Recently, the US National Public Radio published a story on biofuels and nitrous oxide.  I think that it is an excellent description of the reasons that researchers such as myself and others research nitrous oxide.  If you want to hear the full story, click on the link below:

http://www.npr.org/templates/story/story.php?verified=true&storyId=112288478#commentBlock

A recent article in Macleans  (http://www2.macleans.ca/2009/07/28/our-universities-can-be-smarter/4/) makes the argument that there should only be 5 major research institutions in the country.  The remaining universities should train undergraduates and feed their best students to U of A, UBC, Toronto, UM and McGill.  There are so many problems with this that I won’t even attempt to address it.  Instead, I’ve included a post by ‘eddycurrent’ in response to the Maclean’s article.  It is an excellent decoding of the big 5 president’s request:

Eddy Current Writes

I am a faculty member at a Canadian university which is not one of the self proclaimed “Big Five”. Obviously these five presidents would want their universities to receive special treatment. It would make their work more rewarding and most likely easier. I hope their plea, and this article, fall on deaf ears.

I conclude with a statement of personal experience. I was offered a faculty position at one of the Big Five, but turned it down to remain at one of the Lesser Eight (by which I mean the rest of the Canadian G13 universities - which in itself is a kind of self-proclaimed Winners Circle). There are many great things going on in the Lesser Eight, and some crap. The same is true of the Big Five. The question is, is the great to crap ratio better or worse in the Big Five. Would they willing to compare these ratios in a Big Five vs Lesser Eight winner-takes-all competition right now? If they come up short, would they stand aside for the Lesser Eight, volunteer to focus on undergraduate education, and strongly support a program to make the Lesser Eight “Harvards of the North”?

I agree completely.  Transparent competition, resources and commitment to all students (undergraduates and graduates) is the key to a respectful and successful system.

Excitement breeds imagination.  The blind passion of excitement often leads to intuitive leaps of imagination that can lead scientists into new and innovative fields of inquiry.  As a scientist who works in Antarctica, I can attest to this excitement not only in myself but also in my graduate students.  They arrive in Antarctica with eyes as wide a saucers and minds wide open to new ideas.  However, as they step foot on the continent, they bring Canada.

These young Canadian scientists bring -40°C winters, January thaws, quinzees, migrating caribou, seals lounging on the ice looking out for polar bears and the history of the Hudson Bay company men.   As they stay on Antarctic, our Métis, First Nation and Inuit culture surfaces and they view the landscape unlike any other people can.  Canadian’s live and thrive under conditions as hostile and extreme as what is routinely encountered in Antarctica.  As such, Canadian’s don’t view Antarctica as a hostile, foreign land but as a long forgotten home and thus, we are not there to conquer but to nuture.

In turn, Antarctica brings to Canada a level of excitement and innovation that is only possible for extreme explorers. It attracts technical entrepreneurs who are interested in science and risk taking. These students thrive on taking science out of the classroom and into the world.  Students such as these will found Canada’s next high-tech commercial success story.

Canada needs to be working in Antarctica because we are unique in the world.  Our Nation’s history was forged in the North and I believe our future will be as well.  By working in the South, we can demonstrate our national expertise in Polar Regions, confirm our National identity as a polar people and inform our northern science. This will help affirm our northern sovereignty claims and stimulate our innovation economy by providing unique opportunities to the best of our science cadre.

Sam Banerjee has just won the U of S Robson Bursary.  This bursary recognizes academic achievementin an area related to land and resource management with an emphasis on sustainability and ecologically sound management practices.  Sam’s Ph.D. research is focussing on how geospatial relationships of microorganisms influences processes linked to greenhouse gas production in Canada’s Arctic.  His recent work has been investigating at what scale processes are important.  Or in other words, if you are trying to link genes, greenhouse gases with long term geomorphology, should your samples be spaced at less than one meter apart or perhaps several 100 meters apart.  His results are an integral part of the IPY-CiCAT program as it attempts to provide remote sensing experts with the on the ground information they need so that Canada can accurately estimate greenhouse gas emissions under a variety of climate change scenarios.

Congratulations Sam!

A recent article by Girouard and Zagury (doi:10.1016/j.scitotenv.2008.12.019) on the available of arsenic bound in soil highlights a recurring theme in soil environmental toxicology. Our current measurement techniques for contaminants in soil may be significantly underestimating the risk associated with a polluted soil to small children. Typically, we recommend that soils be sieved to pass a 2 mm sieve, or in other words, only particles less than 2 mm are analyzed. Sometimes we suggest that soils should be sieved to pass a 0.25 mm sieve. The reason we do this is that we know that concentrations of pollutants increase as we sieve to smaller and smaller sizes. However, what we don’t know is how ‘available’ pollutants in these smaller size classes would be to small children, or in other words, how easily can pollutants in small sized particles enter our bloodstream. The work by Girouard and Zagury indicates that the answer to this question is: more easily. Thus, the smaller the particles the more risk is posed to small children who might accidentally eat these soils. (as an aside, I’m sure you are wondering how much soil a children will eat. We estimate around 100 mg per day but in some cases, children can eat up to 13 g). As a society we need to revist how we assess risk from contaminated soils and ask the question: are we being protective enough?

A recent article by Dr. Gan’s group in Environmental Science and Technology (DOI: 10.1021/es802966z) investigates how available phenanthreneis to bacteria.  What the group did was measure phenanthrene degradation and also calculate the amount of phenanthrene freely dissolved in soil pore water.  To measure the amount of phenanthrene in pore water, they used solid phase microextraction fibers.  Importantly they checked many of the assumptions about SPMEs and their ability to measure freely dissolved phenanthrene.  Once they did this, they found that the freely dissolved concentration of phenanthrene could only predict the initialy 144 h of degradation but after that was not predictive at all.  This suggests that microorganisms can access phenanthrene directly from soil without the phenanthrene dissolving into pore water.  This is not a brand new observation by Dr. Gan’s group has been able nicely pin it down and also investigate the influence of other soil factors like organic carbon and surface area on bacterial use of phenanthrene.

Why do we care about this?  The concept of chemical activity versus bioaccessibility hinges on this very same issue.  Chemical activity can be linked to the freely dissolved chemical concentration in pore water.  In contrast, bioaccessibility is an estimate of how much of a contaminant an organism can access. One good rule of thumb put forward by Reichenberg and Mayer (2006) is that bioaccessibility is required  when organisms can specifically access a chemical whereas chemical activity is more important for passive uptake systems.  Typically for bacteria we think of them as passive systems for polyaromatic hydrocarbons.  The toxicity of PAHs to organisms is often thought to be due to non-polar narcosis in which the PAHs disrupt the lipid membrane (nitrifiers are an important exception to this).   Based on this recent publication by Dr. Gan, we are going to need to rethink this idea. If microorganisms can specifically uptake the toxicants, then we need some sort of estimate of bioaccessibilty for microorganisms.  This will allow us to modify site specific clean up scenarios to protect biogeochemical cycling at impacted sites.

Well it has been a frustrating week.  Methanol can be substituted but peaks broaden and more non-polar substances co-elute.  The Thermo guideline is a good first step but I think that the method development is going to take longer than I had initially hoped.   Hopefully the acetonitrile shortage will alleviate soon and we can go back to the original solvents.

So, if you are like our lab and use HPLC technology, then you know there is an acetonitrile shortage.  Acetonitrile is a by produce of the automative industry.  As you may have heard, this industry is in free fall and as a result acetonitrile has increased in price 6 to 8 fold and normally can’t be bought.  This is a problem becuase acetonitrile is the solvent of choice for most HPLC applications.  Thus, one can think of HPLC’s as running on acetonitrile.

Luckily, I work in an academic environment so I can change solvents.  Others who need to work with certified methods are stuck and can try to save acetonitrile usage by switching to smaller columns.  If you are going to change solvents, there are two major things to consider.  The first is that other solvents like methanol absorve in the UV spectrum which can pose a problem for UV/VIS detectors.  The second is that methanol has a slightly different polarity than acetonitrile and also results in higher backpressure.  Luckily, Thermo has posted an excellent user guide for replacing acetonitrile with other solvents. Today we are going to try to replace our PAH HPLC method that is acetonitrile based with a methanol based method. PAHs are detected using a fluorescence detector so the UV absorbance of methanol is not a big concern.  Hopefully it will go well and tommorrow I can post the results in case others need to change their PAH methods over.

It is funny that as scientists we normally don’t primarily think of ourselves as consumers and thus are somewhat disconnected from the overall economy.  The acetonitrile shortage is a good example of how interconnected our economy actually is.

Recently the University of Saskatchewan has decided that it needs to increase its graduate enrollment substantially.  It has asked the Department of Soil Science to have 50 graduate students enrolled in its graduate programs. On average the University has a ratio of 2 M.Sc. for every 1 Ph.D.  Currently in Soil Science, we have 38 graduate students, 19 M.Sc. and 19 Ph.D.  There are 12 tenured faculty in the department which means that the University expects the Department to supervise on average 4.1 students (Appendix D:  CGSR Strategic Plan).  This means that we need to teach an additional 12 students.

It has been suggested that we radically need to re-think our teaching strategies.  That is, we should offer a strong non-thesis based program which would be completely course based.  In my opinion, this is not a great option.  Graduate students are not trained but rather mentored.  When I consider my relationships with Brian, Alexis, Wai, Sam, Kyle, and Juliska, I am reminded of my martial arts training.  A black belt is merely an indication that you are a serious student.  Similarily, my Ph.D. merely indicates that I have learned how to learn.  Thus, I try to train my students how to learn.  In turn, they try to train me how to think.

This is why graduate students are so valuable to society, to companies and to the world.  Not because they are highly trained soil scientists and toxicologists.  But rather because they have learned how to grasp difficult concepts, apply original solutions and then evaluate these solutions through sophisticated and rigorous analyses.

It is difficult to imagine how one would do this in a course based approach. Each one of the students who works with me is different.  They are all very smart and creative.  But each in their own way.  This is not a trivial motherhood statement but rather a close observation of how my students achieve their Ph.D.  A graduate student typically faces a data storm. By this I mean a vast amount of conflicting data points that overlap and need to be organized into a coherent story.  Alone they face the unknown and somehow craft a conceptual masterpiece from disparate data.  I am always reminded of Mickey Mouse in Fantasia as the Sorcerer’s Apprentice.  Every one of my students is a Sorcerer’s Apprentice.  My job is to make sure the broom doesn’t run amok.

I know of no way to teach this in a course.  Instead, what is needed is a dedicated, very smart student and a dedicated, very smart professor.  Then, one has a good graduate experience and everyone learns something, society, student and professor.   I don’t think we should change this.  We have great students and professors in our department.  We are one of the best Departments of Soil Science in the country and internationally recognized.  Lets not mess up a good thing.

A recent article (doi:10.1016/j.chemosphere.2007.08.035) by Budinsky et al investigated how readily dioxins and furans that contaminate soil can enter into our bloodstream.  They used two different animals to test this, a rat and a swine model. They used a rat model because the carcinogenic risk factors associated with dioxins and furans have been derived from rat toxicological data.  They also used a swine model because juvenile swine are our best available animal model for human exposure to ingested contaminated soil.

Two key findings jump out of this study. The first is that for rats around 30% of the dioxins reached the bloodstream whereas for pigs it was around 23%.  In contrast, a common chemical test meant to assess exposure to humans predicted only a 17%.  Thus, it looks like certain in vitro digestors might be underestimating exposure by around 2 fold. This should not be too surprising as currently the use of in vitro digestors for organic chemicals is not well accepted and still require substantial research and development before we begin to accept their use to predict human exposure.

The second key finding was that EROD activity varied depending on if the rats were exposed to dioxins in soil compared to oil.  This finding is very troubling.  Often we assess exposure of organic chemicals on the induction of these EROD enzymes (a subset of the P450 enzyme group).   The work by Budinsky et al. indicates that this may not be appropriate.  The reason is that typically an animal is exposed to the organic chemical in some sort of carrier, like corn oil and then this is compared to the organic chemical in soil.  What Budinksy et al. findings show is that the soil itself influences EROD activity.  Thus, if we calculate relative bioavailability through EROD activity it will be confounded by the dosing vehicle.

At the end of the day, I think that the Budinsky et al. article highlights how little we understand about pollutants in soil.  It certainly demonstrated to me that when working with pollutants in soil we need to be extra vigilant that we don’t make any assumptions until they are rigourously checked.

If you want to find this article and read about it yourself, simply open http://dx.doi.org and enter doi:10.1016/j.chemosphere.2007.08.035 in the text box provided, and then click Go