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.

Lab Girl

Lab Girl

Hope Jahren

Alfred A. Knopf, 2016

Hope Jahren is a scientist and a professor and has a blog (www.hopejahrensurecanwrite.com) that I started reading a couple of years ago. Mostly she blogs about her life and her work, which includes plenty of rants about sexism in science and related subjects – she’s a woman scientist, and this isn’t an easy thing to be. This book is her autobiography, potentially Volume I of a series because she’s far from the end of her career and/or life at this point so I assume there are many more stories to be told. But Hope sure can write so I’m quite optimistic that she’ll keep us updated as she sees fit.

This was a highly-anticipated book among the other bloggers I regularly and semi-regularly read. It was also an anticipated book among many of the people I know in real life, who may or may not have their own blogs but many of whom are women and scientists and women scientists. I bought this book in the Chapters in West Edmonton Mall in May; I was at #WEM with my post-doc advisor, Dr. Maria Strack and when I showed her my purchases I promised her I’d loan her the book when I had finished reading it myself. I’ve just loaned it to Charlie so Maria will have to either wait or buy her own copy.

I read Lab Girl in a single weekend. I haven’t read an entire book start-to-finish in a weekend like that for a long time – the last time I’m sure I did that was with Jurassic Park, and I was about 16. I think there’s something about some books that just hooks me at the right age; when I was 16 that hook was in Jurassic Park, when I’m 38 that hook was in Lab Girl. So my opinion of Lab Girl is very positive. But Book Club blog entries have never been about just reviewing a book, they (should) always be about other ideas that flow from reading a book. Such as this idea of age-dependent hooks in books (rhyming is good and fun). Oddly enough, Lab Girl was certainly not written for me, so the hook in it that got me counts as by-catch.

I say that because there is so much in Lab Girl that’s inspiring as a scientist, that gets right at what I want to do as a scientist. More than once, Dr. Jahren describes walking out into an ecosystem, and just letting the environment and her mind interact at some subconscious level until she comes up with a Research Question (capital letters denote things that are more permanent than the daydreams I romp through almost continuously). She kneels in a peat bog in Ireland until an Hypothesis regarding ecohydrology occurs to her, then she starts collecting specimens. She helps a colleague unpack samples and then spends half a decade running fossil carbon through her mass spec. But while I love those stories, they’re not for me – they’re for somebody like me but who has experienced things I have not, things like sexism and manic-depressive mental illnesses interacting with pregnancy.

Having said that, there’s actually less sexism and discrimination and injustice in Lab Girl than I was expecting based on my reading of Dr. Jahren’s blog. My impression of her blog is that she is angry – completely justifiably! – about the institutional sexism and high-level bullshit that infests academic science. That anger is present in Lab Girl, but it’s very much in the background. She may have made her blog about it, but she didn’t make her life about it. Her book, in other words, is not a product of her blog; both her book and her blog are products of her writing, which is itself a product that passes through many filters and checkpoints on its way from her life and her mind. At least, that’s my meta-impression of what of hers I’ve read. I intend to read her scientific papers (well, some of them – at one point in Lab Girl Dr. Jahren mentions a mid-career total in the neighbourhood of 70 peer-reviewed papers) for another look at her overall writing but also because I find myself in a related field. The parts about water-use by plants is especially interesting at the moment.

There are a couple of small errors, and while I really really like Lab Girl, I feel like I need to point them out. The most glaring is a description of DNA and chromosomes as protein. She’s describing the genome of Arabidopsis thaliana, that workhorse of plant genetics, and in two separate paragraphs talks about the length of protein unraveled from each cell. No. Chromosomes do include plenty of protein, but genomes are made of DNA.

In another part of the book, a shocking (to me) casual negligence toward automobile seatbelts is described. Look, just wear your damn seatbelts, OK? Every. Time. Complaints about “Grizzly Adams” field scientists not taking her seriously are much less impressive after reading her laissez-faire attitude towards field work. If you’re going to tell me you don’t feel safe around that creepy post-doc, don’t follow it up with multiple stories of car crashes and heads bouncing off windshields. The creepy post-doc might have legitimately been terrifying, but he didn’t give you a bloody nose and a concussion the way bad car decisions did.

The last thing in Lab Girl I didn’t like – and in a discussion like this I feel I need to remind myself that this is a really good book, like top 10 lifetime books I’ve read GOOD – is a description of what amounts to a “teachable moment”. After her misadventures in Ireland, which culminated in all of her meticulously documented samples being disposed of by an Irish customs agent (Get a permit. It’s not that hard. But I digress), Dr. Jahren has come up with a test of new graduate students that aims to simulate that crushed distress upon having one’s recent hard work destroyed. She describes an exercise in which a new student, somewhat insultingly referred to as a “noob” (LOL OMG BBQ) is made to carefully label a large number of sample vials in anticipation of an upcoming field trip. Then Dr. Jahren and her long-serving research partner (that’s a relationship for a separate Book Club, it’s too big to tackle here) play a game of “Good Cop-Bad Cop” that ultimately results in the entire set of vials being unceremoniously dumped in the trash. This is, on a certain level, a simulation of the end of their Irish trip. But the intent is entirely different, and intent matters.

The intent of the Irish customs agent was to enforce the law, a law that Dr. Jahren should have known about, and Dr. Jahren should have had a permit to export plant material from Ireland. There was a bit of an aside in there about checked vs. carry-on luggage and I don’t think she learned any lessons there; she did claim to have learned the lesson about permits, even if only at the “I’m sorry I got caught” level rather than the truly “I’m sorry for what I did” level.

The intent of Dr. Jahren and Bill in their test-the-noob exercise is to see if an A+ student is really an A+ student or is really a B+ student. The difference, and this is my taxonomy not hers, is that the A+ effort includes something well above-and-beyond expectations, some action that counts as Outstanding. She slyly describes a student who “passed” this bullshit secret test by pulling the vials out of the trash and cleaning them, making them potentially useful for another field trip. There’s so much wrong with that, but I’m going to just focus on the stupid bullshit of a secret test – and that’s all a “teachable moment” is. I went through one or two during my time as a grad student and they were always completely unjust and unfair. If you need me to do something, I’ll do it. If you need me to learn something, I’ll learn it. But don’t “cleverly” combine the two and ruin both. Please. Please, Dr. Jahren, please stop doing that label-vials / good-cop-bad-cop exercise. It shows considerable contempt on your part towards your student, and is a violation of trust. Cut it out.

I would be very happy if pretty much everybody I know could read Lab Girl. It’s a damn good book, a series of great stories told with considerable skill and pushed together into something much bigger than the sum of the parts. I especially want a handful of individuals I know to read Lab Girl; I’m looking forward to presenting this book, this individual copy of a mass-produced hardcover to Maria. And I want to buy more copies for other people. It seems like a mild violation of privacy to describe any of these other future-gift-recipients by name here, but I can plug the wonderful, horrifying, terrifying, fantastic writing of my internet-friend Elise the Great here, and Elise, please read Lab Girl. I’ll send you a copy or an Amazon gift code or something.

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).

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!

Dr. Rob E. Roughley

I received an email today, informing me that a man I was proud to call a colleague and fellow traveller in this business of science has died. Professor R. E. Roughley was not someone I knew well, but I did benefit from knowing him as much as I did, and I am saddened by his death.

Rob was an expert on water beetles, particularly of the family Dytscidae, which is a group I worked on for the time I was based in Guelph. Rob provided excellent advice on methods of capturing, identifying, and generally working on these beetles and other small animals commonly found in the numerous small lakes, ponds, streams, and rivers of North America. His advice was always useful, and I can think of many instances where his help turned my fieldwork, collecting aquatic animals, from hopeless to bountiful.

We shared a glass or two of whiskey while we were both in Churchill in the summer of 2007. I raise my glass now to his fond memory. Goodbye Professor Roughley, you will be missed.

One Good Post

My advisor, Dr. T. Ryan Gregory, has asked a question: How much good can one blog post do? He hopes the answer is "a great deal!"; I share that hope. So, if you're not a regular reader of Genomicron, but somehow ended up here (perhaps by mistake?), please click over to Genomicron and read about the fantastic work Dr. Gregory's parents are conducting.

Donate directly, without the bother of all that reading: DONATE HERE. (look for the paypal button near the bottom)

URLs for the link-averse:
Genomicron the blog: http://genomicron.blogspot.com/
One Very Good Post: http://genomicron.blogspot.com/2007/07/how-much-good-can-one-blog-post-do.html

At this point I'll selfishly and churlishley mention that it was I who got Dr. Gregory a'bloggin' in the first place, so I'm claiming karmic victory if this effort goes as we hope. Say, 1% of the karmic goodness goes to me. A finder's fee, if you will. :)

Another Student Email

Here's one that didn't get sent directly to me. The course instructor forwarded it to me after she asked me about all the students I'd been contacted by, as she's trying to finalize the marks for the course. I haven't replied to this student, yet. Why this didn't come directly to me, I don't know. My name appears at the top of every essay I marked, in bold, next to "Marked by: ". This is a direct copy-paste:

I was very offended by the comments and mark that you gave me. I feel that it was an unfair assessment, especially when you attacked the qualitiy of my interviewees. One has just graduated and the other two are going into their final years. THis is more than good enough for the topics at hand. Also you seemed to pull marks out of now where, giving me 50% on my literature review. Thats just uncalled for. The mark you have given me as it stands now has dropped my overall mark a lot. I just dont think that it is fair to spend so much time on a project, then to have it torn apart unfairly
like this was. A 54% on a very simple 30% final project is an unfair mark.
Please let me know what you are going to do about this.
Thanks a lot,
[name removed]

Oh, won't this be a fun conversation. My first instinct was to reply with just the last sentence and "nothing". I think I'd rather pick this apart here, then take a few deep breaths and actually reply to this person.

Very offended I'm pretty sure I didn't insult this person's parentage, or write racist jokes in the margins, so I'm not sure where that came from. Email is such a lovely feed-back-free medium of communication, isn't it?
Quality of interviewees Let's see, every other student whose essay I marked (n = 41) interviewed PROFESSIONALS in a relevant field for the research question. People studying the use of wood in furniture-making interviewed cabinet-makers. People studying the use of cork stoppers in wine production interviewed winery operators and wine makers. People studying ornamental plants as an invasive species threat interviewed Botanists and municipal garden workers. This asstard interviewed some friends in other botany and environmental-science courses - three of them, all at once, on some couches in a lounge on-campus between classes. Not "more than good enough" at all.
Marks Yeah, pretty much out of "now where", absolutely. What a great idea - insult your TA when you want your mark improved! Fucknut.
Very simple Eh, not so much. This assignment, a 2000-word essay involving a literature review and detailed interviews, was not described as "very simple" by any other student I spoke to. In fact, the student who bothered to come in to campus yesterday to see me (and was actually polite) made the point repeatedly that cramming all the material we asked for into a short 2000 words was very difficult, much more so than a similar amount of material with a 3000 word limit. I agree.
Need I bring out Pedantic Man for the stupid spelling and capitalization mistakes?

"Please let me know what you're going to do about this." I still want to say "nothing". I'd better not reply to this dorkus right away.

Any suggestions? I'm not particularly worried about anything coming down on me based on my reply. I'm not going to swear at Asstard S. McWrongy or anything like that, but I doubt I'm going to hear, you know, reasonable complaints in an email back to me.

Student Emails

So I handed the course instructor a CD-ROM full of marked essays, and she uploaded them to the Distance Education website thingy, and the students downloaded their essays and had a look at their marks and my comments. Not surprisingly, many of them are not very happy.

Now, my email inbox is slowly filling with "i got good marx on first assingment please can i see you talk about it"

1. At least demonstrate the intelligence necessary to spell my name right. TWO Ls!
2. Email is not text-messaging. Type slowly and carefully, please.
3. The marking guidelines were made available to you (in general form) long before the assignment was due - whine about the categories and expectations to someone else, please. You didn't get an "outstanding" mark because your essay was not "outstanding" (at least, not in the positive sense of the term).
4. I'll be here Thursday, Friday, and all next week, including Monday. Pick a time, and I will briefly entertain your whinging voice in person.

Not that any of my students read this.

---

Given that none of my students will ever read this, and I'm going to miss a bus so I might as well hang out here for another 20 minutes anyway, I'm going to do something vaguely unethical. I'm going to post actual snippets of some of these emails (names removed, of course). All are presented as they arrived to me, except elipses - those are mine.

The comments seemed picky. For example, why I chose the word emanate or what do I mean by the words "unique" or "stable". In the results section all comments were specific to the fact that I did not identify a reference number despite the fact that I do say who made the comment.

You were supposed to reference your interviews (those comments) properly, as numerical citations. This was made clear in the assignment.

...and I am a fourth year student hoping to get into medical school. I am writing to you because I am very disappointed with the mark that I received on my assignment... I am not a 70's student and I dont believe that my paper deserved a 70's mark.

Do I look like I care that you're trying to be a doctor? Should I give you special treatment for your medical aspirations? What kind of backwards logic is that - doctors are 'special people' and need a little boost to help them get over their terrible mental illnesses? (Langmann, feel free to comment specifically about this one.) Feel what you like - your paper deserved everything I gave it.

...I think some of your criticisms are redundant. An example is "chemical molecule what other types of molecules are there?" why can't I put the word chemical there

Urgh. This was a particular 'favourite' of mine. My irony detector is not very good - but it's twitching here. My criticisms of your redundancy seem redundant? You can't put "chemical" there precisely for the reason I stated (that you quoted so poorly): "chemical molecules" is a stupid thing to say. So is "mental perception" - you discover another form of perception, you win a prize (from some nice people in Sweden).

I got a very high mark on the first assignment and so I assumed if I wrote the second asignment in the same manner, I would be okay.

You assumed wrong. The two assignments didn't seem rather different to you?

Monday Rant (delayed): Essay Idiocy

This was supposed to be last week's rant, but many of the later essays I marked were not quite so anger-inducing, so I didn't write this up. Oh well, I just handed the CD with all my marked essays on it to the course instructor, so now I'm free to rant away about really, really stupid things students did.

The essays I just finished marking were the result of a project, worth 30% of the course grade, in which the students chose a question relating to human use of plants (it's a botany course) and answered that question by reviewing relevant literature and interviewing one or more people with relevant experience (e.g. work in the industry). It's a pretty broad assignment, so I could have gotten 41 essays about 41 completely different things, but the projects clustered into a handful of (presumably suggested) topics, such as the use of cork stoppers in wine bottles, ornamental plants in municipal landscaping, and 'green roof' technology, in which large buildings have plants growing on their roofs for various purposes. Ho-hum, most were boring, as is to be expected. S.J. Gould, they ain't.

On with the rant. You'd think, perhaps naively, that when writing an essay worth so much of a course's mark, in a science course, some large-ish fraction of the students would take care to, I don't know, PROOFREAD their frickin' essay. I think, out of the 41 I marked, maybe three actually read their own work before sending it in. Common mistakes that these rather dim students made include, but are not limited to:

Use of apostrophes
Go here, read the poster, and try to learn something. Apostrophes NEVER are used for plurals, and are necessary for MOST possessive nouns and pronouns. Urgh.

Spaces and parentheses
Why, oh why, do so many students stick a space between a parethesis ( and the word following? And why do those SAME STUDENTS fail to insert a space between one and the last word of a sentence?

Question marks on non-questions
If you are describing a question, for example "I asked my interviewee how does he make wooden furniture", DO NOT put a question mark at the end of the sentence. You're not fucking asking the question here, you're STATING what question was asked. The voice inside my head (the other one, not the voice of Jwuieeblex the Faceless Lord) that reads your essay aloud raises the pitch of its voice at the end of that sentence, totally ruining whatever narrative effect you may have been trying to acheive.
Note that some semi-professional writers, such as Grrlscientist, do this too. Stop it!

Comma confusion
Why is the humble comma so difficult to master? There are places that need one, and places that do not. I don't think it's really that difficult.

a lot
This is not technically incorrect, but does make your essay look stupid. And it's TWO words, not one.

Numerical citation style
We specified a particular citation style for the students. Yes, I know there are many different styles to choose from, and it can be confusing, especially if one suffers from an excess of certain fatty acids in one's brain. But numerical citation style is really, really easy, and it saves word-count. Is it hard for you to 'sell-out' and actually use the citation style we asked you to use?

Plurals
Yes, English is rather silly with its plurals - goose/geese, mouse/mice, foot/feet, etc. There are also many, potentially unfamiliar, technical terms in scientific writing that have odd plurals, such as the ever-popular-to-fuck-up "species" and "genus/genera". But that's no excuse for the pain of mixed plurals I experienced.

Contractions
"Wouldn't", "Isn't", "Don't" et cetera are legitimate expressions of the English language. But they don't belong in a formal essay (NB: rants are fine places for them).

Couple vs. couple of
Either expression is painfully colloquial when it appears in a formal essay. One, however, is technically incorrect - saying "couple" without "of" after and "a" before is wrong. Stop doing this.

Other words that don't belong (or don't exist)
"phone" - it's a "telephone". NOT ONE student got this right. About half of the essays described essays conducted "by phone". I WILL DESTROY YOU!
"info" - yes, two students actually wrote this instead of "information". YOU SUCK GOAT BALLS!
"pros and cons" - in what universe are these acceptable words? DIE PAINFULLY!

And finally, one student, in an essay about the use of wood in furniture construction, repeatedly misspelled it "would". Seriously. WTF!?!? I don't even understand how that's possible for a non-idiot/savant type writer. Not that that essay's presentation of math was up to 'Rainman' standards.

Reading

Today, my sister took me out for a bit of heavy-item shopping with her car. I bought the supplies and kit necessary to begin production of home-made wine, but I'll write specifically about that when I get some work done on it, and take some (crappy) pictures. I know I also promised (in a subtle way) to rant about something this week; I will, it's about some 'features' of the essays I'm knee-deep in, marking, but I'm just not angry enough about them right now (I've had a string of pretty good ones over the last few days). So there will be (mildly) interesting things coming up here soon, I promise, but here's a little tidbit to mull over in the meantime:

Reading. How much of this activity do you do, let's say on a weekly basis? I read quite a lot, but a large fraction of my total reading consumption is for work / school; I've set a goal for myself of adding about 42 more entries to my annotated bibliography for the first chapter of my PhD thesis, by April 18. So I've been reading lots of scientific papers, lately. I also read a fair bit for fun (Oh! I should also promise here a new book club entry - coming as soon as I sort through all the notes I took). Most of the people I know (a population heavily biased towards people with many letters after their names) also read lots.

During our drive around town and break for lunch, my sister and I discussed reading habits in children - she recently qualified to be an elementary school teacher in Ontario, and is currently looking for a job as such in the Guelph area. Her experience, during 'hands-on' teacher training at various schools in Australia was that, to a first approximation, boys don't read (thereby also leading to the corrollary: Martin is even more odd than previously suspected). It seems that while eight-, nine-, and ten-year-old girls do frequently read books, newspapers, magazines, et cetera for pleasure, their male classmates do not. I was frequently told to turn out the light, put the book away, and go to sleep at bedtime while growing up; I never noticed, but apparently this is a very unusual occurance for boys. One consequence of this, briefly discussed during lunch, may be poor reading skills in adult men as a result of not spending a large fraction of childhood with a book - one example was described of a man, now in his early thirties, who has difficulty watching movies with subtitles, as the subtitles are often presented too fast for him to read - he doesn't have a problem with reading comprehension, his problem is with reading speed.

I've seen some newspaper and similar stories about this phenomenon, but I had no direct experience of it. I still don't, but now I know I'm related to someone who has seen this on multiple occassions. To me, this is just weird - what the hell are you doing during (some fraction of) your spare time, if not reading? If you're like me, and read (and read [past tense]) constantly, can you tell me if you've met grown men without stories of childhood reading? If you're, uh, rather more alien to my experience, and yourself did not / do not read very much, can you tell me what the hell you were up to?

Popularizing Science

A recent post over at Pharyngula, and the associated comment thread, has gotten me thinking about science writing vs. popular-science writing. It's an odd and schizophrenic topic.

Some points now, that I'll write down for later expansion. Please feel free to clog the comments with suggestions about this topic. This is a little messy and poorly formatted; I wanted to get it out there and have people thinking about this as quickly as possible. Of course, given my traffic levels, that's probably a faint hope. Oh well.

From the second article cited by Pharyngula:
As they hump, so too do they evolve, assuring their offspring get only the best of genes.
This annoys me, because it implies that individuals can evolve. NO, only populations evolve.

Comment #1 (Unhappy Writer)
I fail to understand why science writing must be dull and, in this case, poorly structured.
It makes science writing so much harder to read!
Being 'dull' is a subjective measure. Science writing often comes across as 'dull' because it must be precise - the adverbs and adjectives that PZ mentions getting tossed are almost always highly imprecise words - they make 'spin' far too easy.

Comment #5 (cory)
The pervasive use of the passive voice in scientific writing makes my brain hurt. My advisor and I used to argue about this all the time, with him "passivating" everything I wrote and me trying to sneak back in with real writing.
My experience has been that the passive voice in scientific writing is slowly disappearing, replaced by active voice. The good precision-based reason for this, as explained to me, is that writing in passive voice ("PCR was conducted in multiplex reactions for each set of four loci") implies the magic little lab-elves came and did your work for you - which is obviously very much not true! Active voice, to round out the example: "We conducted PCR in multiplex reactions for each set of four loci". It's not difficult, and is often easier to read and understand.

Comment #7 (grendelkhan)
I wonder why scientists are still, as a group, so leery of writing for a popular audience. Doesn't the training process select for an ability to communicate clearly?
The training does not select for an ability to communicate clearly - it's training, so very little selection is involved, at least at later (graduate school) stages, rather it's a process of improvement. The training is geared specifically at clear communication in science writing - which I will argue is very distinct from popular writing. Yes, there is a great deal of overlap between the two styles, particularly in things like basic grammar and organisation and flow, but much of the practice writing that occupies an undergraduate science degree is designed to beat out popular styles and conventions and substitute clear, precise (and, unfortunately, often dry) language.
PZ will make the point in a later comment that one good reason that scientists, "as a group", are leery of popular writing is that there is no motivation for it - one's career as a scientist is not (usually) helped by popular writing.

Comment #9 (William)
Just a quick addendum to the discussion of why scientific writing is so dry, which I think is important enough to deserve a mention: precision! Scientists have to be very careful about the claims they're making, and a loose description of their results can easily imply interpretations not supported by the data. We may be enthused about possibilities for our results, but we (unlike purveyors of woo) have to respect the truth and not take things further than we can support.
I agree completely.

Comment #10 (PZ Myers)
Yes -- the scientific style is well-honed and efficient, and I think we'd all be very upset if PubMed filled up with enthusiastic abstracts loaded with adjectives and pop-culture references. The current style is good for communicating precisely and with brevity to our peers, and I would hope we don't change it.
I'm just saying that when we aren't talking to our peers, we need to be aware of a necessary change in style. What works for fellow experts in our disciplines is a complete turn-off to someone on the outside.

Comment #10 (PZ Myers)
That's something I also mentioned in the Thursday discussion: there is virtually no professional reward for public outreach. I think that's changing -- I've gotten some positive feedback from my peers -- but it's still a simple fact of life that talking to a few hundred laypeople about the importance of a whole scientific discipline has almost no weight in a CV compared to speaking to a handful of your peers at a poster session. It's right that there is a lot of resistance to changing that -- I would hesitate to recommend any changes to tenure and promotion policy along those lines myself -- but there ought to be mechanisms in place to value popularization in addition to (definitely not in place of) traditional scholarship.

Comment #17 (Ian Menzies)
"there is virtually no professional reward for public outreach."
So which rich benefactor, ideally one who is otherwise facing the ravages of history, should we pester to create the "public outreach" version of the Nobel? Does the Gates foundation have enough left over to create such a prize? Is there already a "Carl Sagan" award that needs to get a boost in award level and publicity?
An interesting idea, and probably useful - but rare awards are not going to motivate normal working scientists to popularize their work beyond their disciplines - what's needed for that is some kind of recognition scheme that impacts a majority of working scientists, they way peer- and tenure-review processes do.

Comment #20 (Mona Albano)
Actually, that wasn't at all bad as far as science writing goes. It had "We found" and "Blah should determine X" and so on. I do wonder, sometimes, why scientists can't translate "We found a positive relationship between body size and total number of eggs produced, as well as body size and number of eggs per egg mass." into "We found that the larger the snail, the more eggs it produced and the more eggs were in each egg mass." They have stopped at formal, slightly mathematical language. They could take one more step into standard English, retaining only technical terms where needed, without losing precision. In our minds, I think we translate "a positive relationship" into "bigger snail... more eggs." At least I do.
Something in that bugs me, but I'm not sure yet. A voice at the back of my head is insisting that "a positive relationship" actually does convey more information than "bigger snail...more eggs". Something to do with not being restricted in which direction one moves on a graph. This might require its own dedicated post to sort out, with illustrations. That would definately count as "procrastination".

Comment #23 covers an interesting tangent, about science and policy. I've had very interesting conversations about that, so I'm writing this down now to serve as post-it note on the subject.

OK, I've got to get working, now, and I'll come back to this later.