Below is the text of my formal Letter to Science about the Wolfe-Simon paper. Letter submissions are supposed to be limited to 300 words (this is a bit over at 371), so I'm only bringing up the issues concerning contamination. This is an improved version that incorporates many of the suggestions provided in the comments below. So some of the comments (in the first 10-15) won't make sense any more.
Because this paper has LOTS of other problems, it would be great if many other researchers could also submit Letters and Technical Comments (limit of 1000 words, peer-reviewed). Here's a link to the Instructions for Authors entry page. I won't mind if your Letter gets accepted and mine doesn't.
Wolfe-Simon et al. (1) meticulously eliminated contamination of the reagents and equipment used in their elemental analyses, but they made much less effort to eliminate contamination in their biological samples.
The reagents used for the culture media were not pure. The 3.1 µM PO4 contaminating the As+/P- medium provided enough P for all of the cell growth seen in this medium, using the authors’ estimate of 7.5x106 atoms of P per genome and the generous assumption that phosphate-starved cells use 90% of their P for molecules other than DNA (2). This calculation (not done by the authors) obviates their hypothesis that the cells could only grow by replacing P with As.
An independent contamination problem is the omission of standard DNA purification steps when testing for As in DNA (2). Contamination is typical in DNA/RNA pellets produced by ethanol precipitation of the aqueous phases from phenol:chloroform extractions. This is partly because this fraction contains most of the small molecules from the cytoplasm (contrary to the authors’ assertion), which are often less soluble in 70% ethanol than in water. Pellets are also typically contaminated with small amounts of the ethanol supernatant. Yet the usual step of washing the pellets was omitted, and the dried pellets were simply resuspended in water and loaded on an agarose gel.
Most surprisingly, the chromosomal DNA fractions (boxed in Fig. 2A) were not purified from the gel slices (a standard ten-minute procedure). Instead the authors simply dried the gel slices and assayed them. Not only does this bring in any contaminants present in the gel, but since each gel slice would have contained at least 1 mg of agarose (100 mg of 1% agarose gel), and each DNA band no more than 1 µg of DNA, at least 99.9% of the carbon in these samples would have come from the agarose, not the DNA. No correction can be made for the agarose-derived C because the actual amounts of DNA and agarose are not known. Omission of the gel-removal step for these critical samples is surprising because the authors did use it in preparing the rDNA fragments they sequenced for their phylogenetic analysis.
1. Wolfe-Simon F, Blum JS, Kulp TR, Gordon GW, Hoeft SE, Pett-Ridge J, Stolz JF, Webb SM, Weber PK, Davies PC, Anbar AD, & Oremland RS (2010). Science Express. PMID: 21127214
2. W. Makino, J. Cotner, R. Sterner, J. Elser, Funct Ecol 17,121 (2003).
3. J. Sambrook, D. W. Russell. Molecular Cloning, A Laboratory Manual. 3rd Ed. Cold Spring Harbor Press, New York 2001.