| 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! |
[Hat Tip: GrrlScientist at Living the Scientific Life (How Logical Are You?]
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. Figure Credit: The image of the common (but old) cloning vector pBr322 is from Horton et al. 4th ed. (2006). The ampR gene encodes β-lactamase.]
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.
Here’s how I imagine we might handle this issue: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?
- 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.
"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)]. 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.
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."
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.
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 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.You've all been warned. Your days of crime and condoms are almost over.
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.
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).
[Note: Viola is English for voilà]
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.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?
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? AnNow 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.
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
[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.]
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.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,
God help us, even the usual suspects have finally had enough.
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.
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]. 
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.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.
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: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.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.
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.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].
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."
