Tuesday, July 10, 2012

Rosie Redfield at Evolution Ottawa 2012

Rosie Redfield gave a talk on Sunday night. She described the work she did on the so-called "arsenic-incorporating" strain of bacteria that was made famous in a NASA press release and a subsequent Science paper last year [Arsenic and Bacteria] [Arsenic-associated bacteria (NASA's claims)] ["This Paper Should Not Have Been Published"].

You might recall that Rosie was among the first scientists to point out the flaws in the original paper and this led to a delay in its publication. When it finally was published there were several critical comments—including one from Rosie—that appeared in the same issue.

Rosie obtained the GFAJ-1 strain and tested its growth characteristics. She determined that it absoltutely required phosphate for growth and growth stopped when the phosphate in the medium was depleted. The strain did tolerate high levels of arsenic in but there was no evidence that it could replace phosphorus.

Rosie purified DNA from cells grown in the presence of arsenic and sent it to her collaborators. There was no arsenic in the DNA. (Carl Zimmer takes you through a blow-by-blow summary of Rosie's talk at Live-blogging Arsenic Life].)

The work was submitted to Science and the paper was accepted for publication It was due to be published on July 26th which meant that, under the conditions imposed by Science, Rosie wasn't allowed to talk about her work until then. Rosie informed Science that she intended to violate the embargo and describe her results at this meeting. Science responded by moving the publication date forward and posting the paper on their website at 8pm Sunday night [Absence of Detectable Arsenate in DNA from Arsenate-Grown GFAJ-1 Cells]. Carl Zimmer was watching the website as Rosie spoke and at one point in her talk she turned to Carl to ask if the paper was up—it was.

The audience recognized that this was a major victory for open science. As the moderator put it at the end of her talk, you can mess with NASA, you can mess with Science, but don't mess with Rosie Redfield!

There are two papers being published in Science. The other one [GFAJ-1 Is an Arsenate-Resistant, Phosphate-Dependent Organism] says essentially the same thing as Rosie's paper.

The bottom line here is that the original paper by Wolfe-Simon et al. (2011) was deeply flawed and should never have been published by Science. More importantly, the latest results show that Felisa Wolfe-Simon was dead wrong when she claimed at the NASA press conference that GFAJ-1 incorporated arsenic into its DNA. You can watch her say this in the video I posted at: The Arsenic Affair: No Arsenic in DNA!.

You may be wondering how NASA and the authors of the original paper are handling this issue. In spite of the fact that they held a public press release and in spite of the fact that Felisa Wolfe-Simon was interviewed multiple time in the press and even gave a TED talk, they maintain that the only proper forum to discuss criticism of their paper is in the peer-reviewed literature! (I hate hypocrites.)

When Wolfe-Simon heard that Rosie's paper was in press she said [Arsenic-based life finding fails follow-up] ...
Wolfe-Simon, who says she can’t comment in detail until Redfield’s results appear in a peer-reviewed journal, wrote in an email that her original paper never actually claimed that arsenate was being incorporated in GFAJ-1’s DNA, but that others had jumped to that conclusion. “As far as we know, all the data in our paper still stand,” she wrote. “Yet, it may take some time to accurately establish where the [arsenic] ends up.”
She's right about the fact that the original paper never actually said that arsenic replaced phosphorus in DNA but it did strongly imply that this was the logical conclusion. However, in her press conference, Wolfe-Simon explicitly talked about arsenic replacing phosphorus in DNA and nobody who listened to that talk could have come away with any other impression. You didn't have to "jump to that conclusion" after hearing the presss conference.

So what are they saying today? Read Rosie's blog at: NASA's cowardly responses to their #arseniclife FAIL. And here's what Wolfe-Simon is saying, quoted at: New Studies Say No, Life Can't Live on Arsenic Alone.
These Science authors have made it clear that they are convinced they have tightly shut the door on arsenic incorporation into biomolecules. Yet, low amounts of arsenic incorporation may be challenging to find and unstable once cells are opened," she writes, "so may merit comprehensive and systematic efforts with other assays and conditions.
I don't think it's reasonable to expect Wolfe-Simon to apologize but I do think the scientific community should continue to apply pressure on NASA.

Here's a very good account of what happened and why NASA should be ashamed: Scientist in a Strange Land. It also expresses some sympathy for Felisa Wolfe-Simon.


Photo courtesy of Seanna Watson.

Wolfe-Simon, F., Switzer Blum, J., Kulp, T.R., Gordon, G.W., Hoeft, S.E., Pett-Ridge, J., Stolz, J.F., Webb, S.M., Weber, P.K., Davies, P.C.W., Anbar, A.D. and Oremland, R.S. (2011) A bacterium that can grow by using arsenic instead of phosphorus. Science. 332:1163-1166. Published online 2 December 2010; published in Science magazine Jun 3, 2011 [doi: 10.1126/science.1197258]

Wolfe-Simon, F., Switzer Blum, J., Kulp, T.R., Gordon, G.W., Hoeft, S.E., Pett-Ridge, J., Stolz, J.F., Webb, S.M., Weber, P.K., Davies, P.C.W., Anbar, A.D. and Oremland, R.S. (2011) Response to comments on "A bacterium that can grow by using arsenic instead of phosphorus". Science. 332:1149. [doi: 10.1126/science.1202098]

6 comments :

  1. Frankly, not very impressed with Redfield. Yes, good job and all proofing the scientific record, but how about making some kind of de novo positive contribution of your own? It's pretty standard stuff for the various non-science hype machines to go into rabid overdrive over the smallest result, and maybe FW-S got caught up in it, but the actual paper is considerably more modest.

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    1. From the science paper, pg 1165, third column at the top.

      "These measurements therefore specifically demonstrated that the purified DNA extracted from +As/–P cells contained As. Our NanoSIMS analyses, combined with the evidence for intracellular arsenic by ICP-MS and our radiolabeled 73AsO43– experiments, indicated that intracellular AsO43– was incorporated into key biomolecules, specifically DNA."

      That's a wee bit more than caught up in the hype machine....

      -The Other Jim

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  2. Anonymous fail. Not understanding science or the weakness of the publication system today.

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  3. If Anonymous wants to evaluate Rosie Redfield's science, Anonymous could go read her papers and her blogging about that work. She has studied DNA uptake by bacteria and "quorum sensing" bacterial communication. On both she takes a decidedly nonstandard and controversial position. Her work on the arsenic issue is a sideline. I attended molecular evolution meetings in Canada for many years. Rosie was always there, always with some new and stimulating results or hypotheses, and always great fun to listen to.

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  4. Seems to me that the title of the paper by Wolfe-Simon, et al., leaves no doubt about what Simon and her collaborators claimed (and still do if they're standing by their paper):

    "A bacterium that can grow by using arsenic instead of phosphorus."

    "[I]nstead of" sure doesn't sound the same as "Yet, low amounts of arsenic incorporation may be challenging to find and unstable once cells are opened," she writes, "so may merit comprehensive and systematic efforts with other assays and conditions."

    Instead of can legitimately be construed as 'replacing'.

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  5. In the fourth paragraph from the end:

    "She's right about the fact that the original paper never actually said that DNA replaced phosphorus in DNA but it did strongly imply that this was the logical conclusion."

    I think you mean to say either "...said that arsenic replaced phosphorus in DNA..." or "... said that DNA replaced phosphorus with arsenic...".

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