Portable DNA Sequencer: Cool But Not Really Thought Out

On the theme of “democratizing science” and DIY sensing, Emily Waltz writes for IEEE Spectrum about a “Portable DNA Sequencer”.

MinION is a really cool technology, based on nanopore sensing, which enables low cost, high speed sequencing of DNA, RNA, and proteins. A boon to professional labs, it is being brought to market for widespread use by “everyone”, who can sequence their food, environmental or medical samples, and their own DNA. (As Waltz remarks, this latter possibility is “a dream for the most serious self-quantifiers.“

“Our goal: to enable the analysis of any living thing, by any person, in any environment”

This Is definitely the real thing: they are working out the whole workflow, including analysis and matching to identify samples, e.g., of common microorganisms.

Above all, I was impressed with their development (coming Real Soon Now) of the “VolTRAX: Rapid, programmable, portable, disposable sample processor” and other sample preparation kits.   This is a key piece of the whole process: “garbage in, garbage out” certainly applies to DNA analysis, and the better the measurement, the more sensitive it is to noise and junk in the input.

This is certainly cool technology, and there are abundant brilliant applications.

But…

I’m a bit concerned about their expansive vision of DNA sensors “everywhere”, connected to the Internet. As Waltz reports, they imagine an “Internet of Living Things”, where everyone “will be reading the DNA of their own bodies and the living things around them, and streaming that data on the internet.” On the Internet? What could possibly go wrong?

I note that this device may or may not be “democratic”, but it is definitely not “open” science. You have to use their proprietary software to analyze the data, and the system streams the data to their proprietary “cloud”. This is OK for professional labs, which use commercial tools, provided that there are sufficient open publications demonstrating the validity of the instrument.

But for the general public, I have to wonder if this is a good model. Do you really want your personal DNA sequences controlled by a private company within its proprietary software, out there in “the cloud”?

Unfortunately, the company has thought about the potential issues, but seems to be in a rush to make money regardless of any consequences, by pushing rapidly to sell to the general public. Nanopore’s chief tech officer, Clive Brown  commented “If you get million of people collecting data and thousands of people looking at it, you’ll figure it out as you go,”

Eeek! Are you serious? This is your plan for a beneficent “Internet of Living Things”? Just do it, and see what happens? This is worse than ignorant, it is deliberately negligent.

I’m not saying that this technology is not coming, or that it will not be ubiquitous.  But we really need an open software stack, and some serious privacy options.  And we’re almost certainly going to need considerable legal framework for, say, passing along loosely authenticated DNA samples to third parties, and for making serious decisions based on unchallenged DNA samples.  (Think, for instance, about what your insurance company might do with reams of unverified data supposedly about where you go, what you eat, who you interact with, and what diseases you may have been exposed to.)

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