Moving to Australia

I am deep into moving mode, an emotional state that places a voice inside my head that repeats a few phrases whenever I ponder a wide range of physical objects: "No! Do not buy that!"; "Will this be taken with, packed for storage, sold, or donated?"; "The miniproject you had in mind for this is gone, a dead dream. Let it go.".

This is annoying, I much prefer my normal happy-go-lucky approach to possessions, though this current mood has considerable benefits when it comes to that other major category of possession, money. I would not say I have ever been very good at money, in the sense of avoiding or paying off debts effectively, saving money, and preventing myself from making probably-ill-advised purchases. Between the increased attention I've been paying to my personal finances since late summer and the material needs (i.e., for less material) of my impending trans-Pacific move, my money situation has both clarified and improved. This move to Australia comes with another substantial benefit on this point: a large raise.

As a post-doc in Canada, from my position at the University of Waterloo, through my short half-year at Université Laval, to my current-and-soon-to-end half-year here at Laurentian University in Sudbury, my salary has stayed pretty constant, at about $45 000 / year. My recent improvement in financial self-oversight does not extend far into the past, but I am confident that I can maintain something like my current lifestyle on this level of income. The new position in Australia comes with a salary nearly double that, and while the cost of living will probably be a bit higher, and the move itself represents a significant expense, I anticipate being able to live a slightly more comfortable life there. My current debts would be paid off by mid-to-late 2019 were I to stay here in my current existence, so I anticipate greater chances of success in this goal, even with the currency-conversion and interbank transfer fees I'll incur paying off Canadian debts from Australian income.

So that's one reason why I'm moving. The other, more important reason, is love. Charlie will be starting her PhD in 2019 at the University of New England (as long as certain things go reasonably well, which they mostly have already been doing), and this position for me is in the same laboratory group, so we can STAY TOGETHER! YAY! I have been awarded a University of New England Post-Doctoral Fellowship (UNE PDF), a competitive award that comes with a 3-year contract and considerable support in the form of specific training for professor responsibilities such as effective teaching and applying for outside funding; I am very much looking forward to learning about and practicing both of those.

I think I'll save the application process story for another post, after I arrive in Armidale and take up my new position, just to avoid any public-information weirdnesses - I'll have a chance to clear some things I might want to talk about with the relevant people there.

The third reason I'm moving to Australia is of course ADVENTURE. Ironically, Sudbury is an AMAZING place for EXACTLY the kinds of adventures I am most interested in having. This isn't the canoe capital of Canada - Atikokan, Ontario, a thousand kilometres away, claims that title - but it's a very close second. Greater Sudbury, the coalesced super-municipality of Sudbury plus a large number of suburbs, includes 331 lakes within the borders. My office here looks directly out (I mean, directly - the distance from window to water is about 3 metres) onto Lake Ramsey. Within an hour or two of driving, there are at least half a dozen Provincial Parks with mapped canoe routes, water-access-only campsites, and maintained portages; this includes the jaw-droppingly gorgeous Killarney Provincial Park, which we have managed to visit only once. We'll be back.

I have been spending some of my procrastination time browsing the websites of the State Parks of New South Wales and of Queensland, plus a number of other similar get-out-and-explore Australia websites. The Sunday Drives, which have been dormant here in Sudbury since October (not that I post about them but I do go on them!) will be restarted as soon as possible in Australia. Like Sudbury, Armidale is surrounded by some amazing protected areas that I can't wait to explore.

The move itself has been (and continues to be) a large and seemingly never-ending amount of work. We received the Letter of Offer in late October, so we had about two months to do all things needed for a move like this. Packing, and sorting possessions into take/store/sell/donate has taken much of our time, but some things further from our direct control also require both long times and considerable effort. The visa application, again without talking about it in detail given we have not received it yet, is the obvious example, with published estimates on government websites that our visa may take two months to be processed, though hopefully much less. UNE has hired immigration lawyers to help us, and Visa Lawyers Australia (VLA) have been absolutely wonderful. There's a lot to say in the future about this process, too, but I can say that VLA has been great.

Selling things has been surprisingly effective, I had not expected to make nearly as much money as we have - with more (hopefully) to come - through Facebook Marketplace and eBay. Large things that are not worth shipping, mostly furniture, have gone to local people, organised by Charlie. Smaller things with narrow appeal - mainly my old camera gear - has gone out through eBay. I have bought a bunch of things (including old camera gear) through eBay, but until this move, I had never sold anything. The first to go was my collection of Dragon Magazines, to a few buyers in Ontario and Quebec. Camera stuff has gone to B.C., Alberta, Saskatchewan, Manitoba, Ontario, and Quebec, as well as several American states. In some cases, the cost of shipping exceeds the cost of the item by up to double, but the buyers are willing and the post office is nearby.

That said, if you feel like browsing what I've got up, there are a few more auctions left to run before we drive west (next week), search for "martinb003" on ebay.ca and you'll find me.

Our plan for the move, now well under way, is to drive to Calgary for Christmas, then fly to Armidale by Calgary - Vancouver - Sydney - Armidale. Qantas flies at least once a week on the critical Vancouver - Sydney route, and a few other airlines such as Air Canada also make that trip on most days. We want to avoid stopping in the USA because while it potentially could be less expensive (though not necessarily, as we have seen browsing ticket sellers) there is a large and worrying possibility of all kinds of hassle with US Customs that we would prefer to just dodge. This emotional state comes with strong prioritisation to minimize time and worry requirements in favour of getting stuff done, because there are so very many things to do.

The Death of the Scientific Paper

I’m sitting in my office at Université Laval, waiting for an opportunity to speak with my professor, and procrastinating revising a manuscript. My procrastination, almost always, is to read the internet, and today I’ve found a new article from The Atlantic, “The Scientific Paper is Obsolete”. 

The main thesis of this article is that the scientific paper as we know it today has outlived its utility. The author, James Somers, opens with a description of the niche the scientific paper was invented to fill: a short, incremental advance published as widely as a book but as readable as a letter, and permanent where a lecture is ephemeral. I’ve had conversations with academics in social sciences or humanities disciplines who express their surprise that books, which for argument’s sake are publications longer than about 100 pages, almost never appear in the list of citations in my scientific publications. I list 11 publications – scientific papers – on my C.V. with me as an author (always one of several, I have no sole-author publications) and I’m first author on 7 of those; this means I did most of the actual writing. I feel this experience gives me some perspective to evaluate the article in The Atlantic.

There are the expected jabs at the style and perceived readability of scientific papers, a criticism so widespread and consistent that I now mostly ignore it. I get it, you don’t get the enjoyment of reading a scientific paper that you get out of reading something else, and you put the blame largely on the abundant jargon and dense prose of typical scientific papers; James Somers also adds some mentions of “mathematical symbols”, which is indeed one major feature of many scientific papers that separates them from written works intended for a wider, non-specialist audience. But that’s the point – the intended audience of a scientific paper is not the general public, it’s other experts in that discipline. Know your audience. I guess James Somers does - scientists and non-scientists decrying the difficult prose of scientific papers to non-scientists is very popular in popular science articles.

This isn’t to say that a scientific paper cannot be or should not be highly readable to non-specialists and other members of  the general public, but to approach a scientific paper as a non-specialist and then complain about the jargon is to miss the point. I think one has to approach a scientific paper from a position of self-knowledge, in that I have to read a paper outside my area of expertise in a different (and more difficult) way compared to reading a paper that might cite my own work.

Another major difference between a scientific paper and something like an article in The Atlantic – and these two categories are of similar word-count, on average – is the abundant citations in a scientific paper. Every fact, every suggestion, every piece of information in a scientific paper that is not derived directly from the study itself will be cited; credit is given to the prior work that established those facts or provided those suggestions (unless the fact or suggestion is obvious or already widely known and established; we don’t cite Scheele and Priestly (1772) when talking about oxygen, for example). I find myself wishing for some citations and outside attributions while reading this Atlantic article because James Somers makes so many claims that I would like to dispute.

For example, here’s the third paragraph of the article:

The more sophisticated science becomes, the harder it is to communicate results. Papers today are longer than ever and full of jargon and symbols. They depend on chains of computer programs that generate data, and clean up data, and plot data, and run statistical models on data. These programs tend to be both so sloppily written and so central to the results that it’s contributed to a replication crisis, or put another way, a failure of the paper to perform its most basic task: to report what you’ve actually discovered, clearly enough that someone else can discover it for themselves.

 Are papers really longer in 2018 than they were, on average, in 1998, or 1978, or 1888? Are they more “full of jargon and symbols”? Are the majority of analytical computer programs “so sloppily written”?

And what replication crisis? Mr. Somers, have you not read the recent counterargument to the crisis-in-science narrative by Dr. Fanelli, recently published by PNAS?  

Moving on, one major criticism is that scientific papers are not a good way to express and describe complex results. Animations, something computers are quite good at, are useful tools for visualizing such complex concepts but are very difficult to express on a static sheet of paper, which the modern PDF (Portable Document Format) emulates. I agree, but I do not agree with the follow-up point that this renders the PDF hopelessly useless. A scientific paper is about the words, not the pictures or other visualizations. It’s about the information. Expressing that information in a way the audience can understand and use is the key skill of writing a scientific paper, and is distinct from the skills that create written material intended to be read by as wide an audience as possible. A scientific paper relies heavily on absolute honesty, and presenting all of the available and relevant information to allow the reader to independently decide to agree or not with the author’s arguments and conclusions. A magazine article pushes a particular interpretation of some phenomenon. A scientific paper pushes the phenomenon and then describes one (or sometimes more) possible interpretation of that phenomenon, usually in light of similar phenomena and potential alternative interpretations. A graph is not data, it's an expression of data. An animation is not an argument, it's one support for an argument.

Visualization is a technique, a way to take obscure numbers and show the patterns they contain. I struggle with it, constantly. The paper I am procrastinating working on right now has some decent figures* in it and I don’t see a need for a great deal of work on the visualization side of this paper. I have another project I’m working on that is at a much earlier stage and my current activities there are primarily concerned with visualization. I’m at the “data exploration” stage, where I throw the metaphorical spaghetti of the data at the metaphorical wall and see what sticks. That means lots and lots of images, mostly graphs I get my computer to make for me, and some scribbles on paper in my notebook.

*A figure is any image in a scientific paper, a photograph or map or, most commonly, a graph illustrating the mathematical relationship between two or more parameters. I tend to write papers by making the figures first, but that's a personal style and subjective workflow thing, and certainly not universal among scientists.

Back to The Atlantic

It’ll be some time before computational notebooks replace PDFs in scientific journals, because that would mean changing the incentive structure of science itself. Until journals require scientists to submit notebooks, and until sharing your work and your data becomes the way to earn prestige, or funding, people will likely just keep doing what they’re doing.

This is more interesting to me than the preceding description of competing formats for “computational notebooks”. I have seen suggestions from other people that concentrate on changing other aspects of scientific publishing, often the abolition of for-profit publishing companies (e.g. Here), but these suggestions and discussions do not express a dissatisfaction with the basic unit of scientific communication, the scientific paper. What would my job look like if both scientific papers and the way in which they are disseminated were to go away? Would I just be uploading lumps of code and datatables to some institutional server, whenever I feel like my analyses have answered some tiny question? Does my "Literature Cited" section just become a link-dump?

“At this point, nobody in their sane mind challenges the fact that the praxis of scientific research is under major upheaval,” Pérez, the creator of Jupyter [one of the competing calculation notebooks – MB], wrote in a blog post in 2013. As science becomes more about computation, the skills required to be a good scientist become increasingly attractive in industry. Universities lose their best people to start-ups, to Google and Microsoft. “I have seen many talented colleagues leave academia in frustration over the last decade,” he wrote, “and I can’t think of a single one who wasn’t happier years later.”

I had to look up the definition of “praxis”; I think it’s exactly what I was talking about, what does my job look like if the scientific paper and scientific publishing are drastically changed? Dr. Pérez apparently thinks my job would not change much. I’m not so sure.

There’s also a problem in that paragraph with a possible logical fallacy: confirmation bias. Lots of sad people leave, and then you find a few of them later and they’re happier. Well, good! Happier people is a good thing. But to then claim that it was the act of leaving that made them happier, and then extend that by implication that everybody should consider leaving, is to stretch beyond the available information into unsupported (and idealistic) speculation. If the only people who left were the unhappy people, then what about the happy people who stayed? Would they have also become even more happy had they left? Did the people who stayed unhappy, or became more unhappy after leaving avoid talking to you?

At this point I’m wandering away from the discussion about scientific papers. And I think the article did, too. It concludes with a weak suggestion that maybe some new tools will be useful (who could disagree with that? Tools are useful by definition) and that, hey Galileo, right?

I remain unconvinced in the impending death of the scientific paper. What I got out of this article was a description of some computer programmers and physicists with generally poor social skills but good ideas and skills related to generating and analyzing data. And that somehow this means the time I spend teaching ESL graduate students how to write better English that is also in the demanding, highly technical style of current scientific communication is somehow wasted.

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 - http://carlhoffman.com/ - 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.

Musings on my Career

Yesterday I submitted a manuscript to a journal. The manuscript describes the work I did in the summer of 2010, and has been rejected from another journal and undergone massive revision, repeatedly, in the nearly three years since the raw data was collected. The journal is, in the minds of myself and my advisory committee (i.e. my co-authors) entirely the right fit for our manuscript, even though the publisher is one of the big, evil, for-profit companies that followers of a certain subset of the sciencey blogs will be familiar with (perhaps as an insulting word, spit out rather than merely spoken). My paper will not be open access – I couldn’t find my advisor to ask when that question came up during the submission process.

Oh, the submission process. I’m not going to rant about it now, I feel like yesterday was taken with that episode, with consequences – sometimes I feel the need (i.e. the complete lack of useful motivation) to take an evening and crumple it up into a ball and toss it into the corner (I played Civilization V, while drinking beer). The only noteworthy part for today, I think, was the weird cognitive convolutions I underwent when choosing from the list of topic areas (“Field plots; Greenhouse gases; Methane; Exchange with Atmosphere; etc.), due to the next paper that’s already in my mind – I had to stop myself from selecting all the keywords relating to the molecular biology that forms the core of my next paper.

The reason I went to Tasmania for four months (besides simply it being an awesome, excellent place to go) was to learn some laboratory techniques while applying them to my samples (my soil samples, and microbial DNA extracted from them) with the clear, explicit intention of creating a major manuscript for my PhD thesis – I think of it as “Chapter 3”, where my already-published paper (Brummell et al., 2012) is Chapter 1 and the manuscript I just sent in is Chapter 2. Those numbers might get pushed around a little, for example if I write “bookend” introductory and summary chapters in the actual thesis, but nobody reads an entire thesis anyway so it doesn’t really matter.

Besides “Evil Scientific Journal Publishers” posts, I’ve been reading many blog posts about academic careers, particularly of scientists (especially of biologists). Thus today’s musings. It’s kind of an odd time for me to be devoting time to this, given my departure for a 2-month field expedition in about 5 weeks and my need to scoop my Tasmanian data into a pile resembling something manuscript-like, but there’s a point that the blog posts I’ve read have not addressed but that I have discussed several times with my advisor; I think it’s also notable that he and I have never discussed Open Access publishing or opened the “Evil Publishers” can of worms (we’ve tossed that can back and forth a few times, and placed it on the counter and talked at it, to stretch the metaphor).

The point: Publish or Perish. It’s a cliché, and all most clichés are at least partly true. Rather than take it in the sense of a dire warning (“Thou Shalt Crank Out Pubs at Thine Fastest Rate!”), my advisor and I have several times discussed this point as a focus aid: Publishing is Always Useful. When considering career options, within, beside, or outside of academic science, no option includes “publishing papers is a waste of time if you go down this path.” Even completely non-science career paths will (theoretically) benefit from a CV with a list of publications on it; even to a non-scientist, there’s a certain prestige and value associated with demonstrably undertaking a complex project all the way from genesis to completion; it’s evidence of getting things done.

So, I am spending essentially all of this week working on my data from Tasmania, trying to turn it from an amorphous blob of numbers into a narrative describing my newly-acquired knowledge.

Instead of, you know, choosing which Rival Empire to antagonize based on the label I’m pulling off of the bottle of beer.

Japan is not actually one of the Rivals in the game of Civ V I started playing last night, but I was drinkin Sapporo beer and in the course of building this image I discovered the wonderful thing that is their website. 

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Literature Cited
Brummell, M.E., R.E. Farrell, and S.D. Siciliano, Greenhouse gas soil production and surface fluxes at a high arctic polar oasis. Soil Biology and Biochemistry, 2012. 52: p. 1-12.

ZOMG

OK, it's been more than 7 months, and for that I apologize. It's likely the majority of my posts around here will start with an apology like that, but them's the breaks.

Anyways, just a quick note to say "still alive". Not sure why I'm writing right now, I just felt like writing I think. Which is odd, considering how much writing / rewriting / analyzing / reanalyzing / proofreading / editing / designing / et cetera on my computer at school I've been doing for the past... say... 7 months or so.

News, I suppose, is in order.
1. Not going North this summer, which is sad. Everything was lining up nicely for me to spend an excessive amount of time at Resolute Bay, but funding fell through at the final hurdle.
2. On the other hand, this does give me time to get some serious lab work and data generation done here in Saskatoon. Back to the molecular grind, in other words - which I'm actually looking forward to, I've been telling people "yes, I do PCR" but in that uncertain, hypothetical sense that I'm sure came through in my tone of voice and body language. It's one thing to say "I do PCR", it's another to say "I'm running a PCR right now, stop bugging me this damn pipetting robot is trying to kick-start the inevitable robot uprising again and I'm a little busy suppressing several of the metal ones".
3. I have been on many Sunday Drives since my last post, and I have not improved noticeably in my ability to edit & upload the photographs (and rare video) in anything like a timely fashion. However, I have taken steps that I feel are starting to address this imbalance.
3.1. I have purchased a "pro" Flickr account, visible here: http://www.flickr.com/photos/49837331@N06/ Link for those whose browsers don't like that URL.
3.2. I have purchased Lightroom 3.3, for about $100 using the 'education' discount. I will argue that my educational position fully qualifies me for discounts on photo-editing and photo-management software - a handful of my photos have been published by University publications!
4. I guess I should follow up that last point - back in the fall, a person whose job description includes publicity things for the Faculty of Agriculture and Bioresources approached me about having photos from the 2010 field season in the High Arctic. I did indeed, I put some together and sent them to her, and a few showed up in an article about our work in the University's internal newspaper - uncredited, of course. Oh well. Minor additional upside: she also shoots a Pentax, so there's a possibility for further gear-geekery in future.
5. More driving: I joined the Saskatoon Sports Car Club, and was nearly immediately elected to the exective (with only 17 active members, pretty much everybody has to take turns as director at large, or president, or treasurer, sooner or later). We've got about 18 autocross events planned between the end of May and the beginning of September, and I'm planning to get to every event that I'm in town for (and that my car is up for). New tires are in order, anyways.
6. Good news on the funding / scholarship side of things, but it hasn't been officially announced yet so I can't talk about it. It's very good news, though, and I am pleasantly surprised. Also, somebody done screwed up, 'cuz I sure don't deserve it.
7. Plenty of other things are in the works for the coming year. No promises, but I plan to avoid neglecting this place for quite so long an interval.

One of the reasons I like Flickr is because it supposedly streamlines linking pictures to a blog, as I will now attempt to demonstrate.

Yes, my Flickr username is "Execudork". I chose that name long before I considered the possibility that one day I'd have to spell it out over the phone to my mother. Could have been worse, I suppose. Thanks, Internet!

Proposal II and Car Wars

My first PhD committee meeting was this morning, at which my proposal (see previous post) was discussed, and much feedback was given and recieved. The formal, administrative part of the meeting was the Signing of the Form. My committee members all (there are three of them) APPROVED my proposal, but with the caveat that I need to revise it in line with their recommendations. This revision process is less structured than the basic process of the timing and composition of the meeting, so some of the stress has certainly come off - the hard deadline for the revision doesn't yet exist, just a promise to have it done in a "reasonable time frame"; I'll set a deadline for myself, rather than have one imposed from somewhere. So, overall, pretty good.

The revisions and recommendations of my committee were quite good, actually. Unlike the vibe I'm getting from some of the other grad-student-bloggers I read regularly (you know who you are), the advice I'm getting is mostly relevant and reasonable. Much of the focus of today's recommendations, for example, was on improving my PhD project with two practical goals: make my comprehensive examination committee happy this fall and make my research much more likely to be published in the peer-reviewed literature. I now have a fair bit of work to revise my proposal (essentially, I need to invert it, remove about 1/12 of it, and add perhaps two pages worth of "I will use X to do Y"), and it's been drilled into me that my PhD will be very hard work, very much a "full throttle" kind of project, but for the next couple of days I can perhaps not spend all my time at school obsessing over next summer's plans. Just most of my time.

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Last post's comment thread somehow wandered down memory lane with a discussion about Car Wars and general geekiness. I'm going to expand on that here.

Car Wars is one of my favourite games. It's certainly no role-playing game (much more "roll-playing"), but it's also much more open and unstructured for reasonable comparisons to board games. It's perhaps most similar to minitures table-top wargames, and I believe it has been described as such by one or more of the game developers.

I'm just going to take a moment now and remember some of the good times I've had playing Car Wars.....

OK, I'm back. Anyway, for those unfamiliar, Car Wars is a game in which the players design their own combat vehicles (i.e. cars with guns) and fight against each other, often in arena combat within a well-defined space. It's a tactical wargame in that the strategy part all happens before play, in the choices players make in the design of their vehicles. The time frame is very stretched, such that one second (one turn) of game time can take upwards of 30 minutes of real-time to conduct.

A typical game of Car Wars might involve 4 players and a medium-sized arena, representing an area of land roughly equivalent to a football field. The arena is a piece of paper covered in 1 inch and 1/4 inch grid (faint 1/4 inch lines, heavier 1 inch lines); a map that represents the area of play. The cars are cardboard counters, usually 1 inch long and 1/2 inch wide, with a top-down view of a car. The details (beyond the size) of the counter don't matter; what matters is the design on paper that each player has. Given the number of options in car design, the possible combinations of body style, engine, wheels, weapons, armour and accessories rises to some stupid number. Obviously, a large portion of that combination-space contains illegal (e.g. engine not powerful enough) or simply poorly constructed (e.g. weak front armour) options. But the possible decent combinations are very large in number, and the "optimal" design cannot be predicted before play starts, since this is (in some respects) really a game in game-theory terms; the best decision a player can make at any given time depends to a large extent on the decisions made or possible decisions other players make.

Anyway, once everyone has figured out their cars, and placed them at the entrances to the arena or whatever pre-determined start locations and velocities have been agreed upon, play starts. Each turn represents one second of game-time, and is subdivided into five phases. At low speeds, most of those phases won't matter, but as the cars reach moderate and faster speeds, upwards of about 40 mph, every phase has something happening in it. The usual victory conditions are simply total victory - last car standing. Drive, shoot, crash, burn. Really, it's pretty straightforward. Decisions like loss of control at high speeds and whether one's machine-gun burst hits one's target are determined with dice rolls, with minimum roll for success modified by a long list of factors (e.g. it's harder to hit something that's farther away with a gun, so longer distances on the map inflict penalties in the form of raising the required minimum dice roll to-hit).

Hilarity ensues, when we're not arguing over the exact targetting conditions (I mentioned the list was long; off the top of my head I'd say there are perhaps 40 different factors that can influence any given shot, and a further 20 that might apply only in unusual circumstances). So, it's a pretty math-heavy kind of game, with almost every action accompanied by "roll, uh... 8 or higher" or similar. Computerization (the game was first printed in 1981) would be a huge advantage in Car Wars, but nobody I know has gotten the wherewithal together to put together a spreadsheet or something that will speed up play. I'm not asking anyone to computerize Car Wars (been done, reasonably well, long ago, but Car Wars is a huge potential play space, so...), I'm asking for a program that allows me to rapidly select options and have it tell me what I need to roll to blow my opponent's front-right tire off with my Vulcan machinegun at a distance of 10 inches. Or how many incendiary rockets I need to pump through that hole in his armour to set him on fire. Or how likely I am to roll my car and die taking that corner at 75 mph.

Back in Guelph

Two days ago, Saturday, I flew back to Onterrible from Churchill. Nothing too exciting to report, just a couple of fussy, noisy children on the planes and a delay leaving Churchill that did nothing but shorten my lay-over in Winnipeg.

So, now I'm back, with my less-restricted bandwidth and a larger, more comfortable bed. Some of the pictures I took during my four weeks "up North" were on film, not digital, so I'll wait to post the big photosets until I get those developed, probably to CD-ROM. My plan is to do that this week.

Apparently, the lab moved TWICE while I was away, once to the new building then again immediately after that to a different lab on a different floor - the labs are all mixed groups, with multiple PIs*, and my advisor wanted our lab co-inhabitants to be people studying things more like what we work on, i.e. evolutionary biology rather than ecology. Whatever, I didn't have to carry anything heavy for either event, so I'm not concerned. Tomorrow I'll discover what's what, and get back to work.

In other news, I've been shockingly lazy and antisocial since I got back to Guelph - I have yet to set foot outside since my arrival Saturday evening. I haven't been completely useless, though, as I assembled the bookshelves and organized my books that my parents had been looking after for me since last August - they drove in from Calgary and are spending some time vacationing at the cottage. I think part of my general reclusiveness and low-activity comes from the drastic reduction in my caffeine intake. In Churchill, where free coffee was always plentiful but sleep was not, I was drinking up to six cups per day, compared to a normal weekly intake prior to my trip of about four to five cups per week. In the last two days, I've had one cup of coffee. Other factors include a low-level viral infection (Rhinovirus, I think) and the wonderful opportunity to catch up on my sleep deficit. The latest I was able to sleep in Churchill was 9:00 am, after a late night up until 2:00; yesterday I woke up at 2:00 PM. That was glorious.

Anyway, I couldn't justify NOT writing something here, so this is just a little "still alive" note full of promises about upcoming things (photos) I'll fulfill as other commitments (school/work, family, decaffeination) allow.

* Principle Investigators, a fancy term for "professor"

Rick Mercer visits Churchill

Via Greg Laden, an entertaining story from Rick Mercer.


Also, I wish I could tell stories as well as Rick Mercer.

Short Thoughts

I'm off to Churchill, Manitoba for 4 weeks on Saturday, so I don't feel I have the time or the intellectual energy right now to fully develop some of the ideas rattling around in my head. Also, I expect this blog to be rather quiet while I'm away, since I do not yet know what kind of internet access I'll have in Churchill, and I do expect to be very busy while there, and not have much time for reflection and writing about thngs not directly related to collecting and measuring genomes in arctic invertebrates.

So, this post will serve as a place for me to throw some ideas 'out there', and perhaps my (three or four) readers can talk amongst themselves in the comments. Or just ignore me and come back when I do, after August 4.

1. Lab Notebooks

I discovered a couple of posts at Adventures in Ethics and Science: part 1, part 2; via a post at Sandwalk. I'll put out my opinion here, but leave further discussion for later. To wit: I think lab notebooks belong to the PI of the lab, for reasons of both intellectual property (the PI's grant paid for the work recorded in the notebooks) and because keeping the notebooks in the lab where they happened makes the most sense in light of the very localized information contained therein - e.g. the specific steps required to get that particular quirky, old PCR machine to run the right program.

2. Environmental Metagenomics

This goes to a larger issue in my mind of what I call myself (there's been previous whining about that here somewhere) and this possibly-buzzword "genomics" and derivatives. Do I do "environmental metagenomics"? What does that term even mean? It came from the Beagle Project Blog (give them money).

3. Grad School

Um, yeah. Lots of random, disjointed thoughts in my head here. Money, the front-end loading of administrative tasks, more money issues, further whining and feeble complaining.

4. Communicating science to the public

I've refrained from getting involved in the "framing" debates, and I intend to stay out. But some sub-issues in that debate, particularly the source (and quality, and quantity) of raw data on things like public school systems and science education, do interest me.

5. Science blogging

Many of the people who write the blogs on my bookmarks list attended the recent microbiology meeting in Toronto, and lots of others were at the SMBE in Halifax. I'm jealous of Carlo's invititation from such people, and I don't feel like I write a science blog - this is just a little hobby for me. However, I am considering the possibility of starting a second, science-only blog, and keeping this for personal stuff (book reviews, rants, etc). If I do this, it won't happen soon, probably not until next year. But it's a thought.

More as I think of things.

Update: 5:15 pm

6. Cranks and Science

I did not expect to meet 'cranks' in my field when I started my PhD and dove into the genome-size literature. Nonetheless, the idea of non-coding DNA and associated terminology such as "junk DNA" seems to attract the attentions of a certain group of people who are convinced that they have come up with the hypothesis (or just an idea, sometimes) that either a) thoroughly solves some problem in genomics like describing a universal and until-now poorly appreciated "function" of Junk DNA or b) blows some part of biology completely out of the water. "b)" tends to come more from creationists of various stripes, who I don't normally count as cranks - they're more denialists than cranks per se. I post this now because I just checked the email account that recieves notices of comments here, and discovered two new comments on old posts - I leave it to the readers here to find these if they like - for hints, one is a series of rather well-written and entertaining insults against my scientific abilities (and credentials) on a post I made about a rather poor publication, the other is the return of a commenter I had thought long lost, who returned to the series of discussions we'd had on a nine-month-old post about a fictional womanizer with a lovely combination of insults (against my appearance and emotional state, mainly) and a fine final note exhorting the great advantages of being at all times polite and civil.

I'll write more about cranks (and probably trolls, too) at some point. I find the phenomen somehow interesting.

Eight Facts about TheBrummell

I saw this meme over at PZ's earlier today, and tried to think of some things to put up should I find myself tagged. PZ did not tag me, so I forgot about it until I stumbled across Laelaps' post, and his tagging of me. The rules are a little different between the two editions (PZ vs. Laelaps), but I expect they share a recent common ancestor.

I'll post the full 5 rules of PZ's version, in something akin to horizontal transfer:

1. We have to post these rules before we give you the facts.
2. Players start with eight random facts/habits about themselves.
3. People who are tagged need to write their own blog about their eight things and post these rules.
4. At the end of your blog, you need to choose eight people to get tagged and list their names.
5. Don't forget to leave them a comment telling them they're tagged, and to read your blog

Laelaps' edition includes very similar rules, organised into only three points. Anyway, on with the show. The other "random" facts I've seen have mostly been about childhoods.

A. I lived in England (UK) on two separate occassions as a child - first for about 9 months in 1984, a period I have very few (and mostly very vague) memories of, the second time for about 2.5 years from January 1988 to July 1990. I did not enjoy living there in either instance. I have heard people tell me they wish they'd had such chances to travel (travel we did - France, West Germany, Switzerland, Crete, Benelux...) when they were children; these people do not know what they're talking about. Travelling in the back of a car with one's family when one is 11 years old is never enjoyable, regardless of the locations visited. Also, school uniforms suck.

B. The first one here was too negative, so on to something positive: I went on many great camping trips in the Canadian Rockies near Calgary when I was a teenager. While some camping trips were pretty bad, the majority were either very fun or so extreme and weird that the ability to tell great stories and share in-jokes after the fact make them great. I've crossed the continental divide a few times over saddle ridges between bare rocky peaks 2000 meters tall, with a 15-km view (or more) that contains not a single sign of humanity through 360 degrees. I also have some great photos from those trips; a few were taken by me.

C. I visited Bamfield, BC, in grade 11 on a school trip organised by the (public) education board of the City of Calgary, and I was the only person from my high school to go that year. That trip solidified in me my already-strong desire to become a marine biologist (next year... post on that coming sooner or later), and created a strong desire to attend Bamfield for summer coursework. The easiest way to get to summer courses at Bamfield is to be a third- or fourth-year student at one of the five member universities; those are the only universities I applied to at the end of grade 12. I was accepted immediately to the university of Calgary - not a surprise, any Calgary-resident grade 12 student with halfway decent marks who applies gets accepted there. The university of Alberta also accepted me, eventually, as did Simon Fraser University. UBC, oddly, offered me a place in residence, but did not accept my application. The university of Victoria similarly rejected me; because UVic was my first choice, I appealed their decision based on differing high-school graduation requirements. They had rejected me because I did not take a grade 11 or higher second language, a requirement for graduation in B.C. high schools. I explained to them Alberta's more anglophone requirements, and they let me in. I visited Bamfield again for a third year invertebrate biology course (long weekend) and attended summer courses there in 2000. My father now occassionally jokes that I think Bamfield is the best place on Earth. That's not entirely incorrect.

D. I have two facial scars, though both are small and only one is noticable. Above and lateral to my right eyebrow is the faint scar that resulted from getting hit by my cousin's bicycle (he was riding it; it might not have belonged to him) via the brake handle, at the age of five. I had five stitches, and a scar... perhaps one centimeter over, and I'd have an eyepatch or something. AAARR!!! The other scar is the result of a curling injury. That's right, I have a scar from an injury inflicted upon me while playing CURLING. I'm one step away from maple syrup for blood, ya hosers. To be honest, it's not that exciting. The scar is tiny and hides in my left eyebrow; I got it by pulling myself off my feet while sliding down the ice by hooking my broom onto the leg of an ici-side bench. The spring-hinge-cover of my glasses dug a hole in my head when I faceplanted on the ice. Two or three small stitches.

E. I have little experience of stress. Exams, minor deadlines, travel, personal relationships, all elicit only the weakest of stress responses in me. I've never been in a traumatic situation, though, so I can't say anything about really stressful situations. This summer, however, I am experiencing stress (an inherent part of the PhD process, I gather). Between now and the end of August, three interacting and major things will happen in my PhD. 1) My first ever field season, four weeks in and around Churchill, MB, starting July 7, collecting invertebrates and preparing the specimens for genome size measurement. The stress here comes from a) the fact I've never done this before combined with b) the realization that I have a shitload of things to get done before I go, not least of which is write a rough draft / detailed outline of the review paper that will form chapter 1 of my eventual thesis (and serve as a guide to some of my activities in Churchill), and perform half-a-dozen last-minute mini-experiments in the hope that I will be able to preserve some collected specimens and not need to deal with them (dissections) in Churchill. The first such experiment was disappointing: I do not think I will be able to use a graded ethanol concentration series for preserving arthropods. Shit. 2) The lab is moving! Yay! In fact, the WHOLE DAMN DEPARTMENT is moving to a new building. Moving one lab is one thing. Moving an entire building is something else entirely. The local upshot of this "relocation" process is that I can not do any more lab work as of tomorrow. So I've been trying to get those mini-experiments I mentioned done very quickly, and working on that review paper later at night. The last two nights I stayed at my desk until later than 10:00 pm. This is rather unusual for me, but I expect (and welcome, to some extent) many more long days in future. At least I feel like I'm accomplishing things... there's just so many more things to do. 3) PhD administration stuff: I need to have my first committee meeting before the end of August. Before that meeting can be even scheduled, I need to get a committee. One of the minimum three people on my committee has to be from outside my department (Integrative Biology); getting an outside person involves my advisor submitting a letter and that person's C.V. to the department. So there are some beaurocratic events that I have to coordinate. I have to return the form listing who is on my committee, with signatures, to the department BEFORE I go to Churchill. And when I get back, before I have the meeting, I have to write a PhD proposal that my committee will accept (and sign!). This PhD proposal's requirements are still very unknown and vague to me - the graduate secretary here did not provide me with a straight answer, and passed my questions off (via me, of course) to other people in the department. In other words, I asked "what's the story on this PhD proposal thing I have to do before August 31, you know, in between a month in the Arctic and, oh yeah, a week in New Brunswick grabbing marine squishy things?" and her reply was "ask your advisor and the chair of the department's grad studies committee". Great. MORE contacting people out of the blue, while THEY'RE DEALING WITH THE MOVE, to ask random semi-stupid questions that will (GUARANTEED) have answers that make me sad. I'm expecting my questions about this proposal to be answered by something like "typically, the proposal for a PhD student is a very detailed, 30 page manuscript describing everything..."
Also, I should be working on that review paper right now, or composing polite-but-urgent emails, or something other than writing this blog post that my advisor WILL read and who will almost certainly then ask me awkward questions about the progress of my work (with obvious, but unsaid, implications for my future as a graduate student). Urgh... so this is why people complain about stress.

F. Another thing for me to stress about: money. There are some indications that I will be flat broke, and need to borrow money (from my parents) by approximately September. I have not Monday-ranted about grad salaries because I said I'd only rant about things that are trivial-but-real; grad salaries are non-trivial to me. To look on the bright side, owing yet more money to my parents will serve as strong incentive for me to get NSERC funding; the application deadline is sometime in October.

G. Two negative facts in a row, more happy needed. I appear to be in excellent health. Never in my life have I broken a bone or had surgery more invasive than stitches (see above). I've never had a serious infection, and my (again, non-life-threatening) allergies are limited to a single class of antibiotics that are not widely used, anyways. I recover from colds and other minor illnesses rapidly; I think my average feel-bad time for a cold is about 3 days. Recent work-related health investigations have all come back very positive - the doctor's (cautious) opinion was that I'm certainly fit to dive, and physiological measures such as cholesterol and haematocrit are all well inside the healthy range.

H. I attribute my acceptance into the M.Sc. program at Simon Fraser University partly to my M.Sc. advisor's dogs. When I met him, I had driven to SFU to meet with more than one professor, and met him near the end of the day. Besides us 'hitting it off' well from first meeting, he took me for dinner to an Irish pub near his home, and he was very pleased when I happily agreed to transport his dogs home at the same time (his wife, another professor at SFU, had needed to leave earlier with the car to attend some meeting or something and couldn't take the dogs because she wasn't going anywhere near home until much later that night). My one-and-only vehicle that I have ever owned, a 1990 Dodge Grand Caravan SE (3.3L V6), was well suited to the task. And his dogs seemed happy with the arrangment, too - the larger of the pair, Harry, a mostly-German-shephard massing near 50 kg took the three-seat back bench, and Shasta (also mostly-German-shepard, but with some other traits thrown in), massing about 35 kg took the two-seat center bench. These were also consistently their positions when I drove those dogs around on later occassions, for example when I was house-and-dog-and-cat-and-fish-and-stick-insect - sitting for my advisor's family while they were on vacation. While I'm not much of a dog person, and I've had my differences with those individual canines, I did enjoy their excellent car behaviours.

OK, that's my eight facts. I will tag Carlo, Necator, BronzeDog, Infophile, The Angry Astronomer, Rick of My Biotech Life, The Everyday Scientist, and King Aardvark.

Programming Languages Quiz

Which Programming Language are You?

I don't know very much about programming languages in general or Java in particular, but at least I have met Java before, unlike some of the other programming languages that are possible outcomes of this quiz.

Incidentally, it's nice to be able to see all possible outcomes of a quiz - too many of these very silly things just spit out your 'result' and you have no idea what the other possible choices are.

Yet Another Stupid Intarweb Quiz!

Since I know that my too-long-to-write-and-format 'serious' post I just put up will generate no comments because I'm the only person on Earth who thinks about comparisons between families across classes, I did another stupid intarweb quiz. Apologies in advance for crappy formatting weirdness.


You scored as Scientific Atheist, These guys rule. I'm not one of them myself, although I play one online. They know the rules of debate, the Laws of Thermodynamics, and can explain evolution in fifty words or less. More concerned with how things ARE than how they should be, these are the people who will bring us into the future.

Scientific Atheist		92%
Apathetic Atheist		67%
Spiritual Atheist		33%
Angry Atheist		25%
Agnostic		17%
Militant Atheist		8%
Theist		8%

What kind of atheist are you?
created with QuizFarm.com

Incidentally, I probably can describe the Theory of Evolution in 50 words or less. And I am much more concerned with "is" than I am with "ought". I'm probably a little shaky on the rules of debate, never having participated in a formal debate, and my grasp of the laws of thermodynamics extends not very far beyond the ability to list them, and a willingness to shout like a crazy person and point at the sky, screaming "Mr. Sun!!!" over and over at people who misunderstand the second law to be something that prohibits biological evolution.

What the hell is a "spiritual atheist"?

Existentialist by teh intarweb

You scored as Existentialist. Existentialism emphasizes human capability. There is no greater power interfering with life and thus it is up to us to make things happen. Sometimes considered a negative and depressing world view, your optimism towards human accomplishment is immense. Mankind is condemned to be free and must accept the responsibility. Existentialist 94% Modernist 88% Materialist 88% Postmodernist 69% Cultural Creative 38% Fundamentalist 31% Romanticist 6% Idealist 6% What is Your World View? created with QuizFarm.com

I strongly suspect this result was triggered by my answering "strongly agree" to "Mankind is condemned to be free (there is no outside control)", which now, post-testing, looks like a keyword-loaded statement. I was more agreeing with the part in parentheses than with the vaguely-dogmatic statement about "Mankind". Is that a quote from some famous dead person?

Also, how did I score 31% for Fundie? For the record, I think Fundamentalists of all stripes are dogmatic fools, and the doctrine of Fundamentalism for any ideology is stupid.

Otherwise, a mildly entertaining diversion from what I should be doing (reading papers about squishy things).

Hattip to Larry Moran at Sandwalk.

BBC News

News that could save your life.

That is all.

Making Wine II

Last night I racked the pre-wine from the primary fermenter to the secondary, also known as the carboy (Fig. 1). This took a surprisingly long time, both to get the siphon going (I avoided accidental ingestion of any rotting fruit juice) and just to run. The diameter of the siphon is pretty small, so to move the 23 L of pre-wine took almost ten minutes. I think I managed to avoid almost all of the sludge on the bottom, though I'm sure a little got through. There are two more racking steps before bottling, meaning three siphon runs remaining and three chances to separate the good stuff from the precipitate.

Fig. 1. Pre-wine being siphoned, or "racked", from the primary fermenter to the secondary fermenter.

Anyway, nothing really exciting happened, and I avoided breaking anything made of glass. Now it sits for another two weeks or so (Fig. 2), presumably in a situation designed to encourage anaerobic respiration and the efficient conversion of sugars (fructose) into alcohols (ethanol). I topped up the carboy with about a litre of clean water, to compensate for the lost volume represented by the aforementioned sludge.

Fig. 2. The full secondary fermenter in place, with airlock.

Also, I never mentioned the details of the kit I'm using, so I took a picture of the box using my crappy cell-phone camera (Fig. 3). It's from a company named Cellarcraft, a variety they name Rio Negro. The juice concentrate came from Chile - a nice bonus, as I've had some very good red wine from Chile in the past (Gato Negro Cabernet Sauvignon). The downside of making a red wine kit, as opposed to white, is that this stuff won't be good until it's had a chance to mature in the bottle for a few months - I'm planning on giving bottles of this away at Chimmz, about eight months post-bottling. I expect it to be drinkable by the fall, perhaps September. This, of course, renders the kit's insistence on being "4 week" somewhat laughable - I've had enough immature and very bad wine in the past to know I won't be sampling any of this during or immediately after bottling. If I get really impatient, I might open one bottle a week or two after bottling, but I doubt it.

Fig. 3. Rio Negro Chilean 4 Week wine kit. This cost me about $70.