Dec 06 2010

Alternate Biochemistry

NASA has announced the discovery of a strain of bacteria that is not only able to live in an extreme environment loaded with the toxin arsenic, but is able to incorporate arsenic into its basic structure. The research is part of NASA astrobiology project – exploring the limits of life in order to infer the possible environments beyond earth in which life might exist.

Researchers were investigating bacteria in the harsh environment of Mono Lake – which has been without a supply of fresh water for 50 years and is loaded with arsenic. The discovery of so-called extremophiles – bacteria that have adapted to extreme environments – is nothing new. Bacteria are amazingly adaptable forms of life and have been found in very hot as well as cold environments, and in environments under high pressure and with high salinity. The ability to tolerate the presence of a toxin is interesting, but also not surprising given what has already been discovered about extremophiles.

What is entirely new with this discovery, however, is the fact that these bacteria, a strain (GFAJ-1) of a common type of bacteria called Gammaproteobacteria, appear to incorporate arsenic into their own biochemistry. In normal living cells phosphorous is used as part of the DNA and RNA backbone, in addition to being the energy transporting molecule (adenosine triphosphate), and being part of structural phospholipids. Arsenic is chemically similar to phosphate, and in fact that is partly the reason for its toxicity – it is very disruptive to normal biochemistry. These bacteria seem to have replaced phosphate with arsenic in some of these structures and molecules.

This is an important proof of concept – an alternate biochemistry in which arsenic replaces phosphate is possible.

This raises several interesting points. The one that NASA is primarily interested in is exobiology – life outside of earth. As the number of possible environments in which life can exist expands, so does the probable density of life in the universe and the chance that we will discover such life. The most common alternate biochemisty that I hear (whether in science fiction or speculation) is one in which silicon replaces carbon. Methane-breathers (using methane instead of oxygen for metabolism) is also common. Swapping arsenic for phosphorous now has to be added to the list.

Another interesting point is that “alien” life may exist on earth. So far, all life on earth that we have examined is biochemically similar and is clearly related – the result of one origin of life and subsequent evolution. But there is no reason why there cannot be multiple trunks to the tree of life on earth. Life may have arisen, or been seeded, multiple times. Clearly one origin now dominates, and may be exclusive, but there may be bacteria-like organisms on earth that are the remnants of other origins. Or, they may share a common origin with known life, but have branched off so much earlier than any known life that their biochemistry (even their DNA code) can be vastly different than anything known.

There are many thousands of species of bacteria that we have not yet fully investigated, so this possibility cannot be ruled out. We can conclude that if such a so-called shadow biome exists it must be rare, or else by chance alone we would have encountered it by now.

It can be argued that the discovery of extremophiles, especially this latest discovery, makes the discovery of “alien” bacteria on earth more unlikely because even in extreme environments bacteria that is related to the rest of life have pushed their way in. Perhaps the life that we know was so successful that it managed to invade every possible niche, crowding out any competitors.

Perhaps we will have to look beyond earth to discover the descendants of a truly independent origin for life. Such exploration is underway on Mars, and there are other candidates in our solar system, such as the moons Europa, Titan, and Enceladus. The primary way that we look for microbial life in such locations is by looking for the signs of biochemistry. This is precisely why NASA is interested in this research – they have to know what kinds of biochemistry to look for. This research may partly determine the kinds of experiments that future NASA probes will use to search for the signs of exobiology.

Update: There has been significant criticism of the original Science paper. The harshest I have seen so far is from Rosie Redfield, who not only criticized the interpretation of the results but some core methods, such as the lack of DNA purification. She plans on submitting a paper to the journal. This will be worked out in the peer-reviewed literature, but that will take months at least. Meanwhile it seems that the results should be taken with a huge grain of salt.

Interestingly, NASA retreated to the position that they do not feel they should respond to criticism in blogs – this should be discussed in the journals. In my opinion, this is disingenuous as they made big fanfare about their press conference. NASA appears to want to make a big splash in the public arena, then hide from public debate about the research. Suck it up, NASA – you can’t have it both ways.

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