How Logical Are You?

 

You Are Incredibly Logical

Move over Spock - you're the new master of logic You think rationally, clearly, and quickly. A seasoned problem solver, your mind is like a computer!

How Logical Are You?

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[Hat Tip: GrrlScientist at Living the Scientific Life (How Logical Are You?]

Don't Trust All DNA Sequences

 
I've been interested in sequence errors and cloning artifacts for many years. I have a thick file of papers that have uncovered numerous examples of DNA sequences that are just plain wrong. It's one of the reasons for being at least a little bit skeptical of any unusual discoveries in DNA sequences.

Now, I'm not saying that you should take this skepticism to extremes; I'm saying that you should keep your mind open to the possibility that the data might not be real. Just because it's published in the peer-reviewed literature doesn't mean it's right.

Sandra Porter has an interesting example over on Discovering Biology in a Digital World [Digital Biology Friday: What sequences do you believe?]. She describes the process she went through when she first heard about the discovery of a β-lactamase gene [Penicillin Resistance] that was supposedly from Streptococcus pneumoniae. I'm not going to spoil the punchline by revealing it here. You'll have to read about it on Sandra's blog.

Keep this lesson in mind. It's what good science is all about.

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Figure Credit: The image of the common (but old) cloning vector pBr322 is from Horton et al. 4th ed. (2006). The amp^R gene encodes β-lactamase.]

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.

P. Schubert, Philadephie, un village en mutation entre le IIe et le IIIe siècle ap. J.-C.

Paul Schubert
Philadephie, un village en mutation entre le IIe et le IIIe siècle ap. J.-C.
Schweizerische Beiträge zur Altertumswissenschaft 34, Basel 2007, XV + 190 p.
ISBN 978-3-7965-2305-2
€ 54.50 / CHF 78.-



SBA 34
L’objet de cet ouvrage est d’expliquer le processus de formation de vastes domaines agricoles attestés dans la documentation papyrologique au IIIe siècle ap. J.-C. dans le nome arsinoïte (Moyenne Égypte). Ces domaines appartenaient à des familles de notables entretenant des liens étroits avec le chef-lieu du nome, mais aussi avec Alexandrie. Le fonctionnement de tels domaines est connu par l’existence d’un important lot de papyrus regroupé sous l’appellation d’archives d’Heroninos, du nom de l’intendant qui gérait cet ensemble dans la partie sud-ouest du nome. Ces documents ne nous fournissent toutefois pas beaucoup de renseignements sur la manière dont les domaines agricoles se sont constitués. La présente étude repose sur la documentation disponible une ou deux générations plus tôt dans le village de Philadelphie, dans la partie nord-est du nome. Certains textes étaient publiés depuis longtemps, mais demandaient à être évalués à la lumière des nouvelles connaissances sur le fonctionnement de la société et de l’économie de cette région sous le Haut empire; d’autres témoignages n’ont été publiés que récemment et complètent le tableau. Cette étude permet ainsi de décrire le processus de formation de grands domaines agricoles, en soulignant les rôles respectifs de diverses catégories de propriétaires: les notables privilégiés d’Alexandrie et des chefs-lieux du nome, les vétérans et leurs descendants, ou encore les villageois. Reposant sur l’interprétation des sources documentaires, elle s’adresse aussi bien aux historiens qu’aux philologues.

L’auteur
Paul Schubert a étudié aux Universités de Genève, Oxford et Heidelberg. Il est professeur de langue et littérature grecques à l’Université de Genève. Ses recherches portent notamment sur les papyrus documentaires et littéraires grecs d’Égypte. Il a publié Les archives de Marcus Lucretius Diogenes, ainsi que de nombreux autres papyrus.

Worldcat
source: papyr-L

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.