Archive for April, 2012

Synthetic XNA molecules can evolve and store genetic information, just like DNA

By Ed Yong | April 19, 2012 2:00 pm

Out of all the possible molecules in the world, just two form the basis of life’s grand variety: DNA and RNA. They alone can store and pass on genetic information. Within their repetitive twists, these polymers encode the stuff of every whale, ant, flower, tree and bacterium.

But even though DNA and RNA play these roles exclusively, they’re not the only molecules that can. Vitor Pinheiro from the MRC Laboratory of Molecular Biology has developed six alternative polymers called XNAs that can also store genetic information and evolve through natural selection. None of them are found in nature. They are part of a dawning era of “synthetic genetics”, which expands the chemistry of life in new uncharted directions.

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Brain decoder allows monkeys to control paralysed muscles

By Ed Yong | April 19, 2012 6:40 am

Spinal injuries often leave people with paralysed limbs, as commands from their brains can no longer reach the muscles in their arms. So why not bypass the spine entirely? A team from Northwestern University has used a brain decoder to give monkeys control over their temporarily anaesthetised arms. The decoder deciphers the activity in the monkey’s motor cortex (the part of the brain that controls movements), and electrodes in the monkey’s arm stimulate its muscles in the right way. Even though it can’t feel its arm, it can grab a ball using this electronic middle-man.

I covered this research in more detail at The Scientist, including some comments from a few skeptical scientists, who are concerned about the technique’s limitations.

Scientists transform scar tissue into beating heart muscle

By Ed Yong | April 18, 2012 1:00 pm

In an act of transformation worthy of any magician, scientists have converted scar tissue in the hearts of living mice into beating heart cells. If the same trick works in humans (and we’re still several years away from a trial), it could lead us to a long-sought prize of medicine – a way to mend a broken heart.

Our hearts are made of several different types of cell. These include muscle cells called cardiomyocytes, which contract together to give hearts their beats, and connective cells called cardiac fibroblasts, which provide support. The fibroblasts make up half of a heart, but they become even more common after a heart attack. If hearts are injured, they replace lost cardiomyocytes with scar tissue, consisting of fibroblasts. In the short-term, this provides support for damaged tissue. In the long-term, it weakens the heart and increases the risk of even further problems.

Hearts can’t reverse this scarring. Despite their vital nature, they are terrible at healing themselves. But Deepak Srivastava from the Gladstone Institute of Cardiovascular Disease can persuade them to do so with the right chemical cocktail. In 2010, he showed that just three genes – Gata4, Mef2c and Tbx5 (or GMT)– could transform fibroblasts into new cardiomyocytes.

This only worked in cells growing in a laboratory dish, but it was a start. Srivastava’s team have now taken the next step. By injecting living mice with GMT, they turned some of the rodents’ fibroblasts into cardiomyocytes. Since hearts are already loaded with fibroblasts, Srivastava’s technique simply conscripts them into muscle duty. Best of all, the technique worked even better in the animals than in isolated cells. No transplants. No surgeries. No stem cells. Just add three genes, and watch sick hearts turn into healthier ones.

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Scientists crawl into tower of poo to understand reasons for swift decline

By Ed Yong | April 17, 2012 7:00 pm

For some scientists, an academic career can feel like crawling into a tower of crap. For other scientists, an academic career actually involves crawling into a tower of crap.

Since 1928, thousands of chimney swifts have roosted at Fleming Hall, a university building in Kingston, Ontario. For decades, they fed on local insects, and excreted the remains down one of the building’s chimneys. Around 2 centimetres of droppings, or ‘guano’, built up every year until the chimney was finally capped in 1992. To this date, Fleming Hall contains a hardened guano tower, two metres tall and 64 years in the making, which preserves a layered record of the swifts’ meals.

Now, a team of scientists, led by Joseph Nocera, have used this archive of historical poo to explain why the swift populations have fallen by 90 per cent since their heyday.

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Kangaroos have three vaginas

By Ed Yong | April 17, 2012 11:20 am

We interrupt your regularly scheduled news programming to bring you this wonderful piece of trivia about kangaroo genitals.

Regular readers will know of my love for Inside Nature’s Giants, the British documentary where anatomists cut up large animals to examine how their bodies work and evolved. It’s a truly incredible show, combining unbridled joy at the natural world, drama, and solid educational value.

So far, it has brought us the horrifying throat of a leatherback turtle, the mysterious bloodsweat of a hippo, and the exploding insides of a beached whale. But this week’s episode may have topped all of that with the triple vaginas of the female kangaroo. The diagram above (an annotated screengrab from the show) explains the complicated plumbing.

This set-up is shared by all marsupials – the group of mammals that raise their young in pouches. Koalas, wombats and Tasmanian devils all share the three-vagina structure. The side ones carry sperm to the two uteruses (and males marsupials often have two-pronged penises), while the middle vagina sends the joey down to the outside world.

Note that the ureters, which carry urine from the kidneys to the bladder, pass through the gaps between the three tubes. In placental mammals, like us, the ureters develop in a different way, and don’t go through the reproductive system. As we develop, the precursors to the reproductive tubes eventually fuse into a single vagina. In marsupials, this can’t happen.

The programme also suggested that this might explain why marsupial embryos are born at such a premature stage of development. A kangaroo’s joey is about the size of a jellybean when it leaves the vagina, and it must endure an arduous crawl into the pouch. It’s possible that with such a narrow tube to go down, it couldn’t get any bigger before its birth.

With its complicated reproductive set-up, a female kangaroo can be perpetually pregnant. While one joey is developing inside the pouch, another embryo is held in reserve in a uterus, waiting for its sibling to grow up and leave. Indeed, a mother kangaroo can nourish three separate youngsters at a time – an older joey that has left the pouch, a young one developing inside it, and an embryo still waiting to be born.

How orangutan engineers build safe and comfortable treetop beds

By Ed Yong | April 16, 2012 3:00 pm

We normally think of nests as the creations of birds, but our ape cousins build nests too. Orangutans, gorillas, chimpanzees and bonobos all build tree beds, by weaving branches, twigs and leaves together into a bowl-shaped cradle. These nests may provide safety from predators, or help the apes to sleep warm.* But it seems that their main function is to provide a good night’s rest. Sleeping against a tree bough is hard on a large ape, and nests offer a more comfortable option.

Of all the apes, orangutans reputedly create the sturdiest and most elaborate nests. By studying the physical properties of these treetop bunks, Adam van Casteren from the University of Manchester has found that the apes are skilled engineers. As befits animals of their intelligence, they don’t just mash branches together. Instead, they seem to have an impressive amount of technical knowledge about their construction materials.

Orangutans build their nests between 11 and 20 metres up. Once they choose a good spot on a sturdy branch, they bend or break other branches in towards them, and weave them in place to create a basic foundation. On top of that, they add smaller branches to create a ‘mattress’. That’s the basic model, and some orangutans add deluxe features. They can create blankets, by covering themselves with large leafy branches, or pillows, by clumping such branches together. They can loosely braid branches above their heads to make a roof, or even create a secondary ‘bunk-nest’ over the main one.

Like all apes, orangutans construct new ones every day. This means that intrepid scientists have plenty of old discarded nests to study. Van Casteren, along with Julia Myatt from the Royal Veterinary College, found 14 such nests in the Sumatran rainforest. They hoisted themselves into the canopy, attached ropes to different parts of the nests, and lowered these to the ground where team members were waiting with force gauges. “Climbing up into the high canopy is breathtaking,” says van Casteren. “You enter an area of the forest that isn’t used to having humans hang around in it.”


Van Casteren found that orangutans use thicker branches in the structural foundation of the nest, and thinner branches in the mattress. The structural ones are four times stronger and four times more rigid, and they make the nest sturdy. The mattress branches are thinner and more flexible for comfort.

The orangutans also break the two types of branches in different ways. If you bend a dense branch, it will only break halfway – this is known as a “greenstick fracture (see below). That’s what van Casteren found in the structural part of the nest. Once broken like this, it’s surprisingly hard to fully snap a branch in two, even for a powerful animal like an orangutan. The trick is to twist the branch. The fracture extends outwards until the two halves come apart, producing two pieces with long tapered ‘tails’.  Van Casteren filmed the apes using this technique, and the found plenty of the distinctive tailed branches in their mattresses.

There are plenty of questions about the nests left to answer. For example, orangutans don’t choose their trees randomly, and actually avoid the most common species. What’s special about the ones they pick, and does that factor into the properties of the nests? The apes also learn their craft from adults, so do immature orangutans build nests with less distinctive foundations and mattresses? Van Casteren also wants to look at the nests of other great apes, and of other architects such as beaver or birds, to see if he gets similar results.

But for now, his data already show that orangutans make sophisticated technical choices when they build their nests. He thinks that they account for the different properties of the materials in their environment, and use those properties to make bunks that are both safe and comfortable. While many studies of animal intelligence focus on the use of tools, he argues that nest-building is no less mentally demanding.

Roland Ennos, who was involved in the study, says, “I hope helps to show how the evolution of intelligence can be driven by the need to deal with the mechanical environment, rather than the prevailing orthodoxy that it’s only the social environment that’s important.”

* In writing this story, I stumbled across a wonderful study by Fiona Stewart from the University of Cambridge, who tested the value of chimpanzee nests, by sleeping in them. She spent several nights in Senegal either sleeping in newly made chimp beds or on the bare ground. She was warmer in the nests, and received fewer insect bites. She didn’t get any more sleep, but what she got was less disturbed. “Terrestrial animals, including hyenas, were more concerning during ground sleep, although snakes were always a concern,” she writes, in a wonderfully deadpan way. Van Casteren, however, never tried to sleep in the orangutan nests that he studied. They are higher than a chimp’s and he was “too worried about falling out mid-dream”.

Reference: Van Casteren, Sellers, Thorpe, Coward, Crompton, Myatt & Ennos. 2012. Nest-building orangutans demonstrate engineering know-how to produce safe, comfortable beds. PNAS

Images courtesy of Adam van Casteren

More on orangutans


I've got your missing links right here (14 April 2012)

By Ed Yong | April 14, 2012 12:00 pm

Top picks

The entire population of a species, counted from space! Awesome emperor penguin study

Can a hallucinogen from Africa cure addiction? Very interesting article on ibogaine

Lovely logical paradox (or not) about the infiniteness of universes

Lovely Atlantic photo gallery of water on our world

And another great example of a scientist blogging own research. Crystal-clear explanation of why imperfect mimics survive

Jonah Lehrer interviews the legendary neuroscientist Eric Kandel about Klimt, Freud, neuroaesthetics and “The Age of Insight”

The Chocolate-and-Radish Experiment That Birthed the Modern Conception of Willpower. Great Alexis Madrigal piece.

Controversy Deepens Over Pesticides and Bee Collapse. Very solid reporting by Brandon Keim

Blind woman writing a novel longhand didn’t know her pen had run out. She asked police for help.

Very cool. Scientists use knowledge of local fishermen to understand the fluid dynamics of a lake

Can You Predict a Monkey’s Social Status by Looking at Its Genes? Great Ferris Jabr piece.

This is a superb example of scientists blogging own work: Chris Chambers gives an insightful and thorough look into his work on whether feedback could rebuild vision. Read it.

I love XKCD’s amazing graphic of the world’s watery depths

Check out Paige Williams’ awesome annotated features. It’s the closest you’ll get to shadowing some of the world’s best journalists on assignment.

Early contender for the year’s worst press release. Are there hyper-intelligent alien dinosaurs? Weird paper says yes. Brian Switek says no.

Computer built using swarms of soldier crabs, by Olivia Solon.

A Spoonful of Molybdenum, some Ulysses and the Origin of Life.” Truly excellent writing from Lucas Brouwers about how an odd element may have been essential for life.


Love this. Alexis Madrigal riffs off my take on the baboon-‘reading’ study & compares the monkeys to Google. (My original piece)

“Less time separates us from Tyrannosaurus rex than separated T. rex from Stegosaurus.”

Forget polar bears, science says climate communications should show pics of dying plants

Making a career transition: 13 stories of routes into and out of a career in science

“In 70% of cases where infectious disease causes extinction of an animal/plant, an emerging fungus is behind [it].”

This new paper debunking the compass in bird beaks is interesting – but they still have a quantum compass in their eye!

All the videos from the Royal Society’s H5N1 meeting are now up.

Goshawks single out “odd-coloured” pigeons as prey

Tardigrade eggs might survive interplanetary trip. Badass.

BBC Radio 4’s Today Programme mounts a pathetic defence of their aquatic dinosaur segment. Look folks, no one said you can’t do light-hearted science stories. But maybe, stop covering light-hearted bullsh*t?

Artificial Intelligence Could Be on Brink of Passing Turing Test” Good Brandon Keim piece but not sure I’m convinced.

Enemy me, please. On the benefits of having a nemesis

What birds were once like. Great fossil gallery.

Ancient herbal remedy leaves distinct gene signature of the widespread kidney failure & cancer it causes

The dominoes fall: Rising Ocean Temperatures Prime Amazon Rainforest for Fire

Einstein’s Advice to a Little Girl Who Wanted to Be a Scientist

British polar research is thawing out.

“Perhaps even worse than premature burial was the thought of being dissected while still alive.”

Not a new ant. Actually an ant riddled with worms. Nature punks taxonomists

Google Searches Give Away a Country’s GDP. Fascinating bit of research, covered by Elizabeth Preston.

Okay I LIKE spiders, but even I recoiled a bit at the pic labelled “stash of paralysed spiders

Er, oops. Sorry… Devastating Bat Fungus Invaded From Europe

Fascinating project by Richard Wiseman: is it possible to choose your dreams?

More citizen science – record your bird-watching w/ an app

Independent says “cuddle drug” oxytocin may be new Viagra. No, you blithering idiots. It’s not a cuddle drug, and this was a case report of ONE GUY.

Bird Flu Studies Mired In Export Control Law Limbo.

SciAm Brasil has apologised for its dreadful homeopathy article.

Bats on a plane

Brian Switek on prehistoric driller-killers

Children will pay for this: Tennesse passes ‘teach the controversy’ evolution bill


“Less marketing douchebaggery, more TANKS.”

Twitter Learns The Titanic Was Not Just A Movie. One of these ppl is called “Hope Dies”. Yes.

Hamster bites Spider-Man, gains spider-powers, gets stuck to cage

Ha! “Prometheus may feature ALF, hints Ridley Scott”

Woman recreates Flemish portraits in an airplane toilet

Heh. Funny species names. I love Heerz lukenatcha

Dog eats scientist’s labwork. Paper ensues

This week I learned that there’s a field of hydrothermal vents in the north Atlantic called Loki’s Castle

33 Animals Who Are Extremely Disappointed In You


With “hen,” Sweden officially introduces gender-neutral pronoun

Reporter posts joke press release about new job on his personal site; new employer fires him for doing it

A fantastic tool for analysing Pubmed queries

Subway platforms of the world

Kristina Bjoran mounts an able defence of wordy copy

Great series of interviews with newly fledged science writers


The Wellcome Trust runs into troubled times.

Minimalist Lego renditions of some of your favorite cartoons.

How 25 National Magazine Award Nominations Went To 25 Male Writers

Can computers replicate the human-like cadence of narrative journalism? A good piece, but it fails to convince me at the critical juncture.

The HuffPo’s “science” editor asks readers: Is climate science true?

“There’s a difference between a temple that invites you to gasp open-mouthed & one that invites you in for tea.” – Alice Bell on plans for an atheist temple.

People who like “being gits” may also like “payback”: Big-6 publishers refuse to sign Amazon contracts

Facebook bought Instagram. Also Christmas, hugs, and kittens.

Unmarketing, and what it means for science writers

When Losers Write History: Why legacy-newspaper reporters get their own industry so wrong



Isolated for millions of years, cave bacteria resist modern antibiotics

By Ed Yong | April 13, 2012 9:00 am

The caverns of Lechuguilla Cave are some of the strangest on the planet. Its acid-carved passages extend for over 120 miles. They’re filled with a wonderland of straws, balloons, plates, stalactites of rust, and chandeliers of crystal.

Parts of Lechuguilla have been cut off from the surface for four to seven million years, and the life-forms there – mainly bacteria and other microbes – have charted their own evolutionary courses. But Gerry Wright from McMaster University in Canada has found that many of these cave bacteria can resist our antibiotics. They have been living underground for as long as modern humans have existed, but they can fend off our most potent weapons. Drug resistance may be causing problems for us now, but for bacteria, it’s just an ancient solution to an ancient problem.

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Reading without understanding: baboons can tell real English words from fake ones

By Ed Yong | April 12, 2012 2:00 pm

‘Wasp’ is an English word, but ‘telk’ is not. You and I know this because we speak English. But in a French laboratory, six baboons have also learned to tell the difference between genuine English words, and nonsense ones. They can sort their wasps from their telks, even though they have no idea that the former means a stinging insect and the latter means nothing. They don’t understand the language, but can ‘read’ nonetheless.

At its most basic level, reading is about recognising patterns. We look at letters (or other symbols) and identify them based on their number, position and angles of lines. This is a trivial task, and one that doesn’t require any language. Letters are no different to any other object in our environment that we can recognise. A pigeon can be trained to do discriminate between letters.

The next step is harder. We unite letters into words by looking at their positions relative to one another. This is called “orthographic processing”. It’s the stage where, according to general consensus, language kicks in. As we see clusters of letters, we think about the sounds they represent and we read the word aloud in our heads. But Jonathan Grainger from Aix-Marseille University has shown that orthographic processing can happen without any knowledge of language, or how words are meant to sound.

Grainger trained baboons to recognise English words, and tell them apart from very similar nonsense words. The monkeys learned quickly, and could even categorise words they had never seen before. They weren’t anglophiles by any stretch. Instead, their abilities suggest that the act of reading words is just a more advanced version of the pattern-recognition skill that lets us identify letters. It’s a skill that was there long before the first human had scrawled the first letter.

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Tiny insect soldiers with butch forearms are actually medics

By Ed Yong | April 11, 2012 9:00 am

Many insect colonies have troops of soldiers, which defend their nests with special weapons like massive jaws or chemical guns. Kladothrips intermedius is no exception – this tiny insect, known as a thrips, has soldiers that supposedly crush their enemies to death with butch forearms. But contrary to appearances, these big arms aren’t all that useful for fighting. Instead, they’re living pharmacies. Christine Turnbull from Macquarie University and Holly Caravan from Memorial University of Newfoundland have found that the thrips warriors are actually healers.

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