Ed Yong, Science Writer

In a cauldron of boiling, acidic water, kneeling at the foot of a Russian volcano, one species of microbe is on the cusp of becoming two.

Sulfolobus islandicus is an archaeon – one of many single-celled microbes that thrive in extreme environments. Mutnovsky volcano is certainly one such place. Found at the far eastern end of Russia, it’s full of churning, scalding springs that are nonetheless teeming with microscopic life. S.islandicus thrives in these springs, feasting on the sulphur within the water.

Now, Rachel Whitaker from the University of Illinois has found that the species has pretty much split into two separate lineages. Both share the same water, and they can trade genes with one another, but they have started to part ways and are becoming increasingly distant. In this hot, hostile and acidic world, the origin of the species is playing out before our eyes.

Whitaker collected 12 strains of S.islandicus from one of the Mutnovsky springs, sequenced their complete genomes and charted their evolutionary relationships. They were remarkably similar. At most, any two strains differed in just 0.35 per cent of their genome – far less than the distance between your DNA and a chimp’s.

But the differences were telling. They revealed that the archaea had split into two distinct populations, which Whitaker called the Red and Blue groups. They look the same but they behave differently. The Red strains grow more readily, more quickly, and into denser colonies than the Blue ones.

Microbes like bacteria and archaea can swap genes with great ease, through their version of sex. They’re very promiscuous about it too. Indeed, some scientists have suggested that archaea trade genes so frequently that the very concept of species is irrelevant to them. They don’t subscribe to the neatly branching tree of life that Darwin envisaged. Instead, they’re part of a tangled bush, a thicket, a net.

Not so fast. Whitaker found that her Red and Blue groups were indeed trading DNA, but genes were flowing far more within each group than between them. There was a genetic barrier between them – leaky, sure, but there nonetheless. And it’s closing up. Recently, the Blue group has been donating less and less DNA to the Red one.

The differences in their DNA aren’t building up evenly throughout their genome. Instead, they’re building up unique sequences in three large genetic “continents”, which are changing faster than the oceans of similarity in between. These continents are rich in metabolic genes which allow the microbes to break down the chemicals around them. And that provides a clue about why the same microbes living the same place are dividing into two groups.

It’s easy to imagine how one species can become two, when different populations are separated by a physical barrier, like a mountain or a river. Unable to meet or mate, their genes are free to change along independent lines. The classic example is the separate fates of the Galapagos finches, each one stuck on a different island.

But populations can often split into different species even though they share the same space. They could be separated in time, never encountering each other even though their addresses are the same. They could come to speak separate languages, and split because of a failure of communication. They could develop opposing sexual preferences. Or they could specialise on different lifestyles within the same location. That final option seems to be what S.islandicus has done. Whitaker thinks that they have adopted slightly different ways of life within their shared world.

Reference: Cadillo-Quiroz, Didelot, Held, Herrera, Darling, Reno, Krause & Whitaker. 2011. Patterns of Gene Flow Define Species of Thermophilic Archaea. PLoS Biology http://dx.doi.org/10.1371/journal.pbio.1001265

More on speciation:

New plant species arise from conflicts between immune system genes

How diversity creates itself – cascades of new species among flies and parasitic wasps

Giant insect splits cavefish into distinct populations

Discriminating butterflies show how one species could split into two

British birdfeeders split blackcaps into two genetically distinct groups

One generation, new species – all-female lizard bred in a lab

In African rivers, an electric Tower of Babel

As of this week, I’m starting a new column over at the BBC, as part of their new science and technology super-site. The goal, based on feedback from the BBC’s readership, was to create a space for deeper, richer sources of science writing to complement their typical news pieces. Regular readers of this blog will know that this is a goal that I have a lot of time for. There will be lots of features, and some regular columns. I’m providing one of the latter.

So the column is called “Will we ever…?” The goal is to take far-flung and possibly optimistic applications of basic scientific research and look at the steps and obstacles between now and then. You know that sentence in the fourth or fifth paragraph of most science news pieces? The fluffy one that says, “This discovery could eventually lead to [insert optimistic distant application here]”? This column will expand that sentence into a thousand words.

The first two columns on decoding dreams (up now) and growing new organs (on Friday) illustrate what I want to do with the column. Decoding dreams seems like a relatively straightforward topic but it is fertile ground for exploration. It’s really about the limits of our brain-scanning technology, our ability to understand how the brain processes images, concepts and more, and what makes dreams special. Growing new organs is something we’re doing right now, but I wanted to look at what it takes to do this, where we are technologically, and which organs present the greatest challenges.

In both cases, the leading question could be answered in a simple word: no and yes, respectively. But, as with the topics themselves, the point is in how the question is answered rather than the answer itself. The title provides a nice hook but it could equally be “How will we ever…” or “What’s taking so long for…”

I’m still feeling my way around what topics make for interesting columns. They can’t be too big or the piece will be too shallow (so “cure cancer” is out), and as per the editorial mandate, they have to be of broad interest or importance. But really, the main criterion is that the path to the answer (or the obstacles on that path) should be interesting in specific ways. If you have any suggestions of interesting questions, please feel free to share them.

There is a final and unfortunate catch. I can’t actually read the site. Nor can anyone from the UK. This is the message I get:

We’re sorry but this site is not accessible from the UK as it is part of our international service and is not funded by the licence fee. It is run commercially by BBC Worldwide, a wholly-owned subsidiary of the BBC, the profits made from it go back to BBC programme-makers to help fund great new BBC programmes.

I have absolutely no idea why this means that I can’t read the site at all, but c’est la vie. If this seems crazy to you, I’m not going to disagree. Here’s a hilarious workaround. Meanwhile, the compromise I’ve reached is that I get to republish the column here with a three-day delay.

In the desert of the United Arab Emirates, there is an unusual series of flat discs imprinted in the sand.  Each one is about 40 centimetres wide, and they snake off into the distance in several parallel lines, for hundreds of metres.

They are tracks. They were made by a herd of at least 14 early elephants, marching across the land between 6 and 8 million years ago. The track-makers are long dead, but in the intervening time, nothing has buried their tracks or eroded them away. Today, their social lives are still recorded in their fossilised footsteps.

The site, known as Mleisa 1, provides the oldest evidence for proboscideans – elephants and their close relatives – living in a herd. Covering the area of seven football fields, it’s also probably the largest fossil trackway ever discovered, for any animal. When these beasts strolled across the landscape, the entire area would have been cut through by a river system. Rather than the dry sand of today, it would have been lush and green.

“It’s really an amazing site,” says Brian Kraatz from the Western University of Health Sciences, who was involved in the study. “I wish we had the ability to transport people there so they can stand in the middle of it at sunset. You can’t help but find yourself looking around to see if you can catch a last glimpse of the herd trotting off.”

There are many fossils of prehistoric elephants that show how their bodies evolved from smaller ancestors. But elephants are much more than just tusks and trunks. They have rich social lives, full of empathy, and their behaviours haven’t fossilised as well. We know that some elephants, like the mammoth and mastodon, spent some of their time in groups, thanks to the occasional trackways and mass graves.  But the Mleisa 1 site offers much clearer evidence.

Studying it wasn’t easy. The site is too massive to photograph from the ground, but the individual prints are too small to show up on satellite images. To accurately map the trackways, Nathan Craig from Pennsylvania State University attached a small pocket camera to a kite and snapped a set of overlapping images from above. He stitched the images together into a single large mosaic, which you can see on Gigapan. By calibrating the aerial mosaic with measurements taken on the ground, the team could study the herd’s footsteps from the air.

Faysal Bibi from the University of Poitiers (who worked on the Ardipithecus skeleton) says that the tracks include the footprints of at least 13 individuals, all marching in a straight line. They’re tightly spaced with very few intersections or overlaps, and small variations in direction. Together, they show a herd of early elephants jostling, interacting, and moving together. There was a mix of sizes and ages, as shown by the varying lengths of the animals’ strides and the sizes of their feet. One of them was probably a calf.

Meanwhile, the prints of a single large individual cut across those of the herd. At 260 metres, it’s the longest continuous fossil track ever found. Judging by the size of the prints, this loner was likely an adult male. He was moving in a fairly straight line, and at a slower and steadier speed than the herd. And he probably never met them, for his track was laid down at a separate time.

Together, these tracks suggest that these ancient elephants were both social and solitary, much like today’s representatives. Modern elephants form stable families, led by the eldest female – the matriarch. The males, which are larger, are raised by the families until they reach adolescence. Then, they strike out on their own., only rejoining a herd when it’s time to find a mate. That’s what Bibi saw in Mleisa 1 – a herd of elephants of the same size as a modern family, and a large male who walked alone.

It’s not clear which specific elephant made the tracks, but it certainly wasn’t any of the three species alive today. The most likely candidate is an extinct four-tusked animal called Stegotetrabelodon syrticus. It was the most abundant proboscidean in the area, and the most likely one to be found in open country.

Reference: Bibi, Kraatz, Craig, Beech, Schuster & Hill. 2011. Early evidence for complex social structure in Proboscidea from a Late Miocene trackway site in the United Arab Emirates. Biology Letters http://dx.doi.org/10.1098/rsbl.2011.1185

Images: reconstruction by Mauricio Antón.

Fruits in my fruit bowl tend to rot into a mulchy mess after a couple of weeks. Fruits that are chilled in permanent Siberian ice fare rather better. After more than 30,000 years, and some care from Russian scientists, some ancient fruits have produced this delicate white flower.

These regenerated plants, rising like wintry Phoenixes from the Russian ice, are still viable. They produce their own seeds and, after a 30,000-year hiatus, can continue their family line.

The plant owes its miraculous resurrection to a team of scientists led by David Gilichinsky, and an enterprising ground squirrel. Back in the Upper Pleistocene, the squirrel buried the plant’s fruit in the banks of the Kolyma River. They froze.

Over millennia, the squirrel’s burrow fossilised and was buried under increasing layers of ice. The plants within were kept at a nippy -7 degrees Celsius, surrounded by permanently frozen soil and the petrifying bones of mammoths and woolly rhinos. They never thawed. They weren’t disturbed. By the time they were found and defrosted by scientists, they had been buried to a depth of 38 metres, and frozen for around 31,800 years.

People have grown plants from ancient seeds before. In 2008, Israeli scientists resurrected an aptly named Phoenix palm from seeds that had been buried in the 1^st century. But those seeds were a mere 2,000 years old. Those of the new Russian flower – Silene stenophylla – are older by an order of magnitude. They trump all past record-holders.

Svetlana Yashina from the Russian Academy of Sciences grew the plants from immature fruits recovered from the burrow. She extracted their placentas – the structure that the seeds attach to – and bathed them in a brew of sugars, vitamins and growth factors. From these tissues, roots and shoots emerged.

Yashina potted the plants and two years later, they developed flowers. She fertilised the ancient flowers with each other’s pollen, and in a few months, they had produced their own seeds and fruits, all viable. The frozen plants, blooming again after millennia in the freezer, seeded a new generation.

S.stenophylla is still around, but Yashina found that the ancient plants are subtly different to their modern counterparts, even those taken from the same region. They’re slower to grow roots, they produce more buds, and their flower petals were wider.

This is the first time that anyone has grown plants from seeds tissue deeply buried within permanently frozen burrows. But it’s not the first time that someone has tried. In 1967, Canadian scientists claimed that they had regenerated Arctic lupin from 10,000 year old seeds that had been buried by lemmings. But in 2009, another team dated those same seeds and found that they were actually modern ones, which had contaminated the ancient sample.

Mindful of this mistake, Yashina carefully checked that her plants were indeed ancient ones. She dated the seeds directly, and her results matched age estimates from other samples from the same burrow. The burrows have been buried well below the level that animals dig into, and the structure of the surrounding ice suggests that they have never thawed. Their sediments are firmly compacted and totally filled with ice. No water infiltrates these chambers, much less plant roots or modern rodents. There are a few pores, but they are many times narrower than the width of any of Yashina’s seeds.

This closed world provided shelter, a continuous chill, and an effectively dry environment, that allowed the fruits to persist. At subzero temperatures, their chemical reactions slowed to a crawl. Extreme age was no longer a problem.  A fruit’s placenta is also chemically active, and is loaded with several chemicals that might have protected these specific tissues against the cold.

But the burrows weren’t completely benign environments. The underground rocks contain naturally radioactive elements, which would have bombarded the seeds with low but accumulating doses of radiation. The ones that Yashina regenerated would have amassed 70 Grays of radiation – that’s more than any other plant has absorbed while still producing viable seeds.

S.stenophylla’s resurrection shows how many treasures lie buried within the world’s permafrost. This soil, defined as that which stays below freezing for two years or more, covers a fifth of the planet’s land. It is home to bacteria, algae, fungi, plants and more. In the fossil burrows that Yashina has studied, scientists have found up to 600,000 to 800,000 seeds in individual chambers.

In Norway’s Svalbard Global Seed Vault, scientists have frozen thousands of seeds in an underground cavern, as a back-up in case of agricultural crises. But nature has already produced similar frozen seed banks. Siberia, Alaska and the Yukon could act as one massive freezer, where ancient life has been stored, waiting to greet the world again.

Update: The lead author, David Gilichinsky passed away on 18 February, just two days before his final paper was published.

Reference: Yashina, Gubin, Maksimovich, Yashina, Gakhova & Gilichinsky. 2011. Regeneration of whole fertile plants from 30,000-y-old fruit tissue buried in Siberian permafrost. PNAS http://dx.doi.org/10.1073/pnas.1118386109

More on ancient plants:

2,000 year old “Phoenix” seed rises from the ashes

The 13,000-year old tree that survives by cloning itself

Some people drink alcohol to drown their sorrows. So does the fruit fly Drosophila melanogaster, but its sorrows aren’t teary rejections or lost jobs. It drinks to kill wasps that have hatched inside its body, and would otherwise eat it alive. It uses alcohol as a cure for body-snatchers.

D.melanogaster lives in a boozy world. It eats yeasts that grow on rotting fruit, which can contain up to 6 per cent alcohol. Being constantly drunk isn’t a good idea for a wild animal, and the flies have evolved a certain degree of resistance to alcohol. But Neil Milan from Emory University has found that alcohol isn’t just something that the insect tolerates. It’s also fly medicine.

Insects the world over are plagued by parasitic wasps. The wasps lay eggs in or on the bodies of other insects, turning them into living larders for their developing grubs. The grubs eat their hosts from the inside-out and eventually burst out of their dead or dying husks. It’s a grisly fate, but D.melanogaster can do something about it.

Milan raised some fly larvae on food that contained 6 per cent alcohol, and offered them to the wasp Leptopilina heterotoma. This species is a generalist that targets a wide variety of flies. He found that the wasps laid three times more eggs on teetotal flies than on boozy ones.  Maybe they were sickened by the fumes. Perhaps they detected a hostile environment for their grubs. Either way, among alcohol, the flies were less likely to become a wasp buffet.

Even if the wasps manage to lay their eggs, an alcoholic fly larva proves to be a bad place to grow up. Twice as many of the wasp grubs die if their hosts chow down on alcoholic food. Even those that survive fare badly. When Milan cut them out of the flies, he found that their internal organs were deformed, and they could barely move.

Normally, flies try to deal with wasp infections by imprisoning the unwanted grubs in special cells. But those that get a drink don’t bother. They don’t need a special defence – the alcohol does the job for them.

And the flies seem to know this. Milan found that infected larvae will actively medicate themselves. If given a choice between alcoholic and non-alcoholic food, larvae with wasps inside them will crawl towards the intoxicating meal.  And as a result, they’re more likely to survive their ordeal.

But these defences aren’t unbreakable. A different but closely related wasp – Leptopilina boulardi – only pursues D.melanogaster and it has evolved resistance to its target’s defences. This specialist can take more alcohol than its generalist relative L.heterotoma. It’s more willing to lay eggs on a fly that eats alcoholic food, and its grubs are better at tolerating an alcoholic environment.

This looks like yet another example of an evolutionary arms race, where parasites and hosts are locked in a cycle of ever-escalating counter-measures. Because L.boulardi targets a species that regularly encounters alcohol, it has evolved ways of coping with this defence.

And it’s possible that the larvae know this too. Milan found that infected larvae were more likely to seek out an alcoholic meal if they were infected by L.boulardi (the specialist) than L.heterotoma (the generalist). Alcohol does slightly harm fly larvae, so it’s only worth drinking it if it’ll do more good than damage. If the drink will kill a parasite, that’s a tick in the plus column. If the parasite is resistant, it might be better to stay teetotal and try another defence. (Alternatively, the wasp might be manipulating the fly away from a potentially life-saving medicine.)

The flies are far from the only animals to medicate themselves. Humans obviously do it. Chimps with worm infections in their guts will dose themselves up with the pith of the Veronia plant. Rainforest animals from tapirs to macaws will lick clay deposits to neutralise the poisonous chemicals in their diet. A few years ago, Michael Singer found that woolly bear caterpillars will actively eat toxic plants if they are infected by parasitic wasps.

There are hundreds of such examples, but Milan may have found the first one of animals using alcohol to control an infectious disease or a internal parasite. Whether other species, including ourselves, could do the same is currently anyone’s guess. Certainly, this guy might have found a stiff drink to be quite useful.

More: For a very different and delightful take on this study, see Rob Dunn’s post

Reference: Milan, Kacsoh & Schlenke. 2011. Alcohol Consumption as Self-Medication against Blood-Borne Parasites in the Fruit Fly. Current Biology http://dx.doi.org/10.1016/j.cub.2012.01.045

More on parasitic wasps and defences against them:

• Sex increases risk of being paralysed, buried, eaten alive (for locusts)
• Beetles turn eggs into shields to protect their young from body-snatchers
• Wasps, ladybirds and the perils of hiring zombie bodyguards
• Body-snatching, not socialising, drove the evolution of bigger-brained insects
• The wasp that walks cockroaches
• Wasps use genes stolen from ancient viruses to make biological weapons
• Parasitic wasps hitchhike on butterflies by smelling for chemical chastity belts

“I can see its tail,” says David Attenborough, perched on a small boat. “It’s coming up… it’s coming up! There! The blue whale!” Ever since I first saw The Life of Mammals, I’ve always remembered Attenborough’s joy at seeing the “largest animal that exists or has ever existed”.

I now know how he felt.

On Monday, off the southern coast of Sri Lanka, my wife and I had the privilege of seeing five blue whales.

And not just a gray bump in the far distance, as with many whale-watching trips. Two of them swam within 30 metres of the boat, which, as it happens, is about a blue whale’s length away. They stuck around too, getting closer and closer and gracing us with several minutes in their company.

You cannot talk about blue whales without launching into a litany of breathless stats (see blue whale facts at the bottom). Thirty metres in length. 180 tonnes in weight.  Able to eat half a million calories in a single mouthful. A heart the size of a small car. A major artery so big that a child could fit in it. It’s so big that the so-called “pygmy blue whale” – the Indian Ocean subspecies that we most likely saw – is so-named because it only grows to 24 metres in length.

But there’s a difference between reading the numbers and seeing one in the flesh.

The first sign of a blue whale is the spout of water that issues forth from its blowhole when it surfaces to breathe. The spout is 9 to 12 metres tall – easy to spot from a distance. The whale stays at the surface for a few minutes, taking repeated breaths. One of the animals we saw did a couple of rolls, possibly to clean itself. Here’s one half of its tail.

Then, it dives. That’s when you really understand. As its head angles downward, and its arching back breaks the surface in a smooth roll, it just keeps on going. And going. And going. By the time the tail comes up, you start to wonder if this animal is ever going to actually end. Once it’s gone, it’ll stay that way for around 8 to 10 minutes, swimming 100 metres or so below the surface in search of krill. You check your watch, and 8 to 10 minutes later, you scan the horizon again for that spout.

To give you an idea of the animal’s size, the photo above has one next to a tourist boat. That tiny dorsal fin lies near the tail, about three-quarters down the whale’s body. You see it when the whale dives. So, if you imagine a massive tail in line with the back of the boat, there’s still a huge amount of whale pointing downwards. Most of its head is well out of the frame of the photo.

We sailed with Mirissa Water Sports, the first company to run whale-watching trips in the area and still the best. It’s an offshoot of the Build a Future Foundation, which tries to provides opportunities for young Sri Lankans in areas that had been devastated by the tsunami of 2004.

Sri Lanka has only recently become a hot whale-watching destination, largely thanks to British marine biologist Charles Anderson. Around a decade ago, Anderson hypothesised that blue and sperm whales migrate from the Arabian Sea to the Bay of Bengal, passing by the south coast of Sri Lanka on their way. The frequency of sightings ever since seems to confirm his idea. At the time of our trip, the crew had seen blue whales on all but one day in February.

But don’t be deceived by the regular sightings: these magnificent animals are endangered. Counting such an elusive animal is obviously tricky, but the IUCN puts the global total at somewhere between 10,000 to 25,000 individuals. That’s between 3 and 11 per cent of their numbers in 1911.

Hunting took a big toll on the whales, but it has now been banned internationally. Still, there are other threats. Large ocean vessels sometimes collide with the whales, and their noise might make it harder for the animals to communicate. Here’s a final photo to remind us of how closely the paths of humans and blue whales often intersect.

Some blue whale facts:

• Blue whales are so big that each one can grow as large as a fully grown blue whale. That’s huge!
• If you take all the blue whales in the world and put them on a giant weighing scale, you are on drugs.
• A blue whale’s heart is the size of a Volkswagen beetle, but its steering is rubbish.
• If you take a blue whale’s intestines and lay them in a line, what’s wrong with you, you sick bastard?

Top picks

The second science-of-mysteries tryptich by Deborah Blum, Jennifer Ouellette, and Ann Finkbeiner

Top 10 reasons Erik Klemetti loves volcanoes, and you should too

Oxytocin is not a “love hormone”. It’s much more complicated than that. My new feature for New Scientist – you’ll need to register, but it’s free.

Woman gets a jaw transplant. Her jaw was printed with a 3-D printer

A long feature from Atlantic Magazine about Toxoplasma gondii’s sway over us. I’m not entirely convinced by the personality changes stuff but this is a good read.

Two rival features on the same story – the Zanesville zoo break – in GQ and Esquire. Compare and contrast.

Carl Zimmer profiles the aptly named Joy Reidenberg, arch-dissector from Inside Nature’s Giants

Here’s a song that hasn’t been heard for 165 million years – the reconstructed call of a Jurassic cricket

Marvellous parody paper about neuropsychoanalysis and fMRI, via NeuroSkeptic

Wonderful. 10-yr-old girl discovers new molecule by pissing around with modelling kit, gets published

“When it comes to viruses can we really calculate ratios of costs to benefits?” – Carl Zimmer on the bird flu controversy

A superb mini-profile of the animator behind those bizarre Taiwanese CG news videos by Eliza Strickland

Maryn McKenna has a new feature on Robert Daum, a man who’s trying to make an MRSA vaccine.

What the mysterious death of a 3,500-year-old tree can teach us about impermanence & deep time

If not for a virus, none of us would ever have been born, by Carl Zimmer

Good read about “battle-hardened climate ninja” Michael Mann and the siege atmosphere of climate science

If a pill could erase your most traumatic memory, would you take it? Great feature by Jonah Lehrer

Storming piece from Emily Wilingham on the idea of Asperger’s as a non-disorder. Brings mother’s anger and scientist’s eye

“The exhaustive rendering of our… patterns into data sets” – Charles Duhigg on how companies learn your secrets

We’ve never seen this microbe before, but we have its entire genome. Amazing.

Robert Krulwich on two deaths: a poet’s and a beetle’s. Beautiful

Alex Wild tweets an insect photo that he took, discovers that he may have the only photo of a live member of the species and genus.

“Every elephant that has ever lived started off as a single cell” – Brian Switek on what happens afterwards

Kevin Zelnio’s heartfelt post about raising children without insurance in America’s ridiculous healthcare system.

Good piece by Maia Szalavitz on daft plans to medicalise normal grief

Science/news/writing

What ocean question do you want to see discussed in 2012? Here’s what some ocean scientists at Scio12 thought.

The peppered moth and the final experiment of Michael Majerus

America to collide with Asia… in 50 million years

The tragic fate of the Brighton octopus

Stretchiest spider silk ever

Extreme laboratories: what it’s like to work *inside* a glacier

“The brain is not made of soup. It’s not made of spaghetti either” – Neuroskeptic on the connectome

Tarsiers have secret ultrasonic communications

SciCurious on Nutt’s psilocybin paper: “nothing to address a mechanism… only a picture of your brain on drugs.”

Mini-chameleons, with the world’s saddest scientific name

How can you tell if you’ve hit an Antarctic lake?

Coeclacanths are not living fossils. Like the rest of us, they evolve

Blood of cockroach -> fuel cell

Kate Clancy talks about common myths about menstruation

Alice Bell on debates, climate and otherwise: people with polarised opinions are often least interesting

Is a blood test for depression possible? Or useful?

“What’s clear is that menstrual blood is not exactly a preferential food for black bears.”

Hack your mouth microbiome to get rid of cavities?

From the Yeahbutwha? Files: polar explorers lured penguins with music to kill them for their vitamin C

Sure, let’s introduce elephants to Australia, a country where introducing wildlife has never gone badly

Spider webs are actually stronger as a whole when some of their threads are broken

Alzheimer’s protein seems to spread like a virus from neuron to neuron

Sociologists (and journals) behaving badly: pressure to cite superfluous papers

Jonah Lehrer on a fascinating molecule and the enduring mystery of persistent memories

Vote or nominate psychology findings you’d most like to see replicated

Is the Open Science Revolution For Real? By David Dobbs

Pigeons – feathered rats, or showcases of incredible diversity?

Fallout From Chronic Fatigue Syndrome Retraction Is Far and Wide

Here’s Petra Boynton with everything you wanted to know about penis size. And +1 for “cock quackery klaxon”

How artists remind us of the ocean’s fragility

Trial of drug delivery by wireless microchip shows promise.

We’re going to shove this earthworm-based robot into your anus. Okay?

To Boldly Go – a new blog on astrobiology at the Wired network.

Delusional pregnancy – as common among men as women

If you have a really big pile of manure, you really don’t want it to explode everywhere

Are zebras stripey to repel horseflies?

Good news: the tracks weren’t made by a giant frog! *cough*actuallyagiantseascorpionohlookisthatthetime*cough*

A gallery of creatures that say no to sex

Why We Can’t Just Get Rid of the Genes That Let Us Get Infected

“There was no way the blind mice could see, yet they could.” – Carl Zimmer on the sightless light detector in our eyes

Heh/wow/huh

“Dinosaurs are Jesus ponies” Google Autocomplete FTW

“Consider the perceptual challenges inherent in the robotic manipulation of unseen socks”

“The psychologist or psychiatrist shall wear a cone-shaped hat… imprinted with stars”

NASA releases alternative hi-res “Blue Marble” image for people who don’t want their planet centred on America

Onion: “Huffington Post” Employee Sucked Into Aggregation Turbine

Want free-to-use silhouettes of organisms? PhyloPic is here

“The false teeth disappeared inside the experimental nuclear power plant’s landmark sphere”

Heh. Loving Ben Goldacre’s approach to data visualisation

Want to nuke your house? There’s an app for that.

Rice Krispyhenge!

Shark eats shark

Art by animals (non-human ones), collated in a gallery by one specific animal – Brandon Keim

Corals aren’t just lumps of rock. They’re living animals. Here are some emerging after being buried in sand

Journalism/internet/society

The Atlantic gets more devastating internal docs from Susan Komen. Shorter version: lying

A brief history of blurbs (those short, sound-bite endorsements on creative works)

Embargoes and exclusives don’t mix: NYT story about Neuron study reveals a problem

‘Mobile nature reserves‘ could save marine species from extinction

Why is the African Savanna so full of thorns?

Science, history and London’s blue circles, by Alice Bell. Cool mini-photoessay

Why bullied teens don’t recognise “bullying” rhetoric

The nuclear power plant that never was… and is now a tourist attraction

It’s not easy getting science into women’s mags, as Hillary Rosner knows

Hey hey! I’m back from a wonderful 2.5-week holiday in Sri Lanka. It was tremendous, and the first proper no-writing, no-work break I’ve taken for well over a year. Your normal blogging and tweeting service will now resume, and photos (oh, so many photos) will emerge at some point. But for now, here’s some geekery for you.

This is the full list of what we saw on the holiday. I’ve never been to a country where the wildlife watching opportunities were so thick and easy. The first thing that I saw when I pulled back the curtains on my first morning was a criticially endangered monkey on my balcony. I walked out of a room one afternoon to get some tea and ended up photographing troops of Toque macaques and gray langurs, a mongoose, some water monitors and a giant squirrel. We did a boat trip where a pod of 150 or so spinner dolphins was only the third most exciting thing we saw in an hour (two green turtles mating, and five blue whales).

So, the list. The rules are that they have to be seen in the wild, not in a zoo or nursery, and we had to identify them to the species level (which explains why there are no invertebrates and why the flying fish we saw didn’t make the cut – 65 friggin’ species, are you kidding me?). The asterisks indicate the ones we have photos of.

Mammals

• Blue whale *
• Spinner dolphin *
• Spotted deer *
• Water buffalo *
• Wild boar *
• Indian flying fox *
• Asian elephant *
• Purple-faced leaf monkey (Western and Southern races) *
• Toque macaque *
• Grey langur *
• Black-naped hare
• Giant squirrel *
• Palm squirrel *
• Ruddy mongoose *

Reptiles and amphibians

• Green turtle *
• Star tortoise *
• Water monitor *
• Land (Bengal) monitor *
• House gecko
• Fourclaw gecko
• Kandyan gecko *
• Sri Lankan ratsnake
• Mugger crocodile *
• Sri Lanka bullfrog *

Birds

• Little shag
• Great cormorant
• Indian darter *
• Spot-billed pelican
• Indian pond heron *
• Cattle egret *
• Little egret
• Intermediate egret *
• Grey heron
• Purple heron *
• Painted stork *
• Asian openbill stork *
• Woolly-necked stork
• Black-headed ibis *
• Eurasian spoonbill
• Garganey
• White-bellied sea eagle *
• Brahminy kite *
• Grey-headed fish eagle *
• Crested serpent eagle
• Crested hawk eagle *
• Grey francolin
• Ceylon junglefowl
• Indian peafowl *
• White-breasted waterhen *
• Purple swamphen *
• Pheasant-tailed jacana *
• Black-winged stilt *
• Greater thick-knee
• Yellow-wattled lapwing
• Red-wattled lapwing *
• Common sandpiper
• Brown-headed gull
• Common tern *
• Spotted dove
• Emerald dove *
• Orange-breasted green pigeon *
• Imperial green pigeon
• Ceylon hanging parrot *
• Rose-ringed parakeet *
• Asian koel
• Greater coucal *
• Indian nightjar *
• Little swift
• Stork-billed kingfisher *
• White-throated kingfisher *
• Common kingfisher *
• Little green bee-eater *
• Blue-tailed bee-eater *
• Chestnut-headed bee-eater *
• Indian roller *
• Ceylon grey hornbill
• Malabar pied hornbill *
• Brown-headed barbet *
• Ceylon small barbet
• Black-rumped flameback *
• Crimson-backed flameback
• Barn swallow
• Ceylon swallow
• Orange minivet *
• Pied flycatcher shrike
• Red-vented bulbul
• Gold-fronted leafbird
• Oriental magpie-robin
• Pied bush chit
• Indian robin
• Asian brown flycatcher *
• Paradise flycatcher (Asian + Indian races) *
• Ceylon scimitar-babbler
• Yellow-billed babbler *
• Great tit
• Purple-rumped sunbird
• Loten’s sunbird *
• Black-hooded oriole *
• Brown shrike
• Philippine shrike
• White-bellied drongo
• Indian jungle crow
• Brahminy starling *
• Common myna *
• White-rumped munia

This post was originally published last year. I’m travelling for a few weeks, so I’m reloading some of my favourite stories from 2011. Normal service will resume when I get back.

In 1990, in a depressed area of Buffalo, New York, eleven schoolgirls were raped. According to George Kelling, a criminal justice scholar, eight of these incidents could have been prevented. After the third case, police knew that a serial rapist was on the loose but, even though they had a description and modus operandi, they issued no warning to local parents. They saw their job as catching the criminal rather than preventing more girls from being raped.

Kelling argued that the cops hadn’t wilfully neglected their duties. Their actions were swayed by their views of police-work, which were in turn affected by metaphors. They saw themselves as crime-fighters who trod the “thin blue line” protecting innocent civilians from criminal marauders. With this role entrenched in their minds, they saw their job as catching the rapist, even at the expense of preventing further crimes. As Kelling said, the eight Buffalo schoolgirls “were victims, though no one realized it at the time, not only of a rapist, but of a metaphor.”

As with all complex issues, crime is suffused with metaphors. One common frame portrays crime as a disease, one that plagues cities, infects communities, and spreads in epidemics or waves. Another depicts crime as a predator – criminals prey upon their victims, and they need to be hunted or caught. These aren’t just rhetorical flourishes; they’re mind-changing tools with very real consequences.

In a series of five experiments, Paul Thibodeau and Lera Boroditsky from Stanford University have shown how influential metaphors can be. They can change the way we try to solve big problems like crime. They can shift the sources that we turn to for information. They can polarise our opinions to a far greater extent than, say, our political leanings. And most of all, they do it under our noses. Writers know how powerful metaphors can be, but it seems that most of us fail to realise their influence in our everyday lives.

First, Thibodeau and Boroditsky asked 1,482 students to read one of two reports about crime in the City of Addison. Later, they had to suggest solutions for the problem. In the first report, crime was described as a “wild beast preying on the city” and “lurking in neighbourhoods”. After reading these words, 75% of the students put forward solutions that involved enforcement or punishment, such as calling in the National Guard or building more jails. Only 25% suggested social reforms such as fixing the economy, improving education or providing better health care

The second report was exactly the same, except it described crime as a “virus infecting the city” and “plaguing” neighbourhoods. After reading this version, only 56% opted for more enforcement, while 44% suggested social reforms. The metaphors affected how the students saw the problem, and how they proposed to fix it.

And very few of them realised what was going on. The two reports both contained the same “shocking” statistics about Addison’s crime rates. When Thibodeau and Boroditsky asked the students to say which bits of text had most influenced their decisions, the vast majority circled the numbers. Only 3% noted the metaphors.

Thibodeau and Boroditsky confirmed their results with more experiments that used the same reports without the vivid words. Even though they described crime as beast or virus only once, and without any verbs to continue the metaphor, they found the same trend.

Compared to students who read about crime as a virus, those who read the “beast” report were more likely to suggest enforcement over social reforms. They were more likely to view police officers as people who catch and punish criminals, rather than people who deter crime or act as role models. They were more likely to look for more information about prisons and the size of the police force, than about poverty levels or youth programs. And as before, they thought the statistics in the report were more important than the language.

But these words have no weight on their own; it’s their context that gives them power. When Thibodeau and Boroditsky asked students to come up with synonyms for either “beast” or “virus” before reading identical crime reports, they provided similar solutions for solving Addison’s woes. In fact, the metaphors only work if they frame the rest of the text. If the critical sentence came at the end of the report, it didn’t have any effect.

So metaphors can influence opinions and choices, but how strong are their effects really? At the end of their experiments, Thibodeau and Boroditsky asked the students to state their gender and political affiliation. As you might expect, men and Republicans were more likely to emphasise enforcement, while women and Democrats leant towards social reforms. But these factors only created differences of around 8 to 9 percentage points. The metaphors, on the other hand, created shifts of between 18 to 22 percentage points!

These results show the hidden power that a simple choice of words can hold over our lives. Indeed, it’s virtually impossible to talk about complex issues like crime, the economy, health and so on, without resorting to metaphors. Some people even use these linguistic devices them as the basis of policy. In Chicago, an epidemiologist called Gary Slutkin is leading a crime-prevention programme that takes the crime-as-virus metaphor literally, treating it as a contagious disease whose spread needs to be contained.

These issues apply to science too. Metaphors about electricity as flowing water or teeming crowds can affect a student’s ability to wire up circuit diagrams. Good metaphors can make a complex and obtuse world seem exciting and accessible. A world of telomeres, epigenetic marks and enzymes can be brought to life by comparing them to shoelace tips, Post-it notes, locks and keys.

But bad metaphors can do a great disservice to the public understanding of science. The idea of the “evolutionary ladder” perpetuates the myth that evolution is about a steady linear march towards complexity. The militaristic metaphor of the “war on cancer” threatens to undervalue achievements in treatment that fall short of a total cure. The idea of the brain as a computer creates all sorts of misconceptions about how different parts of the brain work, how memories are stored and whether we will ever be able to download or upload our minds.

In a field where complex ideas must be conveyed simply but accurately, it couldn’t be more important for science writers to pick the right metaphors. Feel free to suggest your own best or worst examples in the comments.

Reference: Thibodeau & Boroditsky. 2011. Metaphors We Think With: The Role of Metaphor in Reasoning. PLoS ONE http://dx.doi.org/10.1371/journal.pone.0016782

Image by Alan Cleaver

More on metaphors:

• Heavy, rough and hard – how the things we touch affect our judgments and decisions
• Social exclusion literally feels cold
• Warm hands, warm heart – how physical and emotional warmth are linked
• The Lady Macbeth effect – how physical cleanliness affects moral cleanliness
• Clean thoughts can soften moral judgments
• Holding heavy objects makes us see things as more important
• Clean smells promote generosity and fair play; dark rooms and sunglasses promote deceit and selfishness

This post was originally published last year. I’m travelling for a few weeks, so I’m reloading some of my favourite stories from 2011. Normal service will resume when I get back.
RM had his first out-of-body experience at the age of 16. Now, at the age of 55, he has had more than he can count. They usually happen just before he falls asleep; for ten minutes, he feels like he is floating above his body, looking down on himself. If the same thing happens when he’s awake, it’s a far less tranquil story. The sense of displacement is stronger – his real body feels like a marionette, while he feels like a puppeteer. His feelings of elevation soon change into religious delusions, in which he imagines himself talking to angels and demons. Psychotic episodes follow. After four or five days, RM is hospitalised.

This has happened between 15 to 20 times, ever since RM was first diagnosed with schizophrenia at the age of 23. He hears voices, and he suffers from hallucinations and delusions. Despite these problems, he managed to hold down a job as a reporter until 2002 and more recently, he has been working in restaurants and volunteering as an archivist. Then, about a year ago, he took part in a study that seems to have changed his life.

For around a decade, RM has taken part in several studies designed by Sohee Park, a neuroscientist from Vanderbilt University who works on schizophrenia. “He’s a very interesting guy,” says Park. “He has very deep insight into his condition.”

Park’s student Katharine Thakkar was testing the idea that people experience psychotic experiences because they have a weak sense of self. It’s an idea that others have suggested before but it seems like something that would be hard to test with experiments. But not so: over the last decade, psychologists have shown that our sense of self is far from the fixed, permanent feeling that we assume it is. Instead, it is disarmingly pliable. You can tweak it. You can study it. Our brain continuously constructs our sense of self using information from our eyes, skin and joints. By tweaking that information using simple illusions, scientists have warped and displaced our sense of self in the lab.

The most famous of these – the rubber-hand illusion – debuted as a party trick at a Halloween bash. Princeton scientists stroked a rubber hand in time with someone’s real hand, which was hidden out of sight. A few seconds later, the volunteer genuinely felt that they owned the rubber hand. Since then, scientists like Henrik Ehrsson have taken the illusion to new extremes, convincing people that they have gained a third arm, jumped into a mannequin or left their own bodies. But the rubber hand illusion is still proving useful.

Thakkar performed the trick on 24 people with schizophrenia, including RM, and asked them to describe their experiences on a questionnaire. Their answers revealed that they experienced the illusion more strongly that 21 people of a similar age and background, but who didn’t have schizophrenia.

Not taking their word for it, Thakkar tested for other signs that people had bought into the illusion: a feeling that their fingers had moved, and a drop in the temperature of their real hand. She found both, and to a stronger extent in people with schizophrenia than in those without. The results suggest that schizophrenia is accompanied by a weaker or more flexible sense of body ownership than usual. Indeed, Thakkar found that people who experienced the most severe hallucinations (and some delusions) also felt the rubber-hand illusion most strongly.

But even among the group with schizophrenia, RM stuck out. The synchronous stroking didn’t just convince him that he had a rubber hand – it brought about one of his full-on out-of-body experiences. He felt that he and Thakkar were both levitating a foot off the floor: back to the ceiling, turning in a circle, and watching themselves on their chairs. The effect lasted for a few minutes, before they landed again. Others have duplicated this effect in the lab, but with more complicated set-ups involving cameras and virtual reality headsets. The rubber hand illusion shouldn’t do anything quite that dramatic.

RM was worried that a psychotic episode was on the horizon, but Park’s team had no idea about his history and he didn’t mention it. “We were so excited when it happened the first time, and he’s very helpful,” says Park. When they asked him to come back and repeat the experiment, he agreed. He wanted to know more too.

When he returned, Thakkar duplicated the same experience and this time, RM actually found the experience to be quite pleasant and wanted the feeling to come back. That was when he told the scientists about his history. “We got really worried, because we’d just induced these twice!” recalls Park. But she didn’t need to worry.

After the experiment, RM wanted to know more, so Thakkar plied him with information and journal articles about out-of-body experiences. He learned that the phenomenon had a name. He learned that scientists could willingly duplicate the effect in a lab. He learned that they had identified parts of the brain that are associated with the experiences. The information was revelatory. “He gained a psychological cause for this apparently supernatural phenomenon,” says Park, “and he has used this knowledge to control his symptoms.” Since then, RM hasn’t had a psychotic episode.

This approach almost certainly won’t work for everyone – bear in mind that RM is high-functioning and self-aware. He is very eloquent and has an IQ of 120. Park notes that similar explanations might also help other people with unusual experiences like out-of-body effects, since these could exacerbate the other symptoms of schizophrenia. “If it feels supernatural, that just feeds into the delusions,” she says.

The study has broader implications for helping people with schizophrenia. Activities that promote a stronger sense of body awareness, such as yoga, dance or playing a musical instrument, might help to alleviate some of the symptoms of schizophrenia.

But for RM, it seems that learning more about his condition was enough. A year on, his diagnosis is unchanged, he still gets out-of-body experiences, and he still hears voices. But gone are the days when his experiences would require a stay in a hospital. He is now hoping to establish himself as a freelance writer, and he’s even had a paper on religion accepted in a peer-reviewed academic journal. For him, knowledge has proven to be a potent treatment. “We check up with him regularly and he’s been doing really well,“ says Park.

Reference: Thakkar, Nichols, McIntosh & Park. 2011. Disturbances in body ownership in schizophrenia: evidence from the rubber hand illusion and case study of a spontaneous out-of-body experience.