• NASA: Arsenic-life saga isn't done

    Mark Wilson / Getty Images file

    "Arsenic life" researcher Felisa Wolfe-Simon is flanked by Mary Voytek, director of NASA's Astrobiology Program, as well as chemist Steven Benner and astrobiologist Pamela Conrad during a NASA news conference on Dec. 2, 2010. Many of the claims made during that briefing have now been refuted in peer-reviewed research.

    By Alan Boyle, Science Editor, NBC News


    Nineteen months ago, NASA's experts on astrobiology hailed the initial report about arsenic-eating microbes as a "huge deal," but with the publication of two peer-reviewed papers that have refuted that report, the space agency now says the picture is "as yet incomplete."

    The statement from Michael H. New, astrobiology discipline scientist at NASA Headquarters' Planetary Science Division, runs counter to the instant reaction that the "arsenic-life" controversy is finished. Since Sunday's online release of the two papers by the journal Science, a lot of folks have been talking about FAILs and nails (as in last nails in the coffin).

    New took a different tack:

    "NASA supports robust and continuous peer review of any scientific finding, especially discoveries with wide-ranging implications. It was expected that the 2010 Wolfe-Simon et al. Science paper would not be exempt from such standard scientific practices, and in fact, was anticipated to generate significant scientific attention given the surprising results in that paper. The two new papers published in Science on the microorganism GFAJ-1 exemplify this process and provide important new insights. Though these new papers challenge some of the conclusions of the original paper, neither paper invalidates the 2010 observations of a remarkable microorganism that can survive in a highly phosphate-poor and arsenic-rich environment toxic to many other microorganisms. What has emerged from these three papers is an as yet incomplete picture of GFAJ-1 that clearly calls for additional research."

    University of British Columbia microbiologist Rosie Redfield, one of the authors of one of the newly published papers, said in a blog posting that NASA's response was "cowardly."

    "I'm at a loss for words," she wrote.

    It's easy to find commentaries on the Web indicting NASA as well as the authors of the original paper, scientific reviewers, the journal Science and journalists for their part in the arsenic-life controversy. Just as some folks scrambled to trumpet the news that evidence of life had been discovered on Titan, now there's a scramble to assign blame. But scientific sagas don't move as quickly as a Twitter stream, and it's a good bet that this particular saga isn't over quite yet.

    Here's a sampling of the reaction:

    Got more reaction? Feel free to pass along links or voice your own thoughts in a comment below.

    Alan Boyle is msnbc.com's science editor. Connect with the Cosmic Log community by "liking" the log's Facebook page, following @b0yle on Twitter and adding the Cosmic Log page to your Google+ presence. You can also check out "The Case for Pluto," my book about the controversial dwarf planet and the search for new worlds.

  • Two studies show 'weird life' microbe can't live on arsenic

    Why was this such a big deal to begin with? In this "Last Word" video from December 2010, MSNBC's Lawrence O'Donnell discusses the arsenic-life controversy with Bill Nye the Science Guy.

    By Alan Boyle, Science Editor, NBC News


    A year and a half after one team of researchers claimed they had bred a type of bacteria that could live on arsenic, suggesting that life is weirder than we imagine, two other teams have found that the microbe really doesn't do anything with the arsenic after all.

    These two teams say that the microbe, known as GFAJ-1, is somewhat weird, due to the fact that it can survive amid ultra-high concentrations of arsenic. But they confirm the widely held view among microbiologists that GFAJ-1 did not rewrite the existing rules of life — an extraordinary claim that was implied by the initial study, which made a huge splash in December 2010.

    "The new research clearly shows that the bacterium, GFAJ-1, cannot substitute arsenic for phosphorus," the journal Science, which published the initial findings as well as today's follow-up studies, said in an editorial statement.

    Case closed?
    One of the authors of the new research, University of British Columbia microbiologist Rosie Redfield, was among the most outspoken critics of the original study — and she said that as far as she was concerned, today's publication closes the case. "This isn't an area I have any special interest in, or any funding for," she told me in an email.

    Over the past 19 months, Redfield has focused on the analysis of GFAJ-1's DNA more as a case study in open science — a perspective that focuses on freely sharing the results of the research process as they come to light. The study that she and her colleagues authored has been available for months on the ArXiv pre-print website. (The other study, conducted by researchers at ETH Zurich in Switzerland, became public just today.)

    Science's editors decided to time today's online publication of the two studies to coincide with a talk that Redfield was due to give at a conference in Ottawa on evolutionary biology. Redfield said last week on her blog that she'd be discussing the results of her group's research, including the Science paper, during her talk. When I contacted her on Friday about the impending publication, she expressed surprise that the journal accelerated its publishing schedule.

    "What? No!" she wrote in an initial email. "Must be because of my Evolpalooza talk that night."

    The print version of the papers released tonight are to appear in Science later this month.

    In the past, the lead researcher for the original study of GFAJ-1, Felisa Wolfe-Simon, has declined to comment in detail about the follow-up experiments that have raised questions about her group's work. She has said such comments would have to wait until those experiments were described in peer-reviewed research articles. But due to the publication in Science, Wolfe-Simon responded to my emailed inquiries at greater length.

    She acknowledged that the follow-up experiments failed to find evidence that compounds containing arsenic, known as arsenates, were being taken up into the molecular machinery of GFAJ-1's life processes, such as DNA. However, she said those experiments were apparently conducted under conditions that differed from those surrounding the original experiment.

    "We do not know the history of the cells in these new papers," she wrote. "In general, it requires more evidence to publish something unexpected — e.g., that cells can thrive in arsenic and that arsenate is found inside the cells, than something that everyone expects — e.g. that arsenate is not found inside cells or DNA.

    "Our original work and data was in fact given high scrutiny, as standards are almost always higher for evidence for things that are unexpected. We are actively following the arsenic in our cells and will know more in the next few months." (The full email exchange is laid out in a comment below.)

    Sensationalism and skepticism
    The original point of the arsenic-life experiment was to see whether organisms on Earth could be coaxed to use arsenic, which generally acts as a poison, in place of phosphorus, which is generally seen as one of the essential chemical building blocks of life. The structure of those two elements on the atomic level is similar, which is a big reason why substituting one for the other is so lethal.

    If some types of organisms, even bacteria, could live on arsenic, that would upset the mainstream view of how life works. Such a finding, if confirmed, would potentially lead to a wider search for "weird life" — not only on Earth, but also in extraterrestrial environments such as the Martian subsurface or the hydrocarbon lakes of Titan.

    Wolfe-Simon and her colleagues conducted their search for arsenic-eating life by taking samples from the arsenic-rich sediments of California's Mono Lake, then turning up the dial on the arsenic and turning down the dial on the phosphorus in their laboratory's cell cultures. They isolated a strain of bacteria that grew in a setting with ultra-high concentrations of arsenic and seemingly negligible amounts of phosphorus. (The strain's name, GFAJ-1, stands for "Give Felisa a Job.")

    Analysis of the cells led them to conclude that arsenic was being used in place of phosphorus, even in GFAJ-1's DNA molecules. The findings created a sensation when they were announced. "We're talking about an organism that we think ... is replacing phosphorus with arsenic," Mary Voytek, the head of NASA's astrobiology program, said at the time. "This is a huge deal."

    The case sparked a huge backlash as well. Many scientists questioned the results — not only in comments to journalists, but also in blog postings and Twitter updates. Redfield suspected that the detection of arsenic was due to sample contamination rather than an uptake into DNA molecules. The experiment in which she was involved, conducted with Princeton's Marshall Louis Reaves as lead researcher, reported finding "only trace amounts of free arsenate" and no chemically bound arsenic compounds in the DNA samples they extracted from GFAJ-1.

    In their Science paper, the researchers say the reason for the dramatically different results "is not clear," but they also note that "differences in DNA purity can readily explain" the discrepancies.

    How GFAJ-1 works
    The other study published today, with ETH Zurich's Tobias Erb as lead author, takes a wide-angle view of GFAJ-1, using mass spectrometry and other tools to trace the bacteria's chemical processes on the molecular level. They found that the microbes could grow with even less phosphorus than the tiny amount that was provided in the experiments by Wolfe-Simon and her colleagues. But when the phosphorus concentration was reduced to nearly nothing (less than 0.3 micromolar), no growth was observed.

    Some arsenic compounds formed in the culture, but at a level that was more likely associated with non-biological chemical processes, Erb and his colleagues said. They noted that such compounds are also found in garden-variety E. coli bacteria when they're grown in cultures containing arsenic. This suggests that the detection of arsenic-containing compounds "might not be of physiological relevance," they wrote.

    The two groups of researchers acknowledged that there was something extraordinary about GFAJ-1, in that it could grow amid ridiculously high concentrations of arsenic — roughly an order of magnitude higher than previously seen for other organisms, the Swiss-based scientists said. "The molecular basis for arsenate resistance in GFAJ-1 might be the subject of further investigations," they wrote.

    It's also noteworthy that GFAJ-1 could survive amid ridiculously low concentrations of phosphorus. Wolfe-Simon and her colleagues said that was because the bacteria switched to metabolizing arsenic. But Reaves, Redfield and their colleagues said it was more likely that GFAJ-1 used a metabolic mechanism to enrich the tiny amount of phosphorus it could grab onto.

    More research ahead
    In her emails, Wolfe-Simon said the data reported in the newly published research did not contradict the thrust of her own studies, which are continuing. She said it's possible that the arsenic compounds taken up by GFAJ-1 become less stable "once cells are broken open."

    "We expect to have our own results ready for publication in the next few months," she wrote. "We are focused on the questions, 'Where exactly is the arsenate going?' and 'How does this microbe survive in high arsenate?' These results will speak to the flexibility of the periodic table for life, so [they] merit the most thorough and careful analysis we can achieve."

    In their statement, Science's editors took a different perspective.

    "The new research shows that GFAJ-1 does not break the long-held rules of life, contrary to how Wolfe-Simon had interpreted her group's data," they said. "The scientific process is a naturally self-correcting one, as scientists attempt to replicate published results. Science is pleased to publish additional information on GFAJ-1, an extraordinarily resistant organism that should be of interest for further study, particularly related to arsenic-tolerant mechanisms."

    Redfield agreed that GFAJ-1 was worthy of further study, even if she's not going to be doing it. "I think all organisms turn out to have interesting tweaks," she told me in her email. "We certainly know very little about the biology of GFAJ-1, and there are complications I never sorted out."

    So just how big of a deal did the "arsenic life" controversy turn out to be? To my mind, the case seems likely to take its place among the other great disputed claims in science, ranging from cold fusion to Martian nanofossils and the missing-link primate. It also feeds into the debate over the best ways to distribute and verify scientific findings. Lots of folks will be weighing in on these questions over the next day or two, and you can have the last word in the comment section below.

    Previous chapters in the weird-life saga:

    In addition to Reaves and Redfield, the authors of "Absence of Detectable Arsenate in DNA from Arsenate-Grown GFAJ-1 Cells" include Sunita Sinha, Joshua D. Rabinowitz and Leonid Kruglyak.

    In addition to Erb, the authors of "GFAJ-1 Is an Arsenate-Resistant, Phosphate-Dependent Organism" include Patrick Kiefer, Bodon Hattendorf, Detlef Günther and Julia A. Vorholt.

    Science said the two papers, along with an editorial statement, were being released at 8 p.m. ET July 8 "to coincide with a related conference." That was a reference to Redfield's talk at the Evolution Ottawa conference.

    Alan Boyle is msnbc.com's science editor. Connect with the Cosmic Log community by "liking" the log's Facebook page, following @b0yle on Twitter and adding the Cosmic Log page to your Google+ presence. You can also check out "The Case for Pluto," my book about the controversial dwarf planet and the search for new worlds.

  • Scientists map the world's microbes

    Nathan Shaner / MBARI

    This tropical postcard consists of a petri dish containing an artistic arrangement of bacteria that have been genetically engineered to incorporate fluorescent proteins.

    By Alan Boyle, Science Editor, NBC News

    Microbiologists are starting to make sense of tens of thousands of samples they've collected from around the world, undoubtedly containing legions upon legions of different kinds of microorganisms. How many kinds? That's just the point: Nobody knows.

    The microbial world is "Earth's dark matter," says Janet Jansson, a senior staff scientist at Lawrence Berkeley National Laboratory in California. By that, Jansson means that the varieties of bacteria and other microorganisms are as mysterious as the unseen stuff that makes up 85 percent of the matter in the universe.

    Jansson held up a spoon of soil during a news conference Friday at annual meeting of the American Association for the Advancement of Science, held in Vancouver, Canada — and noted that there were more organisms in that spoonful than there were stars in the Milky Way galaxy (100 billion).

    Talk about big numbers: Scientists estimate that there are 10 trillion microbes in every kilogram (2.2 pounds) of soil on Earth. Our planet is home about a nonillion cells (that's a 1 with 30 zeroes after it). Most of those are microbes. Each human body is thought to consist of 10 trillion cells, harboring microbial communities that amount to 100 trillion cells. From a microbe's point of view, we're all just lumps of flesh that are convenient places to hang out, said Jack Gilbert, a microbiologist at Argonne National Laboratory and the University of Chicago.

    "Without them, you'd be dead," he told reporters at an AAAS meeting. "Without us, they'd just move onto something else."

    Earth Microbiome Project
    The problem is that far less than 10 percent of the world's varieties of microbes have ever been cultivated in the lab. The rest are out there in the world, beyond the reach of the traditional methods for categorizing and analyzing life forms. That's where the Earth Microbiome Project is aiming to make a big difference.

    Over the past year, more than 100 researchers have been collecting samples from locales as far-flung as the Antarctic Dry Valleys, the Great Indian Desert, Yellowstone's hot springs and a Merlot grape vineyard on Long Island. Swabs have been sent in to document the microbial communities living within ants, iguanas and other animals. The effort meshes with the Human Microbiome Project, a longer-running, federally financed campaign to study the microbes living in us and on us.

    Jansson said about 60,000 samples have been collected during the first year of the Earth Microbiome Project, and about 10,000 of those samples have been processed. Rather than trying to culture individual bacteria, the microbe-hunters are doing wholesale DNA sequencing to piece together as many genomes as they can. Eventually, the project's organizers hope to analyze hundreds of thousands of samples.

    A few more samples are being sent in this week, courtesy of the journalists attending Friday's news briefing. Following the researchers' instructions, we swabbed our smartphones as well as the soles of our shoes, popped the swabs in collection vials, and handed them over to students for analysis over the next few weeks. I'll let you know if I find out anything interesting about the microbial communities living in my pants pocket or on my slip-ons.

    Eventually, the project plans to produce a microbial gene atlas as well as a "field guide" to microbes from regions around the world, said Jonathan Eisen, a microbiologist at the University of California at Davis.

    What's this have to do with us?
    Insights into Earth's microbial dark matter could yield all sorts of benefits for science and our well-being. First of all, shedding light on the planet's microbial dark matter will give scientists a better sense of how Earth's "tree of life" is laid out. Just in the first year, the project has covered 82 percent of the currently known global diversity of microbes, Gilbert reported.

    Charting the human microbiome should be a particularly fruitful exercise. Rob Knight, a researcher at the University of Colorado at Boulder, showed off some visualizations illustrating how the microbial communities on our fingertips, our face and in our mouths have distinct characteristics that can be charted over time — theoretically revealing where our fingers have been. "This raises all kinds of ethical concerns," he said, only half-jokingly.

    Studies have shown that babies delivered vaginally and through Caesarian section have significantly different microbiomes 20 minutes after birth, Knight said. That could mean that those babies face different prospects for immune responses and allergies later in life — prospects that could be changed by postnatal "inoculations" with the right kind of bacteria.

    Gilbert said fecal samples could reveal how our gut bacteria are doing, and whether we need to have our microbiomes adjusted for better health. As icky as it might sound, fecal transplants have already become an accepted therapy for some types of intestinal infections.

    Even the microbiomes that have nothing directly to do with humans could be important. Take that Merlot vineyard, for example. "We're doing the microbiome of a 'good year,'" Gilbert said. If for some reason the wine made from the vineyard's grapes becomes less tasty, it might be possible to load up the soil with the good-year bacteria and restore the vintage to its glory days.

    Gilbert would like to see the Earth Microbiome Project get to a point where it's possible to predict future changes in the ecosystem — including climate change impacts — by checking something like a microbial "weather report." But to do that, researchers will have to manage massive amounts of genomic and environmental data. That's a challenge that Rick Stevens, the Argonne Lab's associate director, compared to unraveling the secrets of subatomic particles with the Large Hadron Collider.

    To study the smallest life forms on the planet, "we need bigger, better computers," he said.

    Is this a job worth doing? The scientists leading the Earth Microbiome Project definitely think so. "I think people should be excited about this," Gilbert said. Are you excited? Feel free to weigh in with your comments below.

    More from the AAAS meeting in Vancouver:

    Alan Boyle is science editor at msnbc.com. Connect with the Cosmic Log community by "liking" the log's Facebook page, following @b0yle on Twitter or adding the Cosmic Log Google+ page to your circles. You can also check out "The Case for Pluto," my book about the controversial dwarf planet and the search for new worlds.

  • Caffeine-gobbling microbe found

    Angelo Cavalli / Getty Images file

    Scientists have found a microbe that lives on caffeine.

    By John Roach, Contributing Writer, NBC News

    Many people say they can't live without caffeine, but few of us would actually perish in the absence of our morning coffee ritual. For the bacterium Pseudomonas putida CBB5 that isn't the case. It really does live on caffeine, according to new research presented today. 

    The caffeine-munching bacterium was found in a flower bed on the University of Iowa campus.

    Ryan Summers, a doctoral student there, identified four digestive proteins that it uses to break down caffeine, which allows it to live and grow, he explains in a summary of his research presented at a meeting of the American Society for Microbiology in New Orleans.

    "This work, for the first time, demonstrates the enzymes and genes utilized by bacteria to live on caffeine," he writes.

    Caffeine is composed of carbon, nitrogen, hydrogen and oxygen. The bacteria break caffeine down into carbon dioxide and ammonia. Ammonia is a compound of nitrogen and hydrogen.

    Further testing showed that the compounds formed during the breakdown of caffeine are natural building blocks for drugs used to treat asthma, improve blood flow and stabilize heart arrhythmias. Since these drugs are difficult to synthesize chemically, Summers and colleagues think their bacteria could ease production of these drugs and lower their costs.

    What's more, the bacteria could be employed to clean up after us human caffeine junkies, Summers notes in the research summary.

    "The caffeine digestive proteins could also be used to remove caffeine and related compounds from large quantities of waste generated from coffee and tea processing industries, which pollute the environment. The decaffeinated waste from these industries can be used as animal feed and for production of transportation fuel."

    More on caffeine and microbes:

    John Roach is a contributing writer for msnbc.com. Connect with the Cosmic Log community by hitting the "like" button on the Cosmic Log Facebook page or following msnbc.com's science editor, Alan Boyle, on Twitter (@b0yle).