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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...
Any major or minor scientific discovery has to be subject to scrutiny in order for it to be proven. If it folds at the first issue or claimed to be above scrutiny it would be called a religion.
What's that thing called.... Ummm... The scientific madness?
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. :)
Amen!
Let's go to one of Saturn's or Mars' moons and test the soil there, why don't we NASA?
He who knows best knows how little he knows. - Thomas Jefferson
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!
I think a better purpose for NASA would be to concentrate on making factories which produce spaceship factories.
What ever did happen to the Virgin funded project to get the (rich only for now) public into space?
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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...
Could they be right? Of course they could be right. It wouldn't change the fact that they sound like five-year-olds.
By the time its dumbed down from the initial scientific review, through the journal, to the PR dept, through the wire service, to the media outlet yes it does.
Where can I go for science news thats not quite as intense as the journals themselves, but more in depth than the normal news outlets? Something that explains whats going on without having to create controversy to justify airtime but recognizes I have a Bachelors and a job and not a PhD?
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.
NASAs ultimate solution is offcourse to become the first space bank! You'll be bailed out whenever you need it, no need to lie to the public nobody does that!
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!"
Scientists can be such whiny, arrogant assholes...whatever happened to science being done for science, rather than recognition?
Scientists are not saints. Science involves a lot of non-science: finding funding, managing teams, etc. and some people are into outmaneuvering others. 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.
I'm not sure about every discipline, but some publications by IEEE are intended specifically for professional engineers who want to keep up with their field but don't require the rigor of a journal publication.
I might also suggest conference proceedings for a prominent conference in your field. Conference papers are usually shorter and less in depth than a journal paper, but still offer a good overview of the research.
...whatever happened to science being done for science, rather than recognition?
This is science. Discoveries are meant to be criticized for their flaws. Now people can try to repeat the experiment while trying to eliminate the previous variables.
Did you bother to RTFA? There are serious flaws in their method. The wrong thing to do would be to blindly defend the original paper or dismiss it completely.
"finding may be based on something a simple as poor sample washing to remove phosphate contamination."
Excuse me? "may be". Well lots of things "may be" but if you can't prove that it was you should keep your mouth shut until you can prove that it "is" instead of "may be"
Thats just it. I keep up on my field just fine. I want to be informed about things outside my field.
My big concern is that I'll hear a story from a generally decent source about something related to my field or to my hobby and they'll get something wrong. Maybe not egregiously incorrect, but just not quite right. That scares me because it makes me wonder what else they're getting not-quite-right when reporting on a field I'm not heavily involved in.
Where can I go for science news thats not quite as intense as the journals themselves, but more in depth than the normal news outlets? Something that explains whats going on without having to create controversy to justify airtime but recognizes I have a Bachelors and a job and not a PhD?
I've always been rather partial to Science Daily. I find it invaluable for keeping up with the latest advancements and discoveries, presented in a way that is understandable yet not insulting to your intelligence.
Living With a Nerd
You are correct, critizing other peoples work is part of the scientific process since it was invented. Just that the public expects our best and brightest to use better debating skills then:
Scientist A: You suck.
Scientist B: No, you suck.
Scientist A: No, you suck.
Scientist B: No, you suck.
etc
Don't know why the general population expects this. It essentially how we all debate. Only diplomats do it better since they know the secret of diplomacy is to tell the other to go to hell in such a way that he looks forward to the journey.
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You may solo them, I prefer them in a group.
I haven't read TFA, but I've read other criticisms of the NASA research, and they said that the microbes had plenty of access to phosphor. And if that's the case, then NASA's assumption that arsenic replaced phosphor in the DNA gets really tenuous.
In fact, I had that very same suspicion when I first read about it. Instead of proving that the DNA contained arsenic instead of phosphor, it really sounded like they just assumed it, because there was so much arsenic and so little phosphor in the environment. Well, sorry, but an assumption that something might be true is just nowhere near as groundbreaking as proof that it really is.
I really hope they do manage to prove that DNA can be based on different elements, but for now I agree with the critics that they haven't done that yet.
Peer review is good. But lets not forget that more and more scientists and physicists are openly complaining of how broken things are in science. These days, all too often, those with the most political clout win in every sense of the word. Meaning, they tend to censor others and in turn receive additional funding. Which ultimately means, most of the whining isn't whining for whining's sake - its for hard cash, more political muscle, and additional prestige.
Its actually fairly easy to argue that better science was done a hundred years ago than is frequently done today.
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."
This conflates two problems mentioned in the article: possible poor washing of arsenic off the DNA, since it apparently likes to glom onto things, and trace amounts of phosphorus in the salts they fed the bacteria that were trying to starve of phosphorus.
Peer review isn't done in blog posts.
...in this great blog. Also check out the rest of the posts, if you're a chemist you'll definitely will enjoy the "stuff I won't work with" series.
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.
"go fever"? So this arsenic-metabolising bug is the O-ring of biology?
If Slashdot were chemistry it would look like this:Cadaverine
The beautiful thing about science is that the person who first made the assertion gets recognition. If someone wants to piss on his corn flakes and discredit his findings saying the sample is contaminated then eventually if/when they do come to a conclusion who gets the credit? The guy who first said there was life based on arsenic that's who. In reality if they really are going to continue on like this citing contamination the best way maybe to test it while it is still in it's original habitat (Mono lake) I.e bring the testing equipment to it. Then again how about if the equipment it's self gets contaminated... This could be a long night.
A loop, by its nature, continues. If that didn't make sense, start reading this sentence again.
Even religions have to contend with philosophers. Science without peer review is worse than that.
How does it feel to be a liar with pants constantly on fire?
As a professional (PhD molecular biology) scientist, I think the starting point is this:
If true, this is the biggest discovery in biology since watson crick, because it really redefines fundamentals of chemistry for life.
This is different from life growing under what seems to us harsh conditions (very acid [pH 1], high temp(boiling water)) etc
Replacing phosphorus with Arsenic is really fundamental, because phosphorus is found in so many different molecules in the cell: in DNA, RNA, tRNA, ATP, phospho lipids, glycolytic intermediates, building blocks for isoprenoid compounds, etc etc; thus you really have to change a lot of very very basic things As the saying goes, extra ordinary claims require extra ordinary evidence.
Coincidentally, there was an episode on a few days ago discussing the possibility of arsenic-based bacteria. I'm guessing that the episode wasn't churned out in 2 days, so there's probably a decent amount of background to this research.
I swear to God...I swear to God! That is NOT how you treat your human!
What's most funny about this is, IMO, is that their criticism isn't peer reviewed and they likely haven't attempted to recreate NASA's experiments, which likely means they are even less knowledgeable, less in a position to comment, and likely extremely hypocritical of the situation.
They may very well be right, especially given how political NASA is these days, but it doesn't change the fact that those throwing stones likely have no cause to do so; glass houses being what they are and all...
that facr is most people in the blogosphere ahve no idea how press release are done, not do they know how information on science is released.
The fact is most people in the blogosphere have no idea how press releases are done, not do they know how information on science is released.
If it was something big, NASA wouldn't have announced they where going to do it. This applies to ANY large entity.
If it was about getting a signal from another life form, they would have confirmed their data, and then just made the announcement. News that big will spread quick on its own.
If it's a small announcement, you let people know you are making the announcement to get ears and a solid reference point to help stop misinterpretation of the complex information.
The Kruger Dunning explains most post on
I cut that whole trying out, put it into a document to spell check, and pasted it back in. /. post what I cut out. Not out of the preview, og no. Just after the submit.
Half the time the spell check doesn't work, need a special work around to past into the text box.
Come on /. fix the thing already.
The Kruger Dunning explains most post on
At any rate, this is all premature. According to Zimmer:
Critics say that a few straightforward tests on the bacteria would show whether they really do have arsenic-based DNA once and for all. And the NASA scientists say they're ready to hand out GFAJ-1 to researchers who want to study it.
So, in a few months we'll either have some very interesting findings from experiments performed to everyone's liking...or a editorial in Science about how the original paper got through.
Here's a summary of the press conference, in case you missed it.
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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.
And if it turns out that this is another sensationalistic claim... like the mud they claimed were microbes from Mars... isn't that going to peg them as fraudsters? If this discovery is indeed invalid because of mistakes made... how many times can they do this before the public just goes "Oh look, NASA 'found' something again. Alert the National Enquirer". If their critics in the research community are right, then they'd have been better served by not jumping the gun with this announcement.
Life is hard, and the world is cruel
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.
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The recent announcement by NASA scientists and their collaborators that the GFAJ-1 strain of the Halomonadaceae bacteria provides hints into the potential biology of alien life-forms and the response of the media and scientific community to this claim have revealed several disturbing trends. These include the desperation of a government-funded science agency to generate publicity at a time when its financial support is in jeopardy; the inadequacy of the experiments by these researchers to support their conclusions; the relatively poor peer-review by one of the most prestigious of scientific journals; and the extra-hype added by the mass media. One rather positive aspect of this affair is the rapid response of the scientific community to question and challenge the most poorly supported and far reaching claims. It is likely that they will be disregarded much faster than the previous announcement by NASA of petrified Martian life in an Antarctic meteorite. A few of my colleagues as well as numerous bloggers have noted that the NASA publicity machine has been coincidently cranked up at a time when the next US budget, including the funding for NASA, is under question. The discovery of the model organism described in the Wolfe-Simon et al. paper in Science is actually not new. Since the mid-nineties, the ongoing study of various strains of Halomonadaceae bacteria and their respiration of arsenic at Mono Lake, the Aberjona Watershed and elsewhere has been reported by Dr. Ronald Oremland (the senior author of the Wolfe-Simon et al. paper) and independently by others. The central claim of the new Wolfe-Simon et al. study is that arsenic can substitute for phosphorus to sustain the growth of the GFAJ-1 bacterial strain, and some evidence is offered that the arsenic is incorporated into macromolecules such as nucleic acids and proteins. The GFAJ-1 cells were cultivated in the near absence of phosphorus in the growth media in the presence of arsenic. However, the media used in the study apparently had about 3 M phosphorus, and one wonders whether phosphorus may have also been introduced with the culture plates that may have been pre-washed with phosphate-containing detergents. In any event, the cultured GFAJ-1 cells were still observed to contain phosphorus at about 1% of the levels seen in cells grown in the presence of high phosphorus. Even under these conditions, bathing in medium containing arsenic, these cells still featured 100-times more phosphorus than arsenic. Moreover, the levels of arsenic incorporated into the phosphorus-depleted bacteria was not that much different from phosphorus-supplemented GFAJ-1 cells grown without arsenic. Ideally, a synchrotron X-ray analysis of arsenic in biomolecules should have been undertaken for both the phosphorus-fed and starved populations of the bacteria rather than just the phosphorus-depleted cells as was performed in the study. Despite the speculations offered in the Wolfe-Simon et al. paper, no conclusive evidence was provided that any arsenic actually replaced phosphorus in the DNA backbone of the GFAJ-1 cells. To incorporate arsenic into nucleotides and proteins, the arsenic would have to be presented with the arsenic-containing equivalent of adenosine tri-phosphate (ATP), i.e. adenosine tri-arsenate (ATAs). No evidence was obtained for the presence of ATAs in the GFAJ-1 bacteria. In fact, I have been unable to find any reports of ATAs in any life-form from PubMed or Google searches. While arsenic and phosphorus are highly related in the periodic table of elements, the arsenic atom is slightly more than double the molecular mass of phosphorus. As atoms get larger, the electronic structure of the atom, particularly those parts that participate in chemical bonds, become increasingly diffuse. Consequently, arsenate esters are very unstable and hydrolyze markedly faster than phosphate esters. This instability of arsenate ester linkages really restricts their utility in the synthesis of macromolecules like DNA. Furthermore, the instability of arsenylation of proteins, would preclude
Yeah... There is a lot of whining going on but having read the paper myself, I can't really say that the detractors don't have a point. The x-ray data from the paper indirectly indicated Arsenic based DNA. There isn't any conclusive proff that it is. The Arsenic DNA was immersed in water which generally destroys Arsenic esters like what Arsenic DNA is but it didn't shatter like glass as it should have. The Phosphorous impurity is several times higher than those levels found to sustain certain microbes. Phosphorous levels found inside these cells were enriched 600 times preferentially to Arsenic. The paper had no mention of how much Phosphorous was required for growth of the microbe. PCR wasn't attempted on the Arsenic DNA (which should fail if it is what they think it is) Honestly, were it up to me, I wouldn't have approved it for publishing either.
Sigs are too short to say anything truly profound so read the above post instead.
Anyone questioning the results should be sent a sample of the bacteria for study. Of course they could contaminate it with phosphorous and then we'd have to question their results too. So instead, we should send them the bacteria, and have them clean and eat them :-)
The finding is controversial because it has been commonly known that arsenic esters (R-AsO3) are rapidly hydrolyzed in water. For example, the main cause of arsenic poisoning is its replacement of phosphorus in adenosine triphosphate (ATP), followed by the quick decomposition of the arsenated compound, preventing cells from performing metabolism. The NASA paper claims that the bacteria have somehow found a way to create stable arsenic compounds despite the fact that cells are highly aqueous environments. I don't believe anybody is disputing that the bacteria can grow in the presence of arsenic. Rather, the controversial claim is that arsenic is replacing phosphorus. For example, an alternative explanation would be that the bacteria possess very effective mechanisms to pump arsenic out of the cell, similar to how halophiles are capable of removing large quantities of salt ions.
On another note, I don't think it's fair to be attacking NASA about this, though their decision to hold a press conference appears politically motivated (i.e. a grab for money/attention). Their space program is consistently underfunded, and they've been deploying robotic missions as much as usual.
As for whether the paper's claims regarding the incorporation of arsenic into molecules stands up, that will have to ultimately be confirmed by independent experiments. It's not like the bacteria are some kind of state secret, so it's premature to call anything "under fire" at the moment.
Disclaimer: I don't know anything about biochemistry, I'm just another IT guy.
The claims of the finding are not Arsenic dependant bacteria, which wouldn't be particularly impressive. The paper claims a Phosphorus INDEPENDENT form of life (one that can use arsenic instead of phosphorus), something which has never been observed before, and is way different than something that is merely Arsenic dependant.
'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,'
Considering releasing it as a paper is asking for serious advice from the peer community, I don't think this individual quite understands the scientific method.
What's most funny about this is, IMO, is that their criticism isn't peer reviewed and they likely haven't attempted to recreate NASA's experiments,
I've heard of an experiment with a purer environment without any phosphor at all, and there the microbes didn't multiply.
But they didn't state that was possible. They state that it can multiply by largely replacing phosphor. Which means some phosphor is still required - just in low quantities. Phosphor is still required and that's explicitly stated. Basically what you're saying validates NASA's experiments and further validates my entire point.
I thought NASA's claim was that phosphor in the DNA was replaced by arsenic. If they only multiply when there's phosphor available, and they don't multiply when there's no phosphor, then how can you possibly deduce that the phosphor in the DNA has been replaced?