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.

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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.