DNA, Phosphorus, and Arsenic

 
Most of you know that DNA strands have a sugar-phosphate background. The bases in each strand are covalently linked to each other by phosphodiester linkages between the 5′ and 3′ carbon atoms of the deoxyribose sugar.

Recently there has been a claim by NASA-funded scientists that a certain bacterium can replace those phosphates with arsenic. Close examination of the Science paper has revealed that, at most, a few percent of the phosphorus atoms are replaced and even that amount is challenged. It has become abundantly clear from reading the paper that the bacteria absolutely required phosphorus and sufficient quantities were present in the media as contaminants.

I've already linked to Rosie Redfield's critiques of the paper and the press conference. Now I want to add Carl Zimmer's take on the whole affair—the title tells all: "This Paper Should Not Have Been Published".

Carl raises an issue that has cropped up in many of the comments sections of various blogs. Is criticizing a scientific paper appropriate outside of the peer-reviewed scientific literature? Is it ethical to cast doubt on the integrity of scientists when questioning the quality of their science?

Felisa Wolfe-Simon¹ is the lead author of the study and she was the main spokesperson in the video below. Carl Zimmer asked her if she wanted to respond to the criticism of her paper and here's what she said, according to the Slate article,

"Any discourse will have to be peer-reviewed in the same manner as our paper was, and go through a vetting process so that all discussion is properly moderated," wrote Felisa Wolfe-Simon of the NASA Astrobiology Institute. "The items you are presenting do not represent the proper way to engage in a scientific discourse and we will not respond in this manner."

Carl asked some other scientists about this and the best quote comes from Jonathan Eisen,

But Jonathan Eisen of UC-Davis doesn't let the scientists off so easily. "If they say they will not address the responses except in journals, that is absurd," he said. "They carried out science by press release and press conference. Whether they were right or not in their claims, they are now hypocritical if they say that the only response should be in the scientific literature."

My own impression of this fiasco is that the scientific authors of the paper can be accused of bad science and the lead author, Felisa Wolfe-Simon, is guilty of grossly misrepresenting her work at the press conference. There really can't be any excuse for that behavior if you want to call yourself a scientist. Those who think this is impolite and unethical are dead wrong. It's an absolute requirement of good science that we point out to the general public when scientists are behaving badly, otherwise we lose all credibility.

As you watch this video keep in mind that the bacteria absolutely require phosphate in the media in order to grow and that only a few phosphorus atoms, at most, are replaced by arsenic in DNA. If you think that's what Felisa Wolfe-Simon is telling you then you need to work hard on your listening comprehension skills.

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1. The name of the bacterial strain is GFAJ-1. Rumor has it that this stands for "Get Felissa a Job." I wonder how that's working out? Do you think the job offers are pouring in?