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.

2014 Major NSERC Prizes continue to under-represent women

I’ve written before about the massive gender imbalance in NSERC’s “Big Prizes”.  Well, the 2014 awardees have been announced, so let’s see how things look:

  • Hamer Prize: 0/1 recipients women
  • Brockhouse Prize: 1/6 recipients women
  • Steacie Fellowship: 1/6 recipients women
  • Polyani Award: 0/1 recipients women
  • Synergy Award: 2/16 recipients women
  • Herzberg Medal (“Canada’s Top Scientist”): 0/1 recipients women


So that’s 4/31 women recipients in 2014, or 13% (which, believe it or not, is below the long-term average of 17%).  And yet again, we see that a woman has NEVER been named Canada’s top scientist (0/24 since 1991).

NSERC was great at responding to my last post, and highlighted the work they do for women in science and engineering.  But do we have to wait 10, 15, 20, 30 years for that to be reflected in the top tier of science?

We also don’t know anything about who was nominated, the gender balance of the review committees, or whether women nominees were specifically solicited.

We still have work to do …

Barriers to open access publishing at a scientific not-for-profit

Things have been going rather well lately. Lots of science, days are getting longer, and I made an awesome curry last Thursday.  Wary of falling into complacency, I thought I’d open a (possible) can of worms. Please, be kind.


Open Access is a wonderful thing.  I appreciate this as someone working at a not-for-profit with a total journal subscription of <40 titles. If we don’t subscribe to a title, or to the full back-catalogue, it’s £12 to the British Library, and one working week if I can’t find a stashed copy on the interwebs.  I’m a classic example of the sort of person who benefits from OA publishing – a practitioner on the ground, working with local partners on applied conservation issues.  But here’s the crux: it’s not easy for me to publish OA.


Now before y’all go for the pitchforks and high tempo bluegrass, hear me out.


I’ve been thinking about this for the last number of years, and I can break down the reasons why I don’t publish more OA papers into the following:

  1. Money
  2. Audience
  3. External forces

Let’s begin.


1. Money

I’ll distinguish between the two types of journals that publish OA – those hybrid journals that let you pay for the option of OA, but will publish your article behind a paywall if you don’t pony up the cash, and those journals that are entirely OA.

Hybrid journals tend to charge significant sums of cash (thousands of your currency of choice).  The same goes for some OA-only journals.  Recently, Zen Faulkes highlighted his lab’s experience publishing many articles in OA journals.  Some journals had complete waivers, while for the majority, the fees were paid by a variety of sources, including research grants, departmental budgets, coauthors, and even apparently his own pocket (!).  I have no external grants, as my work is funded mostly through our core funding.  This core funding does not include covering page charges of any kind (OA or not), and I certainly don’t have the means to shell out for OA from my own pocket (were that it so!).  I’ve lobbied to have *some* publication fees included in our future budget, and we’ll see if that comes to pass, but for now, I am , financially speaking, stuck.

And yes, it’s true that there are several OA journals without any fees.  This recent study on journals indexed by the Directory of Open Access Journals (DOAJ) found a mean fee of $964, and many with no fees at all.  While the DOAJ might seem like a nice dataset with which to work, it presents two problems.  The first is the inclusion of known predatory publishers.  Many of the publishers appear on Beall’s List.  When I reached out to DOAJ via Twitter, they told me that they are in the process of upping the standards for inclusion in the index, and that essentially all journals will have to reapply.  Which is great, but for now, the problem remains.

The second issue is one that falls under #2.


2. Audience

I’m in a fortunate position (but see #3 below) in that I have a permanent full-time job, and one that isn’t (yet) harping on Impact Factors, which means I tend to publish in journals where I think my research best fits, and had the right target audience.  If I’m writing about plastic pollution in the oceans, I’d tend towards Marine Pollution Bulletin, but if I’d rather discuss gull diet, Waterbirds is a better bet.  Last night, I scrolled through the 108 journals listed in the DOAJ under Zoology, and the 393 listed under General Biology.  Many (most?) titles were ones I had never heard of, and were of very local interest in places where I don’t work (Acta Biologica Malaysiana, anyone?).  After filtering out the predatory journals (see #1 above), and those of exceptional local interest, there wasn’t a whole lot of choice aside from the “mega-journals” like Plos One, or PeerJ.  And what few did remain often had considerable fees.  It seems counter-intuitive if I want to publish an article OA, but resort to doing so in journals so obscure, you probably haven’t heard of them (perhaps we could call these “hipster journals”?).


3. External forces

For the overwhelming majority of my papers & projects, I’m not the only one involved, and a number of other folks have a stake.  In some cases, they’re prioritizing different things than I am, such as Impact Factors.  A colleague at a large research university had her department chair tell her that anything published in a journal with an Impact Factor < 4 was a waste of time, and wouldn’t count towards departmental/funding totals.  Collaboration involves negotiation.  In some cases, as in Zen Faukles’ case, coauthors have the funds or departmental support to cover OA costs, but this isn’t that common, particularly when things start running into four-digit invoices per paper.  This is particularly true when we consider that there are few “high Impact Factor” strictly-OA journals in ecology (though most/all? operate on a hybrid system).

Colleagues looking for jobs are also concerned that publishing everything in Journal A, an example OA journal, will reflect poorly on their CV (not because it’s OA, but because of the volume of papers in a single journal).  Whether it’s right nor not, people with power and who make decisions still care about where things are published.  Heck, so are most of us.  I have yet to meet an ecologist who was as excited about their paper in Ecology Letters as they were about one in Southwestern Naturalist. I will be keenly watching (and interested in hearing about experiences) as the “Open Access generation” (roughly those with PhDs since 2010, which is when I’d guess the OA movement gained significant mainstream attention) enters the job market.


I’m well aware of the philosophical arguments for Open Access, and I agree with them.  The concept of OA publishing is a good thing.  My hang-up is in the execution.  Yes, research grants are starting to include / require OA publication as a budget item*.  But if I look at my CV, I’d have a hard time coming up with suitable OA journal equivalents (or thousands of dollars / pounds / euros / pesos / dinari).


Would I like all my papers to be Open Access? Heck yes. But can I make that happen? Not yet.


Before everyone decries my possibly ill-informed orthodox maintenance of the inadequate status quo, here are two questions to kick things off:

  1. What steps have I missed in achieving a goal of OA publishing on a limited/no budget? Are preprints the answer?
  2.  This obviously doesn’t solve the problem of limited access.  What can we do to improve access to already-published literature, particularly for those in the not-for-profit sector?


Please, be gentle.


*And yes, I’m aware of fee waivers, but I’ve had colleagues & coworkers have their waiver requests turned down on a fair number of occasions, or large fees turned into smaller-but-still-large fees.  Hybrid journals also don’t tend to offer such waivers. I don’t see this as a viable solution.

Future of Visiting Fellowship postdoc program in doubt

I was slightly alarmed to see this post indicating that NSERC’s Visiting Fellowship in Government Labs (VF) program had come to an end.  This is (was?) a program administered by NSERC whereby postdocs were placed in Canadian federal research labs for up to 3 years.  The government department (so, Environment Canada, for example) ponied up the money, and NSERC acted as the middleman.

I was a VF from 2013-2014, and had I not found work, I’d still be there.  In an era when finding postdoc funding is particularly challenging in Canada, the VF program was very valuable – applicants just had to find a supervisor in government with the cash.

So when I heard about the supposed demise, I got in touch with a few of my contacts from my days in government to see what the deal was.  At one department, supervisors were effectively told that the program was over without any context.  But at another federal science department, there was a bit more information presented.

According to my anonymous government contacts, the whole issue began when a VF challenged their employment status.  Because VFs are paid directly from NSERC, this person argued, they should be receiving benefits as well, and treated as fully fledged employees.  They took their case to the Canada Revenue Agency, who arbitrates on such matters, and the CRA ruled that VFs are employees of NSERC.  As result, NSERC pulled the plug.

It’s unclear right now how this affects current VFs who are part-way through their position. At present, the application, and program information are still posted on the NSERC site.


But what I think is important to note is that according to my contacts in three federal science departments, this caught everyone off guard.  The researchers in these departments, and yes, even some of their managers, see the importance of the VF program, and are actively looking for solution; it’s just unclear what that solution will be.


It’s very easy to decry this as another example of the current government’s general attitude towards science, but it’s better to look at the evidence presented.  The decision to stop the VF program was made by NSERC for employment/labour reasons.


The NSERC post-doctoral fellowship (PDF) program remains in place and unchanged.  And for now, it’s one of a dwindling number of postdoctoral research opportunities in Canada.

Who are scientists?

One of the blog posts that caught my eye after I got back from Tristan was this entry by The EEB & Flow, wherein they take (much deserved) shots at “creation scientists”, in particular their attempt to define a scientist in a way that excluded people pushing a pro-creationism agenda under the guise of science.  In their table entitled “How to know if you are doing science”, they list four criteria by which scientists should be defined:

  1. Publishing peer-reviewed papers
  2. Being asked to review papers
  3. Securing research funding
  4. Training students

It is with this list that I take umbrage, and with which I disagree.  This is not “how to know if you are doing science”, but “how to know if you are an academic scientist” which, let’s be honest, is only a subsection of scientific endeavour, and a relatively recent one at that.  It’s also one to which an increasing number of researchers don’t aspire.


The terms “academic”, “scientist”, and “researcher” are often thrown about as though they are equivalent, when in fact they are like матрёшка, the nesting Russian dolls. Pardon my pedantry, but I think it’s important to know that these differ, and how.

Most broadly, a researcher is engaged in a line of inquiry. This includes biographers, art historians, sociologists, linguists, economists, and many, many more.  A subset within this group are the academics, which are researchers employed by the academy (usually a university, college, or other school).  Scientists are those,  within and outside the academy, who are researchers in a scientific field (however one chooses to define the scope of those fields; a post for another day).  Though the differences may appear subtle, I assure you they are not without meaning or importance. To suggest otherwise demeans all of us engaged in the pursuit of knowledge.

I work for an environmental NGO. I am a researcher. I am a scientist. I am not an academic.

Taking the list of four supposed requirements to be graced with the moniker of “scientist”, I find fault with each of them.  First, that a scientist must publish, and be asked to review peer-reviewed papers.  For better or worse, this is the mechanism by which we, as a scientific community, have largely chosen to assess merit and progress.  Again, whether this broken system is the best/most appropriate/only way to do so is a topic for another day.  But it excludes the foot-soldiers on the ground doing a lot of the actual work – technicians and research assistants.  “But!” I hear some cry, “They are simply following the instructions of a scientist!” Well done on demoting these people to the role of mindless automatons. Suggesting that they have no independent thought, no ability to find solutions to problems, or to pose unique and important questions is disingenuous, and placing them in a supposedly lower class of “technician” or “field assistant” absent of the word scientist reinforces the strongly hierarchical norms of our profession.  These people are scientists.

We now come to research funding, that fabled mystical land. As above, technicians and field assistants (who, you’ll recall, are also scientists) aren’t expected to secure research funding.  Similarly, some scientists in “industry” (oh, what a wonderfully nebulous term!), in government, and at NGOs are expected to deliver the organization’s scientific program using internal funding.  This is not to say that scientists in these organizations do not, cannot, and should not pursue external funding, but that it’s not necessarily a requirement of their jobs.  But “securing research funding” is sufficiently vague and broad to include meeting with one’s boss to pitch a project, and having it approved, though the typical expectation is that “secure research funding” means a competitive, often external, process.

Lastly, we come to the supposed criterion with which I disagree the most – scientists must train students. Hello there, small-world view! Training students is not a part of my job (though it’s not prohibited, either). The same can be said of scientists in industry and in government. The question of whether there are “too many” PhDs (or other graduate students) has been asked frequently (here, here, here, here, here, here, here, here, and here are just a few examples), and there are no signs that it will slow down.  Even though we, as a community, have been shouting from the rooftops that the days of PhD to postdoc to tenure-track position are largely over, that progression is still the dominant narrative to which graduate students subscribe.  “But!”, some cry, “The universities need to provide/are providing them with the skills necessary to succeed outside academia!”.  When immersed in a research lab “doing academia” for 4+ years, a few hour-long workshops to present alternative careers isn’t going to make a difference. Now, I know that some PIs work at the interface between academia and government/industry/NGOs, and that their students might have a slightly different experience, but they are probably in the minority.  Because “number of students/graduated students” is another criterion against which “success” is measured, they are continually recruited, emerge in their late 20s or early 30s with burdensome debt, having worked for poor salaries (and living with the consequences thereof), and face an abysmal job market. The point of this digression is that recruiting and supervising students isn’t required of, or necessarily good for, science.


Taken together, these four points, while perhaps important for academics are not necessarily the same for scientists, or indeed researchers.  The conflation of these three labels is found frequently in media stories, blog posts, and other discussions, particularly those directed at academics. So please remember that I am a scientist, there are other scientists outside the ivory tower, and we’re not necessarily the same.