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Tuesday, June 17, 2008

With or Without God

 
Come to the Centre for Inquiry's lecture by Gretta Vosper.

With or Without God: Why the Way We Live is More Important than What We Believe

Starts: Friday, June 20th at 7:30 pm
Ends: Friday, June 20th at 9:30 pm
Location: Centre for Inquiry Ontario, 216 Beverley St, Toronto ON (1 minute south of College St at St. George St)

Lecture and Book Launch:
Gretta Vosper, United Church Minister at West Hill United Church, Toronto, and founder and Chair of the Canadian Centre for Progressive Christianity

In Gretta Vosper's church there are no prayers, no miracles-performing magic Jesus and no omnipotent God at all. Vosper's book argues that the Christian church, in the form in which it exists today, has outlived its viability and either it sheds its no-longer credible myths, doctrines and dogmas, or it's toast. With a humanist worldview, Vosper proposes a radical change at the heart of faith. The new church she envisions will play a viable and transformative role in the shaping of a future society. What will save the church from certain demise, Vosper argues, is a new emphasis on just and compassionate living.

A catered receptions shall precede the talk at 6pm exclusively for Friends of the Centre.

Canadian Centre for Progressive Christianity:

MacLeans Magazine coverage "The Jesus Problem":

Globe and Mail coverage "Taking Christ Out of Christianity"

Cost: $6 general, $4 students, FREE for Friends of the Centre


Monday, June 16, 2008

Monday's Molecule #76

 
Name this molecule, being as specific as you can.

There's a direct connection between today's molecule and a Nobel Prize. The prize was awarded for discovering the basic structure of the molecule, although not at the level of detail depicted here. That came later.

The first person to correctly identify the molecule and name the Nobel Laureate(s), wins a free lunch at the Faculty Club. Previous winners are ineligible for one month from the time they first collected the prize. There are four ineligible candidates for this week's reward. You know who you are.

THEME:

Nobel Laureates
Send your guess to Sandwalk (sandwalk (at) bioinfo.med.utoronto.ca) and I'll pick the first email message that correctly identifies the molecule and names the Nobel Laureate(s). Note that I'm not going to repeat Nobel Laureate(s) so you might want to check the list of previous Sandwalk postings by clicking on the link in the theme box.

Correct responses will be posted tomorrow. I may select multiple winners if several people get it right.

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

UPDATE: The molecule is immunoglobulin G (IgG) and the Nobel Laureates are Gerald Edelman and Rodney Porter (1972). The first correct answer was from Jon Turnbull who beat everyone else by more than one hour! Honorable mention (and a free lunch) goes to Haruhiko Ishii of UCSD. Not only did he identify the molecule as IgG, he also showed that it was very likely to be Mab231, a mouse monoclonal anti-canine lymphoma antibody composed of IGg2a heavy chains and κ light chains [PDB 1IGT].


Café Scientifique and Nature Network Pub Night

 
CAFÉ SCIENTIFIQUE PRESENTS
The future of medicine: help, hope or hype? (download the poster)

What lies in the future for medicine and health care? Over the next 50-100 years, how will we conquer illnesses and stay healthy? Join the discussion and debate at the next Café Scientifique, The future of medicine: help, hope or hype?, where experts will peek at the potential for robotics, genomics, alternative therapies and personalized medicine to cure our ills.

Experts:
  • Dr. Tony Pawson – Distinguished Investigator, Samuel Lunenfeld Research Institute of Mount Sinai Hospital
  • Karl Schroeder – Science fiction author and futurist
  • Dr. Calvin Gutkin – Executive Director and CEO, The College of Family Physicians of Canada


Wednesday, June 18, 2008, from 6 to 8pm
Duke of York Pub – ground floor
39 Prince Arthur Avenue -Close to the St. George subway (Bedford exit)

FREE

Presented by the Samuel Lunenfeld Research Institute of Mount Sinai Hospital and Ontario Science Centre, with generous support from Canadian Institutes of Health Research.

Café Scientifique is a place where, for the price of a cup of coffee or a pint of beer, anyone can join discussions that explore the latest ideas in science and technology.

The members of the Toronto hub of Nature Network will meet afterwards in the Duke of York (same place as Café Scientifique) [see Eva Amsen's posting on easternblot]. You get two stimulating meetings for the price of one (i.e. free!).

If you haven't yet joined the Toronto hub of Nature Network you should sign up here. Current members of the Toronto hub are here.


Kansas vs Darwin

 
Jeff Tamblyn, the director of Kansas vs Darwin will be in town this week for the ReelHeART International Film Festival. The film will be shown on Thursday evening. Here's the trailer, details below ...


Kansas vs. Darwin screening Thursday, June 19, 7:00 PM
ReelHeART International Film Festival
RHIFF MAIN PROGRAM B Tickets $8
INNIS THEATER 222
Innis College, University of Toronto
2 Sussex Avenue [1 block south of Bloor Street, on St. George Street]
Toronto, ON M5S 1J5
Advance Sales on line April 21, 2008 at www.reelheart.com

Kansas vs. Darwin
Director, Jeff Tamblyn, USA

Kansas vs. Darwin is a smart, funny, feature-length documentary about the Kansas state school board hearings on evolution. Features intimate revealing interviews with all major players on both sides, and exclusive, multi-camera footage of the hearings. Far more than a political film, Kansas vs. Darwin skillfully weaves multiple themes into a gripping dialectic, putting you face to face with, and inside the heads of, those who oppose your most closely held beliefs. Challenging and entertaining, it’s packed with fascinating characters who will leave you in admiration and astonishment, embarrassment and exasperation, as they feverishly pursue their goals, sometimes stumbling over their own eagerness in the attempt to win the most important battle of their lives.
I'm going. Contact me if you plan to attend and you want to meet up for dinner before the show.


Sunday, June 15, 2008

Fernando

 
Fernando was one of ABBA's biggest hits. There's a lot of debate about which war it refers to. The song mentions crossing the Rio Grande and that prompts many people in America to think of the Mexican revolution of 1910-1920. However, there aren't many examples of fighting that took place near the Rio Grande and there aren't too many examples of revolutionaries who crossed into Mexico from the USA.

Most people assume the song is about the Spanish civil war and the reference to the Rio Grande is just a generic reference to a river. Keep in mind that ABBA is a European group and the Spanish Civil War is still fresh in the memories of many europeans. For many it was glorious, but losing, fight against fascism.

The song refers to Fernando, a man who fought on the losing side against tyranny and fascism. Fernando was a revolutionary and a guerrilla fighter. He is now old and gray like many of the freedom fighters from all over Europe who went to Spain in the 1930's.

John McCain likes ABBA. I hope he appreciates that this song is about people who fought to defend their country from foreign domination. (Franco was supported by Hitler and Mussolini.)




Friday, June 13, 2008

Bias Against Female First-Author Papers

 
This is a follow-up to a posting back in January where I mentioned a recently published article by Budden et al. (2008) [see Bias Against Women?]. That article claimed to show evidence of a systematic bias against papers with women as first authors. The bias was mitigated when a particular journal switched to a double-blind reviewing system. This resulted in a significant increase in the number of published papers with women as first authors.

I was first alerted to the problem when GrrlScientist posted a favorable review of the paper, agreeing with the conclusion that journal reviewers were biased against papers with female first authors [Women, Science and Writing].

My first reaction was skeptical. These are biology papers and it didn't seem plausible that reviewers would be biased against papers with female first authors. There might possibly be a bias against papers from a lab run by women but that's not the same thing. In the biological sciences the principle investigator is often the last author and not the first. Furthermore, in my experience there wasn't any discrimination against female scientists at this level (publication). Half of our graduate students are women—why would we be biased against papers with one of them as first author? The study just didn't make sense.

Many Sandwalk readers interpreted my skepticism as an attempt to dismiss all forms of sexism in science. That was not my intent. Far from it, in fact, because I was very much aware of a particular case of sexism that greatly troubled me. What makes me angry is that I know of overtly sexist behaviors that are not challenged by scientists in the same department who are, themselves, not sexist. The subject of sexism came up at SciBarCamp in February where there was a session organized by physics professors to discuss sexism in physics departments. There seems to be a major problem in physics.

If you read the comments in my January posting you'll see how difficult it was to separate out the issue of whether the particular study on double-blind reviews was a legitimate scientific study, and whether sexism is common in science.

At the risk of encountering the same problem again, let's look at some recent events. A re-analysis of the original publication data has been published by Webb et al. (2008). They looked more carefully at the data from journals with double-blind review and from comparable journals that identify the authors. They found that the number of papers with women as first authors showed a general increase in most journals. The trend in the journal that initiated double-blind review back in 2001 was not significantly different. Thus, they conclude that there's no evidence of systemic bias against female first authors.

This is one of the points that I mentioned in the comments to my January posting but several other readers dismissed it. They implied that any attempt to question the data in the original paper was, itself, sexist.

The following correction appeared in the last week's (June 4th) issue of Nature.
The Editorial 'Working double-blind' (Nature 451, 605–606; 2008) referred to a study(1) that found more female first-author papers were published using a double-blind, rather than a single-blind, peer-review system. The data reported in ref. 1 have now been re-examined (2). The conclusion of ref. 1, that Behavioral Ecology published more papers with female first authors after switching to a double-blind peer-review system, is not in dispute. However, ref. 2 reports that other similar ecology journals that have single-blind peer-review systems also increased in female first-author papers over the same time period. After re-examining the analyses, Nature has concluded that ref. 1 can no longer be said to offer compelling evidence of a role for gender bias in single-blind peer review. In addition, upon closer examination of the papers listed in PubMed on gender bias and peer review, we cannot find other strong studies that support this claim. Thus, we no longer stand by the statement in the fourth paragraph of the Editorial, that double-blind peer review reduces bias against authors with female first names.
I believe that Nature has done the right thing in retracting their earlier claim. The problem of sexism in science is serious and needs to be addressed. But it doesn't do anyone any good if one side is supporting their claims with sloppy science. It would be good if we could get beyond that.

It may not be easy. The authors of the original paper have published a critique of the re-analysis (Budden et al. 2008b). They dispute the re-interpretation although they admit that their analysis is subject to different interpretations.

If the original paper was any other kind of scientific paper the criticism would be harsh. It will be interesting to see if any of the original strong supporters of the claim of sexist bias against female first authors are willing to reconsider their position on that particular issue.


[Hat Tip: R. Ford Dennison]

Budden, A., Tregenza, T., Aarssen, L., Koricheva, J., Leimu, R. and Lortie, C. (2008a) Women, Science and Writing. Trends in Ecology & Evolution, 23(1), 4-6. [PubMed] [doi:10.1016/j.tree.2007.07.008] (ref 1.)

Budden, A.E., Lortie, C.J., Tregenza, T., Aarssen, L., Koricheva, J., and Leimu, R. (2008b) Response to Webb et al.: Double-blind review: accept with minor revisions. Trends in Ecology and Evolution [doi:10.1016/j.tree.2008.04.001]

Webb, T. J., O'Hara, B. and Freckleton, R. P. (2008) Does double-blind review benefit female authors? Trends in Ecology and Evolution [doi:10.1016/j.tree.2008.03.003] (ref 2.)

Alex Palazzo in Toronto

 
Alex Palazzo of The Daily Transcript has been in Toronto for the past few days. We were able to get together for lunch on Wednesday and for some light liquid refreshments on Wednesday evening. It should come as no surprise that we were able to find several things we agree on and several more that we don't. It was a lot of fun. (I made a bet with Alex on Wednesday evening. He'll reveal it on his blog. He will lose.)

Yesterday's departmental seminar was very impressive. Alex has a nice story to tell about targeting mRNA to the endoplasmic reticulum. He has also discovered an unusual pathway for exporting certain mRNAs from the nucleus. This pathway seems to be specific for those mRNAs that encode secreted proteins.

I think everyone in the department was impressed. Maybe he'll be my colleague next year.


Alex Meets Toronto Bloggers

 
Alex Palazzo of The Daily Transcript met with Eva Amsen of easternblot, John Dupuis of Confessions of a Science Librarian, and Phillip Johnson of Biocurious.

Eva posted photos and a description of what they talked about [Science Bloggers].


Friday the 13th in Port Dover

 
It's Friday the 13th and the bikers are gathering in Port Dover. This year they're hoping to set a new Guinness record for the most bikes (>10,000).




Friday the 13th

 
Friday's Urban Legend: FALSE

[reposted from April 13, 2007]

Having a morbid fear of Friday the 13th—paraskevidekatriaphobics—is one of the most widespread superstitious beliefs in western industrialized nations. Believe it or not, there are many people who refuse to leave their house on Friday the 13th because they fear that bad luck will befall them if they venture outside. (Apparently, the bad luck doesn't find them in their homes.)

Personally, I like the attitude of the "eccentric" (rational?) men in the photo.
Members of the Eccentric Club of London at their annual Friday the 13th lunch in 1936 – surrounded by objects that are connected with superstitions. Picture: Getty Images [Unlucky roots of Friday the 13th].
There is no evidence to support the irrational fear of Friday the 13th, with the single exception of a study published 14 years ago in the British Medical Journal [Is Friday the 13th bad for your health?]. That study showed an increase in accidents on Friday the 13th compared to Friday the 6th.

According to scholars, the fear of Friday the 13th is a recent invention. There is no mention of it before 1900 [Why Friday the 13th Is Unlucky]. It seems that people simply combined a fear of the number 13—triskaidekaphobia—with an obscure dead of Fridays. Nobody knows for sure why the number 13 is considered unlucky but there are several popular myths. The most common are a Norse myth about having 13 people at dinner and a Christian myth about the Last Supper.

There is no significant historical record documenting a widespread irrational fear of Fridays although there are plenty of minor examples of Friday avoidance. Some people thought it was bad luck to be married on a Friday or to set sail on a ship. In Christian cultures the day is associated with the fact that Jesus was crucified on a Friday and Friday is the day that Adam was tempted by Eve to eat the forbidden fruit.


Thursday, June 12, 2008

Tangled Bank #107

 
The latest issue of Tangled Bank is #107. It's hosted at Syaffolee [Tangled Bank #107: The CYOA Edition].
You're trapped on a cruise ship in the South Pacific, bored out of your mind. The swimming pool holds no appeal. Gambling is pointless because the advantage is on the house. The books you brought with you have long been finished. You've even resorted to registering for a cha-cha class to relieve your ennui. But that's no fun, because the instructor is always yelling at you for having two left feet.

Then on a Wednesday morning, the ship docks on a small island. Travelers are allowed to go on land for the day. You debark and after wandering past the marketplace filled with locals hawking loud jewelry and ceremonial masks (probably manufactured in Taiwan), you find yourself in a small clearing with several paths meandering off into the undergrowth. There's a sign nearby saying:

"Welcome to the one hundred and seventh edition of Tangled Bank."

At the foot of the sign is a machete.

If you want to submit an article to Tangled Bank send an email message to host@tangledbank.net. Be sure to include the words "Tangled Bank" in the subject line. Remember that this carnival only accepts one submission per week from each blogger. For some of you that's going to be a serious problem. You have to pick your best article on biology.

Religulous

 
Coming to theaters near you in October [Religulous].




[Hat Tip: Brian Larnder at Primordial Blog]

Graduation

 
With 72,000 students, you can appreciate that graduation ceremonies need to be spread out over several weeks at the University of Toronto. At this time of year we have graduations every day and sometimes twice a day.

Today it was the turn of St. Michael's College. It was such a beautiful day that I couldn't resist taking a picture of the graduating class as they walked across the front campus to Simcoe Hall. There were about 500 students in this line.

How many of you went to your graduation? I did.


Charles McVety Visits the ROM

 
I was taking Bryant Ing1 to lunch today when we decided to check out what was happening at the Royal Ontario Museum. There was supposed to be a big anti-racism rally led by "Dr." Charles McVety. He's the man who claims that Charles Darwin was a racist [Canadian Creationist: Charles McVety].

Here he is (left) speaking to his supporters right in front of the museum where the Charles Darwin exhibit is housed. One of his supporters handed us a leaflet explaining why Darwin was a racist. (I'm sure you all know the quotes and I'm sure you all know that Darwin was very enlightened for a man of his time.)

We didn't stay long. McVety was going on about the title of Darwin's famous book. He was making the point that the book is about the preservation of favoured races.2 There were at least three or four people nodding their heads in agreement.

Toronto's finest were there in full riot gear to keep the huge crowd under control. You can see from the photo that they were very suspicious of Bryant and me. Some of them seem to be reaching for their weapons. You can click on the photo to see a larger version where their facial expression tells all.

The last photograph (below) is a view of the entire crowd. I figure there were about ten McVety sycophants supporters present and about ten passers-by who were curious about what was going on. There were almost as many reporters and camera crews. It was a non-event. We went to the Faculty Club for a nice lunch. Mmmmmm, fish and chips!




1. Winner of Monday's Molecule #66.

2. The actual title is On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life.

Canadian Creationist: Charles McVety

 
"Dr."1 Charles McVety is President of Canada Christian College in Toronto.

McVety is currently promoting the movie Expelled in Canada. He claims that it exposes the racism behind "Darwinism" as well as revealing how universities repress academic freedom by firing creationists.

I presume that Canada's Christian College is one of the last bastions of academic freedom where academics are allowed to say and think whatever they believe without fear of reprisal or dismissal. I assume this must be true because McVety feels so strongly about the importance of academic freedom. Evolutionists must be welcome at McVety's college.

The protection of academic freedom is probably behind this statement from the Canada Christian College website on college standards ...
Canada Christian College strives to maintain a distinctly Christian living and learning environment conducive to a rigorous study of God’s Word. Membership in Canada Christian College is obtained through application and invitation. Those who accept an invitation to join the College agree to uphold its standards of conduct. In return, they gain the privilege of enjoying the benefits of college membership and undertake to work for the best interests of the whole community (Phil. 2:4).

Compliance with these standards is simply one aspect of a larger commitment by students, staff, and faculty to live as responsible citizens, to pursue biblical holiness, and to follow an ethic of mutual support, Christian love in relationships, and to serve the best interests of each other and the entire community. Individuals who are invited to become members of this community but cannot with integrity pledge to uphold the application of these standards are advised not to accept the invitation and to seek instead a living-learning situation more acceptable to them.
In an effort to be much more respectful of creationists, no matter how stupid they might be, I will refrain from calling them names, like IDiot. This posting adheres to this new policy. I hope it pleases my atheist friends who favor accommodation.

Larry Moran
Surprising as it might seem, there are some people who don't like Charles McVety and his activities. A recent posting from Kady O'Malley on Macleans.ca blogs isn't all that complimentary [The opposite of YPF?]. (Macleans is a Canadian newsmagazine similar to Time and Newsweek.)
Perhaps he was inspired by the turnout for Young People Fucking, or maybe he misses all that media attention he got after taking credit for getting C-10 through the House with nary a peep over the controversial changes to the film tax rebate. Whatever the reason, Reverend Charles McVety is headed back to the capital to co-host a private screening of a very different kind of film: Expelled: The Movie, the controversial anti-Darwin documentary that purports to expose a sinister anti-creationism bias within the mainstream scientific community.

Interestingly, in his come-one-come-all invite to the film - which was forwarded to all MPs and staffers via parliamentary email by Conservative MP Maurice Vellacott - McVety doesn’t even mention the religious aspect of the debate; instead, he accuses Darwin of “overt racism”, and calls on Canadians to “blot out out this terrible scourge in our society.”
McVety and his friend(s) are holding an anti-racism rally today at 12:30 outside the Darwin exhibit at the Royal Ontario Museum, Toronto. You'd better get there early if you want to be at the front of the crowd where you can touch the great man. I assume traffic on Bloor Street will be tied up for hours.

Canadian Cynic might be there. (Warning! If you follow the link to Canadian Cynic you might be disappointed 'cause Canadian Cynic doesn't adhere to my new policy of accommodating accommodationists. Neither does PZ Myers who uses a rude word in referring to McVety and his somewhat misleading interpretation of Charles Darwin.


1. Here's a description of Charles McVety's degree Degree or Not Degree?.