Prioritizing the flood of ideas

Tags

#NewPI, funding, languishing projects, students

If you’ve been involved in research for more than a couple of years, chances are you quite quickly start to accumulate a list, even if only in your mind, of Things It Would Be Neat To Do. These could be things that you identify as gaps while pursuing your main research theme, or ideas that spark out of a paper you happened to leaf through while waiting for a meeting to start.

And typically starting around the later years of a PhD, and through postdocs and early career positions, the flood of ideas for things to do keeps, well, flooding. You see gaps, methods that need improving, sites that need investigating, and questions that need answering. And very quickly you realize that you do not have time to do it all.

And so it begins: the search for minions!

Or rather, students, collaborators, or others upon whom you can foist your ideas, your existing data, your passion, in the hopes that they will take the torch and run. At some stage, the list becomes too large for your head, and perhaps like me you make a nice text document on your desktop called “Project Ideas.txt”, and just keep adding to it as the ideas pop in, with the hopes that when a prospective minion comes along, you’ll have just the project for them.

But good heavens is that ever difficult. Perhaps I’ve had a skewed view, having never actually worked in a university, but I have tried several mechanisms to try and get homes for existing datasets, or convince others that the project ideas I’ve had are worth pursuing and met with exceptionally low success.

A few years ago, I tried setting up a page here called Languishing Projects, and every 6 months or so I would update it, send around some tweets or emails, and I might get one or two queries. Usually, though, the query didn’t go anywhere because the querier wasn’t at the right career stage (I had several emails from first or second year undergrads – and not to say that those cohorts aren’t suitable for research, but as they would have been in different cities than I, I couldn’t provide them with the mentorship and guidance needed for projects done at that career stage).

It seems ironic, but I just couldn’t give away data.

Now, some of you would surely suggest simply posting the data somewhere like figshare and someone, somewhere would use it. This wasn’t practical because I wasn’t the sole owner of these data, and in many cases, the data would have needed some significant attention before I would want them released into the wild.

A particular challenge I’ve found is funding and recruiting to studentships. I do marvel at PIs who seemingly receive countless emails asking about being a student in their lab – I can’t remember the last time I had one, let alone one that was in my field (again, though, I’m not at a degree-granting institution). And in the few cases where I’ve been able to find a partnering faculty member, the number of applicants, despite quite broad advertising, has been quite low. And university faculty also have their own flood of ideas, so why would they want to take on yet more?

And then there’s the funding. The way the UK funds postgraduate research is, in my view, quite silly. Students don’t apply to PIs, but to thematic or regional Doctoral Training Partnerships, and those admitted to these DTPs then must be wooed by PIs with projects in the hopes that the student will finally settle on theirs. There’s nothing wrong with a little competition, but it means that if a prospective student contacts me, and I think they might be a great fit for a project I have, they can be rejected by the DTP and that’s the end of that. The success rate, particularly for some (like the London DTP) is more akin to a major NERC or NSF grant, <7% last year.

To say nothing of funding for postdocs.

I think that part of the difficulty is that while I work on seabirds and islands, many of the project ideas are desk- or collections-based. This is advantageous on one hand because they involve very little cost, but at the same time, most students in ecology & conservation are in it (largely) for the field work. Which costs money. Sigh.

So as I often, too, I took to Twitter to ask folks how they dealt with the flood of project ideas. The response were basically to prioritize those that had either students or money associated with them. Not great for me, since mine had neither. And without either of those, partnering with a university PI becomes increasingly difficult (because, well, students and money are hard to find, it seems).

But rather than have this a whinging tirade, my question, dear reader, is what do you do with the projects for which you have no time? The bits of data that could be something if they just had some time put into them (time that none of us have)? Are you resigned to letting them slide off this mortal coil?

And lastly, many of my languishing projects or Ideas That Have Little Chance Of Being Realized are perfectly suitable for honours or UK/Australian MSc/MRes degrees, and some could be bundled up into a nice PhD. So if you fancy collaborating, or have a steady stream of students in need of projects, let’s chat!

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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 …)

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.

Making a scientific will (updated)

Tags

archives, data, personal libraries, students

Note: this post is something I’ve thought a great deal about in the last few years, mostly the result of the loss of two wonderful ornithologists, Gary Bortolotti, and Brad Livezey, in 2011. I didn’t know them personally, but I knew their work.

It’s a dangerous business, Frodo, going out your door. You step onto the road, and if you don’t keep your feet, there’s no knowing where you might be swept off to.

– JRR Tolkien, The Lord of the Rings.

While we don’t often like to think about it, the human race has a 100% mortality rate, and  often, this life history event doesn’t occur when we expect it.  We are advised by family members, doctors, and lawyers to keep a will – a statement of what is to happen to our assets (and our body) when we shuffle off this mortal coil.  This attempts to minimise conflict amongst our inheritors by laying out our plans clearly and concisely (in theory at least).

As scientists, we have reams of samples, data, equipment, field notebooks, personal libraries, and in some cases, students.  I’m suggesting that scientists should have an academic will.

In a few cases, like provincial or federal government scientists, everything goes to the crown.  But for the rest of us, I suspect that a fair chunk would be lost if we keeled over.  To say nothing of what would happen to grad students in our research groups.

Many of us also work with collaborators that rely on us for analyses, and in an exception case, it’s possible a current or former student could fill that roll.

So take half an hour sometime soon, look at what “academic assets” you have, and make a plan.  Talk to colleagues, talk to department chairs (who would pay your students? What happens to your grants and lab/office space?), and talk to current and former students, especially if they are continuing in research.  And chat with your current/former advisors – do they have plans?

Much has changed during the proliferation of “scientist” as a profession in the last 100-150 years.  Rarely are our correspondence and notebooks now archived in libraries because most of our correspondence is now by email, and our notebooks replaced with spreadsheets and data files.

But whatever your plan is, make one.  Just like with family, discussing it with our “academic families” won’t necessarily be pleasant, but it’s something we should do.

 

UPDATE

Marc Leger on Twitter made a great suggestion – since you can buy templates for personal wills, why not have universities or academic societies develop templates for an academic will?  It then becomes a simple exercise of updating it every year.

And I think this is especially pertinent to those of us who do field work, often in remote locations.