A Natural Historical Interlude

I’m just emerging from that special juggling act that UK academics perform at this time of year, when a stack of marking is chucked into the air alongside everything else. And given that last time out I provoked a few people (and reinforced a few preconceptions) I thought I’d ease back into things with some nice, non-controversial musings on natural history. Now first-up, I’m not much of a natural historian. Periodically I resolve to learn a relatively manageable group – British trees, say, or dragonflies – but to be honest, I simply don’t have the patience required to work meticulously through a key. Neither do I have that instinctive eye for the salient feature that characterises the great observers. Many’s the time I’ve thought I’ve committed to memory a particular unknown little bird, only to open the fieldguide and find I have no idea of the prominence of its supercilium, or the relative brownness of its legs.

Nonetheless, I muddle on. I am quite good at noticing things, and it’s really important for me to see lots of nature, even if I can’t put a name to absolutely everything. In fact I have a theory that there are two routes into ecology. There are those who as kids collected beetles, who cleaned up and displayed roadkill, or who have subsequently crossed continents to extend their life list of birds. And there are those of us who just sort of liked messing around outside – for whom the important thing remains the experience of nature as a whole, rather than the infinite dissection of its parts.

Over the last four years or so, my major outlet for this interest has been our back garden. One of the advantages of moving back to Sheffield was that a terraced house with a good sized garden fell within budget. And one of the pleasures of staying in the same place for a few years is that early work starts to bear fruit (sometimes literally).

For instance, the other day I trimmed the mixed native hedge that we planted and which is now in its fifth growing season. Originally just a line of sticks, it’s now around 5’ tall, thick and lush. Already populated by sparrows it also shelters blackbirds and starlings, ladybirds and hoverflies. Watching this new habitat flourish gives me as much satisfaction as any paper I might write.

Our pond, in progress (2009) and with water soldiers breaking its surface a year later.

Likewise, the pond I dug in 2009 is an endlessly fascinating mini-experiment. Perhaps I should have kept meticulous records of colonisation dates, but for me it’s enough to remember that the first pond skaters were skating before I’d turned off the tap from filling it; that the frogs appeared to be waiting for me to dig it (I have no idea where they bred before); that great crested newts found it within a year, as did water boatmen, dragonflies and damselflies. The weather’s been rather peculiar this year – the warmth in March got the algae blooming, but then it was too cold for the grazers to do much, so it’s a bit green at the moment. But fishing out some blanket weed at the weekend, I was excited to net three large dragonfly nymphs which I suspect will be climbing up some of the emergent vegetation any day now, as well as the first water beetle I’ve seen there. The birds use it to bathe in and drink from, as do the grey squirrels (which have far less right to be in a Yorkshire garden than the rats that I can’t keep away from the compost heaps, but which have much better PR).

Some of the smaller garden residents: a pioneering pondskater, and its near-mirror image water boatman; frogs in various stages of development; a hoverfly suns itself; and a bee visits a foxglove.

Two more things which have got me into the natural history of my garden. First, buying a good macro lens for my camera – if you look closely, there is always something interesting to see. And of course, sharing it with a 1½ year old for whom all of this is fresh and exciting (and who’s new favourite word is ‘bee’).

Years ago, I studied Candide for my French A level. I’ve never been sure that I grasped in full the philosophical implications of its final line, “‘Cela est bien dit,’ répondit Candide, ‘mais il faut cultiver notre jardin’”. But I like to take it literally, and whenever the stresses and strains of the life scientific start to bite, I take the role of Candide, heading outside with my own version: That’s all well and good, but this garden won’t look after itself.

Confessions of an Open Access Agnostic

The office that I worked in a few years ago had a window that opened onto the main University of Sheffield concourse. Every so often, lunchtimes would be enlivened by a student protest (typically over fees), during which someone with a megaphone would shout a lot. I remember clearly being struck with the thought, “I wonder if anyone has ever changed their mind about anything as a result of something they heard through a megaphone?” It certainly doesn’t work on me. Even if I broadly agree with the shouty person, the louder they shout the more inclined I am to pick holes in their argument. It is a character trait of mine, I’m not sure if you would call it a flaw or a virtue, that I hate being told what to do and, especially, what to think.

All of this explains, perhaps, my ambivalence towards Open Access (OA) publishing. I don’t like being told where I can and can’t publish. I distrust zealots, including well-resourced single-issue campaign groups which will hear no alternative views, which present shades of grey as simple black/white dichotomies, and which (a pet hate) bandy around variants on that tabloid favourite ‘tax-payers’ money’ (when they mean ‘public money’). I worry about people being pressurised into publishing in inappropriate journals, or – if they decide to stick with a non-AO journal, for whatever reason – not receiving the quality of review they deserve because of misguided boycotts. I don’t appreciate non-scientists in the media wading in with their ’aren’t you silly, you’ve been doing this all wrong for decades’ line. And I’m wary of the creeping sense – by no means restricted to science – that content should always be free, regardless of the costs involved in producing it. I’m not comfortable with the big publishers making huge profits from the outputs of science, but I also recognise that good publishers (and their employees) have done, and continue to do a terrific job to ensure the effective communication of science.

Of course, there is a more nuanced debate going on underneath the bluster. From what I see on Twitter, today’s debate at Imperial seems to be a good example (#OAdebate). Some very clever and thoughtful people have weighed things up and come down on the side of OA. And I’m not even sure that I don’t agree with them. Certainly, I am all in favour of the broader Open Science agenda – opening up the data we produce, and the tools we use to access and analyse it. But I remain to be convinced that access to primary research papers is such a big issue that it should be pushed above all else (partly because, with a bit of effort or an email or two, it’s usually possible to access most recent papers), and that all of this energy should be focused on it (whilst overlooking the interesting and potentially profound financial and sociological implications for scientists and their institutions).

My beef is not at all with OA, but rather in the way that the debate has been framed in terms of good and evil, right and wrong (not a million miles from the ongoing GM debate). Subscription-based (reader pays) publication of publicly-funded research costs public money, and has pros and cons. OA (author pays) publication of publicly funded-research costs public money, and has pros and cons. A shift to OA will not (I’m pretty certain) be accompanied by an injection of new cash, but will rather see a shift from funding infrastructure (especially libraries) to funding individuals (e.g. through research grants). And the debate should be on how best we spend limited public money to communicate the outputs of research in the most effective way. It could be that making all primary research available to everyone is the way to do this (although I don’t think accessing papers is quite so difficult as some would have us believe; and in any case, the readership for the vast majority of papers is tiny). It could be that we’d be better advised to concentrate on more effective communication of key results in other formats, or in making other products of our research (especially data) more widely available. Even if we hold OA as something to aspire to, I feel that blindly pushing it as a top priority risks sidelining more important debates about opening up science.

So thanks, but I won’t be signing any petitions just now.

The National Biodiversity Network and Biodiversity Research

Yesterday Nature reported on the launch of the Map of Life project, a new initiative to collate biodiversity records, which allows users to map these, to extract species lists for any area of the planet, and (ultimately) to upload their own data. Limited initially to terrestrial vertebrates and North American freshwater fish, the demo website still looks like a lot of fun. But it also reminded me somewhat of a UK-based project which has been running for a number of years, the National Biodiversity Network (and specifically the data service at the NBN Gateway). This gives me a good excuse to comment on the NBN, which I’ve been meaning to do for a while. Specifically, why hasn’t the NBN Gateway been used more by the research community? Let me first declare some interests. This question was raised by the British Ecological Society around 18 months ago, who convened a scientific working group chaired by Tim Blackburn, of which I was part. And the NBN Trust (@NBNTrust, if you like to Tweet) is actively trying to promote its potential as a research resource, and I’m writing this post partly in response to a request from Mandy Henshall, NBN Trust Information and Communications officer, to spread the word and to find out what it would take to get the data used.

The NBN grew out of the need to standardise and coordinate the many thousands of local, regional or national surveys to provide a national picture of the UK’s biodiversity. The NBN Gateway is simply the portal through which these data can be accessed. And it’s become an extremely impressive dataset: currently >75M records from >700 individual datasets. The Gateway itself if really nicely designed for the general user. You can search on an interactive map, or by site name, or by taxon, and quickly get a list of everything that’s been recorded – fantastic if you’re planning a trip to an RSPB reserve, say, and want to know what birds you’re likely to see; equally good if you’re leading a field trip and want to prime your students about what might be there. (Worth noting too that the NBN encompasses all taxa and habitats, including some limited coverage of marine systems.) As a citizen science / public engagement project, the NBN is absolutely superb, and I urge you to go and have a play.

But does it work as a tool for academic biodiversity research? Some things it does well, for instance the (nontrivial) task of standardising taxonomy across multiple datasets. But we identified several potential shortcomings, most obviously the fact that not all data are publicly available – it can be incredibly frustrating to see a great dataset identified by your search, but not to be able to access it. Of course, the problem of data access is not restricted to the NBN, and they clearly had to make a choice – include everything with restricted access, or include only a subset of available data which can be provided completely open. Other initiatives, for instance the Ocean Biogeographic Information System (OBIS) went this second route, the idea being that if sufficient people can be convinced to make their data available, peer pressure will mount on those who won’t. But this discussion of open data is best left for another day.

Other barriers we identified concerned the different ways that scientists like to access and download data, compared to the public. For instance, we often want to be able to access data programmatically, or at least to have an audit trail of specific queries, rather than working through nice friendly GUIs. And often we want to download data as a simple text file for further analysis, with no whistles and bells.

Finally, there is the matter of the data itself (and pedants: yes, data is a singular noun). The NBN contains some fantastic systematic scientific survey data, but also a lot of more haphazard observational data, which may be reliable in terms of recording the presence of a given species at a particular site, but which tells us little about absences. Suppose Mr Patel has a fascination with limpets, and has been counting them on Filey Brigg every week for years. His data would give us a fantastic picture of the limpet population, but the absence of records for barnacles or periwinkles doesn’t mean that they’re not there – crucial if you’re interested in the whole community.

Such limitations suggest that the researcher proceed with caution through the NBN gateway; but the advantages of such a huge dataset mean that simply to ignore it may be to miss out on a terrific resource. There are already various examples of NBN being used by students for research projects. The question is, what would it take for wider uptake by the research community?