Archive for May, 2012

This post is written in a font made of DNA

By Ed Yong | May 30, 2012 1:00 pm

For more about these DNA sculptures, how they work and what they might be used for, see my piece at Nature News.


Razor clam creates quicksand to bury itself. So does RoboClam

By Ed Yong | May 29, 2012 9:00 am

Anyone who has tried to pull a razor clam from a sandy beach knows that they can dig fast. These edible animals can bury themselves at around one centimetre per second, and they go deep. A clam the length of a hand can create a burrow up to 70 centimetres down.

Like all molluscs, the clam has a muscular foot, but it’s not that muscular. Based on measurements of the foot’s strength, Amos Winter from Massachussetts Institute of Technology calculated that it should only be able to dig a couple of centimetres into the mud. It shouldn’t be able to submerge its body, much less create a burrow five times longer.

But Winter knows the razor clam’s secret: it doesn’t just rely on raw power. The clam adds water to the soil just below it, making it softer and easier to penetrate. It digs by turning part of a beach into quicksand.

The clam’s digging equipment couldn’t be simpler: a pair of long valves that run the length of its body and open or close its shell; and a foot that sits beneath the them. It extends the foot downwards and pushes against it to lift the shell up slightly. Then, it contracts the valves, sending blood into the foot and inflating it. This foot becomes an anchor. By pulling against it, the clam can drag its shell downwards.

To understand how these motions create a burrow despite the foot’s weedy nature, Winter had to capture several clams. And to do that, he had to become a licensed clam digger. Back in the lab, studying the clams wasn’t easy. As Winter writes in a wonderfully deadpan academic way: “The adage ‘clear as mud’ is used to describe the difficulty of visually investigating burrowing animals.” He finally saw what the clams were doing when he created a homemade “visualiser”— a repurposed ant farm. The animal was trapped between two transparent plates, filmed with high-speed cameras, and surrounded by a ‘beach’ of glass beads.

Winter’s videos revealed that when the clam contracts its valves, it does more than just pump the foot with blood. The contraction closes its shell, which relieves the pressure on the surrounding soil. The soil starts to crumble, and mixes with water pulled into the gap from above. The water “fluidises” the soil, making it soft and loose like quicksand. It offers far less resistance, and the clam can move through it with around ten times less energy. It does so quickly, before the soil has a chance to solidify again.

Winter isn’t just studying clams for the sake of it. The list of sponsors for his study is telling: Battelle Memorial Institute, a science and technology development company; Bluefin Robotics; and the Chevron Corporation, an energy company that explores for oil and gas.

Winter used his newfound knowledge to create RoboClam: a robot that duplicates the clam’s burrowing technique. It’s about the size of a lighter, but it comes with a much larger supportive frame of pistons and regulating elements. After further development, RoboClam could act as a lightweight anchor that could be easily set and unset. It could tether small robotic submarines for studying the ocean floor; help to install undersea cables or deep-water oil rigs; or even detonate buried underwater mines.

Reference: Winter, Deits & Hosoi. 2012. Localized fluidization burrowing mechanics of Ensis directus. Journal of Experimental Biology

Photo by Arne Huckelheim

Fire-chasing beetles sense infrared radiation from fires hundreds of kilometres away

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

In the 1940s, visitors watching football games at Berkeley’s Californian Memorial Stadium would often be plagued by beetles. The insects swarmed their clothes and bit them on the necks and hands. The cause: cigarettes. The crowds smoked so heavily that a cloud of smoke hung over the stadium. And where there’s smoke, there’s fire. And where there’s fire, there are fire-chaser beetles.

While most animals flee from fires, fire-chaser beetles (Melanophila) head towards a blaze. They can only lay their eggs in freshly burnt trees, whose defences have been scorched away. Fire is such an essential part of the beetles’ life cycle that they’ll travel over 60 kilometres to find it. They’re not fussy about the source, either. Forest fires will obviously do, but so will industrial plants, kilns, burning oil barrels, vats of hot sugar syrup, and even cigarette-puffing sports fans.

The beetles find fire with a pair of pits below their middle pair of legs. Each is only as wide as a few human hairs, and consists of 70 dome-shaped sensors. They look a bit like insect eyes. In the 1960s, scientists showed that the sensors detect the infrared radiation given off by hot objects. Each one is filled with liquid, which expands when it absorbs infrared radiation. This motion stimulates sensory cells and tells the beetle that there’s heat afoot.

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I've got your missing links right here (26 May 2012)

By Ed Yong | May 26, 2012 12:00 pm

Top picks

This is beautiful. Alexis Madrigal watches an eclipse by turning his fist into a pinhole camera, entrances passers-by

Must-read piece on the NSABB – the board that assessed the risk of those mutant flu papers – by Brendan Maher

Do Plants Smell Other Plants? This One Does, Then Strangles What It Smells. By Robert Krulwich. Love the diagrams!

The ultimate counterfeiter, who fancies himself an artist. A brilliant piece of narrative journalism by David Wolman.

For all the concern about Fukushima, did you know that tobacco smoke contains radioactive polonium? The tobcco industry did.

Deathtraps so beautiful you could cry (and I did). Jennifer Frazer on glow worms.

I love this piece so much. 10 science concepts that would make awesome supervillains

The CIA’s fake vaccination campaign to get bin Laden: still undermining state relations, polio eradication

Human water use on land accounts for 42% of sea level rise between 1961 and 2003; climate change, the rest.

Report about questionable research practices practises questionable research practices

Cancer risk from Fukushima radiation is very low but the mental health risks are high. “I’ve never seen PTSD questionnaires like this.” Essential reporting from Geoff Brumfiel

How One Flawed Study Spawned a Decade of Lies – Forbes covers the man who supported a gay cure, and is now apologising for it.

What is the “Bible of Psychiatry” supposed to do? DSM & challenges of uncertain science, by Vaughan Bell

Space junk piling up around Earth has reached a tipping point. So how are we going to get rid of it? (UK people: use Anonymouse)

What Mark Henderson’s The Geek Manifesto has to say on GM crops. Essential reading for the Take the Flour Back campaign.

Despite all the worry about Fukushima, smokers have been inhaling radioactive particles for decades

Nicotine – murder weapon of choice for the 19th century blackguard, by Deborah Blum.

Citizens in Space is sponsoring… a $10,000 competition to detect organisms at the edge of space.”

“It belongs in a museum!!” Tyrannosaur illegally smuggled out of Mongolia, ends up in auction, by Brian Switek

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Neurons transplanted into mouse spines reverse chronic pain

By Ed Yong | May 24, 2012 11:10 am

Several neural diseases, including chronic pain and epilepsy, involve a lack of restraint. That is, damage to nerves in the spine reduces the levels of a signalling chemical called GABA, which silences excitable neurons. The result: too much neural activity.

There are drugs that can restore GABA, but they don’t always work, they are only temporary and they have unwanted side effects like sedation. There is another option: transplant GABA-producing neurons directly into the spine. Scientists have now done this in mice, with successful results.

I covered the story for The Scientist. Check it out.

Photo by Nanny Snowflake

CATEGORIZED UNDER: Neuroscience and psychology

Virtual resurrection shows that early four-legged animal couldn’t walk very well

By Ed Yong | May 23, 2012 2:00 pm

In a small office north of London, Stephanie Pierce from the Royal Veterinary College is watching a movement that hasn’t been seen for 360 million years. On her computer, she has resurrected the long-extinct Ichthyostega – one of the earliest four-legged animals to creep about on land. By recreating this iconic beast as a virtual skeleton, Pierce has shown that while it looked like a giant salamander, it couldn’t possibly have walked like one. It had some of the planet’s earliest bony legs, but they weren’t very good at taking steps.

Ichthyostega hails from the Devonian period, a time in Earth’s history when swimming transformed into walking. Fish invaded the land and evolved into the first tetrapods—four-limbed animals that include amphibians, reptiles, birds and mammals.  Muscular fins used for steering and balance evolved into legs for walking.

Since its discovery over 50 years ago, Ichthyostega has been an icon of this pivotal transition. Some 300 specimens have been found but many are incomplete, flattened or distorted. Pierce’s new model provides the best look yet at the animal’s skeleton. “It makes Ichthyostega a bit more tangible,” she says. “It’s not just a fossil laying in a rock now. It’s an animal that’s coming to life.”

Pierce built her virtual skeleton by putting dozens of Ichthyostega specimens in powerful CT-scanners, choosing only the best preserved ones out of the 300 or so in existence. “The front end of the animal was mainly composed from one beautifully preserved specimen called ‘Mr Magic’,” she says.

It was painstaking work. These fossils are so old that chemically, they are almost identical to the rocks around them. By eye, the bones stand out. To the scanners, they blend in. Pierce spent over two years scanning the specimens and building her model, but the results were worth it. “This has been on the wish-list for years,” says Michael Coates, who studies tetrapod evolution at the University of Chicago.

Those boots weren’t made for walking…

The model showed that Ichthyostega’s shoulders and hips were oddly restricted. They could move back and forth, and up and down, but they couldn’t rotate about their long axis. Hold your arm out and rotate your palm so it faces up then down—Ichthyostega’s shoulder couldn’t do that.

Most modern tetrapods need long-axis rotation in order to walk. Without it, their legs can’t be thrown forward or pulled backward. Ichthyostega’s limitations meant that despite having four limbs, it probably couldn’t have taken a step. It hind feet would never have been planted flat against the ground or supported its weight. It had invaded the land, but it wasn’t striding across it.

“It highlights the fact that the earliest tetrapods are not just ‘gigantic salamanders’, despite a vague similarity in outline,” says Per Ahlberg from Uppsala University. “The limbs and girdles are very different from anything now living.”

Pierce thinks that Ichthyostega moved by paddle with its front limbs, using powerful muscles and flexible elbows to make rowing motions. The closest living analogue is probably the mudskipper – a fish that drags itself along muddy land with its front fins (as in the video below).

Pierce also compared Ichthyostega’s joints and limbs to those of other living animals with sinuous bodies and interesting gaits, including a salamander, crocodile, seal, otter and platypus. Compared to these modern species, Ichthyostega’s hips and shoulders were similarly flexible in most planes of movements, but along their long axis, they could barely rotate.

Some scientists think that the tetrapods evolved limbs before they could walk, and their first members lived in shallow water. Others think that it’s the other way round, and that muscular limbs, hips and shoulders evolved while fish still had fins. The virtual Ichthyostega supports the former idea, since it had limbs but couldn’t walk. But Coates cautions against “fitting a smooth transition from swimmers to walkers.” He says, “Evolutionary transitions needn’t follow linear routes. Ichthyostega probably represents one of multiple experiments among the first tetrapods with limbs, trying-out life in the shallows.”

So… what made those tracks?

Other early tetrapods had similar shoulders and hips, so they probably had the same limitations too. John Hutchinson, who led the new study, plans to find out. His lab is busy reconstructing other early tetrapods including Acanthostega, one of Ichthyostega’s contemporaries, and Pederpes, a later model.

But Ahlberg notes that Ichthyostega had a very unusual and rigid spine, and may not have been representative of other early tetrapods. “Other tetrapods are known to have had more flexible spines” he says, “and this probably allowed them to overcome the limitations of their shoulders and hips”.

This might explain why Ahlberg and others have discovered tracks that pre-date Ichthyostega by around 20 million years, and had become fairly common by the time it evolved. Many of these tracks showed precisely the kind of salamander-like movements that Ichthyostega was apparently incapable of making. They were clearly made by early four-legged tetrapods, and to this date, we don’t know what made them.

Pierce agrees that the final word on Ichthyostega’s movements will have to wait until she can animate its entire skeleton. “The ultimate goal would be to try and create some sort of dynamic movement,” she says. She has applied for a grant to do just that, to model the motions of the entire animal, and compare them to salamanders or crocodiles. “That’s going to take so much time, but it’ll be very interesting,” she says.

PS: I want to point out that in researching this story, I spent a good minute on my living room floor trying to walk without long-axis rotation. It was really hard, and I looked like an idiot. I did a similar thing when I was writing about hummingbird wing movements for Nature. I’m going to christen this Method Science Journalism.

Reference: Pierce, Clack & Hutchinson. 2012. Three-dimensional limb joint mobility in the early tetrapod Ichthyostega. Nature

Image by Julie Molnar

More on tetrapods:

Fossil tracks push back the invasion of land by 18 million years

Fish fins and mouse feet controlled by the same ancient genetic switch


New sense organ helps giant whales to coordinate the world’s biggest mouthfuls

By Ed Yong | May 23, 2012 1:00 pm

The world’s largest animals have been hiding something. The bodies of the giant rorqual whales—including the blue, fin and humpback—have been regularly displayed in museums, filmed by documentary makers, and harpooned by hunters. Despite this attention, no one noticed the volleyball-sized sense organ at the tips of their lower jaws. Nicholas Pyenson from the Smithsonian Institution is the first, and he thinks that the whales use this structure to coordinate the planet’s biggest mouthfuls.

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Here's where all the magic happens

By Ed Yong | May 23, 2012 10:11 am

And by magic, I mean mixed metaphors, endless hours on Twitter, and tears.

The Open Notebook has a series called Natural Habitat, which looks at the space in which science writers work. I, perhaps foolishly, agreed to take part in it. You can find the resulting video and photos here, featuring the local pub, treelancing (TM), and a cuddly giant squid.




Blind mice regain sight after scientists persuade their optic nerves to grow

By Ed Yong | May 21, 2012 3:00 pm

A mouse optic nerve with new axons (in red) running all the way along it.

A blind man sees his fiancée’s smile for the first time. Another walks around at night, navigating via streetlamps and headlights. Yet another reads his own name (and spots a typo). All three had lost their sight years before, as an inherited disorder destroyed the light-sensing cells of their retinas. But they had since been fitted with retinal implants that took over from the broken cells, sensing incoming light, and converting it into electrical impulses delivered to the brain. The devices are a long way from 20/20 vision, but they have nonetheless restored sight to those who had lived without it for years.

These retinal implants seem miraculous, but they have a major drawback: they rely upon a working optic nerve. This is the main communication line between the eye and the brain. If it’s damaged, no amount of retinal techno-wizardry will help. And that’s bad news for people with glaucoma, the world’s second leading cause of blindness, which wrecks the optic nerve.

But even for those people, there is hope. Silmara de Lima from the Children’s Hospital in Boston has found a way of regenerating the optic nerve in adult mice, partly restoring their vision. Although his techniques cannot be used directly in humans, they provide an important proof of principle that optic nerve injuries can be reversed. We just need to figure out how.

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CATEGORIZED UNDER: Medicine & health

I've got your missing links right here (19 May 2012)

By Ed Yong | May 19, 2012 12:00 pm

Top picks

Manta rays depend on forests. Carl Zimmer on top form.

The evidence for precognition was staring us in the face all along. Hilarious satire of psychology’s problems.

How a professor who fooled Wikipedia got caught by Reddit – implications for ”truth” online. Great story by Yoni Applebaum.

Not allowed to have a small heart: great long read from Greg Downey on Tourette Syndrome

Living photography. This is as cool as it sounds

Committee assesses ethics of trial, in which kids would get an anthrax vaccine unlikely to ever be necessary. But Project “Dark Zephyr”?? Are you kidding me? With a straight face? What about Project “Shadow Mistral”. Or “Hot Air”

My BBC column “Will we ever….?” now has guest stars. First up: John Pavlus on the Turing test.

Helen Pearson talks to The Open Notebook about her seriously good profile of protein-resurrector Joe Thornton

Doctors ‘rewire’ hands of paralysed man. Great story by Ian Sample

This tiny sphere is all the world’s water. (And as usual, America is hoarding it ;-p)

Not all neurons are exactly alike. The brain contains multitudes.” – a new series on neurons by Ferris Jabr, which continues, with a look into the various types of neurons.

Is the Purpose of Sleep to Let Our Brains “Defragment,” Like a Hard Drive? Great piece by the Neuroskeptic.

When an Autism Diagnosis Comes as a Blessing – when Steve Silberman writes book reviews, you know it’s going to be much more than that.

“They look like yearbook portraits from a sanitorium.” Darwin’s creepiest experiment recreated online

With a book on life’s origin & a radio series on extinction, Adam Rutherford is doing life from both ends. So to speak. Listen to his docu.

Tapeworms in the brain are surprisingly common. I warn you: Carl Zimmer has found an image that made even me feel ill

Remember the weird placental jellyfish thing? Here’s some amazing footage of it – Deepstaria enigmatica

Our innate hotness might explain why we’re not being wiped out by fungal blights like bats or frogs. Very cool idea

Deborah Blum christens her new digs at Wired with a post about poisoning the Dalai Lama

Stunning story. How disruptions to the National Children’s Study are hitting the parents who signed up for it

Restoring sight with wireless implants. Very interesting differences to current approaches using retinal implants. Very cool!


“In science, if no one else can make the experiment work, it didn’t happen” – John Hawks riffing on my Nature replication piece

Speaking science to power.

Read Holly Bik’s great post about microbes at sea. I’m never getting on a ship again

Pretty! Trapped in amber, the earliest evidence of pollination

YAWN! Jason Goldman on contagious yawning and empathy

Analyzing an exome to understand a disease is like reading the CliffsNotes version of a classic book.”

“People are quick to assume that what they do is “natural” simply because they don’t know where things are done differently” – Eric Michael Johnson on breastfeeding

Maurice Ward & his secret material Starlite – by Richard Fisher

Why Octopuses Should Run Our National Security Infrastructure

A platonic Tube? World’s subways converging on an ideal form

Fearsome as they are, pliosaurs can still fall victim to churnalism

These folks mapped connection damage in Phineas Gage’s brain (guy who took an iron rod to head). This just seems pointless. Obviously, it’s not Gage’s actual brain. It’s a rod going through a simulation based on lots of other brains, so it’s impossible to say what actually happened with Gage & how that maps to his behaviour changes. So all we really know is that the extent of damage goes beyond specific areas. Erm… yeah. There’s a bloody iron rod in his head. The “Limitations” section basically says: “Could be useless… <awkward shuffle>” Fig1 is fantastic though. I’m not a neuroscientist but I think I’ve worked out where the problem is.

The penultimate para of this Maryn McKenna piece on drug-resistant bacteria will chill your blood


Coffee story in The Atlantic. I winced once at “really does”, twice at “after all” and just wept openly at the rest. Do. Not. Like. Much better in the Boston Globe: Some NEJM editors didn’t want to publish the study on coffee and longer life because of flaws.

Christie Wilcox’s editorial in The Biological Bulletin on why social media is good for scientists.

The climate-change-denying Heartland Institute’s ties to the tobacco industry

The more you know about breast cancer, the more inaccurate your perception of risk

Aquatic dinosaurs?  Darren Naish has a thorough take-down

Scientist resigns from board of journal that restricts access

More on Chabris vs. Lehrer & provisional nature of science + science writing (with a mad Gladwell blurb)

Goblin shark FTMFW! A list of awesome sharks you should get to know

Absolutely wicked visual illusion – beautiful people turn ugly

Guppies lust after killer orange prawn

ADHD Behavioral Therapy May Be More Effective Than Drugs in Long Run (but more expensive)

Explore your microbiome. Absolutely *stunning* graphic (although possible errors)

Block one pit viper eye & the opposite heat-sensing pit, and its strike accuracy gets *really* bad. Now you know.

This long-predicted superweed problem with GM crops has arrived.

SCIENCE! Antarctic Ice Sheet Collapse Recorded In Octopus DNA

A great hilarious video from Virginia Hughes explaining a time-saving technique in neuroscience

We need to talk about Michael. Can You Call a 9-Year-Old a Psychopath?

Why are harps harp-shaped? What does the big curve on the top do?

“The invasion of the Can’t-Help-Yourself books.”

This will go really badly: parents are buying their own oxytocin in attempt at DIY autism ‘treatment’

Which country wants to medicate a prisoner so they can execute him sane? Yep.

What’s actually interesting about covering climate change?

“Childish, misguided and disproportionate” – James Wilsdon on protests about death of British science

Dodgy study about a gene linked to post-traumatic stress syndrome. I didn’t report this after advice on methods from geneticists. Likely to be a false-positive.

Everything you need to know about the scientific controversy that could change Triceratops forever. Not sure about that last bit, but if it means that Triceratops absorbs other species, that’s fine.

Livestock bacteria are as old as the livestock they kill

The pen that lets you draw electrical circuits

Skilled liars make great lie detectors

A brain litmus! fMRI could be used to measure the acidity of the brain

Critical point: mental health diagnoses don’t just categorise behaviour, but *affect* it

Map calculates Roman travel times

Crows recognize familiar human voices

Chimp testing – beginning of the end? Good fair coverage of complicated debate

Man behind a “gay cure” study apologizes. A really good read.

Next to giant snake, a giant-snake-proof turtle

Science’s special issue on conflict, free with registration.

What would count as an alternative form of life? A smart essay by Gerald Joyce

Heh. XKCD on the arse-clenching awfulness that is Klout

Bodes poorly when a reviewer must translate text of a sci e-book for readers. But awesome when it’s Veronique Greenwood.

The Secret to Success Is Giant-Jawed Snake Babies



I’d always wondered about this. Good to see science tackling humanity’s most pressing problems

Collaged images from encyclopedias and nature books suspended in plexiglas

Disappearing hand trick wins illusion of the year. If I’d known it would be that easy, I’d have brought my hacksaw

Amazing. “Above is Andy eating his own brain.” How to make a chocolate model of your brain

Online comment-writers to get own internet. Masturnet – “pics of things w/ ‘Why do you hate this?’ underneath”

100% accurate charts of sea creature anatomy

HA! “France surrenders to Thor

XKCD nails Apple’s biggest problem

LOVE THESE! Photo project memorializes fallen insects

When unrelated tweets just work together



TED: Ideas worth spreading… unless they piss off rich people

It’s 22 years since Jim Henson died. Which means, The Saddest Photo In The World

How Yahoo killed Flickr

Hey, remember when Google did search? So have they.

Aw. Reddit Users Surprise Terminally Ill Man With Random Acts of Kindness

Excellent trolling of bad journalists by an American athlete, using a pair of platypus

Sugar makes embargoes stupid, and doesn’t do wonders for a press release, either

Why promote young writers? An interview with Bora Zivkovic.

Your daily WTF: Kodak had a weapons-grade nuclear reactor in its basement, full of uranium

Stimulating. Can a new and improved vibrator inspire an age of great American sex?

I’m an article about the internet that you repost on the internet.

Tip for journos: try to do things that can’t be done by a robot. Enslave humanity: out. Narratives: in.

Who are the people who use ResearchBlogging? (Very weird to see my own name in a journal paper)

Megan Garber looks at what made Shutterstock so successful.

Pre-release torrent leaks actually benefit album sales



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