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Please begin with an informative title:

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.

Intro

You must enter an Intro for your Diary Entry between 300 and 1150 characters long (that's approximately 50-175 words without any html or formatting markup).

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.

Extended (Optional)

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.

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