The GFAJ-1 microbe: Not quite ready for prime time?

[struggle4progress]

... NASA announced that a group of researchers headed by astrobiologist Felisa Wolfe-Simon had discovered a microbe, GFAJ-1, capable of substituting arsenic for phosphorus in its DNA, proteins and lipids. In a post over the weekend, I explained how this microbe could change what we previously considered science fiction into scientific fact ...

Some scientists take issue with the techniques used or the precision (or apparent lack thereof) with which those techniques were executed. For example, in order to prove that GFAJ-1 was capable of surviving on arsenic alone, the microbe was grown in an environment that was high in arsenic but lacked phosphorus. However, Wolfe-Simon admits that her team couldn't remove all of the phosphorus (a result of "trace impurities" in the salts that were added to the environment for the experiments).

Therefore, some scientists have suggested, perhaps GFAJ-1 wasn’t really incorporating arsenic into its biomolecules as a means to survive; maybe it was living off of scraps of phosphorous instead. These aren't the only points of skepticism: Some researchers don't think that Wolfe-Simon’s DNA purification techniques were appropriate, while others feel that certain figures in the paper are misleading ...

http://www.boston.com/bostonglobe/editorial_opinion/blogs/the_angle/2010/12/the_gfaj-1_micr.html

[struggle4progress]

1. Critics raise doubts on NASA's arsenic bacteria

... One of the critics was Dr. Alex Bradley, from Harvard University, who blogged that there were a number of problems with the research. Firstly, if arsenic had replaced phosphorus in the DNA the molecule would have broken into fragments when the DNA was placed in water, since the arsenic would have hydrolyzed, and yet it did not. Secondly, the paper showed there was a small amount of phosphorus in the medium and Bradley argued that even though small, this could have been enough, since bacteria metabolism is extremely efficient.

Dr. Bradley also pointed out the bacteria live in Mono Lake, which is rich in arsenic but which also contains a higher concentration of phosphate than almost anywhere else on Earth, and this means there would be no selective pressure for a life based on arsenic to evolve ...

Dr. Bradley also suggested a mass spectrum of the DNA sequences would have shown whether or not the nucleotides contained arsenic in place of phosphorus, but this was not done

Another critic was University of British Columbia biologist Rosie Redfield, who reviewed the paper on her blog, and has more recently submitted a letter to the journal. Among her conclusions are that the paper “doesn't present ANY convincing evidence that arsenic has been incorporated into DNA (or any other biological molecule).” She also writes: “If this data was presented by a PhD student at their committee meeting, I'd send them back to the bench to do more cleanup and controls.” ...

http://www.physorg.com/news/2010-12-critics-nasa-arsenic-bacteria.html

[struggle4progress]

2. NASA’s Mono Lake Arsenic Microbes Not Quite As Advertized

... In fact, says Harvard microbiologist Alex Bradley, the NASA scientists unknowingly demonstrated the flaws in their own experiment. They immersed the DNA in water as they analyzed it, he points out. Arsenic compounds fall apart quickly in water, so if it really was in the microbe’s genes, it should have broken into fragments, Bradley wrote Sunday in a guest post on the blog We, Beasties. But the DNA remained in large chunks—presumably because it was made of durable phosphate. Bradley got his Ph.D. under MIT professor Roger Summons, who co-authored the 2007 weird-life report. Summons backs his former student’s critique.

But how could the bacteria be using phosphate when they weren’t getting any in the lab? That was the point of the experiment, after all. It turns out the NASA scientists were feeding the bacteria salts which they freely admit were contaminated with a tiny amount of phosphate. It’s possible, the critics argue, that the bacteria eked out a living on that scarce supply. As Bradley notes, the Sargasso Sea supports plenty of microbes while containing 300 times less phosphate than was present in the lab cultures ...

http://tucsoncitizen.com/wryheat/2010/12/09/nasa%E2%80%99s-mono-lake-arsenic-microbes-not-quite-as-advertized/