Archive for February, 2012

Giant Jurassic fleas sucked but couldn’t jump

By Ed Yong | February 29, 2012 1:00 pm

The shortest poem ever written is known as Lines on the Antiquity of Microbes or, more simply, as Fleas. It goes: Adam/  Had ‘em. It’s a cute verse, but we don’t need Blblical references to know what the first fleas fed upon. As with many questions about ancient life, we can turn to fossils.

Among a horde of insect fossils recovered from China and Mongolia, Diying Huang from the Chinese Academy of Sciences has discovered several species of giant fleas. There are nine individuals from three different species, and they hail from the middle Jurassic and early Cretaceous periods.  “These outcrops have given us thousands of exquisitely preserved insects, but fewer than ten fleas,” says Andre Nel, who led the study.

The fossilised insects had many features that identify them as fleas – ancient precursors to the ones we know and loathe. But they had many unusual traits too. For a start, they were much bigger. While modern fleas are just a few millimetres long, some of these ancient forms were ten times bigger. The males grew between 8 and 15 millimetres in length and the females reached between 14 and 20 millimetres.

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When meeting up at sea, bottlenose dolphins exchange name-like whistles

By Ed Yong | February 28, 2012 7:00 pm

When we meet a group of strangers, one of the first things we’ll do is to introduce ourselves by name. Nicola Quick and Vincent Janik from the University of St Andrews have found that groups of bottlenose dolphins do something similar. When they meet one another in the wild, they exchange “signature whistles”. These whistles are unique to each individual, and they’re strikingly similar to human names. And it seems that they’re a standard part of a dolphin’s meet-and-greet etiquette.

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Full genome of Otzi the Iceman is published

By Ed Yong | February 28, 2012 11:00 am

After years of anticipation, the full genome of Otzi the Iceman, a 5,300-year-old mummy found in the Alps, has finally been published. The genome reveals that Otzi carried a large genomic region known as the ‘Y chromosome’, which significantly increases the risk of traipsing about in the a*se-end of nowhere with very little protective clothing, and getting shot by arrows.

Image © South Tyrol Museum of Archaeology

[For a more serious take, see here. And as Carl Zimmer notes, I'm suffering from YAGS]

CATEGORIZED UNDER: Not Exactly Rocket Satire

Will we ever grow organs?

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

Here’s the second piece for my new BBC column. From now on, they’ll be every two weeks.

In June 2011, an Eritrean man entered an operating theatre with a cancer-ridden windpipe, but left with a brand new one. People had received windpipe transplants before, but Andemariam Teklesenbet Beyene’s was different. His was the first organ of its kind to be completely grown in a lab using the patient’s own cells.

Beyene’s windpipe is one of the latest successes in the ongoing quest to grow artificial organs in a lab. The goal is deceptively simple: build bespoke organs for individual patients by sculpting them from living flesh on demand. No-one will have to wait on lengthy transplant lists for donor organs and no-one will have to take powerful and debilitating drugs to prevent their immune systems from rejecting new body parts.

The practicalities are, as you can imagine, less straightforward. Take the example I have already described. The process began with researchers taking 3D scans of Beyene’s windpipe, and from these scans Alexander Seifalian at University College London built an exact replica from a special polymer and a glass mould. This was flown to Sweden, where surgeon Paolo Macchiarini seeded this scaffold with stem cells taken from Beyene’s bone marrow. These stem cells, which can develop into every type of cell in the body, soaked into the structure and slowly recreated the man’s own tissues. The team at Stockholm’s Karolinska University Hospital incubated the growing windpipe in a bioreactor – a vat designed to mimic the conditions inside the human body.

Two days later, Macchiarini transplanted the windpipe during a 12-hour operation, and after a month, Beyene was discharged from the hospital, cancer-free. A few months later, the team repeated the trick with another cancer patient, an American man called Christopher Lyles.

Macchiarini’s success shows how far we have advanced towards the goal of bespoke organs. But even researchers at the cutting edge of this area admit that decades of research lie ahead to overcome all obstacles.

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CATEGORIZED UNDER: Biotechnology, Medicine & health

Sri Lankan safari – green turtles mating

By Ed Yong | February 27, 2012 5:50 pm



[After a brief problem with the slideshows, they should be working again - Ed]

I can’t escape animal sex, even on holiday.

On our Sri Lankan boat trip, it took us an hour or so to find some blue whales. But the first animals we saw were no less spectacular. From a distance, they looked like buoys, gleaming bright and white against the sea. As the boat drew closer, we realised that the light wasn’t reflecting off a man-made object, but the shell of a green turtle.

Then we realised that the light was actually reflecting off the shells of two green turtles. They were mating at the surface.

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Beetle pest destroys coffee plants with a gene stolen from bacteria

By Ed Yong | February 27, 2012 3:00 pm

For fans of a velvety latte or a jolting espresso, meet your greatest enemy: the coffee berry borer beetle. This tiny pest, just a few millimetres long, can ruin entire coffee harvests. It affects more than 20 million farming families, and causes losses to the tune of half a billion US dollars every year- losses that are set to increase as the world warms.

But the beetle isn’t acting alone. It has a secret weapon, stolen from an unwitting accomplice.

Ricardo Acuña has found that the beetle’s ancestors pilfered a gene from bacteria, most likely the ones that live in its gut. This gene, now on permanent loan, allows the insect to digest the complex carbohydrates found in coffee berries. It may well have been the key to the beetle’s global success.

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Will we ever decode dreams? My first BBC column

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

As mentioned before, I’ve got a new column at the BBC’s new sci/tech site, where I explore the steps we’ll take towards far-flung applications of basic scientific research. For reasons best understood by other people, no one in the UK can actually see the site, but I’ve acquired permission to republish my posts here with a short delay. So here’s the first one:

*****

You wake up. You were dreaming, but in the haze of morning, you cannot quite remember what ran through your head. Childhood acquaintances were there. You were in Australia. One guy was a pirate. There was something about a cow. Perhaps. We have all had similarly murky memories of an earlier night’s dream. But what if you could actually record your dreaming brain? Could you reconstruct the stories that play out in your head?

It appears to be plausible. Science fiction is full of machines that can peer inside our heads and decipher our thoughts, and science, it seems, is catching up. The news abounds with tales of scientists who have created “mind-readingmachines that can convert our thoughts into images, most of these stories including a throwaway line about one day recording our dreams. But visualising our everyday thoughts is no easy matter, and dream-reading is more difficult still.

The task of decoding dreams comes down to interpreting the activity of the brain’s 100 billion or so neurons, or nerve cells. And to interpret, you first have to measure. Contrary to the hype, our tools for measuring human brain activity leave a lot to be desired. “Our methods are really lousy,” says

Professor Jack Gallant, a neuroscientist at the University of California, Berkeley.

Some techniques, like electroencephalography (EEG) and magnetoencephalography (MEG), measure the electric and magnetic fields that we produce when our neurons fire. Their resolution is terrible. They can only home in on 5-10 millimetres of brain tissue at a time at best – a space that contains only a few hundred million neurons. And because of the folded nature of the brain, those neurons can be located in nearby areas that have radically different functions.

More recently, some scientists have used small grids of electrodes to isolate the activity of a handful of neurons. You get much better spatial resolution, but with two disadvantages: you can only look at a tiny portion of the brain, and you need to open up a hole in the volunteer’s skull first. It is not exactly a technique that is ready for the mass market.

Other methods are indirect. The most common one, functional magnetic resonance imaging (fMRI), is the darling of modern neuroscience. Neurons need sugar and oxygen to fuel their activity, and local blood vessels must increase their supply to meet the demand. It’s this blood flow that fMRI measures, and the information is used to create an activation map of the brain. However, this provides only an indirect echo of neural activity, according to Gallant. “Imagine you tried to work out what was going on in an office, but rather than asking people what they did, you went into the kitchen to see how much water they used,” he says.

Seeking Yoda

Despite these weaknesses, Gallant has repeatedly used fMRI to decipher the images encoded in our brain activity. For his latest trick, three of his team watched hours of YouTube clips while Gallant scanned the visual centres of their brains. He plugged the data into a mathematical model that acted as a brain-movie “dictionary”, capable of translating neural activity into moving images. The dictionary could later reconstruct what the volunteers saw, by scanning hours of random clips and finding those that matched any particular burst of brain activity.

The reconstructed images were blurry and grainy, but Gallant thinks that this will improve with time, as we develop better ways of measuring brain activity, better models for analysing it and faster computers to handle the intense processing. “Science marches on,” he says. “You know that in the future, it will be possible to measure brain activity better than you can today.”

While Gallant decodes what we see, Moran Cerf from the California Institute of Technology is decoding what we think about. He uses tiny electrodes to measure the activity of individual neurons in the hippocampus, a part of the brain involved in creating memories. In this way, he can identify neurons that fire in response to specific concepts – say, Marilyn Monroe or Yoda. Cerf’s work is a lot like Gallant’s – he effectively creates a dictionary that links concepts to patterns of neural activity. “You think about something and because we learned what your brain looks like when you think about that thing, we can make inferences,” he says.

But both techniques share similar limitations. To compile the dictionaries, people need to look at a huge number of videos or concepts. To truly visualise a person’s thoughts, Cerf says, “That person would need to look at all the concepts in the world, one by one. People don’t want to sit there for hours or days so that I can learn about their brain.”

Dream album

So, visualising what someone is thinking is hard enough. When that person is dreaming, things get even tougher. Dreams have convoluted stories that are hard to break down into sequences of images or concepts. “When you dream, it’s not just image by image,” says Cerf. “Let’s say I scanned your brain while you were dreaming, and I see you thinking of Marilyn Monroe, or love, or Barack Obama. I see pictures. You see you and Marilyn Monroe, whom you’re in love with, going to see Barack Obama giving a speech. The narrative is the key thing we’re going to miss.”

You would also have to repeat this for each new person. The brain is not a set of specified drawers where information is filed in a fixed way. No two brains are organised in quite the same fashion. “Even if I know everything about your brain and where things are, it doesn’t tell me anything about my brain,” says Cerf.

There are some exceptions. A small number of people have regular ‘lucid dreams’, where they are aware that they are dreaming and can partially communicate with the outside world. Martin Dresler and Michael Czisch from the Max Planck Institute of Psychiatry exploited this rare trait. They told two lucid dreamers to dream about clenching and unclenching their hands, while flicking their eyes from side to side. These dream movements translated into real flickers, which told Dresler and Czisch when the dreams had begun. They found that the dream movements activated the volunteers’ motor cortex – the area that controls our movements – in the same way that real-world movements do.

The study was an interesting proof-of-principle, but it is a long way from reading normal dreams. “We don’t know if this would work on non-lucid dreams. I’m sceptical that even in the medium-term future that you’d ever have devices for reading dreams,” says Dresler. “The devices you have in wakefulness are very far from reading your mind or thoughts, even in the next couple of decades.”

Even if those devices improve by leaps and bounds, reading a sleeping mind poses great, perhaps insurmountable challenges. The greatest of them is that you cannot really compare the images and stories you reconstruct with what a person actually dreamt. After all, our memories of our dreams are hazy at the best of times. “You have no ground-truthing,” says Gallant. It is like compiling a dictionary between one language and another that you cannot actually read. One day, we might be able to convert the activity of dreaming neurons into sounds and sights. But how would we ever know that we have done it correctly?

CATEGORIZED UNDER: Neuroscience and psychology

I've got your missing links right here (25 February 2012)

By Ed Yong | February 25, 2012 4:09 pm

Top picks

From Carl Zimmer and his Amazing Friends: Download the Universe, a new blog that reviews science ebooks:

Great story from Rebecca Morelle on the race to the deepest part of the ocean.

One man controversial ambition to model an entire human brain, and why loads of people think it’s a fool’s errand.

The biggest news this week has to be the fact that climate scientist Peter Gleick leaked the Heartland Institute documents. The Knight Science Journalism Tracker rounds up some of the best coverage.

You have to see this. The Scale of the Universe 2 – it’s back and even better than before

The second photo blew. My. Mind. The Fly That Banks On Arachnophobia

Carl Zimmer profiles Tom Seeley, bee whisperer

Some cultures don’t have a mind, by Vaughan Bell.

Bobbie Johnson and Jim Giles are creating a new digital magazine called Matter for in-depth, long-form science journalism, I watched the vid & hurt my head from nodding too much. Support it.

Robot dinosaurs are the future of paleontology, and possibly the end of humanity.

Lovely in idea + execution: What John Glenn saw from space, by Alexis Madrigal

Interesting Jack Stilgoe post on the term “anti-science” and science’s martyr complex. Plus decent comment thread.

Brilliant. 25 Things To Say To So-Called “Aspiring” Writers, by Chuck Wendig.

The last experiment of Alex T. Parrot, super-genius. His last words got me all teary.

“At 20, he attempted suicide-by-jaguar. Afterward he was apprenticed to a pirate” Most insane obit ever?

Nice. A profile of Susan Lindquist – her of heat-shock proteins and prion fame – in Nature News

Five Kinds of Fungus Discovered to Be Capable of Farming Animals! Nice twist, by Rob Dunn

Huh. So this one Russian scientist stuck his head in a particle accelerator. (He got better)

Bangladesh rickshaw driver earning $6/day saves for 30 yrs & builds village clinic

Amazing “domino chain” of kidney transplants, involving 60 people, and 30 saved lives.

It took a decade to sequence the first human genome. Now, Nanopore’s sequencer does it in 15 minutes

We use Xhosa-like clicks in speech but hardly notice. Why not?

Tourette’s-like disorder in New York school confounds experts

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CATEGORIZED UNDER: Links

The Bruce effect – why some pregnant monkeys abort when new males arrive

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

On a grassy Ethiopian plateau, revolution and death are underway. The plateau is home to a group of geladas – shaggy, grass-eating, and occasionally terrifying relatives of baboons. They’re like a cross between a cow, Animal from the Muppets, and your nightmares.

Geladas live in units where a single dominant male lords over several related females, whom he monopolises as mates. It’s an enviable position, and males often have to fend off takeover bids by eager bachelors. If a newcomer ousts the chief monkey, it’s bad news for the group’s females. A wave of death sweeps through the unit, as the new male kills all the youngsters whom his predecessor fathered. Indeed, babies are 32 times more likely to die after a takeover than at any other time.

But that’s not all. Eila Roberts from the University of Michigan has found that the new male’s arrival triggers a wave of spontaneous abortions. Within weeks, the vast majority of the local females terminate their pregnancies. It’s the first time that this strategy has been observed in the wild.

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In a scalding spring, one species of microbe is becoming two

By Ed Yong | February 22, 2012 9:00 am

In a cauldron of boiling, acidic water, kneeling at the foot of a Russian volcano, one species of microbe is on the cusp of becoming two.

Sulfolobus islandicus is an archaeon – one of many single-celled microbes that thrive in extreme environments. Mutnovsky volcano is certainly one such place. Found at the far eastern end of Russia, it’s full of churning, scalding springs that are nonetheless teeming with microscopic life. S.islandicus thrives in these springs, feasting on the sulphur within the water.

Now, Rachel Whitaker from the University of Illinois has found that the species has pretty much split into two separate lineages. Both share the same water, and they can trade genes with one another, but they have started to part ways and are becoming increasingly distant. In this hot, hostile and acidic world, the origin of the species is playing out before our eyes.

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CATEGORIZED UNDER: Evolution, Speciation
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