Halomonadaceae

[[File:GFAJ-1 (grown on phosphorus).jpg|thumb|165px|Looks like rice, right?]]{{biology}}
'''Halomonadaceae''' are a family of proteobacteria (a.k.a., proteobacteria). In December 2010, it was announced that [[NASA]]-funded research led by Felisa Wolfe-Simon<ref>Known as 'Iron Lisa'</ref> had discovered a strain of this [[bacteria]] that could process [[arsenic]] rather than phosphorus as a [[Metabolism|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]].<ref>[http://www.sciencemag.org/content/early/2010/12/01/science.1197258 Wolfe-Simon et. al. ''Science'' 2010]</ref><ref>[http://www.bbc.co.uk/news/science-environment-11886943 Arsenic-loving bacteria may help in hunt for alien life], BBC News</ref> This was following a 2008 discovery that the Mono Lake bacteria could metabolise arsenic,<ref>[http://news.bbc.co.uk/1/hi/sci/tech/7558448.stm BBC News -Arsenic-munching bacteria found]</ref> 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 [[atom]]s frequently found in the [[molecule]]s that compose living creatures. Adenosine triphosphate (ATP) is used to generate [[energy]] inside [[cell theory|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 [[evolution]]ary 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 [[Bullshit|erroneous idea]] that discoveries that expand [[scientific]] knowledge are actually destroying it or somehow [[falsifiability|falsify]] what came before.<ref>[http://darwins-god.blogspot.com/2010/12/arsenic-based-biochemistry-turning.html Arsenic-Based Biochemistry: Turning Poison Into Wine], ''Darwin's God'' blog</ref>

==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 [[Drake equation|number of stars]] in the [[universe]] may be far higher than originally thought<ref>[http://www.bbc.co.uk/news/science-environment-11888362 'Trillions' of Earths orbit red stars in older galaxies], BBC News</ref> and that the universe may have a cyclic nature that extends before the [[Big Bang]].<ref>[http://www.bbc.co.uk/news/science-environment-11837869 Cosmos may show echoes of events before Big Bang], BBC News</ref>

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."<ref>[http://gizmodo.com/5704158/nasa-finds-new-life NASA finds new life], Gizmodo</ref>

==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."<ref>[http://rrresearch.blogspot.com/2010/12/arsenic-associated-bacteria-nasas.html Arsenic associated bacteria], ''RRResarch'' blog</ref>

These flaws may have been highlighted in [[peer review]] of the submitted paper, hence the cautious tone of the actual ''Science'' article.<ref>[http://www.sciencemag.org/content/330/6009/1302.summary ''Science'' - What Poison? Bacterium Uses Arsenic to Build DNA and Other Molecules]</ref> 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.<ref>http://www.sciencemag.org/content/early/2011/05/26/science.1208877</ref> It emerged that the designation GFAJ actually stood for 'Get Felisa a Job.'{{fact}}

==See also==
*[[Richard Lenski]]

==References==
{{reflist|2}}

[[Category:Biochemistry]]
[[Category:Organisms]]

Categories: Biochemistry, Organisms