Given the choice, I'd vote for a sea lion

For a long time, I wanted to be a behavioural ecologist when I grew up. I had come to biology via watching birds and David Attenborough programmes, read The Selfish Gene (which is bascially a very good book about behavioural ecology) at an impressionable age, and in the early 90s it seemed like a really vibrant and exciting area.

But now it seems to have been a victim of that success — almost (to exaggerate) a completed science. We have a set of ideas that have been very successful at explaining animal behaviour in evolutionary terms — kin selection, optimal foraging, various models of sexual selection, and a few others. Most aspects of animal behaviour seem explicable in terms of one or other, and nothing seems to need a big new idea to explain it. I'd be interested to hear anyone else's thoughts on this (particularly if you disagree).

Anyway, this is really just a preamble before I mention some recent behaviour papers that caught my eye. Behavioural ecology might not be white hot, but it still delivers high on the fancy-that factor.

For example, did you know that sea lions are masters of self control? If you offer them a pile of five fish or a lone fish, and then give them the one they don't choose, they quickly learn to choose the smaller reward — more quickly, in fact than primates, who keep lunging helplessly for the bigger pile (I don't think they offered the primates fish. Probably bananas, or something.).

Not only that, diving seals can hold off digesting their dinner until they surface, to reduce the amount of oxygen they use up underwater.

One area of behavioural research that's still kicking up dust is, of course, evolutionary psychology. Here, for example is a worrying paper from Evolution and Human Behaviour looking at the influence of face shape on voting decision:

We show that differences in facial shape alone between candidates can predict who wins or loses in an election.

Anthony Little and his colleagues took the faces of recent election opponents — Kerry/Bush, Blair/Howard, and several others from around the world. They recreated the differences between the two candidates' faces on neutral models, so that subjects wouldn't recognize them, and then tweaked them to exaggerate the difference (not sure why they did this — it seems to undermine the study's claims to reflect reality). Then they showed the faces to people, and asked who they would rather vote for, without any other information.

The percentage preferences for the simulated faces predicted fairly well the destination of votes cast in actual elections.

The Sunday Times reported on this at the weekend.

Little speculates that voters chose Blair because his skin looked healthier than Major and his face, with a strong jaw and thinner lips, looked more masculine than Hague. “Firm jaws and heavy brows denote masculinity,” he said.

Perhaps more reassuringly, they found that "there may be no general characteristics of faces that can win votes". People asked to choose a peace- or wartime leader, for example, prefer different sorts of faces — wartime voters prefer a more dominant, masculine face, apparently. Sigh. I imagine doctors of spin are already out with the callipers and booking their men and women in for plastic surgery.

An obscenity

This is beyond the usual scope of this blog, and I know there're a lot of bad things happening in the world, but to take a group of people who came to your country to work in your medical system, accuse them, despite an overwhelming body of evidence to the contrary, of infecting children deliberately with HIV, torture them, refuse to hear relevant evidence in court, and then sentence them to death - in what mainly seems to be an attempt to cover-up the shoddiness of one's own procedures - seems particularly shameful and grotesque.

Let's hope that the Libyan government has some sense of justice and humanity, and overturns this decision.

Nature's Declan Butler has done a fine job of reporting this story.

It's lonely out here

There's an interesting post on Evolgen about the paucity of ecology bloggers. Although the discussion seems to have wandered off-message rather. I reckon that one of my previous rambles about ecology's general media-unfriendliness may be relevant to this issue.

The way things go

If, like me, you're a fan of the conservation of momentum, chemical reactions, kettles, stink, bangs, 70s board-game Mousetrap, or 70s BBC2 show The Great Egg Race, get down to Tate Modern and check out Fischli & Weiss's "The way things go' (Der Lauf Der Dinge).

This piece of video art, part of an F&W retrospective showing at the Tate until January, shows an absurdly convoluted and entertaining chain reaction of things bumping, rolling and swinging into each other, not to mention setting each other on fire, inflating, puncturing, foaming, and so on. It's not exactly science, but you can see a sort-of-science (or engineering, at least) thought process behind it that ought to appeal to anyone in the least bit geeky. It reminds me of the great domino-topples that seemed also to be on TV every week in my distant, distant youth (do they still do those?). And apparently it was ripped off by, I mean inspired, that Honda advert of a few years ago.

I didn't stay for the whole thing, which lasts 30 minutes, but what I did watch seemed to go on forever. Some of the slower parts were actually quite painful to witness. If you can't get to the Tate, don't worry. You can get a DVD (and see a trailer) here (I was sorely tempted - I envisioned showing it at Factory-style happenings in my groovy Shoxton loft, and I don't even live in a groovy Shoxton loft. Or own a DVD player.). Or you can see the first 7+ minutes on YouTube:

Make yourself happy

Thank God (or whoever else might be responsible) for the Onion.

Kansas Outlaws Practice Of Evolution.

The cost of leafing

This week's Nature has a news feature by me on leaves (why have they made 'plantecology' one word?). Specifically, it's about the patterns in leaf construction seen across all land plants, what causes them, and the consequences that they have for our understanding of the living world. (Lovers of waffle will not want to miss hearing me talk about this on the Nature podcast.)

[M]ost of the variation in the physical and biochemical properties of leaves can be represented on a single axis running, to put it crudely, from quick and juicy to slow and tough. [This is] the 'worldwide leaf economics spectrum', and it embodies many of the trade-offs that govern how plants deploy their resources within the limits that physics places on biological possibility.

The work … has attracted the attention of everyone, from plant physiologists studying how leaves work to biogeochemists looking at the cycling of nutrients on a global scale. In part, the paper is so popular because of the size and scope of the database that underlies the work; but the popularity also reflects the intellectual excitement that surrounds the discovery that so much can be explained by so little. This has given some ecologists hope that by looking at the large-scale patterns in how organisms work, they can gain a general understanding of why species live where they do, and why some are common and others are rare. Such findings are not of purely academic interest: climate researchers are using them to improve their models of the consequences of global warming.

For me, one of the most interesting aspects of writing this feature was investigating an idea among some ecologists that the best way to understand why species live where they do, and why some are common and others rare is to think not about species, but traits — such as leaf biology, seed size and number, and so on.

In some ways, this is counterintuitive. Most, perhaps all, cultures name the plants and animals around them, and recognize that they split into groups of similar kinds, i.e. species. Many ecologists come to the science through a love of natural history, and identifying and naming stuff. And consequently, many theories of biodiversity are rooted in what's been called 'nomenclatural ecology':

To try to understand things such as what determines the number of species that can coexist in a place, how numerous each species is, and how productive the system as a whole is, ecologists have traditionally looked at what species are present, how they interact, and how their abundance affects that of the others. Such an approach is an extension of ecology's roots in natural history, says Brian McGill of McGill University in Montreal, Canada. "People become ecologists because they love to go outdoors and look at the woods. They get attached to putting names on things, and get focused on knowing lots about particular organisms."

But this approach soon becomes intractably knotty, as the number of possible interactions between species rises geometrically with the number of species. "We don't have the capacity to learn as much as we need to know by studying one species at a time. Studying interactions between species, and then trying to build that up, hasn't panned out. It's too complicated," explains McGill.

Traits — such as, for leaves, mass-per-area, or photosynthetic rate — are measurable, and comparable in a way that species names aren't, and also allow one to quantify natural variation. I think of this as dropping below the species level, to look at the components of biology — how organisms work, and how they differ — and I've a hunch it might offer a way out of the current morass of different theories to explain the origin and maintenance of biodiversity. Of which there are tons — it did my head in trying to get to grips with this area.

Of course, to make satisfying science, one wants to be able to turn trait studies back into predictions about species, because as human beings that's how we perceive the world.

But this looks like it might be possible — Science recently published an extremely cool paper by Bill Shipley and colleagues using trait measurements and, to my satisfaction, maximum entropy theory to predict the abundance and distribution of plants in abandoned French vineyards with 94% accuracy. Which is pretty damn good.

I confess, I really should have covered this in ITBOAH, but it didn't cross my path while I was writing this. Very sorry, ITBOAH-readers.

Review: Genes in Conflict

I've got a piece (registration required) in the current London Review of Books on Genes in Conflict by Austin Burt and Robert Trivers.

The book's a brilliant resource, bringing together what must be pretty much every piece of information on selfish genetic elements, such as transposable elements, selfish sex chromosomes and imprinted genes. These genes can thrive at the expense of the organisms that carry them, causing conflict and selection to operate within genomes and organisms, as well as between them.

Such conflict has led to some extremely odd biology (such as the sperm that can eject the maternal chromosomes from the eggs they 'fertilize'), some extremely fundamental aspects of our biology (such as the uniparental inheritance of mitochondria, and probably some details of mitosis and sex itself), and some extremely interesting potential effects on our behaviour and psychology, caused by different bits of the genome pulling in different directions. I imagine this will be explored further in Trivers' next book, which is apparently going to be about the evolution and uses of self-deception.

This is the sort of book that would work splendidly as an online resource — it doesn't take a linear approach (early on the authors say it can be read in any order, which is a bit dispiriting for a reviewer settling down to read the whole thing), so hyperlinking would be valuable. And this is such a fast-moving field that regular updates would be welcome (such as, say, the power of transposable elements as a creative force in evolution, which is a bit off-message from the book's main thrust, but an exciting area, as a recent N&V feature (registration required) in Nature shows). Magisterial overviews such as this still clearly have a place on academic bookshelves, but they need to cope with the way that the internet has made the information they collate easier to find and access.

Leonardo's notebooks

Anyone interested in science would do worse than go to the Leonardo da Vinci exhibtion at London's V&A museum, running until 7 January. I went last week.

The exhibtion, of material from the man's notebooks isn't primarily an aesthetic experience (although there are some beautiful things there). What it's about is giving you an insight into Leonardo's thinking, and the full range of his preoccupations.

Nowadays, the term 'Renaissance man' is applied to any science PhD who's read a novel and got grade 3 clarinet (women tend to do lots of different things without running around giving themselves grand names). This exhibition shows you better than anything I've ever seen what being a Renaissance man really meant. Leonardo treated the artistic, scientific, mathematical, biological, architectural, mechanical, you name it, as all one and the same - often on the same sheet of paper. Designs for musical instruments are alongside those for palaces, and stage sets, which are alongside plans for epic murals, or engines of war, or anatomical drawings, or clouds. Astonishing.

On the science side, it looks very much as if he was thinking about problems, such as finding a shape's centre of gravity, or a volume's solid, that were solved by Newton/Leibniz's invention of calculus. He also seems to have pondered other Newtonian stuff, such as gravity and mechanics. (And he tried to square the circle, and build a perpetual motion machine. Nothing I could see on thurning base metals into gold, though.)

He also did some drawings on the form of trees, river networks, and blood vessels that (looking at things with a biased eye, I admit) intriguingly prefigures the network models of metabolic rate, river networks, and other stuff by West et al. and Banavar et al.

And here's a quote, presented in the exhibition, which could have come straight out of D'Arcy Wentworth Thompson's mouth, and which sums up world view (one of them, anyway) I write about in ITBOAH:

"A bird is an instrument working according to mathematical law."

Pegged to this exhibtion, there's an interesting piece by Guardian art critic Jonathan Jones on how the notebooks ended up in the hands of the British royal family.

Is natural selection a law of physics?

More on applying the physics of statistical mechanics and thermodynamics to ecology and evolution. This paper by Guy Hoelzer and colleagues appeared recently in the Journal of Evolutionary Biology:

On the logical relationship between natural selection and self-organization

…In this study, we attempt to describe the logical framework that relates the general process of self-organization to the specific process of natural selection. We describe natural selection as a mechanism that coordinates the coevolution of species in an ecosystem to effectively capture, process and dissipate solar energy into the earth’s shadow. Finally, we conclude that natural selection is an emergent process founded on the same thermodynamic imperatives that are thought to underlie all self-organization. This perspective suggests … the possibility that there may be a physical basis for understanding the origin of the process of natural selection. Rather than being merely a fluke of nature, the origin of natural selection that may be driven by energy flows across gradients.

As an example of the kind of links between biology, thermodynamics, and self-organization that they are pursuing, Hoelzer et al. give photosynthesis. They point out how good it is at levelling out the gradient of solar energy, and suggesting either that "photosynthesizing life is a statistically favoured component of the biosphere, or that a high-flux channel for light transduction is a favoured endpoint, towards which perturbed ecosystems recover. Physical principles expressed in terms of stable end states imply a natural teleology, which we have suggested (somewhat imprecisely) is the reduction of the spectral and spatial energy gradient imposed by the situation of earth in a solar radiation bath."

They also invoke metabolic scaling theory, which explains living things' energy use in terms of the geometry of transport networks (something similar seems to apply to the geometry of lightning strikes and river basins), and suggest that a taking a self-organizational view is a good way to try and understand why, the more energy an organism uses (whether metabolically, or, for humans, in society), the fewer offspring it has. (More about all this here and in ITBOAH

Other striking quotes:

We offer the conjecture that the truly ultimate explanation for any dynamical event, and the qualities of any emergent dissipative structure, including organisms and ecosystems, is thermodynamic.

Natural selection is to self-organization as language is to communication. Language is not synonymous with communication, yet it is a quantum leap forward in communicative effectiveness. It is also not merely a more complicated for of simpler modes of communication. … Language has emerged from the drive to communicate just as natural selection has emerged from the drive to break down gradients.

Much of this is not particularly new. Dynamic, complex physical systems can take on orderly, structured states, and physicists such as Stuart Kaufmann have long suggested that the same principle applies to living things — that self-organization, as well as, or instead of, natural selection, can explain the complexity and structure of life.

Likewise, it's not a new idea that thermodynamics can explain the structure of life, and that this structure evolves to flatten out energy gradients as much as possible, and degrade energy/produce entropy as quickly as possible.

And biologists have usually resisted these concepts. Natural selection is so successful that bolt-ons from physics seem superfluous. There's no reason to believe that natural selection should maximize anything thermodynamic, and many biologists take issue with the assumptions and predictions of this approach. Someone once pointed out that the reason horses had evolved was to make more horses, not to make horse manure. John Maynard Smith thought harder about these things than most biologists, and (I think) remained sceptical. (Try here or here.)

So either all the current upsurge of this stuff is just a cyclic blip, or we're really inching towards some kind of new insight. I'm not sure which.

Bee genome

Social insects were my first great scientific enthusiasm, and I still think they're the coolest.

Their behaviour marvellously illustrates the power and subtlety of natural selection. Via kin selection, it can produce altruistic behaviour, but this only works as long as each individual is benefiting — and there is a constant temptation, even for social insects, to choose the selfish path, and rebel against the group.

Honey bees, for example have evolved sophisticated ways to keep selfishness in check, such as worker policing, where workers destroy the eggs laid by fellow workers (but would secretly like to lay eggs themselves).

So, the honey bee genome published in Nature last week is a good thing. But it doesn't tell us much about sociality - when Nature asked project Leader George Weinstock what the most surprising thing about the project was, he replied 'That we did not come up with breakthroughs in understanding social behaviour of the bee'.

Way to hook the public, George. But not really surprising, because the different castes and jobs within a beehive are determined by environment, and developmental factors — queens aren't decided by their genes, but by a diet of royal jelly. What job a worker does depends on its age — they start out as nursemaids, then move outwards, becoming guards, and finally foragers.

So gene regulation is going to be more important than gene content for understanding sociality. Perhaps this is why I found Nature's news and views piece on the genome, by (the great) E. O. Wilson, a tad disappointing — it's more an essay on bees, trotting out a bunch of well-known stuff, than anything that gets to grip with what the genome means.

As well as the Nature paper, it's worth checking out the current Insect Molecular Biology, which has a bunch of freely accessible papers related to the genome.

Besides all the 'how does sociality evolve, and what does it mean for humans' stuff, bees are important, and threatened, providers of ecosystem services. When the genome was completed last year, I had a piece in the Financial Times about this; I'm putting up the director's cut below.

Until last week, I didn't know that bumble bees were also commerically traded and transported, and that this similarly helped to spread disease. Then I saw this paper in the current issue of Population Ecology.

Anyway, here's the FT piece. Science made cool also posted on this issue recently.

A plague has swept the world. Thousands of communities have been infected and wiped out. We are trying to fight back with chemicals and quarantine, but it's a rearguard action, and the threat of a new epidemic is always lurking.

But this isn't Sars or Aids. The victims are honeybees. Across the world, beekeepers are battling with a menagerie of parasites and diseases, trying to stay one step ahead of existing threats, while remaining alert for new scourges.

The honeybee genome recently completed by a team of US scientists gives bees' human allies a powerful tool. It's the first complete genome of any domesticated animal; for thousands of years we have selected bees for docile temperaments and high honey production. Now, scientists can look for the genes that will help bees fight off their ailments.

"I'm optimistic that we'll be able to breed bees resistant to a variety of diseases," says Jay Evans, a geneticist at the US Department of Agriculture's Bee Research Laboratory in Beltsville, Maryland. Dr Evans works on the bees' immune system, and is seeking ways to boost its power. He is also developing tools to diagnose sick bees, by looking for genes that are switched on when insects are sick or starving.

There's more at stake than just the sweet stuff on your breakfast toast. In the UK alone, bees' pollination of crops is estimated to be worth about £200 million - ten times the value of the honey they produce. Fewer bees would mean more expensive food. And the insects perform an unmeasurable service to our environment by pollinating wild plants.

Bees' most serious enemy is a millimetre-long mite called Varroa destructor. The mites suck the blood of adult and larval bees and transmit deadly viral infections. Without treatment, an infested hive is doomed. Beekeepers can control varroa with pesticides, but the mites are starting to evolve resistance.

Varroa originally lived in peaceful coesixtence with a far-eastern bee species. But a century ago it switched to western honeybees. Since then, varroa has spread around the world, reaching the US in 1987 and the UK in 1992, where more than 5,000 hives have been infected. The impact on wild bees has been devastating: "In Europe and North America there are virtually no wild honeybees left," says Dr Evans.

Bees have millions of years of experience of coping with diseases. But we have made them vulnerable, by moving bees around, bringing diseases into contact with hives that have no resistance to them, in the same way that Europeans exported smallpox to the New World. "The movement of bees has increased tremendously, and there's always a risk that you'll introduce an exotic parasite with an exotic virus," says Brenda Ball, who studies varroa at the Rothamsted Research Institute in Hertfordshire.

Rather than create GM bees, researchers will most likely use the genome to steer breeding programmes. The genes that control behaviour could be the key to producing parasite-proof honeybees, says Dr Ball. We know that some bees are more hygenic than others, in their ability to detect and destroy infected larvae, for example. The genome should help us find out how this is determined, and breed more vigilant animals. It could also help us work out how Asian bees are able to resist varroa.

The varroa mite might be beekeepers' worst nightmare, but it's far from the only one. In December the European Commission restricted bee imports, in a bid to keep out two other damaging parasites, a beetle and another mite. And the insects are also prey to a range of fungal and bacterial diseases.

Bees are vulnerable to disease for the same reasons that we are - they live in dense groups, where individuals are in constant contact. Such cities support pathogens and give them the chance to spread. This makes them good models for understanding human disease, and researchers are already testing bees' natural antibiotics to see if they could work against our own infections.

Exclusive offer

Uniquely in the blogosphere, El Gentraso makes its readers this pledge: to keep its thoughts about Richard Dawkins' The God Delusion to itself.

I came to eat, and stayed to learn

This Saturday, I went on a fungus foray and identification workshop on Hampstead Heath, run by Andy Overall of fungitobewith.org.

Beforehand, my main motivation was to gather enough wild mushrooms for a risotto, and to learn enough do the same under my own steam without dying or accidentally tripping. But by the end of the day, I was just as fired up by having had a whole world of biodiversity revealed to me, and also at having learned a new skill. (And we only got enough mushrooms for toast.)

If you look, there really are an immense number of fungi out there, and they’re beautiful. The prettiest ones we found were the sulphur tuft and the wood blewett (the photos don't do them justice). Also, staring at the ground intently really expands your world — Hampstead Heath went from being somewhere nice for a stroll to a universe

Two things struck me. The first is that, to an outsider, the abilities of a skilled naturalist seem almost magical. Andy, armed with years of experience and that marvellous pattern-recognition system known as the human brain, was able to name most species at sight. It's a huge privilege to see someone like that in action.

I would guess that even he might not know how he does it — I am reasonably good at identifying birds, but when someone asks you how you know that something is a heron, or a kestrel, the only answer I can give is that, having seen lots of herons or kestrels previously, perhaps in less ambiguous circumstances, I know one when I see one.

(A bird’s hard-to-define-but unmistakeable signature is what birders call jizz (or jiss, or giss; a quick google reveals that the web is hot with discussion on this topic). Fungi have much the same.)

But the second was how quickly, as a beginner, one accumulates knowledge. Before this, my fungus-identification abilities ended with fly agaric and giant puffball. But now, even though I’m a long way from being able to distinguish between the 100+ different British species of Mycena or Russula, I reckon I could — armed with Roger Phillips’ Mushrooms etc. — assign more than 90% of what I found to a genus.

I’ve also learnt — armed with Richard Mabey’s Food for Free ( a lovely book, although this edition isn't quite as nice as the one I first encountered, an old B&W hardback we found in a holiday cottage) — that the number of good-to-eat species is relatively small, and most are distinctive (no reason to be blasé about safety, of course). When you don’t know anything, you can learn a useful amount of something pretty quickly, and easily.

And, even though I’m no great shakes as a naturalist, it’s tremendously satisfying. It’d be nice if people thought of natural history knowledge as culturally valuable — if people thought that knowing what a hawthorn, or a red admiral, looks like were as important as knowing who wrote Hamlet, or what Pythagoras’ theorem is. It adds another dimension to your enjoyment of the outdoors and, presumably, it’d help us conserve wild plants and animals if more people could recognize them.

Another podcast

You can here me being interviewed here by Judyth Piazza of the Student Operated Press. This is a bit shorter than the Small World interview, and a bit less about the science and what's in the book and more about influences, motivation, and me, me, me.

Website working again (apparently)

www.inthebeatofaheart.com seems to be working again. It went down because I was having some trouble with domain transfer, hosting, and my own ignorance. I hope it'll stay there now, but if not, it shouldn't be gone for long, andwww.johnwhitfield.co.uk isn't going anywhere.

Website technical difficulties

My book's website www.inthebeatofaheart.com is down, owing to difficulties with transferring domain names. But the site is mirrored on www.johnwhitfield.co.uk. Will have the other url working ASAP.

Podcast interview

This past couple of weeks, I've been doing a bunch of radio interviews to promote ITBOAH. But if you've missed my many appearances on AM radio in the US (where were you?), don't despair. You can hear me being interviewed about the book (and gamelan) by Joseph Aleo on this podcast (link goes straight to MP3 file), published on his Small World site. Like the site says, "This episode is work safe". Maybe I should do two versions of my interviews: one radio-friendly, daytime one, and one late-night, foul-mouthed version to play in clubs, like they do for rap records.

Cradle and museum

The greater diversity of life in the tropics compared with the poles is so obvious it barely seems worth thinking about. But explaining it is probably the oldest problem in biology — over the past 200 years (starting with Alexander von Humboldt) there have been more than 100 explanations advanced for what is known as the latitudinal diversity gradient. All these are some variation on: either species are more likely to evolve in the tropics, or they are less likely to go extinct, or both. (In case you hadn't already guessed, there's a chapter on all this in my book.)

Or, as Ledyard Stebbins put it in 1974, are the tropics the cradle of biodiversity, or its museum? 'Both', say David Jablonski and his colleagues in the 6 October issue of Science.

The fossil record shows that biodiversity has been concentrated in the tropics for at least 270 million years. But to answer the cradle/museum question, you need estimates of both origination and extinction rates, which are hard to come by.

Jablobski and co looked at marine bivalves (i.e. clams), one of the few groups with a good enough fossil record to address this question. Going back about 11 million years, into the Miocene, they found that about twice as many groups make their first appearance in the tropics as outside them.

So that's the cradle. In fact, Jablonski had already shown this by looking at marine fossils in what I think is a very good Nature paper from 1993. The new study builds on this by finding that bivalves are also more likely to go extinct outside the tropics: "only 30 exclusively tropical genera go extinct as compared to 107 extratropical and cosmopolitan ones". So that's the museum.

The researchers advocate what they call the 'out of the tropics' (OTT) model: "lineages not only preferentially originate in the tropics, but also persist there as they expand poleward…most extratropical species belong to lineages that originated in the tropics." This includes us, of course.

This seems to me a persuasive general explanation for the underlying driver of the diversity gradient. It certainly seems more general than the various explanations based on ecological factors — there are more ecological niches in the tropics, or competition is fiercer — or on climatic stability, although arguments such as this may be needed to explain why tropical species seem less likely to go extinct.

And, we have a mechanism for why evolution runs faster in the tropics — the warmer temperatures there increase metabolic rates, and so mutation rates, and so (probably) evolutionary rates. This is the 'energetic theory of speciation' that came up the other week at Santa Fe (see previous post); the person doing most work on it is Drew Allen, who is studying how speciation rates in foraminifera relate to temperature, another group with a fossil record to die for.

Blue-sky thinking

1. My new favourite idea
Last weekend, I went to Santa Fe, to be part of a working group meeting at the Santa Fe Institute on 'unifying current theories of ecology'. This comprised 15 researchers representing, broadly speaking, three of the main branches of macroecology: metabolic ecology, neutral ecological theory, and spatial macroecology (for which there isn't really a good link at the moment, but which involves trying to understand the geographical distribution of individuals and species across multiple scales, from fields to continents, as it were).

One idea behind the meeting was to try and find common ground between these models. For example, how do we incorporate information on body size — a cornerstone of metabolic ecology — into the neutral theory? How do we come up with an energetic theory of speciation, explaining evolutionary rates in terms of body size and temperature? If metabolic ecology could provide this, it would allow us to derive, rather than assume, one of the things that the neutral theory uses to calculate species diversities and abundances. In general there was a lot of talk along the lines of 'your theory's inputs are my theory's outputs'.

Another theme was to identify areas of ignorance, and what data are needed. Assuming anyone reads this, I don't want to talk too much about what the meeting concluded — and in truth, much of it seemed quite tentative — because there are publications in the works. But one of the things that excited me, because I've written (subscription required) a bit about it recently, was applying the theories of entropy to these problems. The two relevant models are of maximum entropy (technically known as MaxEnt) and maximum entropy production (MEP), which is different to, but derived from, MaxEnt.

Entropy is My New Favourite Idea. In some ways it's silly to rank concepts (although we do it all the time, of course), but entropy seems to me an extremely powerful and profound way of understanding the world — up there with natural selection, in fact. Even more so than natural selection, its roots are in logic, rather than in the analysis of any particular system. This means that it can be derived, and applied, in lots of different ways — and that it's possible to come up with rigorous mathematical proofs.

It also makes entropy an easy concept to misunderstand. It was only recently, for example, that I discovered that thermodynamics, statistical mechanics and information theory all have their own versions of entropy. Mathematically, these theories can be derived from one another, but I confess I'm still not sure how they relate, and differ. At Santa Fe, I decided I needed to know more about this, so I aim to track down some form of entropy for dummies.

2. Ummm…
I've also started doing publicity for what I like to call ITBOAH (pronounced 'itbo', 'itboa' or 'itbweagh', depending on how I'm feeling). First off, while I was in Santa Fe, I did an interview on Mary-Charlotte Domandi's show 'Radio Café', broadcast by KSFR, the town's NPR affiliate. This cool show comes live each morning from the Santa Fe Baking Company — Mary Charlotte just sets up her gear at a corner table, and gets broadcasting.

I also officially launched the book, to a small (apparently the town's wine and chilli festival was a bigger draw, for some reason) but appreciative crowd at Garcia Street Books, hosted by the shop's owners, the extremely kind and gracious Edward and Eva Borrins. Then, on Monday, I broke my journey home in Washington DC, to see the folks at my publishers, and took part in a Café Scientifique.

I've always told myself that once the book is out there, I've done my bit, and people can make of it what they will — it's not as if I can stand over a reader's shoulder and tell them what to think. When this actually happens, of course, it throws you off balance, but in a good way.

So what's been the most fun aspect of this experience is the questions that you'd never properly thought of and can't properly answer: 'What is energy?', 'If places with the most energy contain the most species, what about hydrothermal vents?'. Given a bit of time, I can kind of give a satisfactory response to these, but at the time, I find myself umming and aahing. The best thing to say is 'I don't know', but it's also the hardest thing — the urge to waffle is always mighty powerful.

3. Mathematical smackdown
Most of the best science journalism, if you ask me, appears not in the specialist press, but in places like the London Review of Books (declaration of interest: I occasionally do stuff for them), New York R of B, and the New Yorker.

For example, on my flight out, I found that, for some reason, they were still selling the 28 August issue of the New Yorker at Dallas airport (surely it doesn't take a month to get a copy into Texas?). I bought it, because it had a feature by Sylvia 'A beautiful mind' Nasar and David Gruber on the current controversy about the Poincaré conjecture. From reading other pieces, I had assumed that the Russian mathematician Grigory Perelman had solved it, and everyone was happy about that. But no.

I confess, after reading it I wasn't much wiser about what the PC is (something about the topological properties of spheres, I think), or how Perelman went about proving it. But it was a riveting read, and a superb piece of reporting. Perelman is, if not exactly a recluse, at least not bothered about giving interviews, refuses prizes, left America to move back to Russia, left his job in Russia to move back in with his mum in St Petersburg, and so on. But Nasar and Gruber got an interview by the brilliantly simple tactic of knocking on his door.

Perelman comes out of the piece pretty well. The person that comes out of it pretty badly is the Harvard-based Chinese mathematician Shing-Tung Yau, who has claimed that two of his students deserve the credit for solving the Poincaré. Yau is basically painted as an unscrupulous empire builder — stomping on those who disagree with him, claiming credit for things that he shouldn't, and not sharing things he should.

I was recently talking with a mathematician who knows people on both sides of the story, and he said paid the piece the tribute of saying that it contained information that was new to him. He also said that, allegedly, Yau plans to sue the New Yorker.

The same issue, incidentally, contained an article on stage fright, including the revelation that Carly Simon overcomes hers by getting band members to spank her shortly before she goes on stage.

At a celebration for President Clinton's fiftieth birthday, at Radio City Music Hall, in 1996, Simon, terrified of following Smokey Robinson, invited the entire horn section to let her have it. "They all took turns spanking me," she says.

You don't get that in New Scientist.

Book website now live

The website to support my book is now live. The main purpose of this — besides advertising, of course — is to host an extended reference list, with notes, for the book. I dithered and agonized a lot about how extensively to cite in the book, and how much to put up elsewhere — I'm not sure I got the balance right, but anyway. There are also links, some photos, and an events list. And because the science I write about is changing so quickly, I've also got a Connotea list of papers relevant to the book that have come out since I finished it, which represents a small attempt to keep up with things.

The site was designed and built by the way talented Charlotte Westney. If anyone's looking for a web designer, I can thoroughly recommend her.

Profile of Vijay Iyer

I've got a piece in the new issue of Seed magazine about the New York-based jazz pianist Vijay Iyer.

Iyer is one of the most interesting jazz musicians around. He recently won Downbeat magazine's annual poll in the 'rising star' categories as both a performer and a composer. He's got a background in maths and physics, and places mathematical tools at the heart of his compositional technique. And, as well as leading an acoustic jazz quartet, he makes electronic music, and creates theatrical pieces in collaboration with the rapper/poet Mike Ladd.

Anyway, it was great fun to meet and talk with him when he visited London earlier this year, and it was fun to do the piece - my first foray into music-ish journalism. Vijay has posted the piece on his own site.

Comment on In the Beat of a Heart

Hello. You've come here either through my regular blog page, or by following the 'comment' link at www.inthebeatofaheart.com. If you'd like to post a comment or observation on the book, bring my attention to some relevant research, or correct a mistake, I'd love to hear from you.

Book launch

On the off chance that anyone in on near Santa Fe, NM, reads this: I'll be talking about my book 'In the Beat of a Heart: Life, Energy, and the Unity of Nature' at Garcia Street Books next Saturday at 3.00 pm.

The Mike Leigh mark-recapture experiment

While standing on the platform of King's Cross Underground station last week (Metropolitan/Circle/Hammersmith and City lines, westbound, since you ask). I spotted Mike Leigh, director of, among others, the films Naked and Secrets and Lies. This is the third time in about four or five years that I have spotted him about the centre of town — I saw him once at an exhibition at the Royal Academy (I can't remember if it was Japanese prints or Renaissance illuminated manuscripts), and once walking down Charing Cross Road.

Now, every Londoner likes talking about famous people they have spotted in the street, pub or wherever (I saw Björk in a restaurant once, and sat opposite David Byrne on the tube). But this set me thinking about something different. How often can I expect to bump into a randomly chosen Londoner? Do I pass the same people every couple of years or so, but don't know it because they're not famous?

This is a problem that ecologists encounter all the time. Perfect knowledge of wild animals and plants is impossible, so we need techniques to estimate things such as population size, movement patterns, and mortality rates. One way to do this is a technique called mark-recapture. You catch say, 1,000 monarch butterflies, or cod, or swallows, mark them, and set them free again. Later, you see how many of the marked ones you can catch again, when, where, what percentage they make up of the recaptured population and so on.

This is used to estimate, among other things, fishing mortality, and was used to demonstrate the action of natural selection acting on the peppered moth: moths were much more likely to be recaptured in their camouflaged environment. Census takers, epidemiologists and others use similar techniques to estimate the true sizes of the populations they are interested in.

But answering my question raises lots of questions about sampling strategy. Who you see depends on where you go, and when. If one commutes into the centre of town most everyone is aged 20-50. If you want to see the elderly or children, you need to go out in the day. If I drove to work every day and spent the weekend playing video games, or doing DIY, my chances of spotting Mike Leigh would be smaller. Although most Londoners probably pass down Charing Cross Road every so often. how often they do so will depend on where they live, income and occupation. So, unless we all start behaving in a standardized way, we will all have different bumping-into frequencies for different (fuzzy) categories of people.

To answer my question, though, Mike Leigh seems like a good bumping-into benchmark, and an ideal subject for mark and recapture. He is random yet recognizable. I am not stalking him. I do not know where he lives, and, apart from being in central London, little connects the three locations in which I have spotted him. Apart from liking Japanese prints (or was it Renaissance illuminated manuscripts?) I would guess that we have little in common. If I were clever at maths I would use the parameters of my encounter rate, movement patterns and the population size of London to draw a curve plotting the probability of seeing him against time. But I'm afraid this is quite beyond me. So as it is, if you're reading this, Mr Leigh, I'll see you in 2008.

The British Ecological Society, and why ecology is unpopular

Last Tuesday (the 5th) I went to Oxford, to spend a day at the British Ecological Society's annual meeting.

A couple of things caught my attention: a talk (the 12.30 slot on this page) by Mairead Maclean of Exeter University, modelling the effect that domestic cats have on sparrow populations. If I remember this rightly, her study found that, in the area of rural Cornwall that she studied, a level of 80 cats per square kilometre would be enough to send the population into decline, whereas the actual level was 93. So it looks as if we might be able to convict cats of being one of the causes of the mysterious disappearing sparrows. She didn't think there was much cat owners could do about it — it seems to be a few cats doing most of the killing, with young and female cats being more avicidal than old and male cats.

The other thing, just 'cos it was related to the whole metabolic ecology, was a talk (the 16.00 slot) by David Coomes of Cambridge, looking at whether metabolic models can explain the size structure — how many big trees and small trees there are in a given area — of forests in New Zealand (this is also known as self-thinning). His conclusion (which was also reached by Muller-Landau et al., working on Sri Lankan forests) was that they can't.

This is not (as far I could tell — I may be misinterpreting here) because the view that metabolic rates influence population density is wrong, but because other things overlay the effects of metabolism, namely that old trees are more likely to die from getting blown over, disease etc., and young ones are more likely to die from being shaded out by big trees. This means that mortality is lowest for middle-sized trees (the graph of size against death risk is U-shaped), whereas (I think) metabolic models predict that mortality risk rises with increasing size.

But on the whole, I was surprised, looking at the meeting programme, by how little either grabbed me by the throat or seemed like it would make a good story, science-journalism wise. Nothing wrong with that, of course — the meeting's not set up for my benefit. But it got me thinking about why there is so little popsci on ecology. Here are some suggestions…

First, ecology is hard. Understanding the questions asked by people tackling say, the spatial and temporal patterns shown by forest tree species, or the influence that food-web structure has on ecosystem stability (to give two examples discussed at the BES), takes a bit of effort, but is not too hard.

Understanding the answers they come up with is a lot harder, particularly as the answers often seem to be uncertain, qualified and localized. Also, these ideas, as with most in ecology, do not have obvious parallels form everyday life, unlike, say animal behaviour, where the parallels between animals and humans are an ever-present reference point.

This complexity and unfamiliarity is also true of particle physics and cosmology, but people are probably more willing to wrestle with trying to understand the big bang, or quarks, because the ideas have more grandeur than, say, understanding the population dynamics of flour beetles. I enjoy quantum entanglement as a mind-blowing spectator sport, without really understanding what on it's all about.

Also, everyone asks her- or himself how the universe began, how the world will end, and so on, so such science taps into a pre-existing market. People love nature, but, I'd suggest, their relationship with it is less philosophical, more sensual and domestic. We marvel at the flowers in a meadow, but most of us don't ponder why the field contains that particular number of species.

Also, unlike animal behaviour, palaeontology or cosmology, ecology is not a narrative science — the work is hard to tell in the form of a story, cause and effect, and so on. One is asking why things are as they are, often trying to find an explanation that doesn't rely on history, rather than how they got that way.

And apart from conservation (in the widest sense, including fisheries, agriculture etc.), there are not many issues that seem to matter to people's everyday lives. And rather a lot of ecology — probably most — has nothing to do with conservation, it's folks trying to work out how the living world is put together. (Nothing wrong with that, of course, and nothing particularly unusual — most genetics isn't going to find a cure for cancer or inherited diseases, although geneticists are good at selling their research as if it might.) In fact, earlier this year the BES had to cancel a meeting on the links between ecology and sustainable development owing to lack of interest. Ouch.

This might come as a surprise, but then perhaps another problem is the very word 'ecology' which people tend to think is a Good Thing that is something to do with having a nice environment: pollution, energy generation etc. (The UK Green Party used to be called the Ecology Party, for goodness' sake. I don't believe density-dependent mortality was high on their list of concerns.) As far back as 1979, Stephen Jay Gould was lamenting (in an NYRB essay about Evelyn Hutchinson, I'm afraid I can't find the exact quote right now) that the word was so debased that its scientific sense had become meaningless to non-scientists.

So how to write about ecology? I've found that using people's stories and biographies can be a good springboard to writing about their ideas and work. I've also found that writing about the roots and origin of a question can lead one into writing about contemporary issues — particularly as most of the oldest questions in ecology are still unresolved. (This isn't such a revelatory solution, I know.) But this doesn't really help when one is sniffing round a conference for a 400-word news story.

How inordinately fond?

Reading a piece on Slate by Jordan Ellenberg about the proof of the Poincaré conjecture (something to do with the geometry of spheres), this caught my eye…

The entities we study in science fall into two categories: those which can be classified in a way a human can understand, and those which are unclassifiably wild. Numbers are in the first class—you would agree that although you cannot list all the whole numbers, you have a good sense of what numbers are out there….

In the second class are things like networks (in mathematical lingo, graphs) and beetles. There doesn't appear to be any nice, orderly structure on the set of all beetles, and we've got no way to predict what kinds of novel species will turn up. All we can do is observe some features that most beetles seem to share, most of the time. But there's no periodic table of beetles, and there probably couldn't be.

Mathematicians are much happier when a mathematical subject turns out to be of the first, more structured, type. We are much sadder when a subject turns out to be a variegated mass of beetles.

Nicely put. But beetles — and biodiversity — are not such a tangled, unknowable mass as you might think. For example, for trees there is a power-law relationship between number of species found in a place and the number of higher groups — genera and families (which are often seen as fairly arbitrary groups constructed for human convenience). Generally, there are also patterns in the relative diversity of different groups — crudely put, most higher groups contain only a few lower taxa (i.e. species), but a few are fantastically diverse. Beetles are one of these — they are often called a ‘hyperdiverse’ group (nematode worms have also been labeled such).

Hyperdiverse groups take up a large chunk of the diversity within their taxonomic level, and are found at all levels: so insects are a hyperdiverse group of animals, beetles are a hyperdiverse group of insects, and the chrysomelidae are a hyperdiverse group within the beetles. (There are also similar patterns in relative abundance — crudely put, most species are rare, a few are very common.)

Of course, describing a pattern isn’t the same as explaining it, and what’s still missing are theories (or at least, theories that most people agree on) that show why these patterns in nature are as they are, and whether they have to be like that. That’s one of the things that my book is about.

Latest reviews

I reviewed two books on human paleontology and evolution for the July issue of Discover. They were: The First Human, by Ann Gibbons, and Before the Dawn, by Nicholas Wade.

Diversity's hidden iceberg

Many of us keep a list of the bird species that show up in our back gardens, or the types of fungi in our local wood. The species is perhaps our most simple, fundamental, and useful tool for describing the living world. But it's a more slippery concept than it might first appear — and the harder one looks, the more slippery it becomes.

Take, for example, the hoverfly Microdon mutabilis. The flies' larva infiltrates an ant's nest — probably by chemically mimicking its host — and spends two years eating ant eggs and larva before pupating. In 2002, entomologist Karsten Schönrogge of the Centre for Ecology and Hydrology in Dorset (soon to be closed by the UK government) and his colleagues showed that M. mutabilis was in fact two species, each specialized to parasitize a different species of ant.

Now, Schönrogge's team have found that the fly's diversity is still finer-grained. Working on the Scottish island of Mull, they moved eggs of M. mutabilis from the ant nests in which they were laid to different nests of the same species.

Almost no eggs survived a move of more than three kilometres. Ants from a different neighbourhood were able to recognize and destroy hoverfly eggs before the larvae could gain entry.

So the species that we have called Microdon mutabilis seems, in fact, to be many populations closely adapted to their local ant hosts, and unable to survive elsewhere. As the fly is found from Ireland to Japan, the one name may conceal a mind-boggling number of cryptic fly species.

This kind of extreme specialisation, and the diversity that comes with it, is especially likely to evolve in parasites, which must trick their hosts into accepting their malign embrace. Faced with overcoming the host's powers of detection, natural selection will hone the parasite's powers of deception, until it may become so expert at exploiting one host that it closes off all its other options, and paints itself into an evolutionary corner.

Microdon, however, might have a trick up its sleeve. It prefers to eat small larvae or eggs. This causes the ant's brood to become biased towards large larvae. These are more likely to be potential queens and males — the sexual forms that found new colonies. And so the hoverfly might be able to promote the reproduction of the colonies that it infests, and ensure a new supply of susceptible hosts.

In general, the smaller you get, the vaguer our notions of biodiversity become. We have a pretty good idea of how many species of bird and mammal there are, and what a species of bird is. But we have almost no idea how many different types of insect, fungi or microbe there are, or how we should classify them. DNA sequencing is revealing yet another world of diversity, that biologists are unsure how to reconcile with their more traditional categories.

Our understanding of what diversity is, and how much of it there is, also has practical implications. Microdon is listed in the Red Data Book as being of conservation concern. But what should we be trying to conserve? The species as a whole? Individual populations? And how should we conserve it? It certainly doesn't look as if one could move hoverflies from one place to another.

The hoverfly is a small example of how important it is to keep the fabric of life intact. It's not even that we won't know what we've lost until it's gone. Even then, we still won't know.

An MRI scanner darkly

I've got a feature in the 22 June issue of Nature about some neuroscientists useing Richard Linklater's films to probe how the brain responds differently to realistic and meaningful, but obviously unreal stimuli.

Raymond Mar and his colleagues used Linklater's 2001 film 'Waking Life', an movie made using a technique called rotoscoping, which involves turning video footage into animation. The researchers sat their subjects in a brain scanner and showed them clips of the original video footage, and then the animated version of the same shot.

They were particularly interested in the brain areas involved in attributing motives to others, and trying to work out what they are thinking and planning on doing. We will attribute intentionality to almost anything - characters in books, cartoons, a malfunctioning computer. But it seems, Mar's team found, that the brain areas involved fire more strongly when the stimuli are more realistic. But no one is quite sure why, or what this means.

The piece also looks at how our brains cope with the reality/fiction divide more generally, and the psychology of narrative. It seems the the suspension of disbelief is a myth, and that, as long as information comes in the form of a story, we are ready to believe almost anything.

One of the reasons I wrote this now is that Linklater has another rotoscoped film out next month, A Scanner Darkly, based on the Philip K. Dick novel. Dick, of course, was well into the untrustworthiness of our brain's picture of reality.

100 conservation questions

Everyone loves a list, including ecologists. And some of the bigwigs of British conservation have now released one with the snappy title of " 100 ecological questions of high policy relevance in the UK".

The list is grouped by topic rather than importance, which will make the five-hour special on Channel 4 less interesting. There are 14 categories, such as forestry, urban development, and invasive species. Questions include: 21. Why have many woodland birds declined? 32. What are the impacts of recreational activities on biodiversity?, 67. How can soil carbon be retained and further carbon be sequestered in the soil?

The authors acknowledge that these are rather vague. This, they say, is the product of input from policymakers, because policy is typically focussed on quite general questions. The challenge for researchers is to derive meaningful specific research projects to address these (I wonder if framing grant applications in terms of this list will help people get funding) and, conversely, to stress what can be generalized from their own tightly focussed projects.

One hundred questions seems to me rather a lot — a shorter list would have been easier to get one's head around, and so perhaps more galvanizing. But these 100 were boiled down from a longlist of 1,003 (!), so perhaps we should be grateful.

The lead author is Bill Sutherland, of the University of East Anglia, who is working hard to promote what (with reference to medicine) he calls ' evidence-based conservation': i.e., making sure that conservation practices are tested, and that they work, rather than doing things just because they're traditional, or seem like a good idea.

You'd be surprised how little we know about whether conservation strategies work or not. I touched upon this earlier this year in a Nature piece on farmland biodiversity called "How green was my subsidy?" [subscription required].

Billions of euros of EU money are spent each year on agri-environment schemes, but many have no clear goals and are not monitored. When people look at whether they do enhance biodiversity, about half seem to have no effect. It would be a mistake to be down on these subsidies as a whole, though — they take many approaches, and have many goals, and some undoubtedly do work. An international project called AE footprint is currently trying to work out how to evaluate them.

How about a global version of the same list (perhaps there already is)? My guess would be that understanding hotspots and carbon sinks and sources would feature large.

Sensible sheep, and cheeky monkeys

A couple of things in the most recent Animal Behaviour caught my eye.

One, Sheep self-medicate when challenged with illness-inducing foods, by Juan Villalba and colleagues, found that lambs can learn which compounds will relieve a stomach ache brought on by, say, tannins. Then, if given the same tannins in the future will choose the appropriate remedy.

I’d put this down in the cute, but not earth-shattering category. Villalba and co write that:

“From prehistoric times, people have looked to the presumed self-medicative behaviour of animals for remedies of ailments but it is still not clear whether animals seek medicinal compounds to recuperate from illness. Evidence of self-medication is based almost exclusively on observations rather than experimental analyses.”

On the other hand, there’re already whole books on animal self-medication.

The other is called Rhesus monkeys, Macaca mulatta, know what others can and cannot hear, by Laurie Santos and colleagues. The researchers set up an experiment where the monkeys competed for grapes with a human experimenter. The monkeys had a choice between picking grapes from a noisy container, and from a silent one.

If the human was looking in the other direction, the monkey preferred the silent container, presumably showing it was out to sneakily get the grape. If the human was paying attention, the monkey didn’t care which container it took — showing that the monkeys understand the connection between hearing and knowing. This also hints that they have theory-of-mind type notions of what others are thinking.

Seals go from the arctic to Siberia. But how?

Lake Baikal in Siberia and the Caspian Sea each has its own species of seal that evolved from marine species a few million years ago. But which species they evolved from, and how they got there, has remained controversial. A new study by Jukka Palo and Risto Vainola at the University of Helsinki challenges existing ideas, and adds new mysteries.

It was previously thought that the Baikal seal Phoca sibirica and the Caspian seal P. caspica were most closely related to the Arctic ring seal P. hispida. But analysing mitochondrial DNA sequences, the two Finns find that the Caspian seal is in fact more closely related to the grey seal Halichoerus grypus, and that several other seals, including the boreal harbour seal, are just as, if not more closely related to the landlocked seals than the Arctic ring seal. It looks as if a bunch of species evolved in a bit of a burst, and that the old triad of Caspian, Baikal and Arctic ring seals — the three species were lumped together in their own sub-genus — does not reflect evolutionary history.

The DNA suggests that the two landlocked seals evolved in the Arctic Ocean about 2-3 million years ago (although DNA dates are controversial), in the Late Pliocene. This raises another problem, of how the seals could have made their journey from the Arctic to their current homes. Previous hypotheses suggested that the seals got to the Caspian first, and then spread out, or hopped across the continent in glacial lakes during an ice age. But the DNA doesn't fit with the paleoclimate data. We have no idea what water features may have existed at this time that let the seals' ancestors make the journey south.

Quick update

Since I last posted I've had a short piece on turtle conservation in Science Now (Green turtles make a comeback) and a longer piece on conservation, agriculture and subsidies in Nature (How green was my subsidy?). I'm going to be regular now, I promise.

A rotten theory

Why don't we like mouldy food? It seems like a no-brainer, but why, in fact, should most foods become unpalatable when colonized by microbes? The existence of Roquefort, after all, shows that mould does not always equal bad food.

1977, Dan Janzen suggested that microbes spoil food so that they can keep it for themselves — it's a trick that helps them compete for resources with animals, and avoid being eaten themselves. It's not just humans that prefer fresh food to rotten — birds do to, given the choice.

The idea has attracted a lot of favourable comment from researchers, but, say Tom Sherratt and his colleagues in Ecological Modelling, it has never been properly analysed. They have done this — and it's not good news for Janzen's idea.

Sherratt's team present a mathematical model that shows that if producing chemicals that spoil food is costly, then the microbes that do it will be displaced by free-loaders, that take the benefit of living on spoiled food, but don't pay the cost.

The 1970s (around the time the Selfish Gene came out) were a bit of a golden age for ideas like Janzen's, that propose for ingenious adaptive explanations for biological phenomena. It's surprising that no one got around to putting the idea through the theoretical wringer before now, but not so surprising that the idea hasn’t stood up to close analysis, because freeloaders are probably a powerful force against group behaviour of this sort.

If all the microbes in a group belong to a genetically identical clone, then spoiling might work, but Sherratt and co suggest that microbes move around too much for clones to maintain their integrity. (Entirely tangentially, for my PhD I worked on a similar problem regarding the evolution of altruism, in the form of soldier behaviour, in aphids.)

The researchers suggest, more prosaically, that spoiling chemicals might be used in competition between microbes sharing a food source, or they might just be a by-product of the process of decomposition.

Big botany

Two papers on plants caught my eye this week. The first is from Nature on the scaling of plant metabolic rate. Peter Reich and his colleagues say that plant respiration increases linearly with plant size — that is, a plant has a metabolic rate twice that of one half its size.

This seems to contradict the West, Brown and Enquist (WBE) model of metabolic rate, which says that metabolic rate in all organisms is proportional to the 3/4 power of body mass — so a plant would have a metabolic rate only about 1.7 times that of one half its size.

Whether this is true, and whether the WBE model is the right way to explain metabolic rate, is controversial. I think that there is good evidence for what's known as quarter-power scaling over a wide range of plants and animals, and I also think that the WBE model makes a lot of sense (but then I've written a book about all this, so I would say that). But these things take decades to sort out, so there will be a lot of to-ing and fro-ing between both sides before any hard consensus emerges. Don't expect the quarter-power people to give up their ideas in the face of this new evidence.

The other paper deals with another big issue in ecology — what maintains the high diversity in tropical forests? Writing in Science, a massive team of ecologists led by Christopher Wills present evidence from forest plots in Panama and Malaysia showing that rare species are more likely to survive than common ones — an advantage that buffers against extinction.

The team don't seem to plump for a reason as to why this should be. One possibility is the Janzen-Connell hypothesis, which says that mature trees attract pathogens, herbivores and so on that make it harder for seeds of the same species to germinate in the vicinity. Another possibility stems from the fact that all species compete most strongly with other members of their own kind — because their needs are so similar — than with other species, and that this competition is weaker for rare species.

I am reading Jonathon Silvertown's new book on plant ecology, Demons in Eden at the mo. He has an excellent discussion of these issues that comes down in favour of the J-C view of things. I don't think things are as clear cut as all that, but there does seem to be good evidence that the process is important in forests.

Darwin, Homer and Austen

I've got a piece in this week's Nature called "Textual selection" that looks at the newish field of Darwinian literary theory (registration required — see here for a summary). These guys (mostly) want to chuck out Freud, Marx et al, and interpret texts from a Darwinian perspective — mate choice, kin selection and all that. It was interesting speaking to non-scientists (including the author Ian McEwan), and try to get my head around someone else's issues and arguments for a change.

These folk think like scientists — they want to make testable hypotheses, collect data, get robust answers, move on. This is very different to a lot of literary criticism, which is also about kicking ideas around, as kicking them out. Many literary critics seem to read Freud, or Marx or Derrida, as if it was a novel, rather than anything with a claim to objective truth — whether an idea is stimulating is as important as whether it is true.

This has got a bit of coverage recently. For more, try here, and here to read Mark Lawson slagging whole idea off in the Guardian. The NY times also had a big piece, but it seems to be subscriber-only now.

Did viruses invent DNA?

What with the threat of bird flu, the reality of HIV, and the general unseemliness of having one's cells pressed into labour on behalf of something alien and microscopic, it is small wonder that people don't much like viruses. But it's possible that we may actually have something to thank the little parasites for. They may have been the first creatures to find a use for DNA, a discovery that set life on the road to its current rich complexity...

This feature in Nature (by me; registration required) looks at Patrick Forterre's idea that viruses invented DNA as a way of invading cells in the RNA world — just as many viruses today use similar genetic tricks to evade cellular defences. It's a neat idea, and raises the useful question of what the original advantage of DNA might have been. It is more chemically stable than RNA (which biologists think came first) and can be used for longer genomes.

But, Forterre points out, no cell could know that it wanted a longer, more complex genome and evolve DNA accordingly, because evolution has no foresight. Not everyone agrees, but there is a lot of excitement about viral diversity and evolution at the moment - there's some crazy stuff out there, virus-wise, much of it currently being discovered by David Prangishvili.