Co-Opting the Genetic Code: DNA Encoding Protocol ITP Design Frontiers in Biology and Materiality, 2010

1. Co-opting the Genetic
Code
DNA Binary Encoding Protocol
Amit Snyderman, ITP Design Frontiers, 2010

2. Genetic Code
The genetic code is the set of rules by which
information encoded in genetic material is translated
into proteins by living cells.

3. DNA
Deoxyribonucleic acid (DNA) contains the genetic
instructions used in the development and functioning
of all known living organisms. The main role of DNA
molecules is the long-term storage of information.

4. Units of the Code
Adenosine (A)
Cytosine (C)
Guanine (G)
Thymine (T)

5. Codons
Mapping between nucleotide triplets and amino acids
43 combinations = 64 possible codons
http://upload.wikimedia.org/wikipedia/en/d/d6/GeneticCode21-
version-2.svg

6. Amino Acids
20 amino acids
Just as the letters of the alphabet can be combined to
form an almost endless variety of words, amino acids
can be linked together in varying sequences to form a
vast variety of proteins.
http://upload.wikimedia.org/wikipedia/commons/3/37/Aa.svg

7. Proteins
Every protein is chemically defined by its unique
sequence of amino acid residues, which in turn define
the three-dimensional structure of the protein.

8. MIME Base64
Encoding scheme that encodes binary data by treating
it numerically and translating it into a base 64
representation.
TEXT M a n
ASCII 77 97 110
BIT PATTERN 010011010110000101101110
INDEX 19 22 5 46
BASE64-ENCODED T W F u

9. Remap
Rather than mapping to a character, map to a codon.

10. VALUE CHARACTE CODON AMINO ACID VALUE CHARACTE CODON AMINO ACID VALUE CHARACTE CODON AMINO ACID
R R R
0 A AAA Lysine (K) 22 W CCG Proline (P) 43 r GGT Glycine (G)
1 B AAC Asparagine (N) 23 X CCT Proline (P) 44 s GTA Valine (V)
2 C AAG Lysine (K) 24 Y CGA Arginine (R) 45 t GTC Valine (V)
3 D AAT Asparagine (N) 25 Z CGC Arginine (R) 46 u GTG Valine (V)
4 E ACA Threonine (T) 26 a CGG Arginine (R) 47 v GTT Valine (V)
5 F ACC Threonine (T) 27 b CGT Arginine (R) 48 w TAA STOP
6 G ACG Threonine (T) 28 c CTA Leucine (L) 49 x TAC Tyrosine (Y)
7 H ACT Threonine (T) 29 d CTC Leucine (L) 50 y TAG STOP
8 I AGA Arginine (R) 30 e CTG Leucine (L) 51 z TAT Tyrosine (Y)
9 J AGC Serine (S) 31 f CTT Leucine (L) 52 0 TCA Serine (S)
10 K AGG Arginine (R) 32 g GAA Glutamate (E) 53 1 TCC Serine (S)
11 L AGT Serine (S) 33 h GAC Aspartate (D) 54 2 TCG Serine (S)
12 M ATA Isoleucine (I) 34 i GAG Glutamate (E) 55 3 TCT Serine (S)
13 N ATC Isoleucine (I) 35 j GAT Aspartate (D) 56 4 TGA STOP
14 O ATG Methionine (M) 36 k GCA Alanine (A) 57 5 TGC Cystine (C)
15 P ATT Isoleucine (I) 37 l GCC Alanine (A) 58 6 TGG Tryptophan (W)
16 Q CAA Glutamine (Q) 38 m GCG Alanine (A) 59 7 TGT Cystine (C)
17 R CAC Histidine (H) 39 n GCT Alanine (A) 60 8 TTA Leucine (L)
18 S CAG Glutamine (Q) 40 o GGA Glycine (G) 61 9 TTC Phenylalanine
(F)
19 T CAT Histidine (H) 41 p GGC Glycine (G) 62 + TTG Leucine (L)
20 U CCA Proline (P) 42 q GGG Glycine (G) 63 / TTT Phenylalanine
(F)
21 V CCC Proline (P)

11. Example: Hello,
world!
BASE64 SGVsbG8sIHdvcmxkIQo=
BASE64 INDEX 18 6 21 44 27 6 60 44 8 7 29 47 28 38 49 36 8 16 40
DNA CAGACGCCCGTACGTACGTTAGTAAGAACTCTCGTTCTAGCGTACGCAAG
ACAAGGA
PROTEIN QTPVRTLVRTLVLAYARQG
Any binary data can be represented: text (unicode),
bitmap, audio, video, etc.
Try It: http://amitsnyderman.com/school/designfrontiers/
encoder.php

12. Disk is cheap.
Who cares?

13. Non-Digital Library
Via recombinant DNA technologies, craft a portable,
reproducible, time-resistant library. Embed, grow and
spread in bacteria. Package as a pill. Organic time
capsule.

16. Spime
"The key to the Spime is identity. A Spime is, by
definition, the protagonist of a documented process. It
is an historical entity with an accessible, precise
trajectory through space and time."
–Bruce Sterling, Shaping Things

17. Spime Ingredients
Unique ID code
History of ownership
Geographical position
Customization details
Public discourse
Etc.

18. Human
Identification
Tools, artifacts, archeology
Bone structure, teeth, dental records, fingerprints, DNA
Yellowpages, resume, Facebook/LinkedIn/etc, Google

23. Narrative
Embedded Histories. Family trees and Lineage. Stories.

24. Junk DNA
Noncoding DNA describes sequences that do not
encode for protein sequences. Much of this DNA has no
known biological function and is sometimes referred to
as "junk DNA".
More than 98% of the human genome is non-coding.

25. Human Spime
Recycle junk DNA by recombining encoded messages
into non-coding DNA regions.
In-vitro manipulation. Gene therapy.
Hereditary storytelling.