The most exciting phrase to hear in science, the one that heralds new discoveries, is not 'Eureka!' but 'That's funny...' --Isaac Asimov
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International Polar Year 2012

May 2nd, 2012 by eric
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I’ve just returned from the IPY2012 conference in Montréal, which was a very interesting mix of science, culture, and politics. On the Science side, there were lots of great presentations wrapping up years of polar research. I spent a lot of time in the Polar Microbes, Polar Marine Ecosystems, and Polar Terrestrial Ecosystems sessions, but also branched out and watched talks on other topics like contaminants, remote sensing, and anthropology. On the culture side, there were some great performances by aboriginal artists like ArtCirq — the Arctic Circus and Beatrice Deer.

Finally, the last part of the conference was political. Speeches by QC Premier Jean Charest and Minister of Aboriginal Affairs and Northern Development John Duncan had the whole conference center in a lockdown the first day. They made me realize that the theme of the conference, “From Knowledge To Action”, meant something very different to them than to most of the scientists I spoke with. None of the politicians mentioned news like the Canadian withdrawal from the Kyoto Protocol, the ongoing student strike against rising tuition and the breaking of a decades-old social contract in Quebec, the firing of 60 Environment Canada scientists, the closing of the Eureka High Arctic Research Station in Nunavut, or the muzzling of Canadian Government scientists at this very conference. Instead, they spoke of rapid development in the Northern regions, especially Charest’s Plan Nord, claiming that he will protect 20% of the pristine northern wilderness (wow! 20%) over the next 25 years (what happens to the other 80%?). John Duncan insisted that development brings jobs and prosperity to northern communities (oh really? since when?). During an “Action Forum” entitled “Creating the Conditions for Arctic Offshore Oil and Gas Development” two oil industry representatives (for Shell Oil and Chevron) earnestly claimed the same thing, and noted that there had been ‘no significant spills’ in the Arctic after decades of exploration (since, technically, Prince William Sound — the site of the Exxon Valdez spill — was only at 61N and not strictly ‘Arctic’). Many, many, many community member comments later, I was simultaneously heartened and dismayed by the topic. It became exceedingly clear that oil and gas development will proceed whether the science is there or not. At one point the Shell spokesman claimed that we have “a very good holistic understanding of the ecosystem” in the Chukchi/Bering Sea region. I would beg to differ, especially as regards the microbial ecosystem, which will prove even more critical to remediation after a spill than the animal ecosystem that relies upon it.

I was very glad when one woman asked the question I had wanted to ask myself (paraphrased): “There has only been discussion of WHEN, not IF, development should occur. Shouldn’t we question the societal necessity of exploration and development of this critically endangered region, especially considering the irony that the use of fossil fuels is the primary contributor to its imminent demise?” Professor Peter Wadhams succinctly explained it thus (paraphrased): “If this were a sane world, we wouldn’t drill in the Arctic.”

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Upcoming Goldschmidt Short Course in Bioinformatics

May 2nd, 2012 by eric
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Short course 2:
Bioinformatics for geologists

Speaker:
Dr. R. Eric Collins, McMaster University, Hamilton, Canada

Date: Tuesday, June 26, 2012
Time: 12h30 – 14h00
Price: Free
Short course description:

This course is an introduction to bioinformatics – the use of computers to study biological processes via information-carrying molecules like DNA and proteins. We will look at how these tools can be useful in interpreting the geologic record, for example by the construction of molecular phylogenies, gene identification, metabolic pathway reconstruction and whole-genome sequencing. We will demonstrate web-based applications that perform these tasks and brainstorm possible future uses, as it becomes cheaper and easier to acquire and analyze massive amounts of sequencing data.

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Astrobiology Science Conference 2012

April 19th, 2012 by eric
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I’m in Atlanta, Georgia this week for AbSciCon 2012, one of my favorite scientific conferences. I’ve only missed one since my first in 2000 at NASA Ames, and over the years I’ve seen Astrobiologists evolve into a more confident, more mature community of scientists. This year I’m excited that there are more presentations on Science Communication, Science Outreach, and Science and Society than there have ever been before, which shows that the community takes those responsibilities seriously. There was also a very nice memorial session for those in the community that have passed away since the last meeting. It was touching and really showed how tight the community has become over the past decade.

My first talk, on Monday, was coauthored with Boswell Wing and entitled “Unraveling the Genetic Basis of an Ancient Geochemical Biomarker: Sulfur Isotope Fractionation” [PDF].

My poster was on Tuesday, re-used from a previous conference: “hima: A Meta-Database for Genomes, Metagenomes, and Phenotypes from Cold Environments” [PDF]. Multiple visitors to my poster offered support, and one is now a potential collaborator on a NASA proposal to fund ‘hima’!

My second talk, co-authored with Paul Higgs, will be on Friday, titled “Testing the Infinitely Many Genes Model for the Evolution of the Bacterial Core Genome and Pangenome” [PDF].

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Guest Lectures

March 23rd, 2012 by eric
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I recently gave guest lectures in Jon Stone’s “Life in the Universe” course (2LU3) and in Paul Higgs’ “Genomes and Evolution” course (4Y03) at McMaster. For “Life in the Universe” I gave a general overview of the prospects for finding life on Earth and elsewhere in the universe. For “Genomes and Evolution” I talked about the DNA sequencing explosion and how it has elucidated the evolution of microbial genomes, using a bunch of examples from ocean-dwelling microbes. The slides for each lecture are available here: 2LU3, 4Y03.

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Third Party Tracking by WordPress+Quantcast Disabled

March 7th, 2012 by eric
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I just installed Do Not Track Plus and I recommend it to everybody, immediately. With it, I learned that my own website was inadvertently invoking 3rd party tracking companies (Quantcast) via the Official WordPress Stats plugin. Yuck!

I’ve now disabled that “functionality” with the DoNotTrack plugin, but I’m still pretty upset that it was in the OFFICIAL plugin to begin with, with no notice to its users and no opt-out feature.

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