Regenesis (46 page)

Fifth and last, we would need a convenient way to read this form of the book—a DNA reader analogous to, for example, the Kindle, Sony-PRS, Android, or iPad. This is discussed briefly in Chapter 8. Sequencing this book using Illumina technology resulted in 692 million paired 100 base pair reads for $2,000. At 91K reads per book, that means $0.26 per 1X reading of the book. No words were lost in the process. Handheld DNA readers are beginning to become available, for example, the 2012 Oxford Nanopore MinIon (Chapter 7), and milestones like this book in DNA might accelerate commercial interest. We have established a DNA Encoded Artifacts Registry (DEAR) to coordinate global use so that mixed samples and updates can be interpreted. Coordination with the Rosetta Project (of the Long Now Foundation) could help make DNA the time capsule. Rosetta 3-inch nickel disk aims at 10,000 year archiving, avoiding the pitfalls of ephemeral digital standards (and even cultures) by intuitively leading the discoverer to higher and higher magnifications and 1,500 languages. In principle, instructions for building a DNA reader could be included in one or more languages and images.

# # # Begin notes and 2-bit/bp DNA encoding notes below # # #

#Decoding self-referential DNA that encodes these notes.

#\Perl\bin\perl bp2bit.pl GMC 25-Jun-02011

sub b2b {return unpack(“N”, pack(“B32”, substr(“0” x 32 . shift, -32)));} open OUT,”>OUT”;binmode OUT;open IN,”IN”; $d{“A”}=“00”; $d{“C”}=“01”; $d{“G”}=“10”; $d{“T”}=“n”; while ($text =) { while ($text =~ s/(^.{4})//i)
{#print “ $text “; $b8=chr(b2b($d{substr($1,0,1)}.$d {substr($1,1,1)}.$d {substr ($1,2,1)}.$d{substr($1,3,1)})); print OUT “$b8”;}}

# # # End of notes and DNA encoding notes # # #

For more information, and to explore the possibility of getting your own DNA copy of this book, please visit
http://periodicplayground.com
.

Afeyan, Noubar,
104
,
170

aging,
84
,
218–219

genetic basis of,
84–85

agriculture, invention of,
151

Air New Zealand,
91

algae,
93
,
100
.
See also
biofuels

amino acids,
21

handedness of,
24

increasing the numbers of,
63

mirror,
63

nonstandard
(NSAAs)
,
68

phenylalanine (F),
65

Amoebaproteus
,
51–52

ancient texts,
38

Anderson, J. C.,
115

Andromeda Strain, The
(Crichton),
225

Anthropocene,
143n
antibodies,
35
,
80
,
110
,
112–114
,
117–118
,
175

monoclonal,
117

as proteins,
113

antigen,
112

antigen binding site,
113–114

anthrax,
26
,
194
,
231

apoptosis,
114

Archean era,
37
,
105

Archer Daniels Midland,
1

Archimedes,
77

arsenic,
6

atomic elements,
16–18
,
252

atoms,

spatial arrangement of,
19

Audubon Center for Research on Endangered Species (ACRES),
141

Bachelet, Ido,
80

bacteria,
4

blinking,
187

changing the species of,
48

minimal,
47

replication-limitation devices,
117

size of,
40

“synthetic”
48-50

bacterial drug delivery system,
115

Baker, David,
171

Bastiat, Frédéric,
99

B cells (B lymphocyte),
112

Bdelloid rotifer,
130

beer brewing,
2
,
103

Beethoven, Ludwig van,
229

Berry, David,
104

Berthelot, Marcelin,
27

Berzelius, Jöns Jakob,
18–20

Bible,
15
,
38
,
270

big bang,
16

BioBrick
(also
biobrick),
161
,
163
,
185–186
,
188–189
,
192
,
199

standard assembly of,
185–186

BioCurious,
234

biodegradation,
2

drawback of,
22

Bio-Fab Manifesto,
160–162
,
181

biofilm,
6
,
191

biofuels,
91–107

algae,
93
,
100

advantages of,
101

disadvantages,
101–102

coconut oil,
94

cyanobacteria,
104–106

E. coli
,
102–104

advantages of,
102–103

ethanol,
98

advantages of,
98

disadvantages of,
99

halo effect of,
92

potential sources of,
98

biogenetic law,
12

biohackers,
234

biological organisms,
4

as high technology,
4

Biological Safety: Principles and Practices
(Fleming and Hunt),
231

biological weapons convention,
240

failure of,
240

Bio-PDO,
3

bioplastics,
1–4

biosafety,
26
,
68
,
89
,
117
,
121
,
139
,
141
,
159
,
175–176
,
230–237
,
253
,
255
,
269–270

biosecurity,
99
,
161
,
231
,
269
,
270

Biot, Jean Baptiste,
27

Black Death,
156
,
226

Black Swan, The
(Taleb),
242

Blattner, Fred,
6–7
,
46

Blue Heron Biotechnology,
189

Boston University,
190

Boyer, Herbert,
44–45
,
46

Brand, Stewart,
249

Branson, Richard,
91

Briggs, Robert,
134–135

Brown, Timothy Ray,
89
,
216–217

bucardo,
9–10
,
133–136

Burnley, Brian,
179
,
199

CAGE (conjugative assembly genome engineering),
78–79

Caltech,
190

Cambrian explosion,
71

cancer,
80
,
83–85
,
111
,
115–117
,
119
,
128–129
,
163
,
174
,
214
,
216
,
220
,
233–234
,
244
,
246–247

Capek, Karel,
180–181

Carboniferous period,
95

carbon-nitrogen cycle,
17

Carlson, Rob,
233

Caruthers, Marvin,
174

CCR5 gene,
216–217
,
228

Celia (ibex),
9

death of,
134

daughter born through nuclear transfer cloning,
133–136

cells,
39

as deterministic systems,
42

attempts to synthesize,
51–54

discovery of,
39

generic,
40–42

minimal,
50

nature of,
39–42

polymeric composition of,
40–41

“synthetic”
48-50
,

Center for Agro-Nutrition Research and Technology,
133

Chang, Timothy Z.,
5

changing the genetic code,
8–9

Children's Hospital of Wisconsin,
110
,
131

chimpanzee (
Pan
)
147–148
,
249

Chinese University of Hong Kong,
195
,
197
,
200
.
See also
iGEM

chips (cheap DNA/oligos),
34
,
76
,
147
,
160
,
171
,
175
,
270

chirality,
23
,
26
,
28

future of,
28

See also
handedness of molecules
;
mirror molecules

Citadel, The,
179–180
,
199
.
See also
iGEM

Clean Genome
E. coli
,
7
,
46

cloning,
9
,
134
,
140–148

arguments against,
221

benefits of,
141
See also
nuclear transfer cloning
;
recombinant DNA

Clostridium perfringens
,
6n
coconut oil,
94

codons,
61
,
64–70
,
79
,
120–127
,
173
,
177
,
196

CodonDevices
(née
EngeneOS, later Gen9),
170–171

Cohen, Stanley,
44–45
,
46

Collins, Francis,
204–205

Collins, Jim,
171
,
255

comparative genomics,
73–86

computational irreducibility,
242

Computer Science and Artificial Intelligence Laboratory (CSAIL),
184

“Conan the Bacterium”
130

conjugative assembly genome engineering.
See
CAGE

Continental Airlines,
92

Ce qu'on voit et ce qu'on ne voit pas
(Bastiat),
99

Crichton, Michael,
138
,
225–226

Crick, Francis,
30
,
213

C-value paradox,
67

cyanobacteria,
38
,
92
,
100
,
104–106
,
162
,
222

cystic fibrosis,
204–205

Danielli, J. F.,
51

Darwin, Charles (Darwinian),
77
,
89
,
107
,
135
,
162
,
234
,
249

Davis, Joe,
196
,
271

Declaration of Independence, stored in
E. coli
bacteria,
195–196

Deinococcus radiodurans
,
130

Denisovans,
147n
,
151