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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."
Murp!
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!"...
If a scientist other than themselves didn't make the discovery, it's obvious the other guy's methods are flawed!
Scientists can be such whiny, arrogant assholes...whatever happened to science being done for science, rather than recognition?
Living With a Nerd
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?
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. :)
Derek Lowe provides an interesting analysis of the NASA paper: http://pipeline.corante.com/archives/2010/12/07/arsenic_bacteria_does_the_evidence_hold_up.php
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?
Why OpalCalc is the best Windows calc
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...
That would be home made kombucha.
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!"
They live in the human digestive tract. Just check the gut of anybody with heavy metal poisoning - like half the population on Bangladesh. I don't think that you have to go to Alpha Centauri to find them.
"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"
Arsenic dependent bacteria can thrive in the human disgestive tract. Just check the gut of anybody with heavy metal poisoning - like half the population of Bangladesh. You don't need to go to Alpha Centauri to find them.
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.
MMO Quests are like orgasms:
You may solo them, I prefer them in a group.
"Extraordinary claims require extraordinary evidence" - Carl Sagan
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.
...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.
"go fever"? So this arsenic-metabolising bug is the O-ring of biology?
If Slashdot were chemistry it would look like this:Cadaverine
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!
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
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
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
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.
I browsed through the science-journal report. Now I do not have that within reach but I do remember some things.
Was it P:C and As:C ratios that they were measuring using NanoSIMS from the DNA extracts? And was it so that As+/P- grown cells had P:C ratios lower than As-/P+ cells?
If DNA was constructed of phosphorous in both As+/P- and As-/P+ cells then would the P:C ratios be the same in DNA extracts? And if this was not the case then there must be something else in the DNA of As+/P- cells than phosphorous. Maybe As.
If they did not wash the DNA before running gel electrophoresis-coupled NanoSIMS then the result that P:C ratios were lower with As+/P- cells would just mean that more C-including contaminants were present in DNA extracts of these cells. I find this unlikely.