Halomonadaceae

Halomonadaceae are a family of proteobacteria. In December 2010, it was announced that NASA-funded research led by Felisa Wolfe-Simon had discovered a strain of this bacteria that could process arsenic rather than phosphorus as a metabolite.

This species was found in Mono Lake, California, which is unusual because of its extreme conditions, including its alkalinity and high arsenic content. When the GFAJ-1 strain of the halomonadaceae bacteria were cultured on arsenic containing compounds, as opposed to phosphorus compounds, the bacteria still survived (although not terribly well) and seemed to even go as far as including arsenic in its DNA. This was following a 2008 discovery that the Mono Lake bacteria could metabolise arsenic, but the 2010 research was the first to "force feed" the bacteria until they began incorporating the toxic element to such a degree.

Phosphorus and arsenic chemistry
Phosphorus is one of the atoms frequently found in the molecules that compose living creatures. Adenosine triphosphate (ATP) is used to generate energy inside cells and phosphate groups are a key component of DNA. Arsenic is in the same group as phosphorus so, in principle, exhibits similar chemical properties such as forming three bonds in a similar fashion to nitrogen, which is on the row above phosphorus. However, the chemical nature of elements in the same group isn't completely identical; silicon and carbon are also very notable for this. Because of the subtle changes in the chemistry of these elements, arsenic is a powerful toxin towards most life because of its ability to mimic phosphorus but not quite well enough.

Implications for evolution
The ability for the bacteria to survive in regions of high arsenic concentration is a clear evolutionary step. Its resistance to the usual mechanisms by which the element is toxic and to incorporate it is an extreme adaptation, although following from extreme selection pressures.

Intelligent design advocates have jumped to the opposite conclusion, seemingly thinking that such a discovery disproves evolution, based on the erroneous idea that discoveries that expand scientific knowledge are actually destroying it or somehow falsify what came before.

Implications for exobiology
Being funded by NASA, the immediate press release was related to the search for extraterrestrial life. Specifically, the ability for life to use a chemical element in this way expands the range of biochemical reactions that are known to support life. Hypotheses and conjectures about different chemistry leading to life are common, but the case of Halomonadaceae GFAJ-1 is a demonstrated example. News of this study was released only a few days after another study suggested that the number of stars in the universe may be far higher than originally thought and that the universe may have a cyclic nature that extends before the Big Bang.

Early rumours seemed to confuse the find with the concept of a second genesis. Although arsenic-containing DNA is pretty exotic, it's clear that the GFAJ-1 strain is still solidly related to life "as we know it."

Criticisms
Importantly, the paper published in Science does not contain direct evidence of arsenic incorporation into the DNA molecule. One example would be the X-ray diffraction structure (the same thing that shows the helical structure of DNA, as was done famously by Rosalind Franklin). Because X-Ray diffraction works by measuring electron density in a molecule, it would show the heavier, and more electron rich arsenic atoms quite readily.The change in the biochemistry of DNA upon substituting phosphorous for arsenic would be considerable. Biological interactions between the DNA and gene expression mechanisms would fundamentally change. The techniques used to extract and analyse the DNA would also be affected.

Several analytical flaws have been pointed out in the paper. The Science paper also lacked some of the rigour required to prove what was claimed in the NASA press release. The researchers didn't seem to report whether the trace phosphorus in their growth mediums could explain the observed growth - if so, this would mean that while the bacteria were resistant to arsenic poisoning, they weren't quite metabolising it in the way claimed. Their labeling methods for testing for arsenic incorporation are also highly prone to contamination, and as such may not offer the conclusive evidence needed to support "arsenic DNA."

These flaws may have been highlighted in peer review of the submitted paper, hence the cautious tone of the actual Science article. However, this caution and uncertainty was not reflected in NASA's press release of the finding. Almost six months after the original publication, Science published a number of peer-reviewed "Technical Comments" criticizing the shortcomings of the finding. It emerged that the designation GFAJ actually stood for 'Get Felisa a Job.'