Canadian government postdocs: revived (well, sort of)

I wrote before about the demise of the Visiting Fellowship program, which placed postdocs in Canadian government research labs, and used NSERC as a middleman (middle-agency?).  Recently, the employment practices around this arrangement, particularly whether postdocs were entitled to benefits.  An employment tribunal reasoned that they were, and the program shuttered (though all current VFs were fine through the remainder of their tenure).

Now, it comes to my attention that an open-ended competition for the Postdoctoral Research Pilot Program (PRP) has been posted on the Government of Canada jobs site.  My guess, and those of some informed government colleagues, is that this is the replacement for the old VF program.  But there has been no announcement, no information page, nothing.

Some other interesting queries… all government jobs are classified based on the broad category and salary scale.  Two important ones for our purposes here are RES and EG.  RES is a Research Scientist, and there are 5 levels (RES-5 being the highest). EGs are scientific technicians, with EG-7 being the highest level.  How are PRPs to be classified?  The old VF program scaled salary to n% of the entry level RES-1 (I think it was 85-90%).  If the new PRPs are to be classified (and they would be, as government employees), an entry RES-1 seems most likely.  This is huge, as the base salary in 2013 (the last year of the current collective agreement) is $53,161 (link; search for “SE-RES-1″).  That’s a big improvement on the $49k of the VF program.  It’s even bigger if it includes benefits, which are quite significant in a government job (pension, medical/dental, etc).  So the actual cost goes up considerably.

Where will this new money be found?  Previously, the VF program paid postdocs from their immediate supervisor’s operational budget.  I wonder if the benefits side of things will be similarly covered, or whether that comes from higher up in the department.  And what about unionization? RES positions are represented by PIPSC, and the current agreement is up for renewal.  Granted PIPSC isn’t known to strike as often as the other major federal government labour union (PSAC), but who knows what the future will bring.

One last, yet troubling, word.  The advertisement linked above excludes two of the most science-heavy departments: Fisheries & Oceans Canada, and Environment Canada.  Sources have told me that there continues to be no internal / government postdoc option in these departments, and no indication that one will be appearing soon.  With an already limited pool of postdoc funding, the loss of the VF program, and unavailability of the PRP in all departments puts further strain on PhD graduates in Canada, and especially those who want experience in the public service.

Publication requirements for graduation are a terrible idea

I’ve come across two cases in my relatively brief foray into post-PhD science where students at either the MSc or PhD level were faced with a requirement from their academic department to have n papers accepted/published, and n papers submitted for publication in order to be awarded a degree.  Here, I will try to explain why I think this does a disservice to both students, and science.


Time (and money)

The most obvious, yet least-planned-for aspect of this policy is the additional time required.  Scientific publication is, in many respects, a stochastic process which by its very definition is difficulty to use in planning.  When universities or departments require accepted (or even worse, published) manuscripts for graduation, the student’s fate is outside the control of the student, the supervisor, the supervisory committee, the thesis examiners, the department, the faculty, and the university.  It’s not uncommon for papers to be rejected, or to require major revisions necessitating an additional series of reviews, and reviews are most often the bottleneck in the whole process. It’s not uncommon for papers to sit on desks, for editors to have a hard time finding reviewers, and for those reviewers to take a long time to complete their assessments.  And if the decision is reject (or another round of review), the time functionally doubles (or very nearly so).


This addition of several months to students’ programs of study is rarely accounted for, meaning graduation dates and thesis submission dates get pushed back, and students fail to obtain their degrees in a timely manner.


This leads to the inevitable question – who will pay for the additional time?  The argument that the supervisor and student should know and plan to have a paper submitted by time x operates on the assumption that a favourable result will be obtained between time x and time y, when the student plans to graduate.  In reality, though, even with the best planning and undivided attention to deadlines of a supervisor, this isn’t possible. Coauthors’ comments, final supervisor’s approval, and stochasticity (coauthor A is on annual leave, coauthor B is in the field/at a conference, coauthor C is busy with a full teaching schedule this term) push things even further outside the control of those with the greatest vested interest.


Students don’t shouldn’t work if they’re not being paid, so someone needs to pay them. The supervisor? The department? The university? Someone’s got to step up and cover salary, but the reality is that supervisors rarely have such amounts of disposable funding, and departments/universities are quick to pass the buck back to the supervisor.



If we accept the above (and I do), then we have a situation where science is being produced under hard constraints of time.  Decisions on where to publish manuscripts become even more important (which has the shortest turn-around time? where is it likely to get the easiest time in review?).  This often results in the proliferation of science published in “local” journals whose main purpose, it seems, is to offer the quick publication required by universities. We’ve all heard of these obscure journals (the <demonym> Journal of <discipline>), and occasionally had cause to search some of them out.

My argument here isn’t that these are terrible journals, but that even if they meet some magical criteria (e.g., listed in the Science Citation Index, have an Impact Factor, etc.), they’re not easy to get at, and they don’t do students any favours.  Like it or not, it still matters where we publish, and publications in these journals won’t make students as competitive in an academic job market (more on this below).

It also fosters the proliferation of predatory journals – those who offer publication with a (falsified) Impact Factor, sometimes with no review at all, but who are happy to take your $500 or £750, or €1000.  Jeffrey Beall has a very useful list of journals and publishers to avoid. But to a student or supervisor facing a looming deadline, this is an attractive (though morally poor) option.



Not all PhD students (and certainly not all MSc students) want/go into a research career, so for them, publishing is less of a priority.  Some will go into policy, or advocacy, or education, or management, or administration, or plumbing, or learning the personal computer.  A PhD (and to a much lesser extent, MSc) does not obligate one to a career in research (and for most, that’s the reality)


And that’s OK. But it does set up competing interests between the student and the supervisor, which is rarely a good thing. It also continues the emphasis that the tenure track is the One True Way™, something we’ve been trying to dispel.


Final thoughts

I’m not suggesting for a minute that publishing science is a bad thing, or that we shouldn’t publish science – of course we should.  But the mechanism by which we achieve that goal shouldn’t be through student degree requirements. It should be through better support and improved funding so that students *can* get their science published, or at least into a state where someone else can take care of things after they’ve left.

I’ve done a fair bit of manuscript necromancy, including two former students’ theses (both MSc).  I’m batting 80% at getting things published, and the last paper will never come out because of poor field methods. It’s tough, it’s hard, but we got the science out there in appropriate journals and with little additional cost.  Both students have successful full-time jobs outside research, and are happy with their choices.

If we want student research to be published, here are some tips/gaps:

  • provide better writing support. Make use of your university’s writing centre if it has one.
  • explain scientific publishing, including how long it can take, to students on a regular basis
  • make sure coauthors are aware of deadlines and enforce them/support the student in enforcing them
  • return manuscripts in a reasonable time. 6 months is not a reasonable time (though it’s far from out-of-the-ordinary in the experiences of some colleagues of mine)
  • discuss career plans with students often, and prioritize actions that will maximize their success in whatever career path they choose.
  • share your publishing successes, and especially failures, with students. The bigger the dataset of “how publications work” the better informed they’ll be.
  • recognize that some students will not publish papers, and some will not publish all of their chapters. Make sure drafts, data, and code are available, have sufficient metadata for reanalysis, and think about other possibilities for publishing (e.g., perhaps it’s a quick analysis & few days of writing for a postdoc, or a colleague’s student, or a collaborator, or …)

FAQ, and answers thereto #3

The latest in a light-hearted look at the search terms folks use to find The Lab and Field.


kroodsma (2000, auk 117:1081–1083)

Probably one of the most under-appreciated papers. You should really read it.


gay canadian scientists



how to make an academic website

Somewhat inexplicably (at least to me), this is by far my most popular post. Ever. By a long shot. I wonder if I should update it. Thoughts?


migration of bird moon

The bird moon is non-migratory (and lacks coconuts)


advantages of academic citation

Jobs, money, power, influence YMMV.


non scientific endeavour

Theatre! Vacuuming! Delivering parcels!


why didn’t i get nserc funding

Sorry to hear. Probably because, though I’m sure it was excellent, your application didn’t make the cut. But you’re not alone.



why do we need to have seminar?

Because it’s good for you. Seriously though, it’s great to hear about other research, and broaden your horizons. If your seminar series sucks (and most of them do), make it better.


when do early view articles show up in google scholar

Give them a few days. You can also add them manually to your profile!


how many applicants per job for postdoctoral position

Depends how widely it’s advertised, among other things. You never get the jobs you don’t apply for.


best site for academics

I like islands, or failing that, aboard a ship. But then again, I’m not an academic.


what if birds didnt migrate

Who would carry coconuts from Mercia?


environment canada post doc

Run! Actually, it was beneficial to see the inner workings. Unmuzzled Science has a post about what it’s like as a postdoc in the Government of Canada.


“hipsters” “github”

Are those meant to be sarcastic of euphemistic?


labrador duck not extinct

Yes. It is. Boo.


if you came to our library..

I’d likely check out a book, or other library material.


http://www.peopple sex vs

Well that escalated quickly. This one is a puzzler.


communication is one of the most

And sometimes one of the least.


Conservation of species: is there a publishing gap?

This post was prompted by two recent/submitted papers, one of which I’m involved with, and the other of which a colleague published.  They both concern what I consider the fundamental building blocks of ecology and conservation: how many of species X are there, what external forces affect those numbers, and how have they changed over time?  The conservation of species is, for better or worse, the basic unit of biodiversity and the main purpose of the IUCN Red List.  Ecosystems consist of species, and the number of their individuals.

Such “status, distribution, & threat (SDT)” papers are often relegated* to “natural history” journals. In the rush to be appeal to a broader audience, many taxon-specific journals (and here I’m referring primarily to ornithological journals) eschew such submissions.  Conservation journals (e.g., Biological Conservation, or Conservation Biology) are more interested in umbrella or big-picture ideas, or at the least, novel methods/approaches (this is  just my interpretation, and I’m happy to hear otherwise!). Not to mention a bias against marine organisms. As someone who works primarily on marine birds, this is particularly bothersome.

SDT** papers generally take the form of reviewing past population estimates & threats, adding in some new data, maybe an analysis, and at the end of the day, should provide the information needed by conservation authorities (international, national, or subnational; more on that below) to adequately know what’s going on. Very often, the historical data relating to seabirds’ distribution and abundance is… how shall I put it?… wrong.  Errors on the ground (or, frankly, just wild guesses) get propagated in monumental (and exceptionally well-cited) tomes, and taken as the Gospel Truth. So SDT papers can be a chance to correct the record, which is crucial for effective (and sound) management and mitigation of things like bycatch. If you thought there were 300,000 of species X, then annual bycatch of 2000, though not good, wasn’t terrible. But if it turns out that a misplaced decimal here, and a poor survey there meant there were only 60,000, that allowable bycatch level becomes very worrying.

As a consequence, SDT papers tend to have lots of information, and some of it is messy. Lots of it is probably from grey literature, government reports, or unpublished data, and a SDT paper is a chance to get that information out into the wider world.  But this is problematic for journals because they thrive on brevity. In one of my case studies, we were advised recently to cut the results section by 90% because “people do not want that level of detail”. Utter bollocks. In the other case study, the paper went through at least 4 formal revisions, and 2 with the handling editor, resulting in a paper that didn’t have a bunch of information in it.

The problem is only compounded when working in the non-English-speaking world, where much of the information is in “foreign literature” that is less accessible to the broader scientific community (that doesn’t mean you should ignore it, though!).  SDT papers are a chance to get information in that Russian technical report, or that Korean government document into the English-speaking world (and let’s face it, science is an enterprise dominated by English, for better or worse).

Conservation is also practiced at a huge range of spatial scales – from global (think the IUCN Red List) to national (think COSEWIC in Canada, or the ESA in the US, or the Nature Directive in Europe), to subregional (states, provinces), or even local levels (individual breeding colonies).  These all, ultimately, matter for conservation because these are the levels at which decisions that will affect species and populations are made.  So if we have a species that has 90% of its population in Country A, and 10% in Country B, it’s important to know what’s going on in Country B because its policies, implementation, and national interest will affect that part of the population, and these can be different from Country A (arguments about genetic distinctiveness and “evolutionary significant units” aside).


So I hope I’ve now established why we need SDT research. The question is how to disseminate it, particularly at the national or subnational level? When I posed this question on Twitter, there were some excellent answers – Endangered Species Research (though when working with species that are globally Least Concern, I’m not sure how well that would go down. And there’s the €1050-1500 fee), and a variety of fish journals.  In the bird world (where there is no shortage of journals!), there are 3 obvious choices.  Avian Conservation and Ecology (of which I’m on the editorial board) generally doesn’t accept SDT papers. The Condor focuses on “the application of scientific theory and methods to the conservation, management, and ecology of birds; and the application of ornithological knowledge to conservation and management policy“, which in my mind doesn’t really fit SDT papers (or my experience with the journal).  Bird Conservation International looks for papers on the “conservation of birds and the habitats upon which they depend“, which is the closest fit I’ve seen, but isn’t known for its speed (it’s also the one with which I have no experience, so again, I’m happy to hear otherwise in the Comments).


Given that the conservation of the natural world is really a broad way of saying the conservation of individual species (and the ecosystems they comprise), which depends on knowing the status, distribution, and threats these species face, I wonder why there isn’t a Journal of Species Conservation? Online-only (so no worries about length or colour figures or number of tables, etc.), of minimal cost to authors, ideally Open Access, and with relatively rapid publication. The focus would be on the conservation status, distribution, and threats to species (or groups of species) at any spatial scale. I know that’s a lot to ask, but a conservation biologist can dream, right?

I’m certainly not offering to start one up, but if an enterprising publisher were looking for an obvious niche to fill*** I’d strongly suggest this one, and would gladly help edit, review, and submit to such an outlet.



*Natural history journals shouldn’t be seen as a lower tier, but they are sometimes less likely to be online (and so more concerned with length and publishing costs), less widely available, and read/cited, and often take long times from submission/acceptance to publication.

** Yes, I chose the order of the words purposely

*** Let’s hold off on the debate about whether niches can, in fact, be empty.

Possibly pedantic points: scientific names

When it comes to certain things, I am a pedant. Not the annoying beat-you-over-the-head type of pedant, but the type that has been known to geek out over methods for reporting taxonomic authorities (it’s all in the parentheses).

This weekend, I had two related thoughts about something that many of us biologists use on a regular basis – those agreed-upon names, comprising species and genus, that transcend our own “common names”.  The first question is what, exactly, we should call them?

It’s rather common to refer to “Alca torda” as the Latin name for the Razorbill, but a more proper title would be the bird’s scientific name. Not all scientific names are Latin. Some are Greek, Arabic, or even Swahili. In this case, Alca is Icelandic or Norse for “auk”*. Calling “Alca torda” the Razorbill’s Latin name is akin referring to all lightbulbs as “fluorescent”; some bulbs are, indeed, fluorescent, while others are not, yet they are all lightbulbs.  Some scientific names are Latin, while many are not, yet they are all scientific names.


Another oddity, and one for which I don’t have an answer, deals with parentheses around such scientific names (we’ll leave the discussion of brackets and braces for another day).  While it’s all well and good to talk about Alca torda eggs, and Diomedea dabennena diet, or even Alle alle altitudes, it’s more common to call them Razorbill eggs, Tristan Albatross diet, and Dovekie** altitudes.  It makes our science more accessible, even among specialists.  While I know that a Fluttering Shearwater is Puffins gavia, it’s different from a Great Shearwater, which is Puffinus gravis. And someone who isn’t up on their classification of the Procellariidae might be easily confused, or have trouble following along.

So for better or worse, we often use common names, and insert the scientific name at each species’ first mention.  But how we do this is inconsistent, and I don’t know if there is a right way.  Some options are:

  • Razorbill (Alca torda)
  • Razorbill Alca torda

I tend to prefer the first, as the italicization doesn’t often render well in some typefaces (notably sans-serif), and it’s easier for my brain to parse the scientific and common names.  It also identifies to me that it’s an aside, and we will use “Razorbill” as our collective shorthand for “Alca torda L. 1758″.

I realize that this is likely discipline specific – some taxa simply do not have common names for all species, and some disciplines have a culture of using scientific names.  Some journals insist on one of the styles above, but the decision appears to be editorial or stylistic, and not founded in any actual logic.  I don’t know what that logic is, but perhaps some fellow pedants could point it out.


*You can check out Roger Lederer & Carol Burr’s fantastic book “Latin for bird lovers“, and ignore the gross error in the title, as I do.

**we’ll discuss common English bird names later.

Manuscript necromancy: challenges of raising the dead

If you’ve been doing research for any length of time, you probably have data that aren’t doing anything but taking up space on your hard drive.  Stick around a little longer, and you’ll eventually have entire projects with half-written (or even completely written) manuscripts that, for one reason or another (or indeed no reason at all) have fallen by the wayside.  At some time in the future, you’re organizing files, or chatting with a colleague and you suddenly think “Oh yeah. Whatever happened to that?”.  Or, if you’re a PI/manager, you’ve had students write their theses/reports, which should have/could be manuscripts, but aren’t.

I’ve dubbed the process of (re)discovering a dead manuscript, and breathing new life into it manuscript necromancy. I think the comparison works.  And like true resurrection from the dead* manuscript necromancy isn’t without its challenges and limitations, and you might need some … interesting tools to get the job done.

I should point out that in a perfect world, necromancy wouldn’t be needed, and all data would be formatted beautifully with wonderful metadata and reproducible analysis scripts.  But this world is far from perfect.  This is the scientific dark arts. Hold on to your tracked changes, boys and girls, we’re going in, and it could get ugly.


Slash and burn

Student theses aren’t often written with tight language, good grammar, and in the style of a journal article.  There’s frequently lots of exposition and background, a verbose writing style, mixed tenses, inconsistent formatting, … the list goes on.  The first step is to go through the current draft with a take-no-prisoners edit to remove unneeded text, straighten out the grammar and style, and to give yourself a general feel for the manuscript.  This is, often, the most labour intensive part of the job.  A recent manuscript we resurrected took me 3 full days of editing, which ultimately reduced its length by almost half.

My next step is to tackle the references.  Theses often cite everything under the sun (Smith et al. 1758), regardless of how useful it is (Jones 1877).** 9 (or 10) times out of 10, the references are incomplete or missing, and almost certainly aren’t in your reference manager of choice (let alone the journal’s style, but that’s another argument for another day).  One trick is to look for references that are only in one place, and ask whether they are truly needed. If they are, keep them. If not, away they go.

The last item on this first step is to look at the tables and figures.  Are they all needed? Are they all necessary?  Are they clear?  Hopefully the answer is yes, or requires minimal changes (though see some spooky possibilities below).

Congratulations! You’re now a Level 1 Manuscript Necromancer (and are entitled to the post-nominals M.N. in certain circles).


The festering wound

But a manuscript can still be alive, though severely wounded.  In some cases, you’ll discovery (to your utter dismay) that you need to re-analyze data, or re-draw a figure.  Both of these require necromancy of the most troubling form: data.

Data management has been improving as  whole ***, but student thesis data is not known to be the most friendly for outsiders to wrangle.  You just have to check out #otherpeoplesdata on Twitter to get a taste of the frustrations.

While your initial reaction would be to re-create the analyses done in the original draft, and obtain the same results before moving on, I strongly recommend against it unless the data are well archived with appropriate metadata and explanations of the analysis (in the form of notes, an R script, etc).  You will not get the same results, and you will tear out your hair (and possible scalp) looking for it.  The situation is already less than ideal, so cut your losses, and use what you have.  By all means, cull anything that’s rubbish (and document it!), and then proceed with your analysis/graph.

Level 2 completed.


Communicating with the dead

One of the biggest challenges of necromancy is in the final stages. You have a draft with the right analyses & figures, and you’re ready to submit. Assuming that someone else started this science (be they a student, technician, contractor, or sorcerer’s apprentice), I’d argue that there’s an obligation to include them as a coauthor.  The exception might be if the end product bears no resemblance to the original, but that is less about manuscript necromancy, and more manuscript transfiguration (a topic for another post).

Make every effort to get in touch with the originator so they can a) see what changes you’ve made, b) approve of them, and c) know your plans for the paper.  This means old email addresses, good old Google searching, contacts through third parties (e.g., friends of friends) and the like.  And keep records of these in case you can’t track them down.  If you can’t, and have made every effort to find them, they should still be listed as a coauthor. Most journals require you to state that all authors have read and approved the submission, so in this case, my pragmatic argument is that, unless there were major changes to the conclusions, their first draft is implied approval****. If there were major changes, you absolutely must track them down, or remove them from the authorship list.


Rest and recharge

Manuscript necromancy can be more work and is certainly more exhausting than writing a manuscript yourself.  Don’t resurrect more than one manuscript at a time, and don’t do more than two or three in a row.  You need time to recharge your mind, and to many resurrections in a short period can lead to botched necromancy (and no one wants that) because of reduced effort, particularly in the Slash & Burn phase.


Preventing (manuscript) death in the first place

The best solution, though, is to avoid necromancy in the first place. This isn’t always possible, though, and just because something doesn’t get written up doesn’t make it less Science.  Some things, though, can vastly improve the chances of successful necromancy, and are good research practices to boot:

  • encourage good writing. This isn’t easy, and Terry McGlynn has some good thoughts on this issue more broadly.
  • give good, timely feedback (which increases the chance of a successful manuscript before it dies for the first time)
  • encourage good data management.  The easier it is for someone else to piece together the analysis, the better chances of necromancy, especially when deeper techniques of the academic dark arts are required.
  • encourage good data management.  Have I said this yet? It’s sort of important.


Glass houses, stones, and all that

One last note – manuscript necromancy need not apply to just someone else’s work, but is equally applicable to your own work from the past that’s being revisited. The same tools and techniques (and problems) apply. In this sort of case, your familiarity with the manuscript may be overwhelming to your necromancy techniques.  Having an outsider read it over as a friendly reviewer is strongly recommended.


Wishing you all much success in your exploration of the scientific dark arts.

— — —

*well, not exactly “true”, sensu stricto, but more widely known

**see what I did there? Not exaggerating either.

***or at least I hope it is.

****ONLY in the absence of actually approving it, mind you, and as an absolute last resort.

On trainees, money, and diversity

Money — it’s the crux of just about everything we do in science.  Want to bring in a new student or staff member? Money.  Want to do field or lab work? Money. Want to go to a conference? Money. It’s one of the things we expect scientists to be good at (and which is also a full-time profession in and of itself).

I get particularly cranky when I see money used as a barrier to diversity.  I’ll explain with two examples that have recently piqued my interest.

The first is something I’ve discussed before – paying staff. I highly recommend Auriel Fournier’s post on the same topic.  For me, it boils down to a simple axiom: no money = no staff.  You’ll note this is similar to the currently accepted adages “No money = no gas”, “No money = no lab analyses”, and “No money = no milk for the tea room”.  As we approach the (northern) field season’s peak time for hiring, I find it particularly frustrating when I see “opportunities” that are entirely volunteer, or even pay-to-work junkets.  That just ain’t right.

The second is something that’s come up on Twitter recently – spending one’s own money “for science”, by which I mean incurring expenses for one’s research/job and not being reimbursed.  This post by Edd Hind lays out the terrible logic, and the damning evidence.

In both cases the result is the same – science becomes only possible for those who have financial means. And that typically means white men. We need more diversity in science.

I don’t think the ideas I’m advocating are all that radical (we should pay people a decent wage for their work, and they should not have to pay for work-related expenses). And while they alone won’t solve the problem of under-represented groups in science, they’ll go a long way to making it a slightly more even playing field.

If you’re a PI – budget for your staff just as you would your lab ethanol or conference travel. Give your trainees travel advances if they’re going to incur large bills over a short period (e.g., a field season). Learn about central pools of money from the department, faculty, or graduate student union to cover conference travel, training, etc.

If you’re a trainee – discuss funding for staff and supplies with your supervisor. Seek reimbursement for costs incurred, and advocate for advances rather than reimbursement (or direct purchasing by the department/university). And know your department’s/university’s financial regs for reimbursement (or pots of money for conferences); your PI may not be up to speed on these.

If you’re an administrator – push for appropriate financial measures so that trainees aren’t out of pocket. Look at having a central pool of funding for things like conference travel (as a grad student, I got 1 conference/year covered this way).

And don’t just assume that because you could cover the cost that others could as well.