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Science —
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New papers deal huge blow to NASA-backed finding on arsenic-based life
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Two labs revisit the study: strange bacteria tolerates, but doesn't use arsenic.
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John Timmer - 7/9/2012, 2:25 PM
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The otherworldly waters of California's Mono Lake were the source of bacteria that, according to NASA, shed light on the search for life on other planets.
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The otherworldly waters of California's Mono Lake were the source of bacteria that, according to NASA, shed light on the search for life on other planets.
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NASA
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reader comments
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A year and a half ago, a cryptic NASA press release focused attention on what it promised would be new evidence in the hunt for life on alien worlds. NASA and the journal involved ( Science ) sat on the results for days as rumors built. Eventually, the paper debuted: NASA scientists had found evidence that life on Earth could rely on alternate chemistry, one that replaced the phosphorus used in many biomolecules for a chemical relative that is usually toxic: arsenic.
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Controversy did not end there. Researchers quickly identified a number of holes in the initial analysis, both logical and experimental. Less than six months later, Science published a series of responses to the original paper that raised significant questions about its accuracy. Now, the topic is back in the pages of the same journal. Two labs have obtained the original arsenic-tolerant bacteria and shown that some of the original paper's conclusions are completely off-base.
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The bacteria themselves were originally obtained from California's Mono Lake, which naturally contains high levels of arsenic. Over multiple generations in the lab, scientists forced them to evolve further, gradually ramping up the arsenic concentrations while lowering the amount of phosphorus available to the organisms. After enough generations, the resulting bacteria reportedly had some rather exceptional properties: they could get by without having any phosphorus added to their growth media, but only if arsenic were added. And, possibly as part of that adaptation, the arsenic started appearing with biomolecules that normally contain phosphorus (although, as our initial coverage noted, the data didn't indicate how the arsenic was being used).
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The responses suggested a couple of problems with the work. On purely theoretical grounds, we know that arsenate compounds should spontaneously fall apart in water. This makes their apparent presence in biomolecules difficult to accept. And, on purely practical grounds, it turns out to be really difficult to get rid of all the phosphorus from the other lab chemicals scientists typically rely on. That suggests these bacteria weren't really doing without the stuff.
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The new papers, from groups in Zurich and Vancouver, nail down a lot of loose ends. The material suggests that the initial results were a mix of artifact and not pushing the experiments sufficiently far.
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First, the inability to grow without phosphate. The Zurich group shows that these organisms can survive down to remarkably low amounts of phosphorus—the equivalent of adding 0.000162 grams for every liter of liquid growth medium (for those of you hung up on English units, that's "almost nothing"). But if you use ultrapure materials that drop the phosphorus levels down to below what the team could detect (somewhere less than 20 percent of that level), the bacteria won't grow. They still need phosphate.
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The original paper reported that when phosphate starved, the organisms needed arsenic in their media to grow at all. But the Vancouver group found that wasn't the case. They suggest this was an artifact: the bacteria also had a requirement for a specific amino acid, something that was not reported in the original paper. They suspect that the arsenic solution used in the original experiments had been contaminated with the amino acid, explaining its apparent requirement.
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So the bacteria don't appear to require arsenic. But, just as clearly, they can tolerate extremely high levels of the substance, and there was evidence that it is incorporated into biomolecules, including DNA. The new papers tackle this as well. The Zurich group used a technique called mass spectrometry, in which every chemical in the cell is separated based on how much an individual molecule weighs. The results can be compared to a database of known weights to identify most molecules very specifically. In this case, the authors updated their database to include molecules with phosphate replaced by arsenate.
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The results largely came back blank. Some arsenate was associated with sugars, but this apparently formed spontaneously, without the need for any biochemical activity. If you let the standard lab bacteria E. coli grow in a medium containing some arsenic, they formed all of these compounds as well. This suggests they have nothing to do with a newly evolved tolerance to arsenic.
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The Vancouver group focused on the reported association of arsenic with DNA, a phosphate-rich molecule. That makes DNA a great candidate for detecting even a rare substitution of arsenate for phosphate, a change that should make the DNA sensitive to breaking down in a simple solution of water. But, even after extended storage in water, DNA obtained from these bacteria was as stable as that obtained from the same strain grown without arsenic. Based on the groups' measurements, that means that less than one-in-25,000 phosphates could possibly be swapped out.
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Given all this data, it's hard to argue with the Vancouver team's conclusion: "The end result is that the fundamental biopolymers conserved across all forms of life remain, in terms of chemical backbone, invariant."
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But an argument may be brewing. MSNBC's Alan Boyle has been communicating with the team behind the original findings, and they suggest there's a paper in the works that backs up their initial findings. Although the two new publications seem like the final word on the topic, more appears to be forthcoming.
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Arsenic and open science
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The researcher who led the Vancouver group, Rosie Redfield, deserves special mention in this saga. Redfield has embraced blogging as part of the scientific process , and was one of the first researchers to publicly raise doubt about the original arsenic results. Her doubts caught the attention of science journalists and led to some of the first skeptical coverage . Once she obtained the bacteria and started working on them, she put results up on her blog as they came in. As she prepared her paper for publication, she also put draft versions up on the arXiv . That is common in physics and astronomy, but almost unheard of in biology.
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Not only is Redfield pushing her fellow biologists for greater openness, she has apparently pushed the journals as well. Science normally distributes papers that will be released in a given week to the press on Sunday night, but asks the press to hold them for a Thursday embargo. Redfield was scheduled to speak at an evolution meeting last night, and let the editors of Science know that her arsenic work would be the topic (and, naturally, she blogged about letting them know, too). In response, Science made these two papers available without restrictions last night.
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Had Science been equally responsible with its embargo of the initial results from NASA, some of the hype that developed in response to the uncertainty might never have become a problem in the first place.
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Science , 2012. DOI: 10.1126/science.1218455 , 10.1126/science.1219861 ( About DOIs ).
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Promoted Comments
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HodyOne | Ars Tribunus Militum
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jump to post
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If you want to see some amazing backtracking and contorted logic from Felisa Wolfe-Simon, read her email exchange between the msnbc correspondent.
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1781 posts | registered Jan 20, 2003
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Promoted Comments
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HodyOne | Ars Tribunus Militum
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jump to post
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If you want to see some amazing backtracking and contorted logic from Felisa Wolfe-Simon, read her email exchange between the msnbc correspondent.
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1781 posts | registered Jan 20, 2003
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reader comments
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31
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John Timmer John is Ars Technica's science editor. He has a Bachelor of Arts in Biochemistry from Columbia University, and a Ph.D. in Molecular and Cell Biology from the University of California, Berkeley. When physically separated from his keyboard, he tends to seek out a bicycle, or a scenic location for communing with his hiking boots.
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Channel Ars Technica
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Unsolved Mysteries Of Quantum Leap With Donald P. Bellisario
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Today "Quantum Leap" series creator Donald P. Bellisario joins Ars Technica to answer once and for all the lingering questions we have about his enduringly popular show. Was Dr. Sam Beckett really leaping between all those time periods and people or did he simply imagine it all? What do people in the waiting room do while Sam is in their bodies? What happens to Sam's loyal ally Al? 30 years following the series finale, answers to these mysteries and more await.
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Unsolved Mysteries Of Quantum Leap With Donald P. Bellisario
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Unsolved Mysteries Of Quantum Leap With Donald P. Bellisario
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Unsolved Mysteries Of Warhammer 40K With Author Dan Abnett
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Unsolved Mysteries Of Warhammer 40K With Author Dan Abnett
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SITREP: F-16 replacement search a signal of F-35 fail?
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SITREP: F-16 replacement search a signal of F-35 fail?
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Sitrep: Boeing 707
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Sitrep: Boeing 707
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Steve Burke of GamersNexus Reacts To Their Top 1000 Comments On YouTube
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Steve Burke of GamersNexus Reacts To Their Top 1000 Comments On YouTube
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Modern Vintage Gamer Reacts To His Top 1000 Comments On YouTube
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Modern Vintage Gamer Reacts To His Top 1000 Comments On YouTube
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How The NES Conquered A Skeptical America In 1985
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How The NES Conquered A Skeptical America In 1985
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Scott Manley Reacts To His Top 1000 YouTube Comments
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Scott Manley Reacts To His Top 1000 YouTube Comments
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How Horror Works in Amnesia: Rebirth, Soma and Amnesia: The Dark Descent
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How Horror Works in Amnesia: Rebirth, Soma and Amnesia: The Dark Descent
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LGR's Clint Basinger Reacts To His Top 1000 YouTube Comments
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LGR's Clint Basinger Reacts To His Top 1000 YouTube Comments
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The F-35's next tech upgrade
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The F-35's next tech upgrade
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How One Gameplay Decision Changed Diablo Forever
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How One Gameplay Decision Changed Diablo Forever
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Unsolved Mortal Kombat Mysteries With Dominic Cianciolo From NetherRealm Studios
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Unsolved Mortal Kombat Mysteries With Dominic Cianciolo From NetherRealm Studios
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US Navy Gets an Italian Accent
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US Navy Gets an Italian Accent
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How Amazon’s “Undone” Animates Dreams With Rotoscoping And Oil Paints
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How Amazon’s “Undone” Animates Dreams With Rotoscoping And Oil Paints
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Fighter Pilot Breaks Down Every Button in an F-15 Cockpit
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Fighter Pilot Breaks Down Every Button in an F-15 Cockpit
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How NBA JAM Became A Billion-Dollar Slam Dunk
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How NBA JAM Became A Billion-Dollar Slam Dunk
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Linus "Tech Tips" Sebastian Reacts to His Top 1000 YouTube Comments
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Linus "Tech Tips" Sebastian Reacts to His Top 1000 YouTube Comments
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How Alan Wake Was Rebuilt 3 Years Into Development
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How Alan Wake Was Rebuilt 3 Years Into Development
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How Prince of Persia Defeated Apple II's Memory Limitations
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How Prince of Persia Defeated Apple II's Memory Limitations
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How Crash Bandicoot Hacked The Original Playstation
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How Crash Bandicoot Hacked The Original Playstation
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Myst: The challenges of CD-ROM | War Stories
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Myst: The challenges of CD-ROM | War Stories
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Markiplier Reacts To His Top 1000 YouTube Comments
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Markiplier Reacts To His Top 1000 YouTube Comments
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How Mind Control Saved Oddworld: Abe's Oddysee
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How Mind Control Saved Oddworld: Abe's Oddysee
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Bioware answers unsolved mysteries of the Mass Effect universe
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Bioware answers unsolved mysteries of the Mass Effect universe
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Civilization: It's good to take turns | War Stories
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Civilization: It's good to take turns | War Stories
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SITREP: DOD Resets Ballistic Missile Interceptor program
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SITREP: DOD Resets Ballistic Missile Interceptor program
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Warframe's Rebecca Ford reviews your characters
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Warframe's Rebecca Ford reviews your characters
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Subnautica: A world without guns | War Stories
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Subnautica: A world without guns | War Stories
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How Slay the Spire’s Original Interface Almost Killed the Game | War Stories
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How Slay the Spire’s Original Interface Almost Killed the Game | War Stories
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Amnesia: The Dark Descent - The horror facade | War Stories
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Amnesia: The Dark Descent - The horror facade | War Stories
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Command & Conquer: Tiberian Sun | War Stories
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Command & Conquer: Tiberian Sun | War Stories
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Blade Runner: Skinjobs, voxels, and future noir | War Stories
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Blade Runner: Skinjobs, voxels, and future noir | War Stories
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Dead Space: The Drag Tentacle | War Stories
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Dead Space: The Drag Tentacle | War Stories
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Teach the Controversy: Flat Earthers
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Teach the Controversy: Flat Earthers
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Delta V: The Burgeoning World of Small Rockets, Paul Allen's Huge Plane, and SpaceX Gets a Crucial Green-light
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Delta V: The Burgeoning World of Small Rockets, Paul Allen's Huge Plane, and SpaceX Gets a Crucial Green-light
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Chris Hadfield explains his 'Space Oddity' video
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Chris Hadfield explains his 'Space Oddity' video
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The Greatest Leap, Episode 1: Risk
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