A new analysis by open-science advocates present a 'clear refutation' of a controversial finding that appears to undermine assumptions about how essential phosphorus is for life
?| January 23, 2012
A scanning electron micrograph of GFAJ-1, the bacterium at the centre of the controversy. Image: Science/AAAS
A strange bacterium found in California?s Mono Lake cannot replace the phosphorus in its DNA with arsenic, according to researchers who have been trying to reproduce the results of a controversial report published in Science in 2010.
A group of scientists, led by microbiologist Rosie Redfield at the University of British Columbia in Vancouver, Canada, have posted data on Redfield's blog that, she says, present a ?clear refutation? of key findings from the paper.
?Their most striking claim was that arsenic had been incorporated into the backbone of DNA, and what we can say is that there is no arsenic in the DNA at all,? says Redfield.
But the authors of the Science paper are not retreating from their conclusions. ?We are thrilled that our results are stimulating more experiments from the community as well as ourselves,? first author Felisa Wolfe-Simon, now at the Lawrence Berkeley National Laboratory in California, wrote in an e-mail to Nature. ?We do not fully understand the key details of the website experiments and conditions. So we hope to see this work published in a peer-reviewed journal, as this is how science best proceeds.?
Open criticism
In the Science paper, Wolfe-Simon and her co-workers reported that they had found a bacterium called GFAJ-1 that can use the element arsenic in place of phosphorus in molecules essential to life (see Arsenic-eating microbe may redefine chemistry of life). This was surprising because phosphorus is thought to be essential for life, whereas arsenic is usually toxic.
But after Redfield and others raised numerous concerns (see Microbe gets toxic response), many of which were published as technical comments in Science, Redfield put the results to the test, documenting her progress on her blog to advance the cause of open science.
Redfield grew GFAJ-1 bacteria in arsenic and a very small amount of phosphorus, as had Wolfe-Simon and her colleagues. She then purified the DNA from the cells and sent it to Marshall Louis Reaves, a graduate student at Princeton University in New Jersey. Reaves used a caesium chloride gradient to separate the cells' DNA into fractions of varying densities, then used a mass spectrometer to identify the elements present in each fraction of DNA. He found no arsenic in any of the DNA.
But Redfield?s methods might leave defenders of the arsenic life hypothesis some wiggle room. For instance, Redfield was unable to grow any cells without adding a small amount of phosphorus. Because it is not clear how much phosphorus was used to grow the bacteria in the original paper, its authors could argue that Redfield's cells were not sufficiently phosphorus-starved to be forced to use arsenic in its place.
Wolfe-Simon also says she would not expect to find arsenic in DNA analysed on a caesium chloride gradient, because the arsenic-containing DNA might be so fragile that it would break apart and appear only in very faint bands separate from the bulk of the cell's DNA.
However, Redfield says that Reaves analysed all of the DNA purified on the gradient, so he would have detected any arsenic. Redfield also analysed the size of DNA from cells that had been stored for two months in her lab refrigerator. The DNA fragments from cells that had been grown with and without arsenic were similar sizes, indicating that DNA from arsenic-grown cells is not unstable.
Source: http://rss.sciam.com/click.phdo?i=8a2d5e66b7c9d68d79d1b7a07956aafa
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