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Saturday, May 31, 2014

The Third Fourth? Way

Back in 1997, James Shapiro wrote an article for the Boston Review entitled "A Third Way." It was a very confusing article. His main point seemed to be that conventional neo-Darwinism wasn't a complete picture of modern evolutionary theory.

That part wasn't news since by 1997 the ideas of Neutral Theory and random genetic drift had been around for thirty years. Apparently, Shapiro was three decades behind in his understanding of evolution.

Shapiro doesn't demonstrate that he understands population genetics and random genetic drift. This just one (of many) criticisms that I mentioned in my review of Shapiro's book Evolution: A View from the 21st Century in NCSE Reports [Evolution: A View from the 21st Century]. Shapiro responded to my review at: Reply to Laurence A Moran’s review of Evolution: A View from the 21st Century] and I discussed his response on my blog [James Shapiro Responds to My Review of His Book].

The "third" way, according to Shapiro's 1997 article, is not classic Darwinism and it's not creationism. Instead, it's a new way of looking at evolution.
What significance does an emerging interface between biology and information science hold for thinking about evolution? It opens up the possibility of addressing scientifically rather than ideologically the central issue so hotly contested by fundamentalists on both sides of the Creationist-Darwinist debate: Is there any guiding intelligence at work in the origin of species displaying exquisite adaptations that range from lambda prophage repression and the Krebs cycle through the mitotic apparatus and the eye to the immune system, mimicry, and social organization? Borrowing concepts from information science, new schools of evolutionists can begin to rephrase virtually intractable global questions in terms amenable to computer modelling and experimentation. We can speculate what some of these more manageable questions might be: How can molecular control circuits be combined to direct the expression of novel traits? Do genomes display characteristic system architectures that allow us to predict phenotypic consequences when we rearrange DNA sequence components? Do signal transduction networks contribute functional information as they regulate the action of natural genetic engineering hardware?

Questions like those above will certainly prove to be naive because we are just on the threshold of a new way of thinking about living organisms and their variations. Nonetheless, these questions serve to illustrate the potential for addressing the deep issues of evolution from a radically different scientific perspective. Novel ways of looking at longstanding problems have historically been the chief motors of scientific progress. However, the potential for new science is hard to find in the Creationist-Darwinist debate. Both sides appear to have a common interest in presenting a static view of the scientific enterprise. This is to be expected from the Creationists, who naturally refuse to recognize science's remarkable record of making more and more seemingly miraculous aspects of our world comprehensible to our understanding and accessible to our technology. But the neo-Darwinian advocates claim to be scientists, and we can legitimately expect of them a more open spirit of inquiry. Instead, they assume a defensive posture of outraged orthodoxy and assert an unassailable claim to truth, which only serves to validate the Creationists' criticism that Darwinism has become more of a faith than a science.
Now Shapiro has joined forces with some other "revolutionaries" and started a new website called "The Third Way." It has grandiose goals ....
The vast majority of people believe that there are only two alternative ways to explain the origins of biological diversity. One way is Creationism that depends upon supernatural intervention by a divine Creator. The other way is Neo-Darwinism, which has elevated Natural Selection into a unique creative force that solves all the difficult evolutionary problems. Both views are inconsistent with significant bodies of empirical evidence and have evolved into hard-line ideologies. There is a need for a more open “third way” of discussing evolutionary change based on empirical observations.
There's only one problem. I'm familiar with Shapiro's ideas and with the ideas of most of the other people listed on the website and I don't think any of them (except Eugene Koonin) have anything significant to say about evolutionary theory. Futhermore, most of them don't seem to understand that there's already been a revolution and population genetics, Neutral Theory, etc. won the day. They seem to have completely missed that revolution.

They are advocating a fourth way that skips right from adaptationism to something else.

They are like a group of would-be revolutionaries marching up Rue de Lyon in Paris only to discover that the Bastille has been replaced by an open square and an opera house.

Note: There aren't many biologists that are interested in this "Third Way" but the creationists are lapping it up [A Group of Darwin-Skeptical Scientists Seeking a "Third Way" in Biology Have Launched a New Website; Welcome to Them!].

Tuesday, May 27, 2014

Begging the Question

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."

Science literacy and "belief" in evolution

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.

Friday, May 23, 2014

The faculty is the university

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.
  1. The faculty is the university.
  2. Budget models that invest in things like $140-million in online learning while cutting normal teaching and research are unlikely to work.
  3. 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.

Thursday, May 22, 2014

The Board of Governors at the University of Saskatchewan fires President Ilene Busch-Vishniac

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 ...
  1. Buckingham has been reinstated as a Professor in the Faculty of Public Health.
  2. The Provost, Brett Fairbairn, was forced to resign.
  3. 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 ...

Tuesday, May 20, 2014

The Provost of the University of Saskatchewan has resigned

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 ....

Monday, May 19, 2014

Monday's Molecule #241

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.)

Friday, May 16, 2014

The Provost and the President of the University of Saskatchewan made a mistake

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.

Thursday, May 15, 2014

Robert Buckingham rehired at the University of Saskatchewan

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.

Why shouldn't you use PowerPoint slides in your classes?

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.

I wonder what he thinks of MOOC's?

Ilene Busch-Vishniac should resign immediately as President of the University of Saskatchewan

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.

Wednesday, May 14, 2014

What did the ENCODE Consortium say in 2012?

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.

Tuesday, May 13, 2014

Happy Birthday to Me!

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.

Monday, May 12, 2014

Monday's Molecule #240

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.)

Friday, May 09, 2014

How does Nature deal with the ENCODE publicity hype that it created?

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.

The Case for Junk DNA: The onion test

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]

Thursday, May 08, 2014

More primordial soup nonsense

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 ...

Tuesday, May 06, 2014

US Supreme Court says that prayer at town council meetings is allowed

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]

Answering creationist questions about Neutral Theory

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 ...

Get Science Right (in Canada)

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.

Monday, May 05, 2014

Monday's Molecule #239

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.)

Saturday, May 03, 2014

Michael White's misleading history of the human gene

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.