Thursday, February 2, 2012

2010 "Arsenic found in DNA", 2012 "We never claimed arsenic was in the DNA" WTF?

Unbelievable.  Check out this news story on some new results relating to the "Arsenic Life" story.  The story discusses a paper from Rosie Redfield that has been deposited in arXiv.  Rosie has been persistent in doing tests on the strain GFAJ-1 that Wolfe-Simon had isolated.  One of their new results is that they cannot detect arsenic/arsenate in the DNA from this strain.  Amazingly, in this news story Wolfe-Simon is reported to have said that they never claimed that arsenic was getting into the DNA:
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.”
Wow.  I recommend people go check out the original paper and see for themselves.  And also check out the press conferences and news stories.  The whole thing was about their claim that the arsenic was ending up in the DNA. 

In their abstract, for example:
Our data show evidence for arsenate in macromolecules that normally contain phosphate, most notably nucleic acids and proteins. Exchange of one of the major bio-elements may have profound evolutionary and geochemical importance.
In their conclusions:
We report the discovery of an unusual microbe, strain GFAJ-1, that exceptionally can vary the elemental composition of its basic biomolecules by substituting As for P. How As insinuates itself into the structure of biomolecules is unclear, and the mechanisms by which such molecules operate are unknown.
I personally am hoping beyond hope that Wolfe-Simon was misquoted in the new story, but I am guessing that that is unlikely.  As I have said before, I feel some sympathy towards Wolfe-Simon and I was one of the first people to call for the community to stop the personal attacks against her and to focus on the science and her claims about the science.  And I still think we need to do this.  But this does not mean we should to not criticize her claims and the almost ludicrous path she is leading some people down with her comments. The notion that they never claimed arsenic/arsenate was getting into the DNA of the strain they isolated is beyond absurd. 

Hat tip to Rosie Redfield for alerting me to this news story.

UPDATE: See these other stories on the new work
UPDATE2: Here are some additional quotes from the original paper to consider:
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
Therefore, our x-ray data support the position of AsO43– in a similar configuration to PO43– in a DNA backbone or potentially other biomolecules as well
UPDATE3: Some quotes from older news stories

From the Christian Science Monitor 12.2.2010
"So far we've showed that it can do it in DNA, but it looks like it can do it in a whole lot of other biomolecules" as well, says Wolfe-Simon, a NASA research fellow in residence at the USGS in Menlo Park, California. 
"It is the first time in the history of biology that there's been anything found that can use one of the different elements in the basic structure," says Paul Davies, the director of BEYOND: Center for Fundamental Concepts in Science at Arizona State University in Tempe, Arizona.
 From CNN 12-2-2010
"We've discovered an organism that can substitute one element for another," said NASA scientist Felisa Wolfe-Simon. "Nothing should have grown. Put your plant in the dark, it doesn't grow." 
The bacterium not only grew but also incorporated the arsenic molecules into its DNA, in place of phosphorus, she said 
"We've cracked open the door to what's possible elsewhere in the universe," Wolfe-Simon said during a press conference Thursday.
UPDATE 4: Here is the text of one of the original press releases entitled "Get Your Biology Textbook...and an Eraser!"
One of the basic assumptions about life on Earth may be due for a revision thanks to research supported by NASA’s Astrobiology Program. Geomicrobiologist Felisa Wolfe-Simon has discovered a bacterium in California’s Mono Lake that uses arsenic instead of phosphorus in its DNA. Up until now, it was believed that all life required phosphorus as a fundamental piece of the ‘backbone’ that holds DNA together. The discovery of an organism that thrives on otherwise poisonous arsenic broadens our thinking about the possibility of life on other planets, and begs a rewrite of biology textbooks by changing our understanding of how life is formed from its most basic elemental building blocks. Astrobiology Magazine has the story. 
Wolfe-Simon’s research is supported by NASA’s Exobiology and Evolutionary Biology (Exo/Evo) Program and the NASA Astrobiology Institute. Among the goals of these programs is determining the evolution of genes, metabolic pathways, and microbial species on Earth in order to understand the potential for life on other worlds. Wolfe-Simon’s discovery represents the first time in the history of biology that an organism has been found to use a different element to build one of its most basic structures. The paper appears in today’s issue of “Science Express“ and will subsequently be published in the journal Science.
UPDATE 5: In 2010 for the press conference about the arsenic story NASA even released a video showing how arsenic could replace phosphorus in DNA.

UPDATE 6: A video of the original press conference shows Wolfe-Simon introducing the video as a model of how they think arsenic replaces phosphorus in the DNA.

UPDATE 7: In a blog post relating to the arsenic life story, Brian Krueger suggests we should in essence discount some new work by Rosie Redfield on the topic because it has not "been properly reviewed." - see his full post here: A peril of "Open" science: Premature reporting on the death of #ArsenicLife

I tried to comment there but something did not work so I figured I would post my comments here. I think his point is completely and thoroughly wrong. What I had tried to post there I thought might be useful to share here:
I cannot disagree more with your post here. You vastly overvalue what happens in peer review. Peer review should not be considered a thumbs up / thumbs down process as you are suggesting here. And it should not be considered a one time event. It should be considered a continuous process and a sliding scale. Some things that get through the normal peer review process for papers are end up being retracted and many things that are presented prior to traditional peer review are fundamental new insights. Scientific results can be evaluated before, during and after the review that happens for a publication. Scientists do this all the time already - at conferences - in hallways - in lab meetings - on the phone - on skype - on twitter - at arXiv - in the shower - in classes - in letters - and so on. It is actually a disservice to science to annoint "peer review" as applied at some journals into something it is not.
Also see Zen Faulkes' post in response to Brian's: Reporting on that non peer reviewed stuff.  Hat tip to @boraz for pointing me to it.

UPDATE 8: Some links to additional stories coming out

UPDATE 9: Found a video of the whole press conference

UPDATE 10: some more links and news stories
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