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Arsenic-based life debate continues

More than a dozen researchers voice their concerns about a 2010 paper that claims bacteria can use arsenic in place of phosphorus in its DNA and other biomolecules

By | June 2, 2011

Scientists are questioning the validity of a linkurl:high-profile paper;http://www.the-scientist.com/news/display/57851/ that claimed to have discovered a strain of bacteria from Mono Lake, California, that can use arsenic in place of phosphorus in its DNA and other biomolecules, such as proteins.
Mono Lake, California
Image: Image © 2010 Henry Bortman
The paper, which appeared online in ScienceExpress last December, immediately sparked a hot debate among the scientific community. Now, fifteen researchers have articulated their concerns in the form of eight technical comments published in ScienceExpress last week (May 27), and, for the first time since its publication, the authors of the controversial study have written a formal response to their critics. In general, the criticisms highlight poor experimental techniques and point to more likely explanations for the results than a straightforward replacement of phosphorous with arsenic in biomolecules. "It's like finding a unicorn in your back garden," said linkurl:Rosemary Redfield,;http://www.zoology.ubc.ca/%7Eredfield/whoRRedfield.html professor of microbiology at the University of British Columbia and an author of one of the eight published comments. "The chances of it being an actual unicorn are small, but if the experiments had been really well done, then they would have been convincing. In fact, the experiments were quite badly done. It's like having a blurry picture of the unicorn. It's unlikely that it's actually a unicorn." Specifically, Redfield takes issue with the DNA extraction protocol, claiming that the genetic material was not purified properly before being tested for arsenic content. Furthermore, the supposedly phosphate-free growth medium on which the bacteria were cultured actually did contain phosphate, the phosphorus-based molecule of DNA backbones, which, Redfield argued, the bacteria may have been using to survive. To be absolutely sure that the bacteria were indeed using arsenate (the arsenic equivalent of phosphate) as the authors claimed, she said, the strain must be cultured without any phosphate. linkurl:Felisa Wolfe-Simon,;http://www.ironlisa.com/ a fellow at NASA's Astrobiology Institute and lead author on the original study, and her colleagues defended their DNA purification techniques, and said that they were transparent in revealing the presence of small quantities of phosphate in the medium. But, she argued, the low levels were not enough to sustain growth, as supported by lack of growth in control cultures in media that contained similar amounts of phosphate but no arsenate. But linkurl:James Cotner,;http://www.cbs.umn.edu/eeb/faculty/CotnerJames/ environmental microbiologist at the University of Minnesota and one of the published commenters, contends that the authors overestimate the minimum amount of phosphorous required for cell survival, noting that many species of bacteria naturally survive on the low levels present in the study. Furthermore, researchers argue that there are simpler possible explanations for why the bacteria cultured with arsenate survived and grew. linkurl:Patricia Foster,;http://www.indiana.edu/%7Ebioweb/faculty/directory/profile.php?person=plfoster professor of biology at Indiana University, said it's possible that the bacterial strain, called GFAJ-1, can only bring phosphate into its cells when it is exposed to a stimulant such as arsenate. Therefore, the control cultures don't prove that GFAJ-1 grows by incorporating arsenate into its DNA, just that arsenate needs to be present in order for the bacteria to grow. She also said that if the cells were actively growing and incorporating arsenate into their DNA, then their DNA should have contained a higher percentage of arsenic than the researchers found. Much of the skepticism stems from the longstanding belief that arsenate is extremely unstable. In his comment, linkurl:Steven Benner,;http://www.ffame.org/people/sbenner.html distinguished fellow at the Foundation for Applied Molecular Evolution and another comment author, calculated that each arsenate linkage inside a hypothetical arseno-DNA molecule would hydrolyze (degrade) after only 1 minute in the environment of Mono Lake while phosphate-DNA can survive approximately 30 million years. Though the specific criticisms vary, the sentiment is clear -- more research is needed to conclusively demonstrate that the bacteria actually incorporate arsenic into their biomolecules. "The experiments weren't done to the standards of a controversial issue," said Cotner. Wolfe-Simon and her colleagues plan to continue follow up experiments, and though they have new data on the organism, Science declined to publish it with the authors' response to comments. They have also made GFAJ-1 available for study by other labs. "We weren't particularly happy with all of the hoopla," said Wolfe-Simon. "But you have to embrace your critics. It gives you the opportunity to be more scholarly."
**__Related stories:__***linkurl:Arsenic supports life?;http://www.the-scientist.com/news/display/57851/
[2nd December 2010]*linkurl:Elemental Shortage;http://www.the-scientist.com/2010/11/1/46/1/
[November 2010]*linkurl:A matter of chow;http://www.the-scientist.com/article/display/55461/
[March 2009]*linkurl:Arsenic and old...photosynthesis?;http://www.the-scientist.com/blog/display/54930/
[14th August 2008]

Comments

Avatar of: N MENHART

N MENHART

Posts: 2

June 2, 2011

at best, if true, this is 'As tolerant' life, not 'As based' life... certainly pushing the envelope on tolerant. but 'based' implies As is the preferred state, with P being unusual and perhaps even toxic... which was not the claim at all. and with all the weird and wonderful things life has created, i'd not be surprised if this is true, at least partly. \n\nsure, the study could have been done more carefully - as could almost any paper i've read, there's always one more experiment to be done. its all a matter of degree... at some point you have to fish rather than cut bait, and they decided to publish. misrepresenting the claim as 'based' rather that 'tolerant' is simply setting up a straw man in the debate, and is not helpful. \n\n
Avatar of: Mike Waldrep

Mike Waldrep

Posts: 155

June 2, 2011

Interesting!
Avatar of: Shi Liu

Shi Liu

Posts: 32

June 3, 2011

On the first day that the online version of the Science paper appeared I PUBLICALLY denounced the discovery of arsenic life as a joke (see http://blog.sina.com.cn/s/blog_502041670100n5rw.html). I submitted on December 14, 2010 to Science my FORMAL Technical Comment, after it had been "peer-reviewed" or -criticized by my trusted microbiological colleagues. However, Science rejected my Technical Comment on March 3, 2011 using an excuse that my "points have been addressed more clearly in other critiques" which is in fact not true at all. If people are interested in learning how Science would even make a lie to reject my solid scientific criticisms they can read my Technical Comment which was FORMALLY PUBLISHED on March 9, 2011 in Logical Biology (http://im1.biz/albums/userpics/10001/LB2011V11N1A1_AsLife_P1.htm). More ever, I have published many blog articles (in Chinese at http://blog.sina.com.cn/im1) and comments (in English in Science website athttp://news.sciencemag.org/sciencenow/2010/12/arsenic-researcher-asks-for-time.html). \nSo if Science has behaved well and accepted my criticisms, this debate should be over already and the firm conclusion should be: There is NO arsenic-based life. A retraction WAS done (early in 2011).\n\nPS\nI was not able to comment on News reported in Nature with my real name for reasons that I cannot tell here. But people are welcome to read others' comments at the following Nature news with the URLs as:\nCritics weigh in on arsenic life\nhttp://www.nature.com/news/2011/110527/full/news.2011.333.html\n\nWill you take the 'arsenic-life' test?\nhttp://www.nature.com/news/2011/110601/full/474019a.html\n
Avatar of: Shi Liu

Shi Liu

Posts: 32

June 3, 2011

Open invitation to truth-seeking and justice-finding scientists and journalists:\nI have kept a series of communications with Editors of Science on my demands for a solid and efficient evaluation of the flawed publication on arsenic life and also my warnings/protests against its irresponsible behaviors in handling the "Arsenogate". Thus, if anyone is interested in exposing some very dark side in Science, please contact me. I promise that you will not disappointed because, entering from this Arsenogate", you will be presented with some even more amazing stuffs that I have collected over the years in my dealing with Science and other "top" journals.\nMaybe those stuffs are needed to fuel the scientific revolution that someone wrote earlier in this magazine.\nMy Email is SVL8EPA_at_gmail.com where "_at_" should be the email character "at".
Avatar of: Nirmal Mishra

Nirmal Mishra

Posts: 22

June 3, 2011

DNA with arsenate constituting the backbone and DNA with phosphate constituting the backbone might flip as transient replacement in spots or as motifs.

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