Tue
Jan 8 2013 12:00pm

The Science of Future Past: Part 3

The Science of Future Past: Part 3In today’s installment of Science of Future Past, we explore some unorthodox uses of those famous “building blocks of life” known as DNA. We’ll start off with Asimov’s Foundation before heading to a galaxy far, far away.

Rapid DNA Sequencing

In part four of Foundation, The Traders, a space-faring trader by the name of Linmar Ponyets is ordered by the Foundation to go and rescue a fellow trader who has been imprisoned by a hostile government. While the issues involved with the actual rescue are extremely interesting, I’m not going to discuss them today. Instead I want to look at the mechanism that the Foundation used to send the message to Ponyet:

The tiny, gleaming sphere changed hands, and Gorm added, “It’s confidential. Super-secret. Can’t be trusted to the sub-ether and all that. Or so I gather. At least it’s a Personal Capsule, and won’t open for anyone but you.”

[Read more]

Biometric locks and authentication certainly qualify as old news by now. But every current implementation I’ve seen uses either voice recognition, fingerprint scans, retinal scans, or iris scans. However the device portrayed here doesn’t seem to use any of those options, instead it opens upon direct contact with Ponyets’ hand, which would seem to indicate some type of genetic recognition.

Reading this made me wonder not only how the device could manage to verify the recipient’s genome in such a timely manner, but also what mechanism could achieve it using such a small size.

The smallest sequencer currently on the market that I’m aware of is the Ion Proton benchtop sequencer, which weighs in at around 130 pounds. However as we know from the reading so far, the Foundation is exceptionally skilled at miniaturization. (Here’s a great introductory video on ion semiconductor sequencing if you’re interested in learning more about the technology behind this machine.)

Regardless of size issues, current sequencing protocols require that DNA samples undergo a series of preparatory steps prior to sequencing which takes around 4-8 hours to complete. After the preparation is complete, it takes an additional several hours to several days to complete the sequencing.

It is of course possible that the mechanism doesn’t need to sequence the recipient’s entire genome, but instead uses something similar to how DNA fingerprinting works, just looking at specific marker alleles within the genome.

More likely is that the foundation has developed superior sequencing techniques that don’t require extensive sample preparation and can be completed rapidly by a machine of very small size. There is some promising research happening in facilitating sequencing without the need for extensive sample preparation as well as breakthroughs in super high-speed sequencing using very small devices, such as the exciting work being done in nanopore sequencing.

DNA Steganography

While I was reading through the current literature to see if any kind of biometric lock based on genetic sequencing, I stumbled across several papers discussing DNA steganograpy.

Just as with conventional steganography, DNA steganography involves concealing important information inside of some other media. However instead of hiding text within text or digital messages inside of image files, DNA steganography encodes a message using a DNA sequence and then hides that sequence within additional DNA to mask its existence.

Decoding the message is a laborious process. First you need to know where the DNA fragment is hidden. It could be preserved in an adhesive, inside a virus or bacteria, or any other place DNA might commonly be found.

Once you’ve found the DNA, you have to sequence it. This can be made extremely complicated if the DNA containing the message is hidden with several other fragments of DNA, as each fragment has to be prepared for sequencing using specific PCR primers before it can be sequenced.

So assuming you knew where to find the DNA, and which primers to use in order to prepare it for sequencing, you still have to know how to decode the sequenced DNA into the original message.

While all of this is extremely interesting, (at least to me), what made it most interesting to me was the timing of the reasearch. This paper outlining all the steps necessary to achieve DNA steganography was published in Nature in 1999. The scientists who carried out that research then applied for a patent in 2000 that was granted in 2001.

However the first time I had heard of DNA steganography was in 1998, when I read about it Michael Stackpole’s, I, Jedi. This book was very memorable for me because it was the first novel I remember reading that was told in the first person. According to Wookieepedia, it is also the first (and, as of this date, the only) Star Wars novel to be written with a first person POV.

At one point in the novel, the protagonist goes to Corellia to learn more about his past. While there he learns that his step-grandfather had used DNA steganography (though it isn’t called that in the novel), to hide ancient Jedi lore in the genetic sequences of the flowers he bred as a horticulturalist.

Conclusion

So while DNA sequencing technology is rapidly improving, it hasn’t yet reached the level of speed it needs in order to send “confidential, super-secret” messages to specific people as used in Foundation. The good news is, we have reached the point where we can potentially hide secret messages in DNA sequences of living organisms, as predicted by Michael Stackpole.


Dr. Lee Falin is a Bioinformatician at the European Bioinformatics Institute, the host of the Everyday Einstein’s Quick and Dirty Tips podcast and the author of the “Science Fictioned” series, in which he takes scientific research articles and turns them into science fiction and fantasy short stories for middle grade and young adult readers.

6 comments
Questionable
1. Questionable
Loving the series of articles (I'm a fan of the Foundation series and of science).

I don't think this sort of thing needs to be far off - just too expensive at present. No doubt the Capsule is sequencing single molecules like nanopores or PacBio's approach. These don't need PCR either (so no primer problems) and I can imagine it mixing buffer and reading sequences constantly until a match to the key is seen. Just a small scale down in size from a minIon or what's out there right now :)

Swabs and stray hairs are the new security risk!
Shelly wb
2. shellywb
It will happen. I worked in a lab doing sequencing of one rat gene in the early 80s. We never got more than a piece of it over 5 years. Today what we accomplished can be done in a day. I'd imagine that in another 30 years they'd have it down to a snap of the fingers.
Questionable
3. entirelyalive
I think you have your timeline mixed up.

Foundation came out in 1951, but Watson & Crick didn't image DNA until two years later, and it was only (according to Wikipedia) in 1952 that DNA was shown to be the genetic information database. Asimov may have been pretty tuned in to the science world, but he doesn't refer to DNA because he didn't know about it at the time.

My suspicion is that a thing "not opening for anyone but you" was just another of the many "basically magic" technologies that Asimov littered throughout the Foundation series, without any hard science basis for them.
Lee Falin
4. leefalin
@entirelyalive Actually it was Rosalind Franklin that "imaged" DNA as you put it, solving its crystal structure using x-ray crystallography, prior to Watson and Crick's publication.

As for knowing that DNA contained genetic information, that had been widely known for some time prior to the 1950's, having been shown in 1944 by the landmark Avery–MacLeod–McCarty experiment.

Considering that Asmiov was a professional biochemist and professor of biochemistry at Boston University prior to becoming an author, I think his knowledge of the most important biological research going on in the 1940s and 50s probably went well beyond merely "being pretty tuned in to the science world". Incidentally, he wrote a children's book on DNA research (How Did We Find Out About DNA) and a parody of The Double Helix called The Holmes-Ginsbook Device.

For more information on the history of DNA research, both The Double Helix by Watson, and The Dark Lady of DNA by Brenda Maddox are excellent resources.
Questionable
5. (still) Steve Morrison
In fact, Asimov referred to the Avery-MacLeod-McCarty experiment as "the breakthrough" (italics his) in genetics research in his 1962 book The Genetic Code.
Questionable
6. ASB210
If I recall correctly, the pilot episode of Star Trek Enterprise featured an instance of DNA Steganography. They had secret information/a message embedded in the Klingon's DNA. To get it, they took a sample of his blood and plugged it in.

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