Every living thing in the Antarctic Ocean mapped

WHALE what's going on here then? Climate change's dramatic effects on the Southern Ocean just got easier to track, thanks to a comprehensive biodiversity map of the region.

Some estimates suggest that the Southern Ocean is home to half of all the human-linked carbon dioxide that the world's oceans absorb, and the consequent drop in ocean-water pH there has already begun to dissolve animal shells in the region.

The new Biogeographic Atlas of the Southern Ocean will make it easier to monitor problems like this. It details everything we know about the life in that ocean: what is there, where it exists and what it is like.

"How do we know if things are changing, and whether they're changing naturally or not, unless we know what's there?" says Graham Hosie, a contributor to the project from the Australian Antarctic Division.

The atlas draws on hundreds of thousands of records reaching back to the 18th century, and describes more than 9000 species, ranging from microbes to whales, including the shrimp-like Antarctic tanaid, pictured below.

The information will inform debates about the creation of marine parks in the Southern Ocean. "This type of bare-bones empirical information is what you need," says Hosie. "Because there are a lot of assumptions that get made in those debates about what is there or isn't there."

This article appeared in print under the headline "Antarctic Ocean life gets mapped"

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Vibrations in rings reveal Saturn's inner secrets

EAVESDROPPING on Saturn's rings is revealing secrets of the gas giant's vast interior.

Conventional wisdom says that Saturn contains a solid central core surrounded by a roiling gassy-liquid mix of helium and hydrogen. "It's like a giant lava lamp – a slow boiling motion," says Jim Fuller of the Kavli Institute for Theoretical Physics in Santa Barbara, California. This flow was thought to keep everything evenly mixed.

But images captured by NASA's Cassini spacecraft revealed steady vibrations at six different places in Saturn's rings. Even though the rings are thousands of kilometres from Saturn's surface, vibrations in them correspond to the way the planet squishes and contracts.

Now Fuller has run a computer simulation of the vibrating rings. The results suggest that Saturn must have a stable, stratified layer, perhaps of liquid and rock, between the core and roiling exterior (Icarus, doi.org/vbh).

This is the first time a seismological investigation has been conducted on another planet. Future work should reveal more about the structure and evolution of gas giants.

This article appeared in print under the headline "To see inside Saturn, watch its rings"

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Swap bad memories for good at the flick of a switch

Memory is a fickle beast. A bad experience can turn a once-loved coffee shop or holiday destination into a place to be avoided. Now experiments in mice have shown how such associations can be reversed.

When forming a memory of a place, the details of the location and the associated emotions are encoded in different regions of the brain. Memories of the place are formed in the hippocampus, whereas positive or negative associations are encoded in the amygdala.

In experiments with mice in 2012, a group led by Susumo Tonegawa of the Massachusetts Institute of Technology managed to trigger the fear part of a memory associated with a location when the animals were in a different location. They used a technique known as optogenetics, which involves genetically engineering mice so that their brains produce a light-sensitive protein in response to a certain cue. In this case, the cue was the formation of the location memory. This meant the team could make the mouse recall the location just by flashing pulses of light down an optical fibre embedded in the skull.

The mice were given electric shocks while their memories of the place were was being formed, so that the animals learned to associate that location with pain. Once trained, the mice were put in a new place and a pulse of light was flashed into their brains. This activated the neurons associated with the original location memory and the mice froze, terrified of a shock, demonstrating that the emotion associated with the original location could be induced by reactivating the memory of the place.

Memory swap

The next step for Tonegawa's team was to see if they could change a place memory from good to bad, or vice versa.

"Emotion is intimately associated with the memory of past events and episodes, and yet, the emotional value of the memories is malleable," Tonegawa told a press conference held yesterday about their latest work.

Male mice with the light-sensitive protein in their hippocampus were given one of two experiences in a specific place. One group encountered female mice – which triggers a positive reaction – while the others were given small electric shocks.

To see if they could switch the remembered emotions, Tonegawa's team reactivated the memory using a flash of light and gave the same mice the opposite experience in a new place. Those that had seen the female mice got a shock, those that had been shocked got their turn to ogle.

The mice that had originally been given the electric shocks showed less fear, and started sniffing in expectation of meeting a female when they returned to the original space. Their associations with the place had been altered, without them having to be there.

A connection is made

In separate experiments, Tonegawa's team showed that these emotional swaps corresponded to changes in connectivity between the hippocampus and the amygdala. Once new associations had formed, stimulating the location memory in the hippocampus triggered the activity of a different group of neurons in the amygdala to the ones that were triggered before.

"While it is well established that a memory can be modified, the underlying mechanisms for this process have not previously been understood," says Jonathan Lee, a neuroscientist at the University of Birmingham, UK. "The findings are highly significant because they have clear implications for the role of different brain regions, and their dynamic interaction in memory processing and updating."

The study validates a therapy currently used in psychotherapy to help depressed patients, Tonegawa told the press conference. "A psychiatrist will talk with the patient and try to make them recall their good memories that they have had in the past. This reduces the effects of bad memories or stress they have had, which leads to some of the behaviours expressed by the depressed patient."

The team also thinks that manipulating the emotional content of memories could prove a novel avenue for mental-health therapies. Lee, however, is more cautious. "It might be claimed that the process could be harnessed therapeutically to alter memories," he says, but he adds optogenetics is a highly invasive technique that is not applied to people.

What's more, the memories changed in this experiment were contextual memories, which Lee says may not be of much use in people that show anxiety sparked by specific stimuli. He suggests that it is important to investigate how best to reactivate happier memories using behavioural methods.

Journal reference: Nature, DOI: 10.1038/nature13725

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Sliding stones of Death Valley: Rocky riddle resolved

I DIDN'T imagine it would be like this. A breath of wind, a crack and then it happened. After seven years of sleuthing, the mystery I'd been pursuing resolved itself instantly before my eyes. Exalted, I rushed down to the edge of the lake bed to watch more closely – slowly but surely, the rocks were moving and now I knew why (see graphic).

Death Valley National Park is an awesome, dramatic place and Racetrack Playa is no exception. The dry lake bed sits 1100 metres above sea level at the end of a 40-kilometre rocky road that climbs up among the Joshua trees. The road can take a heavy toll on vehicles. In a dozen trips, I've had five flat tyres and two busted shock absorbers.

The playa itself is staggeringly flat – its elevation changes by no more than a few centimetres across the whole of its ...

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Fish reared on land replay the transition to four legs

Video: Walking fish replays evolution from land to sea

It was one of the key events in the evolution of animals – and now it has been replayed in the lab. Evolutionary biologists reared air-breathing fish on land for eight months and found that the experience encouraged the fish to develop skeletons better adapted for walking.

Fish first adapted to life on land about 350 to 400 million years ago, when they evolved four legs to form the tetrapods, a group that includes amphibians, reptiles, birds and mammals. This crucial evolutionary transition is preserved in the fossilised remains of animals called stem tetrapods, which have some features of fish and some of four-legged animals.

Bichir fish (Polypterus ), which are native to Africa's Nile basin, are the closest living counterparts of those ancient stem tetrapods. They have true lungs as well as gills, so they can survive on land as well as in their preferred underwater habitat. For these reasons, Emily Standen at the University of Ottowa in Canada and her colleagues decided to try rearing them on land to see whether this made them more adept at walking than bichir fish that were raised exclusively in water.

The short answer is that this is exactly what happened. "The anatomy of the fish raised on land changed, and those changes reflected what we see in the fossil record in the transition from fish to four-legged terrestrial vertebrates," says Standen.

Fin by fin

Bichir fish, which resemble eels, normally "walk" by alternately planting each of their two front fins firmly on the sand. In each "step", they use one fin as an anchor for wiggling the rear parts of their body forward, ready for the next "step" with the other fin (see video).

This walking technique improved in 100 bichir fishes that Standen and her colleagues reared in a tank filled with just a couple of millimetres of water. They doused the fish constantly with mist to stop them drying out and dying.

These fish – and another 50 in a standard water-filled aquarium – were reared for eight months, after which Standen's team tested the walking capabilities of both groups. The researchers filmed the fish for finer analysis of their walking, and examined bones and muscles to see whether there were anatomical differences between the two groups.

"The main outcome was that if Polypterus were raised on land, behaviourally they walked more effectively," says Standen.

Quick evolution

The land-raised fish raised their heads 1.5 times higher on average during walking to reinforce forward momentum, reduced the slippage of their "anchor" fins by a third and planted their fins 3.5 times closer to the midlines of their bodies, providing superior leverage for the rear part of the body.

Their bodies also changed in a way that made them more like stem tetrapods. Their shoulder blades grew slightly longer than normal and were in better contact with a neighbouring bone called the cleithrum. Both of these changes were seen in stem tetrapods as they moved onto land.

There were also changes in bone structures that gave the land-living bichir something resembling the beginnings of a neck. In stem tetrapods, the neck ultimately separated the head from the body and is seen in today's terrestrial animals.

"This data is the first to present evidence that environmentally induced developmental plasticity may have been present in the stem tetrapods, helping facilitate their successful transition onto land," says Standen.

"This research may show us one of the influences acting during the crucial water-to-land transition in tetrapods," says Jenny Clack of the University of Cambridge. "But I'm not sure how it could be tested further or refuted," she adds.

Standen says that ideally, she'd like to study multiple generations of Polypterus to see whether the traits are reinforced over time, but she notes that these fish are notoriously difficult to breed. "We always have breeding as a goal on the horizon, and are continuing to raise fish on land to examine other potential changes that a new environment might induce."

Journal reference: Nature, DOI: 10.1038/nature13708

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Schrödinger's cat caught on quantum film

(Image: Gabriela Barreto Lemos)

Schrödinger's cat is the poster child for quantum weirdness. Now it has been immortalised in a portrait created by one of the theory's strangest consequences: quantum entanglement.

These images were generated using a cat stencil and entangled photons. The really spooky part is that the photons used to generate the image never interacted with the stencil, while the photons that illuminated the stencil were never seen by the camera.

When two separate particles are entangled, measurements of their physical properties are correlated, and they effectively share a single quantum state. Gabriela Barreto Lemos at the Austrian Academy of Sciences in Vienna and her colleagues used this quantum connection between particles to make these images of a cat without directly photographing it.

To do it, the researchers created yellow and red pairs of entangled photons. The yellow photons were fired at the cat stencil, while the red photons were sent to the camera. Thanks to their entanglement, the red photons formed the image of the cat because of the quantum link to their yellow twins.

The silicon stencil was transparent to red light and the camera could only detect red light. This demonstrates that the technique can image objects that are invisible to the detected photons.

Journal reference: Nature, DOI: 10.1038/nature13586

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Supernova find backs dark energy and universe expansion

Astronomers have long had a dark secret: one of the cornerstones of the Nobel prizewinning discovery that the expansion of the universe is accelerating had never been directly tested. The discovery hinged on the assumption that certain kinds of supernovae detonate in thermonuclear explosions that have a fixed amount of energy, but hard evidence that this was the case remained lacking.

Now, more than 15 years later, we finally have firm proof that such supernovae explode as expected.

All type IA supernovae are said to have the same characteristic brightness. Because of this, they are used as "standard candles" to estimate cosmic distances. In 1998, astronomers used measurements of the distances of various type IA supernovae to show that the expansion of the universe is accelerating, which they attributed to a mysterious pushing the cosmos apart.

Astrophysicists theorised that the reason all type IA supernovae have the same brightness is that they are thermonuclear detonations, in which a white dwarf star somehow reaches a critical mass of about 1.4 solar masses and explodes. But this central idea had never been confirmed, because no type IA had gone off near Earth in recent decades.

That changed on 21 January, when Steve Fossey of University College London and his students stumbled upon a type IA supernova in M82, or the Cigar galaxy. At 11.4 million light years away, SN 2014J is the closest such explosion in decades.

Eugene Churazov of the Max Planck Institute for Astrophysics in Garching, Germany, and colleagues observed SN 2014J with the INTEGRAL gamma-ray telescope. They found the classic signature of a thermonuclear explosion of a white dwarf. The process begins with the compression of the white dwarf, leading to the formation of nickel-56, which decays to cobalt-56, which in turn decays to a stable isotope of iron, producing characteristic gamma rays.

"Nobody had directly seen these gamma rays," says Churazov.

Using SN 2014J's gamma rays, the team estimated that the mass of nickel-56 that decayed to be about 0.6 solar masses, within the range predicted by models. That means the status of type IA supernovae as standard candles is secure.

But there are still a few different ways for the explosion to happen, which could change the way astronomers interpret these supernovae in the future. In the favoured model, called the single degenerate system, a white dwarf reaches its critical mass by stealing material from an ordinary companion star. In an alternative, double degenerate model, two white dwarfs orbiting each other cause the explosion, either by merging or by one poaching matter from the other.

Churazov and his colleagues' observations support the single degenerate model. A second team, however, favours the double degenerate scenario. Miguel Pérez-Torres of the Institute of Astrophysics of Andalucia in Granada, Spain, and colleagues used the European VLBI Network of radio telescopes spread across Europe and China to study SN 2014J.

In a single degenerate system, the shock wave from the white dwarf explosion should smash into the surrounding gas from the companion star, generating radio waves. Pérez-Torres and colleagues saw no radio waves, so concluded SN 2014J probably began as two white dwarfs.

Robert Kirshner of Harvard University, who studies type IA supernovae, is not convinced yet. "While it is true that there is no sign of the gas that might be there in a single degenerate, perhaps that gas is more distant and less dense than assumed," he says.

If SN 2014J is a double degenerate, that would imply a greater variation in the intrinsic brightness of such supernovae than if all type IA were single degenerate. It would still be a standard candle, but astronomers would have to account for multiple types of supernovae. "One has to care about this, now that we are in an era of precision cosmology," says Pérez-Torres.

No wonder Kirshner is thrilled to have a nearby type IA to study in detail. "We learn more about the physics of supernovae from one nearby event than from a thousand distant ones," he says.

Journal reference: Nature, DOI: 10.1038/nature13672

The Astrophysical Journal DOI: 10.1088/0004-637X/792/1/38

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Source of sun's power revealed by ghostly particles

ELUSIVE particles from inside the sun are providing a glimpse of the solar forges.

Physicists have known for 75 years that the sun is powered by nuclear fusion, which involves two protons colliding to produce helium and energy. But they have never seen it happening directly.

Photons that arrive in sunlight are hundreds of thousands of years old, so tell us only about fusion in the distant past. One way to spy on recent solar fusion would be by glimpsing elusive particles known as pp neutrinos, which are produced when protons collide.

All neutrinos have no charge and almost zero mass, so interact very weakly with ordinary matter – trillions pass through your body every second, unnoticed. But pp neutrinos are even more aloof because they carry less energy than other neutrinos.

Now the Borexino experiment in Gran Sasso, Italy, has caught some. The team has been hunting pp neutrinos for seven years using a spherical tank filled with a liquid scintillator, which produces flashes when struck by ionising radiation, like that given off by a neutrino. The tank is watched by more than 2000 detectors that count the flashes, and thus the neutrinos.

To shield it from false signals like cosmic rays and radiation from Earth, the tank lies more than a kilometre underground. The materials used to build the detector are also very slightly radioactive, so the team has to constantly purify the scintillator.

Their efforts paid off: the team detected about 90 pp neutrinos hitting Borexino every day. That means the sun produces enough of them to pump about 66 billion through every square centimetre of Earth each second (Nature, DOI: 10.1038/nature13702).

That number agrees with predictions of the standard solar model. Physicists had estimated the number by looking at sunlight, but because photons take hundreds of thousands of years to emerge from the centre of the sun, it's not a measure of what's happening now. Neutrinos punch straight through the sun, giving an up-to-date signal that takes 8 minutes to reach us. "This again confirms that the standard solar model is on the right track and does an excellent job of describing energy production and transport within the sun," says Andrew Renshaw of the University of California, Los Angeles, who was not involved in the work. "This is truly a great feat."

Studying pp neutrinos could also shed light on other mysteries. Previous experiments detected higher-energy neutrinos produced by secondary reactions in the sun, and showed that they morph between three different types. We still don't have a complete picture of how this process works, but Borexino may help.

"With this measurement it will be possible to put better constraints on beyond-the-standard- model physics," says Renshaw.

This article appeared in print under the headline "Ghost particles leak sun's secrets"

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Today on New Scientist

Supercomputers make discoveries that scientists can't

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Supercomputers make discoveries that scientists can't

No researcher could read all the papers in their field – but machines are making discoveries in their own right by mining the scientific literature

IN MAY last year, a supercomputer in San Jose, California, read 100,000 research papers in 2 hours. It found completely new biology hidden in the data. Called KnIT, the computer is one of a handful of systems pushing back the frontiers of knowledge without human help.

KnIT didn't read the papers like a scientist – that would have taken a lifetime. Instead, it scanned for information on a protein called p53, and a class of enzymes that can interact with it, called kinases. Also known as "the guardian of the genome", p53 suppresses tumours in humans. KnIT trawled the literature searching for links that imply undiscovered p53 kinases, which could provide routes to new cancer drugs.

Having analysed papers up until 2003, KnIT identified seven of the nine kinases discovered over the subsequent 10 years. More importantly, it also found what appeared to be two p53 kinases unknown to science. Initial lab tests confirmed the findings, although the team wants to repeat the experiment to be sure.

KnIT is a collaboration between IBM and Baylor College of Medicine in Houston, Texas. It is the latest step into a weird world where autonomous machines make discoveries that are beyond scientists, simply by rifling more thoroughly through what we already know, and faster than any human can.

In a paper to be presented at the Conference on Knowledge Discovery and Data Mining in New York City this week, the researchers say that society is better at generating new information than at analysing what it already has. "This leads to deep inefficiencies in translating research into progress for humanity," they write. KnIT aims to iron out that inefficiency.

"In general, new p53 kinases are discovered at a rate of one per year," says Olivier Lichtarge, who leads the work at Baylor. "We hope to greatly accelerate that rate of discovery."

Studying kinases is important for cancer research, but the Baylor team thinks the approach can extend beyond biomedical studies to all areas of science. And if KnIT's algorithmic discoveries hold up, they point to a future in which everyone could have a personalised algorithm trawling and making sense of the scientific literature to figure out cures for their ailments, including ones tailored at a genetic level.

Expanding KnIT to other areas of biology or the physical sciences isn't straightforward. "We could run into big problems when we try and generalise to more proteins and genes," Lichtarge says. And in subjects like physics, results tend to be presented using equations and graphs rather than words. However, data-mining groups are working to retrieve information from these too.

The idea that new knowledge can be unearthed by finding links between disparate strands of research was first crystallised in 1986 by information scientist Don Swanson at the University of Chicago. He analysed a database of scientific literature manually to deduce that fish oil might be a good treatment for Raynaud's syndrome, a circulatory disorder, because studies showed that fish oil could reverse certain conditions also seen in Raynaud's. His hunch turned out to be right.

Modern science has given us a far larger and more intricate haystack than the one Swanson picked through, but machine intelligence is now sorting through it to find new connections.

Ross King of the University of Manchester, UK, has developed a different kind of automated system, Eve, which he claims has already discovered a novel drug against malaria. Rather than extracting new knowledge from the literature, Eve robotically runs lab experiments focused on finding new drugs to treat neglected diseases. King is keeping the discovery secret until the work is published, but will say that the compound is an ingredient in several brands of toothpaste.

The webs of knowledge that computers create in this automated pursuit of discovery are useful to non-scientists, too. Sophia Ananiadou at the University of Manchester works on Facta+, a searchable database which holds huge amounts of information about cancer, based on data mined from the literature. Although it's designed to help cancer researchers, she says it could be used by the public to learn more about diseases they have been diagnosed with, without having to read scientific papers themselves.

The purpose of data mining can also be flipped. Instead of finding new insights into specialised topics, systems like KnIT can find holes in existing research that need to be plugged.

Natasa Miskov-Zivanov of Carnegie Mellon University, Pittsburgh, is working on using similar techniques to build computational models of cells that can be used to test drugs. Normally, models take time to develop, with input from experimental biologists and theorists. But Miskov-Zivanov's models build themselves quickly and automatically using results in the literature. The models can then be tested by scientists in the lab.

Miskov-Zivanov's work is funded by the US defence agency DARPA as part of its Big Mechanism project, which aims to find new knowledge hidden in big data. "It takes several years to develop a meaningful model of what's going on in a cell, but what we're doing could speed up the process a lot," she says. That would, in turn, speed up drug testing.

New breakthroughs could come by analysing scientific literature across disciplines – physics on the scale of cells and molecular biology, for instance. "I don't think we could ever understand this huge, complicated puzzle without automated help," says King. "There just aren't enough PhDs in the world to do the experiments."

This article appeared in print under the headline "Automated discovery"

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