Get a Job in Newfoundland

 

Memorial University of Newfoundland
Tenure-track Positions in Gene Expression and Metabolic Biochemistry
The Department of Biochemistry at Memorial University invites applications for two tenure-track positions at the level of Assistant Professor, one in each of the targeted areas listed below. Applicants should have a PhD or equivalent degree with a minimum of two years post-doctoral research experience and should possess a strong research record with significant future promise. The successful applicants will be expected to develop externally funded research programmes with relevance to one of the research foci of the department: 1) Development and health, and 2) Membranes and molecular interactions. They will also be expected to show a commitment to effective teaching at the undergraduate and graduate levels. The new faculty members will be encouraged to collaborate with the faculty in the department and elsewhere in the university.

1) Gene Expression (ref # VPA-BIOC-2008-001). The successful applicant for this position will be expected to develop a research programme focused on some area of gene regulation such as, but not limited to, transcriptional regulation by DNA-protein interactions, chromatin structure/remodeling, or gene expression profiling.

2) Metabolic Biochemistry (ref # VPA-BIOC-2008-002). The successful applicant will be expected to develop a research programme focused on some area of metabolic biochemistry such as, but not limited to, metabolomics, gene-nutrient interactions, or metabolic regulation including signaling pathways.

Applicants should submit a curriculum vitae, a summary of past research, a statement of proposed research and reprints of 3 publications. The application must be accompanied by the names, affiliations and contact information of three referees.

Memorial University is the largest university in Atlantic Canada offering diverse undergraduate, graduate and medical school programmes to almost 18,000 students. As the Province’s only university, Memorial plays an integral role in the educational and cultural life of the Province of Newfoundland and Labrador. The Biochemistry Department consists of 18 faculty with expertise in a wide range of biochemical areas. For information about the Department of Biochemistry please see the departmental webpage. St. John’s is a safe, friendly city with great historic charm, a vibrant cultural life, affordable housing and easy access to a wide range of outdoor activities. For more information about St. John’s please see the municipal website.

Memorial University is committed to employment equity and encourages applications from qualified women and men, visible minorities, aboriginal people and persons with disabilities. All qualified candidates are encouraged to apply; however, Canadian Citizens and Permanent Residents will be given priority. Partners of candidates for positions are invited to include their resumes for possible matching with other job opportunities.

Applications should be received by the Department of Biochemistry by May 15, 2009.

Applications should be addressed to: Dr. Martin Mulligan, Head, Department of Biochemistry, Memorial University, St. John’s, NL, Canada, A1B 3X9. Applications may also be submitted electronically to biochead@mun.ca or by fax: (709) 737-2422. Please quote the appropriate job reference number on all correspondence.

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Happy Vernal Equinox!

 
Today at 11:44 UT (= 7:44 AM Eastern Time) the sun appeared to cross the celestial equator in its northward movement. (See Movement of Our Star for the real explanation.)

Most people in the Northern Hemisphere think of this as the first day of Spring. I prefer to think of it as the end of Winter. Springlike days are still a few weeks off in Toronto.

Here's a brief explanation from Wikipedia.

An equinox in astronomy is the moment in time (not a whole day) when the centre of the Sun can be observed to be directly above the Earth's equator, occurring around March 20 and September 23 each year.

More technically, at an equinox, the Sun is at one of two opposite points on the celestial sphere where the celestial equator (i.e., declination 0) and ecliptic intersect. These points of intersection are called equinoctial points—the vernal point and the autumnal point. By extension, the term equinox may be used to denote an equinoctial point.

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[Photo Credit: The photograph shows the position of the sun at various times throughout the year at 12h (UT) over the Temple of Aphaia (490-480 BC), Athens (Anthony AYIOMAMITIS). The image is called the solar analemma. See here for an explanation. The celestial equator is perpendicular to the long axis of the image and half way between the top and bottom. The crossover point of the figure eight depends on your distance from the equator. I'd love to see one taken on the equator or in the southern hemisphere.]

[Image Credit: eSky]

"Science is my job - faith is my rock"

 
"Science is my job - faith is my rock" is the title of an article in today's Globe and Mail. Zosia Bielski is a journalist who writes on a wide range of topics with an emphasis on social issues. She was prompted to write about the conflict between science and religion because of the controversy surrounding Canada's Science Minister, Gary Goodyear.

As usual, there's no mention of the fact that most active scientists are non-religious. The proportion of atheist scientists is much higher than the proportion of atheists in the general public. Apparently this fact has little to do with a conflict between science and religion.

Zosia Bielski takes the standard approach to this issue. She interviews three religious scientists and discovers that they can reconcile their faith and science. What a surprise!

She does not interview anyone who thinks there's a serious conflict between science and religion. If she had written an article about the lack of faith among scientists and had only interviewed atheist scientists, she would have been accused (rightly) of biased journalism. The lack of balance would have been recognized by any competent editor and she would have been told to go out and get statements from religious scientists. It seems like "balance" only works one way.

What's interesting about the article is that she interview Rev. Ambury Stuart, a climatologist who is also a United Church minister. What Stuart has to say about the conflict between science and religion is very interesting.

"I struggled with this all my life. I grew up in the United Church, I always attended. You say, 'Well, can you believe in God if you believe in Newton's laws?' And the short answer is yes, you can, but it takes a while," Mr. Stuart said.

"You have to think through a lot of stuff. It's not simplistic. You try and divide your brain into two bits: One bit you'll use on Sunday and the rest of it you'll use the rest of the week, and it doesn't work. It doesn't have to."

Evolutionary evangelist Michael Dowd's book "Thank God For Evolution" helped Mr. Stuart smooth out his own message at Glebe Road United Church in Toronto. He weaves his scientific passions into his sermons.

"You can look at scripture and say this means a whole lot more than we ever thought it meant before, because it applies to everything," Mr. Stuart said. "The idea that we are related, that we are kin with the rest of life, is essential for Christianity to do anything constructive in the ecological crisis."

This is about as honest as you get. Stuart is telling us that the conflict between religion and science is real and challenging. You have to work really hard at reconciling science and religion. Many religious beliefs don't survive the challenge.

That's an important lesson for people like Gary Goodyear. Any religion that denies evolution is incompatible with science. You have to choose one or the other. You can't be a Young Earth Creationist without being anti-science. If that kind of faith is your "rock" then science can't be your job.

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Nobel Laureate: Willard Libby

 

The Nobel Prize in Chemistry 1960.

"for his method to use carbon-14 for age determination in archaeology, geology, geophysics, and other branches of science"


Willard Frank Libby (1908 - 1980) won the Nobel Prize in Chemistry for using ¹⁴C decay to date organic material. Libby set out to study cosmic rays. He, and others, determined that one of the effects of cosmic ray is to produce carbon-14 atoms from nitrogen-14 atoms in the upper atmosphere.

He determined that the rate of production of carbon-14 and its rate of disintegration (half-life ~5600 years¹) has reached an equilibrium. No matter where you find carbon, in the ocean, the atmosphere, or the biosphere, its radioactivity corresponds to about 14 disintegrations per minute per gram.

Living things incorporate this equilibrium mixture of ¹⁴C and ¹²C. Thus, we, like all other living things, are radioactive and this level of radioactivity can be measured using techniques that Willard Libby developed. When living things die, they stop incorporating carbon and the existing ¹⁴C continues to decay. As time goes on, the level of radioactivity declines with a half-life of ~5600 years. The age of organic material can be determined directly by measuring the remaining radioactivity of extracted carbon.

That's the basis of radiocarbon dating. Libby confirmed the feasibility of the technique by dating Egyptian artifacts, tree rings of known age, and the dead sea scrolls (labeled "Bible" in the figure). The results confirmed that radiocarbon dating works.


The results were published in the late 1940's. Since then, the technology has improved considerably. Today, scientists measure ¹⁴C directly using mass spectrometry so they don't have to wait for it to decay. Detailed calibration curves have been worked out to take account of the fact that cosmic ray intensity has varied somewhat over the past few thousand years.

With current technology, reliable dates back as far as 60,000 years can be obtained. This is about the limit of radiocarbon dating because the half-life of Carbon-14 is so short compared to more long-lived isotopes.

The presentation speech highlights the importance of radiocarbon dating in a number of disciplines.
THEME:
Nobel Laureates

Libby's dating method soon attracted attention from the scientific world, and it was not long before carbon-14 laboratories were set up in many countries. Today, some forty institutions carry on investigations in this field, nearly half of them in America. Also here, in Sweden, we have such institutions, and their investigations have given results of great value. All age determinations - nowadays several thousand every year - are published in a general review, and thus made rapidly available throughout the world. The literature in this field has grown from year to year, and at present covers an impressive area.

One of the scientists who suggested Libby as a candidate for the Nobel Prize has characterized his work in the following way: "Seldom has a single discovery in chemistry had such an impact on the thinking in so many fields of human endeavour. Seldom has a single discovery generated such wide public interest".

Professor Libby. The idea you had 13 years ago of trying to determine the age of biological materials by measuring their carbon-14 activity was a brilliant impulse. Thanks to your great experimental skill, acquired during many years devoted to the study of weakly radioactive substances, you have succeeded in developing a method that is indispensible for research work in many fields and in many institutes throughout the world. Archaeologists, geologists, geophysicists, and other scientists are greatly indebted to you for the valuable support you have given them in their work. The Swedish Academy of Sciences desires to join those who offer you grateful thanks for what you have done for the benefit of so many sciences, and has decided to award you this year's Nobel Prize for Chemistry. May I congratulate you on behalf of the Academy, and ask you to receive the prize from the hands of His Majesty the King.

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1. The modern value is 5730±40 years.

[Photo Credit: University of California History Digital Archives, Copyright © 2006 The Regents of the University of California.]

The images of the Nobel Prize medals are registered trademarks of the Nobel Foundation (© The Nobel Foundation). They are used here, with permission, for educational purposes only.

Science Journalism in Decline

 
There's an editorial in Nature this week on science journalism [Filling the Void]. It's not very interesting.

There's an article by Geoff Brumfiel that's much more interesting [Science journalism: Supplanting the old media?]. Since I'm mentioned in that article, and since I can't comment on their site, I thought I'd make a few comments here.

First, I posted a comment on Chris Mooney's blog where I said, "Most of what passes for science journalism is so bad we will be better of without it." What I meant to say was, "Most of what passes for science journalism is so bad we will be better off without it". I just want there to be a correct version that everyone can quote.

The article correctly points to a trend ...

Traditional journalists are increasingly looking to such sites to find story ideas (see 'Rise of the blogs'). At the same time, they rely heavily on the public-relations departments of scientific organizations. As newspapers employ fewer people with science-writing backgrounds, these press offices are employing more. Whether directly or indirectly, scientists and the institutions at which they work are having more influence than ever over what the public reads about their work.

Over the past decade it has been the "professional" science journalists themselves who were the gullible victims of scientific hype and PR. The scientific accuracy of press releases leaves a great deal to be desired. They are, after all, intended to promote the researcher and the institution. They are heavily biased.

It is not a good thing that individual scientists and their institutions are managing the science news. It's a disaster.

The amount of material being made available to the public by scientists and their institutions means that "from the pure standpoint of communicating science to the general public, we're in a kind of golden age", says Robert Lee Hotz, a science journalist for The Wall Street Journal. But that pure standpoint is not, or should not be, all that there is to media coverage of science. Hotz doubts that blogs can fulfil the additional roles of watchdog and critic that the traditional media at their best aim to fulfil. That sort of work seems to be on its way out. "Independent science coverage is not just endangered, it's dying," he says.

I hear this a lot. Science journalists seem to think that they have served as watchdogs and science critics by tempering the hype and propaganda spewed out by institutional PR departments.

I wish it were true. If science journalists really did their job of separating the wheat from the chaff then I would be their biggest cheerleader. Instead, for the most part they have been completely seduced by the lure of scientific breakthroughs and revolutions promoted by self-serving scientists and their institutions. There are notable exceptions, but the majority of science journalists have failed at the one job they are supposed to do better than non-science journalists.

That's why we would be better off without them.

Coincidentally, Ryan Gregory has just posted an article about Scitable, "A Collaborative Learning Space for Science" hosted by Nature magazine. I'm pretty sure that Nature is proud of this site. They think the articles are good examples of science writing.

Ryan highlights an article by Leslie Pray, a free-lance science writer. The title is: Transposons, or Jumping Genes: Not Junk DNA?. Read what Ryan Gregory has to say at Scitable Again. He thinks the article is "total nonsense." I agree with him.

If this is an indication of the ability of science journalists to cut to the chase and give us the straight dope, then it's no wonder that scientists are skeptical.

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Regulatin' Genes

 
Some of us old fuddy-duddies have been learning about the regulation of transcription for over forty years. When you've been teaching about regulatory proteins, like HOX proteins, for twenty-five years, the novelty sort of wears off.

It's fun to see the enthusiasm of students who have just recently been "turned on" by gene regulation, especially when one of them is also a Toronto Blue Jays fan! Strange that the university looks a lot more like Stanford than the University of Toronto [HumBio instructor, students rap about science on YouTube].

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Time to Change the Channel

 
My local Liberal candidate is Omar Alghabra, who lost the last election to one of Harper's Conservatives. Omar sent me a link to this video. He though I might get a kick out of it.

I did.

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Don't Leave Canada Behind

 
This is a letter sent to Prime Minister Stephen Harper and Leader of the Opposition Michael Ignatieff. It is signed by hundreds of Canadian scientists. I don't expect it to have any effect on Harper but it will be interesting to see if the Liberal Party decides to support science.

March 16, 2009

The Right Honourable Stephen Harper Prime Minister of Canada The Right Honourable Michael Ignatieff, Leader of the Opposition Ottawa

Subject: Don't leave Canada behind

Dear Prime Minister, Dear Leader of the Opposition

U.S. President Barack Obama is taking advantage of the current financial crisis to push his country forward in new directions by greatly boosting funding to scientific research and education as a means to jump start innovation in a new economy. The scope of his vision is stunning, including an increase of more than $15 billion in scientific research, and a promise to double the funding for education in the next 10 years. For more details, see http://www.sciencedebate2008.com.

Our government has also tried to stimulate the research / university sector in Canada, wishing to take important initiatives. At the heart of the plan is a $2 billion dollars infrastructure fund for shovel-ready renovation projects in post-secondary institutions, a fund that was actively solicited by university presidents. There is also an additional $750 million for the Canadian Foundation for Innovation (CFI), and $87.5 million over three years for doctoral scholarships. While these funding announcements are surely welcome, we would like to share our concerns as to the potential effect of some of these decisions, in particular in view of the bold and visionary course taken by the Obama administration south of the border.

1. When the U.S. government is proposing to boost the funding of the National Science Foundation (NSF) by 40% ($3 billion on top of its current $6.9 billion), we see Canada’s "stimulus budget" cutting NSERC's by 5%. When the U.S. administration is proposing to boost the funding of the National Institute of Health (NIH) by 30% ($8.5 billion in addition to its current $29 billion), our "stimulus budget" is cutting CIHR's by 5%, while essentially ignoring the needs of Genome Canada. When US researchers are being actively approached for ideas to use the stimulus money to think big and to hire and retain their researchers, their Canadian counterparts are now scrambling to identify budget cuts for their Labs, while worrying about the future of their graduating students. Recent Tri-council grants competitions, which were post stimulus budget, are already pointing towards sharply lower success rates (by more than 20% in some disciplines), lower start-up grants for young researchers, and negligible research funding for smaller institutions and provinces. These cuts are huge steps backward for Canadian Science and we ask the government to immediately develop a multi-year plan to significantly increase this country’s R&D investment through our granting councils.

2. The infrastructure support for Canada's post-secondary institutions is surely beneficial for their depleted budgets for deferred maintenance. However, the federal support requires 50% in matching funds which few institutions currently have. The net effect of this decision will be to dictate priorities for universities and provincial governments too eager to get the federal funds, and as such to divert further funds from teaching, training and research. We therefore ask government to drop the requirement of matching funds.

3. The CFI has provided a tremendous boost to certain aspects of Canada's research infrastructure over the last 10 years. However, the constraints of the program have left many important research disciplines out of its potential beneficial impact. Moreover, similar matching rules continue to apply to CFI projects, and as a consequence of the present lack of available support from the private sector and from provincial governments, even some of the already approved projects are being postponed and cancelled. At this point in time, we believe that removing the matching requirements for current and future CFI projects would be extremely beneficial for Canada and its research infrastructure.

4. The funding of an additional 500 doctoral scholarships is great news for a country that is committed to have ``the best educated, most skilled and most flexible workforce in the world". However, it seems this funding is coming at the expense of the highly qualified personnel (HQP’s) that could have been recruited more efficiently by our senior researchers through their Tri-Council grants. We believe that a more efficient strategy for ensuring a successful HQP policy is to give our leading researchers the flexibility to manage the selection, recruitment, and support of their own graduate students through their peer-reviewed research grants, and via well-established leveraging procedures with the universities and the private sector. We also regret that the $17.5-million assigned to SSHRC for graduate scholarships have been earmarked towards students in business and finance. As Alain Dubuc writes in La Presse: ``En boudant certains domaines de recherche, nos universités vont perdre leur pouvoir d'attraction. Et bien des jeunes talentueux iront ailleurs.
(See http://www.cyberpresse.ca/)

5. President Obama is proposing to double federal funding for education over the next 10 years, and pledging to “restore science to its rightful place” with billions in new investments. To advise his government, he has appointed leading scientists to his cabinet and as his advisors (including a Nobel laureate as energy Secretary). The Obama administration has also involved the directors of NIH and NSF in federal budget discussions about the future of research. We need a similar approach in Canada, where top research scientists and humanists can help shape directions in Ottawa for research funding.

A new economy is coming out of this crisis and research and development will be the lifeblood to that new economy. We call upon you not to let Canada be left behind.

Sincerely,

Margaret Ann Armour, Chemistry, Order of Canada (University of Alberta) Tom Archibald, Chair of Mathematics (Simon Fraser University) Alejandro Adem, Mathematics (University of British Columbia) Tom Allison (University of British Columbia) Ali Arya, Information Technology (Carleton University) Peter Abrams, Ecology and Evolutionary Biology (University of Toronto) Jim Arthur, Mathematics (University of Toronto) Marshall Agueh, Mathematics (University of Victoria) John Beamish, Chair, Physics (University of Alberta) Edward Bierstone, Mathematics (University of Toronto) Yaacov Ben-David, Biophysics (University of Toronto) Herman Brunner, Mathematics (Memorial University) Margaret Beattie, Mathematics (Mount Allison University) Peter Borwein, Mathematics (Simon Fraser University) Anne Bourlioux, Mathematics (Universite de Montreal) Hans U. Boden, Chair, Math and Statistics (McMaster University) David Brydges, Mathematics (University of British Columbia) Martin Barlow, Mathematics (University of British Columbia) Michael Bennett, Mathematics (University of British Columbia) Kai Behrendt, Mathematics (University of British Columbia) Mark Bauer (University of Calgary) Vijay Bhargava, Electrical Engineering (University of British Columbia) Hichem Ben-El-Mechaiekh,Chair, Mathematics (Brock University) Sydney Bulman-Fleming, Chair, Mathematics (Wilfred Laurier University) Sandra Barr, Acting Head, Earth and Environmental Science (Acadia University) W. Kendal Bushe, Mechanical Engineering (University of British Columbia) Sherryl Bisgrove, Biological Sciences (Simon Fraser University) Mary Berbee, Botany, (University of British Columbia) Jeff Babb, Chair, Mathematics and Statistics (University of Winnipeg) Maxim R. Burke, Chair, Mathematics and Statistics (University of PEI) Susan Baldwin (University of British Columbia) Chris Bose, Mathematics (University of Victoria) Patrick Brosnan, Mathematics (University of British Columbia) Michelle Boue (Trent University) John Bowman, Mathematics (University of Alberta) Walter Craig, Mathematics (McMaster University) John Carter, Applied Science and Engineering (University of Toronto) Rustum Choksi, Mathematics (Simon Fraser University) Dan Coombs, Mathematics (University of British Columbia) Clifton Cunningham, Mathematics (University of Calgary) Mohamed Cheriet, Engineering (École de technologie supérieure, Montreal) Marilyn Chapman (University of British Columbia) Eric Cytrynbaum, Mathematics (University of British Columbia) Jingyi Chen, Mathematics (University of British Columbia) K. Carriere Cough, Statistics, (University of Alberta) Richard Craster, Mathematics (University of Alberta) Vladimir Chernousov, Mathematics (University of Alberta) James Colliander, Mathematics (University of Toronto) Christina C. Christara, Computer Science (University of Toronto) John Clague, Earth Sciences (Simon Fraser University) Laura Cowen, Mathematics (University of Victoria) Paul Deguire directeur, mathématiques et de statistique (Université de Moncton) Karl Dilcher, Chair, Math. and Stats. (Dalhousie) Lawrence M. Dill (Simon Fraser University) Henri Darmon, Mathematics (McGill University) Rob DeWreede, Botany, (University of British Columbia) Gregory Dudek, Chair, Computer Science (McGill University) Dan Dumont, Director, Molecular and Cellular Biology (University of Toronto) David Dunlop, Physics (University of Toronto) Ivar Ekeland, Math Economics (University of British Columbia) George Elliott, Mathematics (University of Toronto) Kadriye Ercikan, Education (University of British Columbia) Yousry Elsabrouty (The University of Calgary) Neil Emery, Director, Environmental & Life Sciences (Trent University) Roderick Edwards (University of Victoria) Ian Frigaard, Math and Mech. Engineering (University of British Columbia) Don Fraser, Statistics (University of Toronto) Richard Froese, Mathematics (University of British Columbia) Don Fisher (University of British Columbia) Eugene Fiume, Computer Science (University of Toronto) John Friedlander, Mathematics (University of Toronto) Jorge Filmus, Molecular and Cellular Biology (University of Toronto) Nassif Ghoussoub, Mathematics (University of British Columbia) Randy Goebel, Computing Science (University of Alberta) Dan Gibson, Earth Sciences (Simon Fraser University) Andrew Granville, Mathematics (Universite de Montreal) Pengfei Guan, Mathematics (McGill University) Ling Guan, Electrical Engineering (Ryerson) Sean Graham, Botany (University of British Columbia) Dmitri Goussev (Gusev), Chair, Chemistry (Wilfrid Laurier University) Stephen Gustafson, Mathematics (University of British Columbia) Terry Gannon, Mathematics (University of Alberta) Veronique Godin, Mathematics (University of Calgary) J. Scott Goble, Education (University of British Columbia) Charles Gale, Chair, Physics (McGill University) Ed Grant, Head,Chemistry (University of British Columbia) Ian Graham, Mathematics (University of Toronto) Jacques Hurtubise, Chair, Mathematics & Statistics (McGill University) Hedley David, Medecine (University of Toronto) Viqar Husain, Chair, Mathematics (U.New Brunswick) Stephen B. Heard Chair, Biology (University of New Brunswick, Fredericton) François Huard, Head, Mathematics (Bishop's University) Nicola J Hodges, School of Human Kinetics (University of British Columbia) Felix Herrmann, Earth and Ocean Science (University of British Columbia) Dr. Holger Hintelmann, Chair, Department of Chemistry (Trent University) Craig Heinke, Physics (University of Alberta) Anita Hubley, Education (The University of British Columbia) Alexander Holroyd, Mathematics (University of British Columbia) Reinhard Illner, Mathematics (University of Victoria) Victor Ivrii, Mathematics (University of Toronto) Andrew Irvine (University of British Columbia) Slim Ibrahim (University of Victoria) Sebastian Jaimungal, Statistics (University of Toronto) Lisa Jeffrey, Mathematics (University of Toronto) Daniel James, Physics (University of Toronto) Robert Jerrard, Mathematics (University of Toronto) Rachel Kuske, Head, Mathematics (University of British Columbia) Young-June Kim, Physics (University of Toronto) Young-Heon Kim, Mathematics (University of British Columbia) Niky Kamran, Mathematics (McGill University) Kalpdrum Passi, Chair, Mathematics & Computer Science (Laurentian University) Boualem Khouider, Mathematics ( University of Victoria) Kalle Karu, Mathematics (University of British Columbia) Maria Klawe, Computer Science (President of Harvey Mudd) Patrick Keeling, Botany, (University of British Columbia) Jennifer Klenz, Botany, (University of British Columbia) Leslie R. Kerr, Biology/Psychology (Trent University) Faqir Khanna, Physics (University of Alberta) Don Krug, Education (University of British Columbia) Raymond Kapral, Chemistry (University of Toronto) Anthony Lau, Mathematics (University of Alberta) Robert K. Logan, Physics (University of Toronto) Michael Lamoureux, Mathematics (University of Calgary) Yue Xian Li, Mathematics (University of British Columbia) Victor Leung, Electrical Engineering (University of British Columbia) Victor G. LeBlanc, Directeur, Chair, Mathematics (University of Ottawa) Wenyuan Liao (University of Calgary) Mark Lewis, Mathematics (University of Alberta) James Lewis, Mathematics (University of Alberta) Aaron Levin (University of Alberta) Alexander Litvak, Mathematics (University of Alberta) Paul Lasko, Chair, Biology (McGill University) Sheldon Lin, Statistics (University of Toronto) Hoi-Kwong Lo, Electrical and Computer Engineering (University of Toronto) Wendy Lou, Biostatistics (University of Toronto) Ben Liang, Electrical and Computer Engineering (University of Toronto) Bill Langford, Mathematics (Guelph University) Marcelo Laca (University of Victoria) Alan Mackworth, Computer Science (University of British Columbia) Bojan Mohar, Mathematics (Simon Fraser University) Richard G. Miller, Biophysics and Immunology (University of Toronto) Greg Martin, Mathematics (University of British Columbia) Robert McCann, Mathematics (University of Toronto) Franklin Mendivil (Acadia University) Akos Magyar, Mathematics (University of British Columbia) Brian Marcus, Mathematics (University of British Columbia) Barrie McCullough (University of British Columbia, Okanagan) Robert Moody, Mathematics (University of Alberta) Patrick Martone, Botany, (University of British Columbia) Peter Minev, Mathematics (University of Alberta) Amy Metcalfe, Education (University of British Columbia) Jim Mattsson (Simon Fraser University) Bill Milsom, Head, Zoology (University of British Columbia) Eckhard Meinrenken, Mathematics (University of Toronto) Sharon Morsink, Physics (University of Alberta) Bonny Norton, Education (University of British Columbia) Raymond Ng, Computer sc. (University of British Columbia) Adrian Nachman, Electrical and Computer Engineering (University of Toronto) Carl Ollivier-Gooch, P.Eng. (University of British Columbia) Fergal O'Hagan (Trent University) Peter Ottensmeyer, Medical Biophysics (University of Toronto) Don Page, Physics (University of Alberta) Anthony Peirce, Mathematics (University of British Columbia),Ed Perkins, Mathematics (University of British Columbia), Marion Porath (University of British Columbia) Roger Pierre, Directeur, Mathematiques et de statistique (Universite Laval) Cindy Prescott, Forestry (University of British Columbia) Arturo Pianzola, Mathematics (University of Alberta) Royann Petrell (University of British Columbia) Peter Pivovarov (University of Alberta) Daniel D. Pratt, Education (University of British Columbia) Erich Poppitz, Physics (University of Toronto) Ue-Li Pen, Astrophysics (University of Toronto) Toniann Pitassi, Computer Science (University of Toronto) Ian Putnam, Mathematics (University of Victoria) Jeremy Quastel, Mathematics and Statistics (University of Toronto) Christiane Rousseau (Universite de Montreal) David J. Rowe, Physics (University of Toronto) Andrew Rechnitzer, Mathematics (University of British Columbia) Cristian Rios, Mathematics (University of Calgary) Chris Radford, Head Mathematics and Statistics (Memorial University) Loren Rieseberg, Botany (University of British Columbia), Dale Rolfsen, Mathematics (University of British Columbia), Reinhard Jetter, Botany (University of British Columbia) Volker Runde, Mathematics (University of Alberta) Omar Rivasplata (University of Alberta) Peter C. Ruben, Director Kinesiology (Simon Fraser University) Steven Rogak, Mech. Eng. (University of British Columbia) Jeffrey Rosenthal, Mathematics (University of Toronto) Jonathan Rose, Chair of Electrical and Computer Engineering (University of Toronto) Nancy Reid, Statistics (University of Toronto) Joe Repka, Mathematics (University of Toronto) William Reed, Mathematics (University of Victoria) Gordon Slade, Mathematics (University of British Columbia) Stephen Strother, Medical Biophysics (University of Toronto) Gordon Semenoff, Physics (University of British Columbia) Mohamad Sawan, Engineering (Polytechnique, University of Montreal) Viena Stastna (University of Calgary) Fred Sack, Head of Botany (University of British Columbia) Paul Stephenson, Head, Mathematics and Statistics (Acadia University) Raj Srinivasan, Chair, Mathematics (University of Saskatchewan),Brian Seymour, Mathematics (University of British Columbia),Anne Scholefield, Education (University of British Columbia) Jedrzej Sniatycki, Mathematics (University of Calgary) K D Srivastava, Engineering (University of British Columbia) Philip Stamp, Physics (University of British Columbia) Dominik Schoetzau, Mathematics (University of British Columbia) Paul L. Smith, Head, Earth and Ocean Sciences (University of British Columbia) Sudarshan Sehgal, Mathematics (University of Alberta) Catherine Sulem, Mathematics (University of Toronto) Theodore Shepherd, Physics (University of Toronto) Vuk Stambolic, Medical Biophysics (University of Toronto) Nicole Tomczak-Jaegermann (University of Alberta) Peter Tiidus, Acting Dean, Science (Wilfrid Laurier University) Phillippe Tortell, Botany, (University of British Columbia) John R. Topic (Trent University) Elisabeth Tillier, Genomics (University of Toronto) Tai-Peng Tsai, Mathematics (University of British Columbia) Derek J. Thorkelson, Chair, Earth Sciences (Simon Fraser University) Mak Trifkovic (University of Victoria) Bill Unruh, Physics (University of British Columbia) Jennifer A. Vadeboncoeur, Education (University of British Columbia) Stephanie van Willigenburg, , Mathematics (University of British Columbia) Andrew Vreugdenhil, Director, Materials Science (Trent University) Frank Weichman, Physics (University of Alberta) Rabab Ward, Electrical Engineering (University of British Columbia) Brent Ward, Earth Sciences (Simon Fraser University) Michael Ward, Mathematics (University of British Columbia) Jason Waywitka (University of Alberta) Doug Wiens (University of Alberta) Eric Woolgar, Physics (University of Alberta) Tony Ware, Mathematics (University of Calgary) Shoshana Wodak, Biochemistry, and Molecular Genetics (University of Toronto) Margaret Wyeth (University of Victoria) Glyn Williams-Jones, Earth Sciences (Simon Fraser University) Reem Yassawi, Head, Math (Trent University) Vlad Yaskin (university of Alberta) Janet Ye, Mathematics (University of Victoria) Nora Znotinas, Chair, Physics & Computer Science (Wilfrid Laurier University) Richard Zemel, Computer Science (University of Toronto) Julie Zhou, Mathematics (University of Victoria)

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[Hat Tip: Genomicron]

John Moore Gets It Right

 
Believe it or not, there are columnists at The National Post who actually understand the issue concerning Gary Goodyear's beliefs. John Moore tells it like it is when he says, ignorance is not a civil right.

Of course it matters whether the Science Minister acknowledges or contests evolution. This isn't a case of a politician who likes to read the Bible and pray -- it's a Cabinet Minister who holds philosophical beliefs that are antithetical to his portfolio. Jonathan Kay insists Christian-hating lefties would never raise similar alarm over a Cabinet minister of another faith. Well this leftie, who holds faith in considerably high regard, would have very serious concerns about an aboriginal justice minister who declined to comment on the efficacy of Western legal systems, and would be even more up in arms if a Scientologist health minister refused to discuss mental illness. And I'm pretty sure the National Post editorial board would have some pretty pointed questions for a Muslim MP given the status of women portfolio.

The first problem with Goodyear is that he fronts the science portfolio in a government that has demonstrated through its most recent budget that it doesn't value the sector. The man delegated to argue the vital importance of science at the Cabinet table doesn't actually know what it is. More significantly, Goodyear's insistence that religion should come to bear on science provides comfort to those who teach their children the falsehood that to follow God you must reject science.

This is the willful dissemination of scientific illiteracy. More frankly put, it is the promotion of stupidity.

I wish I'd written that!

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Gary Goodyear "Clarifies" Some More

 
Minister of State for Science and Technology, Gary Goodyear, is being asked of clarify his position on science. Is he, or is he not, anti-science? Specifically, does he reject the scientific fact of evolution? Yesterday, newspapers reported on his wishy-washy definition of evolution. Most people concluded that he is, indeed, a creationist of the sort that rejects science.

Today's National Post documents the evolving strategy of the Conservative Party and their friends. They are trying to make this into an issue about freedom of religion rather than a simple question of scientific literacy [My beliefs not relevant: Goodyear].

In light of those responses, critics were still wondering yesterday whether someone who believes the Earth is just thousands of years old is heading Canada's science and technology sector.

Mr. Goodyear bucked at requests to clarify his point of view yesterday, cutting short a question into whether he defined evolution in the popular Darwinian sense.

"My entire background has been in science, and my personal beliefs are not important," Mr. Goodyear repeated. "What I'm doing and what the government is doing to move this country forward -- that's important."

When pressed, Mr. Goodyear added that there would be no conflict of interest for a minister heading the science and technology industry to hold a belief in creationism.

"Absolutely not. How ridiculous. It's absolutely ridiculous. That's why I didn't answer the question, because it has no relevance," he said.

Hmmm ... let's think about this for a minute. How many people think it's relevant that a Minister of Science and Technology is anti-science?

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David Asper Doesn't Get It

 
David Asper¹ writes about The Liberal War on Faith in today's issue of The National Post.

Throughout the growth of the current Conservative party, starting with the establishment of Reform, the Alliance and then the merger with the Progressive Conservatives, there has been a festering undercurrent of anti-religious bigotry in the methods of attack used by left-wing critics.

Now, we have a reporter from the Globe following the same script. The essence of the newspaper's front-page slag on Tuesday was that if you have a religious faith that includes the idea of a God who created the heavens and the earth billions of years ago, it must mean you entirely reject the evolutionary process that shaped the life forms that subsequently developed -- and are therefore unfit to be the Minister of Science and Technology.

We need to put a stop to this moving of goalposts. The issue is NOT religious faith. Nobody objects to a Minister of Science who accepts the basic tenets of science and is religious. As Asper points out in his article, it's almost certain that previous ministers of science believed in a God that created the Earth billions of years ago. They also accepted the scientific fact of evolution.

What we can't accept is a Minister of Science who is anti-science. If your religion forces you to reject fundamental facts of science in order to cling to the idea that the Earth in only 10,000 years old then that's a problem. If you believe in such nonsense then you can be a newspaper columnist—or maybe even the owner of a major newspaper—but you can't be in charge of science policy in Canada. It makes us the laughing stock of civilized nations. Even the USA is laughing at us this time, and that's saying a lot.

David Asper is trying to make this into an attack on all religious beliefs but it's not. He should be ashamed of himself for distorting the truth and avoiding the real issue.

On the other hand, anyone who writes this (below) isn't going to listen to reason.

It's also worth noting that the Charter of Rights -- created under a Liberal government --begins with an acknowledgement of the supremacy of God. Our national anthem also calls on God to keep our land glorious and free. So please, enough with the facade of outing people who believe in a higher power.

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1. David Asper is the Chairman of the National Post newspaper and Executive Vice President of CanWest Global Communications Corp. He is a former trustee of the Fraser Institute, a conservative propaganda machine that masquerades as a research institute. He is a supporter of Conservative Party candidates.

[Photo Credit: University of Toronto]

Goodyear's Bad Day

 
Here's a link to Chris Selley's article on The National Post website [Chris Selley's Full Pundit: Goodyear's bad day].

The article has links to several Canadian journalists. I'm pleased to see that many of them recognize the problem. We can't have a creationist Minister in charge of science.

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The Future of Science Blogging

 
Daniel Brown of Biochemical Soul is looking for feedback on the future of science blogging [Science Blogging: The Future of Science Communication & Why You Should be a Part of it].

Personally I don't think the science blogosphere is going to attract more than a few percent of scientists and science students. Most of them don't have the time or the interest. Most of my colleagues are completely turned off by blogs. They see blogs as a negative influence on science.

The science blogosphere is a fun and interesting playground for those of us who have eclectic interests and are willing to invest the time and effort to read a few dozen blogs a day, but that's not going to appeal to the average scientist. Daniel does a good job of listing all the benefits of blogging and reading blogs but, in my experience, none of these benefits are convincing for the average scientist.

Frankly I think that's a good thing. My experience with newsgroups over the past twenty years indicates that it's much better to have a small number of really dedicated and interested participants than to try and expand to cover everyone. Besides, the more science blogs there are out there, the most difficult it is to read them all.

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Four Solar Eclipses on Saturn

 
The inhabitants of Saturn were recently treated to four solar eclipses on the same day. In the video below you can see the four moons and their shadows crossing Saturn. The photos were taken by the Hubble Space Telescope and the video was prepared by National Geographic.

It's exciting to be living at a time when such images are quickly available to the general public. This video would have seemed like magic only a century ago. A century from now it might seem trivial since we may have our own satellites orbiting Saturn.

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Liberal Science Critic Marc Garneau Says that Believing in Evolution Is not a Job Requirement for the Science Minister

 
Marc Garneau (right) is the Liberal science critic in Canada's House of Commons. The same Globe and Mail article that mentioned Goodyear's "clarification" of his position on evolution has the following quotation from Marc Garneau [Minister clarifies stand on evolution].

On Tuesday, Liberal science critic Marc Garneau said that believing in evolution is not a job requirement for the science minister.

“It is a personal matter. It is a matter of faith.… I don't think it prevents someone from being a good minister,” said the former astronaut, who has been a vocal critic of the government for its cuts to the three granting councils that fund university-based research in Canada.

But Jim Maloway, the New Democratic Party science critic, said that if the minister did not believe in evolution that could influence government policy. “I don't see a commitment to a really broad approach if you are encumbered by the denial of evolution,” he said.

Garneau is dead wrong. If you reject evolution you are anti-science. There's no two ways about it. You cannot deny evolution without attacking the very core of scientific reasoning and evidence-based conclusions. What Garneau is saying is that it's OK for a science minister to be anti-science.

That would be like putting a witch doctor (or a chiropractor) in charge of health care, or a soothsayer in charge of finances.

There may be a place for anti-science creationists in the Federal Cabinet but not in charge of science. Acceptance of the core principles of science is a job requirement because part of the job is gaining the confidence of the scientific community. You can't have a science minister who questions the honesty and integrity of Canadian scientists. Make no mistake about it, that's exactly what creationists do.

We need a new minister of science and we need a new Liberal science critic.¹

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1. What do other scientists think about this? See Science minister's coyness on evolution worries researchers. Note that the scientists are worried about a creationist in charge of science while the non-scientists don't see it as a big problem.

Gary Goodyear "Clarifies" His Stance on Evolution

 
Today's Globe and Mail reports that Canada's Minister of State (Science and Technology) has "clarified" his position on the validity of evolution [Minister clarifies stand on evolution].

OTTAWA — Science minister Gary Goodyear now says he believes in evolution.

“Of course I do,” he told guest host Jane Taber during an appearance on the CTV program Power Play. “But it is an irrelevant question.”

....

On Tuesday, Mr. Goodyear said twice during the CTV interview that he did believe in evolution.

“We are evolving every year, every decade. That's a fact, whether it is to the intensity of the sun, whether it is to, as a chiropractor, walking on cement versus anything else, whether it is running shoes or high heels, of course we are evolving to our environment. But that's not relevant and that is why I refused to answer the question. The interview was about our science and tech strategy, which is strong.”

Those of us who have been dealing with creationists for several decades will recognize those words. That's a creationist speaking. They're willing to admit to microevolution within kinds but unwilling to admit to common descent.

Goodyear could have easily said that he accepts common descent and the idea that modern species, including humans, evolved over billions of years from more primitive organisms. That's what "believing" in evolution means to most people. He did not say that.

That pretty much settles it for me. Goodyear is a creationist. He rejects one of the fundamental concepts of biology. That makes him anti-science.

The man in charge of science in Canada is anti-science. Heaven help us.

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Monday's Molecule #112: Winners

 
UPDATE:The equation shows beta decay of ¹⁴C from Wikipedia. The Nobel Prize went to Willard Libby for developing ¹⁴C dating technology.

This week's winner is Dima Klenchin from the university of Wisconsin (again) by two minutes over Ollie Nanyes. The undergraduate winner is Alex Ling of the University of Toronto.

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You may have noticed that today's molecule isn't a molecule. Your task is to identify what this equation is describing.

There's only one Nobel Laureate whose discovery is relevant.

The first person to identify the equation and the Nobel Laureate wins a free lunch at the Faculty Club. Previous winners are ineligible for one month from the time they first won the prize.

There are six ineligible candidates for this week's reward: James Fraser of the University of California, Berkeley, Guy Plunket III from the University of Wisconsin, Deb McKay of Toronto, Maria Altshuler of the University of Toronto, David Schuller of Cornell University and Adam Santoro of the University of Toronto

A previous winner has offered to donate a free lunch to a deserving undergraduate so I'm going to continue to award an additional free lunch 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 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. I reserve the right to select multiple winners if several people get it right.

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

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Happy St. Patrick's Day!

 

Niall Nóigiallach is a very famous man (Nóigiallach is Gaelic for "having Nine Hostages"). He was an Irish King who lived from about 350 to 405 AD. The "nine hostages" refers to hostages that he kept from each of the places that owed him allegiance.

Niall was fond of raiding the coast of Roman Britain and on one of those raids he captured a man named Maewyn Succat, who became a slave in Ireland. Succat eventually escaped, returned to Britain, and became a Christian missionary. He then went back to Ireland to convert the Irish heathens to Christianity. We know Maewyn Succat by his Christian name, Patrick, or Saint Patrick.

Aside from converting the Irish heathens to Christianity, St. Patrick is famous for his skill as a magician. One of his most famous tricks was removing all the snakes from Ireland. At least that's what the legend says.

Connie Barlow describes A St. Patrick's Day Parable.(This is the same Connie Barlow I met last summer—the one who edited Evolution Extended.)

Ireland is a land of no snakes. It has no slithering serpents. There are no rat snakes in Ireland; there are no rattlesnakes; there are no garter snakes. There are no snakes at all.

The absence of snakes in Ireland seems to cry out for an explanation — but only if one regards or ventures to the island from outside: from England, say, or from continental Europe. To the indigenous Celts, there would, of course, have been nothing to explain. The Gaelic peoples no more needed to explain an absence of snakes on their island home than they needed to explain an absence of kangaroos. To those who came to Ireland from abroad, however, a dearth of serpents was a striking anomaly in need of an answer.

We humans must have answers. And so arose the legend of St. Patrick and the snakes. The reason Ireland has no snakes, the story goes, is that Patrick charmed all snakes on the island to come down to the seashore, slither into the water, and drown. So Ireland did once have snakes, but it has them no more. Patrick charmed them all into the sea.

She goes on to explain why there are no snakes in Ireland but I prefer to swtich to the website of the Smithsonian National Zoological Park for their explanation of Why Ireland Has No Snakes.

Now snakes are found in deserts, grasslands, forests, mountains, and even oceans virtually everywhere around the world. Everywhere except Ireland, New Zealand, Iceland, Greenland, and Antarctica, that is.

One thing these few snake-less parts of the world have in common is that they are surrounded by water. New Zealand, for instance, split off from Australia and Asia before snakes ever evolved. So far, no serpent has successfully migrated across the open ocean to a new terrestrial home. As the world's oceans have risen and fallen over the millennia, land bridges have come and gone between Ireland, other parts of Great Britain, and the European mainland, allowing animals and early humans to cross. However, any snake that may have slithered it's way to Ireland would have turned into a popsicle when the ice ages hit.

The most recent ice age began about three million years ago and continues into the present. Between warm periods like the current climate, glaciers have advanced and retreated more than 20 times, often completely blanketing Ireland with ice. Snakes, being cold-blooded animals, simply aren't able to survive in areas where the ground is frozen year round. Ireland thawed out for the last time only 15,000 years ago. Since then, 12 miles of icy-cold water in the Northern Channel have separated Ireland from neighboring Scotland, which does harbor a few species of snakes. There are no snakes in Ireland for the simple reason that they can't get there.

[The book cover is from a book by Sheila MacGill Callahan (Author) and Will Hillenbrand (Illustrator). You can buy it on Amazon.com.]

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Reposted from St. Patrick Banished Snakes from Ireland with a snippet from Niall Nóigiallach - Niall of the Nine Hostages. You find out how Irish I am by clicking here.

You Can Be Good Without God

 
I spotted this ad at the Queen's Park subway station in Toronto.

Kudos to the Humanist Association of Canada.

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NSERC President Praises Gary Goodyear

 
Gary Goodyear is Canada's Minister of State (Science and Technology). His government has just cut funding of basic research grants by $148 million over the next three years. Gary Goodyear is a chiropractor and he may be a creationist.

So, what does the President of NSERC think of this? See the [press release].

OTTAWA — Prime Minister Stephen Harper ventured into the lion's den Monday, defending his government's record on science funding before some of the country's top researchers.

He emerged without a scratch.

Indeed, he actually basked in praise for Gary Goodyear, his minister of state for science and technology.

Goodyear has been much maligned by some scientists who maintain research was shortchanged in the Jan. 27 federal budget. But there was no criticism Monday at an awards ceremony for the winners of prestigious research prizes handed out by the federally funded Natural Sciences and Engineering Research Council.

"It has been a real pleasure for us to work with the Hon. Gary Goodyear," said NSERC president Suzanne Fortier.

"He has already proven himself a champion of the science and technology community."

I know some people who would disagree with Suzanne Fortier. Two representatives of the Canadian Association of University Teachers (CAUT) didn't have such a favorable impression [When Chiropractors Get Angry ....].

Some people would argue that. as a kind of public servant, the President of NSERC should not criticize government policy. Perhaps, but that doesn't mean she has to suck up to the executioner.

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[Photo Credit: NSERC]

Does Canada's Science Minister Accept Evolution?

You might think that's a silly question. How could anyone in Canada become Minister of State (Science and Technology) and not accept the most important scientific fact in biology? Yes, it's true that Gary Goodyear is a chiropractor but he can't also be a creationist, can he?

Apparently he can, according to The Globe and Mail [Minister won't confirm belief in evolution].

Researchers aghast that key figure in funding controversy invokes religion in science discussion

Canada's science minister, the man at the centre of the controversy over federal funding cuts to researchers, won't say if he believes in evolution.

“I'm not going to answer that question. I am a Christian, and I don't think anybody asking a question about my religion is appropriate,” Gary Goodyear, the federal Minister of State for Science and Technology, said in an interview with The Globe and Mail.

A funding crunch, exacerbated by cuts in the January budget, has left many senior researchers across the county scrambling to find the money to continue their experiments.

Some have expressed concern that Mr. Goodyear, a chiropractor from Cambridge, Ont., is suspicious of science, perhaps because he is a creationist.

We are in far worse trouble than I thought. No wonder the Stephen Harper party is cutting back on basic research. They must think most researchers are really stupid for believing in all those silly theories like evolution.

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Monday's Molecule #112

 
You may have noticed that today's molecule isn't a molecule. Your task is to identify what this equation is describing.

There's only one Nobel Laureate whose discovery is relevant.

The first person to identify the equation and the Nobel Laureate wins a free lunch at the Faculty Club. Previous winners are ineligible for one month from the time they first won the prize.

There are six ineligible candidates for this week's reward: James Fraser of the University of California, Berkeley, Guy Plunket III from the University of Wisconsin, Deb McKay of Toronto, Maria Altshuler of the University of Toronto, David Schuller of Cornell University and Adam Santoro of the University of Toronto

A previous winner has offered to donate a free lunch to a deserving undergraduate so I'm going to continue to award an additional free lunch 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 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. I reserve the right to select multiple winners if several people get it right.

Comments will be blocked for 24 hours.

---

Casey Luskin on Junk DNA and Junk RNA

 
Intelligent Design Creationists can't abide junk DNA. Its very existence refutes the idea that living things are designed by some intelligent being. This is why the IDiots go out of their way to make up stories "disproving" junk DNA.

The latest attempt is by Casey Luskin [Nature Paper Shows "Junk-RNA" Going the Same Direction as "Junk-DNA"]. Having failed to explain why half of the human genome is composed of defective transposons, he now pins his hope on the idea that most of the genome is transcribed. Luskin seems particularly upset by my statement that most of these transcripts are junk [Junk RNA].

Luskin thinks that a recent paper in Nature supports his view that a large fraction of the genome isn't junk. The paper by Guttman et al. (2009) says no such thing. Here's the important part ...

Genomic projects over the past decade have used shotgun sequencing and microarray hybridization1, 2, 3, 4 to obtain evidence for many thousands of additional non-coding transcripts in mammals. Although the number of transcripts has grown, so too have the doubts as to whether most are biologically functional5, 6, 13. The main concern was raised by the observation that most of the intergenic transcripts show little to no evolutionary conservation5, 13. Strictly speaking, the absence of evolutionary conservation cannot prove the absence of function. But, the markedly low rate of conservation seen in the current catalogues of large non-coding transcripts (<5% of cases) is unprecedented and would require that each mammalian clade evolves its own distinct repertoire of non-coding transcripts. Instead, the data suggest that the current catalogues may consist largely of transcriptional noise, with a minority of bona fide functional lincRNAs hidden amid this background. Thus, to expand our understanding of functional lincRNAs, we are faced with two important challenges: (1) identifying lincRNAs that are most likely to be functional; and (2) inferring putative functions for these lincRNAs that can be tested in hypothesis-driven experiments.

In other words, most of the transcripts are probably transcriptional noise, or junk, just as I said. This is the consensus opinion among informed¹ molecular biologists.

Guttman et al. wanted to identify the small subset that might be functional. They identified 1,675 transcripts that show evidence of conservation. The average transcript has six exons averaging 250 bp. Thus, each transcript has about 1500 bp. of conserved exon sequence.

Even if every single one of these lincRNAs have a biological function they will only account for 1675 × 1500 = 2.5 million bp. This represents less than 0.1% of the genome. Casey Luskin ain't gonna disprove junk DNA using this paper.

Luskin ends his article with ...

As an ID proponent, I'm still waiting for Darwinists to let go of their precious "junk" arguments for blind evolution and common descent and learn the lesson that you can't assume that if we don't yet see function for a biomolecule, then it's probably just "junk."

This is a point of view that creationists share with many scientists who haven't studied the subject. They assume that the only reason for labeling most of our DNA junk is because we don't know what it does. That's just not true. There's plenty of good evidence that most of our genome can't be functional. We know a lot about the part that consists of transposons and defective transposons, for example [Junk in Your Genome: SINES and Junk in your Genome: LINEs]. That's 44% of our genome.

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1. I added the qualifier "informed" after a commenter pointed out that most molecular biologists probably don't know enough about the topic to have an opinion. Thus, according to this commenter, the consensus opinion would be "I don't know."

Science Cannot Fully Describe Reality, Says Templeton Prize Winner

 
Shocking news: the winner of this year's Templeton Prize says that science isn't everything. He proposes a way to reconcile science and religion [Science Cannot Fully Describe Reality, Says Templeton Prize Winner].

The only shocking thing about this is that Science magazine treats it seriously. Don't they know what the Templeton Prize is for? It's for people who advocate reconciliation between science and religion.

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Censorship at Uncommon Descent

 
Barry Arrington posted this message on Uncommon Descent.

The moderation policy does not apply to you; you are held to a higher standard. I expect your posts to have at least some tangential relationship to Darwinism, ID, or the metaphysical or moral implications of each. The purpose of this site is not to provide a place for you to jump up and rant on one of your pet peeves. DaveScot will no longer be posting at UD.

What in the world did DaveScot do to deserve this?

He posted an article pointing out that religious people were often racist. He challenged the current dogma on Uncommon Descent that was trying to link Darwin to racism. You can read it here but you won't find it at Racism Sans Darwin - other inspirations on Uncommon Descent. Here's an excerpt ...

Since we now seem to be focused on racism instead of design detection and my motto is “When in Rome do as the Romans do” in order to balance the picture of the theory of evolution’s role in racist movements let’s look at some of the other modern history where evolution isn’t the banner around which racists rally.

Selected bits from Religious Tolerance on Christian Identity Movements . Timothy McVeigh, for instance, was a card carrying CIM member.

History:

The Christian Identity movement is a movement of many extremely conservative Christian churches and religious organizations, extreme right wing political groups and survival groups. Some are independent; others are loosely interconnected. According to Professor Michael Barkun, one of the leading experts in the Christian Identity movement, “This virulent racist and anti-Semitic theology, which is practiced by over 50,000 people in the United States alone, is prevalent among many right wing extremist groups and has been called the ‘glue’ of the racist right.”

The largest Christian Identity movement has traditionally been the Ku Klux Klan which was reorganized in 1915 by William Simmons, a Christian pastor. He had been inspired by the film The Birth of a Nation which portrayed the KKK as a champion of white civilization. The KKK slid into obscurity by the second World War, but was revitalized in the mid 1950’s as a reaction to enforced racial integration in the southern US.

I guess the IDiots at Uncommon Descent don't want anyone to distract from their "Darwin was a racist" campaign.

DaveScot was a big fan of Expelled I wonder if he'll complain to Ben Stein?

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[Hat Tip: Afarensis]

What's Up with New Scientist?

 
Amanda Gefter wrote a nice article in New Scientist pointing out the sneaky tricks that creationists use to discredit science. You can read the article here.

As a book reviews editor at New Scientist, I often come across so-called science books which after a few pages reveal themselves to be harbouring ulterior motives. I have learned to recognise clues that the author is pushing a religious agenda. As creationists in the US continue to lose court battles over attempts to have intelligent design taught as science in federally funded schools, their strategy has been forced to... well, evolve. That means ensuring that references to pseudoscientific concepts like ID are more heavily veiled. So I thought I'd share a few tips for spotting what may be religion in science's clothing.

Red flag number one: the term "scientific materialism". "Materialism" is most often used in contrast to something else - something non-material, or supernatural. Proponents of ID frequently lament the scientific claim that humans are the product of purely material forces. At the same time, they never define how non-material forces might work. I have yet to find a definition that characterises non-materialism by what it is, rather than by what it is not.

Unfortunately, you can't read this article on the New Scientist website because it has been removed. If you click on How to spot a hidden religious agenda you'll find the following message ....

New Scientist has received a complaint about the contents of this story. It has temporarily been removed while we investigate. Apologies for any inconvenience.

I can't imagine a complaint that would cause a respectable magazine to withdraw that article. It sounds like New Scientist isn't standing behind its writers.

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[Hat Tip: PZ Myers]

Shepherd's Pie

 
John Wilkins knows about Real Meat Pies.

Janet Stemwedel has a recipe for Vegetarian Shepherd's Pie.

VEGETARIAN SHEPHERD'S PIE!!!! Gimme a break.

Janet, what do you think those sheps are herding out there in the fields? Tofu?

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The Profzi Scheme

 
This cartoon is making the rounds. It's from PHD Comics.

I've been associated with four universities in my career and I've never seen anything that even remotely resembles this. In my experience, departments recruit outstanding junior faculty who may, or may not, work in a field similar to current faculty members. Usually not. No single Professor makes the decision to recruit new scholars to the department.

In my experience, when funding gets tight it is often the senior faculty members who lose and the productive junior faculty survive. Is my experience that unusual?

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Is the Media Being Responsible about Health Issues?

 
Ben Goldacre is a physician and he doesn't think the media is being responsible. In fact, he thinks they may be complicit in the needless deaths of children. Visit his blog Bad Science and read why he says ... Christ I need a haircut. Then watch this video.

We have a problem with health literacy and science literacy. Professional health journalists and professional science journalists have a choice. They can continue to do nothing and blame the marketplace—in which case they become part of the problem—or they can speak out on behalf of good science—in which case they can become part of the solution.

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[Thanks to Chris Nedin for the link.]

The Taste of Gouda

 
Dutch Gouda cheese has a unique taste (pronounced HOW-dah in the Netherlands but Goo-dah everywhere else). Most of the chemicals that make up this unique taste have been identified. The bitter taste is due to CaCl₂ and MgCl₂ plus various peptides derived from incomplete digestion of milk protein. The sour taste is due to lactic acid and phosphates. The salty taste comes from sodium chloride, sodium phosphate and the amino acid L-arginine. Monosodium l-glutamate and sodium lactate contribute the umami taste. (The five tastes are sweet, salty, sour, bitter and umami.)

Combinations of all these compounds at the appropriate concentrations mimicked the taste of Gouda cheese but something was missing. The "mouthfulness," and the complexity of the mature cheese was not present in the artificial concoctions. The missing taste is called the kokumi sensation.

Theme
A Sense of Smell
Toelstede et al. (2009) have found the missing chemicals. They mostly consist of various γ-L-glutamyl dipetides such as γ-Glu-Glu, γ-Glu-Gly, γ-Glu-Gln, γ-Glu-Met, γ-Glu-Leu, and γ-Glu-His. The structure of γ-Glu-Glu is shown below.

Most people don't realize that peptides and amino acids can impart very powerful tastes. Monosodiun glutamate (MSG) is an obvious example. So is aspartame, a powerful sweetener that's a modified tripeptide (Asp-Phe-Ala methyl ester).

Isn't biochemistry wonderful?


Here's a tough question. Let's say you could identify, with absolute certainty, all the chemicals that make up the taste of Gouda cheese. Let's say you make them in a lab and mix them with tofu and get something that tastes exactly like Gouda cheese. Would there be some people who want to ban that artificial Gouda cheese because it has chemicals? Would those same people be happy to eat the "natural" cheese because it doesn't have chemicals?

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Toelstede, S., Dunkel, A., and Hofmann. T. (2009) A Series of Kokumi Peptides Impart the Long-Lasting Mouthfulness of Matured Gouda Cheese. J. Agric. Food Chem., 2009, 57 (4), pp 1440–1448. [DOI: 10.1021/jf803376d]

Mitotic Recombination

 
It is widely believed that recombination, or crossing over, only occurs at meiosis in diploid eukaryotes. Most textbooks reinforce this belief by associating crossovers with chiasmata, which are only seen at meiosis.

In spite of the textbook claims, most people are well aware of the fact that recombination takes place in somatic cells. After all, it's the basis of most recombinant DNA technology and underlies many of the mechanisms that cause cancer. Furthermore, some developmental processes, such as immunoglobulin gene rearrangements require recombination in somatic cells.

Mitotic recombination has been known to occur since the 1930s when it was used for fate mapping in Drosophila so it's somewhat surprising that crossing over is so intimately connected with meiosis in the textbooks. The frequency of mitotic crossing over may be lower than that seen during meiosis, although the differences may not be great in most species.

In yeast, the frequency of recombination during meiosis can be 10,000 times greater than the frequency of crossing over in somatic cells but that's partly because meiotic recombination is very high in yeast cells. Perhaps they have been selected in vitro for high rates of recombination.

Why does recombination occur in mitotic cells? Probably for the same reason it occurs during meiosis—it's a form of DNA repair.

There's a short review of mitotic recombination in the lastest issue of PLoS Genetics [Mitotic Recombination: Why? When? How? Where?]. Let's try and put an end to the false idea that recombination and crossing over only takes place during meiosis.

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