Friday, December 3, 2010

Don't Call It a Comeback

I've been here all month, but finally got motivated to write some stuff down regarding NASA's announcement today: NASA-Funded Research Discovers Life Built With Toxic Chemical. Here is an excerpt:

"NASA-funded astrobiology research has changed the fundamental knowledge about what comprises all known life on Earth.

Researchers conducting tests in the harsh environment of Mono Lake in California have discovered the first known microorganism on Earth able to thrive and reproduce using the toxic chemical arsenic. The microorganism substitutes arsenic for phosphorus in its cell components."

The rest of the writing in the NASA press release is similarly giddy. You might think from skimming the information out there that these researchers found an organism that uses arsenic preferentially, or in the environment, but that is not the case.  The cells were isolated from mud samples collected from Mono Lake, then grown in media with low amounts of phosphorus and high amounts of arsenic. These cells, named strain GFAJ-1, were able to grow in these media despite arsenic's usual toxicity. They do not use arsenic in their natural environment, nor is it accurate to call them an "arsenic-based life form".

Today I read the paper behind this research, published online today in ScienceXpress. (You won't be able to read that unless you have institutional or other access to Science.) I have some questions regarding the results.

  1. Was this testing conducted on other species? NASA is touting this discovery as a whole new type of life. I would be more likely to accept that idea if the researchers had shown that other bacteria did not survive this treatment. According to the phylogenetic tree constructed in the supplementary materials, Escherchia coli is this bacterium's closest relative. More experiments should be conducted to determine E. coli and other common laboratory strains' fitness in this media.
  2. As the cells grow and divide, they should incorporate more and more arsenic into their biomolecules, depleting the phosphorus available in the media and that which was already present in the mother cells. Is there a threshold level of arsenic at which cells can no longer survive? Could they completely replace all phosphorus with arsenic? That hasn't been shown. The data in the paper only shows growth up to 20 days; is there a point at which cells start to die? New Scientist quotes Paul Davies of Arizona State University as saying, "After one year, they are still alive and well"; however, there is no published data to support that, so it could mean anything.
  3. In the paper, cells grown on arsenic-rich medium had a higher dry weight of arsenic that cells grown on phosphorus-rich medium. Similarly, +As/-P cells had a lower dry weight of phosphorus than -As/+P cells; however, even the cells grown on medium with phosphorus had a dry weight of phosphorus (0.54±0.21%) lower than the 1-3% normally needed by bacteria. I can think of two possible explanations: 1) the data is incorrect; 2) this strain typically uses less phosphorus than the average bacteria. I would like to see similar data gathered when the strain is grown on other rich media.
I think that the possibilities created by these findings are fascinating, but as so often happens with science journalism, they have been blown way out of proportion in the media. Far more research is needed before this organism will be accepted as a "parallel form of life".


    1. 1) Very pertinent, this is essentially experimental science and needs to be reproduced, with a large variety of variables. Also I must say, being essentially a layman -- interested though I may be -- that paragraph had a lot of information that was not in any of the articles I'd read today so -- thanks and props.

      2) OK, again, I certainly have not read as in depth as you apparently have but the impression I received was the As only replaced the P in the DNA (or equivalent there of). E. Coli is certainly a highly complex system, so again the point is well taken, just would like to hear your take on exactly what the paper is claiming (re other cellular structures). Though certainly as you point out "After one year, they are still alive and well" needs substantiation, again with ability for other labs to reproduce the results.

      3) ...OK kinda over my head ;-p, however as per point 1) -- yes, essentially the results need to be able to be reproduced with consistency, in addition contamination needs to be ruled out -- of course very difficult given the subject. As for 2) again I didn't comb the paper but that makes a lot of sense, perhaps as far as setting up a control for further testing.

      As you point out: extremely interesting, and I think that's the main import of the findings -- not that "omg aliens on earth!!!" or anything like that, but taking, to put it simply, that DNA -- what we heretofore regarded, along with liquid H20 for instance, as essential to life, simply because we knew nothing else -- and proving that there is indeed an alternative.

      In any event this will surely produce mounds of research, etc in the years to come -- wicked stuff =D