Archive for May, 2011

I've got your missing links right here (21 May 2011)

By Ed Yong | May 21, 2011 12:00 pm

Top thirteen picks

“It’s not a disease. It doesn’t need curing.” Steve Silberman talks to John Robison, a “free-range Aspergian” and best-selling author.

How to fund research so that it generates insanely great ideas, not pretty good ones – an awesome piece by Tim Harford.

Looking for empathy – v.good account of fMRI experiments in action, by Kristina Bjoran. I’m very dubious about whether this approach will yield anything, but Bjoran acknowledges and discusses the controversies about fMRI and describes the process well.

A great three-part series on Alan Turing’s homosexuality & how it was treated as a mental illness, by Romeo Vitelli.

Beautiful article on how one man’s death saved the lives of seven others

How ‘Hotel-Room Journalism’ Uncovered a Qaddafi Bunker

You might get cancer. Oh and your dad isn’t your dad. How a 23andMe test profoundly changed a woman’s life

A “kinder, gentler rib spreader” by Carl Zimmer

Plague in LA. And the man who gave plague his name. This blog is two-posts old but *what posts*!

Prophecy Fail. Vaughan Bell explores what happens to doomsday cults when the world inconsiderately refuses to end.

Levees can make things worse. A great and relevant post by Anne Jefferson on the illusion of flood control.

HELL YES! If you want to hear the actual Robert Krulwich future-of-journalism speech, it’s here! (links to mp3) (The transcript here)

Making a paralyzed man walk! And the research that led to it.

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CATEGORIZED UNDER: Links

Bad gossip affects our vision as well as our judgment

By Ed Yong | May 20, 2011 8:47 am

You’re chatting to some friends at a party and they point out someone standing in a different part of the room. That person, they inform you, is a nasty piece of work. He cheats on his girlfriend.  He picks fights with strangers. Once, he bit a puppy. You’d never seen him before but after this character assassination, you start noticing him everywhere – in other parties, on the street, on Facebook.

This sort of thing happens all the time. If we get information about people from third parties – gossip – we start paying more attention to those people. There’s a simple reason for this. Gossip, especially negative gossip, affects not only our judgment, but our vision too. It influences both what we think about someone and whether we see them in the first place.

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Life’s deliberate typos

By Ed Yong | May 19, 2011 2:00 pm

Within your body, a huge amount of information is copied over and over again, reliably and predictably. Your life depends on it. Typos occur, but they are quickly corrected. Edits are made, but sparingly. Or, at least, that’s what we thought.

It starts with DNA. This famous molecule is a chain of four ‘bases’, denoted by the letters A, C, G and T. These four letters, in various combinations, contain instructions for building thousands of proteins, a workforce of molecular machines that keep you alive and well. But first, DNA has to be copied (or “transcribed”) into a related molecule called RNA. It too is made of four bases: A, C and G reprise their roles, but U stands in for T. Each triplet of letters in RNA denotes a different amino acid, the building blocks of proteins. Small factories read along the RNA like a piece of tickertape, using it to string together amino acids in the right sequence.

So DNA leads to RNA leads to proteins – this is the grandiosely-named “central dogma of life”.

People often assume that this flow of information happens with exacting precision. Every stretch of RNA should be a perfect match for the piece of DNA it is copied from. Take a piece of DNA, and you could predict the exact string of letters in its corresponding piece of RNA, and the amino acids of the resulting protein.

But that’s not always the case.

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CATEGORIZED UNDER: Genetics, Genomics, Molecular biology

Cryptolacerta and the rise of the worm-lizards

By Ed Yong | May 18, 2011 1:00 pm

This animal is not an earthworm. It is long and sinuous, it lives underground, and its flanks look like they’re lined with rings. But it is not an earthworm – after all, it has a skeleton, jaws, scales, and two stubby legs. It is a “worm lizard” or amphisbaenian.

Amphisbaenians are a group of burrowing lizards, and one of the most mysterious groups of reptiles. They’re named after Amphisbaena, a Greek serpent with a second head on its tail – indeed, amphisbaeneans do have tails that look a bit like their heads. They are meat-eaters, and they search for their prey underground, burrowing through the soil with strong, reinforced skulls. Most species are completely legless, but four of them – the ajolotes (including the one in the photo above) – have bizarre, stunted arms.

Their origins are mysterious. Their bones suggest that they are close relatives of snakes and obviously, neither group has any legs. But their genes tell a different story – they say that the amphisbaenians are most closely related to the lacertids, a common group of lizards. Now, Johannes Muller from Berlin’s Natural History Museum has found a fossil lizard whose features might settle the debate in favour of the lacertid camp.

Muller named his animal Cryptolacerta hassiaca, which means “hidden lizard from Hesse”. He found it in the Messel Pit, a disused quarry near the town of Hesse. The quarry has no shortage of famous former residents, including the over-hyped Darwinius, the giant bird Gastornis, and leaves that were scarred by fungus-infected ants. Cryptolacerta is the latest addition to this treasure trove of famous fossils

Muller used a CT scanner to get a glimpse of Cryptolacerta’s body, which was fully preserved except for the tip of its tail. Its huge skull has many features that are characteristic of amphisbaenians, including small eye sockets, indicating tiny eyes, and heavy thickened bone, making it strong and inflexible. That’s a far cry from the light, bendy skulls of snakes. Its body, however, looks far more lizard-like – it obviously has four legs, albeit small ones.

Muller compared Cryptolacerta’s features with those of other modern reptiles, and produced a family tree that linked them together. Cryptolacerta itself sat at the base of the amphisbaenean branch – it was an early member of the group. Meanwhile, the amphisbaenians and lacertids sat on adjacent branches, far away from the snakes.

This supports the genetic view: amphisbaenians are closely related to lacertids, and their superficial similarity to snakes is a great example of convergent evolution. They both evolved long legless bodies in independent ways.

With its legs and squat body, Cryptolacerta clearly wasn’t the specialist burrower that the amphisbaenians have become. By comparing its shape to other lizards, Muller thinks that it spent its days hidden among the leaf litter, burrowing from time to time when the opportunity arose. This concealed lifestyle may have been an intermediate step between open-air scurrying and fulltime burrowing.

Many burrowing animals, from worms to legless lizards (and there are at least 8 groups of those), have long bodies and no limbs, so it’s tempting to think that these features are a prerequisite for an underground life. But Cryptolacerta, with its reinforced skull, tells a different story – it suggests that early amphisbaenians adapted to a digging lifestyle headfirst. Only after they thickened their skulls did they lose their legs and lengthen their body.

Reference: Muller, Hipsley, Head, Kardjilov, Hilger, Wuttke & Reisz. 2011. Eocene lizard from Germany reveals amphisbaenian origins. Nature http://dx.doi.org/10.1038/nature09919

Image by Gary Navis and Robert Reisz

More on lizards:

Tarantulas climb by shooting silk from their feet

By Ed Yong | May 16, 2011 4:59 am

If Spider-Man really could do “whatever a spider can”, he ought to shoot webs from somewhere less salubrious than his hands. All spiders spin silk from their rear ends, using special organs called spinnerets. But one group – the tarantulas – can also shoot silk from their feet, and they use this ability to climb up sheer vertical surfaces.

Tarantulas have been kept as pets for decades, but their silk-spinning feet were only discovered in 2006 by Stanislav Gorb from the Max Planck Institute. Gorb watched Costa Rican zebra tarantulas climbing up glass plates, and saw that they left behind silken footprints – dozens of fibres, just a thousandth of a millimetre wide.

As the spider climbs, four of its legs leave the glass plate at any one time. As the legs land, they begin to slip but small nozzles secrete a viscous silken fluid that rapidly hardens and adheres to the surface. The silk acts as a tether, firmly holding the spider to the pane.

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I've got your missing links right here (14 May 2011)

By Ed Yong | May 15, 2011 12:00 pm

Top thirteen picks

This almost made me cry. Calvin and Hobbes, 26 years later.

David Dobbs’s incredible post on how a family quest exposed barriers to open-access science

The Fracking Song. This is just marvellous. A musical explainer from Jay Rosen’s students. More on fracking from Nature News (Battlestar Galactica fans: try to read this without laughing)

An intrepid New Scientist reporter masturbates in an fMRI scanner to learn about the consciousness of orgasms

From Marietta diChristina, The 1000 Scientists in 1000 Days project – a Scientific American project that aims to create more scientific Americans.

Scientist looks in local pond, discovers entire new branch of fungi kingdom

I’m dying here. It’s “Inception,” summarized in 1 min. with OS X folder management.

Ent seeks entwife. The Loneliest Plant In The World by Robert Krulwich.

XKCD on female scientists, role models, and “being the next X.” Spot on, on so many levels.

Great piece on the science of being buried at sea, w/ flesh-eating shrimps & biodegradable shrouds

Life is beautiful, as is this post by Patrick Clarkin

A test that can distinguish between vegetative and minimally conscious states

Guarding your reputation online and why “Dr Anil Potti Likes Spending Quality Time With His Wife & Three Daughters

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CATEGORIZED UNDER: Links

Building anti-flu drugs on a computer

By Ed Yong | May 13, 2011 9:30 am

You have a sculpture, an intricate piece of modern art, covered in bulges and blisters. Your task is to weave a cover for it. The fit must be exact. You have to fill in every dent and wrap around every lump. Here’s the catch: you have to make this faultless shroud from a single piece of string that must automatically weave itself into the right three-dimensional shape.

This is the challenge that Sarel Fleishman, Timothy Whitehead and Damian Ekiert from the University of Washington have just overcome. Their “sculpture” is a protein called haemagglutinin, or HA, which sits on the surface of flu viruses. Their “shroud” is another protein designed to perfectly fit onto the contours of HA and neutralise it. They have found a way of fashioning these designer proteins on a computer – a feat that could make it easier to create the next generation of anti-flu drugs.

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MORE ABOUT: flu, folding, influenza, protein

Why you should enter science writing competitions

By Ed Yong | May 13, 2011 7:08 am

British readers might have caught wind of a new Guardian/Wellcome Trust Science Writing prize, aimed at finding the “next generation of undiscovered science writing talent.” Since the announcement, the Guardian have been pumping out a series of pieces on tips and tricks for good science writing, penned by established writers.

Alok asked me for something different – he wanted a reflection on the importance of entering and winning competitions. I won the Daily Telegraph’s young science writer prize in 2007, which in many ways was the spiritual predecessor of the new Guardian/Wellcome Trust one. My thoughts on that win, and its importance in my career, is now up at the Grauniad. Read More

CATEGORIZED UNDER: Journalism

Why sons inherit their mother’s curse

By Ed Yong | May 12, 2011 4:00 pm

No expecting mother would ever wish harm to befall her children. Unfortunately, she may have no choice in the matter. Due to the rules of genetics, mums always run the risk of passing a “mother’s curse” onto their sons, but not their daughters.

The curse is an ancient one, the result of events that happened billions of years ago. At a time when all life consisted of single microscopic cells, one of these swallowed another. Normally, the engulfed cell would be digested, but not this time – this time, the two cells formed an alliance. The swallowed cell transferred many of its genes to its host, keeping only those involved in providing energy. It evolved into a mitochondrion – a tiny, efficient battery that would power its host, giving it the energy to become more complex. This alliance is the foundation of all complex life on the planet. All animals, plants, fungi and algae run on mitochondria power.

This means that all animals really have two genomes – their main nuclear one, and a far smaller secondary one in their mitochondria. The two sets of genes work together, each controlling the activity of the other. But they are inherited differently. The nuclear genome is a mash-up of genes from both parents, but the mitochondrial one only comes from mum. And this asymmetry is the reason for the mother’s curse.

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MORE ABOUT: mitochondria

An entire flatworm regenerated from a single adult cell

By Ed Yong | May 12, 2011 2:00 pm

In a lab in MIT, a flatworm is dying. It’s a planarian – a simple animal that is normally very difficult to kill. Planarians are masters of regeneration; whole animals can be reborn from small clumps of tissue. If you cut one in half, it will simply grow into two planarians. But this animal has been bombarded with high doses of radiation that have wiped out its ability to regenerate. Slowly, its cells are bursting apart. With no new ones to replace them, the planarian has a few weeks to live.

But Daniel Wagner and Irving Wang are about to save it, in a fashion. They transplant one special cell from a donor planarian into the terminal individual’s tail. The cell starts to divide. It produces skin, guts, nerves, muscle, eyes and a mouth.

As the planarian dies from the head backwards, the transplanted cells spread from the tail upwards. At its worst, the animal is a stunted mass with no discernible head. But two weeks after the transplant, it has completely regenerated. A new planarian has risen, phoenix-like, from the ashes. Its entire body is now genetically identical to the single transplanted cell. Read More

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