Princeton Team Casts More Doubt On Arsenic DNA Claims

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Princeton Team Casts More Doubt On Arsenic DNA Claims

Posted by timothy on Tuesday January 24, 2012 @03:56AM from the and-that's-what-science-is-and-does dept.

An anonymous reader writes "A team of researchers reports they can't reproduce the most important claim from 2010's controversial 'arsenic bacteria' paper — they find no arsenic in the bug's DNA. Meanwhile, other scientists are looking at different aspects of the bug and at arsenic in biology in general."

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Science! by Anonymous Coward · 2012-01-24 04:00 · Score: 1

I never understood how some people were so incredibly aggressively against the team that made the claim. This is how science works!
1. Re:Science! by zero.kalvin · 2012-01-24 04:08 · Score: 4, Insightful
  
  I don't know who are and what these "people" did. But it is your job as a scientist to scrutinize everything, specially when someone do something that has a flawed procedure. We can't just accept something said by someone, we have to reproduce it, we have to investigate it ourselves and confirm the results. Now unfortunately many times during history many results were refuted by other scientist simply because it didn't agree with the current dogma, look at Mendel it took many years before his results were accepted by the people in that field. So attacking someone's work is valid, but there is a correct way to do it and not attack it for the sake of bashing.
2. Re:Science! by ColdWetDog · 2012-01-24 04:20 · Score: 5, Informative
  
  The big problem with the original researchers was two fold - first, it was very preliminary. They had an unusual hypothesis (the bug, sorry, the bacterium) used arsenic in place of phosphate for the DNA 'backbone'. That's so unusual that it falls into the 'extraordinary evidence' category.
  But they didn't do that - they performed some basic microbiology and some even more basic biochemistry. There were hundreds of other potential experiments that they just ignored, even though they were pretty mainstream and could likely have gotten some grad student to at least to the preliminary ones. Pretty much anyone who has done DNA chemistry would look at the paper and ask why the team didn't bother to do any one of a number of other experiments to tie the arsenic into the DNA. (The original paper basically suggested that since there was arsenic in the bug and the bugs grew where others could not because of the high arsenic and low phosphate levels, the arsenic was being structurally incorporated into the DNA).
  THEN they hyped it to no end - made it sound like the Second Coming of DNA. That was their big error (hubris). It was weird enough in itself to get other people to look at it. That's always a problem with 'new' ideas since most labs are busy doing things they think they're supposed to be doing and don't necessarily have the time (or money) to go chase down other little issues.
  It seems like some PR idiot at NASA got wind of the research and tried to fly with it but it was really a stupid thing to do.
  
  --
  Faster! Faster! Faster would be better!
3. Re:Science! by vlm · 2012-01-24 04:22 · Score: 3, Interesting
  
  I never understood how some people were so incredibly aggressively against the team that made the claim. This is how science works!
  Its sounds like a classic theorist vs experimentalist battle. The experimentalists are trying to think up all kinds of fun ways to disprove her new theory, because its a pretty wide ranging theory so there is an extremely wide front to attack.
  You see a theorist "makes points" by coming up with interesting theories, which she has certainly done. But an experimentalist "makes points" by coming up with interesting experiments, and there sure are a lot of interesting possible experiments to perform in this very wide ranging theory...
  
  --
  "Science flies us to the moon. Religion flies us into buildings." - Victor Stenger
4. Re:Science! by Sockatume · 2012-01-24 04:25 · Score: 5, Insightful
  
  The third problem: they refused to engage their critics. They simply stonewalled their peers. That's not how science is done. Compare it to the OPERA neutrino study, which was an equally hyped and unlikely claim, but the authors openly solicited rebuttals.
  
  --
  No kidding!!! What do you say at this point?
5. Re:Science! by Anonymous Coward · 2012-01-24 04:26 · Score: 1
  
  Did you watch the NASA press conference? Iron Lisa acted like a conceited little princess. Shocking behavior for an alleged scientist. That turned me off to her and her research.
6. Re:Science! by Hatta · 2012-01-24 04:28 · Score: 4, Insightful
  
  They were pretty mean spirited because it was clear from the outset that it was almost certainly a technical error. Scientists don't get anything out of cleaing up someone elses mistakes. These people could have spent their time doing real work if the original researcher had washed her samples properly.
  
  --
  Give me Classic Slashdot or give me death!
7. Re:Science! by Sockatume · 2012-01-24 05:02 · Score: 2
  
  She's not a theorist, she's an experimentalist. It was an experimental study. The criticisms are, largely, on the quality of her experimental protocols.
  
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  No kidding!!! What do you say at this point?
8. Re:Science! by ColdWetDog · 2012-01-24 05:22 · Score: 2
  
  True, but you do that at your peril. Even scientists can be passive aggressive. The bug they found is now being called GFAJ-1 (Give Felisa A Job, Felisa Simon-Wolfe being one the scientists in the original article who has been less than open about the controversy). That's going to be tough to live down. Biologists love to have critters named after themselves, but not quite in this fashion.
  
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  Faster! Faster! Faster would be better!
9. Re:Science! by ColdWetDog · 2012-01-24 05:31 · Score: 1
  
  It may have been a technical error, but if true, would have made an enormous dent in DNA science. Like Nobel Prize type dents. It was plausible although not likely. It piqued other researchers interest (what it should have done) and some researchers are tracking this down.
  So, science worked exactly as it supposed to. Ego got shot down a bit. People got their mental landscapes moved around a bit. Some scientists at NASA might be starting to think out how you would test for the possibility of a non standard backbone on DNA (or whatever you would call it). Electrons get scattered about.
  It's real work.
  
  --
  Faster! Faster! Faster would be better!
10. Re:Science! by ceoyoyo · 2012-01-24 05:52 · Score: 1
  
  It probably had something to do with their media whoring and science by press conference approach.
  If they'd done as you're supposed to and submitted a paper for peer review FIRST, it would have been quietly shredded by the reviewers and they would have been able to either a) do better experiments, b) tone down their claims or c) give up.
11. Re:Science! by ceoyoyo · 2012-01-24 05:54 · Score: 1
  
  You know public (and most private) grants are awarded via peer review of proposals, right?
12. Re:Science! by ceoyoyo · 2012-01-24 05:56 · Score: 2
  
  Um, I'm pretty sure Felisa Simon-Wolfe named it that herself. She was a postdoc when she did the work and it she named it that as a joke about getting a faculty position (i.e. a real job).
13. Re:Science! by the+gnat · 2012-01-24 06:14 · Score: 4, Insightful
  
  If they'd done as you're supposed to and submitted a paper for peer review FIRST, it would have been quietly shredded by the reviewers
  In (partial) defense of the NASA folks, they had indeed submitted the paper for peer review, and it had been accepted to Science magazine - it appeared online the same day (or close to it) as their hand-waving press conference. That it didn't get shredded by peer reviewers is testament to either the laziness of peer reviewers, or the ease with which high-profile journals can be duped into publishing weak but exciting claims. (This happens frequently, I'm afraid.) They should have done much more thorough experiments, but the journals are supposed to filter out hypotheses that haven't been sufficiently proven.
  The problem with the press conference was that they made much more grandiose claims about the importance of their work than the evidence merited. If they'd stuck to publishing the paper and a diplomatically-worded press release, it still would have been very controversial, but it would not have elicited such a passionate response.
14. Re:Science! by Anonymous Coward · 2012-01-24 06:15 · Score: 1
  
  So, science worked exactly as it supposed to.
  No it didn't. Neither the approach nor the magazine (Science). This shouldn't have gone that far at all. This should have been shot down by the reviewers or actually outright rejected. The actual finding is really cool though: a bacteria that can survive high concentrations of arsenic - really cool stuff. Why not stick with that? Why claim arsenate in DNA when you provide no conclusive evidence for it?
  As a result a lot of people had to spend time 'proving' their claims as complete bull-shit. This could have easily been fixed, had the reviewers done their job properly and asked for proper evidence. After all this is really quite an extraordinary claim - please provide some extraordinary evidence.
15. Re:Science! by Frnknstn · 2012-01-24 08:28 · Score: 2
  
  You are incorrect. Evidence can have varying levels of quality. You get weak evidence, you get strong evidence, and you can also get extraordinary evidence.
  If any hypothesis is well-supported by established theory, it is only necessary for there to be mediocre evidence for it. In the absence of any reasonable alternative, it can then be accepted as correct, because it is backed not only by that weak evidence but also by all the strong evidence that supports the established theory.
  If a hypothesis contradicts established theory, the evidence for it must be particularly strong. Accepted theory is based on the BALANCE of evidence being in favour of one hypothesis over another.
  There is always at least some evidence to support a crackpot claim, otherwise that claim would never have been made. To simply abandon a theory because another theory has some evidence to support it is pure folly. The only reasonable action is to compare the sum of evidence for competing theories.
  (Upon re-examining your post, it seems possible that you are mistakenly taking the phrase 'extraordinary evidence' to mean 'evidence of something extraordinary', it isn't clear. If so, you have completely misunderstood the grandparent post.)
  
  --
  If it's in you sig, it's in your post.
16. Re:Science! by geekoid · 2012-01-24 12:34 · Score: 1
  
  No, the media hyped it up. I listened to the researchers in several interviews. She was surprised at what the media did.
  It was presented like any other finding.
  
  --
  The Kruger Dunning explains most post on /. http://en.wikipedia.org/wiki/Dunning%E2%80%93Kruger_effect
17. Re:Science! by geekoid · 2012-01-24 12:35 · Score: 1
  
  "The third problem: they refused to engage their critics. They simply stonewalled their peers.
  that's an outright lie.
  
  --
  The Kruger Dunning explains most post on /. http://en.wikipedia.org/wiki/Dunning%E2%80%93Kruger_effect
18. Re:Science! by geekoid · 2012-01-24 12:37 · Score: 1
  
  She named it, Also, she was open about the controversy.
  Please, you people are a complete fail when it comes to science discussion. People like you are the reason there is so much disconnect between actual science and the public.
  I am so tired of people like you either just making shit up based on some headline or something they heard 'somewhere' and not bothering to actually read up.
  You don't deserve the benefits of a science.
  
  --
  The Kruger Dunning explains most post on /. http://en.wikipedia.org/wiki/Dunning%E2%80%93Kruger_effect
19. Re:Science! by geekoid · 2012-01-24 12:41 · Score: 1
  
  That is exactly why the it's important to get reproducible result in other labs. Falsifying others work is part of science.
  This is a person with little experience, who may have made a mistake. Why people are trying to create a mountain out of this is anybodies guess.
  
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  The Kruger Dunning explains most post on /. http://en.wikipedia.org/wiki/Dunning%E2%80%93Kruger_effect
20. Re:Science! by geekoid · 2012-01-24 12:50 · Score: 1
  
  If you had bothered to look into this issue before spouting off like an ass, you would have noted it HAD BEEN SUBMITTED FOR PEER REVIEW.
  The conference was out on the same day of publication. Something the is normal. the Media went ape shit over it, leaving an inexperienced researcher in a position to defend her work in the media, using common language and not scientific terms.
  Something that is incredibly hard to do and takes experience.
  the media took this:
  "that will impact the search for evidence of extraterrestrial life"
  and twisted far beyond it's intent. Which is "It looks like life can exist in arsenic; which would give us another vector to look for life.
  Her peers saw the media issues, and instead of being professional and explain that the media has taken an inexperienced person results way out of context., the ostersized her.
  shame on them for that.
  .
  
  --
  The Kruger Dunning explains most post on /. http://en.wikipedia.org/wiki/Dunning%E2%80%93Kruger_effect
21. Re:Science! by ceoyoyo · 2012-01-25 15:18 · Score: 1
  
  Submitted hey? Well that's fantastic. You can submit a kermit the frog soliloquy for peer review if you want to. I admit, it's an arduous process, usually requiring twenty or thirty mouse clicks on a web page.
  The proper way to do it is to wait until the paper is accepted, PUBLISHED, and the scientific community has had a look at it. The FTL neutrino guys did that (IIRC their paper wasn't peer reviewed first, but they published it as is normal in the physics community, for review by that community), used cautious language, and have been receptive to criticism. The media still went nuts, but there was no backlash from the scientific community.
  I didn't say it was Wolf-Simon's fault, although it sounds like (I'm not a microbiologist, but there is no shortage of them that have said this) the original work was somewhere between rushed and shoddy, and her responses to criticism haven't exactly been scientifically productive. The real fault lies with NASA though. Without the NASA press conference "A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus" probably wouldn't have attracted much attention from the mainstream media and could have been given a good airing before, if it was justified, being hyped. NASA lost a lot of credibility with that one and, if you want to go with your interpretation, possibly damaged the careers of a few overeager young scientists.
  However, judging by your first sentence, you have some kind of emotional attachment to this story and probably haven't bothered reading this far. If you're involved with the research itself and that's how you respond to criticism, I'm even less surprised at the response you've gotten.
Not a bug by Anonymous Coward · 2012-01-24 04:02 · Score: 1, Insightful

How am I supposed to take a summary seriously when it refers to bacteria as a "bug"?
1. Re:Not a bug by Amorymeltzer · 2012-01-24 04:15 · Score: 1
  
  How am I supposed to take the summary seriously when it refers to the scientists as a "team of researchers"? They aren't actually a group of players on the same side in a competitive sport!
  Maybe we just use different words to mean different things in different contexts, especially when they have a different but slightly related and understandable similarity to the original meaning.
  
  --
  I live in constant fear of the Coming of the Red Spiders.
2. Re:Not a bug by Anonymous Coward · 2012-01-24 04:15 · Score: 3, Funny
  
  It's a feature.
3. Re:Not a bug by ThisIsSaei · 2012-01-24 04:21 · Score: 1
  
  The term 'bug' is used in the main article by Ronald S. Oremland (coauthor of the controversial Science paper and Wolfe-Simon’s postdoctoral adviser at the time), “Even if we are dead wrong with this arsenic-DNA business, with a bit more work this bug could shed light on the limits of what microbes can and can’t do.” Maybe you should be less flippantly critical of the wording.
4. Re:Not a bug by Anonymous Coward · 2012-01-24 04:36 · Score: 1
  
  I know a professional microbiologist. She cultures bacteria for use in medical applications. She always refers to the bacteria as bugs.
5. Re:Not a bug by Rob+the+Bold · 2012-01-24 04:48 · Score: 1
  
  How am I supposed to take a summary seriously when it refers to bacteria as a "bug"?
  I know what you mean. Synonyms make me ill, I mean sick -- oh crap!
  
  --
  I am not a crackpot.
6. Re:Not a bug by geekoid · 2012-01-24 12:52 · Score: 1
  
  a team is a group of people working together.
  team doesn't mean sport.
  
  --
  The Kruger Dunning explains most post on /. http://en.wikipedia.org/wiki/Dunning%E2%80%93Kruger_effect
7. Re:Not a bug by mcgrew · 2012-01-25 07:40 · Score: 1
  
  Bug
  From Wikipedia, the free encyclopedia
  Jump to: navigation, search
  Look up bug in Wiktionary, the free dictionary.
  Contents [hide]
  1 Biology
  2 Geography
  3 Technology
  4 Art and media
  4.1 In characters
  4.2 In films and television
  4.3 In gaming
  4.4 In literature and publications
  4.5 In music
  4.6 Other uses
  5 In acronyms
  6 Other
  7 See also
  Bug may refer to:
  [edit] BiologyInformally, an insect, spider or other small pest other than a rodent; including most arthropods, except marine crustaceans, including individuals or species of
  centipede
  millipede
  mite
  scorpion[citation needed]
  tick
  woodlouse
  Specifically, an insect of the order Hemiptera, known as the "true bugs".
  Bacterium or any microorganism that causes illness and has a superficial resemblance to an insect, or bug, when viewed through a microscope
  Bug, a hybrid dog that is a cross between a pug and a Boston terrier
  One of several species of slipper lobster, such as
  Balmain bug
  Moreton Bay bug
  
  --
  Free Martian Whores!
RTFA by mehrotra.akash · 2012-01-24 04:07 · Score: 1

/. discovered a way to make people RTFA!!!
All Power to the Pedantic Shields, Sir! by eldavojohn · 2012-01-24 04:18 · Score: 2

How am I supposed to take a summary seriously when it refers to bacteria as a "bug"?
While this is seen as probably an oversimplification of describing bacteria, viruses, etc. there are probably a lot of dictionary entries backing this up like the fifth one in Wiktionary: "A contagious illness; a bacterium or virus causing it." You also had media in the late nineties using this virtually everywhere. See this BBC article for an example. The fact that researchers themselves have used phrases like Super Bug to describe resistant bacteria to lay people probably doesn't help. English is viscous. Deal with it.

--
My work here is dung.
Bacteria by Anonymous Coward · 2012-01-24 04:25 · Score: 1

There's a bug in the summary.
Too late now by GodfatherofSoul · 2012-01-24 04:34 · Score: 1

They've already hustled the investors.

--
I swear to God...I swear to God! That is NOT how you treat your human!
If the "DNA" contains arsenic then... by edrobinson · 2012-01-24 04:39 · Score: 1

it's not DNA. DNA is a specific chemical compound. It sounds like these people found some arsenic in the bacteria and decided, with nothing to base it on, that it was part of the organism's DNA.
1. Re:If the "DNA" contains arsenic then... by Sockatume · 2012-01-24 05:01 · Score: 1
  
  Actually there's a lot of leeway in the chemical definition of DNA. It's heavily chemically modified by deliberate and accidental processes. If I wanted to be pedantic I would observe that it's still a nucleic acid based on a deoxyribose sugar and therefore has as much claim to being DNA as the canonical nucleotides.
  
  --
  No kidding!!! What do you say at this point?
This is more common recently by maple_shaft · 2012-01-24 04:51 · Score: 2
It seems we are seeing a lot more of these extraordinary claims and studies become challenged recently ranging from cancer research to climate change denialists skirting the peer review process:
- http://www.npr.org/blogs/health/2012/01/12/145117068/uconn-claims-resveratrol-researcher-falsified-work
- http://classic.the-scientist.com/blog/display/55408/
- http://theconversation.edu.au/whos-your-expert-the-difference-between-peer-review-and-rhetoric-1550
I think money plays a huge part in some of this. Think of the falsified research on the health benefits of Resveratrol and how those studies helped form a legitimacy around diet fad drugs that account for a billion dollar industry. It is an extremely lucrative industry and some of that money may end up funding future studies.
The same thing can be said about the corrupting influence of corporate money in funding climate change denial studies. If as a scientist, my research is being funded by oil companies who clearly want the studies to find a certain conclusion, you would be driving a stake in the heart of your career if you come to any other conclusion than climate change being unclear.
Other times there is enormous competition in research and a successful groundbreaking study will sometimes launch a lucrative career. The temptation can be great to make grandoise claims to jumpstart a career because by the time peer review trashes it, you may have already secured a cushy grant.
1. Re:This is more common recently by ColdWetDog · 2012-01-24 05:41 · Score: 1
  
  It seems we are seeing a lot more of these extraordinary claims and studies become challenged recently ranging from cancer research to climate change denialists skirting the peer review process:
  Only because the general media has hit on this as 'newsworthy'. While it certainly is more interesting that the Newt's latest philosophical, historical and / or moral transgression, being wrong is is one of the occupational hazards of science and as science is conducted by humans, it tends to have all of the other warts and problems inherent human endeavors.
  Read up on the history of science. Today's behaviors are SOP.
  
  --
  Faster! Faster! Faster would be better!
2. Re:This is more common recently by Curunir_wolf · 2012-01-24 05:45 · Score: 2
  
  The same thing can be said about the corrupting influence of corporate money in funding climate change denial studies. If as a scientist, my research is being funded by oil companies who clearly want the studies to find a certain conclusion, you would be driving a stake in the heart of your career if you come to any other conclusion than climate change being unclear.
  Can't you say the same thing about being funded by a government bureaucracy that clearly wants your studies to find a certain conclusion, like a study funded by the DEA to study dangers of marijuana, or by the FDA to show that GMO foods are safe? Wouldn't the EPA have a vested interest in funding studies that can show they need more funding and authority?
  
  --
  "Somebody has to do something. It's just incredibly pathetic it has to be us."
  --- Jerry Garcia
papers regularly retracted in Science and Nature by peter303 · 2012-01-24 05:15 · Score: 2

Its rather amazing to see the glaring headline "Retraction" in the letters section of these distinguished journals on a regular basis now. A dozen major scientists have written Science asking to retract the arsenic life paper. The policy is for authors to request retraction unless its a really extreme case like the XMRV retraction a few weeks ago (principal investigator in jail and authors suing each other). Most authors are honest and sometimes realize they've rushed to print without reproducible results. Then they'll retract.

I dont think there is anything horribly wrong with this process. Labs do rush to print for fame and priority. Readers want to see the newest results. There are many more papers now than decades ago. Reviewers dont have time to replicate the results during the review span of time and have to use their best judgment. Mistakes happen and are corrected. This is merely how good science works.
What's this cracking sounds? by mapkinase · 2012-01-24 05:49 · Score: 1

That's my jaw dislocating as a result of yawning.

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I do not believe in karma. "Funny"=-6. Do good and forbid evil. Yours, Oft-Offtopic Flamebaiting Troll.