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Overenthusiastic science

You all may have noticed that I got very excited about last week’s announcement from NASA of a study by Dr. Wolfe-Simon and others identifying bacteria that could use arsenic instead of phosphorus in their biomolecules, including DNA.

I’m a biologist, but not a molecular biologist, so when I read the Science paper on these arsenic-using bacteria I assumed that the methods used were correct and conclusions reasonable. That is not true, according to many scientists who do know those methods.

My understanding of the methods as intended:
1. Collect bacteria from Mono Lake.
2. Grow them for many generations with phosphorus, arsenic, both, or neither.
3. Divide the bacteria into components: DNA here, proteins there, lipids in the far corner, then check for the presence of arsenic and phosphorus.

I did point out that finding arsenic where you’d expect phosphorus was suggestive but not proof, and also that arsenic is a much weaker and less efficient component of these biomolecules than phosphorus, and so more expensive for the bacteria to use.

What I didn’t realize is that there were a lot of problems with the experimental set-up and execution. Dr. Rosie Redfield provided a critique. There was phosphorus in the growth medium, even in the arsenic-only treatment. Not much, but possibly enough for the bacteria to live on. Despite what they said (and I repeated), the bacteria did grow slowly in the no phosphorus-no arsenic treatment, suggesting contamination, or recycling of phosphorus from the original samples.

Dr. Redfield also explained that the fractionation process wasn’t done in such a way to make sure there was no arsenic contamination of the fragments from the growth medium. And even if Dr. Wolfe-Simon and others did find arsenic in the DNA in the quantities reported, that would make up only a tiny fraction of the still phosphorus-dominated DNA backbone.

Ooops.

Dr. Alex Brady described other likely contamination problems with the methods used. Dr. Brady also points out that arsenic linkages are not stable in water, so if the NASA group had used the methods they described, then the arsenic-based DNA would have come apart during analysis. Thus, the experiment actually demonstrated that the bacteria have phosphorus-based DNA.

And here’s one that bothers me, but that I hadn’t had time to look up before. Mono Lake has lots of arsenic, true, but it also has lots of phosphorus. So why would these bacteria ever need to use expensive and unstable arsenic in their biochemistry?

This is very disappointing, and I look forward to hearing what Dr. Wolfe-Simon and her colleagues say in response. I’m afraid they got overenthusiastic and only presented the results that supported their claim (and according to Dr. Wolfe-Simon they actually went looking for those results). That makes for a lot of excitement, but not for good science.

One Comment

  1. MWT says:

    Well, I guess now someone needs to repeat the experiment with the methodology issues patched up and see if it gets the same results. ;)

    (Probably not, from the sounds of it … oh well?)

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