Sunday, February 27, 2011

Arsenic revisited: discussing arsenic story with a #UCDavis biology writing class next week

Well, this could be fun. Next week I am making a guest appearance in a Writing class at UC Davis. The class focuses on writing in Biology and the instructor invited me to come in as a guest to coordinate a discussion of the arsenic paper and the coverage of it.

When the instructor asked for reading assignments I said they should read:

I think I probably should have suggested they read Zimmer's excellent full write up here.  Going to suggest that now but may be too late.

Any other pointers to good write ups of what has happened since the first week after the paper would be appreciated.

Some suggestions coming in from twitter:


  1. Jamie Fraser on Facebook pointed to a new peer reviewed paper discussing the story. See Arsenate replacing phosphate: alternative life chemistries and ion promiscuity. Not open access but it is out there. Their abstract is:

    "A newly identified bacterial strain that can grow in the presence of arsenate and possibly in the absence of phosphate, has raised much interest, but also fueled an active debate. Can arsenate substitute for phosphate in some or possibly in most of the absolutely essential phosphate-based biomolecules, including DNA? If so, then the possibility of alternative, arsenic-based life forms must be considered. The physicochemical similarity of these two oxyanions speaks in favor of this idea. However, arsenate-esters and arsenate-diesters in particular are extremely unstable in aqueous media. Here, we explore the potential of arsenate to be used as substrate by phosphate-utilizing enzymes. We review the existing literature on arsenate enzymology, that intriguingly, dates back to the 1930s. We address the issue of how and to what degree proteins can distinguish between arsenate and phosphate and what is known in general about oxyanion specificity. We also discuss how phosphate-arsenate promiscuity may affect evolutionary transitions between phosphate- and arsenate-based biochemistry. Finally, we highlight potential applications of arsenate as a structural and mechanistic probe of enzymes whose catalyzed reactions involve the making or breaking of phosphoester bonds."


    On the emerging culture of informal yet impactful post-publication review. (Yeah, yeah, shameless plug).

  3. Is the paper still in Science Express? Isn't that a remarkably long period of time before "official" publication?

  4. Well, I do not even know what exactly Science express is - I guess maybe they use it when they want to put out something before the print edition/final version comes out? 2.5 months is probably not that long. Time from original acceptance to publishing many articles is probably a few months.

  5. I've been keeping an eye on the Science Express list. Judging by the progression of other papers, the Wolfe-Simon paper should have appeared in the paper copy of Science a couple of months ago.

    The only paper older than it is one from July 1, which Retraction Watch points out will probably be retracted because of methodological problems.

    I suspect the authors of the Wolfe-Simom paper are arguing about whether it should be retracted, or waiting to see if the first author can come up with any evidence that suggests it shouldn't be.

  6. Matt Kane pointed out that we should have the students read the original NASA press release - see

  7. I hope it's not too late to suggest my own posts--which may be particularly relevant because they were actually written for science writers and posted on the NASW site.

  8. Thanks Tabitha - too late for my appearance in class which was Wednesday but not too late for them to see


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