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.
#Perlbinperl 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 =
# # # 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.
INDEX
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
diesel (biodiesel), 6–7, 66, 93, 97–106, 201, 239
Diesel, Rudolf, 98
“Diffusion of Synthetic Biology: A Challenge to Biosafety” (Schmidt), 232
DIYbio, 232–237
Dino, 95
DNA, 29. See also oligonucleotides; polynucleotides
as ancient text, 38
encoding digital information using, 90, 177, 195–198
storage of Wikipedia all-languages version as, 197
first appearance of, 38
noncoding (“junk”), 51, 57
origami, 80
plasmid, 44
replication of, 30
commercial synthesis of, 34
as ultimate backup medium, 34
Dolly (sheep), 134
as “raised from the dead”9, 134
Donnell, David, 180, 230–231
Douglas, Shawn, 80
Dresser, Betsey, 141
Drexler, K. Eric, 54
Drmanac, Rade (Complete Genomics), 168
DuPont, 3
E. coli (Escherichia coli), 3
changing codons of, 125
as digital information storage devices, 195–196
discovery of, 43
genetic engineering of, 44
to destroy cancer cells, 115–116
to make diesel fuel, 103
to make ethanol, 103
to suppress appetite, 179–180, 199–200
genome of, 72, 78
inv+ E. coli, 116
K-12 strain of, 6, 46
as rationally designed, 6
as molecular factories, 46
protein-coding genes of, 127
replication rate of, 43, 72
sense-perception ability of, 43
sensor-equipped, 116
synthesis of hemoglobin (“bactoblood”) by, 6, 181, 192
synthesis of PDO by, 3
See also biofuels
EcoRI, 44
E. cryptor, 195–196
E. pluri, 66–67
electricity, 4, 192–193, 240
produced from sewage, 4–5
Elowitz, Michael, 187–188
Emory University, 7
Endy, Drew, 160, 171, 186–190, 237, 255
Engines of Creation (Drexler), 54
Energy from Heaven and Earth (Teller), 96
enhancing the human body, 8–9, 227
Environmental Protection Agency, 3
Escherich, Theodor, 43
“Essay on the Principle of Population” (Malthus), 221
ethanol, 2
eugenics, 8, 86–89, 251
errors of, 59
evolution, 95, 110–111, 119, 125, 155, 161–163, 181, 193, 210, 230, 232
human control of, 13, 74
increasing the rate of, 71–73, 88
laboratory, 31
maximizing, 89
progress in, 61
exponential technologies, 164, 168, 209n, 242–243, 250–252
extinction, 88, 133
successful reversal of, 9–11, 133–136
arguments against extinction reversal, 142–143
Fernández-Árias, Alberto, 133–136
Feynman, Richard, 177
Fleming, Diane O., 231
flies (midges), 72, 130, 250–251
Flynn effect, 88–89
Folch, Jose, 10, 133–136
food-for-fuel problem, 94
Ford, Henry, 98
Forster, Anthony, 52, 66
Fukuyama, Francis, 227–228
fundamental engineering principles, 161
biological equivalents of, 161–162
future, prescriptions for, 243–253
alternative scenarios, 243–249
natural versus exotic, 243–244
staying at home versus jetsetting, 242
personal versus generic, 245
priceless versus worthless, 246
rich versus poor, 246
privacy versus publicity, 246–248
becoming a new species, 248–250
Galton, Francis (Galtonian eugenics), 87–89
Gao, Xiaolian, 174
“garage biology” 232, 233
first example of, 233
Gaston Day School, 194
Gates, Bill, 100, 172
Gen9 (earlier, CodonDevices), 170–171
Genencor International, 3
genetic code, 61
changing, 8–9, 120–128
decoding of, 64
genetic diseases, 204–205
genetic engineering, 11
genome,
synthetic, 74–76
genome synthesis as a business, 176–177
reasons for synthesizing, 75–76
genome sequencing, 73
as a business, 170–174
commercial firms, 215
as enabling the mining of biological talents from other species, 73–74, 83
history of, 165–170
genomic engineering, 9, 11, 59, 119
as a business, 162–164
as enabling increased diversity, 59–66
standardization of, 181–182
Genspace, 234
Gentry, Eri, 233–234, 257
Geobacter metallireducens, 5
Giese, Jeanna, 109–110
recovery of, 131–132
Gilbert, Wally, 118, 165, 255
Gladyshev, Eugene, 130
Glasby, Geoffrey, 97
glycolysis, 42
G-Oil, 93
Gold, Thomas, 97
Goodsell, David, 44
Google, 89, 246, 255
Goto, Kazufumi, 145
“great oxygenation event” 105
green chemistry, 3
green fluorescent protein (GFP), 187
Green Fuel Technologies Corporation, 93
Gustafsson, Claes, 196
H+. See transhumanism
Hadean era, 16
Haeckel, Ernst, 12
handedness of molecules (chirality), 20
defined, 22
reasons to care about, 21–22
See also mirror molecules
Hapgood, Fred, 193
hepatitis C virus, synthetic, 75
Here Is a Human Being (Angrist), 214
Hero of Alexandria, 182
Hippocrates, 204
History of the Peloponnesian War (Thucydides), 111
Holocene epoch, 203
Hood, Lee, 165, 174
Hooke, Robert, 39
houses grown from seeds, 7–8
human genome, modifying, 85, 115, 120–128
for multivirus resistance, 8–9, 119–121
for radiation resistance, 129–131
objections to, 85–86
Human Genome Project, 73, 205
as moon landing of molecular biology, 73, 207
sequenced a “blended person” 207
human immune system, 111–114
limitations of, 111
See also mammalian immune system
HuMAb-Mouse, 118
humanized mice, 118
Hunt, Debra Long, 231
hyperthymesia, 228–229
“Idempotent Vector Design for Standard Assembly of Biobricks” (Knight), 185
iGEM (International Genetically Engineered Machines), 180–181
attempts to make genetic engineering “easy,” 230–231
dangers arising from, 230–232
history of, 189–192
2010 iGEM Jamboree, 192–196, 198–201
Chinese University
of Hong Kong presentation at, 195–196, 197, 200
Harvard iGarden project at, 200
Team Citadel presentation at, 199–200
immortal human components, 217–223
cloning as a possible route to, 220–221
extremes of longevity, 218–219
HeLa cells, 220
Lacks, Henrietta, 220
immune response, 112–114
generation of diversity problem (GOD problem), 113
immune diversity, 113
immune specificity, 113
industrial revolutions, 151–158
first industrial revolution (domestication of time), 152–154
unwelcome consequences of, 154
second industrial revolution (agriculture), 154–157
advantages of, 155
unwelcome consequences of, 155–156
further consequences of, 156–157
parallels to synthetic biology, 157
third industrial revolution (The Industrial Revolution proper), 182
Regenesis Page 30