Nasa news conference (re: Arsenic-based life form?)

I profoundly disagree with PZ Myers on this. I think he is massively underplaying how big a bit of biological news this is. That a bacterium has successfully evolved a means to substitute one of the absolutely fundamental building blocks of every key cellular mechanism and structure is most certainly a "big whoop".The only thing that is a bit disappointing about the announcement is its billing as having major significance for astrobiology.

Disclaimer: not read the paper yet hopefully have time tomorrow.As I understand it: they found arsenate in place of phosphate everywhere. Although they were looking at it by fractionation rather than isolating the particular molecules involved which makes the result less certain than it could be. If it's correct that the phosphate groups in ATP are being replaced by arsenate, at the researchers claim, then this would mean that proteins are being arseneylated. Yeah, it'll be a sidebar at most because, in the end, it's an extremophile living in a pond; it's just not that relevant to life as a whole. I'm astonished by this. And I would put good money that if you'd asked the world's molecular biologists last Tuesday whether this is something we'd find they'd have lumped down pretty heavily on the "not on this Earth" side of the fence.

We're not talking about merely tolerating or incorporating arsenic, we're talking about using it in place of one of the most fundamental building blocks of life and using it in key roles in absolutely central molecules.

Yeah, I still think PZ Myers is hugely underplaying this.It's true, Arsenic is only just below Phosphorous in the periodic table, but then it's also true that Phosphorous is just below Nitrogen and Silicon is just below Carbon - neither can be substituted by the element below.Arsenic and Phosphorous are similar, but this doesn't mean their differences are unimportant. Arsenic-containing analogues of biological phosphorous-containing compounds are radically less stable, which has two consequences: firstly, molecules that should be stable (such as the DNA) will simply hydrolyse and, secondly, whereas the energy release involved in the detachment of phosphate groups is retained, the spontaneous detachment of arsenate would not allow this energy to be retained for useful work. Since this management of energy is the central plank of metabolism this is a massive issue and even if the stability issues of the arsenate can be controlled, the release of arsenate from ATA to form ADA is going to release a slightly different amount of energy to that released by the conversion of ATP to ADP.As well as the stability problem there's also the issue of molecular size; now, Arsenic and Phosphate are similar in size to each other, but they are not identical. A DNA strand made with arsenate, rather than phosphate, linkage will have a slightly different length, with each base pair a slightly different distance apart which means the helix will be a different shape which means that the normal highly sensitive DNA-binding enzymes won't quite match up.If this bacteria is really substituting arsenic for phosphate, the biochemical implications are huge.

The paper does say that their data suggests that arsenate is being incorporated into the DNA backbone. The couch it in cautious terms but they do say it:

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Therefore, our X-ray data support the position of arsenate in a similar configuration to phosphate in a DNA backbone...

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Sure. But you seemed to be saying this was something the press was saying rather than something the researchers were saying. The researchers are saying its in the DNA backbone, they just don't have very strong evidence of this. If you're simply saying that the press is reporting it as more certain than it deserves - then, yes, I agree.

If they had been surviving and reproducing using arsenate in key biological molecules that would still be a finding of staggering biological importance. And as the paper itself says (emphasis mine):

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...GFAJ-1 is not an obligate arsenophile and it grew considerably better when provided with P

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That said, having spent some time looking at the paper and reading what other, more qualified to comment, folks have said about the actual science in the paper it seems to me that it profoundly fails the "extraordinary claims require extraordinary evidence" test. There doesn't seem to have been the testing required to rule out the notion that this bacterium is merely using mechanisms to survive high arsenic and low phosphorous conditions rather than actually substituting arsenic for phosphorous.

this would seem to be pretty much a slam-dunk on the idea that the bacteria is actually using arsenate in its DNA backbone.The skinny: an arsenate backbone should be unstable in water. The researchers theorise that the bacteria uses some unknown means to stabilise it. However, the extraction process they used effectively suspends the DNA in water if it truly had a Arsenate backbone then this should have resulted in it breaking up but their results show it didn't.Disappointing.Edited by Mr Jack, : No reason given.

If you want my idle speculation, I think this is a case of confirmation bias writ large. I've just been reading an earlier paper from Felisa Wolfe-Simon (et al), published last year* - it's basically a paper arguing for the plausibility and existence of life doing pretty much exactly what her group claim to have found. I suspect that because she was already strongly of the position it was possible and would be found, they looked and saw what they wanted to see.* - F. Wolfe-Simon, P.C.W. Davies and A.D. Anbar (2009). Did nature also choose Arsenic? International Journal of Astrobiology. 8: 69-74.

Also, if you listen to what Wolfe-Simon actually said at the press conference she does flat out say that the bacterium is substituting Arsenic for Phosphorous even if the paper is more appropriately circumspect.