We originally submitted our manuscript to Science at the end of January, and posted a copy of it on the arXiv server, asking for comments/critiques from readers. We received a few of these, and on March 16 we received three detailed reviews from Science, and a provisional acceptance. On April 13 we submitted the revised version, and we're waiting with fingers crossed to for final acceptance.
I've just posted the revised manuscript on arXiv, replacing the original version. Here's the link. We tried to incorporate suggestions from blog comments too.
Below I've pasted the text of our 'Response to Reviews' letter. We didn't do a detailed response to the reviews because the Editor had clearly indicated the changes she thought important.
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April 13, 2012
Dr. Caroline Ash,
Senior Editor, Science
Dear Dr. Ash,
Thank you for giving us the opportunity to improve our manuscript. We are now submitting the revised version.
We have closely followed the suggestions in the pre-edited copy of the manuscript that you provided. We felt that the most important request of the reviewers was to directly measure the phosphate concentration in our basal AML60 medium. To this end, we conducted ICP-MS, obtaining a concentration 0.5 µM, in close agreement with our prior estimates based on cell growth. This new measurement fully supports our conclusion that the growth of GFAJ-1 in the hands of Wolfe-Simon et al. was due to residual phosphate in their putative -P conditions. When combined with shortening other text as indicated in the pre-edits, this has reduced the manuscript’s length from 2193 words to 1577 words.
We have retained a few sentences discussing explanations for the discrepancies between our results and those of Wolfe-Simon et al. Since these discrepancies are the point of our paper we feel that possible explanations for them should be considered even when they cannot be directly tested.
We would prefer to retain our original title, as we feel that the word ‘negligible’ puts undue emphasis on the trace of arsenate present in the DNA. Two alternative titles we would be happy with are ‘Absence of detectable arsenate in DNA from arsenate-grown GFAJ-1 cells’ and ‘No covalently bound arsenate in DNA from arsenate-grown GFAJ-1 cells’.
Changes in response to points raised by the reviewers:
The ‘-P’ and +P’ growth conditions we used are now clarified in both the Methods and the legend to Figure 1.
We now explain how cell numbers were determined.
We now explicitly say that we obtained strain GFAJ-1 from the authors of the Wolfe-Simon et al. paper.
The discrepancy in glutamate concentrations and the incorrect formulae have been corrected.
The ingredients of AML60 medium are now given in the Methods.
Reviewer 3 was concerned about our statement (in Methods) that cells were pre-grown in phosphate-limited medium containing 40 mM arsenate. We now explain that the cells were thoroughly washed to remove the arsenate before being frozen, and that the purpose of this pregrowth was to deplete cellular reserves of phosphate and to replicate the standard growth conditions used by Wolfe-Simon et al.
All of the reviewers, but especially Reviewer 3, would have liked more information about GFAJ-1’s growth properties and metabolism. Unfortunately, characterizing these in depth is beyond the scope of this work. We do not know why GFAJ-1 cells need glutamate or another amino acid for growth in our AML60 medium independent of phosphate supplementation, why they reproducibly grew to a higher density in AML60 medium with 70 µM phosphate than with 250 or 1500 µM phosphate, nor why they did not grow in Wolfe-Simon’s low-phosphate AML60 medium unless arsenate was provided.