Tag Archives: academic life

Why I stopped reading the literature

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This year I stopped reading the academic literature. Not entirely, of course — that would be career suicide. Nor is this a deliberately awkward response to the latest hashtag tyranny of #365papers, where fellow academics post how many papers they’ve read either to impress others or make them feel guilty. Mine was an accident that has settled into a default state.

For the last decade I have been able to claim with confidence that I read roughly 1000 papers a year. Now when I say read, you should be given to understand that this doesn’t mean poring over every single word. The normal protocol is to read the abstract, skim the introduction, flick through the figures then read the discussion until it gets boring*. If there’s anything that needs further scrutiny then I’ll look more closely, but it’s rare that the methods will receive more than cursory attention, perhaps checking for a few key words or standard techniques. I think most academics would say that in practice this is how they read papers.

By the end of the week I’m not mentally capable of intellectually-demanding work like writing manuscripts or analysing data, unless the pressure of a deadline forces me into it. So I’ve tended to hold Friday afternoons as a drop-in time for my group, and spent the gaps between meetings looking through recent journal issues and reading papers. This has helped me keep up to date with novel ideas, exposed me to new studies, and honed my awareness of what types of things are getting published.

My pattern of work all changed in the last academic year because I was inflicted with a new module with sessions scheduled in the Friday afternoon slot. No-one wants that time, least of all the students. It’s perhaps only marginally less unpopular than 9am on a Monday morning. Who wants to be in a lecture when there are pubs to go to? (I mean on Fridays, not 9am on Mondays. We’re not all alcoholics in the UK.)

My journal alerts system (I use Zetoc) has build up over the years to incorporate a wide array of sources. There are tables of contents for particular journals, search terms for the fields that I specialise in, and even a few names of colleagues whose work particularly interests me. I’m lucky enough to not need to keep track of competitors because I work in a field that no-one cares about so there’s little risk of being scooped**. At this moment the total number of unread alerts is about to pass 300. Catching up on all of those has reached the point where it’s simply impossible, unless I take a few weeks’ holiday and spend the whole time on academic reading. Which I’m not going to do.

When I was a (more) junior academic I remember being told by (more) senior academics that they didn’t read the literature any more. This struck me as a great pity. One phrase that I heard second-hand, supposedly from Chris Thomas, was that he no longer reads the literature — he raids it. If you’re writing a manuscript and need a reference to make a specific point then you go looking for an appropriate paper rather than attempting to follow everything. Another colleague told me that he expects his group to be his eyes into the literature, and relies on them to spot important new publications, which he gleans from their manuscripts and recycles into the next grant proposal.

With mixed feelings I’ve realised that I’m now headed in the same direction. I’m coming to terms with the idea that, in many cases, my graduate students have a firmer grasp of the frontline of the field than I do. Perhaps this isn’t such a bad thing. Over the last few years while writing a textbook it’s been necessary for me to keep on top of the literature to make sure I’m up-to-date. When covering so many subjects at once this is an overwhelming task. Delivering the final copy to the publishers removed the ongoing pressure to read and read more. But why was that process not fun? How can someone who loves his research and is passionate about his field not unequivocally enjoy the process of reading and discovering more about it?

A clue comes from a Masters-level class on science writing that I’ve just finished. This year I introduced a new exercise: the students were asked to come along with a piece of writing that they enjoyed reading. This could be anything at all — a book, website, magazine, paper — so long as it was in prose. Out of a class of 35, only one brought an article from a scientific journal. There were a handful with popular science books (Dawkins, E.O. Wilson), but the overwhelming majority arrived carrying fiction books.

What does this tell us? A small sample size, I know, but at least it’s an indication. These keen and bright students, at a top university***, immersed in the scientific literature, don’t first think of an academic paper when they’re asked about the most enjoyable things they read. This is probably because, for the most part, academic writing is terrible. Not many people would choose to read it for fun in their spare time. I read constantly at home — but the pile of papers in the corner isn’t the first thing I reach for.

The purpose of our class exercise was to look at the structure of enjoyable writing and see whether there are lessons that can be learnt for our own work. The pointers were perhaps predictable but nonetheless helpful: shorter sentences, simpler words, a focus on engaging rather than impressing the reader. My hope is that one day some of these students go on to produce a higher quality of scientific prose than the general average. Perhaps, in our small ways, we can redirect the tenor of academic writing and make it more pleasurable to read. Who knows, it might get me reading again.

* They all do, even mine. It’s the point where the author switches from actually discussing the results and their implications, and moves on to tenuous speculation or unnecessary criticism of other people’s work.

** This isn’t quite true on two counts. Firstly, there are plenty of people working on spatial self-organisation in natural systems. My experience, however, is that they’re (almost) all nice, supportive and collegiate people who encourage one another. I’ve never got the impression that there’s any competition. The other reason why scooping isn’t so much of a risk is that in ecology, data is king. No-one is going to beat me to publishing papers on Kamchatkan forest organisation because I’m pretty sure that no-one else has those kinds of data.

*** That’s what we’d like to believe, anyway. We do pretty well in some league tables but aren’t as impressive in others. Mostly we end up in the global top 100 and the UK top 20.

Consult the index

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I’m presently mired in what is one of the most tiresome, tedious tasks I’ve had to perform in my academic career. Bear in mind that I say this as someone who spent three years tracking levels of herbivore damage on 20 000 individual leaves as part of my PhD. I’ve counted pollen. I’ve catalogued herbarium specimens. This is an order of magnitude worse.

The task at hand is to produce an index for my textbook, Natural Systems: The Organisation of Life*, which is finally due to be published in March 2016. I knew that indexing would be hard. I didn’t quite appreciate how hard. And that’ while using LaTeX, which makes everything much more straightforward. I can’t even imagine having to do this in hard copy or (shudder) in Microsoft Word**.  There are some useful guides to indexing. There’s even a book called Index Your Book Fast, though one suspects that the time taken in reading it would more than offset any gains. None of them make it any easier.

While it’s not difficult to imagine an ideal index in abstract terms, actually putting one together is trickier. I’m currently working through the book sentence-by-sentence, deciding whether this or that term is a passing or substantive mention, whether it needs to be nested within other groups, and when I might ever finish. Who or what deserves a place in the index? Main concepts are obviously in. What about taxa, important people, study sites, species… where does it end?

As a book reviews editor myself (for Frontiers of Biogeography) I’m acutely aware of that typical complaint by reviewers that ‘subject X doesn’t even make it into the index!’ This could mean any number of things: that the subject isn’t covered by the book, that the index has omitted to mention it, or that the reviewer hasn’t read the book properly. A skim of the index is often one of the first things a prospective purchaser does while browsing and forms a central element of the impression a book makes. Getting it right is crucial because it makes a book more useful to future readers. Too long or trivial and it’s overwhelming; too short and it looks skimpy.

One might ask why I’ve bothered writing a blog post about a topic so dull as indexing (although if you’re finding this particularly fascinating then you should read The Indexer, the international journal of indexing). In part it’s as a corrective to recent posts which may have given the false impression of my life as one of tropical jaunts spent being pursued by dangerous animals. All that happens, but actually 9 months of my year is spent in front of a computer screen. I’m also keen that you realise, when you turn to the back of a book and flick through the index, that a surprising amount of work has gone into preparing it. And, in my case, a surprising amount of wine.

* The blurb on this site is a cut-and-paste from the original proposal, submitted three years ago, and doesn’t really capture the book content. The cover image is also under review right now. All this will be filled in over the next couple of months.

** I haven’t used Word in several years, and it’s made my life immeasurably happier. You could do the same.

We’re all stupid to someone

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I spend an increasing proportion of my time collaborating with engineers and theoretical physicists. It keeps me on my toes and I’ve had to adjust to very different research cultures. The engineers, for example, get particularly excited by designing a technical solution to a problem. The long haul of data collection and statistical analysis has less appeal; once they’ve proven it can be done then they’re itching to move on to the next challenge. Likewise physicists genuinely do spend meetings in front of whiteboards sketching equations, which leaves me feeling a bit frazzled. Nevertheless, I’ve learnt that if an idea can’t be expressed mathematically then it hasn’t been properly defined. That turns out to apply to a lot of verbal models in ecology.

Both engineers and physicists are ready to publish at an earlier stage than most ecologists would, and their papers are a model of efficiency in preparation. Not for them a lengthy waffle of an introduction, followed by an even more prolonged and rambling discussion. Cut to the point, make it clearly, then wrap up. It makes me wonder whether we’re doing something wrong in ecology. I certainly don’t enjoy either reading or writing long papers, and I can’t fully justify our practice.

I also find myself fielding questions or tackling issues that would never come up when chatting to an ecologist. One of the misapprehensions I’ve had to counter is that trees are not lollipops. It might be more computationally efficient to assume that trees are spheres of leaves on a stick, and it can lead to some elegant mathematical solutions, but the outcomes are going to depart from natural systems pretty rapidly. Our disciplinary training leads us to consider particular assumptions to be perfectly reasonable, despite them sounding ridiculous to others or bearing little resemblance to the real world. (Even within their own field, forest ecologists are not immune to this syndrome).

Understanding how another researcher arrived at their assumptions can be informative — sometimes it boils down to analytical frameworks, computational efficiency or technological limitations, all of which are valid reasons to consider accepting a proposition that on first hearing might sound far-fetched. Likewise it helps to have our own assumptions challenged. Sometimes we are able to justify and defend them. Other times they leave us exposed, which is when we know we’re onto something important.

It’s also a sad but common trait within all social groups to mock outsiders for making mistakes about things that appear self-evident to those on the inside. Ecologists can easily play the same game, but make no friends by doing so. I had a chat with one of my collaborators this week who was itching to find a small tree on campus, scan it using ground-based LiDAR, then strip and record the sizes of all its leaves. It’s a perfectly reasonable idea (if a lot of hard work). The main stumbling block is that it’s the middle of February and we’re a good three months at least from having full leaf canopies to play with. An obvious problem? Only to someone who spends their life thinking about trees the whole time. We had a laugh about it then moved back to our simulations, which have the considerable benefit of not shedding their leaves seasonally.

This kind of interaction only makes me wonder what crazy things I’m responsible for coming out with in our meetings. It also makes me grateful to my collaborators for their patience in humouring me, because I’m pretty sure that I come across as an idiot more often than I realise. This to me is the greatest pleasure of interdisciplinary collaborations. We could all spend the rest of our careers treading the same academic paths, publishing in the same journals, and not need to stretch ourselves quite as far. By heading way outside our comfort zones we all end up learning more than we expected to, so long as we don’t mind feeling stupid every now and again (which happens every time I get tangled in algebra). If you’re not willing to be wrong then you’re not willing to learn. And if I end up the subject of an amusing anecdote at a theoretical physics meeting? That’s fine by me. I hope it raises a good laugh. As a wise man once said, ridicule is nothing to be scared of.

The Law of Good Enough (or why your thesis will never be finished)

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I spent quite a bit of time recently meeting our section’s post-graduate students for tutorials. In some cases this is to welcome new arrivals, or to catch up on progress from those who have been away on lengthy field seasons. The ones I most enjoy seeing are those  who are busy writing up — because they’re the ones I’m most able to help.

It can be difficult to persuade a postgrad staring down their thesis deadline that 15 minutes in my office is time well spent, which I fully understand. Usually they are stressed, feeling the pressure and unable to focus on anything other than the thesis. Much of this derives from a sentiment I hear echoed again and again in various forms: “I just want to do the best job I can”.

No. Stop. This is not the way to approach a thesis. You need your thesis to be good enough.

This shift in attitude is hard to accomplish when your whole academic career has been geared towards achieving the highest mark possible, or at the end of four years when you want to have something on your shelf to be proud of, that you can look at and think “I wrote that” and feel a warm glow inside. Allowing yourself to fall into this vanity trap is pathological, and the root cause of a lot of unnecessary stress on the part of post-graduates.

Your thesis is the means to an end, which is graduation. When the day comes, you will walk across a stage for 20 seconds, shake someone’s hand, collect a piece of paper and get a photo taken in a silly gown. It doesn’t matter if you’ve written the most perlucid, inspiring and impressive thesis of all time. No-one will clap any louder, or any longer. No-one will ever judge you on the quality of that thesis, good or bad. All that matters is that it was good enough.

In one of the labs I worked in we had a thesis that did the rounds of the post-graduates who were writing up. You might think that they were sharing a particularly wonderful thesis so as to learn best practice and be inspired by the achievements of others. I’m sure all the supervisors would have preferred that. But no, the thesis everyone wanted to see was singularly atrocious. No-one reading it could fail to spot glaring errors, hideous formatting and some of the worst figures ever committed to print. That’s exactly why everyone was so keen to read it — if this person passed then surely there was hope for others!

I’m not going to reveal whose thesis it was, because that doesn’t matter. They have gone on to a successful academic career where they are respected in their field with an international profile. Does anyone care that they submitted a shoddy thesis? Of course not. It was good enough. On the other hand, the best thesis I ever read remains that by Mike Shanahan, who preceded me by a couple of years and even worked at the same desk. Nothing could be more demoralising than to witness a standard of writing to which I had no hope of aspiring (at the time). Perhaps he still looks with satisfaction upon that thesis. He might do so again if he reads this. My bet is that it hasn’t crossed his mind in a decade or more. Did it benefit his career? Maybe, but probably not that much.

There is an argument that a better thesis will lead to an easier viva, and that’s perhaps the case, but my suspicion is that the correlation is not strong. How a viva goes depends on the personality of the examiners, their particular bugbears, the wind direction and the alignment of the stars. You can no more predict the questions than you can anticipate how many corrections you’re likely to get. The time to be a perfectionist, or at least to aim for the highest standards you can, is when you’re preparing a manuscript for publication. Then you know it’s going to be pored over in great detail. A publication is your contribution to the legacy of science, a work that will be forever associated with you. The thesis? That’s a bookend.

The best advice I ever received while writing up was from another old hand in the group who told me that a thesis is never finished. Eventually you just relinquish it to the examiners. Bear this in mind if you’re tempted to read and reread chapters, add more references, or tinker endlessly with the figures. There’s always something else you could do. Just get it done, make sure it’s good enough, then move on to the rest of your career.

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Edit: @ZarahPattison made an interesting point on Twitter about thesis by publication. Although this is arguably the best possible way to prepare a thesis, it’s not for everyone, and many universities don’t even allow it. I wouldn’t like to give any student the idea that it was an expectation, not least because I didn’t manage it myself. It’s certainly true that a well-written chapter is easier to turn into a manuscript, but that’s missing the point. If you want to write a manuscript, write a manuscript. If you have a manuscript then turning it into a chapter is easy. If you need to finish a thesis then get the chapters done and worry about the manuscripts later.

How to respond to referees’ comments

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The first time I submitted a manuscript, it came back months later with a lengthy list of recommended changes and an equivocal response from the editor which implied that he was reluctant to hear from me again but might deign to respond if I proved myself worthy. I was devastated. It had been an immense amount of work and effort to prepare, and by now I’d moved on to other things. I glumly sloped into my supervisor’s office and was taken aback by his enthusiasm. Apparently this was what passed as good news in science *.

Since then I’ve been through the manuscript submission mill many times and always prepare my students in advance for the likely tone of what they will receive. It doesn’t get any easier. I still can’t read comments as soon as they arrive. Normally I’ll read what the editor says, skim the rest, then go for a short walk around the lake to calm down. Sometimes it takes several laps.

Eventually, however, you need to brace yourself and get down to the revisions. Clear your diary, close the door, unplug the phone (and the internet) and make sure there are no distractions. Don’t leave until it’s done. Unpleasant jobs are always the easiest ones to procrastinate from, and revising a manuscript comes pretty low on my list of favourite ways to spend an afternoon.

Assuming you have an invited resubmission (rather than an outright rejection **), here is a quick guide to how to respond to manuscript reviews that I wrote for my PhD students:

  1. Write back to the editor immediately, thanking them and the referees for their time and helpful comments. Even if you’re not grateful and they weren’t helpful. Even if they rejected the manuscript ***. Being nice works wonders in the long term because they will see your work again. They have also taken their own limited time, usually unpaid, to look at what you’ve submitted.
  2. Compose a response letter, starting in much the same way. List and address every single comment made by the editor and referees sequentially and in full. Keep in the positive ones too, it makes you feel better.
  3. Make it as easy as possible for the editor to tell that you’ve made the changes requested. This means that instead of saying ‘This has been done’, or ‘A paragraph on this has been added to the discussion’, say ‘This is a very helpful comment. We have therefore inserted a new paragraph in lines 283–292 which explains how…’ etc. Editors are busy and don’t like to have to work harder to check whether you’ve followed instructions.
  4. Tread carefully if you disagree with any comment. If it makes no material difference then make the change, even if it’s only a matter of preference. Only contest if you are convinced that the referee is wrong and you can back it up. Even so, apologise for not making the manuscript clear enough and specify where you have added clarifications or extra evidence in the text. If you’ve failed to convince them first time around then it implies that you need to change something.
  5. Try not to use track changes, comments, bold type or other formatting to note changes to the manuscript itself. In my experience (usually when requested to by editors…) this leads to errors in the final copy. Refer to line numbers instead.
  6. Take extra time on the figures. Clear, high-quality figures give your paper a greater chance of being read, cited and used by others. If the figures look amateur then no-one will bother reading the text. Use this opportunity to redraw and tweak them using proper tools (e.g. inkscape, sK1, ImageMagick, gimp). Don’t rely on Microsoft Office products to create publication-quality images.
  7. Never play referees off against each other. If they disagree on a point then compromise and ask the editor for guidance. Also note that if only one referee picks up on something, this does not imply that all the others are on your side. They may simply not have noticed.

Finally, in almost all cases reviewers are doing it because they genuinely care about maintaining standards in the scientific literature and improving the quality of work that gets published. There are some cases when a reviewer might block something too close to their own work, which contradicts them, or out of some personal vendetta against you or your collaborators. This is exceptionally rare though, and can seldom be demonstrated. Even if you suspect it, you’re most likely wrong, and should never say so in your response. No-one is out to thwart you.

Good luck, and remember, we all go through this. If it starts to get you down then go and vent to a colleague. Everyone has stories to share.

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* A friend at a university in a developing country once related that the modal number of papers among his faculty colleagues was zero. Exploring the causes of this, it transpired that in many cases they had once submitted something to an international journal and been so offended by the audacity of the response that they had vowed to never subject themselves to such humiliation again. This was true of even senior professors.

** I would recommend doing all this even if you’ve been rejected. Partly because you have a high risk of coming across the same referees again at a different journal, but mainly because it forces you to confront the criticisms of your work.

*** Don’t contest a rejection unless one of two things apply. Either there has been a gross mistake made by one of the referees, and you can unequivocably demonstrate this. Or you’re submitting to one of the big journals (Nature, Science) when putting up a fight can make a difference. Apparently. It’s never worked for me.