Yesterday, Science published two papers which undercut an earlier paper in the journal claiming to show evidence for an arsenic-based strain of bacteria. Guest poster David Sanders, a structural biologist at Purdue University who was involved in a Retraction Watch story in May, argues that the journal could have avoided publishing the rebuttals—a swift retraction of the original was (and still is) the better move.
Allow me to apologize from the start. This narrative is not a typical Retraction Watch post, because it contains a number of personal elements. However, it would be hard to separate my perspective from my experience.
I will begin by asserting that, despite Rosie Redfield’s many valuable contributions to refuting the Wolfe-Simon paper that have culminated with the publication of data she and other investigators have obtained, there was no need for Science to publish additional articles. The Wolfe-Simon paper never should have been published. The only responsible action on the part of Science would be to retract the original article.
On December 3, 2010, I was listening to Morning Edition on National Public Radio and heard a story about a bacterium that used arsenic instead of
phosphorous phosphorus to live on and that the arsenic had replaced some of the phosphorous phosphorus in the organism’s DNA. Having worked on enzymatic phosphoryl transfer for much of my career (in case you are interested, my collaborators and I discovered that the two-component regulatory system response regulators were phosphorylated on an aspartate residue), I knew that the instability of arsenate esters made the claimed results impossible. Biology may teach us about novel chemistry, but it doesn’t violate the laws of chemistry.
When I arrived at work I went to the Science website and read the article, including the supplementary material. The article has been dissected at length by others (there are eight critical technical comments to it), but I would like to share my initial analysis. There was Figure 1, which purported to demonstrate that the bacteria grew (poorly) in the presence of 40 (!) mM arsenate in the absence of phosphate.
I immediately recognized that the “+As/-P” growth curve resembled that of a bacterium growing with a limiting nutrient (obviously not arsenate—there was many-fold more arsenate present than any nutrient that a microbiologist would include in a growth experiment). There was the statement in the abstract that there were substantial amounts of arsenate in protein. As a graduate student I was in the laboratory of Daniel E. Koshland Jr., where it had been first determined that protein phosphorylation occurred in bacteria, and I can assure you that it is not at very high levels. (Koshland was also editor of Science from 1985 to 1995.) The analytic techniques used to demonstrate incorporation into macromolecules such as DNA were either shoddy or didn’t provide real support to the conclusions.
The most important component of the original article is Supplementary Table S1. There is ICP-MS analysis of the -P/-As and -P/+As media for
phosphorous phosphorus and arsenic content. For each of the media there are two “batches.” Nowhere in the original article is there any mention of which batch was used in which experiments (more on this matter later). The critical data are the phosphorus concentrations. In the April 5, 2010, “batch” of -P/-As medium there is 3.7 +/- 0.4 microM phosphorus (note the standard deviations—we will return to them later as well). In the June 11, 2010, “batch” of -P/-As medium there is <0.3 microM phosphorous phosphorus-normally this result would indicate that the amount of phosphorous phosphorus was below the limit of detection of the instrument. In the April 5, 2010, “batch” of -P/+As medium there is 2.7 +/- 0.3 microM phosphorus, whereas in the July 29, 2010, “batch” of -P/+As medium there is 2.9 +/- 0.3 microM phosphorous phosphorus.
These data are summarized in the main text of the article as follows:
The background PO43- in the medium was 3.1 (+- 0.3) microM on average, with or without added AsO43, coming from trace impurities in the major salts (Table S1).
There can be no statistical or scientific justification for this misrepresentation of the data. One cannot average undetectable and 3.7 microM and get “3.1 (+- 0.3) microM on average, with or without added AsO43.”
No explanation is provided about the divergent analyses. If different “batches” of media have different amounts of
phosphorous phosphorus for no apparent reasons, then none of the data can be trusted.
The obvious explanation, one that others have suggested subsequently, was that the arsenate was contaminated with phosphate! This fact would explain the “optimal level of growth” of 40 mM. The bacteria were growing on the phosphate contamination!
What is the evidence for this proposition? First, the whole basis of the Mono Lake bacterial experiments is that arsenate chemically resembles phosphate. It does. It is therefore a likely contaminant. In my previous research experience I have run into the facts that commercial sources of S adenosyl methionine are contaminated with S adenosyl homocysteine, that D-amino acids are contaminated with L-amino acids, that radiochemicals may be “radiochemicallly” pure but they are not analytically pure chemicals, and that detergents were commonly contaminated with peroxides.
The Wolfe-Simon article, being an article in Science, did not indicate the source of the arsenate. To fulfill our curiosity at Purdue University we conducted some ICP-MS experiments on a commercial arsenate source and found that it was indeed and unsurprisingly contaminated with phosphate. Not a publishable result. For the Wolfe-Simon paper—bad data, misrepresented data, inconclusive data, contamination. Game over. No need for additional research or articles. Article was self evidently wrong and should never have been published. It should now be retracted.
The article itself is, however, only a small part of the story. As we’ll see in future essays, the case provides an illustration of the abysmal failure of scientific peer reviewers, scientific journals, government and academic institutions, the media and numerous individuals to do their jobs with competence and integrity.