Tuesday, November 1, 2016

You May Become Your Own Medical Record

Got any favorite movies on VHS or have any old files on floppy drives?  Too bad you can't read them.  What, you backed everything up on  DVD?  Unfortunately, your new computer doesn't have a DVD drive.  Hard drives?  Don't make me laugh; after 3 - 5 years they start to fail.  Flash drives?  They've got a finite number of read/writes, and after ten years or so start to degrade anyway.  Magnetic tapes?  Keep them away from heat and magnets, and maybe they'll last 20 years.

We love our devices and are storing ever more data from them, but when it comes to long term storage -- and that means as short as a decade or two -- we still can't beat paper.

That may be changing.

Let's start with diamonds.  The slogan "diamonds are forever" was coined by an ad agency to foster the tradition of using them for wedding rings, but it is not far wrong.  They are considered to be the hardest natural mineral, and are chemically very stable.  They might not last forever, but they last a long, long time.  As it happens, they often contain slight impurities, mainly boron and nitrogen, and those are now being exploited for use as a storage mechanism.

Researchers at City University of New York (CUNY) just announced that they had used the nitrogen electrons to encode data (fittingly, images of physicists Albert Einstein and Erwin Schrรถdinger).

In their words:
As a proof of principle, we use multicolor optical microscopy to read, write, and reset arbitrary data sets with two-dimensional (2D) binary bit density comparable to present digital-video-disk (DVD) technology.
Got that?

The New York Times gleaned two key quotes from the authors:
  • "A DVD is like a 2-D puzzle, and this diamond technique is like a 3-D model," (thus allowing for vastly more storage)
  • "There is a no way you can change it. It will sit there forever."
The approach is a long way from being commercialized, but the prospect of a storage device that can be made inexpensively (the researchers said that the industrial diamond they used was the cheapest part of the experiment), has huge storage potential, and lasts "forever" will almost certainly attract entrepreneurs.  If you thought bejeweled DVD cases were cool, then you should really love this.

Using diamonds to store data is pretty nifty, but it seems almost prosaic compared to using DNA to store data.  What's so new about that?  After all, nature has been using DNA to write, store, and read genetic information for, as best we can tell, almost all the time there has been life on earth.

What's new is using DNA to store other types of data.  Earlier this year, Microsoft leapt past previous efforts by coding some 200 megabytes of data into a small amount of synthetic DNA (see below).  That's not much in the scheme of things -- in this case, some 100 literary classics, the seed database of Corp Trust, a music video of "This Too Shall Pass" -- and is still very expensive, but Microsoft believes the effort is important, given the explosive growth in data.

As Microsoft's lead researcher Karin Strauss said, "If you look at current projections, we can’t store all the information we want with devices at the cost that they are."  She estimates that a shoebox of DNA could hold the same amount of data as 100 huge data centers.  Another of the lead researchers, Luis Ceze at the University of Washington, goes further: "You can archive all the data on the internet in a shoebox."

With all this talk of using shoeboxes, you'd think Nike was funding the research.

DNA has one thing in common with diamonds as a storage device; it is extremely durable.  As Dr. Ceze points out: "Some results a few years ago sequenced DNA from 700,000 year-old bones," and I'll bet those bones weren't stored in any nice storage facility, not even a shoebox.

Best of all, it is unlikely that the technology will fall out of favor, unlike most other forms of data storage.  After all, we'll be reading DNA as long as there are lifeforms based on DNA, so unless someday our silicon overlords decide we're superfluous, someone will know how to access data stored in DNA.  

As Dr. Ceze said,
We see DNA as potentially the ultimate backup media—super durable, incredibly dense and never becomes obsolete...We see no fundamental physics reason why the cost and speed of DNA-based storage can’t be cheap and fast enough for main stream storage.
He thinks it will be viable within a decade.  If that sounds far-fetched, consider that there are already DNA storage devices on the market (although with only 512kB).

SingularityHub reported on a recent panel on the topic at SynBioBeta 2016.  The panelists agreed on the need for better long term storage solutions and on DNA's potential as one of those solutions, as well as the need to make the processes much faster and cheaper in order to be commercially viable.  They cited four open questions in the field:

  1. How do we design for security?
  2. What will the user interface look like?
  3. How will the world receive this?
  4. What kind of information do we want to store using DNA?
How we answer those questions may drive our the field advances, and how fast, but, as with diamonds, the potential is too great to ignore.  

Instead of an ever-growing number of massive data-centers, each consuming large amounts of energy, it's nice to imagine a small number of diamond or DNA-based storage centers.  It literally is possible that we could each someday carry around our own data center.

It seems very likely that, within the foreseeable future, you will be able to have your DNA sequenced in near real-time, analyzed for defects/mutations, and have therapies specifically tailored to your results -- possibly even actually editing your genes/DNA.  This is, after all, the goal of Precision Medicine.  

What would make this even cooler is that, as long as we're reading your DNA, your entire medical history is also being read  -- maybe from the cloud, but maybe from synthetic DNA that you've had implanted, or even from your own DNA, if we start writing directly to it.  And, of course, these DNA records would be updated in near real-time as well.  

Talk about owning your own data!

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