[Humanist] 26.289 DNA as storage medium

Humanist Discussion Group willard.mccarty at mccarty.org.uk
Sun Sep 9 10:23:01 CEST 2012


                 Humanist Discussion Group, Vol. 26, No. 289.
            Department of Digital Humanities, King's College London
                       www.digitalhumanities.org/humanist
                Submit to: humanist at lists.digitalhumanities.org



        Date: Sat, 8 Sep 2012 11:57:10 +0100
        From: Andrew Prescott <andrew.prescott at kcl.ac.uk>
        Subject: DNA coding for book digitisation



Dear Willard

This story I think will certainly be of interest to subscribers to Humanist.

Andrew

Professor Andrew Prescott FRHistS
Head of Department
Department of Digital Humanities
King's College London
26-29 Drury Lane
London WC2B 5RL
@ajprescott
www.kcl.ac.uk/artshums/depts/ddh
digitalriffs.blogspot.com
+44 (0)20 7848 2651

------

Book written in DNA code

Scientists who encoded the book say it could soon be cheaper to store information in DNA than in conventional digital devices

Guardian, Thursday 16 August 2012 19.45 BST

http://www.guardian.co.uk/science/2012/aug/16/book-written-dna-code?INTCMP=SRCH

Scientists have for the first time used DNA to encode the contents of a
book. At 53,000 words, and including 11 images and a computer program, it is
the largest amount of data yet stored artificially using the genetic
material.

The researchers claim that the cost of DNA coding is dropping so quickly
that within five to 10 years it could be cheaper to store information using
this method than in conventional digital devices.

Deoxyribonucleic acid or DNA – the chemical that stores genetic
instructions in almost all known organisms – has an impressive data
capacity. One gram can store up to 455bn gigabytes: the contents of more
than 100bn DVDs, making it the ultimate in compact storage media.

A three-strong team led by Professor George Church of Harvard Medical School
has now demonstrated that the technology to store data in DNA, while still
slow, is becoming more practical. They report in the journal Science that
the 5.27 megabit collection of data they stored is more than 600 times
bigger than the largest dataset previously encoded this way.

Writing the data to DNA took several days. "This is currently something for
archival storage," explained co-author Dr Sriram Kosuri of Harvard's Wyss
Institute, "but the timing is continually improving."

DNA has numerous advantages over traditional digital storage media. It can
be easily copied, and is often still readable after thousands of years in
non-ideal conditions. Unlike ever-changing electronic storage formats such
as magnetic tape and DVDs, the fundamental techniques required to read and
write DNA information are as old as life on Earth.

The researchers, who have filed a provisional patent application covering
the idea, used off-the-shelf components to demonstrate their technique.

To maximise the reliability of their method, and keep costs down, they
avoided the need to create very long sequences of code – something that is
much more expensive than creating lots of short chunks of DNA. The data was
split into fragments that could be written very reliably, and was
accompanied by an address book listing where to find each code section.

Digital data is traditionally stored as binary code: ones and zeros.
Although DNA offers the ability to use four "numbers": A, C, G and T, to
minimise errors Church's team decided to stick with binary encoding, with A
and C both indicating zero, and G and T representing one.

The sequence of the artificial DNA was built up letter by letter using
existing methods with the string of As, Cs, Ts and Gs coding for the letters
of the book.

The team developed a system in which an inkjet printer embeds short
fragments of that artificially synthesised DNA onto a glass chip. Each DNA
fragment also contains a digital address code that denotes its location
within the original file.

The fragments on the chip can later be "read" using standard techniques of
the sort used to decipher the sequence of ancient DNA found in archeological
material. A computer can then reassemble the original file in the right
order using the address codes.

The book – an HTML draft of a volume co-authored by the team leader –
was written to the DNA with images embedded to demonstrate the storage
medium's versatility.

DNA is such a dense storage system because it is three-dimensional. Other
advanced storage media, including experimental ones such as positioning
individual atoms on a surface, are essentially confined to two dimensions.

The work did not involve living organisms, which would have introduced
unnecessary complications and some risks. The biological function of a cell
could be affected and portions of DNA not used by the cell could be removed
or mutated. "If the goal is information storage, there's no need to use a
cell," said Kosuri.

The data cannot be overwritten but, given the storage capacity, that is seen
as a minor issue. The exercise was not completely error-free, but of the
5.27m bits stored, only 10 were found to be incorrect. The team suggests
common error-checking techniques could be implemented in future, including
multiple copies of the same information so mistakes can be easily
identified.

The costs of DNA-handling tools are not yet competitive enough to make this
a large-scale storage medium. But the costs and scale of the tools are
dropping much more quickly than their electronic equivalents. For example,
handheld DNA sequencers are becoming available, which the authors suggest
should greatly simplify information stored in DNA.

Kosuri foresees this revolution in DNA technologies continuing. "We may hit
a wall, but there's no fundamental reason why it shouldn't continue."



More information about the Humanist mailing list