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.