Live-blogging Arsenic Life

I’m spending the weekend in Ottawa, where a couple thousand scientists have gathered for the Joint Congress of Evolutionary Biology. I’m drowning in a torrent of fascinating talks, on everything from sexually cannibalistic crickets to the future of the Amazon’s biodiversity. In the evenings, the meeting features high-profile talks–Friday night, the science writer David Quammen spoke about his career, on the occasion of winning the Stephen Jay Gould Prize. I have a particular interest in tonight’s talk, so much so that I’m going to live-blog it. The speaker is one Rosie Redfield, and she’ll be talking about the endlessly intriguing case of Arsenic Life.

Before Redfield takes to the stage at 7:30 pm ET, I want to write a short preface. In December 2010, rumors swirled for a few days that NASA had discovered alien life. When they finally held a press conference, the world discovered that a team of scientists had found a species of bacteria at Mono Lake in California that appeared to be able to build DNA out of arsenic. If true, it would be unlike any known life on Earth.

Rosie Redfield, a microbiologist at the University of British Columbia, read the paper after the embargo at Science was lifted, and didn’t like it. After she posted her complaints on her blog, I got in touch with her, along with a number of other scientists to see what they thought. Most of them didn’t like the paper either. I wrote about their collective reaction in an article on Slate, which was called “‘This Paper Should Not Have Been Published.'” (That was a quote from one of the scientists I spoke to.)

The authors of the paper, who were willing to hold a big press conference, give TED talks, and so on, refused to provide me any comments. They declared that all discussion must be restricted to peer-reviewed channels. Six months later, when Science finally published the arsenic life paper in a print edition, they also published a number of comments from Redfield and other critics.

Redfield and others argued that the arsenic life study had been poorly carried out. To put a scientific claim to the test, critics can try to replicate it. But, as I wrote in the New York Times, that’s a pain in the neck, and a lot of researchers would rather spend their precious time doing something interesting, rather than cleaning up other scientists’ messes. But Redfield decided to replicate the arsenic life study anyway. She had another motivation for doing so: she’s a big fan of open science, and so she used her blog to chronicle her experiences, from receiving the bacteria from the original authors to failing to replicate their results to posting her paper on Arxiv to getting her paper accepted to Science, where it’s now in press.

As Redfield notes on her blog, tonight’s talk presents a certain complication to the traditional way that high-profile journals publish papers. Journals like Science keep their papers under strict embargo, meaning that people are supposed to keep their mouth shut until an appointed time. Science provides pre-publication copies of the papers to journalists, usually a week in advance, so they can write up articles that can appear once the embargo lifts. So…if Redfield talks about her research, what does that mean for her paper? And does the fact that you can download it already from Arxiv make all of this moot?

Stay tuned!

7:36: Getting started. Redfield’s getting introduced.

7:38: “Rosie Redfield led the charge that NASA got it wrong.”

7:41 Redfield is starting: this is a story about the process of science, that starts with a press conference.

7:42 Redfield glosses over the utterly insane week of speculation that NASA had found aliens. Hey, she’s a microbiologist.

7:43 Why was this done? “The researchers were looking for exactly what they found.” (Not always a good thing in science.)

7:44: Looking for alien life is very expensive. So NASA is looking for terrestrial life that can help the search.

7:44: 2009 paper in Astrobiology: arsenci life team pointed out that arsenic is similar to phosphorus. So maybe early life could have used arsenic instead of phosphorus (in DNA for example). And maybe they’re still around.

7:45: Origin of life. You can start forward from early Earth, or go back from life today to figure out what first life must have had.

7:46: Early earth: simple chemicals created complex ones. Also, early Earth was “stinky.”

7:47 Comets delivered dirty water, loaded with polycyclic hydrocarbons.

7:48 All life today is all related. All life descended from a common ancestor.

7:50 Common ancestor of all life today: DNA genome, cellular, lipid bilayer, protein synthesis, many modern biochemical pathways.

7:51 There’s a gap scientists have yet to bridge from prebiotic Earth to last common universal ancestor.

7:52 What properties are essential in living things? Reproduction, heredity, and heritable variation that affects survival or reproduction. Redfield: “That spells natural selection.”

7:53 Natural selection probably kicked in long before our last universal common ancestor. First life could have much simpler metabolism. May not have been based on DNA. Life could have started as RNA. (Check out this story I wrote for Discover.)

7:55 Today, proteins do much of the work of metabolism.

7:57 Creationists seized on this open question. Evolutionary biologists claimed evolution doesn’t include origin of life. But RNA world gets closer to the origin, via evolution.

7:58 Back to arsenic: Poisonous because cells sometimes take up arsenic, which screws things up.

7:59 “Shadow biosphere”–a cool name, but almost certainly wrong.

8:00 Shadow biosphere hypothesis: weird life exists even today, hiding from scientists. Redfield: “This is extremely cool.”

8:01 Redfield recaps arsenic life experiment. Mono Lake bacteria kept growing as arsenic was swapped for phosphorus in medium.

8:02 Once Felisa Wolf-Simon could grow bacteria, brought in other scientists. Sophisticated tests such as NanoSIMS to show arsenic in (or near) arsenic.

8:04 Weirdly, Science has just posted Redfield’s paper, and a second paper documenting a failure to replicate, on their web site without telling journalists.  

8:05 Redfield was suspicious. NASA’s track record was not good, given Martian meteorite debacle.

8:06 Whenever Redfield wants to think something through, she blogs.

8:07 Press release has just gone out on arsenic life. There are TWO  papers refuting it.

8:09 Redfield: Medium in arsenic life had some phosphate in it–same as ocean water.

8:11 Arsenic bacteria got fat. They couldn’t divide any more, so they swelled up.

8:13 Redfield argues that DNA of arsenic life bacteria that was already dirty with arsenic–arsenic not part of DNA.

8:15 Dan Vergano at USA Today is reporting on the new papers. Arsenic life paper lead author Felisa Wolf-Simon declares, “There is nothing in the data of these new papers that contradicts our published data.”

8:17 I forgot to link to my database of the responses from many critics. Here it is.

8:18 For some reason, some people made fun of Redfield for her dyed hair. It’s just gray at the moment.

8:19 Arsenic in DNA would fall apart very quickly. A big problem.

8:19 The bacterium in the arsenic life paper was not part of the shadow biosphere. It was just a member of a well-known genus called Halomonas.

8:21 The bacterium, called GFAJ-1 (Get Felisa Wolf-Simons A Job), is very, very, closely related to other Halomonas. Not much exotic evolution to become arsenic life.

8:22 No reason to think there would be natural selection for arsenic use, since Mono Lake has a fair amount of phosphorus (although a lot of arsenic too).

8:24 NASA suddenly switched from big press conference to shutting up. Felisa Wolf-Simon “had been been tweeting up a storm.”

8:25 Six months after the press conference, paper published, plus criticisms. Response of authors: “We think our research is fine.” –Redfield.

8:27 Redfield’s “selfish reason” for focusing on arsenic life: she blogs about her work, pursing open science. Important that the public see how science is done.

8:29 Redfield lacked all the expertise required for trying to replicate arsenic life. Blog post led to collaboration with experts who could do the job. (Actually, they volunteered their grad student!)

8:30 Redfield spent a month trying to get bacteria to grow, blogging all the way. Trouble with amino acids. Eventually, figured it out.

8:32 Redfield used better reagents with much less phosphate. Arsenic didn’t help growth. Arsenic life team was wrong.

8:33 Her DNA was stable for a couple months. Couldn’t have arsenic in it.

8:35 Redfield et al wrote up a paper, submitted to Science, and uploaded to Arxiv–because this is open science.

8:36 Science planned to publish on July 26.

8:36 Journals use embargoes to control how research is publicized. For more, read Embargo Watch.

8:38 Embargoes enforced by “vague threats.”

8:38 Weirdness of paper being on Arxiv for months and Science enforcing embargo. Redfield informed that embargo being lifted tonight.

8:39 I just told Redfield her paper has been up for half an hour. Applause breaks out.

8:40 Redfield: This is a story of serial failure. Lead author convinced of evidence without good research, senior authors didn’t provide supervision. Co-authors should have accepted responsibility. Reviewers failed, missed a lot of problems. Science failed in selecting reviewers.

8:42 “And finally, NASA failed big time.”

8:42 But the process of science did not fail.

8:45 Talk over. Question–will this episode change science? Redfield: If you blog about it, you mark that it’s your idea.

8:47 Peer review like democracy (as described by Churchill), is terrible, but the best we have.

8:48 Redfield: lots of “seriously flaky” stuff gets published, so we don’t have to worry about strangling science.

8:49 Idea of arsenic life “unlikely to be true,” but an “okay hypothesis.” You always fall in love with your own ideas. “It’s the ultimate high in science.” But you need self-discipline to test your hypothesis and see if it’s wrong.

8:52 That’s it, folks. Good night!

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