Skip to main content

In December 2010, a team of microbiologists from NASA, lead by Felisa Wolfe-Simon, sent shockwaves through the scientific community when they announced their discovery that a particular strain of bacteria - the GFAJ-1 strain - not only could grow in a high-Arsenic environment, but actually incorporated Arsenic into its organic compounds (particularly, DNA).

The very controversial paper was published in Science, one of the top three journals in the life sciences community (the others being Nature and Cell).

This scientific achievement was duly noted here on Daily Kos in a diary by member Rimjob entitled "NASA To Announce New Form of Life".  It made the Rec List and had some really nice discussion.

However, this morning, Science published online dual papers, as well as this news article, that debunk the claim that bacteria can use Arsenic for life processes.

For the full story on why scientists thought this particular strain of bacteria could grow using Arsenic in the first place, please check out Rimjob's diary posted in the intro section.

In brief, Arsenic (Ar) and Phosphorus (P) are in a related group on the Periodic Table, meaning they have the same number of valence electrons.  Elements within a group tend to have similar chemical properties (mostly due to the same number of valence electrons), though differences in electronegativity and atom size give all elements a uniqueness about them.

Phosphorus is the key element that forms our DNA backbone.  It binds very strongly with Oxygen to create a stable scaffold that allows all of our coding nucleobases (the famous A, T, C, and G) in order according to whatever our DNA code may be.

The GFAJ-1 strain of bacteria grows in Mono Lake, California, a lake known with a very high Arsenic (and technically, arsenate) concentration.  This is normally lethal to organisms.  However, not only do the GFAJ-1 bacteria survive in this lake, they in fact thrive.  Additionally, the lake's Phosphate concentrations are very low compared to normal levels.

Thus enters in the initial controversial Wolfe-Simon paper.  In addition to the very peculiar growth ability of the GFAJ-1 strain in a high-Arsenic, low-Phosphorus environment, the authors provided data to show that the DNA of these bacteria actually contain Arsenic instead of Phosphorus.  Thus, the authors claimed, the paradigm of life exclusively using phosphorus as a DNA back bone and energy carrier was to be called into question.

Enter in Rosie Redfield, a microbiologist from the University of British Columbia.  She didn't believe the initial paper from the moment it was published online, and she has been very vocal about it.  She actively maintains a blog that has been very critical of the initial paper.

Redfield presented two key points of data on her blog that eventually ended up in her response paper that was published online today in Science.

The first regards GFAJ-1's supposed lack of growth in what the Wolfe-Simon paper deemed a "no-Phosphorus" growth medium; this medium actually contained 3 micromolar concentration of Phosphorus, but that was thought to be much lower than the minimum required for life.

Redfield demonstrated that the GFAJ-1 strain actually can growth at supposed "No-Phosphorus" concentrations, and even at 1 micromolar Phosphorus, a full 3-fold less than the supposed "No-Phosphorus" growth medium.

Next, and perhaps the most clever reason behind Redfield's disbelief of the Wolfe-Simon paper, was the notion of Arsenic-DNA.  I mentioned above that the Phosphorous-Oxygen bond (known as a phospho-ester bond) in the DNA backbone is very strong and stable in physiological conditions (think water).  However, chemists have long known that the Arsenic-Oxygen bond is instead very weak in water; it can break down within minutes.

The Wolfe-Simon initial paper provided evidence that Arsenic was found in the DNA of the GFAJ-1 strain.  However, as pointed out by several science bloggers and Redfield herself, the Wolfe-Simon paper interpreted their data completely wrong.

First, scientists commented on the Wolfe-Simon methods and materials section, specifically in regard to the DNA isolation protocol they used.  It involved an aqueous incubation for 30 minutes.  If the DNA bonds were really Arsenic-Oxygen, they should have been 100% disintegrated within that 30 minutes.  Intriguingly, the Wolfe-Simon paper showed that their Arsenic-DNA was intact, and explained their result that the DNA must be protected from hydrolysis in some fashion.  However, the Redfield paper showed that another bacterium's DNA known to contain Phosphorus was also protected from degradation.  Additionally, Arsenic should migrate at a different speed on a gel due to a different atomic radius, however migration of the Arsenic+ lane was exactly the same as the Phosphorus+ lane.

Second, scientists commented that the Wolfe-Simon DNA isolation method was messy and could bring along free Arsenic in the growth medium, but not in bacterial DNA.

Redfield proved both correct, as shown from her data figure below.  DNA isolated from GFAJ-1 bacteria grown only in Arsenic-positive medium were resistant from hydrolysis and mass-spec analysis revealed only free Arsenate - i.e. contamination from the Wolfe-Simon isolation method.

F2.medium

F3.medium

Ultimately, the Redfield paper conclusively demonstrated that the GFAJ-1 strain of bacteria does not incorporate Arsenic into its organic compounds, and instead uses Phosphorus like all other known life forms.  The Wolfe-Simon paper's results were incorrectly interpreted, and Redfield has made her opinion well known that she believes the data were not vetted meticulously enough, as needs to happen when you drop a bombshell game changer in the field of biology.

Finally, a corollary paper also published in Science today reports that the GFAJ-1 strain of bacteria is indeed resistant to Arsenate (something pretty cool), but still is Phosphate-dependent.  This explains why the strain can grow in a high-Arsenic, low-Phosphorus environment.

As a graduate student in cell and molecular biology, I followed this story somewhat closer than the average citizen, and I can tell you that I am very proud of the scientific community. It is a depressing reality that journals usually do not publish direct contradictions anymore, despite the fact that we all learned as far back as elementary school that science must be repeated to be verified.

In the world of uber-competition with trying to get grants and such, in addition to journals trying to have the highest Impact Factor possible, journals have gotten into the habit of only publishing new research and never publishing direct contradictions.  So I'm happy to see Science actually doing so when the evidence is there.

I also hope that NASA can quickly rub the egg off its face, since honestly, they really should have been much more meticulous and careful about publishing a claim so revolutionary as this.  Not to say that revolutionary claims are always false, but they require overwhelming evidence, and honestly it wasn't there in the Wolfe-Simon paper.

I know this has been a bit incoherent (I'm currently in lab now trying to write this) but I hope you enjoyed this diary and can have some confidence renewed into the scientific process.

Cheers.

Originally posted to mconvente on Tue Jul 10, 2012 at 10:28 AM PDT.

Also republished by SciTech, Science Matters, Astro Kos, and Community Spotlight.

EMAIL TO A FRIEND X
Your Email has been sent.
You must add at least one tag to this diary before publishing it.

Add keywords that describe this diary. Separate multiple keywords with commas.
Tagging tips - Search For Tags - Browse For Tags

?

More Tagging tips:

A tag is a way to search for this diary. If someone is searching for "Barack Obama," is this a diary they'd be trying to find?

Use a person's full name, without any title. Senator Obama may become President Obama, and Michelle Obama might run for office.

If your diary covers an election or elected official, use election tags, which are generally the state abbreviation followed by the office. CA-01 is the first district House seat. CA-Sen covers both senate races. NY-GOV covers the New York governor's race.

Tags do not compound: that is, "education reform" is a completely different tag from "education". A tag like "reform" alone is probably not meaningful.

Consider if one or more of these tags fits your diary: Civil Rights, Community, Congress, Culture, Economy, Education, Elections, Energy, Environment, Health Care, International, Labor, Law, Media, Meta, National Security, Science, Transportation, or White House. If your diary is specific to a state, consider adding the state (California, Texas, etc). Keep in mind, though, that there are many wonderful and important diaries that don't fit in any of these tags. Don't worry if yours doesn't.

You can add a private note to this diary when hotlisting it:
Are you sure you want to remove this diary from your hotlist?
Are you sure you want to remove your recommendation? You can only recommend a diary once, so you will not be able to re-recommend it afterwards.
Rescue this diary, and add a note:
Are you sure you want to remove this diary from Rescue?
Choose where to republish this diary. The diary will be added to the queue for that group. Publish it from the queue to make it appear.

You must be a member of a group to use this feature.

Add a quick update to your diary without changing the diary itself:
Are you sure you want to remove this diary?
(The diary will be removed from the site and returned to your drafts for further editing.)
(The diary will be removed.)
Are you sure you want to save these changes to the published diary?

Comment Preferences

  •  Most excellent diary and very clear (15+ / 0-)

    even to someone (me) whose technical strengths lie as far away from molecular biology as possible.

    Certainly from our standpoint, this gives us a sense of momentum -- when the United States has accolades tossed its way, rather than shoes. - PJ Crowley

    by nsfbr on Tue Jul 10, 2012 at 10:37:06 AM PDT

  •  No, this is not on NASA . . . . (3+ / 0-)
    Recommended by:
    pgm 01, kyril, pixxer
    also hope that NASA can quickly rub the egg off its face, since honestly, they really should have been much more meticulous and careful about publishing a claim so revolutionary as this.
    Blame Science, they're the ones who published it w/o adequately vetting the work.
    •  It is at least partially NASA (8+ / 0-)

      They took lots of credit for this announcement back in December 2010.  See this story from Nature's news section.

      And today, from Michael New, strobiology discipline scientist in NASA's Planetary Science Division at NASA Headquarters:

      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 micro-organism 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 micro-organism that can survive in a highly phosphate-poor and arsenic-rich environment toxic to many other micro-organisms. What has emerged from these three papers is an as yet incomplete picture of GFAJ-1 that clearly calls for additional research.
      Bold my emphasis.

      They are trying to shift their initial conclusions, which was not merely that this strain of bacteria can grow in a low-phosphate, high-arsenic environment, but that the bacteria strain incorporates Arsenic into its organic compounds.  The first result is neat, but the second one is groundbreaking, that's the one they published in the now-debunked paper.

      "Give me a lever long enough... and I shall move the world." - Archimedes

      by mconvente on Tue Jul 10, 2012 at 10:50:32 AM PDT

      [ Parent ]

      •  Do you expect NASA to throw their scientists (10+ / 0-)

        under the bus?

        I think it's nice that:

        1) in the first place, they (i.e., the scientists) were allowed to publish w/o too much micro-management from above.

        2) that they're now being supported by their superiors.

        Really, the onus here is completely on Science, who fucked up the review of the paper.  What NASA is did, and is doing, is completely understandable wrt to promoting their scientific discoveries.

        In any event, this fits nicely into the the meme of the scientist who can claim (loudly) "I have four Science citations" and then (more quietly) "two papers and two retractions . . . ."

        Also, as far as the title of your diary goes, I never ever understood that this group made the claim that these bacteria could grow "only" on arsenic.   That makes no sense at all!!

    •  Why blame Science or NASA? (7+ / 0-)

      The whole escapade was a triumph of the scientific method. Extraordinary claims require extraordinary evidence. A new theory was proposed, but failed evidentially. Rock on scientists, you make me proud!

      •  This is the lesson to be learned. (2+ / 0-)
        Recommended by:
        mconvente, Don midwest

        Many "discoveries" are "undiscovered" and you never hear about any of them, largely because people wait until the scientific method plays out before they run to the newspapers.

        But this year, we've had the "faster than light neutrino" and the "Higgs Boson" come out of CERN (along with some atmospheric science speculations) that really concern me that the funding cycle precedes the scientific scrutiny.  This is impossible to resist when you work for an agency that feels that its budget is built off newspaper articles instead of scientific papers.

        The Muslim said "I wished I had met Christ before I met the Christians" - Rev. Marvin Winins

        by captainlaser on Tue Jul 10, 2012 at 08:03:38 PM PDT

        [ Parent ]

      •  Agreed (0+ / 0-)

        Not all good science is easily vetted. Sometimes, you have to be patient, and wait for the process to work its way.

        I'd definitely call this a triumph for both science and for Science.

        In graduate engineering classes I teach, I like to stretch students' understanding of published works, by having them read recent papers published on a topic of interest. Then we do some fundamental analysis, and more often than not, we find some serious deficiencies. In published works.

        Just because it's published, doesn't mean it's right. But the analysis of some of these works, and finding the errors, may take quite some time. In the end, scientific truth always wins out.

  •  Great story (10+ / 0-)

    Great of you to point out too that where science is exploring wildly new terrain there will be missteps of corse but that the job of science is to then correct them.  That's what happened here.   I wish the general public understood that science isn't about always being right, it is as much about always correcting where we are collectively wrong if that's what the data show.  

    Fabulous !

    Courtesy Kos. Trying to call on the better angels of our nature.

    by Mindful Nature on Tue Jul 10, 2012 at 10:45:16 AM PDT

    •  Thanks. (11+ / 0-)

      I get so disillusioned by many of my colleague's insistence that you have to publish in Science, Nature, or Cell to be important.  Sure, there is a lot of groundbreaking science published in those journals, but there also is a lot of things that are proven to be incorrect (that's ok, that's what science is about, repetition and verification).  Or... things that are completely fabricated because of the "need" to get published in one of those top journals.

      And when journals state they don't want to publish direct contradictions to papers, to me that flies in the face of literally the first thing I ever learned about science way back in freakin' elementary school - that science, to be demonstrated as correct, needs to be repeated and repeated again.  And then repeated some more.

      But the current system is set up to only want novel things all the time, and then no one takes time to verify.

      Meh, no wonder I want to go to industry when I'm finished with my thesis.

      "Give me a lever long enough... and I shall move the world." - Archimedes

      by mconvente on Tue Jul 10, 2012 at 10:54:28 AM PDT

      [ Parent ]

  •  this is how (9+ / 0-)

    it's supposed to work . . . doubt, test, doubt, test, doubt . . .

    The initial paper was perhaps a little lacking in both (doubt and testing) . . . but that's been corrected now.

    Fake Left, Drive Right . . . not my idea of a Democrat . . .

    by Deward Hastings on Tue Jul 10, 2012 at 11:54:49 AM PDT

    •  one more piece of how science should work... (2+ / 0-)
      Recommended by:
      Bisbonian, captainlaser

      if you're making some wild extraordinary claim, and giving PRESS CONFERENCES about it... you better make damn sure you're right.  

      If the original authors had not made such a media firestorm out of this, there would not have been such a dramatic backlash.  

      Also,it didn't help that the bacteria name (GFAJ)  was an acronym for "Get Felicia A Job".  And she told people that.  Bad form, on her part. In many respects.

      "The death penalty is never about the criminal. They've already done their worst. The question is always "will we join them"?" - jlynne

      by Hopeful Skeptic on Tue Jul 10, 2012 at 04:48:43 PM PDT

      [ Parent ]

  •  Good catch. I knew the first paper was wrong. (6+ / 0-)

    It's great that someone put in the energy to prove how wrong it was.

    Is it true? Is it kind? Is it necessary? . . . and respect the dignity of every human being.

    by Wee Mama on Tue Jul 10, 2012 at 03:12:44 PM PDT

  •  Nice piece. (8+ / 0-)

    I was skeptical of the original paper and sort of guessed it would turn out like this, but stranger things have been proven true.  Just because someone is wrong does not mean that science has failed.

    As a matter of fact, this is an excellent illustration of the scientific method in action.  The peer review process and publication of findings in the journals begs others to try to reproduce the results, and this time they could not be reproduced and the actual facts were exposed.

    No one is correct all of the time, and that includes scientists.  Once again, I find this story to be a triumph not for any individual scientist but rather for the scientific method itself.

    Warmest regards,

    Doc

    I would rather die from the acute effects of a broken heart than from the chronic effects of an empty heart. Copyright, Dr. David W. Smith, 2011

    by Translator on Tue Jul 10, 2012 at 04:21:08 PM PDT

  •  I always wondered why no one did the obvious exp.. (3+ / 0-)

    Replace P with 74 As (Beta emitter with half life of about 17 days and basically replay the Hershey-Chase experiments.  But instead of looking at protein with S and DNA with P, just look at the ability of DNA to replicate with radioactive As.

    "In a battle all you need to make you fight is a little hot blood and the knowledge that it's more dangerous to lose than to win". - GBW

    by 8ackgr0und N015e on Tue Jul 10, 2012 at 04:32:24 PM PDT

  •  I was skeptical of the Arsenic-in-DNA claim (2+ / 0-)
    Recommended by:
    Hopeful Skeptic, mconvente

    but didn't have the ability to test that. What I was really offended by in that media blitz was the breathless proposal that the bacteria were a possible “shadow” form of life – one that had evolved early and still maintained its primitive ability to use arsenic. The authors also presented the phylogenetic tree showing that GFAJ-1 was a member of an existing genus, and shared a common ancestor very recently with other members of the genus. I'm linking the Wiki simplified version, but you can scan down this page about 2/3 of the way to see the original. If the bacterium had fit the "evolved early and has persisted in this metabolism" story, either it would branch close to the origin of life (far to the left of the base of the tree in these figures) or all its relatives and progenitors from the earliest life would be expected also to have this capacity. As you can see from the tree, GFAJ-1 is not a separate lineage, and none of its relatives or progenitors is thought to have used Arsenic (or this would not be a surprise finding). So the scientists knew before the media blitz that the "shadow form of life" intimations were BS. I would have been happier if I'd seen them suppress media hyperbole rather than contributing to it.

    "Maybe this is how empires die - their citizens just don't deserve to be world leaders anymore." -Kossack Puddytat, In a Comment 18 Sept 2011

    by pixxer on Tue Jul 10, 2012 at 05:01:39 PM PDT

  •  but wait a minute. That As for PO4 was disputed (0+ / 0-)

    almost immediately. And NASA was never behind it!

    Dastardly, Sir, you misspoke!

    German Constitution, Article 1 (1) The dignity of man is inviolable. To respect and protect it is the duty of all state authority.

    by Mark B on Tue Jul 10, 2012 at 05:32:35 PM PDT

    •  Not in a peer-reviewed publication (2+ / 0-)

      Sure, scientists were posting on blogs about the major flaws of the Wolfe-Simon paper, but this makes it official - two direct contradictions published in the same journal that published the Wolfe-Simon paper over a year ago.

      And NASA was absolutely involved.  They took credit for the findings.

      See this paragraph from the news article posted yesterday:

      All known forms of life depend on at least six elements: hydrogen, carbon, nitrogen, oxygen, phosphorus and sulphur. Arsenic has some chemical similarities with phosphorus, but is usually toxic to life, so the suggestion that it could sustain life triggered a storm of questions, as well as criticism about how the find was revealed at an enthusiastic NASA press conference (see ‘Microbe gets toxic response’).
      Emphasis mine.

      "Give me a lever long enough... and I shall move the world." - Archimedes

      by mconvente on Tue Jul 10, 2012 at 06:12:05 PM PDT

      [ Parent ]

      •  actually, you cited a secondary source. The actual (0+ / 0-)

        news conference wasn't enthusiastic at all, try you tube.

        citing secondary sources is always a bad practice; the primary source was a joke

        German Constitution, Article 1 (1) The dignity of man is inviolable. To respect and protect it is the duty of all state authority.

        by Mark B on Tue Jul 10, 2012 at 09:15:49 PM PDT

        [ Parent ]

  •  Can arsenic be sequestered with this bacteria? (3+ / 0-)
    Recommended by:
    mconvente, cassandracarolina, ybruti

    I remember reading about certain of the Populus genera that did sequester arsenic and some other toxic metals out of groundwater, wondering if this could be another way to clean up bad water.

    Putting on the spectacles of science in expectation of finding an answer to everything looked at signifies inner blindness. -- J(ames) Frank Dobie

    by cactusflinthead on Tue Jul 10, 2012 at 05:47:07 PM PDT

    •  I believe so, yes (2+ / 0-)

      This was commented on by some scientists online at other sites.  The pictures of the GFAJ-1 bacteria strain in the initial Wolfe-Simon paper appear to have enlarged vacuoles, which are known to store Arsenic (among lots of other elements and molecules).

      Some scientists believed that these potentially Arsenic-enriched vacuoles could be the reason behind the authors' findings of Arsenic in organic compounds.  It is plausible considering the bacteria are growing in a high-Arsenic environment.

      "Give me a lever long enough... and I shall move the world." - Archimedes

      by mconvente on Tue Jul 10, 2012 at 06:14:39 PM PDT

      [ Parent ]

      •  Ok going to cabbage on to this thread while (0+ / 0-)

        it is hot or still smoldering at least.
        Let's say we have a body of water. Polluted. An impoundment pond or remnants thereof. We have some readings of the contents, it isnt good. Lots of things like chromium and Mo and arsenic and other nasties. We go chuck a big barrel of this bacteria and plant some saplings of cottonwood and sycamore and/or birch. Let's also postulate that they actually pull out all this bad stuff and 4 years later (or insert time interval here) the water is passing spec for human or animal consumption.
        The question is after this bacteria has sequestered it in their vacuoles and then subsequently drifted to the bottom of the pond as sediment and the trees have sequestered their portion to themselves...what can we do with it to close the cycle or at least make it as least noxious as possible? Or in other words how can we return it to the soil without poisoning it?

        Putting on the spectacles of science in expectation of finding an answer to everything looked at signifies inner blindness. -- J(ames) Frank Dobie

        by cactusflinthead on Wed Jul 11, 2012 at 04:52:56 PM PDT

        [ Parent ]

  •  And yet.... (2+ / 0-)
    Recommended by:
    mconvente, cassandracarolina

    we still have a group that thinks the earth is about 10,000 years old, haha. Imagine them trying to understand this stuff.  For some reason I just thought of how parents have to stop walking then go back and without any discussion grab the hand of the kid and yank him up to the same place as the rest of the family. Thanks for bringing us up to speed.    

  •  Very well done diary, and a great insight into (3+ / 0-)
    Recommended by:
    mconvente, PeterHug, Mike Kahlow

    how science can and should work. Thanks for the work you've put into making a complex topic understandable.

    Some drink deeply from the river of knowledge. Others only gargle. -- Woody Allen

    by cassandracarolina on Tue Jul 10, 2012 at 06:41:25 PM PDT

  •  And the response from the NASA team? (1+ / 0-)
    Recommended by:
    mconvente

    I bet there will be no "We were wrong" press releases from NASA.

    But this is how science is supposed to work.  If you cannot reproduce it, it ain't real.

    And thus the problem with the Higgs Boson.  Who has the $$$$ to reproduce that experiment?

    The Muslim said "I wished I had met Christ before I met the Christians" - Rev. Marvin Winins

    by captainlaser on Tue Jul 10, 2012 at 07:56:13 PM PDT

  •  The possibility of finding life on other planets (1+ / 0-)
    Recommended by:
    mconvente

    just took a slight dip.

    Thanks for reporting that.  I don't understand all of it, but I try to get the gist of things.  It was exciting when the first news came out because of it's implications for life in other extreme locations.

  •  Thanks for writing this (2+ / 0-)
    Recommended by:
    cassandracarolina, mconvente

    And as you say, the mere fact the bacteria can survive in such a "hostile" environment is fascinating.  I am starting to think that there literally is no limit on where life can thrive, as long as their is some form of energy available in the environment, be it photons, radioactivity, heat, whatever, life will find a way.  Amazing.

    -9.00, -5.85
    If only stupidity were painful...

    by Wintermute on Wed Jul 11, 2012 at 04:51:31 AM PDT

  •  Superb work and very clear. Good science. (1+ / 0-)
    Recommended by:
    mconvente

    How can you tell when Rmoney is lying? His lips are moving. Fear is the Mind Killer

    by boophus on Thu Jul 12, 2012 at 09:46:28 PM PDT

  •  Hey thanks for this, it's great, and although (0+ / 0-)

    it's pretty technical, it's well written for a layperson's eyes, and I enjoyed the read as well as the information and your perspective.

    I'm in the middle of some very low level (compared to this!) chemistry and biochem and physics and engineering and a whole bunch of stuff, prepping for an exam, and some of the info was relevant to some of our current study, so that was a bonus :-)

    Don't use Jesus as an excuse to be a greedy, narrow-minded, bigoted asshole.

    by GammaRae on Wed Jul 18, 2012 at 07:47:32 PM PDT

Subscribe or Donate to support Daily Kos.

Click here for the mobile view of the site