Long story short? The NASA team had a hypothesis and tried to prove it rather than try to find out what actually happened.
1) They improperly cleaned the DNA (or, not at all) before analyzing it. It's like me taking a bath in epsom salts, not showering down after, and then claiming that magnesium sulphate has entered my DNA.
"The Methods describes a standard ethanol precipitation with no washing (and no column purification which would have included washing), so I think some arsenate could easily have been carried over with the DNA, especially if it is not very soluble in 70% ethanol. Would this arsenate have left the DNA during the gel purification? Maybe not - the methods don't say that the DNA was purified away from the agarose gel matrix before being analyzed. This step is certainly standard, but if it was omitted then any contaminating arsenic might have been carried over into the elemental analysis." (link)
2) Further, instead of actually looking at the DNA to make sure, they just analyze my entire body and tell me that because there is such a high concentration of magnesium sulphate attached to me, my DNA must be made of magnesium sulphate. There is a way (mass spectroscopy) to read the DNA directly... but not for NASA!
3) ok, so they did try to at least separate the DNA from the rest of the cell (not clean it, mind you). This process is called phenol-chloroform extraction, and it's apparently a fairly straight forward lab technique. Only one problem; it involves water.
The long standing and well known issue with Arsenic DNA backbones is that arsenic bonds are very unstable, and too unstable to sustain life. So when exposed to water, these bonds break up within minutes (they have a half-life of ten minutes in water). The NASA theory goes that the cell had developed protein machinery to overcome this half-life problem through protection or at least a constant repair mechanism. The problem of course arises when you separate the protein machinery from the arsenic DNA backbone; it should break-up. However, it didn't. The DNA was extracted from the phenol-chloroform process (submerged in water and chemicals) after an hour or so still in long strands! This kinda plainly shows that the DNA did not contain arsenic, and in fact was probably/most likely still made with phosphorus.
4) Apparently this "depleted" phosphorus environment was not so "depleted". The second article below crunches the numbers and shows that there is actually more than enough phosphorus in the final substrate dilution for regular DNA to form.
For these bacteria to be able to form arsenic DNA strands, evolution tells us that there would have to be a selective pressure, or a reason why for the switch from the dependable phosphorus to the arsenic. Just because there is a lot of arsenic around in Lake Mono, doesn't mean that there is not enough phosphorus to form DNA. And in fact, that's the case. There is enough phosphorus in Lake Mono to form regular DNA strands.
The "depleted" phosphate solution provided to the bacteria by the experimenters had concentration of 3 micro molar phosphate. Is that a lot, or a little? Well, the Sargasso Sea has a phosphorus concentration that is 300 times less than the substrate phosphorus concentration provided by the NASA experimenters, and even there, the bacteria still use phosphorus in their DNA (they do succumb to the phosphorus pressures somewhat by removing phosphorus from their lipids, but keep it in their DNA...). So, with no evolutionary pressure, what made the experimenters think that they would take something that was admittedly abundant and incorporate it into their DNA? That's ridiculous.
That's like me saying I'm going to suddenly start incorporating lots of poo into my daily diet, because, ya know, there's a lot of it available!
Fucking NASA. I'm no rocket scientist, but looking for more funding by increasing the public perception that life on other planets is now "easier" to find? Uhhh... this is so frustrating. This is a joke, and will ultimately come back to bite them. Just. horrible. science. Embarrassing. NASA is a joke.
Re: arsenate hydrolysis, improper cleaning techniques without controls, no direct evidence (no mass spectrometer DNA sequencing done) --
http://scienceblogs.com/
Re: more improper techniques, amount of available phosphate in solid numbers --
http://rrresearch.blogspot.
From: http://neuroskeptic.blogspot.com/2010/12/science-bloggers-vs-science.html
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