Growth of GFAJ-1 under phosphate limitation (correction)

Erika Check Hayden's otherwise-excellent Nature News report on our work contained one error, the statement that "Redfield was unable to grow any cells without adding a small amount of phosphorus".

Here's the email I had sent her in response to an earlier query about phosphorus concentrations:

Hi Erika, 
The amount of phosphate in the medium used by Wolfe-Simon et al for their published growth analysis is indeed uncertain.  Their ICP-MS analysis found that most of their media preparations contained 3-4 µM phosphorus, but one batch contained <0.3 µM and a solution containing only the AML60-medium salts had 7.8 µM.  Because we don't know which batch was used for the results in their Figure 1, 3-4 µM is a good estimate of the phosphorus contamination, but the actual amount could have been substantially lower or higher. 
My cells did grow in medium with no added phosphorus*, to about 5 x 10^6 cells/ml.  This is about 1/4 of the density reached by GFAJ-1 in Wolfe-Simon et al's '-P/+As' medium.  Adding 3 µM phosphorus to my medium increased GFAJ-1 growth fourfold, to the same density as reported in Wolfe-Simon et al's experiments.    Simple algebra thus suggests that my unsupplemented medium contained about 1 µM phosphorus.  The correspondence of the cell densities reached in my supplemented (3 µM) and their unsupplemented medium supports the estimate of 3-4 µM contaminating phosphorus in their medium.   
My cells, like theirs, were clearly phosphorus-limited, because they grew to much higher densities when additional phosphorus was provided (see my recent RRResearch post and their Fig. 1). 
I think this is the best that can be done, since Wolfe-Simon et al. apparently did not keep good enough records to determine the actual phosphorus concentration of the medium they used for their reported experiments. 
Hope this helps, 
Rosie 
*The initial growth problem was not due to a lack of phosphorus but to the need for an amino acid, which I solved by supplementing the medium with a small amount of glutamate.

8 comments:

  1. Rosie—
    I have been tracking your blog for some time and generally have
    enjoyed it and admire and respect the work you have been doing to
    address the serious concerns we all have had regarding the
    #arseniclife story. I also have enjoyed your approach to blogging
    Science and having a place for informal, unpublished results to appear
    and be criticized like in a virtual lab meeting. This being said, I
    found the NATURE | News article highly inappropriate and disappointing
    as it creates the impression that your results have been reviewed and
    published, which is obviously not correct and thus premature at this
    point.

    We all recognize there were deficiencies in the Wolfe-Simon paper, but
    another disappointing aspect of this whole story was how they handled
    the presentation of their story. The press conference was an
    embarrassment to scientific due-process; your participation in
    theNATURE | News story is another. I can't WAIT for you to get an
    article like this written about your data AFTER it is published. After
    your refutation of her data has been through the peer review process.
    After you have responded to professional comments and criticisms of
    your own work (and, as there should be for any scientific paper, I
    imagine there will be many—David Borhani's comments for example mirror
    the criticism of a commenter from a few posts back that you have
    ignored). Instead, we find you embracing an opportunity to talk about
    your results as if they've been published and peer reviewed when they
    haven't. This, after lambasting Wolfe-Simon on both a personal and
    professional level for her handling of the media, is bordering on
    hypocritical.

    I look forward to your continued efforts, but it really pained me to
    see this article. Maybe I would have jumped at the opportunity for
    some good press too, but I don't think thats any justification for
    unprofessional behavior. It, in fact, makes your whole effort in the
    #arseniclife saga seem to be little more than a meretricious fling
    with self-promotion.

    I don't believe that it is Rosie, but an article like this sure makes
    it seem that way.

    Cheers,
    Peter Kraus

    ReplyDelete
    Replies
    1. Right, because it's not real science until two anonmyous referees and an editor say so.

      You're missing the whole point of an open notebook. You have the data -- go ahead and review! Got questions about Rosie's methods or conclusions? Go ahead and ask!

      Besides, how many people have been following along, sending comments and questions? This work has probably been more closely scrutinized by more peer reviewers than most manuscripts ever are.

      Delete
    2. I think the article is trying to convey the fact that this topic is still being thoroughly investigated. After a single read-through I felt that purpose of the article was strictly to provide an update on a topic that hasn't been in the public eye since 2010 when the original paper was published and I don't feel it is attempting to report anything that hasn't been peer-reviewed. It is simply giving an update on current research being done and providing a small amount of background information from unpublished results in order to support the questions that are being asked.

      How often do we see unpublished, non-peer reviewed data being referred to in published articles (i.e references of "data not shown" or "unpublished data")?

      Delete
    3. "Right, because it's not real science until two anonmyous referees and an editor say so."

      I understand your point, but the idea that Rosie has presented us with an "open notebook" and that we all "have the data", is ludicrous. We don't know how half of the experiments are performed, controls (that I'm sure Rosie has done) are not shown to us as Rosie would rather show us the 'money shot' experiments, which is fine because its a BLOG not a publication. But if we want to take this blog as science proper, than we should at least have all the details necessary to properly evaluate the work.

      "Besides, how many people have been following along, sending comments and questions? This work has probably been more closely scrutinized by more peer reviewers than most manuscripts ever are."

      While many people have no doubt been following this blog, the expertise of the majority of its readers with respect to the disciplines needed to provide any critical assessment of Rosie's work has been, in general, utterly lacking. When it turns out that the most substantial criticism is coming from trolls as opposed to scientists offering up general criticism instead of just playing fluffer to Rosie's work, you know that your statement holds no water.

      Does peer-review have its problems? Absolutely. Does that mean that we should treat blog-science that gets "reviewed" by RRResearch sycophants as likely-to-be credible? Absolutely not.

      Delete
    4. You want to call me names, sign yours. Anonymous cowards don't merit a response.

      Delete
  2. NotAnAstrobiologistJanuary 21, 2012 at 1:52 AM

    I really have no idea why people have this peculiar devotion to peer review.

    Peer review has a lot of problems (do we need more evidence than the GFAJ-1 paper itself, which was accepted based on peer review). Shennanigans like pseudoanonymous reviewers, asking for buddies on the peer review panel, idea snatching, unfair requests for additional experiments etc. Plenty of retracted papers to be found, all of which passed peer review. Plenty of useless turn-the-crank science out there, all passing peer review.

    The narrative on Rosie's blog is far more compelling than reading a formal publication. She is no doubt going to post a final summary of all the controls etc., but I wouldn't find it any more or less believable if she posted it on the blog or I saw it in Science post peer review.

    I can't come up with an experiment worth doing past what she has shown; and just about anyone who has any interest in this high profile matter can easily post here (and she'll even respond to trolls in the comments, unlike the GFAJ-1 authors)

    I am glad she is publishing the brevia, given the venue of the original GFAJ-1 paper and the fact that grant money allocation systems do (rightly or wrongly) depend publication in traditional journals.

    There is no reason to censor ourselves talking about the science we are doing, there is no reason why someone can't have confidence in someone's results and report on someone's findings without peer review and publication in a journal.

    I find FWS's response in the article (and her inconsistent statements throughout this entire affair) quite banal. Apparently it is ok to post self-laudatory twitter comments, and give talks (and press conferences). Anything critical of the work MUST GO THOUGH PEER REVIEW. Why not a simple casual response (she could even write in the comments on this blog) like:

    "Oh hey, might want to try adding some glutamate, we forgot to add that in methods"

    "Oh are you sending some DNA? I'll throw in from some mine from the bugs I've grown and you should be able to see the As signal clearly"

    etc.

    The fact that we haven't seen such casual comments, is really incriminating in my opinion.

    Yes, getting a consensus (from smart people) is important to help a critical mind understand what is true. It kind of just happens when people, who are interested in this kind of thing, hang out and talk. That's all peer review really is; nothing really holy about it when it happens through a scientific publication company that likes to sell magazines.

    ReplyDelete
  3. Peer review has always been a flawed process for disseminating scientific evidence, it survived because was there nothing better. Dr Redfield's publication of her work in this series of blogs has great advantages. Formal publication may serve the purpose of bean counters, publishers and search systems but will not improve the science.

    ReplyDelete
  4. The Nature News article states :"But it will be difficult to definitively prove the complete absence of arsenic from GFAJ-1 DNA."

    I find this troubling. Surely the burden of proof is on Wolfe-Simon et al. to prove that there is arsenic in the DNA, not on reviewers to prove that there isn't?(yes, Dr. Redfield is a peer reviewer, peer review does not end with publication, in fact, that's when it should really start...)

    ReplyDelete

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