Father and son

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

We are family

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

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

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

Just Science day 3: The H. pylori story

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

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

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

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

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

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

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

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

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

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

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



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

My new £16,000 habit

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

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

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

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

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

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

How many pictures of leopards does the world need?

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

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

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

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

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

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

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

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

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

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