Monthly Archives: March 2009

Scitable again.

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I noted previously that Scitable, a resource from Nature Education, was interesting but had some problems with the content [Scitable (and a weird piece on DNA barcoding)].

Well, more troubles.

Excerpt from Transposons, or Jumping Genes: Not Junk DNA?

Transposable elements (TEs), also known as “jumping genes” or transposons, are sequences of DNA that move (or jump) from one location in the genome to another. Maize geneticist Barbara McClintock discovered TEs in the 1940s, and for decades thereafter, most scientists dismissed transposons as useless or “junk” DNA. McClintock, however, was among the first researchers to suggest that these mysterious mobile elements of the genome might play some kind of regulatory role, determining which genes are turned on and when this activation takes place (McClintock, 1965).

At about the same time that McClintock performed her groundbreaking research, scientists Roy Britten and Eric Davidson further speculated that TEs not only play a role in regulating gene expression, but also in generating different cell types and different biological structures, based on where in the genome they insert themselves (Britten & Davidson, 1969). Britten and Davidson hypothesized that this might partially explain why a multicellular organism has many different types of cells, tissues, and organs, even though all of its cells share the same genome. Consider your own body as an example: You have dozens of different cell types, even though the majority of cells in your body have exactly the same DNA. If every single gene was expressed in every single one of your cells all the time, you would be one huge undifferentiated blob of matter!

The early speculations of both McClintock and Britten and Davidson were largely dismissed by the scientific community. Only recently have biologists begun to entertain the possibility that this so-called “junk” DNA might not be junk after all. In fact, scientists now believe that TEs make up more than 40% of the human genome (Smit, 1999). It is also widely believed that TEs might carry out some biological function, most likely a regulatory one—just as McClintock and Britten and Davidson speculated. Like all scientific hypotheses, however, data from multiple experiments were required to convince the scientific community of this possibility.

Total nonsense.

Open letter: Don’t leave Canada behind

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I received this via email.

Dear colleague,

The following open letter to the Prime minister and the Leader of the Opposition was sent this morning, signed by hundreds of your colleagues across Canada.

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)

Science minister and evolution roundup.

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Here is some of the media coverage of the “acceptance” of “evolution” of Canada’s federal minister of science.

Just a reminder of what he stated:

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.

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.

Canadian politicians who do not understand biology.

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Here’s a brief follow-up to Anne McIlroy’s article about the Canadian federal science minister’s evasion of a question about his acceptance of evolution.

Now he says,

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.

He’s not talking about evolution as it is understood by scientists.

I can understand why Goodyear says such things. He has no real understanding of modern science. What almost bothers me more is the statement from Marc Garneau, the Liberal science critic, who was an astronaut.

It is a personal matter. It is a matter of faith.… I don’t think it prevents someone from being a good minister.

If this is the alternative, we are in very dire straights.

Obama’s statements about science.

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From New Scientist, some quotes of President Obama’s:

“My administration will not deny facts, we will be guided by them.”

“Science holds the key to our survival as a planet and our security and prosperity as a nation. It is time we once again put science at the top of our agenda.”

For once, I actually wish the government in Canada would follow the American lead.

What about the match?

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The federal government in Canada is touting its large investment in the CFI, which provides funding for infrastructure. Many scientists have welcomed this move, but are concerned about the simultaneous cuts that are being inflicted on basic research grants. With no money for operating, what use is a nice new lab?

Another question was recently raised by a colleague that I think is important to consider. The CFI generally funds 40% of a proposed program. Another 40% comes as match from the province, and 20% in match (e.g., in-kind) from suppliers. The question is, will the new federal funds require equal match from the provinces, and if so, have the provinces got the money? If there is no match around, then that substantial new investment may never go anywhere.

Canada’s science minister refuses to answer question about evolution.

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“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.”

So said Canada’s federal science minister, Gary Goodyear, a chiropractor from Ontario, when asked if he accepts that evolution has happened. Who but a creationist would construe a question about a scientific fact as a question about their religious views?

“I do believe that just because you can’t see it under a microscope doesn’t mean it doesn’t exist. It could mean we don’t have a powerful enough microscope yet. So I’m not fussy on this business that we already know everything. … I think we need to recognize that we don’t know.”

Asked to clarify if he was talking about the role of a creator, Mr. Goodyear said that the interview was getting off topic.

I am truly fearful for the future of science in Canada.

Read the story by Anne McIlroy in the Globe and Mail.

Would you act as a consultant on a scifi movie?

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Last week in my first year seminar course “Controversial issues in the life sciences” we watched Jurassic Park and discussed a series of questions about the science included, the portrayal of scientists, and various other issues. This was interesting, because most of the people in the course are not biology majors but had done a good job learning about cloning, genetic engineering, and other topics during the semester. (This was also a nice break from giving weekly presentations, I am sure).

Anyway, as part of the discussion we also read several papers about science in movies. One of them by Kirby (2003) is about scientists as consultants for Hollywood productions. As I was reading it, I thought to myself, “I would probably do it, but not for personal payment — if they funded my research that would be ok”. Then, on the following page, I read:

Based on the available evidence, science consultants are far more likely to accept research funds, or no compensation at all, rather than actual payment for their services. One of the reasons for this situation is the unwillingness of scientists to take money for what they consider a “public service.” Many of the consultants I researched felt it was their “duty” as a scientist to impart knowledge to an uneducated public, including filmmakers, and that it would have been “unethical” for them to take money for this activity. For example, two of the consultants for the 1922 gland-based horror film A Blind Bargain(1922) felt that it would be “disreputable” for “medical researchers” to accept payment for their services, and they even requested that their names not be included in publicity material (see Riley, 1988).Likewise, Donald Francis of Genentech, Inc., who is most famous for his work on an AIDS vaccine, refused financial payment for his work as technical adviser for the film Outbreak(1995), accepting as compensation “only that his 17-year-old son, Oli, be allowed to observe the filming” (see Ganahl, 1995: 1E). Francis’ example underscores the conflict that science consultants face. On the one hand, they believe that as scientists they should give scientific advice freely to anyone who seeks knowledge. On the other hand, they are providing a specialized service for filmmakers and believe they should receive compensation of some type. To resolve this tension, consultants have come up with other forms of compensation that do not involve direct financial payment. In this regard, consultants who accept research funds rather than salary or consultation fees perceive that this action does not compromise their “ethics,” because the money will not go into their pockets but will go toward the production of “new knowledge.”

Science is an intriguing culture, no question.

____________

Kirby, DA (2003). Science on the set: science consultants and the communication of science in visual fiction. Public Understanding of Science 12: 261-278.

"Everlasting antibiotics", wanna bet?

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From Albert Einstein College of Medicine in New York (and several news services):

Einstein Researchers Develop Novel Antibiotics That Don’t Trigger Resistance

Most antibiotics initially work extremely well, killing more than 99.9% of microbes they target. But through mutation and the selection pressure exerted by the antibiotic, a few bacterial cells inevitably manage to survive, repopulate the bacterial community, and flourish as antibiotic-resistant strains.

Vern L. Schramm, Ph.D., professor and Ruth Merns Chair of Biochemistry at Einstein and senior author of the paper, hypothesized that antibiotics that could reduce the infective functions of bacteria, but not kill them, would minimize the risk that resistance would later develop.

Dr. Schramm’s collaborators at Industrial Research Ltd. earlier reported transition state analogues of an enzyme that interferes with “quorum sensing” — the process by which bacteria communicate with each other by producing and detecting signaling molecules known as autoinducers. These autoinducers coordinate bacterial gene expression and regulate processes — including virulence — that benefit the microbial community. Previous studies had shown that bacterial strains defective in quorum sensing cause less-serious infections.

Rather than killing Vibrio cholerae and E. coli 0157:H7, the researchers aimed to disrupt their ability to communicate via quorum sensing. Their target: A bacterial enzyme, MTAN, that is directly involved in synthesizing the autoinducers crucial to quorum sensing. Their plan: Design a substrate to which MTAN would bind much more tightly than to its natural substrate — so tightly, in fact, that the substrate analog permanently “locks up” MTAN and inhibits it from fueling quorum sensing.

To design such a compound, the Schramm lab first formed a picture of an enzyme’s transition state — the brief (one-tenth of one-trillionth of a second) period in which a substrate is converted to a different chemical at an enzyme’s catalytic site. (Dr. Schramm has pioneered efforts to synthesize transition state analogs that lock up enzymes of interest. One of these compounds, Forodesine, blocks an enzyme that triggers T-cell malignancies and is currently in a phase IIb pivitol clinical study treating cutaneous T-cell leukemia.)

In the Nature Chemical Biology study, Dr. Schramm and his colleagues tested three transition state analogs against the quorum sensing pathway. All three compounds were highly potent in disrupting quorum sensing in both V. cholerae and E. coli 0157:H7. To see whether the microbes would develop resistance, the researchers tested the analogs on 26 successive generations of both bacterial species. The 26th generations were as sensitive to the antibiotics as the first.

“In our lab, we call these agents everlasting antibiotics,” said Dr. Schramm. He notes that many other aggressive bacterial pathogens — S. pneumoniae, N. meningitides, Klebsiella pneumoniae, and Staphylococcus aureus — express MTAN and therefore would probably also be susceptible to these inhibitors.

Ok, here we go. How big was the population size tested? How much is 26 generations in bacterial timescales? Let’s think about this. One person taking antibiotics would have billions of bacteria in his/her gut. A week on antibiotics is about 350 generations if you consider 30 minutes per.

How about the possibility of a new mutation or lateral transfer from some other species? Yes, selection may result in resistance easily in bacteria if some individuals already carry a resistance gene, but I would never bet against some mutation occurring down the line and leading to a reproductive advantage — they don’t have to survive while all others are killed for selection to occur and therefore for the new resistant trait to increase rapidly in proportion. Natural selection is about relative reproduction, not necessarily survival alone.

Jon Stewart is awesome.

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This is not supposed to be a political blog, but the current economy is hurting scientific funding and so I feel justified in posting links to Jon Stewart’s absolute thrashing of the sort of people who contributed to the current economic mess by giving nonsensical financial advice.

(If it won’t play, go here).

To watch this in Canada, go here.

By the way, if you think Stewart only came off so well because he was on his own turf, see him on Crossfire: