NASA's Arsenic-Loving Bacteria Don't Love Arsenic After All, Critics Say

NASA: Ahhh..... Oops! my bad

-=SisaR=-

"Ideally, all this should have been resolved in the peer-review process — journal referees should have raised these questions before accepting the paper for publication. "

Peer-review is just group think anymore. You agree with the party lines your 'science' doesn't really need to be examined that well.

Oh, and don't bother publishing if you don't agree with the party.

"In a press conference last week, Wolfe-Simon said the bacteria, known as GFAJ-1, can switch from phosphorus to usually-toxic arsenic in its biomolecules. She said the switch was so complete that GFAJ-1 incorporated arsenic into its DNA. As we pointed out last week, this behavior was not natural — the scientists fed the bacteria an arsenic-rich diet and removed most of the phosphorus."

Well, even if the scientists forced them to eat the arsenic(in a sense). the fact that the bacteria can make use of arsenic(whether forced to or otherwise) is still interesting. It shows how tenacious and strong even the most simple life forms can be.

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 µM 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 precludes it from effectively replacing protein phosphorylation. Protein phosphorylation appears to be the major post-translational regulatory mechanism for the emergence of eukaryotic organisms and seems to be required for the development of multi-cellular organisms.

While the existence of stable ATAs is doubtful, it is more feasible that adenosine-diphosphate, mono-arsenate (ADPAs) might be produced that could fuel arsenylation reactions. Even if ADPAs exists, it is still difficult to reconcile the use of arsenate by a wide range of enzymes to replace all of the diverse metabolic and structural roles (e.g. nucleic acids, phospholipids, phosphoproteins) of phosphate in even bacteria. It is unlikely ADPAs would have a stable enough high energy bond between the gamma arsenic and oxygen atoms to serve as an efficient source of chemical energy. ATP is optimal in all biological systems on this planet with an intermediary position between the higher energy compounds from which ATP accepts phosphate and the lower-energy compounds from which it donates phosphate. Consequently, an organism that exclusively utilizes arsenic and not phosphorus would have a profoundly different metabolism with very different metabolites and macromolecules.

As a member of the wide-spread Gammaproteobacteria, the Halomondadaceae bacteria clearly do not represent an alternatively evolved family of life-forms, but are well adapted to endure extreme conditions. These organisms are also commonly dispersed in environments in which “normal” microbes proliferate, which is most probably where they originated. The GFAJ-1 bacteria actually prospered better in the presence of phosphorus. Those grown in the presence of arsenic and near absence of phosphorus became bloated in size by approximately 60%. This was due to the appearance of large “empty” vacuoles in the bacteria. It seems that this organism functions optimally in phosphorus, but tolerates arsenic. This is not surprising, since the concentration of phosphorus in the Earth’s crust is around 1000 parts per million (ppm), which is about 500-times higher than measured for arsenic. Such a relative distribution of these two elements is likely to be universal, as more energy is required to forge arsenic atoms than phosphorus atoms.

Many metals can poorly mimic each other as cofactors in enzyme-catalyzed reactions. This is why a few are highly toxic such as lead and mercury. The fidelity of enzymes for their optimal elements is not 100%, so it is not surprising if trace arsenic can replace phosphorus in the structures of small molecules and macromolecules. Many marine organisms, including clams and sea weeds can also accumulate arsenic. This is likely to be a protective response to reduce the threat of predation by animals that might try to consume them. Arsenic is particularly toxic in eukaryotic organisms, because amongst other many other problems, arsenic inhibits pyruvate dehydrogenase in the citric acid cycle and it uncouples oxidative phosphorylation in the mitochondria, both of which inhibit ATP synthesis. It seems probable that the Halomonadaceae bacteria have acquired the ability to tolerate arsenic, most likely to avoid being eaten. They may concentrate arsenic-containing compounds in vacuoles for this purpose, and they are known to excrete arsenic, presumably when it becomes too toxic for the bacteria themselves. This ability provides the opportunity for these bacteria to thrive in arsenic-rich environments where most other bacteria cannot.

The lessons from all of this hype from a US government agency, a peer-reviewed scientific journal, and the popular press will likely go unheeded. Unfortunately, too many research institutions that depend on public funding through government agencies and charity will continue to feel pressured to over blow their latest scientific breakthroughs to justify the massive amounts of financial support that they have received. However, with the increasing ability of the wider scientific community to rapidly challenge these assertions in the Internet age, they do so at the peril of their credibility.

@NASA ಠ_ಠ

@S.Pelech-Kinexus That is the longest comment I've ever seen. Its a research article unto itself.

www.geekness.webs.com

I got a crazy idea: SOMEONE REAPEAT THE EXPEREMENT

Lets use the Scientific Method not blogs

congrats to S.Pelech-Kinexus, he can create an account simply to copy/paste his retort from one website to another, I bet his mother must be proud. ...perhaps I'll read it more fully when I don't have other things to do today.

Penzor - I completely agree. If they had taken the time to repeat their experiments under more strictly controlled conditions & under the assumption that their findings would have been picked apart by hundreds of thousands of people, they might have been a little more successful with convincing people of the results for more than just a day or so..

NASA I'm sure is feeling pressured, and they have been under extreme pressure for many years now. I have hope someone out there will understand how important they are to the continuation of the human race & relieve them of some of that pressure (directly, or indirectly) by either helping them, or eliminating them of their duties to compete in certain specific areas.
go NASA, and go private aerospace...you are our future.

The evidence/findings are shady, and controversial.. they will always be ridiculed as such (of course), the fact remains that these microbes THRIVE on arsenic, and that is quite strange. All we can do now (as usual) is wait and see what other tests/results will show us.

Arsenic, an element, 'breaks down' in water?
breaks down into what components? all this time we thought it took so much science to split an atom, and all we had to do was add water to Arsenic!
/sarcasm
/troll

A side note the peer review process is under review. It seems that the peers that are reviewing are taking the information found that relates to their own experiments and turning it down while using the information to further their own studies.

Peer review is dieing because there are to many dishonest reviewers.

everyone makes mistakes,if NASA did actually mess up it is good to see how easily it can come to light, this is good, no conspiracy

Redfields scientific credentials are under investigation due to her failing to disclose 'conflict of interests' so I wouldn't be citing her if you want to be taken seriously.

@ironjustice: Really? Could you post the source of this information?

@ironjustice: I've now looked at some of your other comments. I see that you think that being an atheist is a conflict of interest for doing science. That is, you think that, if someone doesn't believe in a god or gods, we shouldn't trust their science, I guess because science tends to support atheism.

Perhaps you're the only person who's investigating me.

If arsenic does break down in water, that's an even bigger story - cold fission.

Bob Stuart

Quote: I see that you think that being an atheist is a conflict of interest for doing science
Answer: You are fully aware WHAT the 'problem' with your failure to declare your conflict of interests when attempting to sway the opinion of medical journals.
You are an ACTIVIST atheist. You fail to explain that when you comment on religious articles WHEN specifically asked.
THAT means you are a little MORE than a conflict of interest kind of gal aren't ya. It means you might even be considered a liar. THAT is the problem I have with atheists. Low morals and lying do not bode well for Science based investigations. Imho.

Quote: If arsenic does break down in water, that's an even bigger story - cold fission.
Answer: It means it isn't PURE when they tell us it is. It probably has unrecognized debris accompanyiing it. Probably breaks down to iron. Arsenic and iron are found TOGETHER. IF there is a bacteria growing on the arsenic it is probably the unrecognized iron found there allowing it to grow. Same with 'phosphorous growing' bacteria. Phosphate and iron and found together. Sorta like quartz and iron.Imho.

Quote: If arsenic does break down in water, that's an even bigger story - cold fission.

"Under alkaline conditions, the arsenic forms sulfarsenite ions that may combine with heavy metals to form insoluable compounds. If colloidal ferric hydroxide is present much of the arsenic (both arsenate and arsenite) would be adsorbed. The presence of iron in the water could also lead to the coprecipitation of the arsenc along with the iron sulfides (Hounslow, 1980). Adsorption of arsenic is proportional to initial iron concentration of water."

The very title of this article is asinine and inaccurate. Regardless of what you think about the case that the bacteria incorporate As into their DNA (the biggest contention among critics) the bacteria were shown to grow well in the presence of very high As concentrations (40 mM) and they required either this extra As or extra P in order to grow. So "Arsenic Loving Bacteria don't love Arsenic After All"?? Come on Popular Science, people look to you for at least a slightly more scientific treatment of these stories than they get from the knuckleheads in their local newspaper.

Did ironjustice just said religious people have higher morals? Is he suggesting that criminals have lower morals? OMG, did he just call me a liar?