Ian Holmes is a brilliant bioinformatics hacker at UC Berkeley (and also an active happy mutant in our BB community). A few years ago, I wrote about Ian’s efforts to apply Noam Chomsky’s theories about language to the firehose of genetic data spewing from the multitude of DNA sequencing efforts going on these days. Ian just emailed me about his latest research in the mind-blowing area of “paleogenetics.” He writes:
Thought you might be interested to know that we & our collaborators recently put together a DNA sequence for the earliest mammal genome, 75 million years old.
Sure, it’s full of holes, but it’s the first time anyone’s done it on this scale!
This whole field, known as “paleogenetics”, is really taking off. On the experimental side, you might have heard about the recent sequencing of the Neanderthal and the woolly mammoth.
The cool thing is that you can get a lot of information about ancestral genomes just by crunching probabilities — even if you don’t have any fossils, or mosquitos-trapped-in-amber, or time machines, or whatever.
The even cooler thing (to my bioinformatics-geek mind) is that the algorithms used for this are almost exactly the same ones that linguists use to reconstruct ancient languages, like “Indo-European” or “Gondwanese”.
It’s only a matter of time before we can actually synthesize these paleogenetic reconstructions. A very short time, according to the Carlson Curves (the Moore’s Law of DNA synthesis). Which, of course, has its issues (I am currently trying to reconstruct viruses… no plans to actually synthesize them, I hasten to add…)
Still… I wonder what 75Myr-old mammal meat would taste like? What would be the medicinal properties of ancient herbs? How big were ancient octopi, or spiders? How many genes were in the first bacteria? How long was the first self-replicating RNA sequence?
What would you reconstruct, if you could? Dodo, trilobyte, velociraptor?
