Category: Arsenic life

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

A Good Housekeeping Seal of Approval for science? My new piece in Slate

By Carl Zimmer | August 14, 2012 11:26 am

Like a number of other science writers, I’ve become increasingly interested (and concerned) about science’s ability to correct itself. (See my recent pieces about arsenic life, de-discovery, and dysfunctional science.) So I was intrigued by a new project launching today to encourage scientists to embrace the spirit of replication. I write about it at Slate. Check it out.

Tomorrow on Science Friday: Arsenic Life and the Sausage-Factory of Science

By Carl Zimmer | July 12, 2012 5:08 pm

I’m going to be a guest during the second hour of Science Friday on National Public Radio tomorrow. Host Ira Flatow and I will be discussing the latest twist in the ever-intriguing arsenic life saga, and, more broadly, the rough-and-tumble way in which science corrects itself. If you miss the live show, you can listen to it here.

CATEGORIZED UNDER: Arsenic life, Talks

Live-blogging Arsenic Life

By Carl Zimmer | July 8, 2012 4:39 pm

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!

 

 

CATEGORIZED UNDER: Arsenic life, Writing Elsewhere

2011: A Letter from the Loom

By Carl Zimmer | December 31, 2011 1:19 am

In 2011, the Loom reached its eighth birthday. Thanks to everyone who’s paid a visit or become a loyal reader in that time. With the year coming to a close, I spent a little time this week perusing the Loom’s archive, reflecting on the things that obsessed me during 2011.

More than many years, this one reminded me just how huge science is. Even if you limited yourself to the most important stories of this past year, there was just too much to keep up with. (Here’s Discover’s top 100 picks.) As a science writer, my focus is biology, but that didn’t ease my year-long case of head-spinning. The anchors that kept me from spinning away completely were the very small and the very complicated.

At the small end of the spectrum were, among other things, the bacteria that call us home. Like every year, 2011 saw outbreaks, such as the E. coli that sickened thousands in Germany. But now that we can read the genomes of these killers,  as I noted in Newsweek, we can see how chillingly fast new pathogens can evolve.

But the good germs also gained more recognition in 2011. The science of the microbiome is blooming at an astonishing pace, as you can see in the map I created for the September issue of Wired. As I got more familiar with the microbiome, it became clear to me that scientists won’t be able to handle its complexity without thinking like ecologists. I made that point in a talk this spring called “The Human Lake,” which I turned into a blog post in April. (I was delighted when it was selected as one of the best pieces of 2011 by The Browser and Longreads, and was picked to be including in the 2012 edition of Open Lab.)

The microbiome, I predict, is going to become very intimate in years to come. It’s a strangely thrilling experience to discover 53 species of bacteria living in one’s belly button, as I found out this year. In the future, doctors may check our bug types just as they check our blood types today. But all this new knowledge about the microbiome will bring us unexpected  ethical quandaries, some of which I discussed in December in the New York Times.

Bacteria may be small, but they’re positively plus-sized compared to viruses, the subject of my book A Planet of Viruses, which came out in May. (You can read excerpts in Audubon and i09.) Working on the book opened my eyes to just how abundant, diverse, and powerful viruses are–a point I tried to get across in the talks I gave in the spring. The two that I was happiest with were an interview on Science Friday on NPR, and a talk I gave at the Long Now Foundation in San Francisco. As always happens when I write a book about a fast-moving field, the science of virology offered up lots of surprises after the book came out–such as the biggest virus ever, a possible ancestor of hepatitis C in dogs, and signs of a battle between viruses and bacteria in our mouths. When the movie Contagion came out in September, I took a look in Slate at how realistic its story of a new world-wide pandemic was. I found it real enough to be very scary. And in an eerie bit of timing, this fall scientists developed a strain of bird flu that some researchers worry could make the movie a reality.

At the other end of the spectrum from bacteria and viruses is the human brain, those 100 billion neurons that make the universe aware of itself. There seems to be no end of revelatory research coming out of neuroscience and psychology. At the World Science Festival, I talked with three scientists doing extraordinary work on the mystery of sleep (you can watch the video here). In my own stories, I explored genes for language, teen brainsmusic in the brain, the neuroscience of smiles, how our brains make us capable of both war and peace, and the minds of Neanderthals. A lot of the pieces I wrote first appeared in the New York Times or magazines, but some of them have gotten a new lease on life. I published a new ebook in December, More Brain Cuttings, and my feature on the possibility of uploading our brains to achieve immortality was selected for The Best of American Science Writing 2011.

In 2011, it wasn’t just new science that was in the news. The nature of science was, too. Over the course of 2011, some high-profile papers came under fierce criticism, including arsenic-based life and a link between viruses and chronic fatigue syndrome. These studies prompted a debate about how science gets done in the first place, and how some of it then gets “de-discovered.” I pondered the nature of de-discovery in the New York Times in July, and the emergence of a more transparent discussion of science in Slate.

A lot of that discussion happened on Twitter. Twitter was just one of many new media that became more widespread this year. And just as scientists were getting comfortable with these channels of communication, science writers were too. I spent a fair amount of time in 2011 experimenting with different formats. On Twitter, I went after some egregiously bad science with a hashtag: #Greenfieldism. When I wasn’t on Twitter, I was often on Facebook, Tumblr, and Google+. Each medium has different strengths, I’ve found, which only emerge after playing around with it for a while. Google+ has spurred some fascinating discussions; Twitter is a fast way to spread links. I spent some time working with the folks at Radiolab this year, including the newly minted Macarthur genius Jad Abumrad. It was fascinating to see them turn spoken words into symphonies, such as this episode entitled “Patient Zero.” Another form of storytelling can be found at Story Collider, where people tell tales live in front of an audience. An invitation to be a part of a Story Collider evening led me to talk about how a trip to a war zone made me realize just how deeply science speaks to me. And at the end of the year I published Science Ink, a book born out of a blog-based obsession with science tattoos.

It was a strange year indeed when a traditional book felt like a fresh new format. And it makes me eager for the surprises waiting for us in 2012.

[Image: Wikipedia]

Happy Birthday, #arseniclife

By Carl Zimmer | December 2, 2011 10:38 pm

Today marks the one-year anniversary of the Arsenic Life Affair. On December 2, 2010, NASA-funded scientists announced that they had discovered a microbe in Mono Lake that broke the rules of biology. They claimed it could build DNA from arsenic rather than phosophorus. It was a sensational claim, and it was greeted by a spectacular backlash.

Alan Boyle takes a close look at arsenic life on its first birthday over at MSNBC. Other scientists have yet to report whether they can replicate the results or not (the bet of many experts is on not). Meanwhile, other researchers are studying its biology, sequencing its genome, and otherwise investigating it as they would any new microbe. It seems as if the arsenic life affair is morphing into regular science. Which may be about as good of an ending as one could hope.

The year has been an intriguing one for me as a journalist–I’ve found writing about arsenic life as both science and the sociology of science to be very satisfying. Here’s a round-up of my main pieces:

1.Of Arsenic and Aliens, The Loom, 12/2/10

This was the first post I wrote, on the day of the announcement, explaining why arsenic life would be a big deal if it were true.

2. “This Paper Should Not Have Been Published,” Slate, 12/5/10

Over the next couple days, I encountered deep doubts among experts. I summarized their objections in a piece for Slate.

3. Of Arsenic and Aliens: What the Critics Said, The Loom, 12/8/10

I could not delve into the full details of the objections in my Slate piece, but I wanted to make sure readers could see that the critics were not shooting from the hip. So I posted their complete responses on my blog.

4. The Discovery of Arsenic-Based Twitter, Slate, May 27, 2011

Nearly six months after arsenic life was announced, Science finally published the paper, along with lengthy criticisms. It felt fairly anti-climatic to me; at Slate, I wrote about what I thought was the important outcome of the whole affair: an experiment in open science and post-publication peer review.

5. It’s Science, But It’s Not Necessarily Right, The New York Times,  June 26, 2011

As the Arsenic Life Affair was unfolding, several other high-profile papers were also under siege. Together, they got me interested in how science progresses: how scientific ideas are tested, and how difficult it can be for the wrong ones to be “de-discovered.”

6. #ArsenicLife Goes Longform, And History Gets Squished, The Loom, 9/30/2011

The first big feature on arsenic life appeared in Popular Science. I warned that a folk tale about everything being the fault of those pesky bloggers was taking root. (Soon after, the author, Tom Clynes, sent a long message to me, which I posted on the blog.)

 

Along with Boyle’s piece, you can also plunge into Bora Zivkovic’s epic link round-up for more reading.

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

CATEGORIZED UNDER: Arsenic life, Writing Elsewhere

Tom Clynes on arsenic life

By Carl Zimmer | October 1, 2011 9:29 am

Yesterday I wrote about the arsenic life saga, prompted by a long retrospective feature by Tom Clynes in Popular Science. While I recommend the piece, I expressed reservations because it passed along the “scientists besieged by bloggers” spin on the events, when the actual history doesn’t support that.

Clynes (whom I’ve never met) emailed me in the evening with this comments, which he allowed me to share:

 

Carl,

 

Thanks for your comment on my Popular Science feature on Felisa Wolfe-Simon’s arsenic-life saga. In some ways, I think you’re on target, though I would like to provide a bit of clarification: Throughout the story, when I convey an argument made by someone who’s on one side of the issue or another, it doesn’t mean that I necessarily buy into that argument.

To that end, I’d like to add a bit of context to a paragraph that you quote, regarding the storm of criticism and the paper’s authors going “underground.” You follow the excerpt with your comment that “Clynes has us believe that this barrage of extraordinary, brutal criticism (or perhaps questions from journalists) forced Wolf-Simon and her colleagues to go into witness protection.”

Actually, I don’t believe that, nor would I have my readers believe it. I think it would have been useful to your readers for you to have included my next paragraph, which makes it clear that I am in fact spotlighting both sides of a polarized dialogue regarding this particular point:

Microbiologist Jonathan Eisen of the University of California at Davis called the lack of response “absurd” and told Carl Zimmer from Slate, “They carried out science by press release and press conference. They are now hypocritical if they say that the only response should be in the scientific literature.”

Though I didn’t state my opinion in the story (better for readers to decide for themselves), I will here: I think that Eisen is on the money here.

Some other opinions: Do I think that the arsenic-life paper was flawed? Yes. Do I think it that some of its conclusions will be dissolved by further investigation? Yes. Do I believe that NASA’s hyped-up approach to publicizing what was actually a rather understated paper was ham-handed, and damaging to everyone involved? Big time.

Do I think the paper never should have been published? No. In a profession where young scientists are advised to avoid controversy as they build their careers, Wolfe-Simon pushed against a paradigm and sought answers to some very big questions. She passed through the same peer-review hoops (imperfect as they may be) at Science as other scientists must. Yes, her research was imperfect and yes, she likely overreached—but plenty of scientific papers are flawed, and many young researchers go too far. If scientists aren’t willing to subject themselves to the possibility of failure, science can’t possibly progress.

Critically, there’s nothing to indicate that Wolfe-Simon did anything unethical, which might have justified the shrill tone and sweeping proportions of the response—and the fact that she was singled out among the paper’s 11 authors. True, she was the lead author, and it was her hypothesis. But it’s surprising that Ron Oremland, the lab director and principal investigator, is rarely mentioned in the criticisms.

If my story has a bottom line, it’s in this quote by the University of Colorado’s Alan Townsend: “Absent major ethical violations, no junior scientist full of passion for an idea deserves crucifixion for a professional failure or two. If a paper is flawed, it should be dismissed. The scientist should not.”

CATEGORIZED UNDER: Arsenic life

#ArsenicLife Goes Longform, And History Gets Squished

By Carl Zimmer | September 30, 2011 10:00 am

If you haven’t been tracking the arsenic life saga closely over the past ten months, check out Tom Clynes’s big feature at Popular Science. It focuses on the travails of Felisa Wolfe-Simon, the lead author on the paper, who has gone from the Olympian heights of TED talks to getting “evicted” from the lab where she’s worked for the past couple years. (Her word.)

For those of us who’ve been tracking the story for a while, that last fact popped out. Wolfe-Simon had been working in the lab of her co-author Ronald Oremland, but that’s now over. Let’s recall that her senior colleagues dubbed the intriguing microbe she studied GFAJ-1, for “Get Felicia A Job.”

It’s a good article. I won’t be forgetting the opening scene anytime soon, when Wolfe-Simon is ambivalently posing for a television crew, and she sinks into the mud of Mono Lake, where she first encountered GFAJ-1.

But I do share some of the reservations that science writer David Dobbs expresses over at his blog Neuron Culture. As a genre, the profile is one of the most addictive and enjoyable of all. It doesn’t matter if the profile is of a hero or a scoundrel; the story is good as long as it’s full of human nature in all its extremes. But profiles of scientists are tricky, because science transcends any single individual scientist. To do the science justice, you may need to pull the spotlight away and get into the less human stuff, like chemical reactions and pH levels.

The story thus focuses mainly on Wolfe-Simon, with scientific critics effectively reduced to mean chair-throwers, their scientific objections dispatched in a couple lines. People and events are relevant insofar as they affect Wolfe-Simon. And in the process, Clynes writes some mystifying stuff:

What made the level of criticism so extraordinary is that the paper, in itself, is not so flawed that it should not have been published. The argument was compelling, the conclusions were measured, the data was thorough, and the paper made it through the same peer-review process as other articles in Science.

And Clynes has us believe that this barrage of extraordinary, brutal criticism (or perhaps questions from journalists) forced Wolf-Simon and her colleagues to go into witness protection:

Overwhelmed with questions from the media, Wolfe-Simon went underground. Guided by NASA’s PR team, she and Oremland and the paper’s other co-authors began citing NASA spokesperson Dwayne Brown’s position that the authors would not be responding to individual criticisms. The agency, Brown said, didn’t feel it appropriate to debate science using the media and bloggers. Discourse should occur in scientific publications.

“I wasn’t hiding, but I didn’t want to get involved in a Jerry Springer situation, with people throwing chairs,” Oremland says. “There are hundreds of blogs some viable and some off the wall, and they all want an immediate response. To try to engage in scientific commentary that way seems like a descent into madness.”

What the–?

I’ve seen this version of the arsenic life story before, and I can say (as one of the people mentioned in Clynes’s story) that it simply does not square with the facts. I really hope it doesn’t get set in people’s minds like concrete.

Let’s just run through the timeline, shall we?

Thursday, December 2: An eagerly anticipated NASA press conference, the publication of the paper in Science, front-page news in leading newspapers, with no articles I’m aware of dealing seriously with the critics.

[Update: Friday December 3: Chembark, a chemistry blogger, declares, “I am not convinced.”  Jim Hu of Texas A&M writes, “Could there be arsenic-based backbone in the DNA? Maybe. But it would be extraordinary and so I would like to see better evidence.” I for one missed these posts.]

Saturday, December 4: Rosie Redfield, a microbiologist with a blog she mainly uses for her class, expresses deep skepticism. It is the only such blog post I know of that presented a detailed criticism at this point in the timeline. [Update–I should say, the only blog post I was aware of.]

Sunday, December 5: Alex Bradley, another microbiologist, guest-blogs at We Beasties in a similar vein. The criticisms are harsh but deal in the scientific details of the paper.

The audience for both posts is small–an audience of fellow microbe junkies.

By Sunday afternoon, I think it’s time to write something. I’m wondering if Redfield and Bradley are saying what a lot of other scientists are thinking. I start getting in touch with leading experts in the areas that the paper touches on. In the next couple days they will get back to me, and just about all of them say the paper has serious problems, one simply declaring it should never have been published.

Naturally, it’s only fair to give the authors of the study a chance to respond. So on Sunday afternoon, I send links to the two blog posts above to Oremland and Wolfe-Simon. Oremland promptly writes back, “Sorry, but ‘nope.'”

I’m a bit surprised and email back to find out why. Here’s what I get:

It is one thing for scientists to “argue” collegially in the public media about diverse details of established notions, their own opinions, policy matters related to health/environment/science.

But when the scientists involved in a research finding published in scientific journal use the media to debate the questions or comments of others, they have crossed a sacred boundary.

Monday, December 6: Wolfe-Simon emails back at 12:42 AM, a few hours after I emailed her. She cc’s all her co-authors and administrators at NASA, including the director of the astrobiology program:

Mr. Zimmer,

I am aware that Dr. Ronald Oremland has replied to your inquiry. I am in full and complete agreement with Dr. Oremland’s position (and the content of his statements) and suggest that you honor the way scientific work must be conducted.

Any discourse will have to be peer-reviewed in the same manner as our paper was, and go through a vetting process so that all discussion is properly moderated. You can see many examples in the journals Science and Nature, the former being where our paper was published. This is a common practice not new to the scientific community. The items you are presenting do not represent the proper way to engage in a scientific discourse and we will not respond in this manner.

Regards,
Felisa

In the morning I get busy on my story. That evening, the CBC comes out with a story focused on Redfield’s complaint, relaying NASA’s statement that it’s not appropriate for scientists to debate each other in the media. I scratch my head and get back to work.

Tuesday, September 7: I publish a story in Slate about arsenic life, describing the detailed criticisms of a number of scientists (which I’ve posted in full on the Loom). I quote the no-comments of Oremland and Wolfe-Simon.

—Now, we can have a fine debate about whether journalists should ask scientists to respond to criticism from other scientists about their work. Oremland and Wolfe-Simon may truly believe that this crosses a sacred boundary. I say it doesn’t. It’s standard practice. Science, where the arsenic life paper was published, lets reporters get their hands on papers early, and reporters regularly seek out other scientists for comments on those papers before publishing their articles. If two scientists post their thoughts on public blogs, there is no difference in asking authors of a paper to respond to their critiques. Trying to make such a distinction is pointless.

I’ve been doing this kind of thing for a long time, and I have never encountered a response like this one from the hundreds of scientists I’ve interviewed. And that includes scientists who work for or are sponsored by NASA, despite the claims that popped up that NASA policy forbids such open debate. In fact, the scientist who gave me the headline for my story–“This Paper Should Not Have Been Published”–is herself part of NASA’s astrobiology team. Did she say, “Mister, you’ve crossed a sacred boundary”? Nope. She wrote me a long, detailed explanation of why she thought the paper failed.

In other words, I’m pretty sure I’d win that debate.

But the story you get from Clyne and others is not that Oremland and Wolfe-Simon had some a priori policy never to deign to comment on criticism that weren’t published in a scientific journal. It’s that they were overwhelmed by Jerry Spinger-grade hordes of unseemly scientist bloggers and relentless journalists–so overwhelmed that they had to vanish. They were victims.

But for this version of events to be true, the hordes must have stormed their lab in a single day–at some point between Saturday, when Redfield posted her critique, and Sunday, when the scientists told me they wouldn’t comment for the story. As far as I can tell, there were just two blog critiques published during that time, and a CBC news article. If someone can point to any evidence of this alleged horde that I’ve somehow missed–perhaps the gnawed bones of some graduate student left in its trail–I’d love to see it.

Otherwise, this just seems like one of those stories that sounds good in hindsight. And if any good is going to come out of this strange saga, we should strive to get all its stories straight.

[Update: Clynes responds.]

CATEGORIZED UNDER: Arsenic life, Link Love, Top posts

Did Rosie Redfield just refute #arseniclife on her blog?

By Carl Zimmer | August 2, 2011 9:24 pm

Rosie Redfield of the University of British Columbia has steadfastly raised doubts about the headline-grabbing news about arsenic-based life last November. (If neither arsenic life nor Rosie Redfield ring any bells for you, check out my two pieces for Slate, in December and June.) Redfield then did something exceptional: she set out to replicate the initial findings, getting the original bacteria and seeing whether they can build DNA from arsenic when deprived of phosphorus.

And then she did something quite unique: she started to chronicle her experiences on her blog. It’s a fascinating peek into the lab notebook of a practicing scientist. Today’s post is especially intriguing:

“First evidence refuting Wolfe-Simon et al.’s results”

Among other things, Redfield reports that the bacteria seem to be able to grow at very low levels of phosphorus–levels that the original scientists claimed were too low to sustain the growth they saw.

Of course, Redfield has a lot of work left to do. She will have to run this experiment to its bitter end, write up the results, submit a paper to a journal, get it past peer review, and publish it in a peer-reviewed journal. But we can all watch her journey in real time.

[Update: Over on Google+, Richard van Noorden pointed me to a similar (if less headline-grabbing) live-blogged refutation in 2009.]

CATEGORIZED UNDER: Arsenic life

Last year: Arsenic life. This year: Chlorine life?

By Carl Zimmer | July 6, 2011 2:17 pm

[Note: Some folks don’t like the phrase “chlorine-based life.” I welcome suggestions in the comments for a better shorthand descriptor]

Last year, a team of NASA-funded scientists claimed to have found bacteria that could use arsenic to build their DNA, making them unlike any form of life known on Earth. That didn’t go over so well. (See my two pieces for Slate for a quick recap: #1, #2.)  One unfortunate side-effect of the hullabaloo over arsenic life was that people were distracted from all the other research that’s going on these days into weird biochemistry. Derek Lowe, a pharmaceutical chemist who writes the excellent blog In the Pipeline, draws our attention today to one such experiment, in which E. coli is evolving into a chlorine-based form of life.

As I wrote in Microcosm, scientists have been contorting E. coli in all sorts of ways for years now to figure out what the limits of life are. Some researchers have rewritten its genetic code, for example, so that its DNA can encode proteins that include amino acids that are not used by any known organism.

Others have been tinkering with the DNA itself. In all living things, DNA is naturally composed of four compounds, adenine, cytosine, guanine, and thymine. Thymine, shown in the upper left panel here, is a ring of carbon and nitrogen atoms, with oxygen and hydrogens atoms dangling off the sides. Since the 1970s, some scientists have tried to swap thymine for other molecules, such as the one show to the lower left here. This compound is called 5-chlorouracil, the “chloro-” referring to the chlorine marked here in red. No natural DNA contains chlorine.

A team of German scientists recently published the details of an experiment that has taken them a long way towards E. coli that live only on chlorouracil. They didn’t simply sit down and type out a new sequence for E. coli’s genome–we just aren’t smart enough to make such predictions. Instead, they harnessed evolution. The scientists fed a population of E. coli chlorouracil, supplementing their dieet with a little thymine to keep them from starving to death. Bacteria that picked up mutations that allowed them to use some chlorouracil instead of thymine were favored by natural selection. They lowered the thymine levels to increase the pressure on the bacteria to evolve more.

After five months of this evolution, the E. coli underwent a noticeable change. For one thing, they changed shape. They started out in the normal capsule shapes in the top photo, turned into the worm-like shapes below, and then later became capsule-shaped again. The scientists also found that the bacteria were slurping up chlorouracil. Ninety percent of the thymine in their DNA was replaced by chlorouracil. As Lowe writes, the scientists found that the bacteria were still incorporating some thymine into their DNA through a pathway no one had discovered before (which just shows how marvelously mysterious E. coli remains after a century of intensive study). The scientists shut down this new pathway, and found that the bacteria still grew happily. But now they only had 1.5% thymine in their DNA.

This E. coli is different from ordinary E. coli, with over a thousand mutations that enable it to take up chlorouracil. But it is not quite yet off the grid. If it is fed thymine and no chlorouracil, it can switch back to a conventional way of life. So now we’ll see if scientists can further evolve the bacteria so that they can only live on chlorouracil, and starve on thymine.

I checked in with Steven Benner, a chemist who has raised a lot of concerns about the arsenic-life research last year. What did he think of the new research?

“It looks true,” he said.

Benner also pointed out that using chlorine in DNA is a pretty modest changed compared to what would have been required to substitute arsenic for phosphorus in the backbone of DNA. Swapping in chlorine doesn’t change how the compound reacts with other compounds, doesn’t change its size much, doesn’t change its stability much, and so on.

On the other hand, it appears to have the advantage of being real.

[Update: Rosie Redfield, an outspoken critic of the arsenic-life research, just got back to me with nice things to say as well:

“This looks quite solid to me (I read it quickly). The technology is nice, very appropriate for the project. No red flags at all.”]

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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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