Friday, December 14, 2007

Glengarry Glen Research

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

Thursday, November 29, 2007

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).

Monday, November 12, 2007

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.

Friday, November 09, 2007

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.

Thursday, November 08, 2007

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.

Monday, November 05, 2007

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'?

Friday, October 26, 2007

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.

Wednesday, October 24, 2007

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.

Tuesday, October 16, 2007

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.

Monday, October 15, 2007

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.

Wednesday, October 10, 2007

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.

Monday, October 08, 2007

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.

Friday, October 05, 2007

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.

Wednesday, October 03, 2007

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.

Friday, September 28, 2007

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?

Monday, September 24, 2007

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.

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.

Thursday, September 20, 2007

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.

Thursday, September 13, 2007

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.

Wednesday, September 12, 2007

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.

Friday, September 07, 2007

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.

Tuesday, September 04, 2007

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.


Other egregious Fibonaccisms welcome.

Thursday, August 16, 2007

Autumn colours and aphids

In a previous life, before I became a successful, respected and well-balanced science writer, I did a PhD on the evolution of soldier castes in aphids. Happy days (not).

In this life — in 1996, to be exact — I travelled to an entomology conference in Florence. There, at a session on aphid biology, a fellow grad student and more talented researcher than myself called Sam Brown gave a presentation, coauthored with his supervisor Bill Hamilton, on the idea that the autumn colours of trees were a signal to marauding aphids of the strength of their antiherbivore defences.

Bright colours, their argument went, were an honest signal: only well-resourced trees able to make lots of the secondary compounds that plants use to make themselves unpalatable to herbivores would be able to make them. And aphids flying around in the autumn, looking for somewhere to lay their overwintering eggs, would shy away from such vivid displays.

The debate on the worth of this neat hypothesis has rumbled along for more than a decade now. Sceptics have pointed out that yellow pigments were there all along, but are only revealed when the leaf takes back it’s chlorophyll — leaves don’t turn yellow, they unturn green. Also that red pigments have other potential uses, centred on protecting the leaf as the plant takes it apart, chemically speaking. The latest update comes from Lars Chittka and Thomas Döring, two researchers on sensory ecology writing in PloS Biology.

To put it crudely, C and D’s piece plugs a forthcoming paper (this link wasn’t working when I checked) by them looking at colour vision in aphids. They find that Brown and Hamilton might have been deceived by their human’s-eye view. Aphids (and all other herbivorous insects looked at so far) don’t have good vision in the red — so red leaves wouldn’t look anything special to them. And yellow is powerfully attractive — it tickles their green receptors even more so than green itself, and brings insects flocking: ‘If trees wanted to deter herbivorous insects using color, yellow leaf coloration is about the worst strategy they could pick,’ they write.

The piece does such a good job of pouring cold water on the notion that autumn colours are signals that their final (inevitable) conclusion — the good old cry of ‘more research is needed’ rings a little hollow. Speaking as a rampaging adaptationist, who thinks that Hamilton has a good claim to having been the most important evolutionarybiologist since Darwin, I think that’s a bit of a shame, but there you go, beautiful theories, ugly facts and all that.

The essay also has some nice bits of history, and a lovely first sentence: ‘Most living things don't turn beautiful when they senesce’. But some editor should have stopped the use of ‘fascinating’ twice in the first paragraph. I can work out whether something is fascinating or not. (And while we’re about it, can we have a ten-year moratorium on the use of ‘intriguing’ in science journalism? It’s just ‘interesting’ wearing a false moustache.)

Monday, July 16, 2007

Spontaneous order, fungal networks, and circuses

You wait ages to feel moved to post, and then three things come along at once. In no particular order…

Biological modularity can emerge as a spontaneous, self-organized process, say Ricard Solé and Sergi Valverde in J. R. Soc. Interface. By modularity they mean particular sets of interactions in the great web of biochemistry (rather than, say, organs):

Modularity is particularly obvious in cellular networks, where it can be detected at the topological level. These networks include the webs of interactions among proteins, genes, enzymes and metabolites or signalling molecules.

Such a trend seems to call for an adaptive explanation. In particular, what seems to demand explanation are ‘motifs’ in these networks

patterns of interconnections occurring in complex networks at numbers that are significantly higher than those in randomized networks.

Solé and Valverde cite a couple of adaptive explanations “based on a genetic programming approach”. But they don’t agree with them.

Instead, they say such modularity is the inevitable consequence of evolution by gene (or genome) duplication (“the driving force behind the evolution of complex organisms”, they say) followed by divergence, as evolution tinkers with the newly enlarged network of interactions (letting natural selection back in, it looks like)

I’ve clearly, as is my wont, become aware of this debate somewhere in the middle — the paper cites several is-modularity-evolution-or-is-it-self-organization? papers from the past few years. But, as far as I can tell, Solé and Valverde are saying that this is the first explanation for such modularity based on “fundamental, dynamical rules”.

In other network news, Proc R Soc B has just published a paper by Daniel Bebber et al. looking at fungal networks.

they have evolved to explore and exploit a patchy environment rather than ramify through a three-dimensional organism. Unlike all the other biological transport systems studied, the fungal network is not part of the organism, it is the organism.

The challenges such a fungal mycelium faces are to explore its environment, exploit resources, transport them around the rest of the organism, and to be sufficiently robust to resist physical damage and the many fungus-eaters in the soil.

To investigate how fungi meet such challenges, they grew Phanerochaete velutina in the lab, growing it out from an inoculated lump of wood towards other lumps of wood. They found that the fungus began in exploratory mode, sending out lots of narrow filaments. But as it completed searching its environment it consolidated its resources into fewer, bigger bundles of hyphae, growing between maor resource patches, with more exploratory filaments in new territory, and crosslinks to provide some redundancy in the case of network damage. “Netowrk development”, say Bebber et al.
involves over-production of links and nodes in the exploratory phase, followed by selection and positive reinforcement of some links and recycling of the remainder during the consolidation phase … A
similar sequence of events is apparent in the development of other biological transport networks including those formed by acellular slime moulds [and] foraging ant trails … and may well represent a universal feature of self-organized biological networks. However, in each of these systems, the final network structure is likely to represent a context-specific balance between the need for efficient transpor t, cost and robustness.

In other words, they’re stressing the diversity of different structures produced by flexibility and responsiveness to environmental variation, as much as whatever general laws such networks might have.

Philip Loring (who I believe blogs here) approaches questions of resilience, connectedness and persistence from a different angle in Ecology and Society. He proposes the circus as an icon of resilience, in that it has retained its identity while changing its contents — i.e. getting rid of freak shows and (mostly) animal acts.
Through the many forms they have taken over the last 150 yr, circuses have changed significantly while sustaining a singular identity. As a successful and enduring social system, their intriguing history exposes the nuances of sustainability theory, from resilience to pathologies, and illustrates that sustainability requires a complex dynamic between identity, tradition, and change.

The article, to my mind, contains a bit too much on the history of the circus, without exploring the implications of the circus-as-sustainability metaphor. Also, while ‘circus’ has survived for 200 years, most individual circuses haven’t. This is fine for institutions and systems, but not so much for species and ecosystems. But it’s a nice comparison.

Thursday, May 17, 2007

Survival of the likeliest?

There's a feature by me in the current PLoS Biology (and it's free!) on whether natural selection can be explained by the laws of physics, specifically thermodynamics and statistical mechanics. This looks at work of Roderick Dewar on Maximum Entropy Production (MEP), Adrian Bejan's constructal theory, work by Eric Smith at Santa Fe on self-organization and metabolism, and a few other things. The basic idea is that, by looking at the flows of energy and matter, we can predict and quantify the path and results of evolution.

This is something I've been thinking about for a couple of years — I put a bit about it in the first draft of ITBOAH, but took it out, 'cos it wasn't really working. And I wrote a piece for Nature looking at MEP from a more climate- and ecological viewpoint, which didn't go so much into the evolutionary implications. So I'm very glad that this is finally seeing the light of day.

What I did on my holiday

I've just got back from three weeks on holiday in Andalucia. Two things I learnt:

Trenhotel good. If you don't dilly-dally, you can eat lunch in London one day, and in Seville the next, without leaving the ground. The overnight journey, from Paris to Madrid, is comfy and fun (cf flying) – there's a bar and restaurant on the train. The mighty has all the details.

Plasticultura bad. When I saw vegetables in my local supermarket from Spain, I had, I suppose, a dim image of a happy campesino weidling a mattock and whistling a song. In fact, it seems that they are grown in one of a never-ending series of plastic greenhouses that, in eastern Andalucia (around Almeria) fills just about every bit of land between the sea and the mountains.

There's a danger in knee-jerk disapproval of the unsightly — I'm sure there are outdoor forms of farming that have just as much environmental impact, but, because they fit our idea of what farmland should look like, don't make you as depressed as a sea of plastic. And there are arguments that, where we farm, we should do it as intensively as possible, so that is uses the minimum of land and leaves more for nature (whatever one means by that). (Although in a country like the UK, where farmland and countryside are the same thing, this would be tricky.) Plasticultura, or invernaderos, however, do seem to take out more water, and put back more nitrates, than the land can support. Plus they are hellish places to work (although not so hellish that no one wants to work there).

To find out more, try this article from the Ecologist for more on water, the environment and farming in southern Spain, this from John Vidal on the Spanish drought, this lecture by Felicity Lawrence for intensive farming in general, and here (recommended) for photos of plasticultura farming.

I shan't be buying Spainsh veg any more, thus making my winter diet even more cabbage-based than previously.

Oekologie #5

Jeremy Bruno over at the Voltage Gate has done an erudite job on this month's Oekologie blog carnival (my own hosting effort is here).

Wednesday, April 11, 2007

Guardian podcast

I'm on this week's Guardian science podcast, talking about D'Arcy Thompson, polymathy (is that a word?) and ITBOAH with Alok Jha and the other young rowdies.

Father and son

Among the many, many stories I've recently written for recently is one about changing dates of the UK mushroom season. There's been a huge effect in response to warming — the autumn season is twice as long, and some mushrooms are popping up in spring, as well as autumn.

This is a lovely example of you-never-know-when-it'll-come-in-handy data collection. The data — ranging from 1950-2005 — were collected by Edward Gange, stonemason by day and fungal recorder for the Wiltshire Natural History Society in his spare time. The lead author on the paper is his son, ecologist Alan Gange. Isn't that nice?

Another good thing about this piece is that it gave me a gave me a chance to interview Andy Overall, one of whose fungus forays I attended last year.

Back in the dim'n'distant, I had a lot of fun writing a longer piece for Nature about ecologists using data collected by amateurs to measure the effects of climate change on living things. If you ask me, this is probably the most important ever non-specialist contribution to science. Always glad to hear of any other candidates, though.

Tuesday, April 03, 2007

The coming era of jellyfish ascendancy

I admit it, my devotion to the work of George Monbiot (or The Monb, as he's apparently known in some environmental circles) borders on the unhealthy.

But this piece on marine conservation, and the overfishing of top predators such as sharks, is really excellent.

The Spanish fishing industry, he writes, is "traditionally dominated by Galician fascists". There's no fascist like a Galician fascist.

Thursday, March 29, 2007

Some stories what I wrote, and one that I didn't

I'm working for news@nature for a few weeks, so I haven't had a chance to write much stuff for El Gentraso.

What I have written is a story about what the direction a dog's tail wag means, one about 'semi-identical' twins', both of which were subsequently picked up (i.e. copied) elsewhere.

I found them, not by any particular piece of investigative brilliance, but by looking at journal tables of contents. As a science journalist, if you look beyond the press releases on sites like Eurekalert and Alphagalileo, you'll often find that you've got no company.

The twins story, in particular excited a rush of comments to Nature's newsblog, mainly from people who thought they were, or had had, semi-identical twins. But probably aren't/haven't.

Not that incentives for good practice should be necessary, but writing for online is a useful reminder of what people might make of your stories - it's always sobering to see the expressions of hope that come in after any story on a potential cure for a disease or disability, however caveat-laden the story.

More recently, I've written about cane toad distribution and mammal evolution.

So doing all that has prevented me from blogging about John Lanchester's masterly essay on climate change in the LRB. This has one of the best intros I've seen in a long time:

It is strange and striking that climate change activists have not committed any acts of terrorism. After all, terrorism is for the individual by far the modern world’s most effective form of political action, and climate change is an issue about which people feel just as strongly as about, say, animal rights. This is especially noticeable when you bear in mind the ease of things like blowing up petrol stations, or vandalising SUVs. In cities, SUVs are loathed by everyone except the people who drive them; and in a city the size of London, a few dozen people could in a short space of time make the ownership of these cars effectively impossible, just by running keys down the side of them, at a cost to the owner of several thousand pounds a time. Say fifty people vandalising four cars each every night for a month: six thousand trashed SUVs in a month and the Chelsea tractors would soon be disappearing from our streets. So why don’t these things happen? Is it because the people who feel strongly about climate change are simply too nice, too educated, to do anything of the sort? (But terrorists are often highly educated.) Or is it that even the people who feel most strongly about climate change on some level can’t quite bring themselves to believe in it?

It makes you think (and tempts you to act). My guess is that most people don't like doing violence, to property or people, and that we shy away from escalating a confrontation, usually for good reason. Maybe that's another word for cowardice, or apathy, though.

I don't bandy the words 'essential reading' about much, but I'd say that this is. The one thing I might take issue with is Lanchester's approving words on James Lovelock's advocacy of nuclear power.

I don't have an issue with nuclear power per se, and I think it should probably be in our energy portfolio. But George Monbiot's 'Heat' argues that, in practical terms, building a new generation of power stations would take so long that it's not a quick fix - we might as well go all out for renewables and carbon sequestration - and that energy efficiency gives the best return in carbon-saved-per-pound-spent.

One's always tempted to find rational arguments to support things you emotionally favour, but Monbiot makes an effort to do his sums - and also shows that no one really knows what's what when it comes to how we're going to get our energy.

Wednesday, March 21, 2007

One of the best things about being a science writer...

Is sitting down on a Monday, and turning out a story about something that, that morning, you knew less than nothing about - the 248-dimensional exceptional Lie group E8. And then coming in on Tuesday and writing a story about a burrowing dinosaur. Who knew?

Thursday, March 15, 2007

Oekologie #3

Here beginneth the third edition of the Oekologie blog carnival. Thank you everyone who took the time to send in posts. It was great to receive such a diverse bunch — we've got just about every group of organism and every part of the world represented, at scales ranging from the global to the backyard, and addressing just about every issue you can think of. So here we go…

Crime! Julie from The Human Flower Project has sent in a cool story on the banning of the Hungarian hovirag harvest. The hovirag is a snowdrop, sold in Hungary as a mark of coming spring, but now grievously over-picked (and with a street value somewhat greater than crack, apparently). The flower is also the source of the protein that, put into to GM potatoes, led to the controversy around the experiments by (Hungarian-born) Arpad Puzstai.

Deceit! GrrlScientist at Living the Scientific Life posts on a neat piece of mimicry — the moth that pretends to be a jumping spider.

Pestilence! Jennifer Forman Orth at the Invasive Species Weblog reports on beech bark disease, which involves an invasive insect infesting the tree, which leads to a fungal infection, which leads to trouble.

Meanwhile, showing that not you don't need to cross an international borders to be an invasive species, Paul Decelles at The Force that Through… points the finger at red cedar, a native of the eastern US now making trouble further west. And then defends his position.

Goats! Aydin at Snail's Tales discusses the impact of goats on the past and future vegetation of the Mediterranean. "If we want to return at least some of the land to its original, pre-grazing, pre-human state, the goats must go," he says.

The Mediterranean is interesting because it has diverse plant life, even though it has seen millennia of heavy human impact, suggesting that the plants have coevolved with people and their animals. (This has also equipped Mediterranean plants to do well in places like California and Australia.) But, of course, whether this flora was in place before people showed up — and if not, what was — is another matter.

That's enough exclamation marks.

Fish: Stephen Leahy at, um, Stephen Leahy points us to his story discussing the concept of peak fish — global catches have levelled off (not sure what's happened to global fishing effort, but it seems unlikely to have fallen), and may soon start falling.

Another option for providing seafood is fish farming. The US government has proposed to extend fish farming into federal waters, 3 to 200 miles offshore. But Lish at Science Ripsaw is worried it that this would deplete nutrients and increase pollution.

Oil: Tom Elko at Sky Blue Waters reports on the concerns around the environmental impact and property rights issues of the MinnCan pipeline. If built (which is looking likely) it would carry crude oil from Canadian oil sands (which are environmental and carbon-emissions bad news in themselves) to refineries in Minnesota.

Milk(weed): Miconia at A Neotropical Savanna meditates on Asclepia.

I know it's not a very scientific reaction, but…

Eeuuw: GrrlScientist reports on a blind, cave-dwelling Madagascan snake (that looks like a worm), rediscovered more than 100 years after the last known specimens were collected. They avoid the light, and sniff out their prey — the eggs and larvae of ants and termites.

Eeuuw II: The pygmy-hog-sucking louse (as a part-time copyeditor and punctuation geek, I place those hyphens with some confidence). Sticking up for the bloodsuckers at Endangered Ugly Things, Garfman makes the excellent point that every large, cuddly and charismatic species in danger of extinction also has (probably several) parasites that depend on it for their own survival. Coendangered is the technical term, apparently.

Mangroves: On the Ecological Society of America's blog, Edward Barbier has posted an authoritative guide to the issues surrounding the loss and restoration of mangrove forests, particularly regarding their ability to buffer against storm and tsunami damage.

Barbier — who has done lots of research into the interactions between development, mangroves and ecosystem services (the mangroves usually come off worse) — argues that the debate around the benefits and costs of replanting, that have followed from the 2004 Indian Ocean tsunami, is oversimplified.

Cheetahs: Over at Laelaps, Brian Switek highlights something that was new to me — Iranian cheetahs. Brian writes about the Wildlife Conservation Society's work to conserve this population.

(This also made me intrigued about another thing I know nothing about — what issues a US conservation organizations faces when it works in Iran — in terms of dealing with both the Iranian and US governments.)

Bats: Jennifer Pinkley at The Infinite Sphere discusses how the eastern pipistrelle's more catholic taste in habitat and roosts has made it "more adaptable to changing environmental pressures" than its close relative the gray myotis.

Microbes: Coturnix at A Blog Around the Clock alerts us to PLoS Biology's glut of papers on ocean microbial diversity (i.e. metagenomics). This is way-cool stuff right now (see also previous post on this blog).

Semantics: Matt at the Behavioral Ecology blog has sent in a post entitled 'Is rape adaptive?', which also discusses whether 'rape' is a good word to apply to forced copulations in (non-human) animals. The consensus appears to be not and, although I usually favour strong words and try to avoid jargon, I agree.

Celebrity: Mike at 10,000 birds muses on the ethics of twitching, and the motivations of twitchers. Naturalists, paparazzi, rubberneckers, or all of the above?

Memories: for me at least, with Jeremy Bruno, and the Voltage Gate's guide to tropical dry forest.

Jeremy mentions Guanacaste in Costa Rica, conservation success story (thanks to the idea of introducing large domestic herbivores to do the seed-dispersal job once done my extinct species), macroecological hotspot, and a place I visited while researching ITBOAH (I had to get a mention in somewhere). One of the remarkable things about Costa Rica is that this forest is about half-an-hour's drive from cloud forest containing a totally different set of species.

Global: John Feeny at Growth is Madness! muses on whether spreading the news that we're in the middle of the earth's sixth mass extinction since the Cambrian will help turn people on to conservation.

And Vbecer00 at Reconciliation Ecology also touches on the issue of how you get people to care in his/her post on, well, just about every issue in conservation — why do it, how to do it, and how to make it work.

Local: Join Dave Bonta at Via Negativa for a walk in the snow in Plummer's Hollow, and benefit from his sharp eyes. The man knows his neighbourhood, and his shrews.

Or, you could visit Wayne at Niches, and read his reports on the effects of heavy rains on the creeks on his property in Athens, Georgia.

And finally….

Personals: Johan Stenberg is in Sweden, feeling lonely. Cheer Johan up and join his journal club on insect-plant ecology, at (where else but the) Insect-Plant Ecology blog.

So there you have it. Oekologie — opening your minds, grossing you out, winding you up, bringing you together. Thanks again, and be sure to check out the next edition in a month's time on the Behavioral Ecology Blog.

We are family

This week's Nature is a special issue for Linnaeus' 300th birthday, and I've got a feature($) in it looking at what genomics has done for the Linnaean project, in terms of working out the tree of life (and what evolutionary biology can do for genomics). The field is called phylogenomics. One of the surprising things I found when researching this was how uncertain things still are - we have no idea how many of the animal phyla relate to one another, for example.

I'm also talking with Henry Nicholls and Kerri Smith about this on the Nature podcast, recorded at the Natural History Museum in London. Henry has a feature about Linnaeus' raccoon, and has achieved full-spectrum science media dominance by also having a feature($) on metagenomics in today's New Scientist.

Jonathan Eisen's blog is a good place to find out about both phylo- and metagenomics.

Tuesday, March 13, 2007

A quick toot on my own trumpet

Library Journal has just named ITBOAH as one of the best science books of 2006. Picket your local college or public library now, demanding that they buy at least one copy.


The Scientist has a big ol' article, with a fine typo in the last paragraph, on West, Brown, Enquist and their metabolic theory. It's particularly good on recent historical and biographical detail, although a little sketchier on how the idea works, and what else it might apply to besides metabolism.

And I would take issue with the statement that temperature is a "variable necessary to explain the 3/4 scaling of metabolic rates across organisms". It's not, it's an additional variable that explains some of the variation in metabolic rates (between say, reptiles, birds, and mammals, all of which have different body temperatures) not accounted for by size-based 3/4-power scaling.

The article also shows how some of the disagreements about the theory come from differing expectations and goals. WBE are after a theory that gives an abstract, approximate, first-order account of the underlying structure of organisms and ecosystems.

Confronted with Helen Muller-Landau's data on forest population biology that contradicts their predictions they say, well, ok, it shows something else must be going on. Much as, if you see a planet that doesn't follow its predict orbit, you look for something else influencing it before you junk gravity (not that I am saying metabolic theory is as well-established as gravity). Muller-Landau and others, however, see deviation as disproof.

It's a difference partly of philosophy. But it also shows the genuine uncertainty about when you decide that just because a theory can't predict everything doesn't mean it's wrong (as Michael Ruse has written, natural selection's failures are a sign of its strength), and when you decide it's wrong.

WBE's metabolic model is too powerfully predictive, and its foundations make too good sense, to be junked yet. In fact, it seems to be popping up more and more - I have recently spoken to fisheries and foodweb researchers who are using it.

I would also say that people tend not to change their minds, regardless of what data or theory say. A scientific field's centre of gravity depends on when people retire and who gets their job, as much as it does on dialectic.

(The Scientist has published a couple of previous things on metabolic scaling and so on: here and here.)

Wednesday, February 28, 2007

A GUT of ecological scaling?

OK. I'm not going to pretend that I grasp the details of this, but here goes.

A recent paper in Physical Review Letters by Jayanth Banavar et al. presents a general theory of (macro)ecological scaling.

That is, they offer a common explanation for patterns such as that between the area of a place and the numbers of species that live there, area and total biomass, the number of organisms and species of different sizes, the maximum body size of the biggest species in an ecosystem (see here for another view of maximum carnivore size), and relative abundance — the spread of rare and common species.

All these scaling patterns seem to follow power laws, at least over partially. That is, they take the form y=ax^n, and plot as straight lines on a log/log graph.

Here's the abstract:
Scaling provides an elegant framework for understanding power-law behavior and deducing relationships between critical exponents. We demonstrate that scaling theory can be generalized to develop a framework for the analysis of diverse empirical macroecological relationships traditionally treated as independent. Our mathematical arguments predict links between the species-area relationship, the relative species abundance and community size spectra in excellent accord with empirical data.

As far as I can tell, Banavar et al. present a scaling hypothesis, based on a probability distribution of the mass and abundance of different species. Using this, and a set of reasonable assumptions (such as, that an ecosystem's total population and mass is proportional to its area) they derive the relationships described from a single starting point.

Blimey. If all these things can be brought under the one roof — this is the first such attempt that I know of — that's a big deal, I think. These are fundamental ecological parameters. Together, they pretty much sum up most of the questions that community ecology seeks to answer. Even the metabolic ecology models of West et al. (with which I am more familiar) have steered clear of tackling the relationships between species diversity and area, and between body size and diversity and abundance.

But, although much of the criticism of metabolic ecology focuses on its generality, Banavar and his colleagues have an interesting history of seeking yet more general models for the scaling of metabolic rate with body size. Banavar has also worked with Steve Hubbell to develop the neutral ecological theory. It's interesting that this is in PRL. I wonder what a biology journal would have made of it.

Thanks to Phil Ball for bringing this to my attention. I think. If anyone has any thoughts on this, I'd love to hear them.

Tuesday, February 27, 2007

Oekologie blog carnival

Just a reminder that this blog will be hosting next month's round of the Oekologie blog carnival. This follows the grand jobs done so for by Infinite Sphere and Perceiving Wholes.

So, for the period of Feb 15-March 14, please send me your favourite ecological and environmental blog posts by following this link. And I'll bring it to the world's attention, or at least that subsection of the world that reads this.

Thursday, February 15, 2007

Review: Measuring the world

I'm still recovering from the Just-Science exertions of last week, but I have got a review of Daniel Kehlmann's Measuring the World in this week's Nature ($).

They asked me to do this because I write a bit about one of the book's central characters, Alexander von Humboldt, in ITBOAH.

As a rule, I'm not really into historical fiction, or magic realism/postmodern whimsy. But I rather liked MTW (which has been a huge success in German). And I liked it more as it went along.

If you'll forgive me for quoting myself:
Kehlmann tells his story in a relentless deadpan, which is at first alienating but then gets under the skin. As the story develops, your sympathy for the two men grows, as their own does for each other. [He] does a good job of capturing the strangeness and comedy of science, as well as the powerful sense of futility that can afflict researchers from time to time.

Friday, February 09, 2007

Just Science day 5: Kill and cure?

The best way to protect an endangered species might be to ... cull it.

That's the conclusion reached by Michael Bode and Hugh Possingham in a theoretical analysis published recently in Ecological Modelling. The problem that they address is the tendency of some species to show boom-and-bust population dynamics. This seems a particular feature of tightly linked predator-prey systems: if predator is rare, prey booms, predator has lots of food, predator booms, prey crashes, predator starves, predator crashes, and so on. The Canadian lynx-hare system is the most famous example.

At the bottom of the cycles, population sizes might be so small that either predator or prey is highly vulnerable to extinction - by some other event, such as disease or disaster.

Bode and Possingham model various options for damping these cycles by removing some predators, prey, or both, from the system. "Remarkably," they say, "if the interventions are enacted at the appropriate time, infrequent culling of a small number of individuals significantly reduces the probability of extinction of the predator."

My first thought when I saw this, was that we probably rarely know enough about a species' population dynamics to know when the best time to cull is, and that such a move would be politically untenable. But, as Bode points out, the most likely candidates for such a move are large game-park species, such as elephants, about which we know quite a lot. It's also heartening that their (as they say, simplistic) simulation suggests that culling prey (which would be plants for elephants, I suppose) is more likely to be effective than predators, and that culling would be needed only rarely.

They conclude:

Most current methods of ecosystem control attempt to keep a single species population below a certain threshold, or between fixed bounds, leading to highly inefficient management. Furthermore, unnecessarily high levels of culling can generate considerable public opposition. Given the clumsy nature of such static controls, this view may be reasonable. Our dynamic control solution has the substantial benefit of minimising the preventable culling of organisms, and being extremely cost-effective.

I swapped e-mails with Bode, and besides mentioning that, in parks with very high elephant densities, such as Kruger, culling elephants seems 'almost unavoidable' (the issue seems to have flared up most recently in late 2005, judging by this BBC story), he also mentioned that similar issues were arising in Australia regarding koalas and kangaroos. As he says, why is it always the cure animals?

All I can say is I'm glad I don't have to make these decisions. Culling animals is clearly a terrible business - particularly for long-lived, highly social species such as elephants. But we now effectively control the destiny of all large, slow-breeding vertebrates. If the only places they can survive is in the parks we set up, and if we take a truly utilitarian and, dread word, holistic view of conservation, then we also have to take the responsibility of 'managing' their populations. Science isn't he only thing to guide us on such decisions, but it's best ot take as informed and clever a decision as possible, towards which Bode and Possingham's ideas can only help.

Thursday, February 08, 2007

Just Science day 4: Cursory

What's (even) more fun than blogging? Snow!

So, if you'll excuse me, I'm going to recommend that you check out this paper on potential pitfalls of digital photography in biology, and this article by the excellent Jenny Diski, providing a much-needed antidote to all the gush concerning Second Life.

And now I'm off to muck about on Hampstead Heath.

Wednesday, February 07, 2007

Just Science day 3: The H. pylori story

A new Nature paper by Mark Achtman and his colleagues reminds me that today, Helicobacter pylori (Hp) is definitely my favourite member of the human gut flora.

This bacterium is best known for causing ulcers and increasing the risk of stomach cancer. Barry Marshall and Robin Warren won a Nobel prize in 2005 for showing this (famously, few believed that bacteria could survive in the concentrated acid of the stomach, but Marshall chugged down a load of Hp, and got an ulcer.)

But the bacterium is much more than just a baddie. Once upon a time, it was probably in everybody's tummy (although no one is quite sure how its transmitted — vomit seems like the most likely culprit). It's still very common in developing countries and east Asia, but in Europe and North America it's steadily declined — only about 20% of US residents under 40 have it.

A good thing, you might think. But some scientists, such as Martin Blaser, have suggested that there might be a cost to this decline, as well as the benefit of reduced ulcers. Hp reduces the level of stomach acid, so without it there seems to be more heartburn, and possibly an increased risk of oesophageal cancer. There's also the general unknown consequences of having a part of the human ecosystem go extinct: "We have no good sense of the microbial ecology of humans," says infectious-disease specialist Julie Parsonnet of Stanford University in California. "H. pylori infection revs up the immune system - what happens to our ability to respond to other infectious agents when that isn't there?"

Another thing people have argued about is how the bug got into us in the first place:

Most mammals seem to have their own species of Helicobacter in their stomachs, leading some researchers to suggest that the relationship between microbe and host predates the evolution of modern humans. But others think that H. pylori's hook-up with humans, and subsequent spread around the world, was more recent.

That's the view taken by geneticist Douglas Berg of Washington University in St Louis, Missouri. Berg and his colleagues looked at more than 500 strains of the bacterium taken from people in five continents. Native Peruvians had bacteria more similar to Spaniards, they found, even though their genes are more similar to those of East Asians - the group that settled the Americas about 12,000 years ago. This led Berg and his colleagues to suggest that the conquistadors may have carried the bacterium to South America about 500 years ago, and that the continent's first humans arrived with virgin stomachs.

Martin Blaser disagrees. A microbiologist at New York University, he believes that Helicobacter has long been part of the gut flora of all humans. Late last year, Blaser and his colleagues seemed to reaffirm the ancient origins of American H. pylori, when they discovered strains closely related to the East Asian version of the bacterium in native people living in remote regions of Amazonia. And in unpublished work, pathologist Marvin Allison of the Medical College of Virginia in Richmond has detected H. pylori in the stomachs of 1,800-year-old Chilean mummies. In areas where Europeans and Amerindians had mixed, Blaser believes, indigenous strains have fallen victim to microbial imperialism.

The new study seems to confirm that Hp has an ancient origin. Achtman's team had previously shown that the spread of different Hp populations in stomachs around the world reflect the patterns of human migration. Now, they have found that we and them match up on a global scale:

[G]enetic diversity in H. pylori decreases with geographic distance from east Africa, the cradle of modern humans. We also observe similar clines of genetic isolation by distance (IBD) for both H. pylori and its human host at a worldwide scale.

So basically, we've been carrying it since we were human. Achtman has this graphic showing how the two spread:

Those of you with Nature subscriptions can read a 2003 feature by me on all this (which is where the earlier quotes came from). And if anyone's looking to write a short, sharp popsci book, you could worse than tell the H. pylori story. Just remember to give me a cut of the royalties.

Tuesday, February 06, 2007

Just Science day 2: They're only after one thing

Before we begin, I notice that the aggregator at Just Science has given yesterday's post the date of 31 December 1969. Can anyone help with why this has happened, and how to stop it happening again?

Anyway, on with the madness. With Valentine’s day just a week away, this paper in the new issue of Ethology is a must-read. In it, self-proclaimed ‘media friendly expert’, Karim Vahed, of the University of Derby, looks at nuptial gifts — the tasty morsels that many male animals (especially insects and spiders) bring to their intended mates.

The orthodox view of this is that everyone wins — the female gains a meal that increases her fertility, the male gets a mating. Vahed, however, has a rather more cynical take on things:

In this review, I explore the proposition that nuptial gifts act as sensory traps: by exploiting the female's gustatory responses, the male may be able to entice females to accept superfluous matings and/or transfer greater volumes of ejaculate than are in the female's reproductive interests.

Gift composition is more likely to be tailored to increasing the attractiveness of the gift to the female and/or maximizing gift handling time than to suit the female's nutritional needs … evidence suggests that the gift enables the male to overcome the resistance of the female to accepting an extra large ejaculate.

There is some evidence for this notion. Experiments in the fly Rhamphomyia sulcata suggest that females are almost as enthusiastic about worthless gifts as they are about a full dinner. Such indiscrimate behaviour leaves the door open to an invasion of cheating males.

And if Dr Vahed gives you a box of chocolates next Wednesday, beware.

Monday, February 05, 2007

Just Science day 1: cave bugs and shoot-em-ups

Not much time today (or tomorrow), so just a quick one drawing attention the juiciest morsels that popped into my inbox this morning.

First, and most closely related to this blog’s core themes, we have an interesting paper in Micobial Ecology by Raina Maier and her colleagues looking at the impact of tourists on the bacteria living in Kartchner Caverns, AZ.

These caves were opened to tourists in 1999. With admirable foresight (it’s depressing how rare this kind of thing is), researchers surveyed the caves’ microbial biota before opening, and now they reveal what’s changed as a consequence of having 200,000 people pass through the caves each year.

Raina's team found that the most heavily used areas had higher diversity, and different community composition — more Proteobacteria, fewer Firmicutes. This is probably a mixture of people bringing in bugs, and an increase in organic matter in the caves, say the researchers.

What we don’t know is what these changes mean for, say, nutrient cycling, food webs and so on in the caves, and whether they are something that should be of conservation concern. Microbial conservation is something I’d like to know more about, so if anyone has any pointers, please point them.

Three other things caught my eye:
1. Technological Forecasting and Social Change has a special issue of interesting-looking articles on terrorism and technology.

2. The Journal of Experimental Psychology reports that ‘action gaming enhances visuospatial attention throughout the visual field’ – i.e. playing Halo and its ilk makes you sharper-eyed. Whether this does you any good, and whether you get worse at anything else (insert your own joke about leaving the house, talking to girls etc.), is another matter.

3. And Psychopharmacology (always a favourite) finds that people who drink more coffee get more of a kick out of it. Which, given habituation and everything, seems to be the wrong way around. But I can’t tell from this abstract whether this is a consequence or cause of drinking lots and lots of lovely coffee.

There. That wasn't too bad. Back tomorrow.

Wednesday, January 31, 2007

Any other business

El Gentraso has rashly signed up to participate in Just Science. That means there'll be something new and science-related every day here Monday through Friday next week.

Equally rashly, I'll be hosting the March edition of Oekologie, the new ecology blogging carnival. It'll be just like real carnival, except without the samba bands and cross-dressing.

Meanwhile, in the real world, I'm speaking at the Edinburgh Science Festival on 9 April (easter Monday), talking about ITBOAH at 6 p.m. in the National Museum of Scotland's Lecture Theatre. And on 18 April I'm speaking about D'Arcy Wentworth Thompson at the Royal Institution in London. Except it'll be in the Royal College of Surgeons, because the RI's building is being done up. This is part of a series of RI events on polymaths.

Monday, January 29, 2007

Sleep and metabolic rate

Update: the link to the paper is now working. Duh. Sorry.

Sleep is another of those biological phenomena of which we lack a good theoretical understanding, despite there being lots and lots of (good) hypotheses and experiments. Van Savage and Geoff West have suggested a first step to building one, though. And (wouldn't you know it) it's based around metabolic rate.

The amount of time a mammal spends asleep, they find, is proportional to their relative, or cellular, metabolic rate. A fast-burner like a mouse sleeps for about 14 hours a day, whereas an elephant kips for only 3.5 hours. What's cool is that they find that sleep time is most closely matched to the brain's metabolic rate. Their suggestion is that sleep duration corresponds to the amount of time needed either repair brain cells, or reorganize them to process the day's input.

So unlike other organs, perhaps you need to shut down the (conscious) brain to maintain it. Fast-celled animals need more time for repairs (which, if this model holds, seems a more likely function of sleep - or at least of metabolically related sleep - than reorganization), because they do more damage while they're awake. The same argument applies to why small animals have shorter lifespans - fast cells, more free-radical damage, shorter lives.

What's that Lassie? A lot in life seems to depend on metabolic rate? Perhaps by understanding metabolic rate we can inch towards some kind of powerful, simple theory to explain a wide range of biology? You wish someone had written an accessible guide to this vibrant field and its long and strange history? Well, girl, it's your lucky day.

Wednesday, January 24, 2007

My new £16,000 habit

Winter finally came to London today, with a couple of inches of snow falling overnight. It was a nice surprise to wake up to. And not before time: we were hiking in the Peak District over new year, and you barely needed a coat, it was so warm (although the waterproof properties of goretex did come in handy, I admit). Woodland birds were singing, the odd tree was in blossom, and a friend in London has seen bumble bees in her garden. Anyway, enjoy the winter walking before the flood waters rise to engulf us all.

While in Derbyshire, we happened upon the excellent Hawkridge books in Castleton. They have a huge collection nature books, especially ornithology, and also good sections on climbing, mountaineering, etc.

In particular, they major in the Collin's New Naturalist series. This was set up during the second world war by, among others, Julian Huxley (who also popularized the use of allometry, thus earning himself a cameo in ITBOAH), with the intention of educating laypeople about the natural world.

Recently, the books have become collectors' items. The 100th in the series, 'Woodlands' by the legendary Oliver Rackham was published recently. There have also been other off-series monographs, so a complete set numbers around 120 books. The extremely nice man at Hawkridge told us that a set recently went at auction for £16,000 (about $32,000). The Woodlands book also exists in a limited edition, leather-bound version that is already changing hands for hundreds of pounds, apparently. The two rarest, nos. 70 Orkney and 71 Warblers (both from 1985) thanks to their extremely short print runs, are worth thousands. There's an extremely nice article about the whole thing here.

The NN clearly owe their value to a perfect storm of British male nerdiness - we, and especially amateur naturalists, love collecting, making lists, getting the complete set. So something that appeals to both naturalists and book collectors is bound to do well. They are also lovely books, with instantly recognizable covers.

Anyway,I'm not given to impulse purchases (although I'm quite partial to Nonesuch Explorer recordings on vinyl), but Hawkridge had a first edition of NN number 3, London's Natural History by Richard Fitter (with pictures by Eric Hosking, published in 1945 that they were selling for only £8. As a Londonist, this was clearly too good to miss, even though I had to carry it for several more days' walking. Only 102 (they're up to 103 now) to go.

Tuesday, January 23, 2007

How many pictures of leopards does the world need?

We went to the (staggeringly busy) Natural History Museum on Sunday, to see the Wildlife Photographer of the year exhibition. I've been coming to this for 20 years or more now. Usually I ooh and aah at the lovely pictures, and go away saying to myself it's a wonderful world. But this year, for some reason, I didn't react like that (or anyway, not just like that).

Here then, in no particular order, is the case against wildlife photography — or at least the vision of the natural world presented by this competition — that I found myself making as I walked round the show:

The same things seem to come back year after year — comical penguins, majestic birds of prey, big cats, cute baby animals. All set against atmospheric backdrops of sunsets, sunrises, snow, clouds of dust, and so on. It's a fine line between naff and beautiful.

Interestingly, the pictures that win the big prize tend not to be like this — more often, they are impressionistic (which I don't like, because they seem to be trying to imitate painting, which misses the point) or abstract, such as this year's winner, of a walrus, or last year's (which I think is an exciting and original image), of a peregrine attacking some starlings.

Does, and can, wildlife photography develop and change — like, say, portrait photography does. Obviously equipment gets better, but do the genre's aesthetics develop? Not much, would be my suspicion. There seems to be a very narrow version of what's beautiful and impressive about wildlife, that doesn't have a place for anything scary, or horrific (does anyone photograph parasitoids eating their way out of caterpillars?), or strange. Yet, let's face it, nature can be all of these things, and they are meat and drink to other forms of visual art.

The feeling that nature was being boiled down to a series of money shots also came to me while watching the BBC's Planet Earth series which, although it had some staggering images, and showed me lots of stuff I never new existed, lacked the narrative and scientific integrity of David Attenborough's various 'Life' series. Basically, the message was: 'Look at that! And that!'

(If Planet Earth was anything to go by, one thing that has changed in wildlife TV is that filmmakers are much less keen to show the violence that's often thought to be a staple of the genre — usually, the hunt was shown, but we cut off to somewhere else before the kill. This is probably a mixture of Good Taste, and a sense that this sort of thing is getting clichéd. Similarly, in the still photos there was no blood, or shagging.)

Such a highlights-reel approach commodifies nature. These photos blend seamlessly into the high-gloss adverts that surround and tempt us, and a lot of these pictures wouldn't have looked out of place in Condé Nast Traveller, say, or an advert for wide-screen television.

It also exoticizes nature, making it something that happens elsewhere. There's a category for urban wildlife, but it's weak, and this year's winning photo was of that noted urban species, the grizzly bear, pictured on that noted metropolis, the Kamchatka Peninsula. The risk is that we'll think of wildlife as something glossy, impressive, and expensive, not as all the stuff that surrounds us, and is worth checking out and looking after.

You can't blame photographers and exhibitors for this — folks wouldn't queue up to look at a whole roomful of pictures of starlings. But I would applaud the wildlife photographer who actually tried to capture the real experience of watching wildlife, rather than an idealized freeze-frame of wildlife. Usually, this involves a brief glimpse of something's arse as it scuttles into the undergrowth, or squinting at a distant silhouette. But such views are much more satisfying, because they're real, and because we have got them ourselves. Where's the Martin Parr of wildlife photos?