Slashdot Mirror
NASA's 'Arsenic Microbe' Science Under Fire
radioweather writes "The cryptic press release NASA made last week that set the blogosphere afire with conjecture, which announced: 'NASA will hold a news conference at 2 p.m. EST on Thursday, Dec. 2, to discuss an astrobiology finding that will impact the search for evidence of extraterrestrial life.' may be a case of 'go fever' science pushed too quickly by press release. A scathing article in Slate.com lists some very prominent microbiologists who say the NASA-backed study is seriously flawed and that the finding may be based on something as simple as poor sample washing to remove phosphate contamination. One of the scientists, Shelley Copley of the University of Colorado said 'This paper should not have been published,' while another, John Roth of UC-Davis says: 'I suspect that NASA may be so desperate for a positive story that they didn't look for any serious advice from DNA or even microbiology people,' The experience reminded some of another press conference NASA held in 1996. Scientists unveiled a meteorite from Mars in which they said there were microscopic fossils. A number of critics condemned the report (also published in Science) for making claims it couldn't back up."
I can't bear to follow them any more
They used to be able to call press conferences for event like "Hey, we landed on the Moon!" "Hey, we put a telescope in orbit!" Then they started with "Hey, we landed on Mars! Only at a much steeper angle due to some conversion error..." arriving to the current "Hey, we don't have any budget for space stuff, but this paper here looks interesting!"...
Initially, we measured traces of As by ICP-MS analysis of extracted nucleic acid and protein/metabolite fractions from +As/-P grown cells (11) (table S1). We then used high-resolution secondary ion mass spectrometry (NanoSIMS) to positively identify As in extracted, gel purified genomic DNA (Fig. 2A). These data showed that DNA from +As/-P cells had elevated As and low P relative to DNA from the -As/+P cells.
So my question is basically what does it matter what they grew or washed the bacteria with when, in one of the many investigations, they found that gel purified genomic DNA had elevated levels of arsenic in them? Unless I'm misunderstanding what 'gel purified genomic DNA' means, I would assume that there's still several pieces of data in these experiments that point toward an organism that uses arsenic in place of phosphorous -- even if only somehow partially. Would this sort of spectrometry reveal any arsenic at all in my gel purified genomic DNA?
My work here is dung.
... which are very distinguishable down to the DNA level - if of course of you have that kind of microscope - which NASA does...
If you read what the detractors are saying, it sounds like they're whining. This happens with every single major scientific discovery.
Every. Single. One.
Could they be right? Of course they could be right. It wouldn't change the fact that they sound like five-year-olds.
Living With a Nerd
It's a requirement for getting more funding and a bigger budget. With the current emphasis on cutting costs and everyone's budget under the microscope, they are trying to generate as much interest as possible in their work.
The paper made it through peer review. It was published by Nature, and while the peer review process and closed nature of Nature Publishing may not be perfect the paper was in fact reviewed. However NASA is in go-mode, and they desperately want to find life out there. Maybe when they really get serious about finding life they will send a probe down to Europa and sniff around. No telling what they will find.
Also, arguments in the scientific community are nothing new, and a lot controversy occurs because somebodies research infringes on someone else's predetermined view of things. We still don't know about dark matter very well, or even it exists, we still don't know so many things about almost everything! Text books continue to be updated every year, and the current consensus on big things like String Theory, or whatever are laid down to us as authoritative law, yet rescinded just as quickly when we learn something new. This reminds me of the global warming debate a little bit.
Scientists sure like to argue a lot. :)
Wait, wait, wait. The whole point of publication is to open up your results so that other scientists can poke holes in it and the science can be redone and improved upon. Isn't it kind of a bogus statement say something like "this paper shouldn't have been published"? And with outrage, no less. Could the science really have been that bad and still be approved for publication to begin with? It must have been subject to at least a bit of peer review prior to its release. How come no one was outraged about the guy who reinvented integration (http://science.slashdot.org/story/10/12/06/0416250/Medical-Researcher-Rediscovers-Integration)?!
Eek!
That's complete bullshit. This is how science is (and should) be conducted. It's called peer review and it is one of the most important safeguards of the scientific method. Without thorough and ruthless peer review, people are free to simply make outrageous claims and expect to be believed. That's how religion works.
The real reason they are underfire:
http://www.xkcd.com/829/
Laugh,
Love,
Peaceful day.
--- Relax, that mass muderer is just trying to reduce our carbon footprint, one fetus at a time...
You do realize that criticizing research is a crucial part of the scientific method, right? Letting claims go unchallenged is the domain of religion, not science.
People are ripping apart this paper because it makes grand claims based on a potentially flawed methodology. If the results can be replicated with those flaws fixed, then the NASA team's research recieves further validation. If not, hey, I guess they jumped the gun. Either way, you have to identify the potential flaws, which is what people are doing here.
Also, to once again quote Rosie Redfield:
I refuse to believe that NASA would have a press conference for mere PR and self-promotional purposes. That's *completely* out of character.
SJW: Someone who has run out of real oppression, and has to fake it.
If it does- awesome. Really neat microbiology
If it doesn't- well an awful lot of published papers turn out to wrong. Acknowledge the mistake and move on.
I see comments about how peer review failed. I'm not a microbiologist so I can't judge if there were any really obvious errors, but peer review isn't supposed to verify claims in papers- it's a sanity check to make sure that nothing blatantly wrong gets through. Given that Science is the 2nd highest impact journal out there I'm sure they have competent peer reviewers available. Is it possible they screwed up? Sure, but it's not a catastrophe: we're seeing science self-correct in exactly the way it's supposed to.
"Seven Deadly Sins? I thought it was a to-do list!"
There is no "is" in science. Everything is in terms of "maybes." This reflects the epistemological position that nothing in science is certain, but that things can be more or less likely based upon the preponderance of evidence. In this case, the samples may not have been properly washed (the original paper leaves out those details), and if the samples were not properly washed, there is an obvious source of contamination. The correct response is not to attacked Dr. Redfield for disagreeing with the paper, but for Wolfe-Simon et al. to clarify how the experiment was run, and to demonstrate that Dr. Redfield's critique is invalid.
Rhapsody in Numbers
Except that your depiction of the debate is incorrect. In reality, it looks more like this:
Wolfe-Simon et al.: We have made an extraordinary claim!
Redfield et al.: Your methods appear to be flawed.
And that is as far as we have gotten. In other words, the process is working.
Rhapsody in Numbers
As in any other profession, some percentage of scientists are the kind of whiny, arrogant assholes that would attempt to embarrass their colleagues in a mass-market publication rather than put the critique where it belongs: The letters section of Science.
First of all, the article in Slate was written by a science journalist (Carl Zimmer), not a professional research scientist. (Not to bash Zimmer, I think he's a good writer, but he has no personal motivation to sling mud here.)
Secondly, if you'll think way back to. . . last week, there was a breathless NASA announcement of an imminent press conference about a game-changing discovery, which received widespread coverage in mass-market publications. We call this "science by press release". At least they actually had a paper, unlike the cold fusion debacle, but they're still guilty of shameless self-promotion.
Lastly, most of the real debate is happening on blogs, and probably a lot of internal email chatter that we aren't aware of. I don't see anything wrong with this, for quite a few reasons. One is that it's simply an electronic, real-time version of what used to happen only at conferences and faculty meetings; people say far more savage things about each other offline. We could wait around for formal responses to get published, but there's a great deal of scientific value in this real-time analysis and dissection of flaws. I'm learning a lot, and I think we'll arrive at a conclusive answer much faster than if we had to read through several months of stilted exchanges in Science.
The editors of major journals are often reluctant to air controversies about the papers they publish. There was a case several years ago where several scientists wrote a letter to a journal pointing out possible evidence of fabricated data in a paper; the journal made them water down the letter, and allowed the author of the original article to get away with a half-assed, evasive reply. What the editors should have done instead was demand raw data and a reasonable explanation, and thoroughly investigated the paper, but they seemed content to let the matter slide. So, what we ended up with was mob justice, and the accused scientist's reputation was quickly destroyed on mailing lists and at meetings. It turned out that he was a serial fabricator, and he may face federal charges for defrauding the NIH.
That's a much more serious example than this one - there's no evidence that the NASA researchers did anything unethical, but there are some serious holes in the paper, and in general the evidence does not meet the standards one would hope for one of the pre-eminent scientific journals. I really hope that there's some truth in their claims, because it would be a fascinating organism to study, but the paper shouldn't have made it past peer review in this state.
microbes (hell, even complex multi cellular organisms) THRIVE under incredibly hostile conditions right here on this planet. but it's "impossible" organisms eat arsenic because it's "poison"
keep in mind all this shit happens at the bottom of the ocean where the pressure is thousands of PSI.
http://en.wikipedia.org/wiki/Hydrothermal_vent ..... ..... .....
Although life is very sparse at these depths, black smokers are the center of entire ecosystems. Sunlight is nonexistent, so many organisms — such as archaea and extremophiles — convert the heat, methane, and sulfur compounds provided by black smokers into energy through a process called chemosynthesis.
A species of phototrophic bacterium has been found living near a black smoker off the coast of Mexico at a depth of 2,500 m (8,200 ft). No sunlight penetrates that far into the waters. Instead, the bacteria, part of the Chlorobiaceae family, use the faint glow from the black smoker for photosynthesis. This is the first organism discovered in nature to exclusively use a light other than sunlight for photosynthesis.
Other examples of the unique fauna who inhabit this ecosystem are scaly-foot gastropod Crysomallon squamiferum, a species of snail with a foot reinforced by scales made of iron and organic materials, and the Pompeii Worm Alvinella pompejana, which is capable of withstanding temperatures up to 80C (176F).
can you imagine the fish tank you'd need to sustain this life on the surface!? the surface of Mars has to be (marginally) more hospitable than this but "Compared to the surrounding sea floor, however, hydrothermal vent zones have a density of organisms 10,000 to 100,000 times greater."
Peer review isn't done in blog posts.
Mod parent up - this is the most succinct and accurate analysis of the situation so far. We wouldn't be steamed at all if there wasn't some big marketing build-up to some "groundbreaking" discovery with hints of extraterrestrials. NASA was looking for a PR bump to get congresscritters into the mood to fund them more (or at least cut them less), and they took a 3rd rate paper, with 2nd rate review, and tried to make it into a 1st rate media event.
It is these days. And why not? Open science is better than "protected" science, or "sanitized" science. The Science Establishement letting the people see what science is really like, and doing it in the open, is one of the best things we can do for science.
My Suburban burns less gasoline than your Prius.