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.

Fruit-cutting ants

A nice piece of natural history from the latest Ecological Entomology.

The workers of leaf-cutting ants (Atta) fall into two categories — minors, which do the forgaing, and majors, which are more involved in colony defence. But Sophie Evison and Francis Ratnieks at Sheffield have spotted that Brazilian leaf-cutters will also chop fruit (in this case mango) into bits and cart it back to the nest.

But the fruit-cutting is done by the majors - presumably because their jaws are big enough to handle three-diimensional stuff like mango, whereas small jaws are only good for leaves. So we can add a new job to the majors' task list.

The question that occurred to me was - what happens to this fruit in the nest? Leaf-cutters can't digest leaves, so they feed it to fungus in the nest, then eat the fungus. But most of us can digest mango, so does fruit bypass the fungus farm and get eaten raw?

I frass, you frass, he frasses, they frass

A couple of weeks ago, Sara and I were talking, as you do, about the word 'frass', which is the technical term for insect poo.

She said it sounded more like a verb than a noun. It hadn't occurred to me that different types of word sounded different, and I wondered whether they did.

Well, they do. I was chatting with some researchers on Friday, and they mentioned work by Morten Christiansen at Cornell and his colleagues on just this topic. Last year, they published a paper showing that nouns and verbs do cluster together in phonological space.

But the categories aren't rigid. There are 'nouny nouns', which are found in the middle of noun space, but also 'verby nouns' which are closer to verbs. Likewise, there are verby verbs and nouny verbs.

The team did experiments showing that people process nouny nouns more quickly than verby nouns. For example, they are quicker to grasp the meaning of:

The curious young boy saved the marble that he found on the playground.

than

The curious young boy saved the insect that he found in his backyard.

because 'marble' is a nouny noun, whereas 'insect' is more verby.
The same difference was shown between sentences containing verby verbs, such as 'amuse' and nouny verbs, such as 'ignore'.

Last year's paper cites earlier studies showing that 'adults are more likely to use a nonsense word as a noun when it is multisyllabic'. So I would guess that 'frass' would fall amid the verby nouns.

Christiansen et al argue that these cateogries exist in other languages besides english, and suggest that learning these categories is one of the steps in acquiring language.

From idle speculation to scientific resolution - just how I like it.

Batty like a FoxP2

Back in 2001, FoxP2 was the first gene to be linked to human language. The gene was hunted down by studying a British family with extreme difficulties in forming speech. I wrote about (paywall) this work at the time.

Since then, there's been a bunch of studies on the gene - revealing, for example, relatively large differences between the human sequences and that of other primates. But it was thought that, humans aside, there was relatively little variation in vertebrates.

Well, just goes to show how taxonomically restricted our genetic knowledge is, because a Sino-Anglo team has just discovered that the gene varies lots in bats, which don't talk, but do echolocate. There's a news report about their PLoS One paper here.

To see how the variation between closely related bat species really does dwarf that seen between much more distantly related beasts, check out this figure.

Nice. But FoxP2 is not giving up all its secrets just yet. The pattern of evolution - what's been selected for what - is not clear from the sequences, there's just a lot of difference. And comparing bat sequences with other species doesn't help much

Evidence from birds, which likes bats and people show vocal learning, is shows 'no evidence of specific mutations associated with vocal learning abilities...if variation in FoxP2 has a role in vocal learning then it is not straightforward'. Nor are there clear similarities with whales, which also vocal learn and echolocate.

So what is FoxP2 uP2? If it's a 'language gene' it looks as if it's role isn't in what we think of as the clever stuff of language - grammar and syntax - but in the mechanics: the motor control needed to produce tightly controlled sounds, say. But, as far as I can tell, there's no hard and fast links between the gene sequence and this ability. It's just involved somewhere down the line.

One clue is that FoxP2 is a transcription factor - it's product controls the activity of other genes. Maybe this is why comparing species gives few clues as to how its sequence relates to its function: because it's an information processing gene and not making something like haemoglobin, the structure of which is jolly important, maybe its free to vary more, and to mean different things to different animals.

I don't know how much we know about the genes it regulates - I couldn't see anything in the paper, so I'm guessing not much.

Underground networking

Todays's Nature contains a News Feature by me (behind a paywall, I'm afraid), looking at the possibility that mycorrhizal fungi transfer nutrients between plants, and in the process undercut the above-ground competition between plants by robbing the rich to feed the poor - subsidizing plants less able to photosynthesize.

How, why and whether they do this is still uncertain and occasionally controversial. But everyone seems to accept that mycorrhizal networks do exist - namely, that a single fungus can link many plants, potentially of different species, creating a arena for a rich range of ecological interactions. It's just we're not sure what they are. But a bunch of people are doing their damnedest to find out. Mycorrhizal ecology looks like a funky (and fungi) field right now.

For a more technical (than my piece), but freely accessible introduction to this field check out this TREE paper.

Why you will never get everyone to agree with you

Here’s what the recent Nature Neuroscience paper ‘Neurocognitive correlates of liberalism and conservatism’ (See here for one of the many news reports) made me think.

This looks like the (one of the) neural manifestation of a personality axis, such as bold/timid, extrovert/introvert. People and animals spread out all over these — reflected in animals in how quick they are to explore new environments, how far they disperse, and so on. You could probably redefine liberalism/conservatism in terms of these (people probably already have).

So the big question, I think, is: what maintains this diversity in a population? It could be frequency-dependent selection — it becomes more advantageous to be liberal if you’re surrounded by conservatives, and vice versa. Seems unlikely.

More plausible is that it’s balancing selection: there are some environments and tasks that favour a liberal approach, and some that favour conservatism. In great tits, for example, bold, far-dispersing males do better after mild winters, when territories are at a premium, and food is plentiful, whereas stay-at-homes do better after harsh winters. For females, the reverse is true.

So no one strategy can take over. And personality in these birds has a strong heritable component. So, in a variable environment, where genes don't know which sex of bird they're going to be on (unless they're on the females-only W chromosome in birds, or the male-only Y in mammals), a braod range of personality types can persist.

It seems plausible that something roughly similar might be at work in people — the benefits of reaching out, trying new stuff, versus the benefits of staying put and consolidating will depend on the environment. Question here is, why can’t each of us (or each great tit, for that matter) work that out, and adapt to any environment? What is it about our brains, and the genes (and environments) that make them constrains us to occupy our place on the personality axis?

It seems, anyway, that if our politics come from inside us, as well as being a consequence of what the world does to us, we can’t expect political extinction for either liberals or conservatives, just as there are bold and timid great tits.

Of course, when it comes to voting, there’s lots of other stuff at work. It struck me that this is a US study, where, because the different parties don’t offer anything different in the way of economics, peoples’ voting decisions may be more swayed by all that ‘values’ stuff that tickles these particular ‘am I up for this?’ bits of the brain. Also I’m guessing that those studied were students, and occupied a narrow socioeconomic band. It’s perfectly possible to be a left-wing conservative, but more likely if you’re working class, I’d guess.

South Bank Wayang

In non-science-related news, there's a piece by me in today's Guardian about the all-night Javanese shadow puppet play (wayang), including the South Bank Gamelan Players, at the festival hall tomorrow. I doubt it's sold out.

In other news, the Independent newspaper recently put ITBOAH on its list of 10 best nature books. Which is nice. No sign of this online, but Oliver Morton has reproduced the list (which includes his own Eating the Sun) on his photosynthesis-related blog.

Fibonacci watch

One of my partner Sara's bugbears is that all efforts to group art and maths together lazily invoke the Fibonacci sequence (Something, I admit, I've been guilty of myself.)

But my crimes pale next to this absolute humdinger, from the August issue of The Wire. This is Philip Sherburne writing about techno musician and DJ Ricardo Villalobos.

When it comes to rhythm, Villalobos is certainly one of the canniest producers in contemporary electronic dance music. His youthful training in Afro-Latin percussion explains some of his sense of timekeeping, but it doesn't necessarily address the uncanny quality of so many of his beats, which take shape with the same kind of natural/unnatural ease with which a sunflower sprouts seeds according to the Fibonacci sequence.

Let's enjoy that again.

the same kind of natural/unnatural ease with which a sunflower sprouts seeds according to the Fibonacci sequence.

Eh?

Other egregious Fibonaccisms welcome.