May 27, 2011 at 3:27 PM ET
Last updated 8:30 p.m. ET
After five months of battles in the blogosphere, the debate over whether life can be based on an alternate biochemistry is playing out on the highest levels of peer-reviewed research.
Back in December, the journal Science sparked a ruckus by publishing an online report from researchers who claimed that they had coaxed bacteria from California's Mono Lake to live on arsenic rather than phosphorus. That's a big deal, because phosphorus is thought to be one of the six elements essential for life as we know it (along with carbon, hydrogen, nitrogen, oxygen and sulfur). Arsenic, on the other hand, is typically seen as a potent poison.
The researchers, led by astrobiologist Felisa Wolfe-Simon at the U.S. Geological Survey, suggested that such an alien biology could exist in environments beyond Earth that are traditionally thought to be inimical to life — for example, the hydrocarbon seas of Titan, Saturn's largest moon.
That sounds like a wonderful vision, but the claims from Wolfe-Simon and her team instantly came under attack from other chemists and microbiologists. In a flurry of blog postings and Twitter tweets, the critics took aim at what they saw were fatal flaws in the team's methodology. Wolfe-Simon and her colleagues defended their work in a Q&A issued via Science, but said they preferred to pursue the debate through the traditional peer-review process.
Now that process has taken a great leap forward. Today Science posted eight peer-reviewed technical comments from the critics to its Web site, along with a response from the original research group. The journal said all these papers would be printed, along with the original study (which has so far been available only online), in next week's edition.
"There's a lot of stuff that's happened," Wolfe-Simon told me today. "It's been a real challenge for me and my co-authors. ... We think this is evidence that, really, science is moving forward faster."
She held to the original claim that molecules of arsenic were incorporated into the machinery of life, replacing at least some of phosphorus. "We would argue that our conclusion is still viable," she said. "We never claimed 100 percent substitution, and in a way that point was misconstrued."
Wolfe-Simon said more evidence has been amassed to back up the arsenic-life claims over the past five months. However, the fresh evidence had to be held back for future publication. Wolfe-Simon said she was constrained from reporting new data in today's online response to the critics, which was a source of frustration for her. Science insisted on that to keep the cycle of response and counter-response from spinning out of control.
It's not unheard of to publish technical comments and responses in the wake of a controversial paper. Science did exactly that this week, with regard to a study claiming that microbes consumed all the methane that leaked from last year's Deepwater Horizon spill in the Gulf of Mexico. But it's very unusual to publish a research paper, eight critiques of that paper and a follow-up response to those critiques in the same issue of a scientific journal.
Science's editors said they did not expect their data dump "to be the final word on the subject."
"The fact that we received so much feedback to the Wolfe-Simon paper suggests to us that science is proceeding as it should," the editors said in a statement. "The study involved multiple techniques and lines of evidence, and the authors felt their conclusion was the most plausible explanation for these results when considered as a whole. We hope that the study and the subsequent exchange being published today will stimulate further experments — whether they support or overturn this conclusion."
The criticisms — and the responses from Wolfe-Simon and her colleagues — thus set the ground rules for the debate, which will likely continue for months and years to come. Here's a quick rundown of some of the issues involved:
Criticism: The "arsenic-eating" bacteria, known as GFAJ-1, were grown under conditions that still had trace amounts of phosphorus, and it's more likely that the microbes used that trace phosphorus rather than the arsenic. The arsenic-life researchers claimed there was so little phosphorus left that the bacteria couldn't possibly have survived on it — but under extreme conditions, some individual microbes have been found to survive on that little.
Response from the team: They point out that they checked bacteria under three conditions: high phosphorus and low arsenic; high arsenic and low phosphorus; low arsenic and low phosphorus. If the "arsenic-eating" bacteria were actually living off the low levels of phosphorus, they should have done as well in the low-arsenic / low-phosphorus environment. But they didn't. The team also says the survival rate on an ultra-low-phosphorus level should be compared based on wider populations, and not based on individual extremophile microbes.
Criticism: In the course of breeding bacteria to make them live in a high-arsenic environment, the team might have actually created bacteria that adapted to the low-phosphorus concentrations by processing the chemicals differently. That would explain why the high-arsenic / low-phosphorus bacteria did so much better than the low-arsenic / low-phosphorus bacteria.
Response from the team: They saw no evidence that the bacteria's biochemistry processed phosphorus in the way that was suggested, but acknowledged that the chemical pathways used by GFAJ-1 "are important avenues for future investigation."
Criticism: The molecular bonds involving arsenic would simply not be strong enough to hold up in alternate forms of DNA and other biochemical building blocks. What's more, phosphorus is far more abundant than arsenic in the solar system, and most of the arsenic available on rocky planets would be available in a form that is structurally quite different from phosphorus. These considerations point to the unlikelihood of life arising on Earth or elsewhere with an arsenic-based biochemistry.
Response from the team: It's conceivable that the arsenic bonds in large biomolecules are more resistant to a breakdown than the bonds in smaller molecules. "GFAJ-1 may have evolved specific strategies to cope with this issue, such as stabilizing structures," the team wrote.
Criticism: The team didn't devote enough attention to guarding against contamination of their samples and purifying the DNA that they analyzed. What's more, the uncertainties surrounding the measurements may not allow the team to make definite conclusions.
Response from the team: Wolfe-Simon and her colleagues recap the procedures they used and say they "were sufficient to remove any impurities." They also cite multiple techniques that cross-checked their results, through radiolabeling as well as high-resolution mass spectroscopy. They agree that further analysis of the DNA "would be a useful future experiment" because it could shed further light on the chemistry involved. They reworked their calculations on some of the analysis to respond to some of the criticisms about averaging, and said the data still supported their conclusions.
The bottom line is that the debate will continue, with more researchers getting into the act. Wolfe-Simon's team says samples of GFAJ-1 are being made available to other labs upon request, through the Oremland Laboratory at the U.S. Geological Survey.
"We look forward to working with our peers to replicate our observations and to test our hypotheses along the lines suggested by [one of the critics, Stefan] Oehler and others," the team writes.
One of the most vocal critics, University of British Columbia microbiologist Rosie Redfield, said today that she was still unconvinced:
"The authors don't report any new experiments. Most of their responses take the form of 'our interpretation could be correct on this point if...' In many cases there is indeed a small possibility that it could, but there are so many of these points of interpretation, each with only a very small probability of being correct, that I don't think anyone will find the arguments convincing."
Redfield said the team's responses to her comments about contamination were "in some ways the most scientifically valid, as they provide information about their media and DNA purification." She promised to have more about that on her blog later today.
So the blogosphere beat goes on. What do you think? Are you intrigued by this latest chapter in the grand scientific debate, or has the whole subject of arsenic life lost its appeal? Either way, please feel free to add your comments below.
Update for 8:30 p.m. ET: I've added some comments from Wolfe-Simon above after chatting with her this afternoon. She said she and her colleagues took Redfield's concerns about potential contamination very seriously. "Her criticisms are definitely valid," she said. "One of the first things we went back and did was look at all the ways we can get [phosphorus levels] down to zero."
But she said the key observations would come when scientists look at GFAJ-1's molecular machinery, to confirm that arsenic really is being incorporated into DNA, lipids and other molecules where phosphorus is usually found. "The question that people are really asking is, 'Show me the money. Let's see those biomolecules,'" she said.
Wolfe-Simon said she and her co-authors have been getting offers of help from other researchers in fields ranging from molecular biology to astronomy. She's also been getting supportive messages from lots of folks, including a 7-year-old girl who told her she wants to do research at Mono Lake when she grows up. "If I can put my peg on the wall, if we can ask the right questions ... she's going to answer the questions," Wolfe-Simon said.
Meanwhile, Redfield has posted an additional blog item that details her concerns about contamination. She's not satisfied with the response that Wolfe-Simon and her colleagues provided. "Overall, the most striking aspect of the authors' formal response is that they never admit to having made any mistakes or having done anything badly," she writes. "This is a bit disconcerting, given how many concerns were raised."
Update for 9:30 p.m. ET: An additional post from Rosie Redfield addresses how to test arsenic-life claims. Meanwhile, science writer Carl Zimmer looks at the big role that online discussion played in the arsenic-life debate, and Nature's Erika Check Hayden rounds up reactions from other researchers. One theme: Is it worth spending time and effort to try replicating the findings?
The story so far:
Science is making all 10 papers accessible with free online registration. You can see the whole list on Science Express, the journal's rapid-publication website, and here's an item-by-item menu:
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