confusion on this issue stems from differing interpretations based on his contract," Busch-Vishniac said. "Because we hold tenure in high regard, we will immediately reverse that part of our initial decision.”
Busch-Vishniac also said Buckingham was not banned from the university.
Interesting. I assume that "differing interpretations" is a euphemism for "we really screwed up and I hope this will make it go away."
Good luck with that. She admits that her decision needs to be "reversed" and that means she made a very, very, serious mistake.
The Provost should resign (or be fired) today and so should the President. We all know where the buck should stop.
Meanwhile, Lindsay Tedds has a column in today's Globe & Mail that gets it exactly right [When you're a university dean, 'toe the party line' isn't your job].
The role of a dean, such as Dr. Buckingham, is to provide leadership for and protect the integrity of their unit. Dr. Buckingham did exactly that in his criticism of the university regarding the treatment of his unit through the TransformUS process. I expect that his actions were likely met with a great deal of support from his unit, as well as from many academics across this country who wish their deans were equally courageous. In the eyes of many academics, the only ones who ‘damaged the reputation’ of the University of Saskatchewan were those complicit in attempting to censor senior academic staff and the firing of Dr. Buckingham. After all, the University of Saskatchewan is a public institution, supported by taxes and student payments. Debates regarding its management of these resources should be held openly and freely in the public sphere.
Chris Buddle of McGill University (Montreal, Canada) thinks that instructors should stop putting your Powerpoint slides on-line.
He makes some excellent and powerful points but the best ones are directed at not using PowerPoint at all.
Powerpoint is so awesome! Textbook companies provide the slides and all the material is ready to go! Clickity-click-click let’s LECTURE!
Powerpoint is not awesome. Powerpoint slides are an ineffective and rather annoying tool for the University classroom. Text-heavy Powerpoint slides do not promote an active learning environment. Active learning is an important and valuable concept in higher education. Active learning means the classroom becomes a space for debate, discussion, interaction, and the instructor is the facilitator of all of this rather than a ‘voice from a podium’. Powerpoint slides can be used to illustrate concepts, for showing relevant graphs or images, but they should not be used for a long list of bulleted points. Frankly, Powerpoint often becomes a memory tool for the instructor rather than a tool for effective instruction. Try a chalkboard instead…
Students shouldn’t be forced to come to lecture – heck, they are paying for University and we are at their service. It’s their right to have access to course notes on-line.
Yes, students are paying to come to University, and instructors are paid to teach. In most cases, this means teaching in a seminar room or lecture hall. In most cases, this means teaching in a context where direct interaction with students is possible, important and a key part of the University experience! To me, it’s the student’s right to be able to go to lecture and experience an active and engaging environment: an environment that creates opportunity for learning from an expert on a topic, but also learning from peers. These are difficult things to replicate outside of a classroom. So, instead of thinking of it as forcing students to come to lecture, it’s time to create a lecture environment that is welcoming, exciting and engaging. Let’s create environments which make it so students want to come to lecture.
Amen.
I wonder what he thinks of MOOC's?
The university of Saskatchewan fired Robert Buckingham the other day. Buckingham was Executive Director (Dean) of the School of Public Health. He objected to a policy called "TransformUS" that was designed to save the university money. It proposed to abolish the School of Public Health and merge it, and the College of Dentistry, with the College of Medicine.
He was not only fired from his administrative post, he was also fired from his tenured job as a Professor and banned from the University campus.
Buckingham and another Dean (Associate Dean Ken Sutherland of Dentistry) were warned that they should not speak out against the proposals that were being developed by the Provost and the President. He responded by publishing a letter titled "The Silence of the Deans."
According to a CBC article,
Security guards escorted Buckingham out of the building on Wednesday, the same day the Saskatoon-based university stripped him of his tenured faculty position. A termination letter reasoned that by speaking out against the school's restructuring plans, Buckingham "demonstrated egregious conduct and insubordination" and was in breach of contract.
He was also banned for life from the campus.
There are dozens of other articles in newspapers and blogs across the country that confirm these events and condemn the University of Saskatchewan.
Watch this Global TV video to get an overview of what happened and how the University of Saskatchewan Faculty Association intends to respond.
I can understand why the university might want to relieve Robert Buckingham of his job as Dean but, even then, they should tread very carefully if they are firing him only because he speaks out against the destruction of his Faculty. However, under no circumstances should the university fire a professor who is protected by the right to academic freedom—especially if the only cause for dismissal is a disagreement with the university administration.
The letter of termination has (rightly) been made public (see below). It's an extraordinary letter. I don't think this termination has a ghost of a chance in court if it should come to that. The irony is in the Provost's words, "you have damaged the reputation of the university." Any "damage" done by Robert Buckingham in speaking out against the destruction of his Faculty pales in comparison to the damage done by the Provost and the President. The stupid actions of Brett Fairbairn and Ilene Busch-Vishniac are being broadcast all over the world. It will take years to restore the reputation of the University of Saskatchewan after this.
As you can see from this CBC News report, the Saskatchewan Minister of Advanced Education is concerned about the firing. This CTV News video shows the NDP Leader of the Opposition referring to the "outrageous" actions of the university. Oops!
The first step is for the Provost and the President to reinstate Robert Buckingham to his job as professor and then the Provost and the President should resign. This should happen today, or tomorrow at the latest. If they don't resign then the governing body of the University of Saskatchewan should fire them from their administrative posts for cause. Administrative leaders of a public university cannot ignore academic freedom.
When the ENCODE Consortium published their results in September 2012, the popular press immediately seized upon the idea that most of our genome was functional and the concept of junk DNA was debunked. The "media" in this case includes writers at prestigious journals like Science and Nature and well-known science writers in other respected publications and blogs.
In most cases, those articles contained interviews with ENCODE leaders and direct quotes about the presence of large amounts of functional DNA in the human genome.
The second wave of the ENCODE publicity campaign is trying to claim that this was all a misunderstanding. According to this revisionist view of recent history, the actual ENCODE papers never said that most of our genome had to be functional and never implied that junk DNA was dead. It was the media that misinterpreted the papers. Don't blame the scientists.
You can see an example of this version of history in the comments to How does Nature deal with the ENCODE publicity hype that it created?, where some people are arguing that the ENCODE summary paper has been misrepresented.
I don't normally celebrate my birthday in public but I made the mistake of putting my birth date on my Facebook page so lots of people are sending me birthday wishes.
Thank-you very much everyone. Many of your messages are quite touching.
I was born on Monday, May 13, 1946 at 6am. It was the day after Mother's Day so my mother had to wait a full year before she could celebrate her first Mother's Day. We joined her for her 67th Mother's Day a few days ago.
Last week's molecule (right) [Monday's Molecule #239] was 2-carboxy-D-arabinitol 1-phosphate. It's an inhibitor of the enzyme ribulose 1,5-bisphosphate carboxylase-oxygenase, better known as Rubisco. That's the key enzyme responsible for CO2 fixation in the Calvin cycle. Plants have to inhibit Rubisco during the night when the lack of sunlight prevents production of ATP and NADPH by photosynthesis. One of the ways they inhibit the enzyme is to produce 2-carboxy-D-arabinitol 1-phosphate at night. The winner is Piotr Gąsiorowski.
This week's molecule (below) is pretty complicated. I don't expect a complete name; just concentrate on getting the correct name of the core part of the molecule on the left. In addition to identifying the molecule, you need to explain what it is used for and, specifically, the purpose of the -N3 group in the lower left corner of the molecule.
Email your answer to me at: Monday's Molecule #239. The first one with the correct answer wins. I will only post the names of winners to avoid embarrassment. The winner will be treated to a free lunch.
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 email message.)
Let's briefly review what happened in September 2012 when the ENCODE Consortium published their results (mostly in Nature).
Here's the abstract of the original paper published in Nature in September 2012 (Birney et al. 2012). Manolis Kellis (see below) is listed as a principle investigator and member of the steering committee.
The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown. The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification. These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions. Many discovered candidate regulatory elements are physically associated with one another and with expressed genes, providing new insights into the mechanisms of gene regulation. The newly identified elements also show a statistical correspondence to sequence variants linked to human disease, and can thereby guide interpretation of this variation. Overall, the project provides new insights into the organization and regulation of our genes and genome, and is an expansive resource of functional annotations for biomedical research.
Most people reading this picked up on the idea that 80% of the genome had a function.
I draw your attention to a new paper on junk DNA by my friends Alex Palazzo and Ryan Gregory (Palazzo and Gregory, 2014).
You should read this paper if you want a nice summary of the evidence for a high percentage of junk in our genome. They cover genetic load, sequence conservation, and the evidence from the genome sequence itself. There's a brief description of the nearly-neutral theory of molecular evolution and why it's relevant to the debate.1
One of the most important contributions is an explanation of the C-Value Paradox and the Onion Test. The Onion Test was originally published on Ryan's blog (The onion test) but some people won't reference blog posts so here it is in a peer-reviewed paper.
There are several key points to be understood regarding genome size diversity among eukaryotes and its relationship to the concept of junk DNA. First, genome size varies enormously among species [18], [19]: at least 7,000-fold among animals and 350-fold even within vertebrates. Second, genome size varies independently of intuitive notions of organism complexity or presumed number of protein-coding genes (Figure 1). For example, a human genome contains eight times more DNA than that of a pufferfish but is 40 times smaller than that of a lungfish. Third, organisms that have very large genomes are not few in number or outliers—for example, of the >200 salamander genomes analyzed thus far, all are between four and 35 times larger than the human genome [18]. Fourth, even closely related species with very similar biological properties and the same ploidy level can differ significantly in genome size.
These observations pose an important challenge to any claim that most eukaryotic DNA is functional at the organism level. This logic is perhaps best illustrated by invoking “the onion test” [20]. The domestic onion, Allium cepa, is a diploid plant (2n = 16) with a haploid genome size of roughly 16 billion base pairs (16 Gbp), or about five times larger than humans. Although any number of species with large genomes could be chosen for such a comparison, the onion test simply asks: if most eukaryotic DNA is functional at the organism level, be it for gene regulation, protection against mutations, maintenance of chromosome structure, or any other such role, then why does an onion require five times more of it than a human? Importantly, the comparison is not restricted to onions versus humans. It could as easily be between pufferfish and lungfish, which differ by ~350-fold, or members of the genus Allium, which have more than a 4-fold range in genome size that is not the result of polyploidy [21].
In summary, the notion that the majority of eukaryotic noncoding DNA is functional is very difficult to reconcile with the massive diversity in genome size observed among species, including among some closely related taxa. The onion test is merely a restatement of this issue, which has been well known to genome biologists for many decades [18].
1. A little birdy tells me that there's a "better" paper coming out in a few months. 
Palazzo, A. and Gregory T.R. (2014) The Case for Junk DNA. PLoS Genetics (published May 8, 2014) [doi: 10.1371/journal.pgen.1004351]
I just discovered a new paper on the origin of life (Keller et al. 2014). The authors think they are looking at the first primitive biochemical pathways, which they identify as glycolysis and the pentose phosphate pathways.
Here's what they did. They took a bunch of pure sugar phosphates1 and dissolved them in water containing salts and metal ions that were likely present in the primordial oceans. They heated the solution up to 70° C and looked at the degradation products. Low and behold, the sugar phosphates degraded and sometime the products were other intermediates in the glycolytic and pentose phosphate pathway, including pyruvate and glucose.
They conclude that ...
According to Friendly Atheist, there's been a Supreme Court Disaster: In a 5-4 Ruling, Justices Approve of Christian Prayers in Greece, New York.
Apparently a majority of US Supreme Court justices think it's okay to say Christian prayers at the opening of a town council meeting. There seems to be widespread agreement among all justices that there's nothing wrong with prayers as long as the town makes an effort to be inclusive. The majority opinion was written by Justice Anthony Kennedy. He says that making the prayers "nonsectarian" would be equivalent to asking the politicians to "to act as supervisors and censors of religious speech."
He also says that as long as the town tries to accommodate all faiths there's nothing wrong with prayers, even if almost all the churches were Christian [TOWN OF GREECE, NEW YORK v. GALLOWAY ET AL.].
To hold that invocations must be nonsectarian would force the legislatures that sponsor prayers and the courts that are asked to decide these cases to act as supervisors and censors of religious speech, a rule that would involve government in religious matters to a far greater degree than is the case under the town’s current practice of neither editing or approving prayers in advance nor criticizing their content after the fact.
…
Finally, the Court disagrees with the view taken by the Court of Appeals that the town of Greece contravened the Establishment Clause by inviting a predominantly Christian set of ministers to lead the prayer. The town made reasonable efforts to identify all of the congregations located within its borders and represented that it would welcome a prayer by any minister or layman who wished to give one. That nearly all of the congregations in town turned out to be Christian does not reflect an aversion or bias on the part of town leaders against minority faiths. So long as the town maintains a policy of nondiscrimination, the Constitution does not require it to search beyond its borders for non-Christian prayer givers in an effort to achieve religious balancing.
Only one of the judges put her finger on the real issue. Justice Elena Kagan said,
When a person goes to court, a polling place, or an immigration proceeding — I could go on: to a zoning agency, a parole board hearing, or the DMV — government officials do not engage in sectarian worship, nor do they ask her to do likewise. They all participate in the business of government not as Christians, Jews, Muslims (and more), but only as Americans — none of them different from any other for that civic purpose. Why not, then, at a town meeting?
Exactly. Why is it necessary to have prayers at town meetings? Just drop them like most cities and towns in Ontario did when our Appeals Court ruled that they violated the Charter of Rights? [see Prayer at Mississauga City Council]
Many of the creationists are just learning about Neutral Theory for the first time in their lives. (The basics were published in the late 1960s—over 45 years ago.)
Vincent Torley (vjtorley), a philosopher from Australia, has struggled with the idea for several weeks and now he thinks he has some challenging questions for evolutionary biologists. Those creationists are really fast learners. It took me several years of study before I really grasped the basic concepts and the theory behind population genetics. Torley's questions are at: Will the real Neutral Theory please stand up?. The obligatory piling on by "News" is at: Is there a real neutral theory of evolution?.
Torley begins with ...
The Canadian Association of University Teachers (CAUT) has launched a campaign to alert the public about changes in science policy and funding. The Conservative government of Stephen Harper has shifted funds toward directed research and starved Canadian scientists who focus on basic, curiosity motivated, research.
What this means is that young scientists are finding it increasingly difficult to get funding from the government. It means that scientists in mid-career are losing their grants and this means that research technicians have to be fired, graduate students can't be funded, and post-docs have to find another position.
Why is this important? Why should you care? Those are the questions that CAUT wants to answer by sponsoring meetings across the nation to explain why it's important to "Get Science Right." Come to a Town Hall meeting at the University of Toronto (Toronto, Ontario, Canada) and learn more. The meeting starts at 7pm. It's in room 119 at Emmanuel College (Victoria Uiniversity). [Facebook: Get Science Right - Toronto Town Hall]
Let me know if you plan to attend. We could get together before or after the meeting.
Last week's molecules (right) [Monday's Molecule #238] were correctly identified by Dean Bruce (again) who wrote ...
... it is 3-hydroxy-3-methylglutarate-CoA (HMG-CoA) synthetase. HMG-CoA appears to be the only molecule in the active sites of the illustration. Acetoacetyl-CoA and Acetyl-CoA in a Claisen condensation (of the beta-carbonyl of acetoacetyl-CoA) form HMG-CoA.
The mitochondrial one is the isoform involved in metabolic pathology. The disease is called "mitochondrial HMG-CoA synthetase-2 deficiency" in the Online Mendelian Inheritance of Man.
This week's molecule is an important regulatory molecule in some species. Identify it using the standard IUPAC nomenclature and describe the enzyme whose activity it regulates.
Email your answer to me at: Monday's Molecule #239. The first one with the correct answer wins. I will only post the names of winners to avoid embarrassment. The winner will be treated to a free lunch.
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 email message.)
