Synthetic biology and weapons of war

By: | December 5, 2011

A few years ago, Eric Klavins found himself starting at the ceiling of his room in the Athenaeum, a private lodging on the grounds of the California Institute of Technology, in the middle of the night. Unable to sleep, Klavins found himself pondering a question that had been posed to him earlier that day at a meeting.

Klavins, a robotics researcher, was funded by grants from the US Air Force and the Defense Advanced Research Projects Agency (DARPA) on robot self-organization: making many simple robots work together to assemble themselves into a shape or structure. While working on the grants, Klavins would routinely be called into meetings to discuss his work with various defense officials, and it was at one of these meetings that a Defense Department researcher had posed his question.

“He said, ‘Do you think you could figure out how something that has been broken up into lots of little pieces could be reassembled so we could figure out what it was?’” Klavins recalls.

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Guest Post: Why the Secret to Losing Weight and Staying Young Won’t be Found in a Pill

By: | December 2, 2011

In September, a rash of stories appeared about a study contradicting the claim that a class of proteins called sirtuins might be a possible anti-aging cure. “Longevity genes challenged,” Nature declared. “Longevity Gene Debate Opens Trans-Atlantic Rift,” wrote Nicholas Wade at The New York Times.  “New study debunks longevity link for GSK’s sexy sirtuins,” wrote John Carroll for Fierce Biotech, the online tabloid of the biotech industry. “Those sexy ‘fountain of youth’ studies on sirtuins …have failed to live up to the initial hype,” Carroll wrote.

Faced with the barrage of whiplash-inducing headlines, I could only ask, “Haven’t we been here before?”

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Abstruse Goose: Stop the Massacre

By: | December 1, 2011

Our boy, AG, is referring to a joke:  a dairy farmer asks a physicist how to estimate milk production.  The physicist begins the calculations with, “Assume a spherical cow,” and takes it from there.

Physicists are famous for this.  They call it simplifying the model.  Sometimes they have a problem that’s too complicated to be calculated from the bottom up — say, climate change.  So they make a model in which they simplify the parts — an average atmosphere, an average land, an average ocean.  Change one of these averaged parts — make the atmosphere more likely to trap heat — and see how the whole climate responds.

I think in the case that AG presents, the problem is not milk production but something like the distance a cow can be catapulted.  On the whole, simplifying the model is good for finding out roughly where the answer might be.  But it might be hard on the cow.

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http://abstrusegoose.com/406

Pro Tip: Don’t Fall in the Thames

By: | November 30, 2011

Last week, I fell in the Thames. I only fell in up to my thighs, but the gaping, bleeding puncture on my shin, inside which I could see geologic-looking layers of anatomy — that was a bad sign.

So I found myself at the A&E (that’s ER to you, fellow ‘Mericans) at 4 in the morning in Hackney, where everyone was bored by my lack of gunshot wounds. Until, that is, I revealed that I’d taken a dip in the Thames. Then, even hardened nurses blanched and rushed off to confer with other medical professionals.

As the morning wore on and I kept seeing those expressions of pure horror every time I pointed at my leg and said the word “Thames,” I started to get pretty well creeped out. It culminated with the nice NHS doctor lady giving me my marching orders.

“If you see any red streaks, if you get any shooting pains in your leg, or anything feels wrong, come back immediately,” she advised, eyeing my bandage warily. “No one’s going to mind. Just tell them you’ve had your leg in the Thames.”

I started doing some Google-based investigation. Just what was so bad about inviting some Thames water into my gaping, bleeding flesh? My findings led me to conclude that my leg was either about to shrivel up and fall off, or spontaneously sprout 8 smaller legs. Or eyes.

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Breaking Through

By: | November 29, 2011

This past summer, I spent two weeks sitting, working and, once, sleeping next to a hospital bed, trying and failing to communicate with my father.

He had called for an ambulance on the evening of July 25 because he couldn’t breathe. With end-stage emphysema, he often couldn’t breathe, but apparently that night he was frightened enough to call for help. At the hospital, the doctors intubated him and doused him with the sedatives one needs to withstand a hard plastic tube down the throat. My sister and I never knew if he had agreed to the intubation, or if he was too weak or panicked to voice a clear opinion. Over the next few days in the ICU, although still heavily sedated, he sometimes acted in ways that seemed deliberate: he would open his eyes wide, or furrow his brow, or nod to a question or squeeze my hand. But I was never really sure. I wasn’t sure if he would have wanted us to agree to the tracheostomy procedure, on August 2, or remove the ventilator, on August 9.

What if I could have been more sure?

I couldn’t help but think about that a couple of weeks ago while having coffee with Jon Bardin at the Society for Neuroscience meeting in Washington, D.C. A few years back, Jon left the science magazine where we both worked to pursue a PhD in neuroscience. He joined the lab of Nicholas Schiff, an expert on the neural basis of consciousness, and began studying the brain activity of people with severe brain injury. And now at the conference, Jon told me, he would be presenting a poster of unpublished data suggesting that brain waves can reveal whether a somewhat conscious person is tuning in when other people speak.

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It’s Not (Always) About the Lorax

By: | November 28, 2011


I’ve spent a lot of time this past year thinking and writing about extinction, which means I’ve also spent a lot of time drinking thinking about the tragic narrative in environmental journalism.

There’s a lot of genuine tragedy on the environmental beat, and it doesn’t take a partisan to see it. There’s not a whole lot to like about water pollution, or crop failures, or mass extinction. But I wonder if environmental journalists, steeped as we are in bad news, reach too quickly for the Lorax narrative. You know how it goes: The Lorax speaks for the trees, the rest of us keep buying thneeds, and for hope all we get is the Once-ler’s last seed.

Are there other ways to tell environmental stories? With Christopher Booker’s Seven Basic Plots as a field guide, I’ve been searching for examples of environmental journalism with other-than-tragic narratives — archetypal frameworks that still fit the facts, but startle the reader out of his or her mournful stupor. I’ve found some good ones, and I’d love to hear about more.

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Black Friday and Dirty Gold

By: | November 25, 2011

Seventeen years ago, Canadian biologist Adrian Forsyth slipped into lyricism as he described the great wilderness known as Tambopata-Candamo in Peru. The cloud forests there, he wrote in an official report, “are dense with every limb matted with fern, orchid and moss and the only trails are those of the secretive spectacled bear and elusive mountain lion…. Along the banks of the Tambopata brilliant flocks of macaws concentrate by the hundreds to feed on mineral-rich soil pockets. Giant otters hunt the rivers for enormous catfish. Vast expanses of forest extend in all directions.”

This untouched paradise lay near the headwaters of the Amazon, and Forsyth and 23 colleagues explored it, charting its biodiversity for Conservation International. (Sadly, two of the CI team died in the line of action, when their small plane crashed in a treetop survey.) But the team persevered, recording 575 bird species and 1200 butterfly species, the second richest documented butterfly community in the world.  Their final report pleaded powerfully for the protection of this vast emerald wilderness.

But the key to Tambopata-Condamo’s fate lay in just four words in that 184-page-long report: “mineral-rich soil pockets.” Today, nearly two decades after Forsyth waxed eloquent, steepling gold prices and a government seemingly paralyzed by corruption are transforming part of this paradise—the Madre de Dios river and its surrounding forest—into an ecological disaster on a grand scale. “It looks like Mordor,” said Alex Chepstow-Lusty, a paleoecologist at the French Institute of Andean Studies in Lima, in an interview I did with him in February. Continue reading →

Science Metaphors (cont.): Degeneracy

By: | November 24, 2011

I was helping an astronomer write a sentence.  It was about disentangling the color a supernova has intrinsically, from the reddening in its color caused by cosmic dust.  He wrote he wanted to “break the degeneracy” between the colors.  Break the degeneracy.  I got so excited.  I’d always thought degenerates were people who didn’t, for instance, take baths.  But intrinsic color and extrinsic reddening could be degenerate? Oh my yes, he said, and so can stars and electrons.  So what’s science doing, not taking baths? Continue reading →