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One of the most vocal critics of a 2010 claim that a bizarre bacterium might be able to use toxic arsenic as a building block of life has now made public new research refuting that claim. The manuscript, which is not yet peer-reviewed, appears on the site arxiv.org. This site is normally used by physicists to post pre-published papers and receive constructive criticism, but microbiologist Rosie Redfield of the University of British Columbia decided to extend that use to biology, in an effort to promote open science. She has also submitted the paper to the journal Science for publication.|
"This very clearly says you can make research available and still have it submitted and considered for peer review and published, just as if you'd kept it secret," Redfield told LiveScience.
This scanning electron micrograph shows a strain of the arsenic-eating bacterium called GFAJ-1.
Redfield set to work on the research after a group of scientists reported in December 2010 that they had discovered bacteria in desolate Mono Lake, Calif., that could munch on arsenic to survive in the absence of phosphorus, an element long established as a critical building block of life. The bacteria, dubbed GFAJ-1, even seemed to be replacing phosphorous with arsenic in their DNA, the researchers reported in the journal Science
This claim was surprising, because phosphorus is one of the six key ingredients of life on Earth, along with carbon, hydrogen, nitrogen, oxygen and sulfur. If an organism on Earth were found to survive without one of these building blocks, it could mean that life on other planets (as well as our own) is more adaptable than expected.
But the finding soon spurred a lively debate, with outside researchers criticizing the paper's methods. "The basics, growing the bacteria and purifying the DNA, had a lot of contamination problems," Redfield said.
Among those problems was the fact that the medium the researchers used to grow the bacteria they collected from Mono Lake had trace amounts of phosphorus. (The researchers countered that the contamination would not have been enough to sustain the bacteria.)
"That made the results very suspect," Redfield said.
So Redfield decided to test the two main claims in the paper: First, that the bacteria used arsenic to grow when there wasn't much phosphorus around and, second, that the bacteria were incorporating arsenic into their DNA.
Testing the first claim, Redfield grew GFAJ-1 in different media. She found that the bacteria grew just fine in very low concentrations of phosphorus, equal to the trace levels of contaminants in the original researchers' medium.
In the DNA
Next, Redfield and her colleagues took the bacteria grown in arsenic-rich media and extracted and purified their DNA — a more complete purification than in the original study, Redfield said. (A more purified sample means it is less likely to have outside contamination.)
"The results showed that there is no detectable arsenic in the DNA," she said.
That "detectable" qualification may be a sticking point in considering this new study a definitive refutation of the original, according to Steve Benner, a biochemist at the Foundation for Applied Molecular Evolution in Gainesville, Fla. The best and most sensitive way to detect the arsenic in DNA would be to use radioactive arsenic in the medium. That way, if this arsenic showed up in the DNA, it would essentially flash "I'm here!" like a big neon sign.
"Your problem now is having chosen to go in and isolate the DNA without the most sensitive analytical tools at your disposal; you're not going to get to the point where you can absolutely rule out any binding arsenic," Benner told LiveScience, referring to arsenic's supposed placement holding together the DNA backbone.
Nonetheless, he said, Redfield's first result — that the bacteria wouldn't grow in arsenic alone — suggests there is little need to go looking for the arsenic in the DNA, as there seems to be no evidence that GFAJ-1 can grow on arsenic alone. (It doesn't help that researchers need a government permit to work with radioactive arsenic, Benner added. Few researchers have such a permit, he said, and he knew of no one testing out the original results with this method.)
Benner said that nothing can ever be completely proven or disproven in science, but that he would have to "stretch" to come up with ways in which the original arsenic findings hold up.
Ronald Oremland, a research hydrologist at the U.S. Geological Survey and the senior researcher on the first arsenic life paper, declined to respond to the new research.
"It is not appropriate for me to offer commentary upon an un-reviewed manuscript submitted to a journal," Oremland wrote in an email to LiveScience. "My comments would undermine the scientific review process. When (if) the manuscript has passed anonymous peer-review (and in this case the editors at Science) and is published in the journal, that would be the appropriate time for my comments, should I be willing to express them."
The first author of the paper, Felisa Wolfe-Simon, also declined to speak directly about the new research until after peer-review. But she said that she was "thrilled" that other labs were pursuing experiments into the question. DNA may not be the only place in the cell to look for arsenic replacing phosphorus, she said.
"I am working with Dr. John Tainer at Lawrence Berkeley National Laboratory to find out how this organism grows in stupendous amounts of arsenic as our original paper established. It may take some time to accurately establish where the arsenic ends up," Wolfe-Simon wrote in an email to LiveScience. "What is certain right now is that we shall certainly know much more by next year."