Trait databases: the desirable and the possible

Another major traits database has recently come online. This time, all you need to know about the life histories of 21,000+ amniotes (reptiles, birds, mammals), courtesy Nathan Myhrvold, Morgan Ernest and colleagues. I’ve been working with ecological traits for a good while now, and this kind of thing excites me. It also demonstrates the kind of self-interested altruism that typifies the Open Science mentality. As Morgan puts it in her blog post on the paper:

The project started because my collaborator, Nathan Myhrvold, and I both had projects we were interested in that involved comparing life history traits of reptiles, mammals, and birds, and only mammals had easily accessible life history databases with broad taxonomic coverage. So, we decided to work together to fix this. To save others the hassle of redoing what we were doing, we decided to make the dataset available to the scientific community.

In other words, you start by fixing a problem that you yourself have, and then make your solution available to save others the bother. Practical and admirable. The same thing is happening elsewhere, with other kinds of ecological data - take the ‘data rescuing’ example of the PREDICTS project:

https://twitter.com/KatheMathBio/status/676448069890744321

(Compare and contrast with this fascinating, frustrating new book by John William Prothero, The Design of Mammals: A Scaling Approach, another monumental data compilation which includes a multitude of intriguing scaling relationships, calculated from 16,000 records for around 100 response variables, almost none of which are replicable from the subsets of data provided in the Resources section online.)

But Morgan’s blog post becomes really interesting as she muses on the what the end game might be for traits databases. She proposes a centralised trait database, with a focus on individual records, that is easy to contribute to and where data are easily accessible. We had a short exchange on Twitter after reading this, but I’ve continued mulling it over and my thoughts have expanded past 140 characters. Hence, this.

Basically, I have been trying to imagine what this kind of meta-dataset might look like. And my difficulty in doing this in part boils down to how we define a ‘trait’.

The simplest definition is pretty broad, with a trait just any measurable property of an organism (noting that some ‘traits’ apply only to populations - e.g. abundance - or even entire species - e.g. range size). And my own work, like Morgan’s, has typically focused on life history and ecological traits - things like size, growth, reproduction, and feeding. In some respects these are some of the simplest traits to describe, but they can still be tough to measure, and (especially) to classify and record.

Part of this difficulty arises because much work on traits involves imposing categories on nature, and nature abhors a category. Then again, individuals of the same species can do quite different things, or the same individual might display different traits at different times or in different places. Some people have tried to get around this by using a ‘fuzzy coding’ approach - for instance, rather than having to classify me as ‘carnivore’ or ‘herbivore’, you could say that my diet is split, say, 15% carnivore to 85% herbivore. In many ways this seems a sensible solution, but it is of course rather subjective, still requires some rather arbitrary categorisation, and, in the context of this post, is very difficult to incorporate into a more generic database.

Other traits may seem simpler. Body size, for example, the so-called ‘master trait’, us surely easy to measure? You just weigh your organism, right? Or perhaps you measure it’s length. And is that total length, or wingspan, or leg length, or standard length? Oh, you want dry weight? Or mgC? Equivalent Sperical Volume, you say? And so on and on…

Related to body size are other morphological traits. For instance, my colleague Gavin Thomas and his group are busy 3D scanning beaks of all species of bird (you can help, if you like!). Such sophisticated morphological measurement quickly generate individual-level ‘trait’ databases of many dimensions; how might these be incorporated into a more general database? Record each dimension? Or use some agreed (but somewhat arbitrary) composite measure of ‘shape’?

One more example of a different class of traits. On the Marine Ecosystems Research Programme, I’m working quite a bit with ecosystem modellers, and their lists of desired traits are terrifying: Michaelis Menton half sat. uptake const.; Excreted ingested fraction; Respired fraction - all things that seem a long way from the sorts of life history databases I’m familiar with, or from things that can be easily observed in the field. Many of them will be body size and temperature dependent (at least). And so what might be most appropriate to record are the parameters from some fitted scaling relationship; but this means losing a lot of raw data, which surely we would like to retain?

And so on.

So whilst of course I applaud the efforts of people like Morgan to make large trait databases more useful and accessible, and agree completely that we should both think big and think individual, a complementary angle of attack might be to make linking existing databases easier. Of course, they need to be available, well documented, and appropriately licensed as a first step, and straightforward programmatic access should be designed in. But we can also make more efforts to link to taxonomic standards, to ensure we include accurate geographical and contextual information with individual records. Always ensuring our data are nice and tidy so that others can easily do more interesting things with them.

A Rational Optimist's Reluctant Case for Panic

As European rugby fans look back with regret on (yet!) a(nother!!) chastening weekend, one of Monday’s papers put up a poll: When do you think a northern hemisphere team will next win the World Cup? There was a choice of the next five tournaments, 2019 to 2036. (Plus ‘none of the above’, one assumes…) Which got me thinking about something that has been nagging at me for a while. On this kind of timescale - a few years to a few decades into the future - I just don’t think people are very good at conceiving of fundamental change. Rather, and more-or-less regardless (so I contend) of how well informed we might be about the facts of global social, technological, or environmental change - we sort of assume that life will carry on just about how it always has within our experience, with incremental developments maybe, but without major upset. So while the players at major sports events will change, the basic pattern - a big, multi-week jamboree involving mass movement of people around the world, major new infrastricture, huge inputs of cash, energy, water, and so on - will remain, we expect, essentially identical. Hence we start planning for the 2036 World Cup now.

Certainly, this has always been my belief. Although I’ve been concerned about environmental issues for as long as I can remember, I consider myself (favourably, of course) to be towards the optimistic end of rational. So I find it very hard to believe that any of the properly charismatic species will ever really be allowed to go extinct; and I have this powerful faith (i.e., belief without a shred of evidence) that we as a society will in the end, when it really matters, pull something out the bag on climate change. To a certain extent, parenthood enforces such an outlook - first of all we convince ourselves that we are bringing life into what is basically a favourable world; and then we try to ensure our kids have childhoods as good - preferably better - as our own were. Incremental change, on an overall upward trajectory.

But a couple of things I’ve read recently have shaken that stubborn optimism of mine, to the extent that I’m starting to find casual talk of a 2036 World Cup faintly ridiculous.

First, Paul Mason’s Postcapitalism: A Guide to Our Future. Read as a primer in Marxist theory, in economic and industrial history, in neoliberalism and its sinister symptoms, it is compelling. I was less convinced by some of the projections - for instance, his energy analysis seems shaky and whilst Wikipedia is wonderful, it bears an awful lot of the weight of Mason’s arguments about a future of unlimited free stuff and no need to work. (Oh, and his data visualisations are just awful.) But it’s a terrific read nonetheless (subject, I hope, of a full post in due course); and it is, in parts, terrifying. For instance, in laying out the looming pensions crisis - evident already in the imminent downgrading of my own (excellent, public sector) policy. And the economic consequences of taking climate change seriously (as he argues that we must), which include a collapse in the share value of some of the world’s largest companies, if (when!) we tell them that large fractions, perhaps 60-80%, of the assets on which this value is based - as yet unburnt fossil fuel reserves - must stay in the ground. In fact, I was convinced enough to adapt the title of his ninth chapter for this post. And, reluctantly, I'm leaning towards seeing our current, post-crash situation as more than a painful period of austerity that will end as soon as we vote the nasty posh boys out of office, but rather as a sign of far less pleasant things to come. As Mason puts it,

“The OECD’s economists were too polite to say it, so let’s spell it out: for the developed world the best of capitalism is behind us, and for the rest it will be over in our lifetime.”

The second key book for me has been David Mitchell’s wonderful novel The Bone Clocks. I’m a long-time Mitchell fan, I just love the worlds he creates, and suspend my disbelief willingly for his forays into the supernatural simply because of the power of his characters and the beauty of his prose. The Bone Clocks follows one of his most vivid creations yet, Holly Sykes, through six intertwined novellas and across seven decades, from the 1980s to the 2040s. And it is the final section, set in rural Ireland in 2043, that presents such a stark imagining of a drastically different future. Here is Holly, a few years older than me but basically of my generation, who has lived - as I have - with the rise of technology into every aspect of life; but who in her 70s is now experiencing the ‘endarkenment’ - chaotic times of 21^st Century tech that still works occasionally, of power for those who can generate their own energy or grow their own food, or who have the might to take that from others. My copy of The Bone Clocks includes a short interview with Mitchell, in which he is asked whether this dystopian end to the novel reflects his own view. “Yes”, he responds,

“I’m afraid our civilisation is defecating in the well from which it draws life. We’re leaving our grandchildren a hotter and less secure world… We’re intelligent, but we’re not wise.”

Now I’ve read similar sentiments countless times from environmental prophets of doom, but taken alongside my research into the implications of population 10 billion  for this adventure, as well as Postcapitalism and the rest, I find myself concluding that life in twenty or thirty years time - and forget the grandkids, this is for me, for us - might very well be very different from how it is now. So I’m actually not too fussed about losing perks from my pension, simply because the I can't really imagine the plan of retiring comfortably sometime in the 2040s panning out…

The optimist in me still thinks of the resilience of nature - a different, feral, nature maybe, but nature nonetheless - and of humanity. Sure, we’re seeing the what Kevin Gaston call’s the ‘extinction of experience’, the sad loss of connection with nature; but as I’ve written before, I think baselines shift: people just get used to this new normal and find joy where they can. I fervently hope my kids get to see some real nature, but I know too that they won’t regret what they have not known; that regardless they will be complex, connected, happy-sad members of the 10 billion.

But I will regret.

And thus underperforming sports teams are placed in proper perspective.

Peer Review, Amis Style

I have read for pleasure for as long as I remember, some books haunting me for years after I finish them, others drawing me in only while they last. But two authors had a particularly formative influence on me in my late teens, in very different ways. Richard Dawkins caused me to reassess my position in the world. And Martin Amis showed me that so-called literary novels could also be pretty good fun. In the couple of decades since, my tastes have changed. Amis’s early novels, which made such an impression, were written while he was much younger than I am now. They are probably best left to sixth formers and twentysomethings. And as for Dawkins, well, I was convinced early on, argumentitatively so for a while; but the need to fight those fights left me as I drifted into the happy state of live and let live that Ben Goldacre wonderfully characterises as ‘apatheism’: "I'm an apatheist. It's not that i don't believe, it's more that I find all discussion of the issue shit-boring". Dawkins, of course, is still fighting; and Amis is still writing. Indeed, superficially the two seem to have followed similar trajectories from exclusive schools through Oxbridge and early brilliance and into… well, if satirist Craig Brown’s name hadn’t appeared at the bottom of this set of (supposed) Dawkins tweets would you have known they were in Private Eye? And his second volume of memoirs was greeted in Nature thus: “Brief Candle is about as edgy as Sir Mick and the Rolling Stones cranking out the 3,578th rendition of 'Brown Sugar' — a treat for fans, but reinscribing boundaries rather than crossing them”. Amis is also an easy target for ridicule, expressing with apparent seriousness not enormously sophisticated opinions on grown-up issues, like (according to the magnificent Chris Morris) 'a senile 12-year-old'. Nearly time (he's 66) for him to consider his own advice:

“Novelists are stamina merchants, grinders, nine-to-fivers, and their career curves follow the usual arc of human endeavour. They come good at thirty, they peak at fifty… at seventy, novelists are ready to be kicked upstairs.”

As with so many things I got up to when I was young, then, reading Dawkins and Amis is probably best remembered fondly than attempting again now.

And yet.

I just read a Martin Amis book. True, it was not a novel, rather a book of his literary criticism and journalism (The War Against Cliche - just the kind of ‘bits and pieces’ book I enjoy). But it was good fun, and reminded me of Amis’s twin saving graces. First, he can really write. It’s partly the technical stuff - elsewhere, he writes that you should never start successive paragraphs with the same word, unless for effect, in which case do three in a row. Impossible to unread that command and I’ve obeyed it ever since. Whether or not it makes a difference stylistically, it makes you think about your writing in useful ways. More generally I just derive great pleasure from reading a sentence like:

“Excluding a few dry-outs, in hospitals and prisons, and the very occasional self-imposed prohibition, Malcolm Lowry was shitfaced for thirty-five years”

or:

“The book bristles with beauties, charm, sublime comedies; it is also, for long stretches (approaching about 75% of the whole), inhumanly dull… The question ‘What happens next’ has no meaning, because there is no next in Don Quixote’s world: there is only more.”

The second reason to re-try Amis is that he’s funny.

For instance, he decides to review Desmond Morris’s The Soccer Tribe by writing six pages of anecdote about the travails of being an intellectual football fan (note for younger readers: in the 1980s football fans were a trainspottery bunch, before Sky required us to profess to enjoy the lucrative game), not mentioning the book until the final sentence, whereupon:

“I have only time to add that Morris’s book is handsomely packaged, that the pictures are great, magic, brill, etc., and that the text is an austere, an unfaltering distillation of the obvious and the obviously false.”

For instance, on Norman Mailer:

“He isn’t frightened of sounding outrageous; he isn’t frightened of making a fool of himself; and, above all, he isn’t frightened of being boring. Well, fear has its uses.”

For instance, the new monster in Michael Crichton’s The Lost World

“…shows promise. It is a carnotaurus, a light-heavyweight with horns… ‘Diet: Meat’, as my dinosaur encyclopaedia bluntly assures us. This is good. In the Jurassic era, as in our own, vegetarians are a drag.”

So he can write, he can amuse, and he can, of course, be cruel. (On Crichton again: “Animals — especially, if not quite exclusively, velociraptors — are what his is good at. People are what he is bad at. People, and prose.”) But Amis’s reviews are also, in aggregate, much nicer than I had expected. He states as much himself: as a critic,

“[y]ou hope to get more relaxed and confident over time; and you should certainly get (or seem to get) kinder… Enjoying being insulting is a youthful corruption of power. You lose your taste for it when you realise how hard people try, how much they mind, and how long they remember… ”

This surprising (and admittedly somewhat self-interested - note the ‘how long they remember’…) sensitivity to the efforts of others - no matter how substandard - is echoed in his review of a volume of John Updike’s collected journalism:

“Kind to stragglers and also-rans, to well-meaning duds and worthies, and correspondingly cautious in his praise of acknowledged stars and masters, Updike’s view of twentieth-century literature is a levelling one. Talent, like life, should be available to all.”

Think on this, then, before you set upon the next unfortunate manuscript to land in your inbox. And try always to get kinder.