Wednesday, June 6, 2012

Arsenic Life Wrap-Up: The Good, the 'Not-So-Good'

"Arsenic Life," a hot-button issue for much of the past year, reemerged this week with two new papers, one propitious, and one, well...not so much.

GFAJ-1 bacteria
Source: nasa.gov
As covered by Curious Wavef(n), the first paper related Prof. Rosie Redfield's well-documented efforts coaxing the GFAJ-1 strain to flourish in arsenic-rich media, which, if successful, would imply arsenate linkages in the bacterial DNA. Redfield bursts the bubble nicely, utilizing multiple tools (LC-MS, cell growth assays, gels) to cast doubt on the earlier study, even mentioning that most of the detected arsenate could be washed away with distilled water.

Well, if timing is everything, then the second #arseniclife publication really missed the boat. Last week, a commentary appeared in the open-access online journal Biomolecules, bearing the epic title From Phosphorus to Arsenic: Changing the Classic Paradigm for the Structure of Biomolecules. Heavy stuff!

This summary takes the opposite tack, casting "Dr. Wolfe-Simon's discovery" as a fighting underdog - viewed skeptically today, but enshrined and glorified by future generations much like Copernicus or Darwin (both name-dropped inside). The prose shakes the reader with thrilling, emphatic statements, lines you might find in a rousing stump speech or an action movie. A few choice selections:
"...Some have died as a result
of these discussions
..."
Image Credit: Silver Lining
"It is no surprise that this work has come under what some may consider a brutal attack in the past year; the proposed repercussions almost beg of it."
"...members outside of the scientific community may view the criticisms and other events that have transpired as superfluous, vindictive, and outright scathing.
"...the implications of [arsenic life] have the potential to shake the foundation of biology as we have known it for centuries."
 "This discovery...would be absolutely groundbreaking to all of science."
You get the point. These excesses, coupled with a few cut-and-paste sources (N.B. Don't include "page-access" dates in references) and a passing remark to Wolfe-Simon's potential scientific martyrdom, complete the commentary. Yesterday, several Twitter denizens, led by the industrious Carmen Drahl, noted a very familiar vibe to this piece. To borrow a phrase from Derek and Leonid, it sounded suspiciously like a "term paper," final reports students submit to wrap up specific college courses.

My feelings, reading Paper #2
Source: Jobbing Scriptwriter
Was it? A very strong maybe. Check out this editorial, culled from the Colorado State University Journal of Undergraduate Research  (p. 16), scribed by the lead author. Bears a rather striking homology to the Biomolecules piece, sources* and all. The second author, currently an undergraduate at Boston University, may have interacted with the CSU authors at a conference, or perhaps on a summer REU.

As corresponding author, Prof. Mark Brown (CSU) would, I'd believe, have final say over the manuscript. Did he check it against the lead author's previous work? The journal's Author Information section mentions that five external reviewers must be named, although "...the Editor will not necessarily approach them."

So, to round up this bizarre publishing escapade, we have undergraduate authors submitting previous work in an open-access, loosely-reviewed, and barely-edited online journal, all with the benediction of a faculty member? Sounds dubious...much like arsenate linkages in DNA.

*Can someone please tell me where to find Ed "Young" at Discover Blogs? : )


Update, 6.8.12 - Commenter Stuart Cantrill (Editor, Nature Chemistry) points out on Twitter that the original piece also misspelled "phosphorous" in the title. Sigh.

7 comments:

  1. Yippee-ki-yay, #arseniclife.

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  2. Wherefore art thou, Dolph Lundgren?

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  3. "Arsenic is a chemical analog of phosphorus, just as copper is to iron, mentioned above."

    He tries to suggest that iron and copper have similarities, "namely orbital configuration, electronegativity, and quantity of valence electrons," which, according to the author are "largely due to the elements belonging to the same periodic group." *Facepalm*

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    1. So, by his logic, lead is an analogue of...gold?

      Get those retorts, spirits, and elixirs ready, alchemists. We're in business!

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    2. THE START-UP FUNDING WILL POUR IN

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  4. Thanks for the plug. I especially liked this part from the abstract: "Mounting evidence supports the claim that these bacteria substitute arsenic for phosphorus in macromolecules". Strange, since there seems to have been much mounting evidence that indicates the exact opposite.

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    Replies
    1. Couldn't have said it better myself.

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