Science / AAAS
A photomicrograph shows GFAJ-1 bacteria that were coaxed to grow in an arsenic-rich medium.
Did scientists really coax microbes found in a California lake to act like alien life forms? Last week I wrote that some scientists just couldn't believe the claims that were reported in the journal Science, and since then the controversy has only grown more contentious.
"This paper should not have been published," science writer Carl Zimmer quotes University of Colorado microbiologist Shelley Copley as saying in a roundup of highly critical commentary gathered for Slate.
The key claim in the Science paper was that a strain of salt-loving bacteria from California's Mono Lake, known as GFAJ-1, was weaned away from consuming phosporus and forced to use arsenic instead. The researchers said the experiment showed that arsenic -- which is poisonous to life as we know it -- could serve as a substitute for an element that is generally considered an essential for life.
The implication was that life forms may well exist in arsenic-rich environments on Mars or the moons of Jupiter or Saturn, and that they might go unnoticed unless we expand our view on what life requires.
That big-picture view still holds true: Few biologists would insist that the recipe for life elsewhere in the universe has to use Earth's main ingredients (carbon, hydrogen, oxygen, nitrogen, sulfur and phosphorus). But if last week's buzz focused on how bacteria could be taught alien tricks with arsenic, this week's buzz is about how the researchers may have left out some essential steps for making their case.
"Something's wrong," Steven Benner, an astrobiologist at the Foundation for Applied Molecular Evolution, told me last week. "This is a recipe for creating these kinds of confrontations."
Benner said the case of arsenic-based life might well end up like the case of cold fusion, or the case of Martian nanofossils, with researchers from different disciplines arguing for years over the details of how the experiments were done. There was some of that even last week: Benner contended that there was still just barely enough phosphorus left in the experiment to sustain the bacteria, but during a NASA news conference to discuss the results, lead researcher Felisa Wolfe-Simon of the U.S. Geological Survey said the trace amounts of phosphorus couldn't have kept the microbes alive.
Wolfe-Simon's colleague at USGS, Ron Oremland, repeated that view today during a NASA webcast about the research. "There's a smidgen of phosphorus in the medium ... but it's not enough to sustain growth," he said.
Oremland acknowledged that "we can't do everything" to make an ironclad case for arsenic-based life, and said it would be up to other scientists to repeat the experiment and assess the results. "They may prove us wrong, or they may reproduce the results and find new stuff," he said.
If the bacteria were still living off that "smidgen of phosphorus," why did they contain so much arsenic? The critics say that the arsenic was contamination, and they continue to doubt that the arsenic molecules were actually incorporated into GFAJ-1's cellular machinery. In a detailed blog posting over the weekend, University of British Columbia microbiologist Rosie Redfield said the researchers failed to give the DNA from the microbes a thorough enough cleaning to remove contaminants. That may have been why their analysis led them to claim that "arseno-DNA" had been created.
"If this data was presented by a Ph.D. student at their committee meeting, I'd send them back to the bench to do more cleanup and controls," Redfield wrote.
Other researchers said that if arsenic was truly incorporated into the DNA, the relatively unstable molecular bonds should have fallen apart when they came in contact with water.
All this is what led Benner to bet Wolfe-Simon $100 that the DNA was not arsenic-based after all. But that $100 may be in dispute for a while. In the Slate article, Zimmer quotes Wolfe-Simon as saying "any discourse will have to be peer-reviewed in the same manner as our paper whas, and go through a vetting process so that all discussion is properly moderated."
Which raises another question: If there's so much griping about the research now, why weren't these concerns raised during the peer-review process?
"I don't know whether the authors are just bad scientists or whether they're unscrupulously pushing NASA's 'There's life in outer space' agenda," Redfield wrote. "I hesitate to blame the reviewers, as their objections are likely to have been overruled by Science's editors in their eagerness to score such a high-impact publication."
Stay tuned to hear more about that angle in the days ahead. Meanwhile, here's a roundup of week-after reconsideration:
- Slate: 'This paper should not have been published'
- LiveScience: Debate over arsenic-based life gets lively
- Embargo Watch: An arsenic bacteria postmortem
- Wired Science: Doubts brew about arsenic life
- Nature News: Microbe gets toxic response
- CBC News: Arsenic microbe science slammed
- Seed Magazine: Death for 'arsenic-based life'?
- We, Beasties: Arsenate-based DNA: Big idea with big holes
- Highly Allochthonous: This is what peer review actually looks like
- The Observatory at CJR: The right place for scientific debate?
"My research team and I are aware that our peer-reviewed Science article has generated some technical questions and challenges from within the scientific community. Questions raised so far have been consistent with the range of issues outlined by journalist Elizabeth Pennisi in her Science news article, which was published along with our research. For instance, other scientists have asked whether the bacteria had truly incorporated arsenic into their DNA, and whether the microbes had completely stopped consuming phosphorus. Our manuscript was thoroughly reviewed and accepted for publication by Science; we presented our data and results and drew our conclusions based on what we showed. But we welcome lively debate since we recognize that scholarly discourse moves science forward. We've been concerned that some conclusions have been drawn based on claims not made in our paper. In response, it's our understanding that Science is in the process of making our article freely available to the public for the next two weeks to ensure that all researchers have full access to the findings. We invite others to read the paper and submit any responses to Science for review so that we can officially respond. Meanwhile, we are preparing a list of 'frequently asked questions' to help promote general understanding of our work."