Bacteria not made of arsenic after all
Claims of ‘new biology’ and ET life fall flat
Published: 12 July 2012 (GMT+10)
At the end of 2010, we commented on claims that NASA scientists had found evidence of arsenic-eating bacteria that supposedly supported the idea of ET life (see NASA’s ET suffered arsenic poisoning!) and followed the controversy as it unfolded (see the two postscripts appended to the original article). The whole controversy started with a cryptic press release by NASA that said this:
“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 [emphasis added].”
The mere mention of ‘ET’ set the media and the blogosphere ablaze with speculation. It had some more radical commentators prognosticating that NASA was going to produce a live ET, or some other such nonsense. The find was much more prosaic than this, but was still very significant for our understanding of biology on Earth if true. Research was published in Science that announced evidence of the discovery of the first life we knew of that incorporated Arsenic (As) into its biomolecules, including its DNA.1
Arsenic is a close chemical analogue of phosphorus (P), and this research was presented as evidence that an organism was able to replace P with As in its biochemical structure. Phosphorus is essential for numerous biomolecules, including essential ones like DNA, RNA, and ATP (adenosine triphosphate), and the substitution of such an essential and ubiquitous nutrient was completely unheard of. Arsenic is certainly not identical to phosphorus,2 and is better known as a poison.
However, upon hearing the news the blogosphere was again set abuzz. However, this time it was not by radical speculations about ET, but by numerous highly qualified scientists slamming the work as bad science. The researchers defended their work, and basically said: “The blogosphere is not the place for scientific debate—let our detractors refute us in the scientific literature.” While this was rather disingenuous given the way the news was revealed, scientists took up the challenge. Two research papers from independent teams seeking to confirm the original claims have just recently been published—again by Science.3,4 It looks like the skepticism this claim was met with was justified—the results are not pretty for the idea that these bacteria (called GFAJ-1) incorporate As into their biomolecules.
What was wrong with the original claim?
The research teams identified numerous problems with Wolfe-Simon et al.’s1 claims. One problem identified by both Reaves et al.3 and Erb et al.4 was that numerous tests failed to find any detectable As in the DNA of GFAJ-1 regardless of As or P concentrations. Both studies found that no As was found in the structure of the DNA of GFAJ-1 when analysed by mass spectrometry,5 and the DNA didn’t behave in water outside of the cell as would be expected if it contained As in its structure.
Moreover, As was not found in any molecules linked to metabolism in GFAJ-1 regardless of As concentration, but P was always found. This was confirmed by the fact that when the P levels were too low for growth, even high As concentrations didn’t enable growth, which directly contradicts Wolfe-Simon et al.’s claims. Some potential As ‘metabolites’ were found in low concentrations, but Erb et al. concluded that they were due to abiotic reactions and only a negligible amount might have been due to biotic reactions—certainly not enough to significantly impact either core or secondary metabolism in GFAJ-1.
Perhaps the most overtly damning result of both studies for the original research is that they were both able to grow GFAJ-1 on concentrations of P lower than the “–P” trials of Wolfe-Simon et al. even at high As concentrations. This not only suggests that As has nothing to do with the growth of GFAJ-1, but it also suggests that the methodology of Wolfe-Simon et al. was sloppy. If the so-called “–P” trials had enough residual P in them to facilitate growth of GFAJ-1 regardless of the As concentration, then there is no evidence that As actually contributes to the growth of GFAJ-1, and Wolfe-Simon et al. failed to purify their trials well enough to demonstrate what they purported to demonstrate.
It is interesting that this was exactly what one of the original scientific skeptics of the claims with relevant expertise to comment, Dr Alex Bradley, predicted would happen. Dr Bradley’s whole blog comment is eerily predictive of most of what both research teams did, and the results they got—and he was not involved with either research paper. For those interested in the original research, I recommend reading Dr Bradley’s comments alongside the current research—it’s an instructive look at science at its predictive best.
With the original claims basically invalidated, the onus is now on the proponents of the ‘As-eating bacteria’ claims to put forward some proper evidence.
Proponents of As-eating bacteria respond?
Not surprisingly, the proponents of the original claims have not been silent in response. Lead researcher of the original claims Felisa Wolfe-Simon intimated that she and others are seeking to publish new data in support of their original interpretation in the future.6 It will be interesting to see if they can successfully address the criticisms levelled at the original claims. But she also made this rather bizarre comment:
“The original GFAJ-1 paper emphasized tolerance to arsenic, but suggested the cells required phosphorus, as seen in these two new papers. However, our data implied that a very small amount of arsenate may be incorporated into cells and biomolecules helping cells to survive in environments of high arsenate and very low phosphate. Such low amounts of arsenic incorporation may be challenging to find and unstable once cells are opened [emphasis added].”7
There are a number of excuses offered in this statement, despite the fact that there were numerous ways in which these present studies were much more careful in their methods than her own. However, one aspect of this statement left me completely bewildered. Her article “emphasized” As tolerance and only “suggested” the replacement of P with As? I have to say that if this is true, then everything I’ve heard or read on this controversy—including her original research article—has profoundly misrepresented her intended point. The very title of her original paper explicitly contradicts what she says: “A bacterium that can grow by using arsenic instead of phosphorus”.1 The emphasis is clearly on As replacing P as an essential part of biomolecular structure, not As tolerance. She has blatantly contradicted herself and everyone else who has ever written on this controversy.
The title of one science news article deserves special comment. The LiveScience.com article is titled “Arsenic-munching bacteria doubted, but still alien-like”.7 It is the only article I have come across on this latest research to mention ET life. The recent research completely crushed the original claims, and the text of the article doesn’t mention anything about ETs. The closest the article comes is at the end, where the writer and one of the researchers say that GFAJ-1 is a “remarkable” organism given its extreme As tolerance. And this is true, but what’s that got to do with ET life? Life is an amazing phenomenon, but that doesn’t mean ETs exist! It just goes to show that some still want to use this whole controversy to promote the ET agenda. The fact is, however, even I was aware of numerous As-tolerant microbes and plants nearly 10 years ago as an undergraduate environmental science student—and they are all most definitely earthly organisms. There’s nothing new or ET about As-tolerant microbes, which now appears to include GFAJ-1. They are just another type of extremophile (see Life at the extremes).
A publicity stunt gone bad
This was a publicity stunt from the beginning promoting the ET/evolutionary worldview, and it backfired almost immediately. Microbiologist Rosemary Redfield of the University of British Columbia, and co-author of ref. 3, was among the first outspoken critics of the initial study, with a scathing blog comment:
“I don’t know whether the authors are just bad scientists or whether they’re unscrupulously pushing NASA’s ‘There’s life in outer space!’ agenda.”8
And now we’ve got two independent studies presenting strong support that it should have backfired from the beginning. Even if some organisms, even GFAJ-1, can incorporate As as a replacement for P into their biomolecules, there is at present no evidence supporting the claim—and such a claim wouldn’t even be antithetical to biblical creation. But all the evidence put forward to date has been invalidated. So now it’s time for the proponents to provide new evidence—if they can. These two research papers are examples of how science should work—it’s just a shame that good science almost invariably only gets the spotlight whenever bad science gets the spotlight first.
- Wolfe-Simon, F. et al., A bacterium that can grow by using arsenic instead of phosphorus, Science 332:1163–1166, 2 December 2010. Return to text.
- Arsenic is larger, and its V oxidation state—the state of phosphorus in most biochemicals—is less stable, easily reduced to III. Return to text.
- Reaves, M.L. et al., Absence of detectable arsenate in DNA from arsenate-grown GFAJ-1 cells, Science (DOI:10.1126/science.1219861), Published online 8 July 2012. Return to text.
- Erb, T.J. et al., GFAJ-1 is an arsenate-resistant, phosphate-dependent organism, Science (DOI: 10.1126/science.1218455), Published Online 8 July 2012. Return to text.
- See www.magnet.fsu.edu/education/tutorials/magnetminute/spectrometer.html for a helpful definition of a mass spectrometer. Return to text.
- Kaufman, M., Journal retreats from controversial arsenic paper, Washington Post, www.washingtonpost.com/national/health-science/journal-retreats-from-controversial-arsenic-paper/2012/07/08/gJQAFQb7WW_story.html, as at 10 July 2012. She made this statement with Dr John Tainer. Return to text.
- Emspak, J., Arsenic-munching bacteria doubted, but still alien-like, LiveScience, www.livescience.com/21484-arsenic-bacteria-alien-like.html, 9 July 2012. Return to text.
- Redfield, R., cited in: Scientists disprove arsenic life form claim, ABC News, abc.net.au, 9 July 2012. Return to text.