Field of Science
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From Valley Forge to the Lab: Parallels between Washington's Maneuvers and Drug Development4 weeks ago in The Curious Wavefunction
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Political pollsters are pretending they know what's happening. They don't.4 weeks ago in Genomics, Medicine, and Pseudoscience
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Course Corrections5 months ago in Angry by Choice
Sorry for lack of posts...
We're busy finishing the Science/arseniclife paper, and the postdoc's uptake paper, and the RA's E. coli competence paper (submitted!), and an old visitor's competence paper, and my article about teaching genetics....
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I caught the CE&N article and found FWS's comments mind bogglingly inconsistent (and a touch dismissive "it's a great thing to check"):
ReplyDeletehttp://cen.acs.org/articles/90/web/2012/01/Arsenic-Based-Life-Aftermath.html
Once GFAJ-1 cells are cracked open, any arsenic linkages in DNA are liable to fall apart, she writes. As a result, “arsenate-containing bands may then also be shifted in the gradient—so that the expected amounts associated with DNA would be undetected because the band is so faint.”
I don't know how much of the above paragraph is coming from the author vs. FWS, but it doesn't make any sense.
The DNA can fall apart once cells are "cracked open", so you won't see anything? But Fig 2A in the original paper claims just the opposite!
“We will be purifying DNA, RNA, and proteins and seeing whether or not the arsenic tracks with these components.”
Forget about the rather odd circumstance of Ron Omerland's lab not working on this anymore and him not renewing FWS's contract....surely there would be some strong intermediate result (+ve or -ve) from MS by now (what about all those papers that FWS was about to finish? Remember, the ones she referred to in the press conference?)...
“We want to solve the structure of the ribosome and see what it’s going to tell us,”
This reeks of someone trying to simply trying to slow the game by holding the ball. Ribosome crystallization is tricky (as the guy who won a Nobel prize for doing it, points out in the article), and it would make no sense to try crystallizing before running MS to see if As is covalently present. One needs relatively high levels of incorporation to detect As unambiguously (otherwise, people could just use trace SeMet to phase). If you can't see it in MS, you won't see it in your crystal.
FWS is directly implying a lower bound on substitution rate by suggesting that solving a crystal structure (of a whole ribosome, no less) could be definitive. I'm going to guess it is something like 10% (I think that is generous), that would be very very easy to see in MS (or on a gel for that matter).
It seems that the ribosomal RNA is somehow magically stable outside the cells, but the DNA isn't?
I wouldn't be the first to say it, but I will do it here: shenanigans.
Going after the ribosome structure to solve this problem definitely qualifies as one of the most monumentally, uh how shall I say this, "misdirected" things I've ever heard of. “We think structure is the way to go,” Wolfe-Simon says. Who is the "we" here - is her group really pushing this approach? Apparently FWS is setting in for a long haul of dragging this out as long as she can (goes along with what's said here: http://www.michaeleisen.org/blog/?p=606 ). It will be interesting to see how long Tainer keeps funding her but apparently she enjoys her role as "science martyr".
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