Chromosomes, Drift, and Demes

One of the characteristics of evolution is change in chromosome number and organization. These large-scale changes are often associated with speciation events although it would be a mistake to assume that there's a causal relationship.

One particular chromosomal rearrangement has been getting a lot of press recently because it has been featured on blogs and in some recent trade books on evolution.

Humans (H) have only 23 pairs of chromosomes while most other apes, such as the chimpanzee (C), have 24 pairs. Evidence for a fusion of two of these ancestral chromosomes into a single chromosome 2 in humans has been well supported by genome sequence data. Our fusion chromosome contains remnants of telomeres at the fusion point and it has another centromere-like region at just the right position.

Intelligent design proponents have a hard time explaining this event. They don't propose an explanation based on their concept of intelligent design—that would be too ridiculous—instead they concentrate on raising questions about evolutionary explanations. One of the common objections is that the new fusion chromosome would screw up mitosis and meiosis because it would initially have two centromeres. According to them, the chromosomal rearrangement would be detrimental and could never be fixed by natural selection.

As it turns out, the latter part of this statement is correct. Natural selection is not responsible for this kind of evolution. But no serious scientist would suggest otherwise.

The first part of the statement isn't as serious as the IDiots would like to think. Rearrangements of this sort aren't much of a problem. Many species are heterozygous for such rearrangements and we can see that it has little effect on the viability of dividing cells. Nevertheless, a newly rearranged chromosome is unlikely to be completely neutral. It's probably slightly deleterious with respect to the ancestral chromosome(s).

So, how does a slightly deleterious mutation become fixed in a population? The answer, of course, is random genetic drift. But in order to understand the importance of random genetic drift you have to understand the substructure of species. Species are usually subdivided into many smaller, locally inbreeding, populations or "demes." Slightly deleterious (nearly neutral) mutations can easily become fixed in a deme by accident.

Over at Panda's Thumb, Dave Wisker Arthur Hunt has been writing about chromosomal rearrangements and how they become fixed in a species. His latest essay talks about how fixation within a deme can lead to fixation by random genetic drift in the entire population: The Rise of Human Chromosome 2: Beyond the Deme.

This is a nice, short, explanation of a very important mechanism of evolution. I urge everyone to get on over to Panda's Thumb and read it right now.

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[Image Credit: This drawing is from: Chromosome Fusion: Chance or Design?. I don't know the original source.

The Old Cavendish Laboratory: Maxwell to Watson & Crick

 
For scientists, some places are more "holy" than others. Here's the story of one such place. "The moral of the story is that 'place matters'."

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How Granting Agencies Destroy Young Scientists

 
Peter Lawrence has an article in the latest issue of PLoS Biology: Real Lives and White Lies in the Funding of Scientific Research.

He's not saying anything we don't already know but he says it so well. Peter describes the typical example of a young researcher (K.) who is frustrated and discouraged by the way science is funded in the UK. The details may differ but it's the same basic story at universities in North America and everywhere else.

He then describes his own experience and highlights the problem.

After more than 40 years of full-time research in developmental biology and genetics, I wrote my first grant and showed it to those experienced in grantsmanship. They advised me my application would not succeed. I had explained that we didn't know what experiments might deliver, and had acknowledged the technical problems that beset research and the possibility that competitors might solve problems before we did. My advisors said these admissions made the project look precarious and would sink the application. I was counselled to produce a detailed, but straightforward, program that seemed realistic—no matter if it were science fiction. I had not mentioned any direct application of our work: we were told a plausible application should be found or created. I was also advised not to put our very best ideas into the application as it would be seen by competitors—it would be safer to keep those ideas secret.

The peculiar demands of our granting system have favoured an upper class of skilled scientists who know how to raise money for a big group [3]. They have mastered a glass bead game that rewards not only quality and honesty, but also salesmanship and networking. A large group is the secret because applications are currently judged in a way that makes it almost immaterial how many of that group fail, so long as two or three do well. Data from these successful underlings can be cleverly packaged to produce a flow of papers—essential to generate an overlapping portfolio of grants to avoid gaps in funding.

Thus, large groups can appear effective even when they are neither efficient nor innovative. Also, large groups breed a surplus of PhD students and postdocs that flood the market; many boost the careers of their supervisors while their own plans to continue in research are doomed from the outset. The system also helps larger groups outcompete smaller groups, like those headed by younger scientists such as K. It is no wonder that the average age of grant recipients continues to rise [4]. Even worse, sustained success is most likely when risky and original topics are avoided and projects tailored to fit prevailing fashions—a fact that sticks a knife into the back of true research [5]. As Sydney Brenner has said, “Innovation comes only from an assault on the unknown” [6].

You know, what's really puzzling about this phenomenon is not that we are unaware of the problem—it's that we haven't done anything about it. If the system isn't working then let's fix it.

There are several innovations that could fix the problem. Peter suggests that only the best papers from a lab should be evaluated and that young investigators could be interviewed by the granting agencies to evaluate promise. Others suggest that funds could be given to departments and the departments could distribute the money in the most efficient and effective manor.

Many scientists advocate shorter grant proposals with more of an emphasis on past productivity than on what's in the actual proposal. If you've been successful in the past then you will probably be successful in the future. It's time to stop rewarding grantsmanship and start rewarding science.

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Hawks on Campus

 
It's probably just a coincidence but now that students have returned from their summer break there are more and more reports of hawks flying over the main open space on campus just outside my office. I seen them (it?) as well.

The latest issue of the University of Toronto eBulletin has a photo of a red tailed hawk—one of the regular visitors. Darryl Chow took the picture.

Does this explain the noticeable lack of doves on campus? I haven't seen any significant gathering of doves for many years. It used to be a regular occurrence on university campuses.

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Evolution and "Modern" Religion

 
Karen Armstrong, a former Roman Catholic nun, was asked to write an article about evolution for The Wall Street Journal. They also asked a scientist [Man vs. God]

We commissioned Karen Armstrong and Richard Dawkins to respond independently to the question "Where does evolution leave God?" Neither knew what the other would say. Here are the results.

Most us have heard what Dawkins has to say, so let's concentrate on Karen Armstrong's defense of religion in the light of modern science. She starts off with ...

Richard Dawkins has been right all along, of course—at least in one important respect. Evolution has indeed dealt a blow to the idea of a benign creator, literally conceived. It tells us that there is no Intelligence controlling the cosmos, and that life itself is the result of a blind process of natural selection, in which innumerable species failed to survive. The fossil record reveals a natural history of pain, death and racial extinction, so if there was a divine plan, it was cruel, callously prodigal and wasteful. Human beings were not the pinnacle of a purposeful creation; like everything else, they evolved by trial and error and God had no direct hand in their making. No wonder so many fundamentalist Christians find their faith shaken to the core.

That seems to be the inescapable conclusion. Religious people who want to accept science have no choice but to fall back on a wishy-washy kind of religion where God plays no direct role and life has no purpose.

What kind of religion is that? Well, you'll have to read the rest of her article in order to appreciate the kind of mental gymnastics required to "evolve" a "modern" religion that doesn't conflict with science. Here's a taste ...

The best theology is a spiritual exercise, akin to poetry. Religion is not an exact science but a kind of art form that, like music or painting, introduces us to a mode of knowledge that is different from the purely rational and which cannot easily be put into words. At its best, it holds us in an attitude of wonder, which is, perhaps, not unlike the awe that Mr. Dawkins experiences—and has helped me to appreciate —when he contemplates the marvels of natural selection.

This is typical of so-called "modern" and "sophisticated" theology. It's so "sophisticated," in fact, that the only people who understand it are those who practice it. Those people are completely incapable of explaining their version of spiritualism and mysticism to the rest of us because it's a very personal feeling. It's that feeling you get when you appreciate natural beauty or the awesome knowledge that comes from science.

Problem is, Richard Dawkins also has that feeling, and so do I. If the "God" feeling is indistinguishable from that of atheists then what's the point? Why not just cut out the middle man?

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[Photo Credit: Reuters]

It seems like I'm not the only one who recognizes a vacuum when I see one.

Jerry Coyne: Dawkins 17, Armstrong 0

PZ Myers: Saving gods by making them even emptier of meaning

Richard Dawkins Speaks About Evolution

 
During last week's class I asked my students if they had heard of Richard Dawkins. Very few hands were raised.

Here's a recent video of Dawkins speaking about evolution and his latest book, The Greatest Show on Earth—Evidence for Evolution. I leave it as an exercise to identify those ideas of Dawkins where there is legitimate scientific controversy. (The course is about controversies and misconceptions.)

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[Hat Tip: RichardDawkins.net

Monday's Molecule #136

 
Today's "molecule" is an easy one in celebration of the start of a new academic year for many university students. Name this structure and provide a very brief description of it's function.

The Nobel Laureate should be obvious.

The first person to describe the "molecule" and name the Nobel Laureate wins a free lunch. Previous winners are ineligible for six weeks from the time they first won the prize.

There are only three ineligible candidates for this week's reward: Markus-Frederik Bohn of the Lehrstuhl für Biotechnik in Erlangen, Germany, Maria Altshuler of the University of Toronto, and Philip Johnson of the University of Toronto.

I have an extra free lunch for a deserving undergraduate so I'm going to continue to award an additional prize to the first undergraduate student who can accept it. Please indicate in your email message whether you are an undergraduate and whether you can make it for lunch.

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(s) and names the Nobel Laureate(s). Note that I'm not going to repeat Nobel Prizes 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.

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

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No Creation in America

 
According to the Telegraph: Charles Darwin film 'too controversial for religious America'.

Creation, starring Paul Bettany, details Darwin's "struggle between faith and reason" as he wrote On The Origin of Species. It depicts him as a man who loses faith in God following the death of his beloved 10-year-old daughter, Annie.

The film was chosen to open the Toronto Film Festival and has its British premiere on Sunday. It has been sold in almost every territory around the world, from Australia to Scandinavia.

However, US distributors have resolutely passed on a film which will prove hugely divisive in a country where, according to a Gallup poll conducted in February, only 39 per cent of Americans believe in the theory of evolution.

Movieguide.org, an influential site which reviews films from a Christian perspective, described Darwin as the father of eugenics and denounced him as "a racist, a bigot and an 1800s naturalist whose legacy is mass murder". His "half-baked theory" directly influenced Adolf Hitler and led to "atrocities, crimes against humanity, cloning and genetic engineering", the site stated.

I didn't see the film on Thursday evening when the Toronto film festival opened but it got favorable reviews and lots of press in the local newspapers. Creation looks like a very good movie. It's a shame that it won't be seen in America.

UPDATE: It may have been a tempest in a teapot or (gasp!) a publicity ploy. Latest word is that there's a bidding war going on for distribution rights in the USA. It will soon be coming to a theater near you ... or maybe not so near.

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The Good People of Halifax

 
The second part of this posting is a re-post from two years ago to commemorate September 11, 2001. Before getting to it, let's remember another connection between September 11, 2001 and Stephen Jay Gould. His last essay in This View of Life—his regular column in Natural History—was published in January 2001. The title of the essay was "I Have Landed." Those are the words his grandfather wrote on September 11, 1901 when he arrived at Ellis Island, exactly one hundred years before September 11th became one of the most famous dates in American history.

Mike Dunford posted excerpts from a Stephen Jay Gould essay Apple Brown Betty [9-11]. This is another connection. It brings us to the third, and more direct, influence of 9/11 on Gould.

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I hope you'll forgive my Canadian chauvinism on this occasion as I post parts of another Stephen Jay Gould essay [The Good People of Halifax].

My latest visit among you, however, was entirely involuntary and maximally stressful. I live in lower Manhattan, just one mile from the burial ground of the Twin Towers. As they fell victim to evil and insanity on Tuesday, September 11, during the morning after my 60th birthday, my wife and I, en route from Milan to New York, flew over the Titanic’s resting place and then followed the route of her recovered dead to Halifax. We sat on the tarmac for 8 hours, and eventually proceeded to the cots of Dartmouth’s sports complex, then upgraded to the adjacent Holiday Inn. On Friday, at 3 o’clock in the morning, Alitalia brought us back to the airport, only to inform us that their plane would return to Milan. We rented one of the last two cars available and drove, with an intense mixture of grief and relief, back home.

.......

I know that the people of Halifax have, by long tradition and practice, shown heroism and self-sacrifice at moments of disaster -- occasional situations that all people of seafaring ancestry must face. I know that you received and buried the drowned victims of the Titanic in 1912, lost one in ten of your own people in the Halifax Explosion of 1917, and gathered in the remains of the recent Swissair disaster.

But, in a sense that may seem paradoxical at first, you outdid yourselves this time because you responded immediately, unanimously, unstintingly, and with all conceivable goodness, when no real danger, but merely fear and substantial inconvenience, dogged your refugees for a few days. Our lives did not depend upon you, but you gave us everything nonetheless. We, 9000 strong, are forever in your debt, and all humanity glows in the light of your unselfish goodness.

And so my wife and I drove back home, past the Magnetic Hill of Moncton (now a theme park in this different age), past the reversing rapids of Saint John, visible from the highway, through the border crossing at Calais (yes, I know, as in Alice, not as in ballet), and down to a cloud of dust and smoke enveloping a mountain of rubble, once a building and now a tomb for 5000 people. But you have given me hope that the ties of our common humanity will bind even these wounds. And so Canada, although you are not my home or native land, we will always share this bond of your unstinting hospitality to people who descended upon you as frightened strangers from the skies, and received nothing but solace and solidarity in your embrace of goodness. So Canada, because we beat as one heart, from Evangeline in Louisiana to the intrepid Mr. Sukanen of Moose Jaw, I will stand on guard for thee.

Some of us can watch the movie Diverted on television this evening. It's about the response of the people of Gander, Newfoundland when 38 planeloads of people landed at their airport on September 11, 2001 following the closure of American airspace.

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CFI CANADA CONFERENCE: LEADERSHIP (DAY 1) + THE INTERSECTION OF ART & SCIENCE (DAY 2 & 3)

 

The Centre for Inquiry Canada is excited to announce our first national conference. It will take place in Toronto from October 29 to November 1 at the University of Toronto and at the Centre for Inquiry in downtown Toronto.

Starts
Thursday, October 29th 2009 at 5:00 pm

Ends
Sunday, November 1st 2009 at 12:00 pm

CLICK HERE TO SKIP TO REGISTRATION

There are two parts to this conference. On Friday, October 30, there will be a one day Leadership & Organizational conference for representatives and leaders of all CFI affiliated student groups, Communities for Inquiry and city organizations.

On Saturday, October 31 and Sunday, November 1, there will be an educational conference, featuring the theme "Art and Science: Freethought at the Intersection of Two Worlds." Leading thinkers will explore a wide range of topics. Art exhibits, special entertainment and musical presentations, as well as catered meals, will be included.

TAREK FATAH TO GIVE KEYNOTE PUBLIC ADDRESS
Friday, October 30, 2009, 7:00pm

Tarek Fatah is a secular Muslim Canadian political activist, writer and TV host. He is the author of "Chasing a Mirage: The Tragic Illusion of an Islamic State," which suggests that the idea of an Islamic state is merely a mirage that Muslims have been made to chase for over a millennium. The book was short listed for the prestigious Donner Book Prize. Tarek Fatah has joined CFRB 1010 as a co-host of the radio station's 3PM daily show. Fatah is the founder of the Muslim Canadian Congress.

Fatah's advocacy for a separation of religion and state, opposition to Sharia law, and advocacy for a liberal, progressive form of Islam have been met with considerable criticism from various Canadian Muslim groups. The Muslim Canadian Congress has been a longtime supporter and ally of the Centre for Inquiry.

Our Art & Science Conference will feature discussion panels and talks on subjects including:

Science & Art Panel
We will explore the awe and wonder of science. Can art be turned into a science? Can science be turned into an art? Where does art and science come together, where do they depart

Art, Prehistory & Evolution
Why was there a sudden explosion in late stone age art? How is art appreciated by the human mind/aesthetics of art? Why is art appreciated, from an evolutionary, aesthetics and neuroscience perspective

Atheism, Skepticism & Philosophy
We will explore the philosophical school o fscientific naturalism, the impact of atheism on 20th century philosophy, the origins of postmodernist philosophy in skepticism/atheism and its effects on art today.

Science & Ethics Panel
We will explore ethical decision making in science research and the ethics of choosing among competing lifestyles

PLUS: AN ART EXHIBIT "ART INSPIRED BY SCIENCE" WITH PRESENTATIONS BY SELECT EXHIBITORS

Confirmed speakers include:

Christopher DiCarlo, who will Chair the Panel "Art, Prehistory & Evolution"

Ontario's Best Lecturer 2008 and Canada's Humanist of the Year 2008, Christopher diCarlo is a Philosopher of Science and Ethics whose interests in cognitive evolution have taken him into the natural and social sciences. His personal research focuses on how and why humans reason, think, and act the way they do. He is interested in how and why the human brain has evolved to its current state and what cross-cultural and cross-species behaviour can provide insight into universally common modes of reasoning. He is also interested in the application of neuroscience (specifically fMRI work), in an effort to better understand psychoneuroendocrine feedback looping in problem solving. Dr. diCarlo is currently an Assistant Professor at the University of Ontario Institute of Technology where he teaches Critical Thinking, Bioethics, and other courses. His most recent book (just released by McGraw-Hill Ryerson) is entitled: How to Become a Really Good Pain in the Ass: A Practical Guide to Thinking Critically. He is also a past Visiting Research Scholar at Harvard University in the Department of Anthropology and the Peabody Museum of Archaeology and Ethnology where he conducted research for two books he is currently writing called: The Comparative Brain: The Evolution of Human Reasoning and The Evolution of Religion: Why Many Need to Believe in Deities, Demons, and the Unseen.

James Robert Brown, who will speak on the panel "Atheism, Skepticism & Philosophy Panel"

Fellow of the Royal Society of Canada and experienced debater in defense of scientific realism, Professor Brown appeared on TVO's The Agenda on their programs on Science and Religion, and Assault on Science. He is a Professor of philosophy at the University of Toronto.

Guillaume Loignon, who will speak on the topic "Is Art an Evolutionary Adaptation"

Spokesperson from the Ontario Science Centre on the important topic of "Selling Science to the Public"

LEADERSHIP & ORGANIZATIONAL CONFERENCE

Designed for representatives of CFI affiliated group and projects across Canada, and other special guests, this conference will run from the evening of Thursday, October 29 to the end of Friday, October 30.

The conference will feature an exciting panel on Canadian political issues to be run by various representatives from the new Canadian Secular Alliance. After hearing reports on well researched and analyzed policy positions, delegates will be invited to contribute to a discussion on building a coordinated national lobbying effort to approach critical issues:

• Secularism and Science Education, with Mike Evans
• Tax exemptions for religious charities, with Greg Oliver
• Public Financing of Religious Schools, with Mike Evans

Mike Evans is an M.A. student in philosophy at York University and an aspiring teacher. He joined the CSA in June 2009 and is currently a spokesperson and Policy Advisor with the organization. In his work at York, he puts a particular emphasis on science and its importance in society. As a teacher, he is commited to promoting a widespread culture of science and reason. Outside of his studies and his work with the CSA, Mike is a piano teacher, science educator, and musician.

• Religious Accommodation, with Michael DeDourek
• Free Expression, with Justin Trottier
• Heritage Issues (God in the national anthem, God in the Charter), with Leslie Rosenblood

Leslie Rosenblood has a Bachelor of Mathematics degree in Computer Science with a minor in Drama and Speech Communication from the University of Waterloo, and a Masters of Business Administration for Science and Technology from Queen's University. He has held diverse roles in his career, including programmer, technology researcher, market analyst, journalist, and national sales manager. Born and raised in Canada, Leslie has lived in several countries, including Japan, England, the United States, Albania, and Kazakhstan. He is currently an IT project manager at a major Canadian retailer. Leslie lives in Toronto with his wife and two sons.

Plus, student leaders will address issues affecting science, secularism and skepticism on campus:

• Violations of church-state separation at university (eg. Campus graduation prayers)
• Student unions and censorship
Student newspaper and the treatment (or lack thereof) of science
• Alternative medicine endorsing campus programs
• Working with faith groups on campus - multifaith dialogues, multifaith centres, chaplaincies

We will also host sessions on a variety of topics, to be presented by CFI leaders in cities like Vancouver, Saskatoon, Montreal, Toronto, Ottawa, Halifax, Calgary and elsewhere! If you are interested in addressing any of the issues below, or any we may have missed, please contact jtrottier@centerforinquiry.net

• The road to a CFI branch in your city, featuring Kendra Getty, who leads the high successful new CFI Saskatoon/Saskatoon Freethinkers. Listening to Point of Inquiry podcasts motivated Kendra to start community and campus groups in Saskatoon when she moved back in 2008 after several years living in Sweden, Taiwan, and Vancouver. Kendra is particularly interested in issues related to the public understanding of science and to religion in different cultures. Kendra holds degrees in Chemistry and Sociology and currently works in private industry. Kendra started the Saskatoon Freethinkers along with George Williamson in November of 2008.
• Launching your own Multimedia projects, featuring presentations from leaders of freethought themed radio shows, podcasts and even Canada's first freethought TV show.
• Press & Activism: Tips from Toronto, CFI's most media covered branch
• Public Relations & Outreach
• How to give a kick-ass interview
• How to raise money
• How to promote your groups and its activities
• General group organizing
• How to attract members
• Forging campus/community partnerships

To open both conferences, on Thursday and Friday evenings, introductory remarks will be made and a toast led by representatives of CFI Canada's Board of Directors & Advisory Fellows, including:

Carol Parow, President of the Board of CFI Canada

Dr. Carol M. Parlow is a clinical psychiatrist, a fellow of the Royal College of Physicians and Surgeons of Canada, a psychiatric consultant on occupational health and disability to businesses and a member of the Advisory Board of the Centre for Inquiry Canada.

Jeffrey Rosenthal, Advisory Fellow

Jeffrey Rosenthal is a professor in the Department of Statistics at the University of Toronto.For his research, he was awarded the 2006 CRM-SSC Prize, and also the 2007 COPSS Presidents' Award, the most prestigious honour bestowed by the Committee of Presidents of Statistical Societies. For his lecturing, he received a Harvard University Teaching Award in 1991, and an Arts and Science Outstanding Teaching Award at the University of Toronto in 1998. Rosenthal's book for the general public, Struck by Lightning: The Curious World of Probabilities, was a bestseller in Canada, and is being published in a total of fifteen countries. He has also worked as a computer game programmer, musician, and improvisational comedy performer. He maintains the web site probability.ca. Despite being born on Friday the thirteenth, Rosenthal has been a very fortunate person.

Gordon Precious, Advisory Fellow

Preliminary Schedule:

Thursday, October 29: LEADERSHIP & ORGANIZATIONAL CONFERENCE
Registration and check in (starting at 2pm)
Opening round table

Friday, October 30: LEADERSHIP & ORGANIZATIONAL CONFERENCE
Sessions
Evening: Public Keynote Lecture (TBA)

Saturday, October 31: ARTS & SCIENCE CONFERENCE
Sessions
Art Inspired by Science exhibit
Halloween Party & Awards Banquet

Sunday, November 1: ARTS & SCIENCE CONFERENCE
Final sessions (ends at 12 noon)

Lodgings:The following is a small sample of accommodations available in downtown Toronto, with some diversity for cost and quality

* Holiday Inn: 111 Lombard Street - (416) 367-5555‎
* Delta Chelsea Hotel: 33 Gerrard Street West‎ - (416) 595-1975‎
* Days Inn: 30 Carlton Street - (416) 977-6655‎
* Metropolitan Hotel: 108 Chestnut Street - (416) 977-5000‎
* Sutton Place Grande Hotel: 955 Bay Street‎ - (416) 924-9221‎
* Bond Place Hotel: 65 Dundas Street East‎ - (416) 362-6061‎

Transportation:The conference is held in the University of Toronto and at the Centre for Inquiry Ontario. CFI is located at 216 Beverley St., just south of College St. at St. George St.

Registration: Students $99.00, Non-students $115.00, CFI Members $79.00
 

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Get Two Jobs in Toronto

 

DEPARTMENT OF IMMUNOLOGY TWO TENURE STREAM POSITIONS

The Department of Immunology, University of Toronto invites applications for two tenure‐stream positions. The appointments will be at the rank of Assistant Professor and will begin on September 1st 2010, or a mutually agreed date.

As part of a continuing program to build on strength in Immunology, the University of Toronto is recruiting for two tenure track positions, one of which will be in the field of Human Immunology. The successful candidates will be expected to mount an original, competitive and independently funded research program and to have a commitment to undergraduate, medical and graduate education in Immunology.

Outstanding applicants working in any area of Immunology complementary to our existing faculty will be considered, with the expectation that one of the positions will be in Human Immunology. Candidates must have a Ph.D. or equivalent degree, postdoctoral experience, and an established record of research excellence. The appointments are expected to be at the Assistant Professor level with a salary commensurate with qualifications and experience. The positions will be located in newly renovated space in the Medical Sciences Building on the downtown campus of the University of Toronto.

For details about the Department of Immunology see www.immunology.utoronto.ca and to apply online, please visit http://www.jobs.utoronto.ca/faculty.htm (see Ad # 0900694 under Faculty positions). Applications should be submitted by November 6th, 2009 and include a curriculum vitae, bibliography, an outline of current and future research objectives and the names and addresses of three referees.

The University of Toronto is strongly committed to diversity within its community and especially welcomes applications from visible minority group members, women, Aboriginal persons, persons with disabilities, members of sexual minority groups and others who may further contribute to the diversification of ideas.

All qualified applicants are encouraged to apply; however, Canadians and permanent residents will be given priority.

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Get a Job in Toronto

 

DEPARTMENT OF MOLECULAR GENETICS
UNIVERSITY OF TORONTO
Applications are invited for a Tenure-Stream Position in Developmental Biology

The Department of Molecular Genetics at the University of Toronto invites applications for a tenure-stream appointment in developmental biology. The appointment at the rank of Assistant or Associate Professor, will commence on or after July 1, 2010, and will be located in the Medical Sciences Building on the downtown campus of the University of Toronto.

We seek candidates whose research addresses a fundamental problem in animal developmental biology using either established (mouse, frog, fish, fly, nematode worm, sea urchin, tunicate, etc.) or up-and-coming (stickleback, cnidarian, planarian, arthropod, choanoflagellate, etc.) models. The successful candidate will complement and enhance the Department’s existing strengths in developmental biology, model organism genetics, and other areas.

The Department is one of the premier academic life sciences departments in Canada, with 90 full-time faculty members and 300 graduate students (Molecular Genetics). The candidate will benefit from the interdepartmental Collaborative Graduate Program in Developmental Biology as well as from recent efforts at the University of Toronto and affiliated teaching hospitals to expand research in stem cell biology; cell, tissue and whole-animal imaging; proteomics, genomics and bioinformatics through new infrastructure and academic programs. Candidates must have a Ph.D. degree or equivalent, postdoctoral experience, and an established record of research accomplishment. The successful candidate will be expected to mount an original, competitive, and independently funded research program, and to have a commitment to undergraduate and graduate education.

We encourage you to submit your application online (Jobs: faculty). Please ensure that you include a Curriculum vitae that includes current and long-term research objectives. If you are unable to apply online (or alternatively have large document to send), please submit your application and other materials to: Dr. Howard Lipshitz, Chair, Department of Molecular Genetics, University of Toronto, 1 King’s College Circle, Rm. 4286, Toronto, Ontario M5S 1A8 Canada. Applicants should also arrange that three letters of reference be sent directly to Dr. Lipshitz, or have them emailed to mogen.chair@utoronto.ca Applications and referee letters will be accepted until November 15, 2009 or until the position is filled.

The University of Toronto offers the opportunity to teach conduct research and live in one of the most diverse cities in the world. The University is strongly committed to diversity within its community and especially welcomes applications from visible minority group members, women, Aboriginal persons, persons with disabilities, members of sexual minority groups, and others who may contribute to further diversification of ideas.

All qualified candidates are encouraged to apply; however, Canadians and permanent residents of Canada will be given priority.

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The Last Universal Common Ancestor

 
Jeffrey Wong is a former member of our Department¹ and the author of the best theory on the origin of the genetic code [see: Amino Acids and the Racemization "Problem"]

LUCA, LECA and LBACA--Root of Life and Roots of the Biological Domains

Dr. Jeffrey Wong
Department of Biochemistry
Hong Kong University of Science and Technology

4:30 pm, September 10
Medical Sciences Building room 4171

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His mother's photograph is on the wall of graduates on the first floor of our building. She graduated from medical school in 1929.

The Most Expensive Health Care System in the World

 
The USA has the most expensive health care system in the world. They're number 1 by a long shot.

But does the USA have the "best" health care system in the world? Is it going to change?

Change doesn't look promising. Apparently it's a lot easier to make up campaign slogans about change than it is to actually deliver.

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[Hat Tip: Genomicron]

Monday's Molecule #135: Winner!

 
Yesterday's molecule was the type II reaction center from the photosynthetic purple bacterium Rhodobacter spaeroides.

When light shines on the special pair of chlorophyll molecules known as P870, a single electron is boosted to a high energy level by absorbing a photon. This electron is transferred to an adjacent bacteriochlorophyll a heme group in a typical oxidation reaction. The single electron then travels down the electron transport pathway to a bacteriopheophytin heme and then to a quinone molecule that's part of the pathway.

In the final step, the electron reduces another quinone bound to the "mobile" site. This reduction is mediated by an iron atom (red ball). Quinol (QH₂) is released after two electrons have been transferred sequentially. The quinol molecule carrying two electrons then diffuses to a cytochrome bc complex that pumps protons across the membrane. The creation of a proton gradient drives the synthesis of ATP.

The electron deficient P870 chlorophylls are re-supplied with electrons from cytochrome c, which gets them from the chytorchrome bc complex in a cyclic reaction [see A Simple Version of Photosynthesis].

Purple bacteria are strict anaerobes—oxygen is poisonous to them so their The purple bacteria version of photosynthesis does not involve the splitting of water and generation of O₂. This is an important point since many students think that water (H₂O) is the only possible electron donor in photosynthesis. In fact, the ability to oxidize water evolved much later.

It's much better to think of photosynthesis as a light-activated oxidation-reduction system where there are several possible electron donors and acceptors.

The type II reaction center molecules are embedded in a membrane-spanning protein complex whose structure has been solved [see Nobel Laureates: Deisenhofer, Huber, and Michel]. In the version shown here, the electron donor is cytochrome c, which binds to the top part of the molecule on the exterior surface of the membrane.

Photosynthesis is a complex example of an electron transfer reaction. Rudolph A. Marcus was awarded a Nobel Prize for his work on understanding this type of chemical reaction.

This week's winner is Philip Johnson of the University of Toronto. He blogs at Biocurious. While Philip was the first to get the right answer, an honorable mention has to go to Wibowo Arindrarto from Jakata, Indonesia for the best answer.

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Your task for today is to identify the molecules with the question marks and explain (briefly) what's going on.

There's a Nobel Prize associated with the type of reaction that you're seeing here. Focus on the red arrows. The prize wasn't for this particular reaction although it is depicted in the Nobel Lecture as an example of the type of reaction that was being described. Name the Nobel Laureate.

The first person to describe the reaction and name the Nobel Laureate wins a free lunch. Previous winners are ineligible for six weeks from the time they first won the prize.

There are only three ineligible candidates for this week's reward: Alex Ling of the University of Toronto, and Markus-Frederik Bohn of the Lehrstuhl für Biotechnik in Erlangen, Germany, and Maria Altshuler of the University of Toronto

I have an extra free lunch for a deserving undergraduate so I'm going to continue to award an additional prize to the first undergraduate student who can accept it. Please indicate in your email message whether you are an undergraduate and whether you can make it for lunch.

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(s) and names the Nobel Laureate(s). Note that I'm not going to repeat Nobel Prizes 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.

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

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