Bloggers for Peer-Reviewed Research Reporting

 
Bloggers for Peer-Reviewed Research Reporting is a fledgling organization that's going to try and impose some standards on the reporting of peer-reviewed papers by bloggers. Here's their mission statement at [BPR3.org].

Bloggers for Peer-Reviewed Research Reporting strives to identify serious academic blog posts about peer-reviewed research by developing an icon and an aggregation site where others can look to find the best academic blogging on the Net.

The idea is to list all blog posts about peer-reviewed scientific literature on one site (with an RSS feed) and to identify all such blogs with a copyrighted icon.

What's the point of that, you might ask? Well, it's because BPR3 wants to impose some sort of standards on the blogging community. Here's how Dave Munger describes it on the BPR3.org website.

Here’s how I imagine we might handle this issue:

• Credentialling of blog authors is probably a bad idea — some expert bloggers have good reasons for being anonymous, and there are many blogs run by graduate students, journalists, and others without PhDs that offer thoughtful commentary on peer-reviewed literature


• Instead, we could have bloggers register their blogs here. Then we will (eventually) have an aggregation system which will allow links to those blogs’ posts about peer-reviewed research to appear on this site.


• If a blog appears to be abusing the system, either by not meeting our definition of peer review, or not commenting thoughtfully on the article, then readers could alert us and we could remove them from the list of registered blogs. How exactly would that process work? We’re open for suggestions.


• A secondary process could be used to combat abuse of the icon itself (whether or not the blog is actually aggregated here). This would require BPR3 to maintain copyright of the icon, so that we could deny permission to use the icon to those who abuse it. Again, we’d love to hear suggestions about how that might work.

Any other ideas/suggestions? Let us know in the comments.

I write a lot of articles about peer-reviewed research so this is right up my alley. I've got to say right up front that I'm not very enthusiastic about the proposal. Any attempt to impose order on the blogging community is doomed from the start, in my opinion. Furthermore, I don't see any advantage for most bloggers. What's in it for them?

We already have a sort of system that mimics this "peer review" of blog articles. It's the various carnivals that are published every week (see my list in the sidebar). The idea is that the carnival moderator will pick the best of the blog articles that have appeared recently and collect them on a single site. You can judge for yourself whether this has been a remarkable success over the years. From my perspective the quality of the articles in most carnivals varies enormously and I've no reason to suspect that the same won't happen on the BPR3 site.

What does everyone here think? Is this an idea that's going to work?

Adaptive Evolution of Conserved Noncoding Elements in Mammals

 
"Adaptive Evolution of Conserved Noncoding Elements in Mammals" is the title of a paper that's just been published in PLoS Genetics [Kim and Pritchard (2007)].

With a title like that you'd think the paper would be really interesting because conserved noncoding elements are a hot topic. Recall that these are short sequences in the genomes of diverse mammals that are highly similar. They were thought to be examples of regulatory sequences but deleting them from the mouse genome seems to have no effect [The Role of Ultraconserved Non-Coding Elements in Mammalian Genomes]. It's a little puzzling to see "adaptive evolution" in the title since the very fact that these short sequences are conserved implies adaptation.

I took a look at the paper. Here's the abstract.

Conserved noncoding elements (CNCs) are an abundant feature of vertebrate genomes. Some CNCs have been shown to act as cis-regulatory modules, but the function of most CNCs remains unclear. To study the evolution of CNCs, we have developed a statistical method called the “shared rates test” to identify CNCs that show significant variation in substitution rates across branches of a phylogenetic tree. We report an application of this method to alignments of 98,910 CNCs from the human, chimpanzee, dog, mouse, and rat genomes. We find that ∼68% of CNCs evolve according to a null model where, for each CNC, a single parameter models the level of constraint acting throughout the phylogeny linking these five species. The remaining ∼32% of CNCs show departures from the basic model including speed-ups and slow-downs on particular branches and occasionally multiple rate changes on different branches. We find that a subset of the significant CNCs have evolved significantly faster than the local neutral rate on a particular branch, providing strong evidence for adaptive evolution in these CNCs. The distribution of these signals on the phylogeny suggests that adaptive evolution of CNCs occurs in occasional short bursts of evolution. Our analyses suggest a large set of promising targets for future functional studies of adaptation.

Okay. It's confusing but what they seem to be saying is that the sequences of these conserved noncoding elements change in various lineages. A lot of them seem to be evolving at a "neutral rate"—which raises the question of why they are "conserved" in the first place. Does it mean that the ancestor to all mammals had a functional sequence but that function has been lost? Some of these conserved elements evolve at a very rapid rate in some lineages and this is taken to be evidence of adaptive evolution in that lineage.

I read the entire paper. It's pretty much Greek to me. If anyone else can figure it out please feel free to post an explanation in the comments.

John Tory Tries To Clarify

 
According to CityNews ,John Tory is trying to put his goof behind him. He's asking people to stop focusing on this one issue. Just because he doesn't understand what science is all about is no reason to not vote for him, is what he's saying [John Tory Tries To Clarify "Creationism Vs. Evolution" Controversy]. One nice thing about this controversy is that nobody is listening to him, even his so-called supporters. Another nice thing is that the Premier, Dalton McGuinty, makes it pretty clear where he stands.

Don't make this a one-issue election.

That was the plea from Conservative leader John Tory Thursday as the PC boss found himself awash again in a sea in controversy over his faith-based school funding platform. The plan was already contentious enough, when Tory openly mused on Wednesday about the possibility of creationism being taught alongside evolution in religious schools.

Since then, he's been assailed by those who oppose his idea and those who support it. "In the course of an election campaign, you have to have an open, honest discussion about these kinds of issues and you always have to choose your language with precision," Tory admits about his statement. "I understand that this issue is controversial ... But it doesn't mean that you shouldn't discuss it or try to sweep it under the carpet."

He attempted to bridge the gap by clarifying that the creation theory would only be allowed to be taught during a true religious lesson and not in a science class. But it's clear what pundits believe will be the most controversial part of the election has left the Conservative leader between two different worlds that don't seem likely to ever meet.

Dalton McGuinty is taking a different road on the issue. "Creationism is not a science," he reminds. "Evolution is a science. When we're teaching science in our public schools, we should be teaching evolution."

One School System Network Sponsors a Debate

 
The One School System Network (OSSN) is sponsoring a debate on Friday, September 21st from 7-10 pm in MacLeod Auditorium.

Catholic Public Schools: Constitutional Right or Archaic Privilege? Featuring Jan Johnstone, Progressive trustees network and trustee for the Bluewater District School Board.

The One School System Network includes the University of Toronto Secular Alliance and a variety of civil rights, faith-based and secular humanist advocacy organizations. The OSSN is lobbying the government to merge our two school boards into one secular school system.

University of Toronto Secular Alliance

 
Well, it's that time of year again. The Meds students have already begun classes and the undergraduates start next Monday. It's time to start putting those important events on your calendar.

The University of Toronto Secular Alliance is hosting a BBQ at the Centre for Inquiry on Thursday Sept. 13 from 5 to 7pm. If you haven't joined yet then sign up on the website.

The Centre for Inquiry is located at 216 Beverly St. just south of College St. Following the BBQ you can stay for the Flying Spaghetti Monster Dinner and Movie Night.

Don't Say We Didn't Warn You

 
The editor of the Lebanon Daily News has made a prediction. It's so important that it deserves a posting on Uncommon Descent [Matter of time for intelligent design].

Now I don't know where Lebanon is—other than it's in Pennsylvania, USA—but this editor must be one of the big guns of Intelligent Design Creationism. Here's the bad news ...

The public needs enlightenment on the truth of intelligent design as increasing numbers of the world’s greatest scientists are yielding to the compelling and mounting evidence of this burgeoning movement. In recent years the erroneous teaching of Darwinism and life by random chance is becoming unraveled and exposing itself for what it really is: a bankrupt philosophy masquerading as a science with the aid of fake fossil mills loose in the world.

I’m confident that in the not-to-distant future the information-revolution will sound the death knell for Darwinism. The hard evidence of technology will shake the pillars of evolutionary theory and toss them into the dustbin of history. When America restores true Bible science and accountability to our Creator God into our political and educational institutions, we’ll have taken a giant step toward healthier national character and the prevention of crime, life without purpose and the consequences of our condom culture.

You've all been warned. Your days of crime and condoms are almost over.

"IDiot" doesn't even begin to describe this nonsense.

Intelligent Design Creationism: Frontloading

 
You're not going to believe this.

A few days ago I reviewed some work from Edward Rubin's lab at the Lawrence Berkeley National Laboratory in Berkeley, California (USA) [The Role of Ultraconserved Non-Coding Elements in Mammalian Genomes]. What they did was identify short stretches of DNA that are identical in the mouse, rat, and human genomes. Most of these pieces of DNA are 200-300 bp in length but some are larger. Rubin's group deleted four of these "ultra-conserved" non-coding elements in mice and discovered that the resulting strains seemed perfectly normal. This raises questions about the role of these short sequences that appear to have been highly conserved.

The IDiots have an explanation. DaveScot describes it on Uncommon Descent [Ultra-conserved DNA with no evident immediate purpose].

Edward Rubin again finds hard evidence supporting a front loaded evolution. Front loading is a design engineering term generally used to describe design elements inserted for possible use in the future (contingency) as opposed to immediate use. The mechanism of random mutation and natural selection is incapable of contingency planning. RM+NS can build based on experience but can’t build based on an abstract future. It is reactive not proactive. The front loading hypothesis in essence says the complex specified information necessary to construct the more complex machinery of life has been around since life appeared on the earth but much of it was preserved for expression in the far distant future.

According to Intelligent Design Creationism this DNA is for future use by the Creator. Apparently the Intelligent Designer can't just make up some new DNA whenever (s)he needs to evolve some new function. Instead, (s)he has to stick the DNA in the genome of all organisms then take steps to protect it from mutation. In a few years the Intelligent Designer will activate these little bits of DNA and viola!—rats will get smarter (or something).

The other good news is that there's not much of this ultra-conserved DNA in our genomes. The Intelligent Designer must have just about finished with us. I don't know about you but I think it's time to get ready for the Rapture. Life is going to be so much better without the Christians.

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[Note: Viola is English for voilà]

Defining Life

 
The August issue of SEED has a wonderful article by Carl Zimmer, the best science writer on the planet. The article, The Meaning of Life, has just appeared on the SEED website so you can all read it [THE MEANING OF LIFE]. You should read it.

Zimmer asks an important question,

We create life, we search for it, we manipulate and revere it. Is it possible that we haven't yet defined the term?

What do you think of the definition(s) in the article?

Denyse O'Leary's University Course on Intelligent Design

 
One of my friends alerted me to a course taught by Denyse O'Leary at the University of St. Michael's College in the University of Toronto. This is a continuing education course under Religion, Scripture, Spirituality. Here's the complete description.

RSS7-F By Design or By Chance? An
Introduction to the Intelligent Design Controversy

The intelligent design controversy is best understood as a conflict between materialist and non-materialist views of the origin and nature of the universe. Reputable scientists can be found on both sides. Because the two sides proceed from different assumptions, they do not agree, as Thomas Kuhn would say, on what would constitute a falsification of their premises. The controversy continues to grow because, while the materialism is prevalent in academia and the media, it is widely discredited in the population at large, including the professional classes.

INSTRUCTOR: *Denyse O’Leary is a Toronto-based journalist, author, and blogger, who is the author of Faith@Science, By Design or By Chance? and co-author of The Spiritual Brain with Neuroscientist Mario Beauregard.

Date: 6 Tuesdays, Oct. 23 – Nov. 27 2007
Time: 7 – 9pm
Fee: $130.00
Blue Card: Free
Partner School: $20

Now that sounds really interesting. The good part is that she will focus on materialist vs non-materialist views of the nature of the universe. This is, indeed, the core of the problem. The bad part is that she identifies Thomas Kuhn with the idea of falsification—that doesn't bode well for the accuracy of her lectures.

It might be fun to learn what the "professional classes" think about Intelligent Design Creationism. Is the entertainment worth $130?

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[Photo Credit: The photograph is from the University of St. Michael's College website. Marshall McLuhan was a Professor a St. Mike's and the photograph shows him walking to his office on Queen's Park Cresent.]

Creationism: Even the Blogging Tories Have Their Limits.

 
Canadian Cynic has an amusing posting about the John Tory creationism disaster [Creationism: Even the Blogging Tories have their limits]. As you may or may not know, Canadian Cynic is no fan of conservatives and has exposed their stupidity on many occasions.

You know, I've always wondered whether there was a right-wing position so indefensible, so appalling, so absolutely batshit crazy that even the Blogging Tories would finally pull up short, saying, "No, I don't think so. That's too stupid, even for us." And I believe we've finally found it.

God help us, even the usual suspects have finally had enough.

Read the list of Blogging Tories who have turned on John Tory for promoting creationism. I never thought I'd be proud of right-wing conservatives. Canadian Cynic is also impressed,

You know, with these signs of intelligent life over there, maybe -- just maybe -- I'll stop saying such snarky things about them.

Don't hold your breath.

New York Times "Forgets" to Mention Their Blogger Source

 
Effect Measure carries a story about a New York Times article that used a blogger (Dr. David Michaels at The Pump Handle) as their primary source [New York Times uses story, neglects to mention blogger is the source]. Their excuse is that the reference was cut out of the article by an editor. Shame on you, New York Times.

PZ Myers is also angry [Time for another blogger ethics review panel].

Ontarians Want Public, Catholic Schools to Merge

 
According to this CBC poll a majority of the citizens of Ontario want to end discrimination in our school systems by abolishing the Catholic school board [Ontarians want public, Catholic schools to merge: poll].

This is, of course, exactly the opposite of what the Progressive Conservative Party is proposing. They want to extend funding to all religious schools. We have just discovered that their leader, John Tory, has doubts about evolution and favors creationism [ John Tory Promotes Creationism].

With a bit of luck this will blow up in their faces and we'll be able to get rid of the parallel public and Catholic school boards. Maybe it's just the stimulus we needed. Thanks, John Tory, for being an IDiot.

[Hat Tip: Jeffrey Shallit at Recursivity (Stupid Tory Tricks: Religious Schools In Ontario Could Teach Creationism, Get Public Funds)]

John Tory Promotes Creationism

 
This man is John Tory. He's the leader of the Ontario Progressive Conservative Party. Right now he's the leader of the Opposition but he's hoping to become Premier after the election on October 10, 2007.

If elected, Tory promises to extend public funding to all religious schools in Ontario. Right now we fund the Roman Catholic Schools as a result of a deal struck at the time of Confederation. I favor abolishing this funding and restricting government funding to the public school system [One School System Network [OSSN]].

Today John Tory stuck his foot firmly in his mouth when he revealed his ignorance of evolution. John Cowan of The National Post—a conservative newspaper—reported it like this [John Tory on creationism, the theory of evolution and why ducks have wings].

It should be said that Ontario Progressive Conservative leader John Tory is usually a thoughtful, articulate guy. But this week, the man has had nothing but a mouthful of foot. First, he referred to the University of Ottawa as the “University of Zero.” Another stumble came today, during an event to promote Mr. Tory’s promise to extend public funding to faith-based schools. A radio reporter asked whether schools would be allowed to teach creationism. Mr. Tory responded: “The Christian-based school would have to teach the Ontario curriculum, which of course has a different explanation. It’s still called the theory of evolution, but they teach evolution in the Ontario curriculum, but they could also mention to children the fact that there are other theories out there that are part of some Christian beliefs.”

Hmmm ... where have we heard that before? Do you know anyone who emphasizes that it's only a theory who isn't a creationist? Tory is in big trouble. He might get away with this in another country but here in Ontario he's going to look like a real fool.

Fortunately for him, his handlers got on the job real quick.

What Mr. Tory did not say was whether evolution would be taught as part of science class or religious studies -- which is, we submit, a pretty important distinction. So important that late this afternoon, the Conservative campaign issued the following press release:

JOHN TORY 2007 CAMPAIGN
STATEMENT OF CLARIFICATION

(Toronto, ON) – In an interview with reporters earlier today, John Tory was asked whether ‘creationism’ could be taught in faith-based schools, if they wished to receive funding under his proposed policy.

POINTS OF CLARIFICATION:
1.) The Ontario curriculum does not allow for creationism (or any other religious theory) to be taught in science classes in Ontario’s public schools.
2.) Mr. Tory clearly stated that any school to be included in the proposal must teach the Ontario curriculum.
3.) Mr. Tory’s proposal would allow creationism to be discussed only as part of religious studies programming, as is now the practice in Ontario’s publicly-funded Catholic schools.

Nobody's going to buy that. Tory clearly questioned whether evolution is true by mentioning that it is a "theory" and other "theories" should be taught.

Tory is running against the current Education Minister Kathleen Wynne (Liberal) in the riding of Don Valley West (Toronto). According to this article in the Canadian Press [ On eve of Ontario election, Conservative leader muses about creationism in schools] she nailed him on the issue.

Education Minister Kathleen Wynne - who is running against Tory for her Toronto seat - said his comments prove his policy hasn't been properly thought out. Creationism is currently not part of the provincial science curriculum and isn't given the same weight as evolution, she said.

Catholic schools may talk about creationism, Wynne said, but only in the context of a broader religious discussion.

"It's useful for students to have the opportunity to know the ideas that are out there and are part of our history," Wynne said.

"What we teach as the truth is the question. The scientific truths are the ones that are included in the Ontario curriculum. That's the curriculum that we support."

The Canadian press is all over this: See this article from the Globe & Mail [Creationism raised as Ont. election issue], and this from Canada.com [John Tory grilled on faith-based schools proposal], and this from The Toronto Star [Tory ignites debate over creationism in schools].

It will be interesting to see what happens tomorrow.

What is the latest theory of why humans lost their body hair?

 
This is the question asked in this month's issue of Scientific American. Mark Pagel, head of the evolutionary biology group at the University of Reading in England and editor of The Encyclopedia of Evolution gives three adaptationist explanations.

Now, here's the question of the day for all you adaptationists. Why didn't he mention neoteny? Do you think it's because he has carefully reviewed all the evidence and reaches the conclusion that there's more data to support running on the savannah?

Nobel Laureate: Richard Kuhn

 

The Nobel Prize in Chemistry 1938.

"for his work on carotenoids and vitamins"



In 1938, Richard Kuhn (1900-1967) won the Nobel Prize in Chemistry for his work on the structure of several different vitamins, including the carotenoids [Vitamin A (retinol)] and the B₆ family [Pyridoxal Phosphate and the Vitamin B6 Family].

The award overlaps considerably with the prize for the previous year [Nobel Laureate: Paul Karrer], which suggests that the prize committee may have been pressured to recognize Kuhn after slighting him in favor of Karrer. The two men were friendly competitors for many years and much of their work is similar.

Kuhn was not able to accept the prize in 1938 because at the time he was working at Heidelberg University and the political situation did not allow him to travel to Sweden. There was no formal presentation speech but the following account of his work is posted on the Nobel Prize website.

When Richard Kuhn in 1926 took over the Chair for General and Analytical Chemistry at the Federal Institute of Technology Zurich he set in motion a comprehensive series of investigations into the so-called conjugated double bonds which make up the essential arrangement of the atoms of the polyenes.

The group of the diphenylpolyenes had at this time aroused especial interest because the presence in the carotenoid Crocetin of a chain of double bonds had been successfully demonstrated. Kuhn's sixth report on conjugated double bonds already contains structure determinations of polyene dyes from vegetable materials. With his syntheses of over 300 new materials belonging to this group Kuhn has by no means sought merely to liberate new substances. In this work he was much more concerned to clarify the general relationships between the chemical structure of these unsaturated substances and their optical, dielectric, and magnetic properties. The results which he has obtained in this respect form the starting-point for new lines of development in organic chemistry.

Kuhn's work on polyenes led him straight into the chemistry of the carotenoids. In 1930 Karrer clarified the constitution of carotene. The elementary composition of carotene, C40H56, had previously been ascertained by Willstätter. In 1931, R. Kuhn (at that time already Professor at Heidelberg), Karrer in Zurich, and Rosenheim in London discovered simultaneously and independently of each other the fact that the carotene in carrots consists of two separate components: one of these, b-carotene, rotates the plane of polarized light to the right, while the other, a-carotene is optically inactive. In 1933 Kuhn discovered a third carotene isomer which was called g-carotene.

The great physiological and biological significance of carotene lies in the fact that it is hydrolysed in the liver of certain animals so that from one molecule of b-carotene or from two molecules of a-carotene two molecules of Vitamin A, Axerophtol, are formed. This substance is necessary for growth in higher animals and especially for maintaining the normal condition of the mucous membranes.

With several collaborators Kuhn carried out a large number of investigations into the occurrence of carotenoids in the animal and vegetable kingdoms. Among his most important results, his discoveries of the following carotenoids and their structure determination should be mentioned:

Physalien from berries of species of Physalis, Helenien, Flavoxanthin, isolated from species of Ranunculus, Violaxanthin from Viola tricolor, unstable Crocetin from saffron, Taraxanthin, Cryptoxanthin from Zea Mays Rubixanthin.

Kuhn also had an important share in establishing the composition of Rodoxanthin and Astaxanthin as well as in discovering the connection of this latter carotenoid with the chromoproteids of the Crustaceans.

Of great interest also are the many contributions Kuhn and his school have made to the perfection of the chromatographic method which is one of the most important aids to the isolation and synthesis of the different representatives of the carotenoid group.

Kuhn's second great field of activity concerns the clarification of the Vitamin B complex. Kuhn has the great merit, together with von Szent-Györgyi and Wagner-Jauregg, of having been the first to isolate the extraordinarily important substance Vitamin B2 (Lactoflavin or Riboflavin). He has made very important contributions to the elucidation of the chemistry of this substance.

From 5,300 litres skim milk Kuhn and his collaborators succeeded in liberating about 1g of a pure yellow substance, Lactoflavin, whose composition was found to be C17H20O6N4. A breakdown product of the Lactoflavin, which was called Lumiflavin, could be identified with a substance previously prepared from the yellow ferment occurring in yeast. By drawing up a structural formula for Lumiflavin later confirmed in various ways, Kuhn furnished a key to the chemical clarification of Lactoflavin. He himself demonstrated the Lumiflavin formula, which had been found by analytical methods, by a synthesis - namely through the condensation of an odiaminobenzene derivative with Alloxan.

At the beginning of 1939 Kuhn made his second significant discovery in relation to the Vitamin B complex. Together with Wendt, Andersag, and Westphal, he succeeded in isolating that component of the Vitamin B complex which is designated Vitamin B6, the antidermatitis vitamin, and in a remarkably short time he was able to establish its chemical composition and structure (Ber., 71 (1938) 1534; 72 (1939) 309). The substance which Kuhn thus elucidated, which he called Adermin, proved to be 2-methyl-3-hydroxy-4,5 -dihydroxymethylpyridine.