Arsenic-based life debate continues

Scientists are questioning the validity of a high-profile paper that claimed to have discovered a strain of bacteria from Mono Lake, California, that can use arsenic in place of phosphorus in its DNA and other biomolecules, such as proteins.

Mono Lake, California Image: Image © 2010 Henry Bortman

The paper, which appeared online in ScienceExpress last December, immediately sparked a hot debate among the scientific community. Now, fifteen researchers have articulated their concerns in the form of eight technical comments published in ScienceExpress last week (May 27), and, for the first time since its publication, the authors of the controversial study have written a formal response to their critics.

In general, the criticisms highlight poor experimental techniques and point to more likely explanations for the results than a straightforward replacement of phosphorous with arsenic in biomolecules.

"It's like finding a unicorn in your back garden," said Rosemary Redfield, professor of microbiology at the University of British Columbia and an author of one of the eight published comments. "The chances of it being an actual unicorn are small, but if the experiments had been really well done, then they would have been convincing. In fact, the experiments were quite badly done. It's like having a blurry picture of the unicorn. It's unlikely that it's actually a unicorn."

Specifically, Redfield takes issue with the DNA extraction protocol, claiming that the genetic material was not purified properly before being tested for arsenic content. Furthermore, the supposedly phosphate-free growth medium on which the bacteria were cultured actually did contain phosphate, the phosphorus-based molecule of DNA backbones, which, Redfield argued, the bacteria may have been using to survive. To be absolutely sure that the bacteria were indeed using arsenate (the arsenic equivalent of phosphate) as the authors claimed, she said, the strain must be cultured without any phosphate.

Felisa Wolfe-Simon, a fellow at NASA's Astrobiology Institute and lead author on the original study, and her colleagues defended their DNA purification techniques, and said that they were transparent in revealing the presence of small quantities of phosphate in the medium. But, she argued, the low levels were not enough to sustain growth, as supported by lack of growth in control cultures in media that contained similar amounts of phosphate but no arsenate.

But James Cotner, environmental microbiologist at the University of Minnesota and one of the published commenters, contends that the authors overestimate the minimum amount of phosphorous required for cell survival, noting that many species of bacteria naturally survive on the low levels present in the study.

Furthermore, researchers argue that there are simpler possible explanations for why the bacteria cultured with arsenate survived and grew. Patricia Foster, professor of biology at Indiana University, said it's possible that the bacterial strain, called GFAJ-1, can only bring phosphate into its cells when it is exposed to a stimulant such as arsenate. Therefore, the control cultures don't prove that GFAJ-1 grows by incorporating arsenate into its DNA, just that arsenate needs to be present in order for the bacteria to grow. She also said that if the cells were actively growing and incorporating arsenate into their DNA, then their DNA should have contained a higher percentage of arsenic than the researchers found.

Much of the skepticism stems from the longstanding belief that arsenate is extremely unstable. In his comment, Steven Benner, distinguished fellow at the Foundation for Applied Molecular Evolution and another comment author, calculated that each arsenate linkage inside a hypothetical arseno-DNA molecule would hydrolyze (degrade) after only 1 minute in the environment of Mono Lake while phosphate-DNA can survive approximately 30 million years.

Though the specific criticisms vary, the sentiment is clear -- more research is needed to conclusively demonstrate that the bacteria actually incorporate arsenic into their biomolecules. "The experiments weren't done to the standards of a controversial issue," said Cotner.

Wolfe-Simon and her colleagues plan to continue follow up experiments, and though they have new data on the organism, Science declined to publish it with the authors' response to comments. They have also made GFAJ-1 available for study by other labs. "We weren't particularly happy with all of the hoopla," said Wolfe-Simon. "But you have to embrace your critics. It gives you the opportunity to be more scholarly."


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Elemental Shortage
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A matter of chow
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Arsenic and old...photosynthesis?
[14th August 2008]