Slashdot Mirror
Using Bacterial DNA For Data Storage
NPV writes "January ACM Communications has an article on the use of DNA in genetically modified bacteria to store information. This is an attempt to achieve the ultimate in archival storage (one of the modified bacteria can tolerate 1000X more radiation than a human being). Now just suppose that the "junk DNA" in the human genome is the documentation package for the machine code. Who wrote that manual?" Here's the article abstract.
Just to be clear, no non-coding segments have been found in bacteria yet (last I heard).
My first impluse was that this is way off. I'm used to working with plasmids where frequently like 60% of the sequence is junk. They use E. Coli and D. radiodurans in the study mentioned in the article. A brief survey of E. Coli K12 (the parent of most common lab strains) sez that about 5-10% of it is non-coding. The old initial reference claims about 11% is non-coding, but a good chunk of that may be regulatory. The radiodurans genome is about 9% non-coding. The up shot is that there is actually a fair amount of 'junk-DNA' in (at least the Coli) bacterial genomes. Not a lot by human standards but enough to be able to squeeze in a chunk here or there if you're careful.
Another impulse was 'gad... that made it into Nature!?' (the journal, the article cited is a self congratulatory summary of their Nature paper). A lot of it follows a well duh kind of reasoning. 'Well duh' science is often the really good kind, but I wasn't particularily amazed by this. The DNA manipulation methods are beyond standard now, the only really clever thing was proposing the use of radiodurans as the host. Even that was sort of obvious (a blazingly well studied organism that is transformable). The DNA -> text using a 6 bit space? Well if you've ever designed linker regions in proteins I'm sure you were at least thought about spelling out you name or something in amino acids (unless your name is BOB). In part this is because every one learns the amino acids by doing stupid things like spelling out their name. Few people actually do this, mind you, as it usually would have some deleterious effect, but the point is I'm sure they weren't the first ones to try something like this, probably just the first to get funded to do this explicitly. Their big addition was to come up with a 3-letter code that includes all the letters and, ooo, punctuation. Then they spelled out bits of 'It's a small world.' My point is that it's not that far fetched and a bit surprising (to me) that it made it to Nature.
As to the utility of these things for information carriers... Mutation would be a problem in the long term. Sure radiodurans would survive nuclear war (these guys put cockroaches to shame) but they do it using lots of mismatch repair and recombinatorial repair methods. These are not perfect repair systems, they can and frequently do introduce many errors, especially in non-essential DNA space. Tying it to a functional protein isn't a bad idea, but unless the added sequence adds some survival advantage it won't enhance the lifetime of the measage (ie. if uncorrputed data gives an advantage then it is statistically less likely to propagate). Also, as you mentioned, the bacterium might notice long chunks (they're using 100 characters here) of useless DNA and excise it. For that kind of text, it might be better to just etch it into stone or something, at least you have some hope of seeing it intact in 2000 years.