We spend so much time discussing manufactured controversies about science that it's a bit refreshing to be able to report on a real one. And one has been brewing since late last year, when Science released a report that suggested that researchers had forced bacteria to evolve to the point where they no longer simply tolerated arsenic, but incorporated it into their DNA. The publication quickly attracted criticism on a few blogs that were written by scientists, leading mainstream reporters to dig into matters. Now, the scientific community is having its say in the pages of Science, with eight separate technical comments on the work.

We covered the publication when it was first released, describing the major claims of the authors. They had isolated bacteria from an environment (California's Mono Lake) that is naturally high in arsenic, and then grew them in the lab, gradually raising the levels of arsenic while dropping those of its close relative, phosphorus, which is a component of DNA. After sufficient selection, they tested the surviving bacteria, and found some evidence that indicated arsenic may have been used in place of phosphorus in DNA.

The evidence, however, was indirect; arsenic was associated with DNA, and linked to carbon as arsenate (just as phosphorus in DNA is in the form of phosphate), but there was no conclusive demonstration that it was in the DNA backbone. As Yun Xie, who did the initial reporting noted, "high resolution analysis of purified products would provide more concrete evidence."

But harsher criticisms of the paper quickly followed (Carl Zimmer talked with a number of unconvinced scientists). Arsenate compounds are unstable in water; the medium contained residual phosphorus; its claims about DNA shouldn't have made it through peer review. The paper's authors declined to respond to the critiques, and some of them displayed a fair bit of contempt for online criticism, even that of their scientific peers.

Some of that same criticism, however, was sent in to Science, and has elicited a response from the paper's original authors. In the eight comments, the initial complaints are repeated and then some. A selection of quotes should give a flavor.

The assays performed were insufficient: "Straightforward experiments that could verify incorporation of arsenic into biological macromolecules were either not performed or not reported." "The presence of contaminating phosphate in the growth medium, as well as the omission of important DNA purification steps, cast doubt on the authors' conclusion that arsenic can substitute for phosphorus in the nucleic acids of this organism."

Residual phosphate found in the cells is significant, as "although low, [it] falls within the range we observed for environmental bacteria from a diverse set of aquatic environments."

Arsenic simply doesn't have the chemical properties implied by its presence in DNA: "Arsenate should correspondingly be slowly reduced to arsenite, a compound that is stereochemically quite different from phosphate."

And, most damningly: "If such arseno-DNA exists, then much of the past century of work with arsenate and phosphate chemistry, as well as much of what we think we know about metabolism, will need rewriting."

In general, there seems to be a significant divide. Everyone agrees that these are interesting bacteria. Some researchers are willing to accept that arsenic has found a home in biomolecules, while others question whether this is even chemically realistic.

The authors were given the opportunity to respond, and some of their responses are more compelling than others. For example, they argue that the cells grew better on arsenic alone than they did in a control experiment where neither arsenic and phosphorus were absent, even though these should have the same concentration of phosphate. That latter part of the claim appears to be a point of contention, though, as at least some people have indicated the arsenic source may provide some small amount of phosphorus.

Their response about the stability of arsenic in a biological environment boils down to noting that most of what we know about its chemistry comes from work with small molecules. Biomolecules are large and complex, and may shield arsenic sufficiently to provide a greater degree of stability. To me, that seems like a pretty weak argument, as does their response to the claims that the low levels of phosphorus seen in their cells overlaps with those in environmental samples of other strains of bacteria—they split hairs regarding populations and individual cells.

Overall, the sum total of the comments are likely to shift the controversy from the online sphere into the pages of Science. The authors have stuck to their guns, but have reiterated arguments that their critics are likely to find unconvincing. And that's somewhat surprising; it should have been possible for them to accept at least a few of the criticisms and indicate further work was under way that would handle them. I'd be tempted to think that they already knew what some of the answers were or they wouldn't have put up the arguments they had if the whole thing hadn't been handled so awkwardly from the start.

In any case, the authors have announced they'll mail out the bacteria to anybody who wants to independently check their work. For a case like this, where the claims in a paper are truly radical, getting more of the scientific community involved and letting them reach a consensus is the obvious route to clarity.

Science, 2011. DOI: 10.1126/science.1208877 (About DOIs).

Listing image by Photo illustration by Aurich Lawson