Midsummer Indulgence

Sorting through some papers recently, I came across a printout of a piece I wrote in (I think) the summer of 2002, fresh out of a PhD and wondering what happens next, looking after the ailing family dog at my parents’ house in West Norfolk, playing with the idea of natural history writing. Short of cash too - this was intended for some essay competition or other, probably at BBC Wildlife, though it certainly didn't bring me riches, even if I actually entered it. I re-read it, a decade on, expecting to cringe much more than I actually did. Things have moved on since then - the dog didn’t last the summer, mum and dad have migrated to the coast, I know a few more birdsongs, and I’ve somehow managed to remain employed doing what I enjoy, pretty much continuously. But Sheffield is also rich in swifts, and their screeching arrival each May signals the start of summer, regardless of what the weather tries to tell me. It’s still nice to stand in a field and remember that ecology is about real organisms interacting in a complex, wonderful world, and not simply points on a graph. So, 11 midsummers on, here’s the piece, retyped with one or two minor edits, but essentially an authentic blast from my past. What I’m saying, I suppose, is: indulge me… SWIFT

I wouldn’t mind being a swift for an hour or two. The thought cartwheels into my head as I crane to count them circling, screeching, avoiding bedtime on midsummer’s night. I’m on a hopeful excursion, looking for a barn owl that I’d seen on patrol months earlier, on the shortest morning. Noticing earlier that the meadow next to the river - its meadow - was freshly mown, I’d thought that on such a luminous evening as a barn owl I’d be hunting there. But my own hunt, always vague, tonight is in vain. In fact the full statistics of my stroll would hardly excite an expert - not even a hare, a rare absentee in these fields, in this part of Norfolk.

But I do calm my nerves before tomorrow’s job interview. Manage to reassure myself that this is who I am, this is what I like, all of it is worth it. And I take my communion, on the bridge over the Wissey, watching the lifeblood of this rich land flow beneath me, suffused still with water-crowfoot blooms and guarded by stroppy moorhens. I follow the meanders, going with the flow a way as I used to daily when the dog was younger and more sprightly.

Tonight the newly airborn midges, mozzies, mayflies could sustain a filter-feeding zeppelin, though for some reason (I won’t complain) they decline to feed on me. A malaise trap might catch a million a minute; back home, I could magnify, tease out, count veins and setae and quantify this diversity. But that sounds like a day job, and this is an evening stroll, so I leave them in as much peace as their brief and frenzied adult lives allow.

Soon I annoy a more ponderous beast, a heron sighing as it lifts off and flaps further downstream. How to tell it just to let me past, or I’ll disturb it again soon enough, round the next bend, or the next? Usually, I consider the heron’s solitary, stationary, mobbed lot a poor one, feeling I would soon tire of holding yogic postures in chilly, drizzly esturine mud. But tonight I would happily stand an hour or two with toes in this lucid summer stream.

A field of cows on the opposite bank: a score of mums and leggy calves processing dinner, long faces panning as I progress. A young coot, grey and ugly, panics, setting a partridge chucking behind. A rabbit retreating rapidly from the water’s edge gets my binoculars twitching - my heart insists on associating mammals near water with the frolicking otters that would complete the scene. But I’ll not see them on such a casual amble, I know. With the rampant June vegetation even water voles are invisible, betraying their presence with squeaks from deep within the tangled reeds.

Level with the old willow that marks my usual turning point, I finally set up the heron again. He shows his disdain by projecting a great skein of bright white shit in my general direction, but happily I’m out of range - a friend’s car acquired an uneven but surprisingly thorough re-spray in similar circumstances. I turn and head homewards with more urgency, conscious that my bare legs are unlikely to escape the insect clouds a second time. Birds are still settling in the bushes, and I pick out the odd wren or blue tit. In this prime riparian corridor there must be others, and indeed I’ve seen a few - whitethroats, reed warblers - but I’ll need more sessions with the CD before I’m confident in my ear. This new world of song feels tantalisingly close, but for now with no-one to confirm otherwise I’ll assume the lone thrush is a blackbird and not a nightingale. Still, another excuse for returning…

Pausing again on the bridge - a habit since I once saw the day-making flash of a kingfisher there - tonight I see just bubbles. Perhaps chub? With the low sun I can’t make out shapes or count fins. My angling friend would have sized them up by now I know, determined optimal bait and tactics. But I’m convinced that a lifetime on river banks has left him with polarizing retinas.

Now back past the barn owl’s vacant paddock, into the village, to the contemplation of chasing, screaming swifts. Their action calls to mind a skateboarder: seconds of vigorous pumping affording a blissful few seconds of glorious gliding before a new input of power is needed to avert the risk of stalling. Trying to focus binoculars on them, I may as well try focusing on flames. But I’m sure they are smiling, exhilarated anew each day by the sheer joy of flight. And really, that would be a fine thing, wouldn’t it?

The Clunky Mechanics of Collaborative Writing

Forget the myth of the lone genius: science is a collaborative enterprise, requiring cooperation within large teams of people. Often, this is both a joy and a necessity: many hands make light work in the lab or the field, and collaborations massively extend the scale of research questions we’re able to address. More and more, however, writing of papers, reports and funding applications is becoming collaborative too, and that’s seldom so pleasant; the best writing is personal, and writing by committee is difficult. There are counter-examples - the teams of writers beavering away on blockbuster US sitcoms spring to mind - but attempting to write something coherent when authors are scattered over multiple institutions, sometimes across many time zones, brings significant challenges. Although this post has been triggered by big collaborative writing project that's consuming my time recently, it would be inappropriate and hugely unfair to comment on some of the issues of content that plague all such enterprises; what I want to focus on instead is the actual mechanics of how we write. Some of the orthodox habits of academic collaborative writing seem incredibly frustrating, but I’m unsure of how to address them in a way that is accessible to all. The first issue feels like it should be a non-issue, given that content is platform-independent: what software do you use to write? For almost everyone I’ve ever worked with, the answer is: MS Word. My view is that Word is fine for individual writing. Sure, ‘features’ like its habit of second-guessing your formatting choices or its eccentric decisions regarding wrapping text around figures are frustrating. But as a simple typewriter it’s OK, and although I’m trying to shift to Scrivener more for my own writing (using it now), I do still use Word daily. The commenting system in Word - comments and tracked changes - also works fine as long as the number of commenters is small. But in a team of 20 or so, and with a heavily edited document, it becomes very unwieldy and, more importantly, very unstable - I’ve lost so many annotations through crashes.

What are the alternatives? I’ve never really got on with Google Docs, or at least haven’t seen anything that would place it substantially above Word. I know papers are now being written with full version control in GitHub, but even the advocates of this approach admit that, for now, the technical barriers to entry are too high to expect all collaborators to use it. And to be honest, a 20-author document is always going to be unwieldy, regardless of the platform. Perhaps we just have to learn to live with this.

Then there is the profusion of files which again, inevitably results when lots of people are simultaneously working on different parts of a complex document. How do we track these? Emailing individual docs around is a recipe for disaster, so some kind of file sharing system needs to be adopted. I’m a big fan of dropbox, but not everyone is (some institutions actively block it, I’ve recently discovered). On this application we’ve been using MS SharePoint, which I have to admit I’m not a great fan of, perhaps because it’s just more of an effort than dropbox. Perhaps if we used its full features, e.g. signing out documents for editing, rather than downloading and re-uploading everything, it might have won me over. Upshot anyway is that I have both a SharePoint site and a Dropbox folder each containing close on 200 files, with many combinations of initials and dates appended, which must be suboptimal… (Incidentally, sticking a date at the end of a filename is useful, but if you do so yy-mm-dd format allows for the most logical sorting.)

That’s a lot of problems raised, with little in the way of solutions. So if you have any killer tips, do let me know! But I will finish with two more constructive points. First, I said I didn’t want to talk about content, but I think there is one thing worth emphasising: Nothing is Sacred. There is no place in a piece of collaborative writing for egos and intransigence. By all means argue your corner if you feel a coauthor has completely missed your point. But think: if your coauthor doesn’t get it, no chance that a reviewer will, or any other reader. So don’t just dismiss their concern; take their criticism on board, re-work your text, and get back to them. In this sense, collaboration is the first stage of peer review. (A related aside on comments and tracked-changes, in the context of multi-author documents: comments can be useful, if they take the form of “X please write two sentences on that thing you know about here…”. But before adding comments like “This needs more detail” or “This doesn’t work for me”, stop and think whether you could preempt your own comment by actually editing the document.)

Second, a couple formatting tips. Every proposal I’ve ever been involved with has ended up bouncing off the page limit, and so it’s useful to be able to make maximum use of available space. One tip I got from Twitter (whoever it was, thanks!) is to turn on automatic hyphenation in Word (Tools > Hyphenation…), which gains a surprising amount of space. Apart from that, I’m a bit wary of pushing font size and margins right to the limit, simply because confronting your reviewers with massive blocks of dense text is not going to do you any favours. The key then is to edit, edit, and edit again (see also the point above about nothing being sacred).

I take a strategic approach to this: any paragraph that ends with a line less than half full is ripe for reduction by one line, easily, simply by cutting unnecessary words and rephrasing. Be really harsh on repetition, verbiage, impressive-but-meaningless words, and repetition. (See what I did there?) Use short words like ‘use’, no need to utilise longer synonyms like ‘utilise’; this will help readability too. Funnily enough, this is an area where Twitter really helps, as it gets you used to fitting ideas into a strictly delimited space.

So anyway. I now open this to input from coauthors…

On endlings and singletons

There can be few words as poignant as ‘endling’, the name given to the last surviving individual of a species. Tell me you don’t find this image of Benjamin, the last Thylacine, heartbreaking? Or that you weren’t moved by the plight of Lonesome George? And what about Martha, the passenger pigeon? Doesn't her story make you weep at our limitless environmental profligacy? But what links all of these endlings is that we know they were once members of a thriving population - in Martha’s case, one of the most abundant vertebrate species on the planet. There are other species which are known only from a single individual. These species, perhaps lacking the poignancy of endlings but arguably more significant to students of biodiversity, are known as 'singletons'.

Singletons of course are to be expected when your survey area is small, or if your look for only a short period of time. If I counted the birds in my garden for an hour tomorrow morning, I’d expect to see multiple individuals of a few species - magpies, wood pigeons, house sparrows - but I’d be very surprised to see more than one sparrowhawk or wren. However, if I extended my search to my whole street, or to the whole of Sheffield, the number of singletons would drop off precipitously. And at the scale of the UK, over the course of an entire summer, any breeding bird species by definition must be represented by at least two individuals, so there should be no singletons at all in our core avifauna. Any that remain can be dismissed as shivering vagrants blown across the Atlantic, ornithological curiosities but ecologically insignificant.

Enter the sea, though, and the number of singletons remains stubbornly high, even when we expand enormously our study region. For instance, in an analysis of European benthic invertebrates I did a few years ago, I found that about 10% of the species in our very large database (2,300 species sampled from >15,000 locations throughout European seas) were singletons. Similar patterns appear when interrogating the Ocean Biogeographic Information System database I blogged about recently. For instance, OBIS contains records for >11,500 species occurring in the seas around Britain, yet over 45% of these are represented by a single record. At the global scale, 20% of the almost 80,000 marine animal species which occur in OBIS are singletons.

What's happening here? Are these singletons simply very rare species? We expect most species to be rare, but do our surveys of marine habitats really cover so small an area that we never pick up their conspecifics? And if this is so, what does this mean for marine ecosystem functioning? Do these rare species play a role? Individually, maybe not - Kevin Gaston has written on the dominance of common species in terms of numbers, biomass, and probably ecosystem functioning, in most communities. But collectively the singletons in a sample can be abundant, and if there were particular biological characteristics associated with being a singleton, then this could be significant. Unfortunately, about the one generalisation we can make about rarely observed marine species is that we know little about their biology, so we’re not yet in a position to answer this question.

An alternative explanation is that many singletons are mistakes. When analysing diversity surveys, we can take steps to ensure that taxonomic names are consistent, for instance by using the World Register of Marine Species to ensure that we use the accepted name for each species and not one of its (often many) synonyms (I've done that in the cases mentioned above). But what if the person who sorted the sample simply got their identification wrong? There’s not much we can do about that kind of mistake, although one would hope that errors of identification are not so frequent as to explain the very high prevalence of singletons.

Probably we won’t know the answers to such questions until sampling of a few large marine ecosystems reaches a sufficient intensity that we can have confidence that surveys accurately reflect the composition and relative abundance of the species present. For now, we can at least use the presence of singletons to tell us something about how far away from such complete knowledge we are. As I suggested in my last post, in certain marine systems the answer to this is: a very long way indeed. In the meantime, we are becoming more and more aware of the threats facing many marine species. We must hope that the singletons we find in our surveys are only statistical loners, the first observed rather than the last remaining individual. If they do in fact represent the Benjamins, Marthas and Lonesome Georges of their kind, then marine biodiversity is in more trouble than we thought.