Good science happens because of good people – thoughts on coauthorship

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authorship, publishing

The title of this post if often how I end my talks and show that even though I’ve been the one talking for the last 45-50 minutes, there’s a whole cadre of students, mentors, and collaborators behind the science. And I will admit that I have had, on the whole, generally good experiences with coauthors. Perhaps so much so that when things don’t go as smoothly, I really notice it. And I’ve only had one coauthoring experience that I would describe as truly awful (and perhaps unsurprisingly, that paper was never published).

So below are a few nuggets. It’s not advice, or meant to be prescriptive, but is more about the ethos that we (my coauthors and I) have tried to adopt over the last 15 years. It’s never been something that someone sat me down to explain, and I’ve picked it up over the years working for (and with) folks at universities, NGOs, quasi-NGOs, government, and community groups.

 

Authorship

Always (ALWAYS) discuss this up front, but be open enough to discuss it again as projects change. I am a huge fan of the CLEAR Lab’s Equity in Author Order post, and highly recommend it. Different folks in different places (geographically, career-wise) have different pressures. Read Max’s post above which lays it out better than I ever could.

 

Journal

We all have preferences for journals, and different factors that go into picking one. Some folks do/don’t have funds for open access. Some have to play the impact factor game. Some need something out quick (more on this below). We always try to come up with a list of 2-3 so that there isn’t a lot of back-and-forth in the case of desk rejects (which happen often enough).

 

Time

With very few exceptions, there are no hard limits on getting things submitted. Not necessarily everyone on the team has a huge time allocation for research, and speaking from personal experience, timelines of “get this back in a week” aren’t likely to be met with compliance. It obviously depends on one’s team, but I found that at least 3 weeks for minor comments worked for a bunch of our papers (especially with larger teams). And obviously longer for things like first drafts or major changes. Whenever we suggest a deadline, we usually include the caveat that if someone feels they can’t make it, we can happily accommodate if they let us know.

The same goes for revisions. I have yet to be denied additional time from a journal to complete revisions, so long as they know it’s coming. And believe me, I have certainly asked frequently.

 

Software

There are lots of tools for writing papers these days. Overleaf, Google docs, Word, TeX, papyrus, and no doubt others. There are likely to be legitimate preferences for one over the other, and finding a consensus (with rationale for why) is another piece that brings everyone on board. For several years, I was in the field & working offline for large chunks of time so Google Docs was less than ideal, for example. Each has its advantages and disadvantages.

 

Communication

I mean, this one is pretty universal. But in this context, I mean keeping everyone in the loop about where things are. Not all journals email all coauthors about decisions, and sometimes folks who aren’t coauthors will need to be kept in the loop. Send around submitted (and indeed accepted versions) of manuscripts for folks to decide to keep for their records. In the case of accepted versions, many institutional repositories need these, and so it saves an email.

 

Develop a checklist

If you work with the same team, or supervise students, having a quick checklist for common issues can be helpful and save time. Are all references cited listed? Are the figures colour-blind-friendly? Our students submit this checklist with each new submission, and it means we can focus on the more substantive parts of the manuscript.

 

A note about process

With all the above, we try to come to a decision by consensus and after hearing from everyone. Sure, we have suggestions and can have informed starting suggestions, but we get the OK from all before proceeding. Yes, it can take a bit longer, but it means that everyone’s involved in the decisions, and has a bit more invested in the project and its success. At the end of the day, everyone’s name is going to appear on it, so if there’s something grating someone the wrong way, it’s not great (from either side).

The above is just a few of the major “process” things we think about when writing a paper. There are indeed more, and as I said, this isn’t meant to be prescriptive or a complete list. My point is that finding a system that eliminates (or mitigates hurdles before they manifest in a collaborative way has been a huge benefit for us, and when we end up working in other collaborative circles without some (or any) of these, it’s quite noticeable, and sometime unpleasant.

An understanding of everyone’s pressures, institutional requirements, and logistical situation up-front can help ensure smooth(er) passage of papers through the part of science publication where we have the most direct control – producing that manuscript for submission.

 

Happy coauthoring!

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Suggestions for responding to reviewer comments

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peer review, publishing

One of the often frustrating things about the scientific process is finally getting the manuscripts published. This is true of reports, theses, journal articles, white papers, and more. Anything that undergoes any mechanism of external review where a response is needed. Journal manuscripts are the most common in my line of work, so that’s where I’ll focus, though this applies elsewhere, too.

When scientists submit manuscripts to a journal, journal editors who think the submission is suitable for their journal (in terms of scope and quality) will send it out to other experts in the field to comment on and provide an assessment. But in a throwback to the pre-computer age, where carbon copies of types manuscripts were mailed and returned, reviewers provide this feedback by referring to page or line number in a separate document rather than, say, a tracked changes function in a word processor.

If the manuscript isn’t rejected at this stage, authors are invited to respond to these comments, and either comply, rebut, or present new arguments to convince the editor that the work is publishable in that particular journal. Again, as a separate document, often called a “response to review”. And it’s this document that is the focus of this post because seldom is any guidance given, and how one approaches it can be one of those “unwritten rules” about science.

Steve Heard has this covered well on his blog as well, and in his excellent book on science writing (and I hasten to add, he was the first person who explained this process to me when I was a wee masters student, n years ago!).

Here’s an example reviewer comment:

L283 – while this may be true for chocolate cookies, what do the authors expect in their study system of apple pies?

As reviewer comments go, this one is pretty good. It’s specific, and makes a clear suggestion, highlighting what they see as a weakness (in this case, perhaps applying an incorrect interpretation from a different system).

So, how to respond?

If the journal system lets you upload a response to review as a separate document (my preferred method!), then my approach has 3 parts:

1. Put the reviewer comment in boldface. Just copy & paste it. It’s then easier for you, your coauthors, the editor, and other reviewers to see which comment you’re replying to. I dislike colours because some folks print things out, and bold text is easily distinguished.
2. Immediately below, explain what you did (or didn’t do) to address the comment in normal type.
3. Quote ANY new or changed text in italics. Don’t refer to line numbers (which can get easily muddled); just put it right here for everyone to see.

So if we take our example above, it might look something like this:

L283 – while this may be true for chocolate cookies, what do the authors expect in their study system of apple pies?

We thank the reviewer for pointing out this comparison. Indeed, the approach for consuming chocolate cookies (i.e., using one’s hands) is less often applied in the case of filled pastries, including apple pies. We have changed the text to: “Desserts are easily consumed with hands (Monster, 2018) or can be eaten with assistance from cutlery (Garfield 2015)”

Garfield [The Cat]. 2015. Refined dining for modern felines. J. Arbuckle Press, Samoa.

With a quick look, the editor (or reviewer, as it often gets sent back for Round n+1) can see how the comment was addressed, and doesn’t have to wade through the entire manuscript, comparing it to an old version. And a happy editor/reviewer is often a kinder reviewer/editor.

For minor suggestions, like word choice, typos, or where the reviewer comment is obvious, it’s fine to respond with “Fixed” or “Changed as suggested”. But when in doubt add more information rather than less.

At the end of the day, though, the precise formatting doesn’t matter. What matters is that the information is presented clearly and can be easily assessed. Some journals (or some programs) use plain text for responses to review. In this case, I paste the reviewer comment, and below start my comment with “Response” or “R:”, and sadly the new/inserted text part gets left off.

Few things frustrate reviewers or editors more than a response of “Changed” without indicating where or how. I just stumbled on these formatting methods, and I’m sure there are others. The general advice of clearly indicating a response (to each and every comment) and marking any new or inserted text can be accomplished in many ways.

Happy responding!

 

In praise of researching (and publishing) “local” conservation science

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conservation, local, publishing

If you’ve published a scientific paper in a journal, you’ll know that part of the challenge is making it relevant to a broad audience. Why should a conservationist in Outer Mongolia, Zambia, Murmansk, or Baton Rouge care about your study? Chances are they study )or are concerned with/interested in) different species in different places. The pressure, therefore is to wrap much of our conservation science in global policy and priority frameworks: the Aichi Targets, multilateral environmental agreements, globally threatened species, or highly imperilled habitats. Which is good and fine and has resulted in lots of policy relevant science and conservation action.

But conservation also operates on a much smaller, more local scale, and with individuals on the ground in communities who can influence local, regional, and national policies and conservation actions. And this requires the science underpinning these actions to be, at least in part, local in nature. Sure, we all know that global warming is driving our planet further down the 6th Great Extinction, but most people will only take action when they see this manifest in their own backyards. Why have the doves returned a month early? Where did all the swifts go? Weren’t there fish in this lake?

And this is where “local” conservation science comes in. And it’s some of the most rewarding science with which I’ve been involved, even though it can be some of the most difficult science to publish. Providing the evidence base for local problems gives scientists and conservationists a better bargaining chip when holding governments to account, to speaking with the public and with media. A local story is usually more relatable than one from a seemingly abstract land far away.

Local conservation needn’t be novel, ground-breaking, cutting-edge, or revolutionary. It’s purpose is rather different, though from an implementation perspective just as important (if not more so). But this very nature makes it a more difficult problem for academic researchers to tackle as it’s unlikely to be of global significance, gain copious citations, or end up in a journal with an impact factor >4. It therefore often falls to scientists in government agencies, independent researchers, and non-governmental organizations to contribute to this science.

I’ve been lucky enough to be involved in a couple of these kinds of studies, and have a few more in the pipeline. We showed migratory patterns and geographic distribution of a Flesh-footed Shearwaters in the northeast Pacific Ocean (Bond & Lavers 2015), and described the current status & threats facing Streaked Shearwaters in the Korean peninsula (Hart et al. 2015). In these papers, we learned a heck of a lot about the species involved, and hope that these will become go-to papers when someone compiles details into whole-species assessments of status, distribution, and threats.

Overall, the key to success with local conservation science is the involvement of local people. The paper on shearwaters in Korea was only possible because of people in Korea. The same is true of the other (as yet unpublished) bits of work I’m involved with. These local connections make the work more likely to be well received (if received at all) by the people who matter (those who will enact policy or implement conservation interventions on the ground). The days of colonial science, where outsiders (often from the UK, US, or other countries with an advanced state of scientific inquiry) come in, do something, leave, and then issue what amount to scientific edicts (which are often promptly ignored) are over (or at least should be).

But, for me, the bottom line is that I find this kind of science fun. It’s adding a piece to a puzzle, and I find it very rewarding, especially when it’s highly driven by local collaborators (I usually just provide some stats, and editing… they do the real work of data collecting, and then working with the community to influence change). And at the end of the day, I like to think that it has some benefit for the species and sites we’re trying to look after.

On finding an error in my own published paper

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correction, publishing, scoters

Dan Bolnick (on Eco-Evo-Evo-Eco) and Meg Duffy on Dynamic Ecology have both posted stories of how they were confronted with, and subsequently addressed, the need to retract or correct their published papers. This fall into the “scientists are humans; humans make mistakes; therefore scientists make mistakes” logical tenet, and they both addressed it wonderfully. Sadly, that’s not always the case.

So to further demonstrate that scientists, as all humans, make mistakes, here is my tale of finding a fairly significant error in my first ever paper.

In my undergrad, I spent a spring at the Point Lepreau Bird Observatory in southern New Brunswick. Yes, past the nuclear exclusion zone and next to a 19th-century lighthouse was a little hut with electricity, a portable heater, radio, and view of the majestic Bay of Fundy. As a one of the more southerly points in the area, it was also a hotspot for migratory birds, mostly seaducks, on their way north to breed. My job: figuring out how many scoters (3 species of mostly-dark seaducks: the Black, Surf, and White-winged Scoters) passed the site in April and early May. I was also generously allowed to analyse the previous 8 years’ data (and have since heard through the grapevine that a student may be updating this work soon!).

The Point Lepreau Bird Observatory in 2004.

I was, at the time, terrible at data analysis and statistics. I had more pivot tables than I knew what to do with, graphs were made in Excel, and I think I used JMP for the various ANOVAs.

But I, and my supervisors, were able to churn out some basic stats on the timing of migration, the peaks, and come up with a crude estimate of how many birds passed the point each year. I would almost certainly analyse the data completely differently today (and I hope the aforementioned student does!). After some fairly minor revisions, it was published in 2007 in Waterbirds, and I was elated – my first publication!

One of the challenges was that the counts were done in 15-minute stints (15 on, 15 off), so in essence I had to double all the counts with the assumption that the number and composition of birds was identical in the counted and uncounted periods.

Except I forgot to do that.

Is that one Black Scoter?

Or two?

I got an email from a member of one of the naturalist club’s members (the observatory was run by the Saint John Naturalists Club at the time) in 2009 pointing out that he thought my numbers were too low. I dug into the terribly formatted awkward files, and realised what we had done (or rather, not done).

I was devastated.

I immediately wrote my supervisors, contrite, and apologetic. We quickly prepared a correction (which essentially doubled the population, so not that insignificant), and emailed the editor who agreed a correction was in order, which we subsequently published.

Unlike Dan or Meg’s stories, this wasn’t a high profile paper, but it was my first one, and one of the very few for which I have a printed issue of the journal on my shelf. But everyone understood it was an honest mistake, and we did what we could to fix it.

I’ve opined before about why there are so few retractions or corrections in conservation biology/ecology, and I don’t see this changing, or being any different. But in the meantime, if anyone finds an error in any of my other published papers (I’m sure there are some floating around), I will happily try to set the scientific record straight.

Publication requirements for graduation are a terrible idea

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degree requirements, publishing, students

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.

 

Science

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.

 

Priorities

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)

 

Where will a biology PhD take you? Data from the 2012 NIH Workforce Report. TT faculty: ~8% http://t.co/GJQlE7P77V pic.twitter.com/1IVdrE7hg2

— Alex Bond (@thelabandfield) April 13, 2014

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 …)

Conservation of species: is there a publishing gap?

Tags

conservation, journals, publishing

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.

Manuscript necromancy: challenges of raising the dead

Tags

data management, manuscript necromancy, manuscripts, necromancy, publishing, students, writing

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.

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

Tags

journals, open access, publishing

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.

The whirlwind of returning – recommended reads

Tags

LGBTQ, links, natural history, publishing, sexual assault

I’ve just returned from about 4 months away doing field work on Tristan da Cunha, the most remote inhabited island in the world.  I had an absolutely fantastic time, and will reflect on my experiences a bit over the winter.  One of the things I look forward to on returning from the field (where there is little or no internet connectivity, poor email and phones, and a myriad of amazing experiences in nature and natural history) is catching up on all the amazing blogging and writing from my time away.  Below I’d like to highlight a few that caught my attention or various reasons, and add some thoughts of my own.  These are certainly not the only amazing stories from the last few months, and there are others that gave me much more to think about that I’ll write about later.  So without further ado, here we go:

 

#IAmANaturalist reclaim the name campaign celebrates natural history research

It’s no secret that I believe natural history is important and has a place in the modern scientific curriculum, so I was thrilled to see this initiative from the Ecological Society of America’s Natural History section.  The photos and stories on Twitter embody the innate curiousity about the natural world, and the importance of observing the world around us.

 

Ninety Minutes

Kate Clancy recounts three experiences that each took place in an hour and a half.  In particular, her musing that keeping the grass watered and green is a metaphor for the struggles and uncertainty of working to improve the learning and research environment while others seek to overhaul/decimate/table-flip it is worth thinking about.

 

Science’s sexual assault problem

I’m obviously late to the much-lauded New York Times op-ed by Hope Jahren but it’s too important to not include here.  Personally, I really identified with her sadness (and perhaps frustration) at not being able to travel to countries where she felt unsafe, even though this changed her research path, and obviously influenced the questions she pursued.  I’ve mentioned this in passing in the context of LGBT field scientists, too. We still have work to do.

 

Deconstructing creationist “scientists”

This piece from The EEB and Flow makes some excellent points in the context of how non-scientists use credentials to pass themselves off as scientists.  But what struck me and made me twinge a bit was the table that highlighted the four things needed in order to be a scientist.  It included:

• publishing peer-reviewed papers
• being asked to review papers
• securing research funding
• training students

What I take exception to is that the list seems to be very/entirely academia-centric.  As a scientist working for an NGO, supervising students isn’t part of my job description.  And I doubt it is for many in government (though many do).  Similarly, I would argue that many field staff that I’ve worked with are indeed scientists even though they have not published papers, secured funding, reviewed papers, or trained students.  I’ll be writing more on non-academic science in the future, so stay tuned.

 

Making science more welcoming for women and minorities: a workshop

Along the same lines, Ambika Kamath led a workshop on how to make women and minorities more welcome in science, and posted her thoughts and recommendations for others wanting to tackle topics of bias in a workshop environment.  Props for including orientation and gender!

 

Busy is no myth

In which Tim Poisot casts the “I’m always busy!” trope as an example of the Red Queen.  Teach those time management skills early!

 

Conservation Basic Training

Dez Huber tackles a comment by National Geographic Explorer-in-Residence Enrick Sala and makes the case that teaching is the “basic training” or boot camp for the next generation of conservation scientists. Couldn’t agree more.

 

Homage to the squished mosquito

A student in Chris Buddle‘s field biology class had a squished mosquito in their field book, and wrote a poem about it. Natural history can be an inspiration for the arts as much as for science.

 

No you’re not paranoid – there is a bias against publishing marine conservation papers

Chris Parsons has an interesting analysis over at Southern Fried Science of the number of marine conservation papers in various journals, and finds them less likely to be published in general conservation journals.

 

Two interesting papers

I don’t often highlight specific papers, but there are two that have come across that are worth looking at.  AS Glen writes in the Bulletin of the Ecological Society of America on the “golden rule” of reviewing – review for others as you would have others review for you.  And over at PLoS Computational Biology, Rougier et al. gives some advice for improving figures.  I’ll also plug what I see as a “classic” paper by Don Kroodsma on figure legends.

 

Systematic gender bias in editorial boards in ecology

Again from Tim Poisot, an analysis of the gender disparity in various ecological journals.  Spoiler: it’s not great.

 

The Campus Alcohol Problem That Nobody Talks About

Rebecca Schuman nails it once again in this must-read on the prevalence of alcoholism among faculty, and the consequences for those who don’t partake (or even with less frequency).

 

A handy guide to UK-US feedback

How to tell what your UK or US prof/colleague means in handy tabular format.

 

Finally, but certainly not least, I’d like to highlight a new initiative to profile LGBT scientists that Beth Hellen started recently called LGBT STEM.  I highly recommend you check it out, and if you’re an out worker/student in STEM, submit your own story.  Jeremy Yoder highlighted (again) the perceived lack of queer STEM mentors for young scientists, as was described in Jack Andraka’s op-ed in The Advocate.

“Old” meets “New”: the role of preprints in natural history

Tags

Aleutian, cackling goose, glaucous-winged gull, natural history, PeerJ, preprint, publishing

The title of this post is a little tongue-in-cheek because preprints are a relatively recent adoption in ecology, conservation, and environmental science, and natural history is, of course, the foundation of ecology, conservation, and environmental science.  Regardless, though, I think preprints have a huge role to play in natural history.

Preprints are non-peer-reviewed documents that are posted in online repositories where others can comment on them, authors can upload revised versions, and most importantly, get information out.  Preprints are often submitted to journals, and their ultimate version usually contains the same text as the journal article.  Importantly, the preprint is archived, is citable (with a DOI), and gets the information into the world and out of our filing drawers (or more likely, computer folders and field books). The case for preprints in biology is fairly strong, and I’ll add one more: natural history and conservation.

Natural history, I’ve argued (as have many, many, many, many, many others) is an important part of modern science. Sadly, not everyone agrees (but this is my blog, and they’re wrong). But there are still journals that value (and are dedicated to!) natural history, and rightly so.  But even putting together a “natural history paper” isn’t trivial. There are still hypotheses, observations, analyses, and interpretation.

Now, maybe it’s a particular proclivity of ornithologists, but we tend to write a heck of a lot of reports – to government agencies, for permits, and to funders.  These often have some preliminary analyses, lots of methodological detail and background, and in the case of most of my field studies, heaps of “ancillary information”.

During my PhD, my primary field site was Kiska Island, a lovely volcanic island in the Rat Islands group of the Aleutian Islands, Alaska.  It’s a fantastic spot, and cumulatively over the four years, I spent nearly 300 days there (probably the 2nd largest amount of time of anyone alive right now).  Each year, we filed a summary report with the US Fish and Wildlife Service that detailed the effects of introduced rats on Least and Crested Auklets.  But we also did much more than that.  In particular, we (and the other 3-6 ornithological research camps in the Aleutians each summer) compiled an annotate list of bird sightings.

“Hey!” I hear you exclaiming, “That’s some pretty awesome natural history data form a neat part of the world! When will you write it up?”.  Sadly, the answer is not anytime soon.  This makes me sad, but my current job doesn’t allow for Natural History Fridays.  What if you were interested in the distribution and effect of introduced predators on Aleutian Cackling Geese? Or were examining range-wide variation in Glaucous-winged Gull egg size?  You would have no way of knowing that I collected useful data because it’s in an unpublished government report (or other “grey literature”), and doesn’t merit a paper or note on its own.

If I had deposited my annual reports in a preprint repository like PeerJ PrePrints, or bioRxiv, not only would these data be out there, but others could cite my report/preprint.  Furthermore, the publicly available copy wouldn’t just be the one on my old lab’s webpage, but it would be available after I’m long gone, and since it would have a DOI, it would be easy to find.

Tracking down grey literature is a royal pain.  Reports are rare, are often poor black-and-white reproductions, and usually hard to find in the first place.  Citations of grey literature also tend to be more prone to errors, which exacerbates the whole process of finding them.  And, I think most importantly, the information they contain doesn’t always make it into a paper.  All solved if they were deposited on a preprint server.

We are, after all, already producing these reports, and more importantly, they’re already cited frequently, and data appearing in these reports is also in published papers.  So the reality is that nothing would really change, except that the information would be more widely available, better curated, and citable.  I don’t see a downside.

So if you are, in fact, interested in the distribution and effect of introduced predators on Aleutian Cackling Geese, or variation in Glaucous-winged Gull egg size, you will hopefully soon be able to add my wee bits of data to your analysis.  When my various colleagued return from the field, I’ll convince them that we need to deposit our annual reports in a preprint archive.  In the meantime, you can see them on the “Downloadable reports” section of the Kiska webpage.