As It Turns Out, Not all Conservatives Are Smart ....

 
In an earlier posting I commented on how pleased I was that some of John Tory's supporters realized that teaching creationism is wrong [see John Tory Tries to Clarify]. I'm still pleased with the majority of conservative commentators but, naturally, there are some who still don't get it.

One of them is Matthew at ThePolitic.com, a widely read Canadian political blog. Mathew reveals that some Canadians are IDiots [Warren Kinsella’s Documentary Sequel]. Matthew really crams his foot in his mouth all the way up to his kneecap but I won't bore you with all the details. Instead, let me just mention one or two of the most obvious examples of stupidity.

5) Creation science is a real scientific theory — if you want to challenge it, please don’t insult us by just offering a fancy and long-winded “nuh-huh”. I find it funny that Wikipedia attempts this too, but I’ve seen this movie before; it’s called the Consensus on Climate Change (and we all know how that one will end!).

Where do these IDiots come up with stuff like this? Creation science is not a real scientific theory by any stretch of the imagination. If Matthew is talking about Biblical Creationism then that fairytale has been disproved by science. If he's talking about any other version of "Creation science" than it's either; (a) also disproved, or (b) vacuous.

The fact that Matthew is so confused about this means that it's extremely important that we teach evolution in school. It's pretty clear that Matthew skipped all the science classes when he was in school. Probably because they required more than 6th grade mathematics.

6) Someone still has to address for me how teaching an alternative view on the origin of species will forever ruin students’ lives and deny them jobs, houses and weekends up at the cottage. They’re not your kids so what do you care what they learn if it doesn’t affect you?

Look at it this way Matthew. We have basically two choices in the classroom. We can teach children things that are correct or we can teach them lies. Call me old-fashioned, but I think it's better to teach the truth. It makes for better citizens in the long run.

I actually think we should address Creationism in school. Traditionally we use astrology as the example of something that masquerades as science. It's a way of teaching what science really is and it provides a good lesson on how to think. Creationism would be another good example. We should make sure that all children learn why Creationism is not science.

9) Ala the Flintstones comment, blindly believing in evolution is like believing Star Trek is a documentary about the future. Reality is though that we’re not eliminating all wars, humanity isn’t evolving past its character flaws and evil tendencies and no matter how much some in our society might like it, we’re not going to grow beyond religious faith. Even the television series outlived this optimistic faith in the human will by DS9. Evolution might be wonderful science fiction with things spontaneously mutating everywhere, but we shouldn’t be confusing it with a scientific principle. Maybe we should also be keeping it in it’s proper place too — media class!

No comment, other than to point out there's a reason why we call them IDiots.

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[Photo Credit: The photograph shows a typical Boston Red Sox fan celebrating something that got them all excited (Red Sox Connection). (I think their team just lost another game against Toronto.)]

[Hat Tip: Canadian Cynic]

Gene Genie #15

 

The 15th edition of Gene Genie has just been published on Cancer Genetics [Gene Genie #15].

As you might expect, there's a lot of stuff about Craig Venter's genome. You won't read anything about it here so if you're really interested in Craig then your kicks from the carnival postings.

Play Creationist Bingo!

 
The rules are on Skeptico [ID Creationist Bingo].


[Hat Tip: FriendlyAtheist]

Theories Don't Become Laws

 
I'm pleased by the almost universal condemnation of John Tory's remarks about creationism in schools [John Tory Promotes Creationism]. Letters to the newspapers are running overwhelmingly against the leader of the Ontario Progressive Conservatives. However, there's still lots of misunderstanding out there even though their hearts are in the right place.

In today's Toronto Star there's a letter from a reader in Barrie, Ont. The title is Misunderstanding of the word `theory'. I'll quote most of the letter ...

John Tory's statement appearing to equate Darwin's theory of evolution with "other theories that people have out there" comes from a common misunderstanding the general public has about the scientific meaning of the word "theory."

When a scientist has an idea he or she wishes to test through observation or experimentation, this is termed a hypothesis.

Once a body of scientific data has been accumulated in support of the hypothesis, it is elevated to the status of theory.

After a time, certain theories receive considerable support from various scientists and no contradictory evidence turns up. Then, the theory may be elevated to the status of law.

There is now so much evidence from many branches of science supporting Darwin's theory of evolution by natural selection, that it may be time to give it the status of a law.

This is not right. Theories are explanations of natural phenomena and laws are simple descriptions of phenomena. Boyle's Law, for example, simply states that "For a fixed amount of gas kept at a fixed temperature, P and V are inversely proportional." It does not explain why this is so. That's what the theory of the behavior of gases would do.

Evolutionary Theory is a complex subject that attempts to explain how species evolved. It incorporates Darwin's Theory of Natural Selection and other things like random genetic drift and mechanisms of speciation. Evolutionary Theory will never become a law. Theory is as good as it gets in science.

Waiting for the Paradox

 
John Dennehy's citation classic for this week is Gunther Stent's Molecular Biology of Bacterial Viruses [This Week's Citation Classic]. This reminds me of the time when I was an undergraduate in 1966 and I first read about the Phage Group in Phage and the Origins of Molecular Biology (1966). The book was a collection of articles by workers who had been influenced by Max Delbrück, on the occasion of his 60th birthday.

A few years later I got to meet most of them at the annual phage meetings in Cold Spring Harbor. It was an exciting time. I remember Stent as one of those people who is so smart it's scary. Little did I know at the time that I was witnessing the end of an era.

Stent's contribution to Phage and the Origins of Molecular Biology was an essay with the cryptic title "Waiting for the Paradox." He describes some of the early history of the phage group and Delbrück's attempts to define the gene in 1940. This influenced the physicist Erwin Shrödinger who wrote a famous little book called What is Life?. It stimulated many physicists to enter biology—including Francis Crick.

The key passage from Shrödinger's book is described by Stent. Schrödinger defines an important credo (quoted by Stent) ...

In fact, this credo was probably the most important psychological incentive for physicists to turn to biology in the first place: "From Delbrück's general picture of the hereditary substance it emerges that living matter, while not eluding the 'laws of physics' as established up to date, is likely to involve 'other laws of physics' hitherto unknown which, however, once they have been revealed will form just as integral part of this science as the former." Thus it was the romantic idea that 'other laws of physics' might be discovered by studying the gene that really fascinated the physicists. This search for the physical paradox, this quixotic hope that genetics would prove incomprehensible within the framework of conventional physical knowledge, remained an important element of the psychological infrastructure of the creators of molecular biology. [my emphasis - LAM]

By 1966 it was clear that no new laws were going to be discovered although there was still the hope that something mysterious was going on inside the brain. Some people were still waiting for the paradox.

Today we teach our students that the most remarkable thing about biology is that life obeys the laws of physics and chemistry.

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[Photo Credit: The book cover shows the 1992 expanded edition of Phage and the Origins of Molecular Biology. A new Centennial Edition is due out next month.]

John Tory's Self-Immolation

 
This is from the National Post. They're supposed to be on the same side as the Progressive Conservatives. It's too cute to pass up [Colby Cosh: Tory's tumble].

EDMONTON -Where were you when John Tory lost the Ontario election? I was at my usual post in far-off Alberta, but even here Tory's Wednesday self-immolation cast a glow that you could almost warm your hands by.

As I hear it told, a radio reporter looking for a new angle asked the Conservative leader whether the fully funded religious schools he wants to pay for as premier would be permitted to teach creationism.

There's no word on whether Tory actually expressed gratitude for the layer of gasoline he had just been super-soaked with: he just went ahead and whipped out the Zippo. Creationism? Sounds great! Why, it's just one more of the menu items our $400-million will buy us! Say, why's my tie melting?

Genomics Is Dead! Long Live Systems Biology!

 
When you're an old fuddy-duddy like me you've lived through several revolutions in biology. I still remember when recombinant DNA technology was going to change the world. Then it was developmental biology and evo-devo. Along the way were told with a straight face that sequencing the human genome would cure cancer and everything else.

After a while it all got very boring. We put up with the hype on the grounds that it was good spin framing for the general public. If it brought in lots of money then what's the harm? Well it turns out there was some harm done. We scientists are losing our credibility.

I've gone way beyond being bored by this kind of nonsense. Now I'm angry—especially when it seems that those who are ignorant of history are doomed to misrepresent it. Here's the opening paragraph of a press release on Systems Biology [Systems Biology poised to revolutionize the understanding of cell function and disease]. It summarizes the contents of a report to the European Science Foundation.

Systems Biology is transforming the way scientists think about biology and disease. This novel approach to research could prompt a shake up in medical science and it might ultimately allow clinicians to predict and treat complex diseases such as diabetes, heart failure, cancer, and metabolic syndrome for which there are currently no cures.

I wonder if they just reuse the reports from years past substituting "systems biology" for "genomics," or whatever the last cure for cancer was supposed to be? This kind of stupid motherhood hyperbole would be laughable if it wasn't for the fact that these people are deadly serious. That makes it pathetic.

Look what one of authors of the report has to say ...

Until recently, researchers tended to focus on identifying individual genes and proteins and pinpointing their role in the cell or the human body. But molecules almost never act alone. According to Lilia Alberghina from the University of Milano-Bicocca, Italy: “There is a growing awareness in medical science that biological entities are ‘systems’ – collections of interacting parts."

I suppose this depends on what you mean by "recently." If it's 40 years then maybe the statement might make some sense but even then it's a gross misrepresentation of the truth. Of course we isolated genes and proteins one-at-a-time but the goal was always to put them back together to make molecular machines. Does Lilia Alberghina really think that older scientists were completely unaware of the fact that biological entities are "systems"? I wonder if Alberghina is aware of metabolic pathways that were worked out half a century ago, or ribosomes, or DNA replication complexes, or muscle, or the complement system, or Drosophila embryogenesis, or any number of other systems that haven't just sprung into existence in the last few years.

Most scientist are already tired of these fads masquerading as revolution. I wonder how long it will be before the public and the politicians catch on?

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.

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.

The Role of Ultraconserved Non-Coding Elements in Mammalian Genomes

Ultraconserved elements are stretches of DNA that are 100% identical in mouse, rat, and human genomes. In order to qualify as an ultraconserved element, the length has to be greater than 200 bp. This eliminates most sequences that might be identical by chance.

The most interesting elements are those that fall outside of coding regions. These ultraconservative elements are most likely to be involved in regulating gene expression or some other essential feature of non-coding DNA. The fact that they are identical in species who last shared a common ancestor 100 million years ago is powerful evidence of adaptation.

Ahitiv et al. (2007) set out to test this hypothesis by selecting four examples of ultraconservative elements for further analysis. They discovered that the elements function as tissue specific enhancers in a test designed to look at how they control expression of a maker gene in mouse embryos. The results are shown in Figure 1 (left) of their paper, which was just published in the open access journal PLoS Biology.

The figure shows the genomic location of the four ultraconserved elements; uc248 (222 bp), uc329 (307 bp), uc467 (731 bp), and uc482 (295 bp).

Of these, uc467 is the most remarkable because it is 731 bp in length and resides in the last intron of the DNA polymerase alpha 1 gene (POLA1) on the human X chromosome. The enhancer trap experiment shows that this segment of conserved DNA directs expression of the marker gene in embryonic brain cells (shown as the dark blue area in the embryo above the 467 site). This is usually taken as evidence of specific regulatory sequences that bind transcription factors.

Ahituv et al. then deleted the four ultraconserved sequences from the mouse genome using standard knockout technology. Mice that were homozygous for the knockouts showed no evidence of any defect compared to wild-type mice. In other words, the ultraconserved elements seemed to be completely dispensable—a result that is not consistent with their extreme conservation.

THEME:
Junk DNA
What are the possible explanations? It's possible that the authors missed a phenotype that can only be detected outside the laboratory. It's also possible that the sequences really aren't conserved because they perform an important function but for another reason. Here's how the authors explain their results,

Based on the compelling evidence that ultraconserved elements are conserved due to functional constraint, it has been proposed that their removal in vivo would lead to a significant phenotypic impact [7,8]. Accordingly, our results were unexpected. It is possible that our assays were not able to detect dramatic phenotypes that under a different setting, for instance, outside the controlled laboratory setting, would become evident. Moreover, possible phenotypes might become evident only on a longer timescale, such as longer generation time. It is also possible that subtler genetic manipulations of the ultraconserved elements might lead to an evident phenotype due to a gain-of-function-type mechanism. All four elements examined in this study demonstrated in vivo enhancer activity when tested in a transgenic mouse assay (Figure 1) [6], which would suggest regulatory element redundancy as another possible explanation for the lack of a significant impact following the removal of these specific elements. Just as gene redundancy has been shown to be responsible for the lack of phenotypes associated with many seemingly vital gene knockouts, regulatory sequence redundancy [22] can similarly provide a possible explanation for the lack of a marked phenotype in this study. While our studies have not defined a specific need for the extreme sequence constraints of noncoding ultraconserved elements, they have ruled out the hypothesis that these constraints reflect crucial functions required for viability.

[UPDATE: Ryan Gregory at Genomicron discusses the same paper with a more thorough coverage of the background information and the relevance to junk DNA (Ultraconserved non-coding regions must be functional... right?). R. Ford Denison at This Week in Evolution has some thoughts on the paper (If it's junk, can we get rid of it?")]

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Ahituv, N,, Zhu, Y., Visel, A., Holt, A., Afzal, V., Pennacchio, L.A., and Rubin, E.M. (2007) Deletion of Ultraconserved Elements Yields Viable Mice. PLoS Biol 5(9): e234 doi:10.1371/journal.pbio.0050234.

Denyse O'Leary's New Book

 
We've been waiting with baited bated^* breath but the big day has finally arrived. Denyse O'Leary announces that we can now buy her new book The Spiritual Brain [ Just released - a neuroscientist's case for the existence of ... the soul!].

The first author is Mario Beauregard, a scientist at the Université de Montréal (Canada). According to Denyse, Beauregard is one of the "One Hundred Pioneers of the Twenty-First Century" selected by World Media Net. What the heck is "World Media Net"? Canadian Cynic also wants to know The hilarity just never ends].

Beauregard (and O'Leary) have solved the mind-body problem. It turns out that there's more going on inside the brain than just the firing of neurons. Apparently, your brain is capable of contacting a different reality during intense religious experiences.

Beauregard uses the most sophisticated technology to peer inside the brains of Carmelite nuns during a profound spiritual state. His results and a variety of other lines of evidence lead him to the surprising conclusion that spiritual experiences are not a figment of the mind or a delusion produced by a dysfunctional brain.

I'm not going the buy the book. If someone wants to read it I'd be happy to see a review from a real scientist.

^* I actually knew that "baited" was wrong but I typed it anyway. For an explanation of what "bated" means see World Wide Words.

Pyridoxal Phosphate and the Vitamin B6 Family

 
Vitamin B₆ is actually a family of related molecules consisting of a six-membered ring with a single nitrogen atom. The various members differ only in the group attached to position 4 of the ring. The ring is called a pyridine ring and the various derivatives are named after the pyridine ring (see below and Monday's Molecule #41). The most common vitamin B₆ molecules are pyridoxal or pyridoxamine. They are widely available from plant and animal sources and it's unusual for human diets to be deficient in vitamin B₆.


By definition, a vitamin is a compound that humans can no longer synthesize. Some vitamins act directly as cofactors or coenzymes but many them serve as precursors for the synthesis of the final product. This is true of the B₆ vitamins. They are rapidly converted to pyridoxal 5′-phosphate (PLP). Humans have retained the ability to catalyze this conversion.

PLP is a cofactor that's bound to many enzymes in the cell where it participates in a number of different reactions. The most important reactions are those involving transfer of amino groups from one molecule to another. There is a large class of transaminases that require PLP.

The transaminases are required for amino acid synthesis and for synthesis of many neurotransmitters such as serotonin and epinephrine. An example of a transamination reaction is shown below. Note that PLP is covalently bound to the enzyme through a lysine side chain. An amino acid donates its amino group to PLP in an exchange reaction giving rise to pyridoxamine phpsphate (PMP), which remains firmly bound to the enzyme. The entire sequence of reactions can then be reversed using any α-keto acid as a substrate to generate a new amino acid.

Many of the transaminases are evolutionarily related. Similarly, the transaminases are often related to enzymes that catalyze different PLP-reactions such as isomerizations and decarboxylations. The evidence indicates that a primitive PLP-enzyme gave rise to a number of different enzymes that make use of the basic mechanism shown below. The enzymes differ in a few amino acids that bind the substrates.

The Evolution Poll of Sandwalk Readers

 
The poles are closed and the results are in. Richard Dawkins is the clear winner (boo!).

The good news is that 87% (499/573) Sandwalk readers have legitimate scientific views of evolution (Dawkins + Gould + Futuyma). Only a small number of readers are creationists or proponents of theistic evolution.

The bad news is that most readers are split between three different views of evolution. Some people have asked me to explain these three views so here's a brief summary of how I distinguish between Dawkins, Gould, and Futuyma.

Richard Dawkins holds the Charles Simonyi Chair for the Public Understanding of Science at Oxford University (UK). In his first book, The Selfish Gene (1976), he promoted the idea that evolution can be viewed as a competition between genes. This concept was amplified in The Extended Phenotype (1982) where he also answered the main criticism of the selfish gene concept. Dawkins' most popular book was The Blind Watchmaker, first published in 1986. In that book he made the case for design by natural selection and attempted to dismiss, or minimize, all other mechanisms of evolution. The emphasis on the power of natural selection was expanded in Climbing Mt. Improbable (1996).

Dawkins is the leading exponent of adaptationism—or Ultra-Darwinism—the idea that everything interesting in evolution can be explained by adaptation. This is especially true of traits that give rise to visible phenotypes. Dawkins is not very interested in macroevolution and he dismisses punctuated equilibria and species sorting. He believes, along with most adaptationists, that macroevolution is just an extension of natural selection acting on populations. (See RichardDawkins,net for a complete list of books and articles.)

Stephen Jay Gould was Alexander Agassiz Professor of Zoology at Harvard University from 1967 until his death in 2002.

He published Ontogeny and Phylogeny in 1977 where he made the case for a relationship between development and evolution. In The Mismeasure of Man (1981) he criticized biological determinism. Wonderful Life (1989) described the Burgess Shale fossils and explained Gould's ideas about the role of chance and contingency in evolution. In 2002, Gould published The Structure of Evolutionary Theory where he attempts to explain macroevolution, punctuated equilibria, and species sorting. These are part of Gould's hierarchical approach to evolutionary theory. Gould identifies himself as a pluralist—one who recognizes many different mechanisms of evolution that can give rise to important and interesting features. He tends to place much more emphasis on chance and accident in evolution than Dawkins.

Gould, along with Niles Eldredge, is famous for the concept of punctuated equilibrium. This is the idea that much of the change in the characteristics of species is concentrated in brief speciation (by cladogenesis) events.

Gould wrote a regular column for Natural History magazine and many of his articles have been collected in a series of anthologies: Ever Since Darwin, The Panda's Thumb, Hen's Teeth and Horse's Toes, The Flamingo's Smile, Bully for Brontosaurus, Eight Little Piggies, Dinosaur in a Haystack, Leonardo's Mountain of Clams and the Diet of Worms, The Lying Stones of Marrakech, and I Have Landed. Some of his essays and some of his scientific articles are widely cited. (For a complete list see SJG Archive.)


Douglas J. Futuyma is a Professor of Ecology & Evolution at the State University of New York at Stoney Brook. He is best known for his textbooks on evolution; Evolutionary Biology (1998) and Evolution (2005). His major research interests are evolutionary theory [see Hypotheses, Facts, and the Nature of Science] and the interactions of plants and insects [see Insect Pests: Resistance and Management].

Futuyma's view of evolution is different from that of Richard Dawkins because Futuyma is interested in random genetic drift and speciation. Futyuma is much more aware of population genetics than Dawkins or Gould and he (Futuyma) frequently refers to it in his books and papers. Unlike Gould, Futuyma is skeptical of punctuated equilibria and particularly species selection/sorting, although, ironically, he is credited with proposing the best explanation of the connection between cladogenesis and evolution.

You can check out some of Futuyma's ideas in this interview. In response to the question, "Is natural selection the only mechanism of evolution?", Futuyma replies,

No, certainly not. There cannot be evolution without genetic variation in the first place. So there must be mutation and often recombination to generate the different genotypes or the different versions of the genes, known as alleles, which then may or may not make a difference in the ability of an organism to survive and reproduce. You can’t have any evolutionary change whatever without mutation, and perhaps recombination, giving rise to genetic variation. But once you have genetic variation, there are basically two major possibilities:

First, there is simply no difference between the different genotypes or different genes in their impact on survival or reproduction, and in that case, you can have random changes of one versus the other type in a population or a species until eventually one replaces the other. That is an evolutionary change. It happens entirely by chance, by random fluctuations. That is what we call the process of genetic drift.

Genetic drift is very different from possibility number two, natural selection, which is a much more consistent, predictable, dependable change in the proportion of one gene vs. another, one genotype vs. another. Why? Simply because there is some consistent superiority, shall we way, of one genotype vs. another in some feature that affects its survival or some feature affecting its reproductive capabilities.

Neither Gould or Dawkins would respond in this way. Dawkins would admit to random genetic drift but downplay its importance. Gould would focus on higher mechanisms of evolution like species sorting.

Futuyma also thinks about the role of mutation in a different way than either Dawkins or Gould, especially Dawkins. While Dawkins is very much opposed to crediting mutations per se with any substantial influence on evolution, Futuyma is more sympathetic to a limited mutationism point of view. For example, when asked what would happen if the tape of life were re-played he says.

Of course, it wouldn’t be the same, because first of all, random processes are involved in the evolutionary process. For example, the origin of new mutations: a lot of evolution is dependent on particular mutational changes in genes that were very, very rare or unlikely, but that just happened at the right time, in the right species, in the right environment, but it need not happen that way. So, there’s this unpredictability.

This is very unlike Dawkins who is more inclined to think of evolution as design and strongly resists any attempt to sneak randomness into the equation. For the most part, Dawkins believes that all possible mutations will be available for selection so mutations can never determine the direction of evolution. Gould prefers to focus on developmental constraints as possible limits to the effectiveness of natural selection.

Monday's Molecule #41

 
Today's molecule is actually three related molecules. You have to name all three by giving the common names and the complete IUPAC names. There's a direct connection between these molecules and Wednesday's Nobel Laureate(s). (Hint: The Nobel Prize winner was not allowed to receive the prize.)

The reward goes to the person who correctly identifies the molecules and the Nobel Laureate(s). Previous free lunch winners are ineligible for one month from the time they first collected the prize. There are two ineligible candidates for this Wednesday's reward. Both of them are waiting to collect their prize this week or next week. The prize is a free lunch at the Faculty Club.

Send your guess to Sandwalk (sandwalk(at)bioinfo.med.utoronto.ca) and I'll pick the first email message that correctly identifies the molecules and the Nobel Laureate(s). Correct responses will be posted tomorrow along with the time that the message was received on my server. This way I may select multiple winners if several people get it right.

Comments will be blocked for 24 hours. Comments are now open.

UPDATE: The three molecules are:

1. pyridoxine: 3-hydroxy-4,5-bis(hydroxymethyl)-2-methylpyridine


2. pyridoxal: 3-hydroxy-5-(hydroxymethyl)-2-methyl-pyridine-4-carbaldehyde


3. pyridoxamine:
   4-(aminomethyl)-5-(hydroxymethyl)-2-methyl-pyridin-3-ol

Nomenclature for Vitamins B-6 and Related Compounds

Modern women are excellent gatherers

 
Here's an article form this week's New Scientist [Modern women are excellent gatherers]. I'd be curious to know what our adaptationist friends think about it. Is this a good example of how to do research?

Men hunted, women gathered. That is how the division of labour between the sexes is supposed to have been in the distant past. According to a new study, an echo of these abilities can still be found today.

Max Krasnow and colleagues at the University of California, Santa Barbara, have discovered that modern women are better than men at remembering the location of food such as fruit and veg in a market.

The researchers led 86 adults to certain stalls in Santa Barbara's large Saturday farmer's market, then back to a location in the centre of the market from where the stalls could not be seen. They were then asked to point to each stall's location. This requires dead reckoning - a skill that men may once have used to return from hunting, and one that men today still usually perform better than women in experiments. Despite this, the ...

The news report refers to a paper that will soon be published in Proc. Roy. Soc. B [New et al. 2007]. Here's the abstract.

We present evidence for an evolved sexually dimorphic adaptation that activates spatial memory and navigation skills in response to fruits, vegetables and other traditionally gatherable sessile food resources. In spite of extensive evidence for a male advantage on a wide variety of navigational tasks, we demonstrate that a simple but ecologically important shift in content can reverse this sex difference. This effect is predicted by and consistent with the theory that a sexual division in ancestral foraging labour selected for gathering-specific spatial mechanisms, some of which are sexually differentiated. The hypothesis that gathering-specific spatial adaptations exist in the human mind is further supported by our finding that spatial memory is preferentially engaged for resources with higher nutritional quality (e.g. caloric density). This result strongly suggests that the underlying mechanisms evolved in part as adaptations for efficient foraging. Together, these results demonstrate that human spatial cognition is content sensitive, domain specific and designed by natural selection to mesh with important regularities of the ancestral world.

As indicated in the news report, 86 adults (41 women and 45 men) were tested for their ability to remember the location of food stalls in a farmers market. The women were 9% better at this than the men.

The result confirms the authors' hypothesis that women are genetically superior at this task because of adaptation during our hunter-gatherer past.

Silverman & Eals (1992) argue that the female advantage on pencil-and-paper and desktop measures of object location memory reflects a selective pressure on ancestral women for plant-foraging efficiency. But their measures did not involve foods, tested spatial memory on a very small scale, and included no measure of vectoring; as a result, a female advantage on their measures is open to many alternative interpretations. For this reason, we deemed it important to examine whether a female advantage could be demonstrated on a task that closely resembles foraging for plant foods. From this theory, we predicted that women should remember the locations where they have previously encountered immobile resources (e.g. plants, honey) more accurately than do men.

The authors don't explain exactly how this adaptation might have happened. Presumably it went something like this ...

At some time in the ancient past all humans had a single allele for the (unknown) gathering gene. A mutation in this gene arose producing an allele where the ability to gather food was improved. Since women were the principle food gatherers, this mutant allele conferred a selective advantage on women who carried it: presumably because they didn't share their food with their friends who carried the old allele. Over time, the new allele became fixed (or very frequent) in women but men did not benefit.

The first three authors are in Departments of Psychology and the senior author is in a Department of Anthropology.

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New, J., Krasnow, M.M, Truxaw, D. and Gaulin, S.J.C. (2007) Spatial adaptations for plant foraging: women excel and calories count. Proc. Roy. Soc. B. DOI 10.1098/rspb.2007.0826.

[Photo Credit: The drawing is "An artist’s impression of early Hunter-Gatherers" from Manx National Heritage]

Adaptationomics

 
Jonathan A. Eisen is an evolutionary biologist with a blog called The Tree of Life. He's also one of the authors of a new textbook on evolution published by Cold Spring Harbor Laboratories [A New Textbook on Evolution]. I'm about to order a copy.

I mention this because Eisen is a pluralist. He's as annoyed by adaptationist just-so so stories as I am. Over on the Dennett on Adaptationism thread I'm encountering commenters who question whether there really are modern scientists who believe in the adaptationist program. I can assure you there are. Eisen has discovered some of them in the field of genomics—he didn't have to look very hard—and he decided to label their approach adaptationomics [Adaptationomics Award #1 - Wolbachia DNA sneaking into host genomes]. This is tongue-in-cheek so don't all you adaptationists get your knickers in a knot.

Here's how Jonathan sets up the issue.

For years I have been fighting against the tide on the tendency for people doing genomics work to resort to silly adaptationist arguments for observations. The argument goes something like this. We sequenced a genome (or did some type of genomics). We made an observation of something weird being present (take your pick - it could be a gene order or a gene expression pattern or whatever). We conclude that this observation MUST have an adaptive explanation. We have come up one such adaptive explanation. Therefore this explanation must be correct.

Gould and Lewontin railed against this type of thing many years ago and others have since. Just because something is there does not mean it is adaptive (e.g., it could be neutral or detrimental). And even if something is adaptive, just because you can think of an adaptive explanation does not mean your explanation is correct.

And this is so common in genomics I have decided to invent a new word - Adaptationomics. And I am giving out my first award in this to Jack Warren and colleagues for their recent press release on their new study of lateral transfer in Wolbachia (plus it lets me plug their new study which is pretty ^$%# cool).

Does this sound familiar?

What did the authors say that makes them adaptationists? In order to understand their statement you have to be familiar with their findings. They discovered that the genome of a parasite (Wolbachia) has been integrated into the geonome of their insect host. There are several reasons why this might have happened. It could just be an accident, since these kind of recombinant events occur frequently and most insects don't carry a full complement of their parasite's genome. In other words, it could be junk.

On the other hand, the parasite genome could possibly confer some (unknown) selective advantage on the host. But here's the rub. When the author of the article, Julie Dunning Hotopp, was interviewed for the the Nature News article here's what she said.

You're talking about a significant portion of its DNA that is now from Wolbachia," says Julie Dunning Hotopp, a geneticist at the J. Craig Venter Institute in Rockville, Maryland, who led the study. "There has to be some sort of selection to carry around that much extra DNA."

That's a classic adaptationist statement. The result "must be" explained by natural selection. There are no other options. I agree with Jonathan Eisen, this is a fitting recipient of his new Adaptationomics Award.

Congratulations to Julie Dunning Hotopp.

Theories of Speciation

 
In order to understand real evolution you have to understand speciation. This fact usually comes as a great surprise to adaptationists who tend not to think of such things. (Or, if they do, they adopt a grossly simplified version of speciation based on adaptation.)

John Wilkins tries to explain theories of speciation in his latest posting on Evolving Thoughts [Theories of Speciation]. John is a philosopher but don't let that fool you. He's an expert of speciation. The problem is, he explains it like a philosopher. :-)

Here's a nifty chart that I stole from John's article (he published it in his latest paper). If, after looking at the chart, it all becomes crystal clear to you then you have my sympathy. This is a very difficult problem but it can't be swept under the rug if you want to debate hierarchical theory and punctuated equilibria.

A genetic trigger for the Cambrian explosion unraveled?

 
Here's an interesting press release [A genetic trigger for the Cambrian explosion unraveled?]. This is the abstract, there's much more but I can't make sense of any of it.

A team of scientists led by young Croatian evolutionary geneticist Tomislav Domazet-Lošo from Ruder Boškovic Institute (RBI) in Zagreb, Croatia, developed a novel methodological approach in evolutionary studies. Using the method they named 'genomic phylostratigraphy', its authors shed new and unexpected light on some of the long standing macroevolutionary issues, which have been puzzling evolutionary biologists since Darwin.

We won't be able to discuss this "revolutionary" paper because it won't be published until November. The journal is Trends in Genetics, which is billed as "the most established monthly journal in Genetics."

RPM at Evolgen didn't seem to be too impressed either [Genomic Phylostratigraphy]. Go there if you want to see a list of the really best journals in genetics.

I wish there were some way of enforcing standards on places that issue scientific press releases. This one from the Ruder Boškovic Institute (RBI) is worse than useless.