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.

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:

• Washington Post: Journal retreats, authors stand ground
• Guest opinion on Retraction Watch: Science should issue retraction
• Phylogenomics on Storify: Twitter stream for #ArsenicLife
• Q&A on USA Today: Arsenic life studies released

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.

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:

• DNA study counters arsenic-life claims
• One year later, 'arsenic life' debate still percolates
• Strange find on Titan sparks chatter about life
• Mars methane mystery: What's making the gas?
• What exactly is life, anyway?
• Cosmic Log archive on arsenic life

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.

This image shows a type of bacteria called GFAJ-1 that was said to incorporate arsenic in its cellular machinery.

Researchers say they ran a more rigorous version of the experiment that sparked a yearlong debate over the prospects for arsenic-based bacteria — but found no trace of arsenic within the organisms' DNA.

The findings, submitted to the journal Science this week and distributed openly via the ArxiV.org website, serve as the most definitive refutation to date of the "weird life" claims that caused such a stir in December 2010. "They match with what basically all the scientists had concluded a year ago," University of British Columbia microbiologist Rosie Redfield, the paper's senior author, told me.

Redfield had criticized the original study from the start, suggesting that the arsenic detected in a strain of bacteria known as GFAJ-1 was not actually incorporated into the machinery of life but was merely the result of insufficient purification. "We were much more meticulous about purifying the DNA before we analyzed it," she said today.

She and her colleagues worked with the same bacteria used for the original research, which had astrobiologist Felisa Wolfe-Simon as lead author and was published in Science. The bacteria were bred to live in a high-arsenic environment, with virtually no phosphorus present. The aim was to see whether arsenic compounds known as arsenates, which are typically poisonous to life as we know it, could be substituted for chemically similar phosphorus compounds known as phosphates. If that turned out to be the case, that would suggest that alien life forms could operate using biochemical processes radically different from Earth's.

In their paper, Wolfe-Simon and her colleagues said they saw evidence that the bacteria could be bred to live in the arsenic-rich environment, and that arsenates were detected in "macromolecules that normally contain phosphate, most notably nucleic acids and proteins."

Redfield and her colleagues were able to grow the bacteria amid high arsenic levels, under special conditions, but they found that the arsenic wasn't necessary for the bacteria's survival — and that the highly purified DNA from the bacteria did not contain detectable levels of arsenate.

Redfield noted that some arsenate stuck to the DNA even after what she thought would be sufficient purification, but was removed during a second round of washing. "That shows that arsenate does persist through steps in the DNA purification, but in a form that will wash away," she told me.

The researchers acknowledged that arsenate might occasionally get into the bacteria's biological machinery.

"Given the chemical similarity of arsenate to phosphate, it is likely that GFAJ-1 may sometimes assimilate arsenate into some small molecules in place of phosphate, such as sugar phosphates or nucleotides. Our results do not rule out the possibility that such assimilation could be beneficial," they wrote. "When it comes to DNA synthesis, however, GFAJ-1 does not appear to productively assimilate any arsenate."

Open review for results
The scientists behind the original study have said they would refrain from commenting on follow-up research until the peer-review and publication process is completed. Wolfe-Simon did not immediately respond to an emailed request for comment, but Science News' Rachel Ehrenberg quoted her as saying she and her colleagues never actually claimed that arsenate was being incorporated in GFAJ-1’s DNA.

"As far as we know, all the data in our paper still stand,” Science News quoted Wolfe-Simon as saying in an email. “Yet, it may take some time to accurately establish where the [arsenic] ends up."

That response left Redfield figuratively scratching her head — and literally wondering "WTF??" in a Twitter update. She pointed to several references in the original Science paper referring to DNA, including a sentence saying that the measurements "specifically demonstrated that purified DNA extracted from +As/-P [high-arsenic, low-phosphorus] cells contained As [arsenic]."

The paper written by Redfield and her colleagues is open for review and comment even in advance of its consideration for journal publication. That's consistent with Redfield's advocacy of an "open science" approach to research, as reflected in the regular updates posted to her RRResearch blog. Thanks to the blog, avid followers of the #ArsenicLife issue have known for weeks that the original results couldn't be replicated.

Redfield said she has received assurances that freely distributing the draft paper won't hurt the prospects for publication in Science — which goes against the traditional grain for peer-reviewed publication.

"What's happening, and I'm really pleased by this, is that interested people are reading the manuscript, and they're putting comments on it," she observed.

Redfield said she and her colleagues appreciated the feedback being posted to her blog by experts — as well as by non-experts. "Their comments are going to let us polish the manuscript to make it more accessible to non-experts," she told me.

More about the arsenic-life debate:

• A year later, the debate still percolates
• Nature: Study challenges existence of arsenic-based life
• Chemical & Engineering News: The arsenic aftermath

In addition to Redfield, the authors of "Absence of Arsenate in DNA From Arsenate-Grown GFAJ-1 Cells" include M.L. Reaves, S. Sinha, J.D. Rabinowitz and L. Kruglyak.

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 or adding Cosmic Log's Google+ page to your circle. You can also check out "The Case for Pluto," my book about the controversial dwarf planet and the search for other worlds.

Henry Bortman / 2010

Other scientists are analyzing the controversial strain of bacteria that biologist Felisa Wolfe-Simon and her colleagues found in California's Mono Lake.

It's been one year since researchers shook up the scientific world by claiming they bred bacteria that used arsenic in place of phosphorus, and the controversy is still simmering: The lead researcher and her critics say they're taking a closer look at the microbe at the center of the "weird life" claims.

After hitting the highs and the lows of academic acclaim, Felisa Wolfe-Simon has left her original research group and joined up with Lawrence Berkeley National Laboratory in California to continue her research into the bacterium known as GFAJ-1, which gets its name from the acronym for "Give Felisa a Job." (No joke!)

"There is so much work to do we're focusing on that and look forward to communicating our efforts in the coming months," Wolfe-Simon told me in an email this week.

Meanwhile, Wolfe-Simon's highest-profile critic, University of British Columbia microbiologist Rosie Redfield, took on the task of replicating the GFAJ-1 experiment. "I'm doing this even though I agree with all the other researchers who said this result is almost certainly wrong," Redfield told me. "Scientifically, it's really kind of a waste of time to try to replicate this yourself. But there's always the possibility that you could be wrong. And more than that, there was just a general sense that, you know, somebody should try."

Redfield has sent purified DNA samples to collaborators at Princeton University for mass spectrometry analysis — to see whether any arsenic was really taken up into the molecular structure. "We just got the DNA from Rosie Redfield," one of those collaborators, Leonid Kruglyak, told me this week. A graduate student in Kruglyak's lab, Marshall Louis Reaves, is currently working out the protocols for analyzing the DNA.

"We want to be able to fragment the DNA and run the fragments on the mass spectrometer," Krugylak said. "Those fragments should look quite different in the mass spectrometer if there is arsenate."

Just today, another team of researchers, led by Simon Silver of the University of Illinois at Chicago, announced that they have sequenced GFAJ-1's genome and will be analyzing it for new clues in the case.

Argonne National Laboratory's Jack Gilbert, a member of the team, characterized himself as a "100 percent skeptic" about the findings announced a year ago, but said that the gene sequence was still worth having. He and his colleagues have already found some interesting genetic twists, even if there's no evidence of arsenic in the DNA. "It's interesting to have this information to determine what the mechanism might be if other evidence shows this to be true," he explained.

Gilbert said it was mere coincidence that the genome sequence was published online exactly one year after Wolfe-Simon and her colleagues kicked off the controversy. "I hadn't even considered that today was the anniversary," he told me.

Why all the fuss?
The case of GFAJ-1 is significant on more than one level.

If the central claim of the original paper holds true, that means the machinery of life can be tinkered with to replace one seemingly essential chemical — phosphorus — with a different chemical that's seemingly inimical to life. One of Wolfe-Simon's original collaborators, Arizona State University astrobiologist Paul Davies, has long maintained that "weird life," built on a different biochemical platform, could exist right under our noses and we wouldn't know it.

The prospect of weird life on Earth would also argue in favor of widening the search for weird life on other worlds, perhaps as close as Mars or the Saturnian moon Titan. That's what led NASA to tout the research a year ago as having extraterrestrial implications. "The definition of life has just expanded," said Ed Weiler, an associate administrator at the space agency. The news reports went even farther. Here's a typical headline: "NASA Discovers Alien Life in California."

Actually, what Wolfe-Simon and her colleagues did was to take an existing strain of salt-loving bacterla from California's Mono Lake, and try to breed it in the presence of high concentrations of arsenic. GFAJ-1 emerged as the best prospect: The research team said it seemed to take hold in the high-arsenic environment, and they said their molecular analysis suggested that arsenic-based compounds known as arsenates were incorporated in the place of phosphates.

The bacteria in the arsenic-rich culture weren't aliens at all. But for many chemists and microbiologists, the research team's claims, published online by the journal Science on Dec. 2, 2010, were as hard to believe as reports of a UFO landing.

One chemist, Steven Benner of the Florida-based Foundation for Applied Molecular Evolution, said he bet Wolfe-Simon $100 that the arsenic wasn't taken up in the DNA. Benner said in an email this week that the proposition was "still in limbo ... so the bet is not yet collected." (Wolfe-Simon told me she doesn't remember the bet.)

The skepticism over the reported results erupted almost immediately in a wave of blog postings and Twitter updates from commentators and scientists, including Redfield. As a result, the #arseniclife case quickly became a case study for instant peer review, mediated by the Internet. It also turned into a case study for open science, in which researchers share their results as they become available rather than holding them back until they're published in a journal.

Redfield emerged as a strong voice, for the skeptics as well as for the open-science movement. Her technical criticisms focused on the way that the bacteria samples were handled. "The way they isolated their DNA was almost 'I can't believe they did this' badly done," she told me this week. Such criticism led Science's editors to hold back the on-paper publication of the research for months, until eight sets of technical comments could be collected from Redfield and other observers and vetted through peer review. Wolfe-Simon and her colleagues were also given space to respond to the technical comments.

"That was pretty unprecedented," said Ginger Pinholster, director of the Office of Public Programs at the American Association for the Advancement of Science, which publishes the journal Science.

The next steps
Since then, the focus has shifted from the headlines to the labs. A Popular Science profile of Wolfe-Simon created a bit of a stir a couple of months ago: She was quoted as saying that she was "basically evicted" from her research group and worried that "it's quite possible that my career is over."

But during this week's email exchange, Wolfe-Simon told me that the "Popular Science article quotes were not what I said," and that "what matters now is what these organisms are telling us about biology, and that is my focus." Here are some reflections on the one-year anniversary from one of her emails to me:

"What a busy year it has been!

"With the generous support of NASA, we are able now to dive deep and explore this scientific discovery. After such a discovery comes the time-intensive process of rigorous testing. We aim to unravel the mechanisms behind how this microbe accomplishes the ability to flourish and grow despite uptake and utilization of arsenic. This systematic rigorous testing is critical and needed to build upon an initial discovery of this type.

"To this end, I have joined the Lawrence Berkeley National Laboratory in collaboration with Dr. John Tainer and his group there. LBNL provides the diverse intellectual and material resources of a major national laboratory, affording us the opportunity to pursue our efforts to test multiple aspects and implications of the work efficiently and stringently. LBNL synergistically complements the generous financial support from NASA.

"Currently, we have made significant headway in optimizing the growth conditions of GFAJ-1 and preparing samples for a wide range of analyses, including biomolecule crystallization and metabolite characterization. There is so much work to do we're focusing on that and look forward to communicating our efforts in the coming months. ...

"I maintain my serious commitment to science and the process of data-driven research. I look forward to speaking with you some time in the not too distant future after we make additional scientific progress."

Other researchers are delving into the mysteries of GFAJ-1 as well, even though they don't think the claims about arseno-DNA and other "weird life" wonders will hold up. "I don't have any money for this," Redfield told me. "This is just a side project in what would be my spare time, if professors have any spare time."

Redfield says the projects she gets paid for are more likely to be scientifically productive, but they're not as interesting to the general public. "This struck me as an opportunity to do science openly in a circumstance where people would be actually interested in what I'm doing, and what the results were," she said.

Now the fruits of her GFAJ-1 labors are in the hands of Kruglyak and his colleagues. If the arsenic in the samples has really been incorporated in the DNA, rather than merely representing sample contamination, traditional genetic sequencing techniques would not work. "They could give all sorts of unpredictable results," Kruglyak said. That's why mass spectrometry has to come into play.

Kruglyak can't predict how long it will take to get the answers. "It always takes longer than whatever I would say," he told me. "I would hope it's weeks, not months."

Meanwhile, Gilbert and his colleagues will continue studying GFAJ-1's genetic makeup. He told me "there's nothing spectacularly amazing" about the bacteria, which was not subjected to the high-arsenic treatment applied by Wolfe-Simon's team and by Redfield. But Gilbert said the raw bacteria's genome has some intriguing twists nevertheless.

"What is quite interesting is that this has very few arsenic resistance genes, i.e., it does not have the typical suite of genes that would make the cell resistant to arsenic in the environment," he told me in an email. Further study of the genome may at last point to an explanation for GFAJ-1's affinity for arsenic — but as of today, one year after the bacteria came onto the world scene, Gilbert can't predict what that explanation might be.

"We will prod and poke at this thing for another year, and see if there's anything more interesting," he said.

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.

Henry Bortman / 2010

Astrobiology researcher Felisa Wolfe-Simon works with samples at California's Mono Lake.

Last updated 8:30 p.m. ET

After five months of battles in the blogosphere, the debate over whether life can be based on an alternate biochemistry is playing out on the highest levels of peer-reviewed research.

Back in December, the journal Science sparked a ruckus by publishing an online report from researchers who claimed that they had coaxed bacteria from California's Mono Lake to live on arsenic rather than phosphorus. That's a big deal, because phosphorus is thought to be one of the six elements essential for life as we know it (along with carbon, hydrogen, nitrogen, oxygen and sulfur). Arsenic, on the other hand, is typically seen as a potent poison.

The researchers, led by astrobiologist Felisa Wolfe-Simon at the U.S. Geological Survey, suggested that such an alien biology could exist in environments beyond Earth that are traditionally thought to be inimical to life — for example, the hydrocarbon seas of Titan, Saturn's largest moon.

That sounds like a wonderful vision, but the claims from Wolfe-Simon and her team instantly came under attack from other chemists and microbiologists. In a flurry of blog postings and Twitter tweets, the critics took aim at what they saw were fatal flaws in the team's methodology. Wolfe-Simon and her colleagues defended their work in a Q&A issued via Science, but said they preferred to pursue the debate through the traditional peer-review process.

Now that process has taken a great leap forward. Today Science posted eight peer-reviewed technical comments from the critics to its Web site, along with a response from the original research group. The journal said all these papers would be printed, along with the original study (which has so far been available only online), in next week's edition.

"There's a lot of stuff that's happened," Wolfe-Simon told me today. "It's been a real challenge for me and my co-authors. ... We think this is evidence that, really, science is moving forward faster."

She held to the original claim that molecules of arsenic were incorporated into the machinery of life, replacing at least some of phosphorus. "We would argue that our conclusion is still viable," she said. "We never claimed 100 percent substitution, and in a way that point was misconstrued."

Wolfe-Simon said more evidence has been amassed to back up the arsenic-life claims over the past five months. However, the fresh evidence had to be held back for future publication. Wolfe-Simon said she was constrained from reporting new data in today's online response to the critics, which was a source of frustration for her. Science insisted on that to keep the cycle of response and counter-response from spinning out of control.

It's not unheard of to publish technical comments and responses in the wake of a controversial paper. Science did exactly that this week, with regard to a study claiming that microbes consumed all the methane that leaked from last year's Deepwater Horizon spill in the Gulf of Mexico. But it's very unusual to publish a research paper, eight critiques of that paper and a follow-up response to those critiques in the same issue of a scientific journal.

Science's editors said they did not expect their data dump "to be the final word on the subject."

"The fact that we received so much feedback to the Wolfe-Simon paper suggests to us that science is proceeding as it should," the editors said in a statement. "The study involved multiple techniques and lines of evidence, and the authors felt their conclusion was the most plausible explanation for these results when considered as a whole. We hope that the study and the subsequent exchange being published today will stimulate further experments — whether they support or overturn this conclusion."

The criticisms — and the responses from Wolfe-Simon and her colleagues — thus set the ground rules for the debate, which will likely continue for months and years to come. Here's a quick rundown of some of the issues involved:

Criticism: The "arsenic-eating" bacteria, known as GFAJ-1, were grown under conditions that still had trace amounts of phosphorus, and it's more likely that the microbes used that trace phosphorus rather than the arsenic. The arsenic-life researchers claimed there was so little phosphorus left that the bacteria couldn't possibly have survived on it — but under extreme conditions, some individual microbes have been found to survive on that little.  

Response from the team: They point out that they checked bacteria under three conditions: high phosphorus and low arsenic; high arsenic and low phosphorus; low arsenic and low phosphorus. If the "arsenic-eating" bacteria were actually living off the low levels of phosphorus, they should have done as well in the low-arsenic / low-phosphorus environment. But they didn't. The team also says the survival rate on an ultra-low-phosphorus level should be compared based on wider populations, and not based on individual extremophile microbes.

Criticism: In the course of breeding bacteria to make them live in a high-arsenic environment, the team might have actually created bacteria that adapted to the low-phosphorus concentrations by processing the chemicals differently. That would explain why the high-arsenic / low-phosphorus bacteria did so much better than the low-arsenic / low-phosphorus bacteria.

Response from the team: They saw no evidence that the bacteria's biochemistry processed phosphorus in the way that was suggested, but acknowledged that the chemical pathways used by GFAJ-1 "are important avenues for future investigation."

Criticism: The molecular bonds involving arsenic would simply not be strong enough to hold up in alternate forms of DNA and other biochemical building blocks. What's more, phosphorus is far more abundant than arsenic in the solar system, and most of the arsenic available on rocky planets would be available in a form that is structurally quite different from phosphorus. These considerations point to the unlikelihood of life arising on Earth or elsewhere with an arsenic-based biochemistry.

Response from the team: It's conceivable that the arsenic bonds in large biomolecules are more resistant to a breakdown than the bonds in smaller molecules. "GFAJ-1 may have evolved specific strategies to cope with this issue, such as stabilizing structures," the team wrote.

Criticism: The team didn't devote enough attention to guarding against contamination of their samples and purifying the DNA that they analyzed. What's more, the uncertainties surrounding the measurements may not allow the team to make definite conclusions.

Response from the team: Wolfe-Simon and her colleagues recap the procedures they used and say they "were sufficient to remove any impurities." They also cite multiple techniques that cross-checked their results, through radiolabeling as well as high-resolution mass spectroscopy. They agree that further analysis of the DNA "would be a useful future experiment" because it could shed further light on the chemistry involved. They reworked their calculations on some of the analysis to respond to some of the criticisms about averaging, and said the data still supported their conclusions.

The bottom line is that the debate will continue, with more researchers getting into the act. Wolfe-Simon's team says samples of GFAJ-1 are being made available to other labs upon request, through the Oremland Laboratory at the U.S. Geological Survey.

"We look forward to working with our peers to replicate our observations and to test our hypotheses along the lines suggested by [one of the critics, Stefan] Oehler and others," the team writes.

One of the most vocal critics, University of British Columbia microbiologist Rosie Redfield, said today that she was still unconvinced:

"The authors don't report any new experiments. Most of their responses take the form of 'our interpretation could be correct on this point if...' In many cases there is indeed a small possibility that it could, but there are so many of these points of interpretation, each with only a very small probability of being correct, that I don't think anyone will find the arguments convincing."

Redfield said the team's responses to her comments about contamination were "in some ways the most scientifically valid, as they provide information about their media and DNA purification." She promised to have more about that on her blog later today.

So the blogosphere beat goes on. What do you think? Are you intrigued by this latest chapter in the grand scientific debate, or has the whole subject of arsenic life lost its appeal? Either way, please feel free to add your comments below.

Update for 8:30 p.m. ET: I've added some comments from Wolfe-Simon above after chatting with her this afternoon. She said she and her colleagues took Redfield's concerns about potential contamination very seriously. "Her criticisms are definitely valid," she said. "One of the first things we went back and did was look at all the ways we can get [phosphorus levels] down to zero."

But she said the key observations would come when scientists look at GFAJ-1's molecular machinery, to confirm that arsenic really is being incorporated into DNA, lipids and other molecules where phosphorus is usually found. "The question that people are really asking is, 'Show me the money. Let's see those biomolecules,'" she said.

Wolfe-Simon said she and her co-authors have been getting offers of help from other researchers in fields ranging from molecular biology to astronomy. She's also been getting supportive messages from lots of folks, including a 7-year-old girl who told her she wants to do research at Mono Lake when she grows up. "If I can put my peg on the wall, if we can ask the right questions ... she's going to answer the questions," Wolfe-Simon said.

Meanwhile, Redfield has posted an additional blog item that details her concerns about contamination. She's not satisfied with the response that Wolfe-Simon and her colleagues provided. "Overall, the most striking aspect of the authors' formal response is that they never admit to having made any mistakes or having done anything badly," she writes. "This is a bit disconcerting, given how many concerns were raised."

Update for 9:30 p.m. ET: An additional post from Rosie Redfield addresses how to test arsenic-life claims. Meanwhile, science writer Carl Zimmer looks at the big role that online discussion played in the arsenic-life debate, and Nature's Erika Check Hayden rounds up reactions from other researchers. One theme: Is it worth spending time and effort to try replicating the findings?

The story so far:

• December 2010: Life as we don't know it ... on Earth?
• 'Weird life' claims spark a backlash
• 'Weird life' reveals science at work
• 'Weird life' researchers answer critics
• February 2011: Arsenic debate just won't die
• April 2011: Alien life revisited

Science is making all 10 papers accessible with free online registration. You can see the whole list on Science Express, the journal's rapid-publication website, and here's an item-by-item menu:

• Comment by James Cotner and Edward Hall
• Comment by Rosemary Redfield
• Comment by B. Schoepp-Cothenet, W. Nitschke, L.M. Barge, A. Ponce, M.J. Russell and A.I. Tsapin
• Comment by Istvan Csabai and Eors Szathmary
• Comment by Stefan Oehler
• Comment by David Borhani
• Comment by Steven Benner
• Comment by Patricia Foster
• Response by Felisa Wolfe-Simon, Jodi Switzer Blum, Thomas Kulp, Gwyneth Gordon, Shelley Hoeft, Jennifer Pett-Ridge, John Stolz, Samuel Webb, Peter Weber, Paul Davies, Ariel Anbar and Ronald Oremland
• "A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus" by Felisa Wolfe-Simon et al.

You can connect with the Cosmic Log community by "liking" the log's Facebook page or following @b0yle on Twitter. Also, give a look to  "The Case for Pluto," my book about the controversial dwarf planet and the search for new worlds.

Science / AAAS

A photomicrograph shows a strain of bacteria called GFAJ-1 that was said to incorporate arsenic into its cellular machinery.

Last updated 2:15 p.m. April 2:

Is there life beyond Earth? Over the past few months, scientists have repeatedly suggested that there could be — but the science behind those suggestions remains frustratingly murky and controversial.

Astrobiology's X-Files were the subject of a talk I gave on Saturday in the Second Life virtual world, at the invitation of the Meta Institute for Computational Astrophysics. Here's the vidcast of the talk — which gives you a taste of how Second Life works as well as how the search for extraterrestrial life works.

Arsenic life
This talk came exactly four months after researchers shook up the scientific world with claims that they were able to get the cellular machinery of microbes from California's Mono Lake working with arsenic instead of phosphorus. That's an amazing result, because arsenic is supposed to be poisonous to living things. If organisms on Earth could be tweaked in such a dramatic way, perhaps life could arise in other environments that don't seem conducive to life as we know it ... the Saturnian moon Titan, for example.

The implication of the research, published in the journal Science, would be that we might be missing strains of "weird life" that just might exist under our noses. (Perhaps literally under our noses, as a "second Genesis" that has gone undetected.)

The study ran into a lot of skepticism from the start. Some microbiologists and chemists have faulted the research team's laboratory techniques, or the conclusions that the team drew from their data. In response, the research team insisted their science was sound — but also encouraged their detractors to run their own experiments and report the results. Science pledged to publish a follow-up.

That follow-up is still in the works, but commentaries on the "arsenic life" are showing up in peer-reviewed journals such as BioEssays and FEMS Microbiology Letters. These papers have sparked a secondary controversy: Does scientific criticism really count if it's just on the Internet?

The BioEssays paper sees no "fatal flaw" in the original paper, and the paper's authors contend that Internet-only discussions "are not components of the peer-reviewed literature and thus are not placed on record as part of the official scientific discourse." The Microbiology Letters commentary complains about "the magic and nonsense that floods cyberspace."

As you can imagine, that's sparked a lot of counter-criticism from the folks who have been using the blogosphere and Twittersphere as a sounding board for their own review of the research. To get that side of the story, check out the postings from Rosie Redfield at the University of British Columbia, Zen Faulkes from the University of Texas-Pan American and Michael Eisen from the University of California at Berkeley (who attended an informal seminar given by Felisa Wolfe-Simon, the lead author of the arsenic-life study).

R. Hoover / Journal of Cosmology

A field-emission scanning electron micrograph shows one of the filaments that was found in the Ivuna CI1 carbonaceous meteorite. The filament looks similar to those seen in earthly cyanobacteria.

Meteorite life
Less than a month ago, NASA astrobiologist Richard Hoover published a paper in the online-only Journal of Cosmology, suggesting that a number of meteorites contained microbes that could have come from outer space. Once again, the study created a splash, in large part because of the NASA connection. There was quite a furor over whether or not Hoover was misinterpreting what he was seeing, and some critics pointed out that the research had been submitted to (and rejected by) other, better-known journals before it wound up in the Journal of Cosmology.

The story went big on a Saturday, but by the following Monday, executives at NASA disavowed the research, and the debate quickly died down. The Journal of Cosmology's editors said they were selling off the publication. Hoover, who has had a long and distinguished career as a researcher at NASA's Marshall Space Flight Center, faced sharp questions about his academic credentials.

Today, Hoover came in for an added dose of indignity: The James Randi Educational Foundation named him one of the year's "five worst promoters of nonsense," alongside anti-vaxxer Andrew Wakefield, televangelist Peter Popoff, TV doctor Mehmet Oz and the CVS pharmacy chain (for offering homeopathic remedies). The last thing Hoover needs right now is a "Scientist Pigasus Award" from the Amazing Randi.

NASA / LPI

Some scientists have suggested that tiny wormlike structures seen within the Mars meteorite known as ALH84001 may be "nanofossils" of biological origin.

Life on Mars
You could argue that the sharp debate over the prospects of detecting microbial life from beyond Earth began 15 years ago, with Science's 1996 publication of research about "nanofossils" found in a meteorite from Mars. Some might go two decades further back, to the much-debated life-detection experiments that went to Mars aboard the Viking landers.

Even after 15 years, the microfossil debate is still percolating. The researchers behind the original study have been setting out other lines of evidence to argue that they're seeing the fossilized traces of ancient organisms rather than modern-day contamination from Earth, or geological shapes that just happen to look like critters.

Other studies, conducted as part of NASA's Phoenix Mars Lander mission, have shown the presence of perchlorate, a chemical that could be associated with particular kinds of exotic life on Earth. Those findings have revived discussions over what Viking found (or failed to find).

Although the debate over past life-on-Mars experiments is continuing, most astrobiologists say it's going to take additional  studies on the Red Planet to resolve the controversy. That's the goal of an experiment being proposed by MIT and Harvard researchers, known as the Search for Extra-Terrestrial Genome, or SETG. Right now the researchers are facing one big challenge: They don't yet have a spot on a future Mars probe.

Even if SETG's genome sequencer went to Mars and detected a snippet of DNA or RNA, would that serve as sufficient evidence that life arose on other planets? Or would such a claim end up in the same limbo that surrounds earlier claims for alien life. I suspect that the latter would be the case — but what do you think? Feel free to weigh in with your comments below, and check out Saturday's hourlong presentation.

More controversies in astrobiology:

• Strange find on Titan sparks chatter about life
• Mars methane mystery: What's making the gas?
• Search for alien life may take giant leap forward
• What exactly is life, anyway?

Join the Cosmic Log community by clicking the "like" button on our Facebook page or by following msnbc.com science editor Alan Boyle as b0yle on Twitter. To learn more about my book on Pluto and the search for planets, check out the website for "The Case for Pluto."

Henry Bortman

Astrobiology researcher Felisa Wolfe-Simon works with samples at California's Mono Lake.

The continuing controversy surrounding the announcement of strange bacteria deep in a California lake that can apparently survive on arsenic and even incorporate the element into its DNA is being held up as a shining example for how the scientific process works.

The latest to point this out are the folks at Real Climate, a blog on climate science — a discipline that is no stranger to controversy.

The arsenic-DNA study, published in the journal Science, was announced at a NASA news conference on Dec. 2 that was hyped in advance as an opportunity "to discuss an astrobiology finding that will impact the search for evidence of extraterrestrial life."

What's groundbreaking about the find is it suggested that salt-loving bacteria gathered from California's Mono Lake could be coaxed to substitute atoms of arsenic, which is toxic to life on Earth, in place of the usual phosphorus atoms in DNA and other parts of their cellular machinery.

If that's possible on Earth, then it's also possible that such alternate forms of life could be thriving elsewhere in the universe. This, in turn, might expand the definition of "life" and require a broadened search for extraterrestrial organisms.

Since the study was published, a number of microbiologists and chemists have questioned whether the experiments actually proved the researchers' point.

Among their criticisms are concerns that inadequate care was taken in purifying DNA samples from the bacteria in the arsenic-rich medium, and that the arsenic found in the DNA was merely contamination. They said that the bacteria might have been using trace amounts of phosphorus left as impurities in the growth medium.

As these criticisms played out in the media and on the Internet, the researchers behind the original paper issued a statement responding to their critics — and said more would be forthcoming in Science.

So that's the story so far. Has this high-profile airing of claims, counterclaims and counter-counterclaims hurt the credibility of the scientists involved? Not at all, Real Climate's bloggers say. Instead, they contend that the controversy "has demonstrated the credibility of scientists, and should promote public confidence in the scientific establishment."

Climate scientists are keen to point out the scientific process at work, in part to counter their own critics. Such critics say many researchers are afraid to go against the scientific consensus that human activity is a driving factor in global climate change because it might staunch their flow of funding from agencies such as NASA.

Real Climate flagged a comment on the Watts Up With That blog, a hub of climate skeptics, that reads:

"It’s amazing how fast the scientific community came out to attack NASA for what they claim is plainly flawed science. Then again, NASA isn’t funding any of the attackers.

"In the Climategate mess, however, we still have heard very little from an awful lot of so-called scientists who should have been saying a lot more about flawed science but are too afraid to lose their grant money."

The reality is more complex: Science writer Carl Zimmer has done the work to show that many of the arsenic-DNA study's critics are indeed NASA-funded, including Norman Pace at the University of Colorado, extremophile expert Hazel Barton at the University of Northern Kentucky, and John Roth at the University of California at Davis.

Real Climate notes: "Scientists offer opinions based on their scientific knowledge and a critical interpretation of data. Scientists willingly critique what they think might be flawed or unsubstantiated science, because their credibility — not their funding — is on the line."

While the Real Climate bloggers have mixed feelings about the arsenic-DNA controversy playing out in the blogosphere and media, rather than strictly within the confines of the peer-review process, they are far from alone in using the controversy to help explain the merits of the scientific process.

Over on the NeuroLogica Blog, for example, Steven Novella has a post up that responds to a comment on the ScienceNOW website in which the criticism is characterized as "unfair."

"The commenter is confusing being fair with being nice. The self-critical aspect of science is not nice. It’s brutal – necessarily so. But it is still fair and professional, just not politically correct.

"This is one critical aspect of science that I feel the public needs to better appreciate. This is also a fun and dramatic aspect of science — real-world mud fights where scientists go at each other’s throats. The mass media needs to appreciate this real drama more so that they will rely on their hackneyed Hollywood cartoon of science less."

In USA Today, science columnist Dan Vergano recaps the controversy and notes that the back-and-forth is likely to continue, though it will eventually be settled via the peer-review process.

What do you think about the way in which the "weird life" controversy has been playing out on blogs and in the media, rather than strictly through the peer-review process? Is it actually a shining example of science at work? Feel free to weigh in with your comments below.

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).

Henry Bortman / 2010

Astrobiology researcher Felisa Wolfe-Simon works with samples at California's Mono Lake.

The controversy over findings that suggest life can grow using arsenic entered a new phase today: The researchers behind the radical claim issued a statement responding to their critics — and said the comments and responses generated by their experiments would be reviewed and published in a future issue of the journal Science.

In their original study, published online by the journal Science on Dec. 2, the researchers suggested that salt-loving bacteria gathered from California's Mono Lake could be coaxed to substitute atoms of arsenic, which is toxic to life on Earth, in place of the usual phosphorus atoms in DNA and other parts of their cellular machinery.

Since that study was published, a number of microbiologists and chemists have questioned whether the experiments actually proved the researchers' point. The critics said inadequate care was taken in purifying DNA samples from the bacteria in the arsenic-rich medium, and that the arsenic found in the DNA was merely contamination. They said that the bacteria might have been using trace amounts of phosphorus left as impurities in the growth medium, and that arsenic bonds in the DNA could not have stood up to exposure to water.

For the past couple of weeks, members of the Mono Lake research team have declined to respond in detail to the criticisms, saying that they preferred to address questions through a peer-reviewed process. But today, team leaders Felisa Wolfe-Simon and Ron Oremland of the U.S. Geological Survey said they were providing additional information about the experiments "as a public service ... while more formal review of their responses to comments sent to Science continues."

In a preliminary Q&A, Wolfe-Simon and Oremland recapped the procedures they went through to purify arsenic-laden DNA and said they felt the critics' concerns about the procedures were not valid. They also said "it is conceivable" that DNA containing arsenic is more resilient to water exposure than previously thought, although they acknowledged that "more research is warranted" on this question.

They pointed out that the Mono Lake bacteria could not grow unless either arsenic or phosphorus was added to the medium. Such data "clearly demonstrate" that the trace amounts of phosphorus left in the medium were insufficient to support further growth, they said.

In their conclusion, the research team reflected on what they've gone through and what lies ahead:

"For all of us, our entire team, what this was like was unimaginable. We are a group of scientists that came together to tackle a really interesting problem. We each used our talents, from technical prowess to intellectual discussion, to objectively determine what exactly was happening in our experiments. We freely admitted in the paper and in the press that there was much, much more work to do by us and a whole host of other scientists. The press conference even included a technical expert, Dr. Steven Benner, who voiced some of the concerns we responded to above. Part of our reason for bringing this work to the community was to make the intellectual and technical connections for more collaborations to answer many of the lingering questions. We were transparent with our data and showed every datum and interesting result. Our paper’s conclusions are based on what we felt was the most parsimonious way to interpret a series of experiments where no single experiment would be able to answer the big question. 'Could a microbe use arsenic in place of phosphorus to sustain its growth?' The best science opens up new questions for us as a community and sparks the interest and imagination of the general public. As communicators and representative of science, we feel that support of new ideas with data is critical but also to generate new ideas for others to think about and bring their talents to bear on.

"We look forward to working with other scientists, either directly or by making the cells freely available and providing DNA samples to appropriate experts for their analyses, in an effort to provide more insight into this intriguing finding."

Science is making the original study as well as its news article about the research available for free online with registration. If you're interested in this issue, be sure to read today's full statement — and feel free to comment below.

Update for 11:55 p.m. ET: Rosie Redfield, a microbiologist at the University of British Columbia who was a prominent critic of the original "arsenic life" research, has posted her critique of the today's statement.

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).