Archive for March, 2012

I've got your missing links right here (31 March 2012)

By Ed Yong | March 31, 2012 1:18 pm

James Cameron sunk to the bottom of the Mariana Trench and tweeted (by proxy… still) from the bottom. He brought back footage – the narration is thrilling but the video, less so. Rebecca Morelle had the best official coverage at the BBC but the Deep Sea News crew did an amazing job. Craig McClain and Al Dove asked if it was a scientific milestone or rich guy’s junket, and offered 10 reasons why we should explore the deep. Craig created a storify of the reaction to his descent. And Holly Bik explains what we can do with the cup of mud that James Cameron grabbed from the bottom of the ocean? Holly Bik explains.

“Of 7 friends/colleagues of Thornton’s who spoke to Nature, 6 called him intense. 7th described him as “beyond intense”. This profile of protein-resurrector Joe Thornton is a masterclass in science writing. Helen Pearson is among the best of the best.

FOSSIL RAINDROPS. 2.7 billion-year-old fossil raindrops. That’s so wonderful, I might tear up a bit.

I’m utterly mesmerised by NASA’s animation of the world’s ocean currents. It’s like watching an animated Monet. And a real-time map of wind patterns across the US

A 4th grader asks Jonah Lehrer,“What is the downside of creativity?” He answers with this post about the creative treadmill

The many ways that that machines can hurt you, shown on warning labels

Tomb raider… in SPAAAAAACE. Meet the world of aerial archaeology.

Sip carefully: murky science on drinks with neurotransmitters and hormones

Nice analysis by Declan Butler highlighting serious problems with global flu surveillance

“I want to help him fight the bad guys.” His mom said, “You need to help your sister fight cancer.” Batman sped away. A really moving story about the guy who got pulled over as Batman.

Great long feature from Ian Sample on the mutant bird flu controversy.

Screenshots of Despair.

Bacterial outsourcing! The Black Queen hypothesis: Why evolution tells microbes to be lazy

A tornado as wide as five Earths.

“The [Daily] Mail is less a parody of itself than a parody of the parody” – a New Yorker profile

“Why’s this so good?” No. 35: Malcolm Gladwell on ketchup, by Tim Carmody

Great coverage of the terrifying Waspzilla (I like Waspthulu)

Amazing things that happen in nature in a single second, illustrated

In cancer science, many “discoveries” don’t hold up. And how the cancer drug that wasn’t highlights widespread flaws in preclinical studies

Fossil foot of human ancestor hints that tree-dwellers lived alongside species built for walking.

Chris Chambers dismantles a flawed paper and dodgy PR about a brain-zapping “thinking cap”. I loved: “I don’t even know what to call this problem. Appeal to…prose?”

Why suicide is a really hard thing to study

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CATEGORIZED UNDER: Links

The two faces of rapamycin – why a life-extending drug also increases risk of diabetes

By Ed Yong | March 30, 2012 9:00 am

A plaque on Easter Island commemorates the discovery of rapamycin

You don’t have to go far to find supposed ways of delaying the ageing process, from oddball diets to special supplements. But these fountains of youth are all hype and no substance. For now, there are only a few methods that have consistently extended the lives of mammals. Eating less – formally known as “caloric restriction” – is one of these. Rapamycin, a drug originally found in Easter Island bacteria, is another. It can lengthen the lives of old mice by 9 to 14 per cent, and it boosts longevity in flies and yeast too.

But rapamycin has its downsides. For a start, it strongly suppresses the immune system. That is why it is currently given to people who receive new organs, to stop them from rejecting their transplants. Rapamycin can also increase the risk of diabetes. In mice, rats and humans, the drug weakens the ability to stabilise levels of sugar in the blood. Individuals who take it for a long time become resistant to insulin, and intolerant to sugar.

You’d expect the opposite. Longer-lived animals ought to be better at dealing with sugar, and less likely to suffer from insulin resistance. Indeed, that’s what you see in individuals that cut down on calories. So why does rapamycin behave so paradoxically?

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CATEGORIZED UNDER: Ageing, Medicine & health

The brain is full of Manhattan-like grids

By Ed Yong | March 29, 2012 2:00 pm

London’s streets are a mess. Roads bend sharply, end abruptly, and meet each other at unlikely angles. Intuitively, you might think that the cells of our brain are arranged in a similarly haphazard pattern, forming connections in random places and angles. But a new study suggests that our mental circuitry is more like Manhattan’s organised grid than London’s chaotic tangle. It consists of sheets of fibres that intersect at right angles, with no diagonals anywhere to be seen.

Van Wedeen from Massachusetts General Hospital, who led the study, says that his results came as a complete shock. “I was expecting it to be a pure mess,” he says. Instead, he found a regular criss-cross pattern like the interlocking fibres of a piece of cloth.

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More from the peculiarly introspective world of science journalism

By Ed Yong | March 28, 2012 9:00 am

Recently, I took part in a debate about improving science journalism, hosted at the Royal Institution. It was somewhat mixed, but at least, it allowed a variety of viewpoints to rise to the surface. The videos are now up. I’m at 31:00 in the first one, acting as a first-responder to the initial two speakers. I’m basically writing this on the spot, so it’s a bit rambling. For those who can’t be bothered to watch, basically my points are these:

    • Science journalism suffers from big systemic problems that are not unique to science, and that won’t be solved by the typically suggested solutions of “send ‘em all on a stats course”.
    • Time pressure is one of those problems, although the fact that many journalists working under the same pressures produce quality results suggests that it isn’t a critical factor.
    • Many science journalists have come to accept a frankly unacceptable level of mediocrity in our own practice, including playing an odd blame game whenever mistakes are made, and tolerating stenography.
    • Many of the errors in science journalism are made commonly and repeatedly, and we can find out what these are by paying attention to blog commentaries, Twitter, other social media, and more.
    • Likewise, it would help if the people producing those critiques could frame them in a constructive and helpful way. As examples (not mentioned in the video), T. Ryan Gregory’s rants about junk DNA have been very helpful to me, and Jon Simons and Russ Poldrack are working on a guide to interpreting fMRI studies for journalists. Those resources allow those of us who want to do better to do better.
    • Debates like the one in the video above are all well and good but the people in the room are (largely) the ones who are interested in quality science journalism. How do you reach the ones who are down the pub and don’t give a toss?
CATEGORIZED UNDER: Journalism

Will we ever… talk to dolphins?

By Ed Yong | March 27, 2012 9:00 am

Here’s the fourth piece from my new BBC column

“What’s that Flipper? The treasure is over there?” So went a typical plotline for the popular TV series featuring the cute, bottlenosed dolphin who could communicate with his human guardians, and who – in the time-honoured fashion – used his animal powers to apprehend criminals.

The idea that animals like Flipper can communicate with humans is not just the preserve of the small and big screen. History is littered with celebrity animals who have communicated with human scientists, with varying degrees of success. Many apes, including Washoe and Nim the chimps, and Kanzi the bonobo, have learned to communicate by using sign language or symbols on a keyboard. Alex, an African grey parrot learned over 100 English words, which he could use and combine appropriately; his poignant last words to Irene Pepperberg, his scientist handler, were “You be good. I love you. See you tomorrow.”

Dolphins hold a particular fascination; we are captivated by their intelligence and beauty, and swimming with dolphins features regularly on lists of things to do before you die. Denise Herzing has a lifetime of such experiences. For the last 27 years, she has been swimming with a group of Atlantic spotted dolphins in Florida as part of the Wild Dolphin Project. She can identify every individual and they, in turn, seem to trust and recognise her. It is a solid foundation for the boldest attempt yet to talk with dolphins.

One-way chat

“Talk” is tricky to define. A SeaWorld trainer who prompts a dolphin to jump for fish is arguably communicating with it. But such simple one-way interactions are a far cry from the conversational world of Dr Doolittle. Here, the dolphin responds, but says nothing intelligible back. Herzing’s vision is much more ambitious – she wants to establish two-way communication with her dolphins, with both species exchanging and understanding information.

The idea of talking to dolphins has a long and chequered history. It was widely publicised in the 1960s by John Lilly, who argued that dolphins have such large brains that they must be extremely intelligent and have a natural language. All we had to do was to “crack the code”. Much of Lilly’s work was highly questionable. He once flooded a house to keep a captive dolphin, instigated failed attempts to teach them spoken English, and even gave the animals LSD (while taking the drug himself). But there is no denying his influence in popularising the idea of two-way dolphin communication. “He said that in a few years, we will have established complex dialogue with them,” says Justin Gregg from the Dolphin Communication Project. “And he was saying that every few years.”

Lilly was right about dolphin intelligence, but not dolphin language. A true language involves small elements that combine into larger chains, to convey complex, and sometimes abstract, information. And there is no good evidence that dolphins have that, despite their rich repertoire of whistles and clicks.

Little less conversation

Wild dolphin communication is hard to study. They are fast-moving and hard to follow. They travel in groups, making it hard to assign any call to a specific individual. And they communicate at frequencies beyond what humans can hear. Despite these challenges, there is some evidence that dolphins use sounds to represent concepts. Each individual has its own “signature whistle” which might act like a name. Developed in the first year of life, dolphins use these whistles as badges of identity, and may modulate them to reflect motivation and mood. This year, a study showed that when wild dolphins meet, one member of each group exchanges signature whistles.

But beyond this, dolphin chat is still largely mysterious. “To communicate with dolphins, we need to understand how they communicate with each other in the natural world,” says psychologist Stan Kuczaj at the University of Southern Mississippi. “We still don’t know basic things like what the units of dolphin communication are. Is a whistle the equivalent of a “word” or a “short sentence”? We don’t know.”

We may not be able to understand them yet, but we know that dolphins can learn to understand us. In the 1970s, Louis Herman taught an invented sign language, complete with basic syntax, to a bottlenose dolphin called Akeakamai. For example, if he made the gestures for “person surfboard fetch”, Akeakamai would bring the board to him, while “surfboard person fetch” would prompt her to carry the person to the board. His experiments showed that dolphins could understand hundreds of words, and how those words could be combined using grammatical rules.

What’s my motivation?

Herman’s work was groundbreaking, but this was still one-way communication. It focused on comprehension, not conversation. In the 1980s, Diana Reiss had more luck by showing that dolphins could use underwater keyboards to make basic requests. When they prodded keys with their snouts, a whistle would play and Reiss gave a reward like a ball. Eventually, the dolphins used the artificial whistles to ask for the associated rewards.

But as conversations go, these were shallow ones. “The dolphins were only really interested in communicating about needs that they had, like a tool they needed or a fish they wanted,” says Kuczaj, who was involved in a similar project at DisneyWorld’s EPCOT Center. “We hoped they would also comment on other things going on in the aquarium but they didn’t.”

It is difficult persuading dolphins to learn some arbitrary signals, like a whistle signifying a ball, and then use them in a social context, admits Gregg. “They don’t seem to run with it the same way that chimps or bonobos have. The big stumbling block is motivation. Dolphins don’t seem to care.”

Herzing disagrees. She notes that captive animals, which often lack stimulation, will respond to systems like the underwater keyboards. She thinks that these experiments disappointed because they were cumbersome. “The dolphins swim very fast and went to where they were requested, but humans are very slow in the water. There wasn’t enough real-time interaction.”

Chat line

Herzing is trying to solve that problem with Cetacean Hearing and Telemetry (CHAT) – a lighter, portable version of the underwater keyboards. It consists of a small phone-sized computer, strapped to a diver’s chest and connected to two underwater recorders, or hydrophones. The computer will detect and differentiate dolphin sounds, including the ultrasonic ones we cannot hear, and use flashing lights to tell the diver which animal made the call.

The CHAT device can also play artificial calls, allowing Herzing to coin dolphin-esque “words” for things that are relevant to them, like “seaweed” or “wave-surfing”. She hopes the dolphins will mimic the artificial whistles, and use them voluntarily. By working with wild animals, and focusing on objects in their natural environment, rather than balls or hoops, Herzing hopes to pique their interest.

Herzing emphasises that her device is not a translator. It will not act as a dolphin-human Rosetta stone. Instead, she wants both species create a joint form of communication that they are both invested in. She hopes that CHAT will tap into the “natural propensity” that dolphins have “for creating common information when they have to interact”. For example, in Costa Rica, distantly related bottlenose and Guyana dolphins will adopt a shared collection of sounds when they come together, using sounds that they don’t use when apart.

As with past projects, all of this depends on whether the dolphins play along. Kuczaj says, “It’s a remarkable challenge because she is working with wild dolphins so they’ve got the option to participate or not.” Here, Herzing has an edge, since the animals know her, and vice versa. “We’ve been observing them underwater every summer since 1985,” she says. “I know the individuals personally – their personalities and relationships. We’ve got a pretty good handle on what they’d be interested in.” Perhaps this combination of cutting-edge technology and old-school fieldwork will finally produce the conversations that have eluded scientists for so long.

The surprisingly toxic world of lichens

By Ed Yong | March 26, 2012 3:00 pm


Peltigera membranacea – one of the species analysed in this study

One of the most successful alliances in the natural world often goes unnoticed. It involves either an alga or a bacterium that harvests energy from the sun to make its own nutrients. It shares this bounty with a fungus, which reciprocates by providing it with shelter. Together, the associates form a dual organism known as a lichen.

This alliance is so successful that lichens have colonised every continent, including Antarctica. They’re often ignored, but look closely, and you’ll find a hidden world of jellies, bushes, worms and pixie cups. Look even closer, and you’ll find a world of poison.

Ulla Kaasalainen from the University of Helsinki has discovered that one in eight species of lichens wield microcystins, a group of poisons that cause liver damage in humans and other animals. These chemicals are manufactured by blue-green bacteria known as cyanobacteria. These microbes are best known for creating large ‘blooms’ in lakes and rivers, which discolour the water with greenish swirls, and poison it with harmful toxins like microcystins. These toxins can accumulate in the food chain, affecting humans via shellfish and fish.

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CATEGORIZED UNDER: Evolution, Fungi

Sequencing our gut bacteria: the hype and hope of another big science project

By Ed Yong | March 26, 2012 9:00 am

I regularly write about the microbiome – the trillions of bacteria that share our bodies with us, and the genes that they carry. At the recent International Human Microbiome Congress in Paris, I was immediately struck by two things. First, the field is clearly growing. It’s full of scientists who are doing great work to understand our bacterial associates, and who are glad that the microbes are finally hitting the big time.

But I also felt a familiar twang. When one of the initial speakers described the quest to sequence our microbiome as the “biggest life sciences project of all time”, and when people spoke of new ways to diagnose and treat diseases, I was reminded about the hype that surrounded the Human Genome Project, back when our DNA had not yet been fully sequenced. When people showed communities of microbes that were associated with diseases, with no clear sense as to which caused which, I thought of the endless number of observational studies looking at risk factors for cancer, heart disease, autism, and other conditions.

And it worried me. While I’m fascinated by the microbiome, and was thrilled to be part of the conference, I also wondered if the current optimism would lead to a backlash down the line. There’s precedent for this. The Human Genome Project is currently experiencing just such a backlash, as are large studies that try to find genetic variants that underlie human diseases. The so-called War on Cancer is still being fought several decades later, and patients are getting impatient. And I found many other microbiome scientists who shared my concerns, at the conference and beyond.

This was the basis of a piece that I wrote for Nature News. It looks at the potential for hyping yet another ‘Big Science’ endeavour. But it also considers legitimate reasons why the microbiome may deliver on its promises more quickly than the genome has. In particular, diagnostic tests seem to be a rich area to focus on, with a good chance of providing short-term gains. Check out the full piece for more.

CATEGORIZED UNDER: Bacteria, Microbiome

I've got your missing links right here (24 March 2012)

By Ed Yong | March 24, 2012 12:00 pm

Top picks

A video of a debate on science journalism. I’m at 31:00, saying that we must not accept mediocrity

What can James Cameron expect at the bottom of the ocean? Dunno. Maybe nothing, maybe Cthulhu.

Is Silence Going Extinct? Great piece on the science of soundscape ecology

Big meta-analysis finds no genes that are associated with personality traits. Neuroskeptic ponders what that means

Wonderful Robert Krulwich piece on what you gain and lose when you record the data of your entire life

“Despite what most people think, it’s not vomit.” The dirty, lucrative business of sperm whale ambergris

“On the internet today, watching something twice is a radical act.” Fish – a truly wonderful tap essay for the iPhone/iPad by Robin Sloan.

Important news: judge orders FDA to restart 35-year-old effort to examine, and maybe ban “growth promoter” farm drugs

“You don’t write like a scientist.” Wonderful piece of satire.

Helen Pearson is an awesome writer. Here’s her latest piece on Joe Thornton, the man who resurrects ancient, extinct proteins

How appropriate is it to frame overeating and obesity as “food addiction”? SciCurious investigates.

John Hawks on why humans aren’t apes. Not entirely sure I buy it. Meanwhile, is Brian Switek a fish? He thinks so.

UNC physicist faces 16 years in an Argentinian jail, says cocaine found in his suitcase in Argentina was planted by friend of online girlfriend. He’s still writing papers…

Wind-powered kinetic sculptures crawl down a beach and take my breath away.

Incredible! A camera that sees round corners, explained in a funky video by Geoffrey London.

“Across the street… a rhesus monkey named Thor is strapped into a chair.” On the quest to create a true bionic limb

Jaguars in the night… Meet the man who has been recording nature for three decades.

“THIS is why we invest in science,” says Phil Plait, and he’s right. Rocket engine tech leads to a design for a better fire-hose pump.

Not a caterpillar… Incredible illusion photo.

Kill all viruses – Carl Zimmer’s new feature for Wired

Steve Silberman talks to Charles Duhigg about the habits that drive us, and how we can drive *them* instead.

If you really need to puncture someone’s airway with a pen, the BIC soft feel Jumbo is the brand of choice

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CATEGORIZED UNDER: Links

What goes on in my head…

By Ed Yong | March 23, 2012 2:32 pm

I tweeted a link to a video of a talk I did, and asked people to caption the screengrab. Joe Hanson did an uncannily accurate job…

CATEGORIZED UNDER: Personal, Uncategorized

Scientists create mice that automatically label new memories for easy reactivation

By Ed Yong | March 23, 2012 12:30 pm

Finding a specific memory in your brain is not easy. Is it held within a particular group of neurons? If so, which ones? Are they clustered together, or spread throughout the brain? In science-fiction, a goofy helmet and a fancy operating system is all it takes. In real life, we need a subtler and cleverer technique.

Two independent groups of scientists have devised just such a method, and used it to awaken specific memories in mice. One group even planted a slightly artificial memory. These techniques have great promise. They will allow us to study how memories are formed, how our existing memories affect the creation of new ones, and what happens during the simple act of remembering.

Scientists have long been able to reactivate old memories, but only in a crude and undirected way. Back in the 1940s, brain surgeon Wilder Penfield found that when he electrified the brains of some epileptic patients, they recalled vivid random memories. The results were scattershot, and expectedly so. Even the tiniest of electrodes will shock thousands of neurons. There’s no way of directing the electricity to the specific neurons involved in any particular memory.

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