Being Human: A New Site About Our Species (With An Essay From Me On Brains in Vats)

By Carl Zimmer | October 13, 2012 2:39 pm

I was recently invited to write an essay for a promising new web site that launches today, called Being Human.  It’s all about what it means to be Homo sapiens, and I chose to focus on our brain, which is so fundamental to our unique place in the natural world. In fact, we like to think of ourselves as our brains. You could, after all, imagine yourself as just a brain in a vat. It might be hard to manage, but if someone could figure out the right liquids to put in the tank and the right wires to stick into it, it “ought” to work. Hence, The Matrix.

This is actually a new notion, and in my essay, I take a look at our ideas about the brain over the past couple thousand years. Check it out.

CATEGORIZED UNDER: Brains, Writing Elsewhere

That GMO-cancer study? It gets worse.

By Carl Zimmer | October 10, 2012 5:32 pm

Last month I blogged about the unsavory practices of French scientists who unveiled a study purporting to show that genetically modified corn and herbicide cause cancer in rats. Not only was the study weak, but the scientists required reporters to sign an oath of secrecy to see it in advance. As I explained to the NPR show On the Media, this strategy raised the odds that all those pesky questions about statistical significance from meddling outsiders would be absent from the first wave of reporting.

In Nature today, Declan Butler continues his great reporting on the affair, unearthing additional disturbing parts of the story. My favorite was this passage from the agreement that some reporters–incredibly–agreed to sign:

“A refund of the cost of the study of several million euros would be considered damages if the premature disclosure questioned the release of the study.”

Who knew that doing basic science reporting could land you catastrophically in debt? Well, aside from Simon Singh…

[Update: Link to Nature fixed]

CATEGORIZED UNDER: Darwinius, Meta

Tuesday in Hartford: Viruses in the Movies!

By Carl Zimmer | October 7, 2012 9:42 am

On Tuesday I’ll be in Hartford to participate in the Science on Screen series. It started in Boston last year, and now it’s spreading across the country. Each evening consists of a science-themed movie paired with a talk about some of the science involved. On Tuesday, Real Artways in Hartford will be screening the virus-zombie movie, 28 Days Later. And I’ll talk about what real viruses can do to their hosts. Details here.

CATEGORIZED UNDER: A Planet of Viruses, Talks

Weirdly Unweird: A Better End to the #Arseniclife Affair

By Carl Zimmer | October 3, 2012 5:59 pm

It’s getting close to two years now since a NASA-funded team of scientists announced they had found a form of life that broke all the rules by using arsenic to build its DNA. It’s become something of an obsession for me. If you want to follow the saga, click here and start back at the earliest post. In July I live-blogged the announcement that other scientists had replicated the experiment and failed to find the same results. In some ways, that was the logical end to the story

My fascination with this story has been tempered from the start by a creepy feeling. As a science writer, I most enjoy reporting on advances in biology: the research that opens up the natural world a little bit wider to our minds. The “#arseniclife” affair was less about biology than about how science gets done and the ways it goes wrong: the serious questions it raised about peer review, replication, and science communication. That fierce debate did some collateral damage. The microbe in question, known as GFAJ-1, went from being the species that would force us to rewrite the biology textbooks to yet another bacterium that offered no serious challenge to the uniformity of life. It became boring.

But biology is not boring. Elephants and redwoods may both be made of the same elements, may both build genes from DNA, may both use the same genetic code book to build proteins–but they’re very different from each other in some respects, and, each in their own way, are most certainly not boring. Neither is GFAJ-1. And so it’s a pleasure to see a new paper in the latest issue of Nature in which a group of scientists pick apart the biology of the microbe and discover something very interesting.

The whole search for arsenic life got its start because arsenic, despite being toxic, is very similar to an essential element, phosphorus. Phosphorus is part of the backbone of DNA, for example, and it is an ingredient in the energy-storing molecule ATP–in each case in a form known as phosphate, with four oxygen atoms tacked on. Arsenate (arsenic linked to three oxygen atoms) is just about identical in size, has a similar charge to its oxygen atoms, and has many other chemical similarities to phosphate.

So the arsenic life team wondered if life might be able to survive with arsenic instead of phosphorus. One way to test that idea would be to rocket off to a planet where there is only arsenic and no phosphorus and look for life. Another would be to look for life on Earth that can swap arsenic for phosphorus. The arsenic life team opted for the latter and headed to Mono Lake in California, the waters of which are loaded with arsenic. They brought a strain of bacteria back to their lab, weaned it off of phosphorus, and supplied it with arsenic instead. The bacteria still grew. That fact and other studies they conducted convinced them that the bacteria had, indeed, become arsenic life.

The consensus today is that the scientists unwittingly fed the bacteria just enough phosphorus to survive, and the tests that seemed to indicate the arsenic was inside the DNA weren’t executed carefully enough.

But think about that for a moment. Imagine what it’s like for a microbe in Mono Lake, or in the lab of a particularly sadistic scientist. You’re drowning in arsenate, and in order to stay alive, to keep growing, you need to grab the precious few phosphate molecules drifting by.

Dan Tawfik, an expert on protein function at the Weizmann Institute in Israel, and his colleagues have uncovered some of GFAJ-1’s secrets to survival.  GFAJ-1 and other bacteria absorb phosphate through their outer membrane, into a sandwiched layer of fluid called the periplasm. Once there, the phosphate is grabbed by so-called phosphate binding proteins, which then deliver the phosphate to the interior of the microbe. Tawfik and his colleagues examined these proteins in unprecedented detail to see how they work.

The scientists offered the proteins a mixture of arsenate and phosphorus. Even when they raised the ratio to 500 molecules of arsenate to every phosphate molecule, the proteins still managed to pluck out phosphate over half the time. The scientists then examined the proteins to figure out how they make such fine discriminations. When the proteins encounter a molecule of phosphate, they enfold it in a tight pocket, which ties down the phosphate with 12 different hydrogen bonds. When arsenate falls into that pocket, it doesn’t quite fit in, and the bond between one of the oxygen atoms in the arsenate and one of the hydrogen atoms in the protein gets twisted. It gets pushed to such an uncomfortable angle that the arsenate drops out.

This finding suggests that ordinary microbes are well-adapted to picking out phosphates when they’re scarce, using their fussy phosphate binding proteins to reject abundant arsenate. GFAJ-1 is stuck in a place where phosphate is always scarce and arsenate is always dangerously copious. Tawfik and his colleagues found that one form of their phosphate binding proteins is spectacularly fussy, preferring phosphates by a factor of 4,500. What’s more, GFAJ-1 produces many copies of this super-fussy protein. As a result, GFAJ-1 can thrive in Mono Lake. In fact, it can handle arsenate-to-phosphate ratios up to 3,000 times higher than found in the lake.

Finding alien life on Earth would have been grand. But seeing how life as we know it manages to adapt to our planet’s extremes is also a pleasure. And it’s a good place for the story of arsenic life to stop: at the point where new science begins.

[Update: Rosie Redfield, the University of British Columbia microbiologist who became a leading skeptic of arsenic life, Maneesh points out in the comments that phosphates are actually abundant in Mono Lake. Thanks for pointing that out, Rosie Maneesh!]

 More: 

The paper

C & EN article

Nature News

[Image of Mono Lake by .Bala via Flickr, under Creative Commons License]

CATEGORIZED UNDER: Arsenic life, Top posts

Fraud: My story in tomorrow’s New York Times

By Carl Zimmer | October 1, 2012 3:35 pm

A new look at retracted papers since 1975 paints a picture that’s none too pretty. Retraction rates are zooming up, and most of those retractions, a new study finds, are due to misconduct such as fraud and plagiarism. I write about the study in tomorrow’s New York Times. Check it out.

The Infected Air (NSFH [Not Safe For Hypochondriacs])

By Carl Zimmer | October 1, 2012 1:59 pm

As I was putting together a talk today about our microbial world, I just came across this interesting paper in the August issue of The Journal of Virology.

A team of Korean scientists set up some traps to catch viruses and bacteria floating in the air. They set up their traps in Seoul, in an industrial complex in western Korea, and in a forest. Based on their collection, they came up with the following estimates…

**In each cubic meter of air, there are between 1.6 million and 40 million viruses.

**In each cubic meter of air, there are between 860,000 and 11 million bacteria.

Given that we breathe roughly .01 cubic meters of air each minute, a simple calculation based on these results suggests we breathe in a few hundred thousand viruses every minute.

Half of the viruses the scientists trapped didn’t match any known virus species. But most belong to groups that infect plants or mammals.

A note to hypochondriacs: holding your breath may keep viruses from coming into your body, but as a lifestyle choice, it has some drawbacks.

 

CATEGORIZED UNDER: A Planet of Viruses

Ben Goldacre on more bad data: this time from drug companies

By Carl Zimmer | September 30, 2012 10:47 am

This morning I was accused of writing “corporate sponsored blogs whoring themselves out to all and sundry.” Actually, I was arguing that science writers have a duty to call out weak science and press manipulation rather than cave into it. That applies to any kind of research. I happened to be talking about research on genetically modified foods and their health risks. But it applies just as well to pharmaceutical corporations that deep-six drug trials that don’t support their drugs. The most eloquent critic of this bad behavior is Ben Goldacre. You can watch this video of a TED talk he recently gave on the subject, read this essay in the Guardian, or pre-order his new book, Bad Pharma.

If highlighting Goldacre’s vital work means I have to return my gold-plated corporate-whore Corvette, so be it.

[Update: Guardian link fixed, book title fixed]

CATEGORIZED UNDER: Link Love, Meta

Walk Away! My Interview on "On the Media"

By Carl Zimmer | September 28, 2012 8:01 pm

My outburst last week about scientists trying to get reporters to sign a confidentiality agreement to see a paper on genetically modified food landed me on the radio. I spoke to Brooke Gladstone of “On the Media” for this week’s show. I’ve embedded the interview here.

CATEGORIZED UNDER: Meta, Talks

A Paddleboat for Lakes of Gasoline

By Carl Zimmer | September 27, 2012 10:15 am

Saturn’s moon Titan is speckled with lakes of liquid hydrocarbons that might just the sort of places you’d want to visit in order to look for weird forms of life.

A Spanish engineering firm has designed a probe that could explore the lakes of Titan: a paddleboat. All it needs now is a seat, and I’ll be ready to take a spin on it…

[Source: Europlanet]

CATEGORIZED UNDER: Life Elsewhere

When Food Webs Flip: My New Story in Scientific American

By Carl Zimmer | September 24, 2012 11:25 am

New England’s fisheries are in such bad shape that the Department of Commerce has now declared them a disaster. It’s not merely the sheer volume of fish we’re catching that explains the woeful state of these fish stocks. Even in places where governments have established strict limits on fishing, some fisheries have been unexpectedly slow to recover. That’s because fish don’t exist in isolation. They’re part of ecological networks. And when we hammer these networks, they can suddenly flip into a new state. Getting them back to their old state can be surprisingly hard.

In the new issue of Scientific American, I’ve written a feature on recent research into how ecological networks flip, along with attempts to detect warning signs of food webs on the brink (subscription required).

P.S. A needless snarky commenter objected to having to pay for the article. As I pointed out to him or her, if you want to read two lengthy scientific reviews on the subject for free, here is a pdf and here’s another one.

[Image: Lake Michigan food web/NOAA]

CATEGORIZED UNDER: Environment, Writing Elsewhere
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The Loom

A blog about life, past and future. Written by DISCOVER contributing editor and columnist Carl Zimmer.
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