Sunday, May 10, 2015

Summer 2015 Plans

I successfully moved to Kitchener, and spent April with my friends there. On my first day at work, we (Dr. Strack and I) worked out plans for the summer that can be summarized as “Alberta for four months”, so I did not look for an apartment and just enjoyed the company of my fine friends and their lovely house in Kitchener.

I am now in the tiny Alberta town of Seba Beach, about 80km west of Edmonton. I have two field assistants this summer, Stephanie and Ali, and so far – less than a week into the season – we all seem to be working well together. We’re living in a house in Seba Beach rented by the company, Sun Gro, which owns the lease on the peatlands we’re studying. It very much feels like a summer home, with an unusual layout – the three bedrooms are on the ground floor, the kitchen and living room are upstairs – and a clear history of renovation and addition, such as the electrical subpanel in my bedroom. The furniture is a typical summer home mix of new and second-hand, but it’s actually a very nice place to spend time when we’re not working out at the field site.

Our site is a set of patches of peat wetlands – properly called fens due to their hydrology – that Sun Gro previously harvested. Some areas were harvested more or less intensively than others, and some areas have had various restoration efforts applied to them while others have been left to regenerate on their own. My work will focus on the nitrogen cycle processes in these ecosystems, especially N2O fluxes and the mineral and organic nitrogen pools in the soil and groundwater that contribute to N2O fluxes. Another post-doc, Cristina, will be working here as well, with her work centred on the dissolved organic carbon and its relationship to different types of vegetation (mosses vs. sedges, primarily) and the fluxes of CO2 and CH4.

Data collection is structured around weekly measurements of greenhouse gas fluxes with large chambers placed on permanently-installed collars in various places on the fen. Other measurements, such as dissolved carbon and nitrogen and water-table height, will fit around that weekly schedule. The workload appears moderate, which means we’ll have plenty of free time to explore this part of the world and/or analyze data and come up with fun new research ideas. 

Seba Beach First Look 1
Seba Beach First Look 2
Views of our main field site, from our first day, May 7.

I’m also shopping for a vehicle. I’m currently car-less, again, which is a state of affairs I always find mildly distressing; I like having my own wheels. This is Alberta, and for reasons of plans I have in mind for later in the summer, I’m shopping for a small pickup truck. My modest budget – I could afford up to about $4000 – covers a range of compact trucks from Ford, Mazda, Dodge, Toyota, and Chevy with model years from the mid-1990’s to the early 2000’s. I’m prioritizing 4-wheel drive and a manual transmission simply because I want both of those features, and I’ve been told to avoid V8 engines for reasons to do with not completely abandoning any sense of environmental responsibility – trucks don’t get good fuel efficiency compared to cars as a general rule, but I’m not supposed to go hog wild here. It seems unnecessary to stuff a big 5L+ V8 into a compact truck, but then I don’t work for Dodge.

Monday, March 16, 2015

Scientific Writing

I was informed, about a month after my defense, that my PhD dissertation was both well-written and the writing was not liked by the examining committee. This puzzling combination - good but not enjoyed - was explained as my writing lacking elegance. I was advised to seek a creative writing class when I am in Waterloo, because my technical writing is suitably technical but lacks a certain story-skill. I'm not sure I'm making that clear, which may be a function of my apparent weaknesses as a writer.

As a form of slightly-more-productive-than-nothing procrastination, I've been reading some of the opinion papers that scientific journals publish every once in a while bemoaning the current state of this enterprise of Science. Soil Scientists have contributed their share of these articles, mostly written by senior, established scientists and expressing ideas regarding how to write a good paper (or how papers were better back when they were young, or both - those two concepts can dissolve in each other with the help of some sneering condescension as an emulsifier).

Currently open is a scan of Janzen (1996), a paper with the provocative title "Is the Scientific Paper Obsolete?". After an opening in which Dr. Janzen answers the title question with "no", there are a few sections describing the trend of increasing publication productivity by (soil) scientists, and some speculation on the effects this trend is having on the average quality of papers. This follows closely the paper I have just read, Hartemink et al., (2001), in which the lead author invites contributions to his essay from a range of colleagues, built around a similar quantity-vs-quality argument.

I'm not all the way through Janzen (1996), but mid-way in the essay he is describing a trend of increasing specialization of the literature, and uses as an example the number of papers published on earthworms; the per-year rate of those papers doubled every year from 1930 to 1980 (here Janzen cites Satchell, 1992 - which also has a provocative title. This is an interesting rabbit-hole I'm down). Janzen continues:
"At this rate, 6.5 new papers will be published every week by the year 2000, on earthworms alone."
(emphasis original)
Earlier comments in this paper included a description of the growing presence of scientific publishing on the then-nascent World Wide Web; I have access to a much-expanded Web compared to what Janzen had in 1996, so I ran a quick check on his prediction.

In Web of Science, I ran an advanced search with the following string:
TS=(earthworm or Lumbric* or Moniligastr*) and PY=(2000) 
TS is for topic, or a word that appears anywhere in a paper's title, abstract, or keywords, and PY is for publication year. I chose those terms based on the wikipedia page for earthworms: - Lumbricina and Monligastrida are two suborders that animals commonly called "earthworms" fall into.

Web of Science returned 783 hits (there may be some duplicates or other false positives), or nearly 15 papers for each week of the year 2000. Janzen missed it by more than a factor of 2, which I think only strengthens the argument in these papers about the increased productivity derived from the effectively-universal adoption of computers for both analyzing data and composing papers for publication. Actually, come to think of it I'm having a very hard time imagining writing a paper without a computer, and never mind the statistical analyses.

Literature Cited
Janzen, H.H. 1996. Is the scientific paper obsolete? Canadian Journal of Soil Science 76: 447-451.  
Hartemink AE, Buurman P, Dick WA, McBratney AB, van Cleemput O, Young A. 2001. Publish or Perish (6) - Soil science for pleasure. Bulletin of the International Union of Soil Sciences 100: 50-56.
Satchell J. 1992. Take the money - call the tune. Soil Biology & Biochemistry 24: 1193-1196.

Post-script. I tracked down Satchell, 1992 and Janzen mis-cited that paper - earthworm papers did not double every year from 1930 to 1980, they doubled on average every 13 years.
It's hard to get precise numbers from the rambling introduction to Satchell (1992), but he seems to state that by 1984, 3000 papers on earthworms had been published cumulatively since 1930.
Satchell (1992) states directly the 6.5 per week figure, so I suppose it's not Janzen (1996) that missed the mark.

Thursday, March 05, 2015

Post-Doc: University of Waterloo

I have a new job: a post-doctoral position at the University of Waterloo, in Kitchener/Waterloo (K/W), Ontario. My first day on the job will be April Fool's day, so I will be departing Saskatoon on the morning of March 28. This will give me four full days to cover the approximately 3000 km to K/W, and as long as I don't slide off the road (again) I should be able to make that distance easily.

Wipeout 1
The last time I drove through northern Ontario in late winter / early spring, I had some traction difficulties.

I will be working in the Department of Geography and Environmental Management, with Dr. Maria Strack. Her work has included considerable research into the greenhouse gas exchanges of wetlands, particularly peatlands that have been harvested and restored. Most wetlands are nitrogen-limited; the abundant plants and other organisms living there have adapted to scarce nitrogen supplies and as a result most wetlands are not thought of as strong sources of N2O. N2O is a powerful greenhouse gas, and while wetlands are strong sinks for CO2 (because of vigorous photosynthesis) and sources of CH4 (because of anaerobic, organic-matter-rich conditions below the surface), their contributions to N2O emissions are not well known. My job will be to try to fill that knowledge gap by examining N-cycle processes such as nitrification and denitrification - both of which are potential sources of N2O - in some Canadian peatlands.

I plan to move to K/W with as little in the way of possessions as I can. If I take no furniture (the desk I am currently writing this on can be dissassembled, and I might bring it) I have no need to rent a truck, thus saving potentially $1000 or more - when I moved from Guelph (effectively next door to K/W) the rented truck cost several hundred dollars and burned several hundred dollars more in gasoline. My car - formerly my parents' Chrysler 300M - isn't the most fuel-efficient vehicle in the world, but it gets much better mileage than a truck. Once I arrive, I'll need to find a place to live (friends in Kitchener have graciously offered to let me stay in a spare bedroom while I conduct this search) and presumably then buy some furniture. My bed, the single largest item I own that isn't self-propelled, is a little more than six years old. It's in fine shape, but when I bought it (when I first moved to Saskatoon) the salesmen informed me it "should last" about 10 years. Nothing else big enough to need a truck to move it is worth anywhere near that much money, so I should be able to buy new and new-to-me furniture in K/W for less than the cost of moving the items currently in Saskatoon.

SD 140 1 Aspirations of Canoe Unloading The Chrysler 300M, named "Nikki", beside Buffalo Pound lake in southern Saskatchewan.

Charlie will be keeping the apartment in Saskatoon, so it makes sense to leave furniture here for her, anyway. We plan to live together again, after she completes a M.Sc. here* and we have a chance to look for new and exciting opportunities again.
My contract is for one year, with the possibility of extension for another two years; current (rough) plans are for a project that will last two years total. So, in early 2017, Charlie will be looking for a PhD position and I'll be applying for faculty positions - at least, such is the plan today.

* In Canadian university biology departments, M.Sc. degrees are expected to take about two years; mine took about three-and-a-half but I'm abnormally slow when it comes to higher education, apparently.

I'm looking forward to the new job, I'm happy to be moving on from the lab and work I've been doing here in Saskatoon, but I am sad to go, too, and I will miss living in the Paris of the Prairies. It will be strange to be back in southern Ontario, and so close to Guelph, but I have friends and family in the area and I fully expect to enjoy my time there.

Wednesday, January 28, 2015

Book Club: The Lunatic Express

The Lunatic Express
Discovering the World... via Its Most Dangerous Buses, Boats, Trains, and Planes
Carl Hoffman
Broadway Books, New York

Last Friday, having spent most of the day plowing through the revisions to my PhD dissertation as suggested by members of my examining committee, I took a break and went to the Starbucks coffee shop in the Murray Library (the main library branch) at the University of Saskatchewan. Charlie gave me a gift card a while ago that I've been refilling every so often for my froofy pseudo-Italian coffee beverage fix; go ahead, call me names because I unironically say the phrase "Grande Latte, please" on a somewhat regular basis. Hey, the uni library isn't as intolerably yuppie / hipster as what I used to do, which was drive my BMW to the Starbucks on trendy Broadway Avenue and order a Grande Latte. 

Pictured: BMW, Anachronistic Yuppie-ness. Not pictured: Latte, Starbucks, Fax Machine.

Where was I? Oh, right, in line at the university Starbucks. To take advantage of the captive audience in the queue for caffeine, the staff of the Murray library have (excellently) installed a set of bookshelves near where one stands when the line is particularly long, as it was on Friday afternoon. Onto these shelves they place the newest books the library has just acquired, and a selection of books through the SPL on Campus program. The SPL is the Saskatoon Public Library. Public libraries, unlike university libraries, tend to focus their acquisition efforts (and budget) on books with mass appeal; best-selling novels and popular non-fiction are much more available at a public library than at a typical university library. Obviously, a decent university library will not only also have those best-sellers (in single copies compared to the public library's half-dozen or more per branch) but also access to esoteric academic materials, including broad swathes of the scientific literature and obscure, long-out-of-print materials that never rose to the leve of "classic". 

I was feeling a strange need to read for fun to balance the intense proof-reading I'd been doing pretty much all week. This book was standing up in a small metal bookstand on top of the SPL on Campus shelf unit, and I picked it up and started reading while I was standing in line. I made it to page 20 by the time my latte was ready, so I checked it out and took it home.

Mr. Hoffman is an experienced travel writer and it shows in this book. According to the micro-biography in the back, he's a contributing editor to National Geographic Traveller and Wired - and while I like most things National Geographic, Wired has always struck me as pretentious and excessively neophilic. Some parts of this book read a little like a Wired article, with essentially common experiences or not-particularly-interesting events presented as stunning revelations about life, the universe, and everything. Fortunately, such episodes are few and far between.

I enjoyed this book, and this is a Book Club so I won't really review it. I will note that the match between the text and the map at the front of the book is not close - Mr. Hoffman simply does not talk at all about large segments of his journey around the world. I assume the passage from Sao Paulo, Brazil, to Nairobi, Kenya, by way of Johannesburg and Dar es Salaam by air and from Tanzania to Kenya by bus, was not interesting or dangerous enough to describe. This omission is a little strange, like the editor decided this book had to come in under 300 pages (the Appendix - regarding communication with an insurance actuary - starts on page 281) and so cut some of the slightly less hair-raising adventures. 

The theme of the latter half (or so) of the book is about loneliness and interpersonal connections. Mr. Hoffman, it emerges in slow parts, is separated from his wife, mainly for reasons of his constant travel and his wanderlust when at home in Washington, DC - at least, according to him. His experiences among the less-than-affluent, especially in South America, Indonesia, and India strike him with a mixture of feelings regarding the Unity of Man and the Need for Connection and other such ennui. I believe him when he describes his own feelings, of course, but it was difficult for me to sympathise. Perhaps if I had also thrown myself into a project that necessarily included episodes where "the very idea of silence was unheard of" (pg 88, Kenya) or if I'd stood "in a line next to roadside stalls, a trillion insects flying and buzzing in the lights, pissing into a trench that had years of plastic water bottles, plastic wrappers, toilet paper"... (pg 203, India) I might be more inclined to identify with his crisis of traveller-mindset and his apparently intense realization that what is missing from his life is strong human contact. Mostly, though, I read about his escapades with the kind of fascinated dread normally associated with graphic depictions of violence.

The book mentions his blog, but all I found was his website - - and his twitter feed - @lunaticcarl - I think I'll follow him, he doesn't tweet very often and when he does there are often pictures. He travels widely and writes clearly and very well, even if (to me) he comes across as a bit emo sometimes.

Book Club: Mind of the Raven

Mind of the Raven
Investigations and Adventures with Wolf-Birds
Bernd Heinrich
Harper Perennial
New York

I picked up this book from a discount bin at a local bookstore; I like ravens (Corvus corax) and I wanted to learn more about them. This book provides lovely information about raven life-history and behaviour, so I succeeded there. Book Club entries here are not supposed to be book reviews, I will say I enjoyed this book and I would recommend it.

The author is a professor emeritus of biology at the University of Vermont; he is an ecologist by training, with some specialization in ornithology though I don't think he would describe himself as an ornithologist; his interests are too broad for one vertebrate class. At several points in this book I was struck by the evidence of his career as a scientist, such as when he talks about his model of raven behaviour being congruent with the observational data, and his frequent references to the trouble he's had getting some papers published. I have been criticised in the past for not providing a summary of my project or proposal that was written for an "interested non-scientist" or having too much jargon in my attempt at such a piece. It's very difficult to write about science for a non-specialist audience without coming across as condescending or dumbing it down too much. I don't know if Dr. Heinrich succeeds, because I have enough training in ecology to skip right past the words and phrases that presumably lead non-scientists to pause and scratch their heads (or roll their eyes). 

I enjoyed this book, so I think I'll try again to find some more science writing that I can read and evaluate for a different audience (i.e., different from me).

Wednesday, January 14, 2015

Tomorrow I Defend

Tomorrow, January 15 2015, I will defend my PhD. I expect to pass, with some revisions required to my dissertation. I had a committee meeting in late October at which the consensus was "looking good", I've written my presentation, and I'm not feeling particularly nervous. I assume tomorrow morning I'll be a bit more nervous, increasing up to the start of my talk, when I hope I'll get over it and get on with it.

I've practiced my talk a few times and I'm pretty happy with it - it's about the right length (around 25 minutes) and covers what I think are the main points of what I've been doing for the past 5 years (with the procrastination and spinning-wheels-frustration omitted, of course). I've received a few very nice emails and other messages from people wishing me good luck and bolstering my confidence, and overall I'm very optimistic. Obviously, there is a distinct possibility that I'm delusional in some way and tomorrow will not be the positive-but-hard event I'm anticipating, but there's little I can do regarding my own delusions on that front.

On the other hand, I have been spending some time today searching for the next thing: a post-doctoral position, somewhere. This presents a mix of emotions, but most of them are positive - I find the prospect of traveling to a new place, starting a new project, and learning new skills quite appealing. Getting paid to do that sounds pretty good, too.

Besides looking up advertisements for positions, I've been reading a fair bit about the current state of science, scientific research, and scientific careers. That's where some other possibly-delusions come in. Much of what I've read, not just lately but stretching back several years, have been articles and blog posts decrying the horrible prospects for fresh PhDs in the academic career field. Nearly all of these articles are based entirely on the situation in the United States; I've seen very little about Canadian post-docs and nothing about post-docs in Europe or Australia. I am looking at post-doc positions in the USA, so some of what has been said, such as discussions of cost-of-living and salaries, or academic culture, certainly applies to me. But I do not wish to become a professor in the States, because I do not wish to live there for longer than a few years; I like Canada and I like living here, though I would very much like to live a few years in other places.

It's frustrating because so many of these articles are essentially "only a delusional idiot would accept a job as a post-doc. The smart thing to do is to leave science because the whole enterprise is broken". I don't want to leave science. I love doing science, and I cannot see myself gaining real satisfaction from an occupation that didn't include the raw intellectual curiosity - the ability to pursue any avenue, regardless of its predicted utility - and celebration of intellectual achievements that I see in the modern practice of scientific research.

"Go to industry!" - sure, if there were a) actual jobs on offer in "industry" for someone with my skills* and b) those jobs included 1/10th the intellectual freedom offered to even a constrained PhD student.

"Consulting!" - this sounds like a reflex word, something said when all other options have been discarded. Surely a job as a consultant - without any description at all of what such a job might entail, short-term and long-term, day-to-day and paths of promotion - is an option? For somebody?

"Government!" - Um, you've seen the current state of Canadian government science, right? They're firing people (when they're not simply gagging them), not hiring. I could see myself happily employed by a branch of the federal or a provincial government, but not this month. Maybe not this year. Maybe next year, if the election this year leads to a major change in government science policy.

My current plan - OK, I'm just using that word, rather than looking for a better word to describe my mix of optimism, cynicism, and whatever-else-ism - is to find an interesting post-doc position that will provide me some useful new scientific skills and introduce me to new people and new ways of approaching fascinating questions. I'll start on that next week; most of the post-doc applications I've found ask for evidence of my completed PhD, and that should be easy to provide after I get those revisions done.

* My skills center around walking around outdoors and working out the characteristics of the environment I'm standing in. Seen here:

Sunday, November 23, 2014

Book Club: Crawling from the Wreckage

Crawling from the Wreckage
Gwynne Dyer
Random House, 2010

This book is a collection of Gwynne Dyer's columns - syndicated in many, many newspapers around the world - from 2005 to the end of 2009, re-organized into thematic chapters such as "South Asia" (chapter 8) and "Nukes" (chapter 17), each containing 3-5 essays ranging in length from about two pages up to about five. He also includes introductory or post-script remarks before and after almost every essay, where he points out changes that occured since he wrote that essay (i.e., between the time of the essay and sometime in 2010), emphasises certain points, or says things he thought he wouldn't be able to get published in a newspaper but fit into the book - most of these have to do with direct insults to various individuals (a former deputy Prime Minister of Japan is called "old and stupid" for example), or greater emphasis of his opinions regarding religion (he's not a fan, generally speaking).

I quite enjoy Gwynne's writing, he maintains a simultaneous tone of both exasperation and sarcasm at just a light level that works well to combine cynicism with, surprisingly enough, optimism. The theme of the book is that despite the overwhelming bad news generated daily - wars, poverty, crime, et cetera - the signs of progress are there if you're willing to look for them. He's a supporter of international organizations such as the U.N. dedicated to preventing wars and promoting human rights and expansion of democracy, and many of the essays centre on victories, minor and otherwise, of such organizations.

This was a good read, a series of thought-provoking short works arranged logically. I suspect I would have enjoyed this book even more if I'd read it shortly after it came out. Chapters dealing with Ukraine and Russia, for example, are fairly optimistic, having been written years before the current crisis. Similarly, the predictions regarding parts of the Arab middle east - Syria, Egypt, and Morocco are each mentioned specifically several times - were all written before the "Arab Spring" of 2011 and the Syrian civil war. Presumably, Gwynne has updated his long-term predictions accordingly, and I'm looking forward to reading his new opinions.

Saturday, May 31, 2014

Time and Money

I am approaching the end of my PhD, after approximately a decade as a graduate student. What can I say, speed is not my forte when it comes to large-scale academic projects. This time comes with a large number of interesting thoughts and emotions, which I'm going to try to make sense of here.

1. Money
This is the big issue at the moment. My PhD at the University of Saskatchewan was supported by a scholarship from NSERC, the "Canada Graduate Scholarship - Doctoral" (CGS-D). This was for 36 months, the last of which was April, 2014. I didn't get paid at all in May (today being the last day of May), though through a weird little side project and some creative financing by my advisor I'll receive around $350 once the casual-labour paperwork gets sorted out. Similarly, I'm not expecting (as of right now, things can change) any real income in June, aside from a similar amount from the casual labour I will devote (probably around 20-25 hours) to that side project.

The other inflows of money I'm expecting in the near term are all reimbursements for things like conference travel from the last few months. I beat my head against the particularly rocky wall of the university's expense-claim system last week, apparently successfully and I'll be able to pay down a large majority of my credit-card debt (where those expenses went - airline tickets, conference registration, hotels, etc.) as soon as that clears - probably this week.

So, while my income is close to zero and my debts are several thousand dollars (and tied to obnoxiously-high interest rates) I'm not actually feeling too money-stressed, yet. If things go to THE PLAN (see below) over the next month I should be able to avoid anything too nasty on the financial side. 

I've been to the real world, and found it a dark and scary place. Thus, my overall career goal is to barricade myself inside the Ivory Tower of academia; the view is nice, at least. Anyway, a key sub-goal in this is getting my PhD. There are some who know me who believe I can finish my dissertation by July 1 - that I can hand in my dissertation to my supervisor by that date. Such "deadlines" have come and gone before, recently and further back, so I essentially have no firm opinion of that opinion - it's possible, I suppose. That doesn't sound very optimistic, so I'll emphasize that I also think it's very possible, and a good, useful goal to work towards.

My dissertation is not *yet* finished, but it's close. I like to quantify things, it's a side-effect of training as a scientist, but I can't really say any numbers that would have any meaning in this case. Anyway, there are a few components that need finishing, or starting, including the Introduction (here's a number: 95% done), the Literature Review (85% done), the third data chapter (a manuscript to be submitted to a journal around the same time I hand in the whole thesis, call it 40% done, though as many readers might know, writing a scientific paper is a very non-linear process), and the overall summary of my dissertation (0%, not started yet). That non-linearity and large uncertainty is why I'm uncomfortable talking about an overall "this much completed" value for my dissertation, but it does exist and represents a series of solvable problems.

3. Uncertainty
My life at the moment is made of uncertainty. Obviously, there are many things I'm quite certain about, but some of the things that I'm used to being able to answer questions about in an intelligible manner leave me shrugging and muttering. I've got a few post-doc applications out there, though of course those are highly uncertain (mostly in the sense of not-bloody-likely), but without a solid offer I have no idea where I'll be living and working in a few months' time - nor do I know how many months away my eventual move and job change will be. One possibility, for example, is that I move to Australia for a 2-year appointment (though that could be more accurately stated as 1-year with [strong] possibility for extension) starting in September. Another possibility (more likely? less?) is that I stay in Saskatoon until December or January, then move to some other university in Canada. 

It's an exciting time, both in the sense of the many, equally-possible possibilities (Australia! United States! United Kingdom! Germany! various parts of Canada!), and the stress and inability to make plans that come with this impending change.

Anyway, there's some blather to fill space on this chronically under-used blog.