John Wilkins has it right: Begging that damned question.
For hundreds of years, the phrase "begging the question" meant something like "avoiding the question." It is an important fallacy in logic and philosophers should fight hard to keep the original meaning.
Unfortunately, in the past decade or so the phrase has come to mean "raising the question." That's probably because the original meaning was too subtle for the average person who preferred a much more literal interpretation of "begging the question." If you are going to use the new interpretation you should be aware of the fact that a lot of people are gong to think you're stupid.
My next post on evolving language will discuss an announcement that I hear frequently on my train. See if you can guess why it annoys me. It goes like this: "On behalf of myself and the crew I'd like to thank you for riding the train today."
On May 24th 2014 Ed Yong (@edyong209) tweeted ....
Those surveys about views on evolution are a terrible guide to “science literacy” (which is itself a silly term) [Weekend update: You'd have to be science illiterate to think "belief in evolution" measures science literacy]
You can follow the Twitter thread here but it's not very enlightening.
The article that Ed Yong linked to is by Dan Kahan, a Professor of Law and a Professor of Psychology at Yale University (New Haven, Connecticut, USA). He has a B.A. from Middlebury College and a law degree (J.D.) from Harvard.
The issue that upsets Ed Yong and Dan Kahan is a serious one. It's about how one measures scientific literacy and what it means to be capable of using the scientific way of knowing to distinguish between reality and superstition. The specific issue is whether asking people if they "believe" in evolution is a valid measure of scientific literacy.
An old high school friend1 added a comment on a previous post where he alerted me to a new (for me) blog called "Piece of Mind." The author is Nassif Ghoussoub, a Professor of Mathematics at the University of British Columbia (Vancouver, Canada) and a member of the Board of Governors of that university.
His blog post is: Return on investment in faculty rarely captured by university CFOs and it makes three important points.
- The faculty is the university.
- Budget models that invest in things like $140-million in online learning while cutting normal teaching and research are unlikely to work.
- Cutting normal faculty positions while advocating an increase in "professional programs" and an increase in enrollment seems illogical.
I like the opening and the closing ....
"Mr. President, We are not employees of the university. We are the university."
With these words, Isidore Rabi, a distinguished faculty member at Columbia University, interrupted Dwight Eisenhower, who had started off a speech by addressing the faculty as "employees of the university." [At the time, Eisenhower was President of Columbia University.] Generation after generation of faculty members has repeated this inspirational anecdote from the early 1950s, though they know very well that their universities are increasingly becoming about everything other than the faculty. And the situation appears to be worsening. To the professional managerial class that nowadays run the neoliberal version of post-secondary education, the faculty is often seen as merely the source of the university’s problems. So, before too many of my colleagues get used to being seen as a cost, not something that provides net positive value to the university, I would like to use charter accountants’ speak to argue that investment in university research excellence could be and should be viewed as a possible driver of future revenue.
....
As to the end of the Eisenhower tale, people assumed he might have taken offense by the somewhat confrontational remark of Rabi. Instead, the latter became his closest friend on the faculty – "and when Eisenhower became President of a somewhat larger organization than Columbia, he appointed Rabi to a number of influential positions."
1. It was Bob Woodham, and I mean a high school friend from a long time ago not a high school friend who is old. None of us are "old" yet.
Last week the Provost of the University of Saskatchewan fired Robert Buckingham, Dean of Public Health, for his outspoken criticism of plans to disband his Faculty and for his public criticism of the administration for attempting to muzzle him. Buckingham was not only removed from his job as Dean but fired from his tenured position as a Professor and banned from the campus.
One week later ...
- Buckingham has been reinstated as a Professor in the Faculty of Public Health.
- The Provost, Brett Fairbairn, was forced to resign.
- The President, Ilene Busch-Vishniac, has been fired.
This has been a good week for universities in Canada and for the principle of academic freedom. All the major TV networks and all the major newspapers were appalled at the actions of the University of Saskatchewan. Even the Premier of Saskatchewan and the minister in charge of higher education expressed their displeasure.
Watch the CBC excerpt at: University of Saskatchewan board fires president Ilene Busch-Vishniac. It gives you a good flavor of the way this is being covered in Canada. Nobody is defending the university.
Some of the best coverage of this sorry episode is by the Star Phoenix of Saskatoon: University of Saskatchewan president Ilene Busch-Vishniac fired. According to their reporters, the Chair of the Board of Governors (Susan Milburn) announced late last night that President Busch-Vishniac has been fired "without cause." She will retain her position as a tenured Professor in the College of Engineering where presumably she will assume normal teaching and research duties.
[Susan Milburn says] "The board feels strongly that the university’s ongoing operations and its reputational rebuilding efforts will be more effective with new leadership."
The board in its statement said it had been "a painful week for the University of Saskatchewan. Many students, faculty, staff, and alumni of the U of S, and the people of the province generally, were dismayed by news emerging from the campus over the last seven days. The board was deeply troubled by this situation and committed itself to repairing the university’s reputation."
The StarPhoenix went to the president's home on the U of S campus but husband Ethan Vishniac said Busch-Vishniac would not comment.
Busch-Vishniac, who began her term at U of S on July 1, 2012, was terminated without cause, which means she is eligible to collect severance and can take up a faculty post in the university’s college of engineering.
The backdrop to this story about academic freedom is "TransformUs"—a plan to drastically cut expenses in order to meet a $45M deficit. Apparently, students and faculty at the University of Saskatchewan were not brought on board during the discussion leading up to the decision and they are not happy with a budget plan that appears to be imposed by a small number of senior administrators.
The Board of Governors has restated its support for "TransformUS" in spite of widespread protests on campus. It looks like the Board will be the next target.
Meanwhile, the faculty is upset because the Board of Governors granted the President the right to veto tenure recommendations made by peer-group tenure committees. The Faculty Association will likely take legal action against the Board because their action violates the agreement between faculty and the university. (The faculty at the University of Saskatchewan is not (yet) unionized.) (The Faculty Association is a certified union under the Trade Union Act. They have been certified since 1977.)
Stay tuned.....
This is my fifth post on this subject. The others are at ...
The provost of the University of Saskatchewan, Brett Fairbairn, resigned yesterday (Monday, May 20, 2014) just before an emergency meeting of the university's Board of Governors. The President of the university, Ilene Busch-Vishniac, announced that she had accepted the resignation.
Last week the Provost fired Robert Buckinham, the Dean of Public Health, from his tenured position for disagreeing with the policies of the rest of the university administration, specifically the Provost and the President. They want to disband the Faculty of Public Health and the Dean disagreed and protested the attempt to muzzle him. Two days later the President offered Buckingham a tenured position and admitted that a terrible blunder had been committed on her watch.
The Provincial Minister of Advanced Education, Rob Norris, called the emergency meeting of the Board of Governors in order to determine if recent events at the University of Saskatchewan had violated the "University of Saskatchewan Act." He spoke to the Board at their 8pm meeting then addressed the press. According to CBC News ....
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.)
There are many ways of defining the gene but only some of them are reasonable in the 20th and 21st centuries [What Is a Gene?]. By the 1980s most knowledgeable biologists were thinking of a gene as a DNA sequence that's transcribed to produce a functional product.
They were familiar with genes that encoded proteins and with a wide variety of genes that produce functional RNAs like ribosomal RNA , transfer RNA, regulatory RNAs, and various catalytic RNAs. It would have been difficult to find many knowledgeable biologists who thought that all genes encoded proteins.
By the 1980s, most knowledgeable biologists were aware of RNA processing. They knew that the primary transcripts of genes could be modified in various ways to produce the final functional form. They knew about alternative splicing. All these things were taught in undergraduate courses and written in the textbooks.
Here's how Michael White views that history in: Your Genes Are Obsolete.
Creationists in general, and Intelligent Design Creationists in particular, feel very threatened by the idea that most of our genome is junk. We know why they feel threatened: it's because a genome full of junk doesn't seem like something gods would design on purpose. It's pretty hard to reconcile junk DNA with with gods that spend so much effort designing bacterial flagella.
The creationists get very excited whenever a group of scientists publish evidence for function in junk DNA and they could hardly contain themselves when the ENCODE preliminary results were published in 2007 because the ENCODE Consortium said that most of the human genome was functional. You will recall that the creationists fell hook line and sinker for the ENCODE publicity hype in September 2012 when the ENCODE leaders came right out and said that their analysis of the entire genome shows there is almost no junk in the human genome.
The creationists, just like the ENCODE leaders, were very resistant to all of the scientific evidence for junk DNA. Both groups showed a remarkable ignorance of four decades of work leading to the conclusion that our genomes are full of junk DNA [see ENCODE, Junk DNA, and Intelligent Design Creationism ]. Creationists, and even some scientific opponents of junk DNA, quote Jonathan Wells' book The Myth of Junk DNA as an authority of the issue.
Now, I wrote a pretty extensive review of The Myth of Junk DNA showing where mistakes were made and why the evidence still favored lots of junk DNA in our genome [The Myth of Junk DNA by Jonathan Wells]. That was in 2011. Here's how Jonathan Wells responded ... [Jonathan Wells Sends His Regrets].
Oh, one last thing: “paulmc” referred to an online review of my book by University of Toronto professor Larry Moran—a review that “paulmc” called both extensive and thorough. Well, saturation bombing is extensive and thorough, too. Although “paulmc” admitted to not having read more than the Preface to The Myth of Junk DNA, I have read Mr. Moran’s review, which is so driven by confused thinking and malicious misrepresentations of my work—not to mention personal insults—that addressing it would be like trying to reason with a lynch mob.
The ENCODE Consortium has decided that it had better backtrack a little on the subject of junk DNA. Their recent PNAS article (Kellis et al., 2014) pretends that the publicity hype of September 2012 never existed and, even if it did, they may have been right to conclude that 80% of our genome is functional. It all depends on how you define function. Apparently they have just discovered that lots of scientists define it in a way that the ENCODE Consortium overlooked in September 2012.
Now they just want to make sure that everyone knows they have done their homework and they acknowledge that there's a wee bit of a controversy—but they weren't wrong! They just have a different way of defining function.
This puts some of the creationists in a difficult position. Some of them are actually willing to conceded that there's a lot of junk DNA in our genome while other are only willing to concede that the case for function may not be quite as rock solid as they thought.
Here's how an anonymous creationist explains the backtracking of the ENCODE Consortium on Evolution News & Views (sic): Defining "Functional": The Latest from ENCODE.
He/she starts off with the obligatory snipe at "Darwinists" and the obligatory misrepresentation of the case for junk DNA. He/she is referring to the Kellis et al. paper ...
First, the paper is a remarkably restrained and balanced response to some of the rather intemperate criticisms of ENCODE from hard-core Darwinists who insist that (a) ONLY an evolutionary approach yields valid information about functionality, (b) evolutionary theory necessarily implies that most of our DNA is junk, and (c) junk DNA provides evidence that Darwinian evolution is a fact. In other words this paper is a model of rational and civil scientific discourse, in contrast to what we have come to expect from some hard-core Darwinists.
(See the quote above from Jonathan Wells for an example of "a model of rational and civil scientific discourse.")
The Evolution News & Views post concludes with ...
The authors conclude that all three approaches must be taken into account, though a simple intersection of the three (which would include only DNA sequences that meet the test of functionality for all three approaches) would be far too restrictive. Unfortunately, the authors do not specify exactly how the three approaches could be integrated to yield a single reliable estimate of the percentage of functional DNA.
So the debate continues.
Believe it or not, that last sentence ("So the debate continues") is pretty remarkable considering that the creationists have steadfastly refused to admit that there is a scientific debate. Over the past decade, they have consistently claimed that the evidence is in and it shows that gods did it after all most of our genome is functional.
Maybe I'm being overly optimistic but it looks to me like some creationists are actually disagreeing with Jonathan Wells. Stay tuned.
Kellis, M. et al. (2014) Defining functional DNA elements in the human genome. Proc. Natl. Acad. Sci. (USA) April 24, 2014 published online [doi: 10.1073/pnas.1318948111 ]
Last week's molecules (right) [Monday's Molecule #237] were α-D-glucopyranosyl-(1➝4)-β-D-glucopyranose, the β anomer of maltose and α-D-glucopyranosyl-(1➝6)-α-D-glucopyranose, the β anomer of isomaltose. The winner is Dean Bruce. A surprising number of people got it right.
This week's molecules (below) are related. They are cytoplasmic (PDB 2P8U left) and mitochondrial (PDB 2WYA right) versions of very important enzymes. The human versions are shown. Name the enzymes and the products bound in the active sites (complete common name of the product). Mutations in one of the genes coding for one of these enzymes cause a rare genetic disease. Which one? Why are there no known diseases associated with genetic defects in the gene for the other version of the enzyme?
Email your answer to me at: Monday's Molecule #238. 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.)
I'm in San Diego (California, USA) attending Experimental Biology 2014 (EB2014). This is a large meeting of several differnent societies. The one I belong to is ASMBM (American Society for Biochemisty & Molecular Biology).
I'm mostly interested in the sessions on teaching. The two I went to yesterday were on "Measuring Success in Undergraduate Education" and "Mentoring and Networking: Preparing for the Future."
There are far too many science talks. It's a bit overwhelming. I tend to focus on the plenary sessions where you can get an overview of a subject. This is where I'm most likely to find new material for my textbook. (No luck so far.)
All the cool people are here.
Here's Voet & Voet (Don Voet and Judy Voet). I also met John Tansey and several of the other authors on the paper covering ASMBM Core Concepts [see ASBMB Core Concepts in Biochemistry and Molecular Biology: Molecular Structure and Function ].
We've had some interesting discussions. I don't think I've convinced them, yet.
Sometimes you just want to throw up your hands and say something very rude. This is one of those times.
Salvador Cordova is trying to explain non-Darwinian evolution to his friends over on Uncommon Descent [Cost of maintenance and construction of design, neutral theory supports ID and/or creation].
Here's the punchline ....
But if most evolution is non-Darwinian, maintenance much less construction of design cannot be explained by Darwinism, then the case for ID is strengthened.
Now if most evolution had been non-Darwinian, one would rightly argue it would have been a random walk, and thus not much better than a tornado going trough a junkyard. Creationist have seized on this and said, "well we’re not a junkyards, therefore some non-random process must have created designs in nature, hence we are designed". In contrast, Larry Moran and friends have said "evolution is a random walk and we are obviously junkyards and you’re an IDiot if you think biological organisms are mostly functional."
It's very, very, difficult for me to believe that Cordova isn't lying through his teeth. He can't be that stupid, can he?
The faculty at most Canadian universities are unionized. Faculty unions are important for negotiating fair salaries and benefits but they play a much more important role in defending academic freedom and protecting faculty from administrators who don't understand what a university should be about. I served for many years on the Grievance Committee and I can assure you that conflict between faculty members and administrators is common. In 99% of cases, the issues are resolved by negotiations between the union and the administration.
We don't have a union at the University of Toronto. Instead, we have an "Association" that functions a lot like a union without the right to strike. Right now the University of Toronto Faculty Association (UTFA)is negotiating with the university to set up ways for faculty to play a more direct role in governance issues. Those negotiations have nothing to do with certification (unionization).
I suppose there's another option. University faculty members could abandon collective bargaining and rely entirely on the goodwill of administrators, much like the situation in the business world where you can be fired if the boss doesn't like you. I suppose it's possible that academic freedom could be protected entirely by the administration and individual faculty members could fend for themselves if administrators ever abused their authority.
That's apparently what some professors in the Rotman School of Management want. They wrote letters to the President of the University protesting an imaginary move toward certification. I assume they misunderstood what the University of Toronto Faculty Association was doing because they don't read the newsletters that all us received.
Here's one of the letters from Roger Martin, Premier’s Chair in Competitiveness and Productivity in the Rotman School of Management. It illustrates quite nicely why schools of management and business don't belong on university campuses.
Dear President Gertler:
I am writing to express in the strongest possible terms how outraged I am by UTFA’s decision to attempt certification. UTFA does not represent anything related to me, nor, I suspect, does it represent the faculty of the Rotman School.
The notion of unionization of employees who make six figure salaries and have job security and protection of the sort enjoyed by professors is ridiculous on its face. It is really an insult to all real laborers who fought for the right to unionize and collectively bargain. Those workers coped with subsistence wages, unsafe and inhumane work environments, and absolutely zero job security. They didn’t have intellectually rewarding jobs in completely safe environments with lifetime job security. Collective bargaining was put in place to protect basic human rights, not to enable highly paid employees to argue for richer dental plans.
It is simply outrageous that that the ideologues who purport to represent us even raise the notion. They should be embarrassed. Sure they can say that it happens at other Universities in Canada. But when ever was that robust logic for doing something incredibly stupid and destructive?
We simply can’t let University of Toronto be ruled and ruined by ideologues. This is a fight for the future of a great institution. UTFA, when not run by ideologues, works perfectly well and creates a positive dialogue with university administration and a pleasant work environment for the faculty.
My fond hope is that this gambit is defeated by the weight of faculty members across the University. Failing that, I believe that my colleagues at the Rotman School will disassociate themselves from the bargaining unit and refuse to be represented by a completely foreign force. But in the end, if that can’t happen, it will be a sad day for me. I can’t insult every brave union activist in history who fought for human rights for workers by accepting becoming a member of one of the cushiest unions on the planet. That is not the way to live a principled life.
Sincerely,
Roger Martin
Premier’s Chair in Competitiveness and Productivity
Rotman School of Management
University of Toronto
In case some of you aren't familiar with unions, let me explain what would have to happen if UTFA ever wanted to certify. There would have to be a vote and a majority of faculty members would have to vote in favor of forming a union. That vote would be called by a group of faculty members and there's absolutely nothing that the President of the University of Toronto could do to stop it. It falls under labor laws of the province.
The current President knows this and I'm certain that he would have no objection to a certification drive if there ever was one. Apparently there are several professors in the Rotman School of Management who think that the President of the University could put a stop to certification. They must think the President functions like the CEO of a big corporation. (But even a corporate boss couldn't stop certification, so I don't know what they were thinking. Maybe they don't think.)
The one good thing about the letter from Roger Martin is the suggestion that the faculty at the Rotman School of Management might want to dissociate themselves from the university if the faculty ever forms a union. That might be a good reason for certification. If we play our cards right, the entire school of management might leave the university.
Last week's molecules (above) [Monday's Molecule #236] were the stereoisomers of L-threonine (D-threonine, L-allotheronine, and D-allothreonine). Nobody got the right answer so there was no winner last week. I guess that one was too hard.
It's not going to get any easier. This week's molecules (right) are related. You need to give the common names of each one and the complete IUPAC names. You'll have to be very careful in identifying and naming each one of the stereoisomers.
Email your answer to me at: Monday's Molecule #237. 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.)
A few Intelligent Design Creationists are beginning to learn about evolution. A few days ago, I speculated about what would happen if they really did start to understand modern evolutionary theory and the massive amount of data that supports the basic facts of evolution [What would happen if Intelligent Design Creationists understood evolution?].
Vincent Torley has responded. He illustrates the problems they will face and reveals some of the rationalizations that they might use to avoid the most severe symptoms of cognitive dissonance [see Professor Larry Moran poses five questions for the ID movement].
Let's take a look at what has to say. Remember that Vincent Torley doesn't speak for all Intelligent Design Creationists but he does have posting privileges on Uncommon Descent and he is frequently praised by some of the ID leaders who post there. I think we can assume that his views are typical.
Here's his response to each of the five questions.
I stumbled across an article in Science & Education that caught my eye. The authors discuss the way genetics is taught in introductory university courses (McElhinny et al. 2014). They quote several sources that define the core concepts of genetics that students must learn.
Here's the list ...
- DNA is the universal information molecule in living organisms, encoding genes and allowing for genetic variation within and genetic continuity between generations (DNA);
- Mendelian patterns of inheritance are directly related to the mechanisms of meiosis (MENDELIAN);
- Traits result from the expression of one or more genes working alone or together, with the environment, often in unpredictable ways (GENE EXPRESSION);
- The activities of genes and the environment regulate all developmental processes (GENES + ENVIRONMENT);
- Genetic variation underlies variation in traits, which is the basis for the differential survival and reproduction that allow populations to evolve (VARIATION); and
- The ability to analyze and manipulate genetic information raises a variety of complex issues for individuals and society (GENES + SOCIETY).
These six concepts for genetic literacy will hereafter be referred to as the core genetics concepts.
This is a strange list. Let me explain why.
- The structure of DNA and how it is expressed should be covered in other mandatory courses, including introductory biology and biochemistry. You should not have to spend any time at all on these topics in a genetics course. (P.S. DNA does not "encode genes.") You may want to spend some time on the biochemistry of recombination if it's not covered elsewhere. Students should understand Holliday junctions and how they are resolved.
- Mendelian genetics is important. Students should learn and understand the three laws he discovered. They should also learn about meiosis and sex. However, it's important for students to understand that simple transmission genetics is not limited to diploid eukaryotes. Bacteria also do genetics.
- Traits (phenotype) are due to information in DNA (not just genes) but most of those traits have very little to do with the external environment.
- Of course the activities of genes regulate development. They also regulate the citric acid cycle, photosynthesis, and protein synthesis. Surely you don't want undergraduates to think that development is the only thing that's important in genetics?
- It's important for students to understand that populations contain genetic variation. That means they have to learn about MUTATION and how it happens. They also have to learn why there's so much variation in populations—one of the most important discoveries in genetics in the last century. The answer is Neutral Theory and random genetic drift. No genetics course should leave out this important concept, especially because so few students will have never heard of it before enrolling in the course.
- Discussions about cloning, GM foods, and personal genomes are interesting but, unfortunately, there are very few scientists who can handle those issues in a genetics course. The important core concept is to get the science right and make sure students understand that getting the science right is absolutely essential whenever you discuss controversial issues.
- POPULATION GENETICS is an essential core concept in an introductory genetics course. You can't teach students about the genetics of EVOLUTION without it.
The authors discovered that only the first three "core concepts" were taught in every genetics course. Variation and mutation were taught in only 88% of the courses they surveyed. Only 63% covered GENES + ENVIRONMENT and only 9% covered GENES + SOCIETY.
McElhinn et al. (2014) discuss one possible change in the curriculum. It's a suggestion originally made by Dougherty (2009) and echoed by Redfield (2012). The idea is to "invert" genetics courses by beginning with coverage of poplations, variation, and complex traits. I strongly disagree with Rosie Redfield's proposal [see Questions for Genetics Students] but what surprises me in the McElhinny et al (2014) paper is that they can seriously list those core concepts without mentioning mutation and population genetics.
McElhinny, T.L., Dougherty, M.J., Bowling, B.V., and Libarkin, J.C. (2014) The Status of Genetics Curriculum in Higher Education in the United States: Goals and Assessment. Science and Education 23:445-464.
[doi: 10.1007/s11191-012-9566-1]
Redfield, R. J. (2012) "Why do we have to learn this stuff?’’—A new genetics for 21st century students. PLoS Biology, 10, e1001356 [doi: 10.1371/journal.pbio.1001356]
Branko Kozulic has asked me to post some additional comments. I'm happy to do so since it reflects a sincere attempt to learn about evolution and come to grips with the concepts of neutral alleles and random genetic drift. We should encourage the creationists to continue this effort whenever possible.
As usual, my policy is not to comment on posts from guests, especially those that disagree with my views. So here's Branko Kozulic's latest take on the "evidence" as he see it.
I thank Professor Moran for posting my text.
This reply to the comments has grown in size much more than initially anticipated. At the outset, to prevent misunderstandings, I declare my complete ignorance of paleontology and, in general, that my ignorance is by far larger than my knowledge. And I am prepared to repeat this as many times as the readers are willing to read it.
From this discussion up to date, it seems that we do not have a simple model that could show the fixation of 22,000,000 mutations. And that no simple model will work becomes evident, for example, with just a glance at the Beerli & Felsenstein paper.
The referring of our colleague McBride to the Li & Durbin paper provides an opportunity to touch upon two other topics. In addition to the Li & Durbin article, I have carefully read also the paper by Gronau et al., dealing with the same topic. Both research groups started with the data derived from the sequenced genomes of several humans (7 and 6, respectively) from various sub-populations, with the goal of illuminating past fluctuations of the effective population size. Both groups arrived at similar results: thus the first paper reports for the Yoruba population the Ne of 15,313 ± 559, while the second paper gives the range of 7,500 to 10,500. Given this congruence of the results and the quality of the journals in which the results are published, I have no doubts about correctness of the results: I trust in internal consistency of these results. But they depend on certain starting assumptions, like all other results that are an outcome of scientific models. Now it´s time to look closer at the starting assumptions of these models because there is an external inconsistency – with another set of experimental data – as will become apparent in view of other three papers.
Figure 1 of Nielsen et al., paper shows multiple (up to 21) synonymous and non-synonymous substitutions in thousands of chimp proteins compared to the related human proteins. In the second paper Behe & Snoke conclude that in order to generate a new function that requires mutations of two amino acids, like forming a disulfide bridge, 108 generations are needed with a population size of at least 109. In the third paper, Lynch countered that much smaller populations could reach this goal in less time. Now, if we take the human population size from the above two studies (Ne about 104) for the population size in Figure 3 of the Lynch article, we can see that it would take 108 generations for the arrival of a new function, even if the two changed amino acid were any 2 of 50 (with a high s = 0.01). For humans, 108 generations mean 2 Billion years: an impossibly long period. Needless to say, a new function requiring 3, 4 … up to 21 amino acid changes would take much longer than 108 generations. And yet there about 3,000 proteins with 3 amino acid substitutions, over 1,000 proteins with 5 substitutions, etc. A contradiction is thus evident between the experimental data on the one side and the Lynch model plus Li & Durbin and Gronau et al., modeled results on the other, by a wide margin. Therefore, either the starting assumptions of the Lynch model, or of the human population size models, or of both, are false.
Furthermore, we should not lose sight of singletons/orphans found in all sequenced genomes. Population genetics – which deals with changes of allele frequencies in populations – necessarily will remain “agnostic” in relation to the singletons: they are, simply put, beyond its horizon.
Some of the comments referred to religious implications. I deny the existence of direct contact between scientific conclusions and religion. In my view, each particular scientific conclusions must pass through the filter of philosophy and exit at the other side as part of a general statement (universal); then universals are incorporated into a philosophical system, and that philosophical system may or may not be in accordance with philosophy (or theology) of a religion. The only level at which the implications of scientific conclusions can be meaningfully discussed is the philosophical level, in my opinion.
Allow me to conclude with additional philosophical thoughts. Science is no democracy, but a dictatorship. A dictatorship of experimental data: and only of experimental data. Can a scientist ignore the experimental data that contradict his favorite theory without betraying his vocation of scientist? I do not think so.
Moreover, I do not expect other scientists to provide answers to all my questions; nor can I answer all their questions: this is the normal state of affairs.
I wish to extend my thanks to all participants, especially Professor Felsenstein, for their courtesy shown during this discussion.
Beerli, P. and Felsenstein, J. (2001) Maximum likelihood estimation of a migration matrix and effective population sizes in n subpopulations by using a coalescent approach. Proc. Natl, Acad. Sci. (USA) 98:4563–4568. [doi:10.1073/pnas.081068098]
Behe, M.J. and Snoke, D.W. (2009) Simulating evolution by gene duplication of protein features that require multiple amino acid residues. Protein Science 13:2651–2664. [doi: 10.1110/ps.04802904]
Gronau, I., Hubisz, M.J., Gulko, B., Danko, C.G., and Siepel, A. (2011) Bayesian inference of ancient human demography from individual genome sequences. Nature Genetics 43:1031–1034. [doi: 10.1038/ng.937]
Li, H. and Durbin, R. (2011) Inference of human population history from individual whole-genome sequences. Nature 475:493–496. [doi: 10.1038/nature10231]
Lynch, M. (2009) Simple evolutionary pathways to complex proteins. Protein Science 14:2217–2225. [doi: 10.1110/ps.041171805]
Nielsen, R., Bustamante, C., Clark, A.G., Glanowski, S., Sackton, T.B., Hubisz, M.J., Fledel-Alon, A., Tanenbaum, D.M., Civello, D., White, T.J., Sninsky, J.J., Adams, M.D., and Cargill, M. (2005) A Scan for Positively Selected Genes in the Genomes of Humans and Chimpanzees. PLoS Biology doi: 10.1371/journal.pbio.0030170
