Thursday, February 02, 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
UPDATE 11: July 7, 2012: lots of new things since March when I did the last update
UPDATE 12: Storify of Redfield's talk at Evol2012 and related tweets

-
Labels:

10 comments:

  1. Jeff Gralnick2/02/2012 8:15 AM

    Some very interesting parallels with #arseniclife and the publication from Woese and Wolfe's groups on finding the third domain of life - Archaea in 1977. Watch Wolfe recount this story here (it starts about 15 min in or so, though the entire talk is fascinating (http://archaea.igb.uiuc.edu/abstracts/wolfe.php?video=true&directory=./Ralph%20Wolfe.flv) - Thanks to D. Bond for finding it!

    The day that the paper is published, Wolfe fields phone calls from Luria and one unidentified member of the National Academy who asked him "What's this bullshit you guys are putting out?!"

    The media mostly gets it wrong - a headline from the Chicago Tribune reads 'Martianlike bugs on earth?'

    Wolfe's father-in-law advises him that 'if you don't overstate your case, no one will listen!'

    The big, big difference here is the data. Woese and Wolfe were right, and the data presented was solid.

    As a side note, Wolfe claims this is his first powerpoint lecture! I'm glad its online!!

    ReplyDelete
  2. Jonathan Eisen2/02/2012 8:43 AM

    I do not think the Stories are so parallel -Wolfe Simon and NASA have been the ones doing the overhyping - not the media --

    ReplyDelete
  3. Jonathan Badger2/02/2012 9:38 AM

    Well, at first the media were on the hype bandwagon too -- I probably wouldn't have even noticed the Wolfe-Simon article if newspapers and TV stations hadn't presented it as a huge, possibly Nobel-worthy discovery. It's true that within a week or so the media did shift sides as critics began to appear. But the main reason the stories aren't parallel is (as Jeff notes) that Woese & Fox *did* make the most important biological discovery of 1977 (and arguably of some years before and after).

    I really don't understand Wolfe-Simon's strategy at this point. She could live this down and go on to a successful career -- it's no crime to be wrong in science. But like Pons & Fleischmann (of cold fusion fame) she is sticking to her original interpretation long after more convincing ones have been presented.

    ReplyDelete
  4. garwuf2/02/2012 1:26 PM

    2 Jeff Gralnick: 'if you don't overstate your case, no one will listen!'

    It's a good advise for a showman or politician, not for a scientist. In science, extraordinary claims should be supported with extraordinary proofs. Otherwise, the whole body of modern scientific knowledge will quickly loose its coherence. When some unconfirmed results of scientific research are being released directly to general public without passing through peer review, it makes me feel suspicious about intentions of the authors.

    ReplyDelete
  5. Stevo2/02/2012 9:12 PM

    Peer review in the shower. lol.

    ReplyDelete
  6. Jonathan Eisen2/03/2012 7:03 AM

    JB - I disagree with your assessment of the role of the press here. Certainly the press did have a lot of hype initially. But that all can be blamed on NASA and the authors - NASA announced in a teaser that they were going to have a very important press conference about life in the universe. And then they basically told everyone that textbooks needed to be rewritten and our world had changed. The press just went with the hype NASA created.

    ReplyDelete
  7. Unknown2/04/2012 7:46 AM

    I can't comment on Iron Lisa's comment until it has been peer-reviewed. Gimme a minute.... OK: rejected. Come on now, this is just ludicrous. (not sure why Google is signing me in as unknown.... Benoit Bruneau)

    ReplyDelete
  8. mcleary2/06/2012 11:46 AM

    I too disagree with Gralnick and agree with Eisen. The parallels to Woese and Wolfe are ephemeral, except that extraordinary claims require extraordinary evidences. The third domain of life was proposed, based on the application of a new genetic analytical method, 16sRNA analysis, which gave very different results from the widely accepted and long standing, phenotypic (morphological and biochemical) methods of the time. Woese and Wolfe continued to inexorably pile up more and more data to the point that it was generally accepted. We are waiting for that to be provided by Wolfe-Simon, and the first attempt at replicating the original analysis has been negative.

    ReplyDelete
  9. Jordi Cirera8/13/2012 4:47 PM

    Although as a scientist I do agree that we should focus on science and stop personal attacks, I do have to say that in this particular case, this whole story is really upsetting me. We all work hard and put time and care in our experiments. We are all tested by peers who ask for more data, experiments, tests and so on before getting published. And yet, we have to keep following on this discussion. How is it possible that Wolfe-Simon stands so much by her paper? No one can reproduce her experiments, not even come close to the outlined results. And yes, she was claiming arsenic biomolecules such as As-DNA. Now she hides behind semantics, and pretends she never said what we all know she was claiming as the biggest 21st century revolution in life-sciences. How can anyone keep believing in her experiments when no one can reproduce it? She needs to stop this fight, the same way she started the fire. It is her responsibility. And the other authors, please stop hiding. You are all responsible for that fiasco

    ReplyDelete
  10. Jordi Cirera8/13/2012 4:48 PM

    Although as a scientist I do agree that we should focus on science and stop personal attacks, I do have to say that in this particular case, this whole story is really upsetting me. We all work hard and put time and care in our experiments. We are all tested by peers who ask for more data, experiments, tests and so on before getting published. And yet, we have to keep following on this discussion. How is it possible that Wolfe-Simon stands so much by her paper? No one can reproduce her experiments, not even come close to the outlined results. And yes, she was claiming arsenic biomolecules such as As-DNA. Now she hides behind semantics, and pretends she never said what we all know she was claiming as the biggest 21st century revolution in life-sciences. How can anyone keep believing in her experiments when no one can reproduce it? She needs to stop this fight, the same way she started the fire. It is her responsibility. And the other authors, please stop hiding. You are all responsible for that fiasco

    ReplyDelete

Subscribe to: Post Comments (Atom)

Most recent post

Talk on Sequencing and Microbes ...

I recently gave a talk where I combined what are normally two distinct topics - the Evolution of DNA Sequencing, and the use of Sequencing t...