The Mike Leigh mark-recapture experiment II

The discovery of Neptune. Gauss's calculations of the orbits of asteroids. The 1919 solar eclipse that caught light bending. Science is filled with masterly predictions, triumphantly confirmed.

Add a new one to the list.

In Sept 2006, I wrote, in a quite poorly punctuated post, of my repeat sightings of film director Mike Leigh around London. I suggested that Leigh could be a model for measuring the bumping-into-frquency of any two Londonders. And, based on three sightings, I ended the post with

if you're reading this, Mr Leigh, I'll see you in 2008.

Well, we were in the NFT on Sunday afternoon, queuing up to get tickets for The Lady Vanishes, and there he was, right in front of us in the queue!

Imagine my pleasure. Conclusive proof that any two Londoners (of similar cultural interests/socioeconomic level) can expect to cross paths just under every 18 months. I released the director back into the wild, to go on making his finely observed portraits of lower-middle-class desperation, secure in the knowledge of another encounter in summer 2009.

Glengarry Glen Research

A conversation I was having today made me think of this sketch. I wanted to share. Contains swearing.

Ecologists rule (well, advise)

I see (belatedly) that John Beddington is going to be the UK government chief science adviser, succeeding David King in January. Beddington is an applied ecologist - specializing in fisheries biology. He'll be the second ecologist out of the past three science advisers - King's predecessor was the legendary Bob May (who, like Beddington, used to work at Imperial College London).

Add to this behavioural ecologist John Krebs' (who, I see, now has the magnificent title of Baron Krebs, making him sound as if he should be wearing a monocle and shooting down British biplanes over the Somme) chairmanship of the Food Standards Agency, and it looks as if ecologists are doing rather well at getting their mitts on the UK's levers of power. (And Krebs and May are now both at Oxford, making it basically an Imperial-Oxford operation).

Why is that? Within science, ecology doesn't strike me as a particularly powerful discipline, in terms of its level of jobs and funding. It's a lot more quantitative than, say, cell biology, which I guess is useful in government, but that doesn't seem like much of an argument. Maybe it's just a blip - May's predecessors were a microbiologist (William Stewart) and a computer engineer (John Fairclough).

The Future of Amazonia

The current New York Review of Books has an excellent piece by John Terborgh looking at the history of development in the Brazilian Amazon, and the forest's future prospects.

Terborgh's story and his arguments are too detailed to do justice here, but this, roughly, is his conclusion:

Brazil will continue to pursue its long-cherished goal of integrating the Amazon into the national economy. Much of the forest will go. But I would be surprised to see it vanish entirely because an increasing portion of the Amazon in Brazil, and in neighboring countries, is under formal, legal protection...Short of a complete breakdown of civil authority, the Amazon won't be entirely "lost".

He then sounds a note of caution: "Unforeseen developments are likely to determine the future of th Amazon... One such unforeseen development is fire, which holds the potential to be the undoing of the Amazon." Pristine tropical forest, he say, doesn't burn. Logging changes that:

Logging synergizes fire in two ways. First, cutting down trees opens the forest canopy, admitting sunlight and drying out the leaf litter on the forest floor. Second, the debris of branches, chips, and stumps left behind by logging operations serves as fuel for any subsequent fire.

The first time a tropical forest burns, the damage can hardly be detected from above because the destruction is largely confined to saplings and small trees whose crowns lie below the canopy. But the subsequent presence of large numbers of dead trees greatly increases the fuel available to stoke the next fire. Consequently, second fires burn hotter and more destructively, killing large trees as well as practically all smaller ones. And, of course, second fires generate even more fuel for the third fire. Colleagues of mine who study this subject, notably, Carlos Peres and Jos Barlow of the University of East Anglia (UK) and William Laurance of the Smithsonian Tropical Research Institute in Panama, assert that the third fire spells doom for the forest, since it kills all remaining trees.

Then, he adds, there's climate change, which will reduce rainfall, and dry the Amazon out from west to east (becasue the rain comes off the Atlantic) and threatens the 'savannaization' of the forest. In total, Terborgh's essay is all the more sobering for being balanced and unalarmist.

Do escaped transgenes persist in nature?

Of the things I get worked up over, genetically modified crops aren't that high up the list. (As an aside, I think the UK farm-scale trials of a few years back did a good job in showing that GM crops tended to reduce agricultural biodiversity, but that this was a result of the changes in farming methods associated ith them, rather than any property of the crop per se. Likewise, I think the issues around GM crops are more to do with big agribusiness controlling the food chain, loss of varietal diversity and so on, rather than that the technology is somehow immoral or that eating them is bad for you. It's striking that in places where they don't have the luxury of squeamishness about agriculture, such as India and China, GM is rather less of an issue.)

That said, I think this paper in Molecular Ecology by Suzanne Warwick et al is interesting. They show that herbicide resistance genes from oil-seed rape (Canola) have crossed into a weedy relative, Brassica rapa and set up home there (they've been there for 6 years, apparently).

"Most hybrids had the [herbicide resistance] trait, reduced male fertility, [and] intermediate genome structure", say Warwick et al. Whether they are more or less fit than the wild variety - and what consequences this has for the weediness of B. rapa - they don't say in the abstract. That's clearly something worth studying; I don't think panic is in order, but vigilance is, so well done to these researchers for playing the long game. Although by the time we find out we've created a super-weed it may be a bit late.

Who's the queen? Ask the genes

Is the title of a piece by me in the current issue of Science looking at genetic caste determination in social insects (mostly ants, of which mostly harvester ants, with the occasional termite).

Here's the introduction:

In 1712, the English scholar Joseph Warder dedicated his treatise, The True Amazons: Or, The Monarchy of Bees, to Queen Anne, citing the caste divisions of the hive--the queen built for breeding and the workers tending her and her brood, foraging, and dying to defend their home--as evidence that nature adored royalty. But much of what entomologists have learned since then has made the lives of bees and other social insects seem closer to the American dream: Given the right nurturing--a diet of royal jelly in honeybees, or being reared at a certain temperature in some ants--any female grub in a beehive or in an ant's nest can grow up to be queen.

At least this nurture-over-nature paradigm was the prevailing wisdom, backed by theory that argued that any gene that required a developing insect to become a sterile worker would be committing evolutionary suicide. But a few years ago, social-insect research was rocked by the discovery that in some ant species, workers and queens are determined by their genes--in other words, born, not made.

Gonzo my arse

I thought John Bohannon's piece on the Libyan AIDS scandal in the November issue of Discover (can't see it online) was excellent. So I was interested to learn that he's just started a column called the Gonzo scientist over at Science.

I dimly remember a piece by Jon Turney from years ago asking where the gonzo school of science writing was. My guess is that science writers don't often get the opportunity to get deeply/improperly involved in their stories (although to a small extent I tried for ITBOAH, going off to collect vegetation samples in Costa Rica with Brian Enquist and his group. It really helped the book.). Scientists, meanwhile, have an excess of amour propre, which makes tham worried about dropping the veil of objectivity/looking like idiots.

The most honourable exception that I know of is Robert Sapolsky's A primate's memoir, which has some brilliantly funny passages (one about learning to fire tranquilizer darts from a blowgun springs to mind), in which he isn't afraid to look foolish.

So, what does Bohannon's gonzosity consist of? Well... he...(wait for it)...goes to vaguely off-beat conferences! And writes about them! At great length!

This, from the latest piece, might not be the worst line of science journalism written this year (the competition's always stiff), but...

"So those were American crayfish?" I asked, resisting an ironic smile.

Listen, sunshine. When you're in a Guatemalan brothel, having a naked fistfight with Martin Rees, after sinking a dozen temazepam and a bottle of Flor de Caña, then you can go around comparing yourself to Hunter S. Thompson. Until then, why not rename your column 'The wussy scientist'?

Sharks, sheep and viruses

Three recent conservation biology-type papers worth a look:

Do shark declines creat fear-released systems?
A model sugesting that if you take pacific sleeper sharks out of the ocean, seals swim deeper, and eat more pollock - which live deep - and fewer herring.

Are cattle, sheep, and goats endangered species?
The "rise of the breed" 200 years ago, followed by more recent selection for increased productivity has led to a dangerous drop in the genetic diversity of domestic animals. "Many industrial breeds now suffer from inbreeding, with effective population sizes falling below 50... It is therefore important to take measures that promote a sustainable management of these genetic resources; first, by in situ preservation of endangered breeds; second, by using selection programmes to restore the genetic diversity of industrial breeds; and finally, by protecting the wild relatives that might provide useful genetic resources."

(Andrew Marr says that whenever you see a newspaper headline ending in a question mark (Is this the most evil man in Britain?; Are working mothers poisoning their children? and so on) you should answer 'no'. I'm not sure if the same applies for the scientific literature.)

Barley yellow dwarf viruses (BYDVs) preserved in herbarium specimens illuminate historical disease ecology of invasive and native grasses
Invasive species are often thought to thrive because they escape all the diseases and predators that keep them in check back home. But this study suggests that the diseases that invaders bring with them are just as important as the ones they leave behind.

In California, over the past two centuries European grasses have almost completely displaced the native prairie. Carolyn Malmstrom and her colleagues think that one factor in their success was the viruses they brought with them. For example, they have previously shown that native grasses growing alongside exotics have higher levels of cereal yellow dwarf viruses.

But this doesn't put the viruses at the scene of the crime. Now they've taken a step towards that (although how you ever prove such an idea, I don't know). Using herbarium specimens from 1917, they have recovered some of the oldest plant viral sequences so far and, by comparing them with European relatives, show that the disease probably showed up along with the plants — and also hopped from California to Australia in the late nineteenth century — and may have been a useful ally in the invaders battle against the natives.

Galaxy 2 Galaxy

One of museum directors' great worries is how to get more good-looking people to visit their collections. They employ world-class architects to create buildings filled with beautiful and enlightening objects, and then the spotty, balding, punters in their unsightly leisure wear come along and spoil it all.

Of course, I would never dream of visiting a museum without stopping off at Trumper's, taking a freshly pressed tweed suit out of the wardrobe, and selecting an appropriate cravat and handkerchief, but not everyone is so public spirited. But I think the American Museum of Natural History could have solved the problem.

In a neat piece of mountain/Mohammed reasoning, the museum has figured out that, although nightclub patrons might not be all that into science, they are, on average, relatively easy on the eye. So the museum has started booking DJs. Not some no-hoper playing 'Superstition' at an unobtrusive volume to be ignored by drink-sipping-late-night-opening types. No, proper DJs what beat-match, and twiddle the knobs on the mixer, and whose names you might have heard of, and who play their records at conversation-negating volume, and everything.

Last Friday they had Josh Wink and Axsel 'Superpitcher' Schaufler (whose haircut, wardrobe and moves come straight from a English synthpop band circa 1981, not that there's anything wrong with that), playing several hours of techy beats in the Rose Center for Earth and Space. And the trendy twentysomethings came in their droves.

(One thing, though: why did the VJs deploy the usual bog-standard psychedelia? When you're surrounded by the most amazing sights in the Universe, you need to up your game a bit. Next time, get off to the NASA site and download some nebulae shots.)

This is more appropriate than it might at first appear; techno and space go back a ways. Several of the early Detroit acts had a futuristic, sci-fi aesthetic. Specifically Drexciya, and Underground Resistance, whose 1992 album "X-102 Discovers the Rings of Saturn" has tracks called Titan, Enceladus, and so on. (I believe that on the original vinyl, the tracks are each in their own groove, so that they don't play continuously, but you have to lift the needle and move from track to track. This is cool, but I couldn't tell you why.)

This worldview seems a little bit quaint now; at the club night, it struck me how there's nothing more retro than the future. Today's dance-music subgenres tend to emphasize the dirty, grimy and nasty (hell, one of them's even called grime). Which seems more fitting to today's world. Whereas dancing to techno under the giant white sphere of the Hayden Planetarium feels more like a party out of Barbarella.

Why Al Gore deserved the Nobel peace prize

When AG won the NPP last week I was pleased, but I suspected that the academy had given it to him mainly because his campaign was A Good Thing rather than because of any direct link with world peace.

But this piece in Slate makes the good point that addressing climate change might be a matter of stopping wars before they start, rather than cleaning them up once they get going. And that really does deserve a peace prize.

The pygmy possum: a tribute

What's better, sleeping or being awake? Exactly. As Jeremy Hardy once said, "Saying 'I'll sleep when I'm dead' is like saying 'I'll bathe when I'm drowning'."

So, as a devotee of shut-eye, El Gentraso salutes the marsupial pygmy-possum Cercartetus nanus, "an opportunistic nonseasonal hibernator with a capacity for substantial fattening" (hey, before you get all judgemental, maybe it had just been through a difficult break-up, and was comforting eating, yeah?) according to Fritz Geiser of the confusingly named University of New England, in Australia.

Geiser's newly published study found that possums hibernate for an average of 310 days, with the champion snoozer clocking up 367 days. That, according to my calculations, is more than a year. I have only seen the paper's abstract, so I don't know how or why he discovered this. Do they just naturally kip this long, or did he regulate environmental conditions to induce maximum snooziness?

Either way, it's a heroic effort, both on the part of the possums, and of Geiser, for giving up a year to watch them sleep. I imagine his lab notes read: "Day 238. Possums still hibernating. Day 239..." and so on.

Talking about D'Arcy

Earlier this year, I gave a talk about D'Arcy Thompson as part of a Royal Institution lecture series on polymaths.

I notice belatedly that the Royal College of Surgeons (where the talk took place, cos the RI is being lotterified) has put audio of the talk online.

I think that link should take you straight to the sounds. If not, go here, where you can also hear Andrew Robinson talking about Thomas Young and him, me and Oliver Morton talking about poymathy in general, and whither it. Plus lots of other stuff.

Perhaps the least original thought I've ever had

With each passing press release, it's looking more and more like Craig Venter has missed his true calling as a Bond villain.

The Guardian can reveal that a team of 20 top scientists assembled by Mr Venter, led by the Nobel laureate Hamilton Smith, has already constructed a synthetic chromosome, a feat of virtuoso bio-engineering never previously achieved.

Any fule kno that 'assembled' is journalistic shorthand for 'kidnapped and forced to work in a hollow volcano'. Still, Hamilton Smith sounds like the sort of chap who ought to be able to fashion a glider out of latex gloves and pipette tips and escape to alert Her Majesty's Secret Service.

Scientific meetings - a lot of hot air

Earlier this year, I heard evolutionary biologist Hervé Philippe speak at the Royal Society's Linnaeus 300 meeting. Before he mentioned anything phylogenomic, however, he spoke about the carbon footprint of his research.

With labs, computers and travel to meetings this added up to a whopping 40+ tons. Philippe's suggestion to help get this down was to make all annual scientific meeting biennial, thus halving the massive emmissions of flying scientists.

It struck me as an excellent idea (and one that he should publicize - I can see no obvious mention of it anywhere online). As well as cutting down emissions, it would send a powerful signal if the scientific community en masse could institute such a change. And it came back to me when I read the piece Greening the meeting in today's Science.

Regarding the discplines that El Gentraso is mostly interested in, it's good to see that many attendees at the Society for Conservation Biology and Ecological Society of America meetings offset their flights - although given the uncertainty about offsetting, you might be better off giving the money to a group that campaigns against climate change.

But it was disappointing to see that the SCB couldn't agree to cut down on the frequency of meetings: "some members considered the meeting's exchange of ideas too important to forgo".

Get over yourselves. I know that e-mail, message boards, the phone, video-conferencing, Second Life and so on aren't as immediate, or necessarily as productive as face-to-face, but isn't that a price that a bunch of conservation biologists, for crying out loud, ought to be willing to pay once every other year? It seems like a major failure of imagination (or maybe junket lust). If people really threw themselves into finding alternatives, they'd find better ways to use the technology and to structure meetings to get the most out of it.

The ESA, meanwhile has "slimmed down the program book, began using soy-based inks, and now distributes its advertiser kit only electronically. The society also arranges with hotels to change linen less frequently and has removed Styrofoam from the meeting entirely. Some of the changes make more of a difference than others, but "every little bit helps," says Michelle Horton, a meeting organizer at ESA."

The words 'burns' and 'fiddling' spring to mind.

Woo hoo!

In news of marginal interest: I submitted my PhD thesis just over ten years ago. But thanks to the diligence of others, data from it continue to leak out.

Most recently, BMC Evolutionary Biologist has just accepted Ecological correlates of sociality in Pemphigus aphids, with a partial phylogeny of the genus. I did the phylogeny ('partial' being the operative word). Thanks to Nathan for getting these data into the public realm.

At my count, that makes three peer-reviewed publications with my name on. For any completists out there, the other two are:

Behavior and morphology of monomorphic soldiers from the aphid genus Pseudoregma (Cerataphidini, Hormaphididae): implications for the evolution of morphological castes in social aphids Insectes Sociaux 44, 379-392 (1997).

Clonal mixing in the soldier-producing aphid Pemphigus spyrothecae (Hemiptera: Aphididae) Molecular Ecology 11, 1525–1531 (2002).

Snappy titles, I think you'll agree.