Iraqi Children Throwing Rocks

This video from YouTube is poignant in so many ways ... It's the same situation that Canadian forces face in Afghanistan. If the children hate us then why are we there?

        

A Simple Act of Kindness

This morning I drove over to my local Tim Horton's to get a coffee. There was a lineup in the drive-through, as usual. The woman in front of me stopped by the garbage bin and tossed out an empty cup. She missed, and the cup bounced off the receptacle and rolled under her car. She opened the door a crack, peered out, saw nothing, and drove on.

I have to admit I'm really annoyed at this kind of behavior. I hate it when people throw garbage on the street, especially when there are garbage bins everywhere. I've been known to pick up litter and hand it back to the owner. Rather than drive over her discarded cup, I stopped, picked it up, and put it in the bin. I was not thinking nice thoughts when I did this and I made sure that she saw me do it.

Back in the car, I drove up to the window to get my coffee. Imagine my surprise when the server told me my coffee was free today! She informed me that the woman ahead of me had paid for my coffee.

Thanks, whoever you are. You made my day. In fact, you made my week.

City of Toronto

Here's a 360° view of Toronto.

Click here to see a larger image.

Ten Worst Science Books

John Horgan has upped the ante with his Ten Worst Science Books. I haven't read most of the ones on his list but I certainly agree with Consilience. I disagree with The Tipping Point 'cause it's not a science book and I disagree with Rock of Ages 'cause when you read it carefully you see that Gould has a valid point.

PZ Meiers adds Darwin's Black Box by Michael Behe and The Language of God by Francis Collins. I'm not sure if the Collins book qualifies as science. It's in the superstition section of my local bookstore.

John Lynch over at Stranger Fruit has an even more interesting suggestion for John Horgan's list of worst science books. Lynch would add The End of Science by John Horgan. Ouch!

I have three suggestions. The one everyone is forgetting is Icons of Evolution by Jonathan Wells. This one's a no-brainer.

One of my personal favorites is Sudden Origins: Fossils, Genes, and the Emergence of Species by Jeffrey H. Schwartz. This is a really, really, bad science book.

Another book that gets my vote is Darwin's Dangerous Idea by Daniel Dennett.

The Three Domain Hypothesis (part 2)

Jan Sapp sets the tone by outlining the history of bacterial classification and phylogenetic analysis. We’re mostly concerned with the fourth era—the one that begins in the 1990's with the publication of the first bacterial genomes.

By the late 1990's, just when the three-domain proposal and the outlines of a “universal phylogenetic tree” were becoming well established, the microbial order based on rRNA was challenged by data from complete genome analysis of bacteria. Phylogenies based on genes other than those for rRNA often indicated different genealogies, and indeed a somewhat chaotic order. The new genomic data also indicated that archaebacteria and bacteria had many genes in common: perhaps they were not that different after all.

Sapp then goes on to discuss the attack on the Three Domain Hypothesis by Ernst Mayr in an oft-quoted PNAS paper (Mayr, 1998). Mayr’s objections have more to do with classification and taxonomy than with any real dispute over the validity of the molecular data. It’s about the fact that Mayr doesn’t like cladistics. He doesn’t want molecular phylogenies to trump visible phenotypes and “common sense” (Mayr’s, of course). Mayr argues that archaebacteria and bacteria both look like bacteria so they should be lumped together in a single prokaryotic empire.

I’m not interested in that debate. If the gene trees say that archaebacteria form a separate domain then that’s good enough for me no matter how much they resemble other prokaryotes. Woese (1998) has published an adequate reply to Mayr.

The real arguments are based on conflicting gene trees and the increasingly obvious similarity between bacteria and archaebacteria at the molecular level. How do we resolve the conflicts between the ribosomal RNA trees and examples of equally well-supported trees from proteins? The first thing that comes to mind is that some of the gene phylogenies are just wrong. They are artifacts of some sort and don’t really represent the history of the genes. Most of the debate on this topic concerns the validity of the SSU trees since they are based on nucleotide sequences. It’s well-known that ribosomal RNA trees are prone to long branch attraction artifacts to a greater extend than trees based on amino acid sequences. It’s also well-known that there are some famous mistakes in rRNA trees.

For the time being, let’s assume that all genes trees are accurate representations of the gene history, bearing in mind that the opponents of the Three Domain Hypothesis are not prepared to concede that point.

Conflicting gene trees then have to be artifacts of a different sort. Some of them will accurately represent the evolution of the species while others will not. The ones that don’t follow the phylogeny of the species will deviate because the genes have a different history. Either they have been transferred singly from one species to another or they have been transferred en masse by some sort of fusion event. Sapp discusses both these possibilities.

Lateral gene transfer (LTG)—also called horizontal gene transfer (HGT)—is the latest fad in microbial evolution. You can explain away all the conflicting gene phylogenies by invoking interspecies transfer. But here’s the problem: which genes were transferred and which ones represent the “true” species phylogeny? Several papers in the book address this problem and we’ll cover them in separate postings.

Keep in mind that LGT can get you out of a messy situation but there’s a price to pay. If you envisage a time when cells were frequently swapping lots of genes to form a “net” of life, then that, in and of itself, is enough to refute the standard version of the Three Domain Hypothesis. What you’re left with is a hypothesis about the phylogeny of “some” genes and a different phylogeny for others. This gets us into playground fights about “my gene is better than your gene.” Supporters of the Three Domain Hypothesis are willing to go there in order to save the hypothesis. Do their arguments hold up?

The other way of explaining the conflict is to invoke whole genome fusions followed by selective loss of half the genes. There are several models to explain the origin of eukaryotic cells by fusion of a primitive archaebacterium with a primitive bacterium. Such an event would account for the data, which shows that most eukaryotic genes are more closely related to bacteria but some are closer to archaebacteria. There are other interesting models, for example one model postulates fusion of a primitive eukaryotic cell with a primitive bacterial cell to form the first archaebacterium! This also accounts for the data but it pretty much wipes out one of the three domains!

Most people take these fusion models seriously. If one of the fusion models is correct, then the original Three Domain Hypothesis is refuted. (One of the complications is the transfer of genes from mitochondria to the eukaryotic nucleus. We’re not talking about those genes. Those ones are relatively easy to recognize.)

Jan Sapp closes his introduction with a summary of the problems that will be addressed in the rest of the book.

... with the development of genomics, the hitherto unappreciated ubiquity of LGT was postulated to explain many gene histories other than those for rRNA. The species concept was again considered to be inapplicable to bacteria, not because of the absence of genetic recombination, as long thought, but because there seemed to be so little barrier to it. Doubts about the inability to construct bacterial genealogies arose anew because of the scrambling of the genetic record from LGT. While debates continue over which (if any) provide the most reliable phylogenetic guide, so too do debates over the origin of the eukaryotic cell nucleus and over the inheritance of acquired bacterial genomes.

---

Microbobial Phylogeny and Evolution: Concepts and Controversies Jan Sapp, ed., Oxford University Press, Oxford UK (2005)

Jan Sapp The Bacterium’s Place in Nature

Norman Pace The Large-Scale Structure of the Tree of Life.

Woflgang Ludwig and Karl-Heinz Schleifer The Molecular Phylogeny of Bacteria Based on Conserved Genes.

Carl Woese Evolving Biological Organization.

W. Ford Doolittle If the Tree of Life Fell, Would it Make a Sound?.

William Martin Woe Is the Tree of Life.

Radhey Gupta Molecular Sequences and the Early History of Life.

C. G. Kurland Paradigm Lost.

---

Mayr, E. (1998) Two Empires or Three? Proc. Natl. Acad. Sci. USA 95:9720-0823.

Woese, C. R. (1998) Default taxonomy: Ernst Mayr’s view of the microbial world. Proc. Natl. Adad. Sci. USA 95:11043-11046.

---

High School Dropouts

ABC News reports that Students Dropping Out of High School Reaches Epidemic Levels. According to the article ...

A recent study by the Department of Education found that 31 percent of American students were dropping out or failing to graduate in the nation's largest 100 public school districts.

Is 31% too high? I suspect so, but it depends on so many things. The real question—the one that's never addressed in the popular media—is, "What should be the ideal success rate in high school?" Clearly it shouldn't be zero or even 50% because we need to have public high schools that educate the majority of students to the level of high school graduate.

Should it be 100%? Of course not. It would be silly to have a situation where everyone was capable of graduating from high school. High school wouldn't mean anything. In order to be meaningful, a high school graduation diploma has to be a significant achievement and that means that some students won't succeed.

What's the ideal number? Does a 20% "dropout" rate sound about right to you? It does to me, but I'd like to hear other opinions. A 20% "dropout" rate translates to an 80% success rate. It means that the degree of difficulty of high school courses is set at a level achievable by the vast majority of students, but not all. The bar isn't too high and it's not too low. The important point is that there is a bar.

Nobel Laureates: Jacques Monod

 

The Nobel Prize in Physiology or Medicine 1965.

"for their discoveries concerning genetic control of enzyme and virus synthesis"

Jacques Monod was a biochemist who shared the Nobel prize with François Jacob and André Lwoff for their work on understanding how genes work. Part of their contribution was demonstrating that mRNA was the key intermediate between genes and proteins. Part of it was their discovery of gene regulatory sequences and repression in the lac operon. They also worked on gene regulation during bacteriophage infection of E. coli.

Monod, who was born in 1910, led a very full life. He was active in the socialist movement in France and played an important role in the French resistance during World War II. He did most of his scientific work at the Pasteur Institute in Paris after the liberation of France in 1944.

I highly recommend Monod's Nobel Lecture "From Enzyme adaptation to allosteric transitions." It reveals a state of knowlege and understanding in 1965 that most of us don't appreciate. There are figures in the lecture, especially a diagram of allosteric transitions (with "relaxed" and "stressed" conformations), that are remarkably similar to what's in modern biochemistry textbooks.

In 1971 Monod published Chance and Necessity: An Essay on the Natural Philosophy of Modern Biology (Le hasard et la nécessité). This insightful book influenced an entire generation of scientists. Monod died in 1976.

The privilege of living beings is the possession of a structure and of a mechanism which ensures two things: (i) reproduction true to type of the structure itself, and (ii) reproduction equally true to type, of any accident that occurs in the structure. Once you have that, you have evolution, because you have conservation of accidents. Accidents can then be recombined and offered to natural selection to find out if they are of any meaning or not.

                                                                Jacques Monod (1974) p.394

Mélissa Theuriau

The voters over at digg are getting all excited about news anchor Mélissa Theuriau. I don't see why. It's just the news—old news at that. She has a funny accent. I don't think she's from Québec.

I have to admit she's better looking than Lou Dobbs.

A Picture Is Worth a Thousand Words

 

   Sometimes even

   two thousand.

   Ed, is that you? :-)

Ed Brayton Speaks

I'm going to respond to a number if things Ed Brayton says in "With Friends Like These". Let me begin by saying it doesn't really sound like I'm Ed's friend. :-)

Ed Brayton's opening attack on me refers to my tongue in check suggestion that students who reject evolution should be flunked, or not admitted to university in the first place. Anyone with a brain can recognize the humor and sarcasm in such a remark. The fact that it sets the Intelligent Design Creationists all atwitter is part of the fun.

However, behind the humor is a serious point. If students entering university have already made up their minds that evolution should be rejected, then that's a serious problem. It's not a question of ignorance. Those students have made an active decision to choose superstition over science. Given a choice of students to admit into university science programs, I would choose the ones who show some understanding of science over those who reject one the fundamental facts of biology. Wouldn't Ed?

Ed then says, ...

To be honest, I'm rapidly becoming convinced that there are two very different groups involved in fighting against the ID public relations campaign to distort science education. The distinction between the two groups is that one is fighting to prevent ID creationism from weakening science education while the other is fighting, at least in their minds, to eliminate all religious belief of any kind, even those perspectives that have no quarrel with evolution specifically or science in general, from society.

I'm mostly in the first group but I also have an interest in elminating the worst parts of religion; namely, those parts that conflict with reason. The fight against Intelligent Design Creationism and Young Earth Creationism is only part of the battle—there's a lot more involved in trying to improve science education. Some of it requires us to take a long hard look at the way science education is being eroded by well-meaning theists who don't belong in one of the obvious hard-core Creationist camps. Let's call them Theistic Evolutionists for want of a better term.

People like Ed Brayton think it's okay for Theistic Evolutionists to nibble at science and undermine its principles in subtle ways. He probably thinks it's okay because at least they aren't taking big bites. Well, Ed, I'm here to tell you that it's not all right. The little nibbles are just as bad, perhaps worse, and if you defend even a little bit of sloppy science then you are still defending sloppy science and you should be ashamed.

When Eugenie Scott and others promote a theistic version of science they seem to think they are allowing for a safe middle ground where Theistic Evolutionists like Francis Collins, Simon Conway Morris, and Ken Miller can find common cause with scientists who don't let superstition masquerade as science. They are wrong. There is no common ground between the rational and the irrational. I've written a little essay to try and explain why [Theistic Evolution: The Fallacy of the Middle Ground].

Ed continues, ...

How else to explain Moran's earlier comments here that bluntly accuse Ken Miller, the single most effective and tireless advocate of evolution and critic of ID creationism in the nation, of being anti-science merely by virtue of the fact that he attempts to reconcile science with his religious faith? In the battle Moran is fighting, theistic evolutionists are the enemy despite their advocacy of evolution, because his battle is not for evolution or against ID creationism, it is against theism, hence theists, in any form.

I'll tell you how else to explain it, Ed. I'm not a fan of religion but I'm not dogmatically opposed to religion in any form. What I'm opposed to is the attack on science by religious apologists of any stripe. You can't claim to accept evolution and then turn around and say that God is behind it all and He can tweak it whenever He wants. That's not science.

In my essay I included a diagram from a talk given by Rev. Ted Peters, a leading Theistic Evolutionist. I'll include it here.
Note that Ken Miller is way out on the left of the diagram, not far from the Intelligent Design Creationists. As a matter of fact, it's difficult to distinguish his belief from those of some Intelligent Design Creationists. Take a look at where evolutionary biology is positioned. That's where I am.

Let's not forget that this is a fight between rationalism and superstition. Science is on the side of rationalism, and so am I.

Stop the Presses: Godless Dawkins Is Subverting Schools in the UK!!

The Sunday Times in Great Britain reports that Godless Dawkins Challenges Schools.

RICHARD DAWKINS, the Oxford University professor and campaigning atheist, is planning to take his fight against God into the classroom by flooding schools with anti-religious literature.

He is setting up a charity that will subsidise books, pamphlets and DVDs attacking the “educational scandal” of theories such as creationism while promoting rational and scientific thought.

He's doing no such thing. The goal of The Richard Dawkins Foudation for Reason & Science is to promote rationality. Of course that means attacking the IDiots and religious superstition but that's just a consequence of promoting rationalism and common sense.

Here's a video where Dawkins explains his objectives.

Why the US Should Spring for a New Particle Accelerator

Harold T. Shapiro explains in SEED "Why the US Should Spring for a New Particle Accelerator". He writes, ...

The US must develop a compelling bid to host the International Linear Collider in order to safeguard American science.

Sounds good to me. It's in all our best interests that America maintain an active presence in international front-line science. Besides, it's quicker for Canadians to fly to the US than to Geneva. :-)

The photograph shows workers celebrating the connection of the first sector of the Large Hadron Collider in Geneva on November 10, 2006. It won't be long now 'till they start bashing things together. That's what physicists do these days and it cost a lot of money. Biochemists can smash things for much less money.

Noam Chomsky - What's All the Fuss About?

I've long admired Canada's decision not to participate in the war on Iraq and I've been critical of the American decision to start the war.

Whenever the topic comes up on talk.origins you can count on the resident coterie of kooks bringing up Naom Chomsky. Apparently it's a grave insult to be associated with Chomsky. I don't know whether to be insulted 'cause I'm not familiar with his writings.

Today I accidently stumbled on a link to a speech by Noam Chomsky. Here it is.



Chomsky says lot of things that make a great deal of sense to me. For example, when taking about American policy in the Middle East he says,

If somebody was watchng all of this from outer space they might be led to believe that George Bush was embedded in the White House as an agent of Osama Bin Laden. He's certainly acting that way.

With respect to Us foreign policy, ...

The US declares the sovereign right to use force as it wishes. It's gonna lead even if nobody's following.

I'm not an American but I don't see why I should feel insulted to be on the same side as Chomsky. I know many Americans who aree with what I saw in the video. Am I missing something? Is Chomsky much more evil than he appears in this clip? Is there something I should know? Is he mean to old people, or something?

Name This Molecule #2

 

Twenty-three different amino acids can be incorporated into polypeptides by the translation machinery. They all have their own codons.

The molecule on the left is one of the 23, which one?

The Greatest Science Books of All-Time

Discover magazine has published a list of The Greatest Science Books of All-Time.

I have no problem with Darwin being at the top of the list (#1 and #2) and the next six choices seem reasonable. But The Selfish Gene by Richard Dawkins at #9? No way. That book will be forgotten in a few more years. If you must put Dawkins on the list then The Blind Watchmaker is the book to pick.

The Double Helix by James D. Watson at #11 is controversial, but I have to admit it's justified. #14 is The Insect Societies by E. O. Wilson. I can't imagine who voted for that.

The top Stephen Jay Gould book is The Mismeasure of Man at #17. It's a good book but I would have put The Panda's Thumb ahead of it ... way ahead.

Some of the other choices are very strange. The most obvious omissions, in my opinion, are Chance and Necessity by Jacques Monod, The Nature of the Chemical Bond by Linus Pauling, and The Eighth Day of Creation by Horace Freeland Judson.

Neanderthal genome FAQ

I've hesitated to comment about the sequencing of Neanderthal DNA 'cause I haven't read the papers. Fortunately John Hawks has made the effort and posted the Neandertal genome FAQ. It should answer all your questions, except why John Hawks calls them "Neandertal" when Science and Nature use "Neanderthal." Personally, I prefer the original "Neanderthal."

If you want more information, Nature has a special webpage devoted to Neanderthal DNA.

They Just Don't Get It

The discussion about UCSD students being ignorant of evolution was stimulated by an article that appeared in the San Diego Union-Tribune on February 16, 2006 ["Designed to Create Controversy"]. The article quotes UCSD evolutionary biologist Joshua Kohn,

At UCSD, which is known for its strength in science and engineering, faculty members are realizing they need to pay more attention to the controversy. Two years ago, a UCSD survey found that 40 percent of incoming freshmen to the university's Sixth College – geared toward educating students for a high-tech 21st century – do not believe in evolution, said the college's provost, Gabriele Wienhausen.

The university now requires students who major in biology to complete a course in biological evolution, Kohn said. The policy became effective with freshmen who enrolled last fall. Professors had discussed the change for years, he said, but the Sixth College poll made it more urgent.

“Our own faculty has gotten sensitized to the issue that there's a bunch of people that just don't get it,” Kohn said.

If UCSD is accepting such a large number of students who don't understand one of the basic tenets of science then maybe it's time to re-examine their admissions policy? I wonder how many of the students are from Kansas?

Will the Real IDiot Please Stand up?

Bill Dembski writes, Larry Moran — Will the real idiot please stand up?. He says,

Larry Moran has been getting some play on this blog, so I’ll throw in my two cents. I met Larry in 2002, when he attended a lecture I gave at U of Toronto and confidently explained to me and the audience how indirect Darwinian pathways explain the evolution of the flagellum from the type three secretory system. To this day it amazes me that people find so bogus an argument a slam dunk for evolutionary theory. Try explaining to an engineer that the origin of the laptop computer is the product of trial and error tinkering from a cathode ray tube. If anything, this analogy fails to capture the full measure of self-delusion that evolutionary theory has become.

That's not a very accurate description of what I said. I pointed out that scientists have a pretty good explanation of irreducible complexity. In the case of the bacterial flagella, that explanation includes evolution from a more simple, primitive, secretion complex. There was good evidence for that pathway back in 2002, as I stated. The evidence is even stronger today. (See Mark Isaak's description of flagella evolution on the Talk.Origins Archive.) Is it a "slam dunk" explanation? No it isn't. We might find a better one tomorrow.

There are lots of other irreducibly complex systems that have much better evolutionary explanations. Isn't it strange that you never mention those? What I was pointing out to your audience was the fact that you did not present the views of your opponents during your talk. This is not what we expect of a seminar on a university campus. Intellectual honesty requires that we address the views disputing our favorite hypothesis. This is especially important when you are presenting the argument that irreducibly complex systems can't possibly be explained by evolution. That speculation is challenged by any known scientific explanations that have been published. You knew about those explanations but you "forgot" to mention them. In fairness, you've been more honest about this since your visit to Toronto. At least you now mention the scientific explanations in your books and lectures.

I'm sure you're well aware of the fact that irreducbibly complex systems can evolve. In fact, there are many different ways that such systems can arise by purely naturalistic means. You probably know in your heart that the main argument of the Intelligent Design Creationists has been refuted. It's time to move on, Bill. Find something else to promote your anti-science viewpoint. This one won't work any more.

Now let's talk about IDiots. You and your friends have been writing books and giving talks where you attack all professional biologists, especially the ones who have devoted their lives to studying evolution. You claim we are so stupid that we don't even realize that the fundamentals of our discipline have been proven wrong. You claim that lawyers, journalists, and mathematicians know more about evolution than researchers who have published tons of papers on evolution. You insult our intelligence, question our integrity, and denegrate our profession. You're doing it right now.

Have you heard the story about the pot and the kettle? When I call you and your friends IDiots, you're getting back a small taste of what you've been dishing out to me and my colleagues for years.

Celebrity Atheists and Wimps

Over at talk.origins they're having a debate on Is it becoming fashionable to be an atheist?" One of the participants asked about well-known atheists and quickly received a reply. I'm posing the names here from Celebrity Atheist List...

Douglas Adams, Ayaan Hirsi Ali, Woody Allen, Lance Armstrong, Darren Aronofsky, Isaac Asimov, Dave Barry, Ingmar Bergman, Lewis Black, Richard Branson, Berkeley Breathed, Warren Buffett, George Carlin, John Carmack, Adam Carolla, John Carpenter, Asia Carrera, Fidel Castro, Dick Cavett, Noam Chomsky, Billy Connolly, Francis Crick, David Cronenberg, David Cross, Alan Cumming, Rodney Dangerfield, Richard Dawkins, Daniel Dennett, David Deutsch, Ani DiFranco, Micky Dolenz, Harlan Ellison, Brian Eno, Richard Feynman, Harvey Fierstein, Larry Flynt, Dave Foley, Jodie Foster, Janeane Garofalo, Bill Gates, Bob Geldof, Ricky Gervais, Ira Glass, James Gleick, Seth Green, Robert Heinlein, Nat Hentoff, Katharine Hepburn, Christopher Hitchens, Eddie Izzard, Penn Jillette, Billy Joel, Angelina Jolie, Wendy Kaminer, Diane Keaton, Ken Keeler, Neil Kinnock, Michael Kinsley, Richard Leakey, Bruce Lee, Tom Lehrer, Tom Leykis, James Lipton, H.P. Lovecraft, John Malkovich, Barry Manilow, Todd McFarlane, Sir Ian McKellen, Arthur Miller, Frank Miller, Marvin Minsky, Julianne Moore, Desmond Morris, Randy Newman, Mike Nichols, Jack Nicholson, Gary Numan, Bob Odenkirk, Patton Oswalt, Camille Paglia, Steven Pinker, Paula Poundstone, Terry Pratchett, James Randi, Ron Reagan Jr., Keanu Reeves, Rick Reynolds, Gene Roddenberry, Joe Rogan, Henry Rollins, Andy Rooney, Salman Rushdie, Bob Simon, Steven Soderbergh, Annika Sorenstam, George Soros, Richard Stallman, Bruce Sterling, Howard Stern, J. Michael Straczynski, Julia Sweeney, Matthew Sweet, Teller, Studs Terkel, Tom Tomorrow, Linus Torvalds, Eddie Vedder, Paul Verhoeven, Gore Vidal, Kurt Vonnegut Jr., Sarah Vowell, James Watson, Steven Weinberg, Joss Whedon, Ted Williams, Steve Wozniak.

Here's a list of famous wimps (also called agnostics) ....

Margaret Atwood, Antonio Banderas, Susie Bright, Vincent Bugliosi, Robert X. Cringely, Clarence Darrow, Charles Darwin, Alan Dershowitz, Richard Dreyfuss, Umberto Eco, Timothy Ferris, Carrie Fisher, Stephen Jay Gould, Matt Groening, Bob Guccione, Robert (Bob) James Lee Hawke, David Horowitz, Bob Hoskins, Robert Jastrow, Matt Johnson, Jack Kevorkian, Larry King, Tony Kushner, Dave Matthews, Larry Niven, Neil Peart, Sean Penn, Roman Polanski, Bertrand Russell, Carl Sagan, Dan Savage, James Taylor, Charles Templeton, Uma Thurman, Ted Turner, Robert Anton Wilson.

Some of those so-called agnostics sound an awful lot like atheists to me and others sound like spiritualists of various sorts. Some of you may not be familiar with the name Charles Templeton. He's a former evangelical Christian from Toronto who abandoned his faith near the end of his life.

Most of the agnostics are probably wimps. We could expand the atheist list if only we could get Jodi Foster to talk some sense into Margaret Atwood ...

Or maybe Bill Gates could work on Antonio Banderas?

Dover, the Movie

Paramount Pictures is planning to make a movie about the Dover trial. They've hired a screenwriter, Ron Nyswaner, who says, "This story is about the place where faith intersects with science, where what we believe in intersects with what we know. This was a town that was split in half, neighbor against neighbor."

Ed Brayton is pretty excited and so are the readers over at Dispatches from the Culture Wars. Calm down guys, it's a friggin' movie ... you know, love scenes, car chases, ... that sort of thing. It ain't gonna be another "Inherit the Wind." Instead think "Contact."

I can see it now. There'll be a character from NSCE like Nick Matzke (that's him on the left of the photograph) or Wesley Elsberry (second from the left). The hero will be an atheist. (Sorry Nick and Wes.) Paramount should get Antonio Banderas (a real agnostic) to play Nick. (Incidently, the other handsome dude in the picture is John Harshman. Steve Steve is sitting on the table.)

Nick will fall in love with a sexy Christian school board member, played by Madonna. There'll be a car chase when some of the local yokels try to run Nick off the road. At the end of the movie Nick has to leave town realizing he can never make it with the Christian, ... but there will be at least three attempts. The trial itself will be irrelevant.

This is not something that evolutionists should look forward to. First, it's about one of our biggest failures—a situation were we completely failed to get our message out to the general public and had to rely on lawyers and legal trickery to defend evolution. Second, it's likely to be very sympathetic to the Christians, just like "Contact." The story will end with the audience thinking that good Christians can triumph over atheism. Nick the movie character might even convert to theistic evolution.

Go, Leafs, Go!!!

Tonight is hockey night in Canada. We get to watch Don Cherry on TV.

Last Thursday, the Leafs played Boston, home to Boston University, MIT, and some other schools. The hated Bruins managed to squeak out an overtime victory.

Tonight, the Leafs play New Jersey at the Air Canada Centre. New Jersey is home to Rutgers and my alma mater Princeton. Poor New Jersey won't know what hit 'em. This is the year the Leafs are going to win the Stanley Cup.

Surprise!- Intelligent Design Creationists Trash Peer Review

Denyse O'Leary has posted a four part article on peer review at The ID Report and also at Post-Darwinist.

Mike Dunford of "The Questionable Authority" responds in a well-reasoned and well-researched article. The bottom line is, peer review isn't perfect but it's way better than the second choice (whatever that is).

Horrible Horganism

John Horgan claims that Collins Whups Dawkins in TIME Debate!

David Van Biema, the TIME interviewer (who deserves a pat for good questions), asks both men to comment on the observation that “if the universal constants, the six or more characteristics of our universe, had varied at all, it would have made life impossible.”

Dawkins responds that “maybe the universe we are in is one of a very large number of universes. The vast majority will not contain life because they have the wrong gravitational constant or the wrong this constant or that constant. But as the number of universes climbs, the odds mount that a tiny minority of universes will have the right fine-tuning.”

Collins, no fool, pounces: “This is an interesting choice. Barring a theoretical resolution, which I think is unlikely, you either have to say there are zillions of parallel universes out there that we can't observe at present or you have to say there was a plan. I actually find the argument of the existence of a God who did the planning more compelling than the bubbling of all these multiverses. So Occam's razor--Occam says you should choose the explanation that is most simple and straightforward--leads me more to believe in God than in the multiverse, which seems quite a stretch of the imagination.”

I hate to say this, but Collins is right. The multiverse theory is just as preposterous and lacking in evidence as divine creation. Dawkins is often denounced for his arrogance, bluntness, rudeness--in short, his style. When it comes to multiverses, substance, not style, is Dawkins’s problem. Incredibly, Dawkins’s defense of multiverses has allowed Collins--a Christian who believes in miracles, fer crissake--to score a rhetorical victory in a national forum.

In the actual TIME article Collins replies first to the question. He says,

When you look at that evidence, it is very difficult to adopt the view that this was just chance. But if you are willing to consider the possibility of a designer, this becomes a rather plausible explanation for what is otherwise an exceedingly improbable event—namely our existence.

Dawkins replies to this by pointing out that there are two other possible explanations that don't require us to create a cop-out God. Dawkins says ...

People who believe in God conclude there must have been a devine knob twiddler who twiddled the knobs of these half-dozen constants the get them exactly right. The problem is that this says, because something is vastly improbable, we need a God to explain it. But that God himself would be even more improbable. Physicists have come up with other explanations. One is to say that these six constants are not free to vary. Some unified theory will eventually show that they are as locked in as the circumference and the diameter of a circle. That reduces the odds of them all independently just happening to fit the bill. The other way is the multiverse way. ...

I think Dawkins has given a perfectly adequate response to the question. What it boils down to is we don't know why the universe is constructed as it is but there are some reasonable ideas that make the fine-tuning argument superfluous.

The fact that Collins thinks a God who built the universe is more probable than a multiverse is nonsense. The fact that Horgan thinks it's a valid response only proves that if you repeat an ancient superstition enough times it begins to sound reasonable, even to someone who should know better.

Upside Down World Map

In his new book The God Delusion, Richard Dawkins talks about consciousness raising. He points out that we often need a jolt from radical thinkers to get us to start looking at things in a different light. Sometimes all it takes is a strange image to make us realize that we have biases and prejudices. He gives the example of the upside down world map.

Here's an example from The Upsidedown Map Page. Think about it.

A Fin Is A Limb Is A Wing

I highly recommend A Fin Is a Limb Is a Wing by Carl Zimmer, probably the best science journalist in the world. It's in this month's issue of National Geographic. I bought it on the newsstand just so I could have a copy of the article and the wonderful photographs.

As a special bonus, we get to read Carl's posting about this article on the Loom.

It gets a lot better. The IDiots at the Discovery Institute couldn't resist making fools of themselves once again. Casey Luskin posted a critique of Carl's article where he (Luskin) pretends to be a scientist. Imagine the stupidity of someone like Luskin lecturing Carl Zimmer on misrepresenting science! The mind boggles.

The upside to this silliness is that Carl Zimmer has responded in detail to Luskin's charges by posting a lengthy article on his blog [Getting the Mooney Treatment]. It's a wonderful explanation of how a good writer creates a top quality science article in a leading magazine. Thanks Carl.

Flunk the IDiots

Casey Luskin over at the Discovery Institute reported that University of California, San Diego Forces All Freshmen To Attend Anti-ID Lecture. Apparently, the university has become alarmed at the stupidity of its freshman class and has offered remedial instruction for those who believe in Intelligent Design Creationism.

Salvador Cordova has picked up on this at Dembski's blog, Uncommon Descent in an article titled "Darwinian indoctrination required at UCSD? Or will the other side be heard someday?". He notes that 40% of the freshman class reject Darwinism.

I agree with the Dembski sycophants that UCSD should not have required their uneducated students to attend remedial classes. Instead, they should never have admitted them in the first place. Having made that mistake, it's hopeless to expect that a single lecture—even one by a distinguished scholar like Robert Pennock—will have any effect. The University should just flunk the lot of them and make room for smart students who have a chance of benefiting from a high quality education.

Why I'm Not a Darwinist

Charles Darwin was the greatest scientist who ever lived. This may seem like an exaggeration to many people who take evolution for granted, and it appears downright ludicrous to those who reject evolution for religious reasons. But really, who are the other candidates? Newton is the only one who comes close and his contributions were nowhere near as significant and far-reaching as those of Darwin. Biology is much harder than physics.

Darwin discovered natural selection and he promoted and sold the idea of common descent. He founded evolutionary biology. Today evolutionary biology is one of the largest and most exciting fields in all of science.

We all know about evolutionary biology, but what is "Darwinism?" Ernst Mayr has an entire chapter devoted to the question ("What is Darwinism") in his book One Long Argument (Mayr, 1991). At the end of that chapter he says, ...

After 1859, that is, during the first Darwinian revolution, Darwinism for almost everybody meant explaining the living world by natural processes. As we will see, during and after the evolutionary synthesis the term "Darwinism" unanimously meant adaptive change under the influence of natural selection, and variational change instead of transformational evolution. These are the only two truly meaningful concepts of Darwinism, the one ruling in the nineteenth century ... and the other ruling in the twentieth century (a consensus having been reached during the evolutionary synthesis). Any other use of the term Darwinism by a modern author is bound to be misleading.

I agree with Mayr on this point. Darwinism refers to evolution by natural selection. But a "Darwinist" is not just someone who accepts the fact of natural selection, it's more than that. It's someone who prefers this explanation to all other possible mechanisms of evolution. This is the point made by Stephen Jay Gould in his famous 1982 Science paper, "Darwinism and the Expansion of Evolutionary Theory." (The Gould quote about semantics in the left sidebar is from that paper.) Gould defines modern Darwinism as ...

If we agree, as our century generally has, that "Darwinism" should be restricted to the world view encompassed by the theory of natural selection itself, the problem of definition is still not easily resolved. Darwinism must be more than the bare bones of the mechanics: the principles of superfecundity and inherited variation, and the deduction of natural selction thereform. It must, fundamentally, make a claim for wide scope and dominat frequency; natural selection must represent the primary directing force of evolutionary change.

Richard Dawkins is a Darwinist and Daniel Dennett is a Darwinist. I am not a Darwinist. I prefer a modern pluralist view of evolution as I explain in Evolution by Accident.

I am not a Darwinist, just as most of my colleagues in the Department of Physics are not Newtonists, and most of my friends who study genetics are not Mendelists. All three of these terms refer to the ideas of famous men (Charles Darwin, Isaac Newton, Gregor Mendel) who made enormous contributions to science. But in all three cases, the modern sciences have advanced well beyond anything envisaged by their founders.

Call me an evolutionary biologist.

The Three Domain Hypothesis (part 1)

 

The Three domain Hypothesis is dead. It passed away peaceably sometime in the past ten years. Most people didn't notice.

Last year a wake was held. Friends and enemies of the Three Domain Hypothesis were invited. Many gave eulogies and these were published in a book called Microbial Phylogeny and Evolution: Concepts and Controversies. This is a collection of papers by leading scientists in the field. It's edited by Jan Sapp, a Professor of Biology at York University here in Toronto. I've listed the most interesting articles at the bottom of the page and I'll stick to comments on these articles for now.

Surprisingly, some of the guests at the wake did not know the hypothesis had been falsified. They thought the corpse was still breathing!

The Three Domain Hypothesis refers to the proposal by Carl Woese that; (1) archaebacteria form a monophyletic group, (2) this clade is sufficiently different from all other prokaryotes to deserve elevation to a separate Domain called Archaea (the other two Domains are Bacteria and Eukarya), (3) eukaryotes are more closely related to archaebacteria than to other prokaryotes, and (4) the root of the universal tree of life lies in the branch leading to Bacteria.

The "standard" universal tree of life is based on the Three Domain Hypothesis. It is mostly derived from sequences of the small ribosomal RNA subunit (SSU).

In recent years, all four of the major claims of the Three Domain Hypothesis have been challenged. Some would say that two have been falsified. Furthermore, there is growing recognition that SSU-based trees are not as reliable as we once thought. Surprisingly, this skepticism among evolutionary biologists has not reached the ear of the average scientist who continues to act as though the Three Domain Hypothesis is a done deal.

The literature is large, varied, and controversial. I've been following it for twenty years and it's not possible to write a short note covering all the bases. Instead, I'll concentrate on reviewing a few of the papers in the book.

---

Norman Pace The Large-Scale Structure of the Tree of Life.

Woflgang Ludwig and Karl-Heinz Schleifer The Molecular Phylogeny of Bacteria Based on Conserved Genes.

Carl Woese Evolving Biological Organization.

W. Ford Doolittle If the Tree of Life Fell, Would it Make a Sound?.

William Martin Woe Is the Tree of Life.

Radhey Gupta Molecular Sequences and the Early History of Life.

C. G. Kurland Paradigm Lost.

Student Evaluations

Dave Munger of Cognitive Daily is discussing student evaluations in an article titled "Blink" methods now being applied in the classroom". The word "Blink" refers to the best-seller by Toronto author Malcolm Gladwell (an excellent book, BTW). Gladwell mentions a study by Nalini Ambady and Robert Rosenthal in (1992) where they exposed students to short video clips of a lecturer and asked for evaluations. The evaluations weren't much different from those done at the end of the term.

Unfortunately, Dave Munger seems to draw the wrong conclusions from this study as he explains in an earlier posting [The six-second teacher evaluation]. In that article from last May he says ...

So we do appear to be quite effective at making judgements about teaching ability even after viewing only a total of 6 seconds of actual teaching, and without even hearing the teacher's voice.

This is dead wrong. Students are good at evaluating something after six seconds but it sure as heck ain't teaching ability. It's probably whether the students like the teacher or not. We can make snap judgements about personality but not about ability. The correlation with end-of-term evaluations suggests that even after several months, students are still only evaluating the personality of the teacher and not teaching ability.

It makes no sense whatsoever to assume that students can judge how good a teacher you are from a six second video clip. How can they tell whether the lecturer is well prepared, knows the subject, writes fair exams, chooses the appropriate level of difficulty, and communicates important concepts?

The Canadian Association of University Teachers (CAUT) has developed a policy regarding student evaluations. The CAUT report discusses the pros and cons of student evaluations, including the Ambady and Rosenthal (1993) study. Here's what it says in footnote #10 ...

More recently, Ambady and Rosenthal (1993) report findings which point to the conclusion that student ratings of instructors can be strongly influenced by factors that probably bear only a slight relationship to critical dimensions of teaching effectiveness (though one must hasten to add that this is not the conclusion that Ambady and Rosenthal argue for in their study). They report that trained observers' evaluations of very brief segments (30 seconds or less) of silent videotape of college teachers yielded ratings of specific behaviors that correlated positively with students' ratings of the instructors. The experimenters found that appearing to be more active, confident, dominant, enthusiastic, likable, optimistic, supportive and warm, etc., in these "thin slices" of observation correlated positively with students' ratings of the instructors. In one of the experiments, student ratings of the instructors also were found to be "somewhat" influenced by the physical attractiveness of the teachers (p. 435). Whatever aspects of the teaching act have been accessed in this study, and no matter their positive relationship with student ratings, it must be obvious that there is more to effective teaching than demonstrating behaviors that can be documented in 30 seconds or less of silent videotape.

In his discussion of instructor personality and the politics of the classroom, Damron (1994) reviews the extensive literature that suggests that student ratings may be especially sensitive to students' perceptions of instructor personality or aspects of instructors' demeanour that bear little relationship to student learning or achievement.

Conestoga College Teaches Pseudoscience

Check out Jeffrey Shallit's blog Recursivity. He reports that Conestoga College in Kitchener is offering courses in Homeopathy, ESP, and Reincarnation. Shame!

Lost in a Haystack

John Pieret over at Thoughts in a Haystack has weighed in on the agnostic/atheist debate with his article "Agnostic About Atheism."

You'll have to read the comments before gettng a clear idea of John Pieret's position. He says,

...But what I think Dawkins' own example (inadvertently) demonstrates is the correctness of PAP. The scientific community itself, through its practices, recognizes that miracles (assuming, as you must for the sake of this argument, that they exist) cannot truly be addressed by empiric investigation. "Miracles" may be debunked (at least by showing fraud or trickery -- merely showing a sufficient naturalistic cause for something does not mean you have shown the phenomenon is not miraculous) but they may not be empirically confirmed. That inability to truly engage the issue means that empiricism is not capable, in the end, of answering the question of whether God exists.

And since I share with Dawkins the view that empiric investigation is the only game in town for obtaining knowledge, and that the rest is mere opinion, refusing to claim knowledge of God's status is not fence-sitting, it is good scientific practice.

I've heard this before. John's opinion is that science can never absolutely disprove the existence of anything, including the most ridiculous claims of miracles and magic. Thus, according to him, you have to remain agnostic about everything if you are being a good scientist.

While philosophically sound in principle, this doesn't work in practice. Taken to the extreme it says that science can never be sure of anything because there's always the possibility that we could be wrong. I wonder if John proclaims his agnosticism about evolution and intelligent design?

I suspect not. I suspect that religion gets special treatment for some strange reason. It's okay to take a stance and say you don't believe in astrolgy but it's not okay to say you don't believe in God. Strange.

On-line Access to Scientific Journals

One of our students (Sabina) recently posted this comment to our university newsgroups [BIOME].

However, we are VERY fortunate at [the University of Toronto] because we can download any full PDF of an article from almost all possible journals imaginable for free with just our UTorID from the Gerstein off-site access which leads into PubMed, so, we don’t even need a subscription to anything (unless you really enjoy having all those shiny pages at your disposal). So we don’t need to worry about costs for an individual article, most people that need them are associated with an institution that will already have a subscription.

This reminded me how lucky we are to enjoy such open access. Our library currently subscribes to 31,000 journals that allow faculty and students to download articles/abstracts as PDF files. What this means for teachers is that we can assign an article from the scientific literature knowing that every student can print it out at home or on one of the university computers in the "information commons." They can even print it out on a color printer—an important consideration in my field where many of the journal images are in color.


How much does this service cost the university? I asked our librarians for an estimate and they told me it costs several million dollars (<$2,000,000) per year.

Just how lucky are we? I know that some of my friends at other universities don't have access to the same journals we get. I presume that everyone can get articles from Nature and Science but what about the Journal of Biological Chemistry (JBC) or the Journal of Molecular Evolution?

She's Baaaaaack!

Watch Ann Coulter and Tucker Carlson commenting about Canada in these clips on YouTube in December 2005. The second half of the video features Carolyn Parrish, my former MP, in an interview with Carlson in November 2004.


Some of you may remember Carolyn Parrish. She made quite a name for herself by stomping on a George Bush doll and proclaiming that she hated American "bastards." She was kicked out of the Liberal party in 2004 and didn't run in the last Federal election in January 2006.

Nobody in our riding was sad to see the last of her. It wasn't because she didn't like Bush—that's not unusual around here—it was because she's a jerk and doesn't know enough to think before she opens her mouth. Here's a list of quotations from someone who doesn't know that silence is sometimes golden. Parrish also didn't like Paul Martin, Prime Minister at the time and leader of her party, and that probably had a lot to do with her ejection. If you're going to belong to the party you have to agree with it's policies or get out.

Anyway, she's back. Caroline Parrish was just elected to the city council in Missisauga. I didn't vote for her. She ran in another ward north of my home. I'd probably have voted for Bush if he had run against her in Ward 6.

Now all decent citizens of Mississauga have to get together and make sure she will never, ever, be elected to replace Hazel McCallion as mayor of our city.

Some Buildings Look Better at Night

 

This is the new Leslie L. Dan Pharmacy Building at the University of Toronto. It's right next to where I work so I pass it every day. I think the building is quite unattractive during the day but the nighttime view is spectacular. I took this photo last night.

The colored pods hold lecture theaters.

Jay Ingram Speaks to our Students

 

Last night Jay Ingram spoke to our students about carreer opportunities after you graduate from university. Jay was the long-time host of Quirks and Quarks on CBC radio and he is the current host of Daily Planet, a daily science show on Discovery Channel Canada. He has published many books; the most recent is Theatre of the Mind [amazon.ca].

Jay graduated from the University of Toronto some years ago with a M.Sc. degree in Microbiology. His talk was held in the same building where he used to take classes as an undergarduate. He told the students that his carreer path has been somewhat unusual but he encourged them to take advantage of any opportunities that come their way. Fortune favors the prepared mind, as Louis Pasteur once said. The best advice he could give was "to not always listen to what well-meaning mentors tell you to do." (He wasn't referring to me, of course.)

One of the most interesting parts of his talk was when he deconstructed yesterday's Daily Planet show in order to explain what one has to do to keep an audience's attention. The idea is to make each segment short and simple and have lots of pictures.

During the question and answer session he expressed his frustration over the lack of scientific literacy among the general public. He pointed out that it's almost a badge of honor among pseudointellectuals to claim they know nothing about science. They should be as embarrassed about their ignorance as the rest of us would be if we had never heard of William Shakspeare. (Personally, I think we should make a point of telling such pseudointellectuals that they are ignorant.)

Ingram's talk was sponsored by the Molecular Genetics & Microbiology Students Union (MGYSU). Schreiber Pereira of MGYSU was the man who did most of the work. That's him in the photograph with Jay Ingram.

Canada Wins "Fossil of the Day"!!!

 

This is so exciting! Canada hardly ever wins anything except international hockey tournaments.

All we had to do was rack up one of the worst environmental records in the world. It was a close race—we were barely edged out by the USA and they're a lot bigger than we are!

Here's the story in the Toronto Star. The first three paragraphs say it all ...

Canada has been handed its second consecutive "fossil" award for its poor performance on the environment - attention that’s richly deserved, an expert says.

Climate Action Net work, a coalition of environmental lobby groups, singled out Canada at in ternational talks today in Nairobi. But Environment Minister Rona Ambrose is fighting back.

In a brief scrum outside the conference hall, the minister said the federal government is intensively negotiating with Canadian industry on cutting greenhouse emissions, and short-term targets should be in place by mid-January.

Yeah, right. Don't bet on it. We'll be back next year looking for revenge. We'll settle for nothing less than first place. Those Americans better watch out, Harper is gunning for you, Dubya.

Agnostics Are Wimps

Jason Rosenhouse over at EVOLUTIONBLOG has challenged John Wilkins' position on agnosticism in Wilkins on Dawkins. It didn't take John [Evolving thoughts] long to respond with Agnostic Still.

They are both discussing an issue raised by Richard Dawkins in The God Delusion. In his section on "The Poverty of Agnosticism" (pp. 46-54), Dawkins describes agnostics as fence-sitters, and this was not meant as a compliment. Dawkins knows full well that there is a deep metaphysical sense in which we can never know anything for certain.

If we're all being perfectly philosophical, then we have to admit to being agnostics about the tooth fairy and Santa Claus. But what good is that? Do we really go around telling everyone that we just don't know whether Santa Claus will visit on Christmas Eve? Of course not. We don't believe in Santa Claus, even though we can all write an essay in Philosophy 101 about not being able to prove a negative.

This is what Dawkins means when he says, "I am agnostic only to the extent that I am agnostic about fairies at the bottom of the garden" (p. 51). He makes the same point a few pages later when he says,

That you cannot prove God's non-existence is accepted and trivial, if only in the sense that we can never absolutely prove the non-existence of anything. What matters is not whether God is disprovable (he isn't) but whether his existence is probable. That is another matter. Some undisprovable things are sensibly judged far less probable than other undisprovable things.

John knows this but, nevertheless, he says, "Do I think there is a God? No, I don't. Am I an atheist? No, I'm not."

John, with all due respect, if you walk like an atheist and talk like an atheist then, to all intents and purposes, you're a practicing atheist, whether you want to admit it or not. You can be an agnostic atheist in the sense that you act as if there's no God but still want to be true to your profession. They won't drum you out of the philosophers' union if you confess your atheistic lifestyle as long as you make the right noises from time to time. I've was with you at a conference of philosophers last year and we met several atheists who were still card-carrying philosophers.

We spent a whole Sunday together and I know you didn't go to church. You are not a theist. The word that describes that non-believer lifestyle is "atheist," not "agnostic." Please join Jason Rosenhouse, Richard Dawkins, and me, and come all the way out of the closet. :-)

Biochemistry v Bioinformatics

Michael White over at Adaptive Complexity has posted an article on the growing conflict between biochemists and bioinformaticians [The problem with computational biology papers]. Michael White is a biochemist postdoc at Washington University working on cell cycle regulation in yeast so he's well-positioned to appreciate the problem.

Thanks to RPM at evolgen for finding the article. This is a problem that RPM has addressed before; you should follow his links in today's posting [Computational Work without Experimental Validation].

There are important issues here. My department has made a serious effort to develop and nurture the growing field of bioinformatics over the past ten years and we have recruited a number of excellent scientists. Nevertheless, there's still a two-solitudes problem that threatens to undermine the effort. The real bioinformaticians, and their students and postdocs, don't communicate well with the pure wet-bench biochemists. The more "traditional" biochemists still resent the fact that bioinformatics students don't get their hands dirty.

It's clear that there has to be give and take on both sides. Bioinformatics graduate students simply must learn enough biology to recognize the significance of their project. You can't get a Ph.D. in biochemistry if you don't understand what all those interaction networks really mean or you don't know how to interpret EST data.

Similary, older biochemists have to adapt to the new ways of thinking about scientific problems. There's nothing magical about working at the bench and mixing buffers. Some of the most important advances in biology are coming out of computers. This does not mean that everything in bioinformatics is valid science—far from it. A lot of what passes as bioinformatics is highly questionable, but that's also true of more traditional biochemisty. Neither side has a monopoly on truth and accuracy.

Carnival of the Godless #53

The 53rd edition of Carnival of the Godless was put up on Debunking Christianity last Sunday. As a new blogger I'm still getting used to the cornucopia of excellent blogs. Thanks to PZ Myers for bring this to my attention.

I especially like The God Conundrum by Sean Carroll (the physicist, not the biologist) over at Cosmic Variance. Carroll does a good job of addressing the question that Terry Eagleton raised in his review of Dawkins' book. You need to read all of "The God Conundrum" but here's a teaser ...

Some of you may be wondering: “Does God exist?” Fortunately, Richard Dawkins has written a new book, The God Delusion, that addresses precisely this question. As it turns out, the answer is: “No, God does not exist.” (Admittedly, Dawkins reached his conclusion before the Cards won the World Series.)

Nevertheless, there remains a spot of controversy — it would appear that Dawkins’s rhetorical force is insufficient to persuade some theists. One example is provided by literary critic Terry Eagleton, who reviewed The God Delusion for the London Review of Books. Eagleton’s review has already been discussed among some of my favorite blogs: 3 Quarks Daily, Pharyngula, Uncertain Principles, and the Valve (twice), to name a few. But it provides a good jumping-off point for an examination of one of the common arguments used against scientifically-minded atheists: “You’re setting up a straw man by arguing against a naive and anthropomorphic view of `God’; if only you engaged with more sophisticated theology, you’d see that things are not so cut-and-dried.”

There are several other contributions of interest to biologists. Shalini at Scientia natura looks at the Time magazine "debate" from the non-believer perspective. Her article, Francis Collins Does It Again, exposes some of the silly thinking behind the Collins' version of religion.

Mr R. of Evolving Education adds his voice to the growing number of people who are getting tired of Theistic Evolutionists. His blog is about a talk by Ken Miller at N.C. State University. You can see my take on this issue at Theistic Evolution: The Fallacy of the Middle Ground.

There's lots more in this Carnival of the Godless—44 articles in total. Enjoy.

Technicolor Money

On a recent trip to the UK I had to get used to British currency. The coins were a problem but not the banknotes since each denomination was a different color. The £10 note was not only a pretty color but it had a picture of a famous scientist.It's hard to imagine an American bill with a picture of Darwin. It's also hard to imagine an American bill that's any color but green. Why is that? Is America the only country that does not have technicolor money?

I asked my American travelling companion about this but he didn't seem to care. In fact, I got the distinct impression that he preferred boring monchrome money.

Denyse O'Leary Needs Help (again)

Over on Pre-Neanderthal Denyse is quoting Douglas Futuyma from the 1998 edition of his book Evolutionary Biology 3rd edition. She lifted her quotation from a Discovery Institute quote-mining project. Here are the words that she puts in Futuyma's mouth ...

Darwin showed that material causes are a sufficient explanation not only for physical phenomena, as Descartes and Newton had shown, but also for biological phenomena with all their seeming evidence of design and purpose. By coupling undirected, purposeless variation to the blind, uncaring process of natural selection, Darwin made theological or spiritual explanations of the life processes superfluous. Together with Marx's materialistic theory of history and society and Freud's attribution of human behavior to influences over which we have little control, Darwin's theory of evolution was a crucial plank in the platform of mechanism and materialism ...

It's clear that Densye doesn't have one of the world's leading textbooks on evolution because she didn't even check to see if the Discovery Institute got it right. Perhaps Denyse doesn't realize that the Discovery Institute sometimes makes the occasional—always inadvertent, I'm sure—error. Here's what Douglas Futuyma actually says on page 5 in my copy of the book ...

Darwin's immeasurably important contribution to science was to show how mechanistic causes could also explain all biological phenomena, despite their apparent evidence of design and purpose. By coupling undirected, purposeless variation to the blind, uncaring process of natural selection, Darwin made theological or spiritual explanations of the life processes superfluous. In the decades that followed, physiology, embryology, biochemistry, and finally molecular biology, would complete this revolution by providing entirely mechanistic explanations, relying on chemistry and physics, for biological phenomena. But it was Darwin's theory of evolution, followed by Marx's materialistic (even if inadequate or wrong) theory of history and society and Freud's attribution of human behavior to influences over which we have little control, that provided a crucial plank to the platform of mechanism and materialism—in short, of much of science—that has since been the stage of most Western thought. [Futuyma's emphasis]

The sense hasn't been changed much by the Discovery Institute's quote-mining but it's not a true quotation in any legitimate sense of the word. Why can't these people get it right? Do they have a mental block?

Denyse then goes on to ask, "I would be interested to know if this paragraph appears unaltered in the just-released 2006 edition, but Toronto Public Library seems to have nothing later than the 2nd edition." Here's a bit of advice, Denyse; if you're going to attack evolution then you should buy a textbook instead of relying on the words of people who are notoriously unreliable.

Guess what, Denyse? I have a copy of Futuyma's latest book. You are more than welcome to come to my office and check it out if it's really that important to your cause. I'm almost as close as the public library.

Nobel Laureates: Otto Fritz Meyerhof

The Nobel Prize in Physiology or Medicine 1922

Otto Fritz Meyerhof was awared the Noble Pize in Physiology or Medicine in 1922 "for his discovery of the fixed relationship between the consumption of oxygen and the metabolism of lactic acid in the muscle."

Meyerhof was born in 1884 and graduated with an M.D. in 1909. He did most of his work in Germany at Kiel University and, later on, at Heidelberg. In 1938 he fled to France and after the fall of France in 1940 he escaped to the United States where a position at the University of Pennsylvania was created for him. He died in 1951.

Meyerhof is best known for his work on glycolysis where he was one of the first to discover the role of phosphorylated intermediates. The classic glycolytic pathway in bacteria is known as the Embdem-Meyerhof-Parnas (EMP) pathway in honor of Meyerhof and his colleagues Gustav Embdem and Jacob Parnas.

Name This Molecule #1

 
The mystery molecule is an aldohexose. There are 16 different aldohexoses. The structures and names of 8 of them are show below in order to help you out.

This is a tough one. You have to know several carbohydrate naming conventions and you have to understand Fischer projections. Good luck.

I'm Voting for Hurricane Hazel!

 

Today is voting day in Ontario. I live in Mississauga and I'm voting for Mayor Hazel McCallion. Hazel, who is 85 years young, has been mayor of Mississauga since 1978. I reckon she's good for another few years. She won her last election in 2003 with 92% of the vote and she hasn't bothered campaigning in this one. She doesn't need to. We all love Hurricane Hazel.

McCallion was nominated for the title of World Mayor in 2005 [Locally revered and internationally honoured] and finished as runner-up to Dora Bakoyannis, Mayor of Athens. If you wanna see what it's like to run against Hazel check out this newsclip from CityTV.

University Rankings: Toronto Drops to #3

The Macleans annual issue on ranking universities is now on the newsstands. The new rankings have the University of Toronto at #3 behind McGill and Queen's. Toronto was #1 for the past 12 years.

This year the rankings are controversial because 26 universities, including the University of Toronto, refused to cooperate with Macleans. Other major universities that joined with Toronto are:

Queen's University (#2)
University of British Columbia (#4),
University of Western Ontario (#5)
University of Alberta (#6)
Université de Montréal (#7)
University of Ottawa (#8)
McMaster University (#12)
University of Calgary (#13)
Dalhousie University (#14)
University of Manitoba (#15)

Last summer, these schools declared that they would not cooperate. They cited
problems with the methodology and claimed that the rankings were unfair. President David Naylor of the University of Toronto also noted that responding to the Macleans questionaire was time-consuming because it required compiling data in a different format than what the university normally does. Professor Naylor wondered why a public university should be devoting so much time and effort to helping a for-profit company.

I was waiting for Macleans to hit the newsstands before blogging about this because I was hoping that the University of Toronto would still be #1 and I could complain about the rankings without making it look like sour grapes. Oh well, at least my university is on record as objecting to the unfairness of the rankings when it was still in first place.

The main problem seems to be the huge emphasis on things over which universites have very little control. The importance of student surveys, and surveys of the business community are also causes for concern. Read David Naylor's report, University Report Cards, Ratings, Rankings, and Performance Measures, for a serious discussion about the flaws in rankings such as Macleans.

The Evolution Crackpot Index

 
Check out John Wilkins' Evolution Crackpot Index over at Evolving Thoughts.

I prefer to call them "kooks" or "idiots" but "crackpots" will do in a pinch. There are lots of them on talk.origins and sci.bio.evolution.

My Neighbourhood Tim Hortons

 
Last week PZ Myers posted a map showing all the churches in his neighbourhood Small Town Churches. I thought this was very interesting so I decided to make my own map. Here are all the Tim Hortons in the 'hood.

Here I am!

 
Taking a page from The Daily Transcript here's the campus of the University of Toronto. We have about 71,000 students but you can't see them in this image 'cause they're all inside studying.

Sea Urchin Genome Sequenced

The sequence of the genome of the California purple urchin, Strongylocentrotus purpuratus was reported in the November 10 issue of Science magazine. The Science webpage contains a number of links to important articles and, more importantly, a link to a special interactive poster.

The sea urchin genome is 814,000 kb or about 1/4 the size of a typical mammalian genome. Like mammalian genomes, the sea urchin genome contains a lot of junk DNA, especially repetitive DNA. The preliminary count of the number of genes is 23,300. This is about the same number that we have in our genomes. Only about 10,000 of these genes have been annotated by the sea urchin sequencing team. We can expect the number to drop as annotation proceeds because most of the gene prediction programs tend to over-estimate the number of genes. I've looked at the current draft of the sequence to see how many HSP70 genes are in the genome and discovered that there are more pseudogenes and gene fragments than real genes. This is not unusual in a first draft.

There are two important links to the Sea Urchin genome project. The first is at CalTech, the home of Eric Davidson who is one of the key movers and shakers in the study of sea urchins. The second site is at the Human Genome Sequencing Center at Baylor College of Medicine. This is one of the large sequencing centers that sprung up during the rush to finish the human genome sequence.

The first assembly has been deposited in GenBank and the National Center for Biotechnology Information (NCBI) has set up a website for Sea Urchin Genome Resources.

According to the original proposal [White Paper] the cost of sequencing the sea urchin genome would be about $30 million. The proposal gives several different reasons for funding the project but one of the key motives is to fill in a gap in the phylogeny of sequenced animal genomes. The figure above shows the position of sea urchins relative to chordates (including mammals) and most invertebrates. The phylum Echinoderma clusters with the phylum Chordata (shaded area on the right) in a group known as Deuterostomes. Thus, sea urchin genes are more closely related to chordate/vertebrate genes than to mussel or arthropod genes. In other words sea urchins are more like humans than octopus or squid.

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From PhysOrg.com .....

Scientists have sequenced the genome of the sea urchin, an invertebrate surprisingly similar to man, a step that could help develop new treatment for human disease such as cancer, said a study released Thursday. [more ...]

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From the National Center for Research Resources (by Aaron Levin) ...

For more than 30 years, Dr. Eric Davidson and his research team at the California Institute of Technology in Pasadena have steadily teased apart the molecular genetics of a common ocean-dwelling creature, the purple sea urchin (Strongylocentrotus purpuratus), searching for the regulatory mechanisms that underlie its development from fertilized egg to free-swimming larva. The Caltech scientists have long recognized what a growing segment of the biomedical community is beginning to appreciate—that the sea urchin is a unique and tractable organism with enormous potential for shedding light on the most basic biological processes, including many that are relevant to human health. Indeed, the National Human Genome Research Institute recently selected the sea urchin as a top priority for genome sequencing, along with the genomes of the chimpanzee, dog, cow, and other animals of scientific interest. [more ...]

United Nations Ranks Countries

 
The Human Development Report ranks countries according to life exectancy, literacy rate, enrolment in schools, and GDP per capita. Norway is the best country.

    Here are the top 10.
        1. Norway
        2. Iceland
        3. Australia
        4. Ireland
        5. Sweden
        6. Canada
        7. Japan
        8. United States
        9. Switzerland
        10. Netherlands