Friday, June 24, 2011

DNA Replication In Silico

"Did you get that new Anti Virus Software?"
"For my computer?"
"No for your gene sequencer!"

So I read an interesting post on an MIT blog about Mycoplasma contaminating "the human genome." I think its a bit of a stretch, but in fact it looks like bacterial DNA has corrupted what we call the "human genome." Literally bacterial DNA has slipped in via contaminated cell cultures. Now when we test gene expression from a human sample, it appears we are also frequently checking for mycoplasma genes as well.

How does this happen? The article mentions another study that indicates a large amount of human cell contamination in samples from other species that we have sequenced. This is no surprise as biologists ARE human (right?). But this means we are slowly corrupting the data that we use to compare other species for similarity using tools like BLAST and other methodologies. On the flip side viruses and mycoplasma which are VERY small, hard to detect, and hard to filter are all over the place, and easily contaminate and multiply with laboratory samples.

So in a sense there is "replicating" DNA propagating through gene chips, sequencing tools, and our knowledge, though it doesn't QUITE meet our definition of a living organism, much like viruses and prions they are replicating simply one way or another. What's really scary is that once we start working gene therapy by for example splicing DNA into a retrovirus, which then starts re-writing our DNA with synthesized strings we could complete the loop.

This will be just another example of horizontal gene transfer. For all eternity we have had ways of exchanging DNA without literally being related, or through a myriad of epigenetic ways, by viruses which infect us by splicing their genetic material into OUR DNA and using the cellular apparatus to reproduce, occasionally leaving pieces behind, or taking a piece of our code along to the next host. This has occurred NOT just between humans, but humans and animals, plants, and other organisms some as close as the bacteria that live symbiotically in our gut.

Soon the list of things we exchange genetic code with will not just contain carbon based plants, animals, bacteria, and fungi, but carbon based silicon chips and information networks. We could have a bit error in an encoded DNA strand, or a virus that re-writes a character. Imagine a future where machines can directly affect our bodies through a myriad of ways.

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