Monday, July 25, 2016

Carl Zimmer's series on exploring his genome

If you haven't yet read Carl Zimmer's series of articles (one, two, three), you should go out and read it now!

Because after all, it's Carl Zimmer, one of the best science writers around, especially when it comes to biology.

But even more so because when you read the story of his personal quest to understand his genetic story in all its multifaceted glory, you understand the terrifying opportunities and dangers in the use of genetic information for predictive and diagnostic medicine. You also realize the intricate way that computation is woven into this discovery, and how sequences of seemingly arbitrary choices lead to actual conclusions about your genome that you now have to evaluate for risk and likelihood.

In a sense, this is the tale of the use of all computational approaches right now, whether it be in science, engineering, the social sciences, or yes, even algorithmic fairness. Zimmer uses the analogy with telescopes to describe his attempts to look at his genome, and this explanation is right on the money:
Early telescopes weren’t terribly accurate, either, and yet they still allowed astronomers to discover new planets, galaxies, and even the expansion of the universe. But if your life depended on your telescope — if, for example, you wanted to spot every asteroid heading straight for Earth — that kind of fuzziness wouldn’t be acceptable.
And this quote from Robert Green, one of the geneticists who was helping Zimmer map out his genome:
Ultimately, the more you know, the more frustrating an exercise it is. What seemed to be so technologically clear and deterministic, you realize is going through a variety of filters — some of which are judgments, some of which are flawed databases, some of which are assumptions about frequencies, to get to a best guess.
 In this is a message for all of us doing any kind of data mining.

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