by Frank Ryan
Definition of genomic creativity: Ryan, F. P. “Genomic creativity and natural selection: a modern synthesis.” Biol J Linnean Soc 2006; 88: 655–72.
Chapter 10: The Advantage of Living Together
Epigraph: Margulis, L., 1970. Preface.
The Selfish Gene: Dawkins, R., 1976.
I have written a lot more about the history of symbiosis and its development in my book Darwin's Blind Spot, 2002.
For Maynard Smith and symbiosis: Smith, J. M., and Szathmáry, E., 1999.
For Lynn Margulis, chloroplasts and mitochondria: Margulis, L., 1970.
Chapter 11: The Viruses That Are Part of Us
Epigraph: Wimmer, E. “The test-tube synthesis of a chemical called poliovirus.” EMBO Reports 2006; 7: special issue: S3–S9. The first sequencing of polio virus was published in Kitamura, N., Semler, B. L., et al. “Primary structure, gene organization and polypeptide expression of poliovirus RNA.” Nature 1981; 291: 547–53.
The viral components of the human genome: Ryan, F., 2009.
HIV-1 and human HLA-B types: Kiepiela, P., Leslie, A. J., et al. “Dominant influence of HLA-B in mediating the potential co-evolution of HIV and HLA.” Nature 2004; 432: 769–74.
Screening for viral proteins in various tissues: Chen, F., Atterby, C., et al. “Expression of HERV-R ERV3 encoded Env-protein in human tissues: introducing a novel protein-antibody-based proteomics.” J Roy Soc Med 2013; 107(1): 22–29.
Chapter 12: Genomic Level Evolution
Epigraph: Jablonka, E., and Lamb, J. M.: vi.
C. elegans: Brenner, S., 2001.
Chapter 13: The Master Controllers
Epigraph: Brenner Nobel speech, 2002.
Chapter 14: Our History Preserved in Our DNA
Epigraph: Judson, H. F.: 10.
Clovis discovery: Rasmussen, M., Anzick, S. L., et al. “The genome of a Late Pleistocene human from a Clovis burial site in western Montana.” Nature 2014; 506: 225–29.
Siberian child discovery: Raghaven, M., Skoglund, P., et al. “Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans.” Nature 2014; 505: 87–91.
Richard III story: Ehrenberg, R. “A king's final hours, told by his mortal remains.” Sciencenews.org, March 9, 2013.
Chapter 15: Our More Distant Ancestors
Epigraph: Cavalli-Sforza, L.: 33.
First Wilson paper: Cann, R. L., Stoneking, M., and Wilson, A. C. “Mitochondrial DNA and human evolution.” Nature 1987; 325: 31–36.
For a more recent overview: Pakendorf, B., and Stoneking, M. “Mitochondrial DNA and human evolution.” Ann Rev Genomics Hum Genet 2005; 6: 165–83.
Stringer's drawing attention to lack of agreement on date of Adam and Eve: Stringer, C. “Out of Ethiopia.” Nature 2003; 423: 692–95.
Y–chromosome sequencing: Poznik, G. D., Henn, B. M., et al. “Sequencing Y chromosome resolves discrepancy in time to common ancestor of males versus females.” Science 2013; 341: 562–65. Also Cruciani, F., Trombetta, B., et al. “A revised root for the human Y chromosomal phylogenetic tree: the origin of patrilineal diversity in Africa.” Am J Hum Genetics 2011; 88: 814–18.
Mount Toba and Asian dispersal: Mellars, P., Gori, K. C., et al. “Genetic and archaeological perspectives on the initial modern human colonization of southern Asia.” PNAS 2013; 110(3): 10699–704.
HERV-K106: Jha, A. R., Nixon, D. F., et al. “Human endogenous retrovirus K106 (HERV-K106) was infectious after the emergence of anatomically modern humans.” PLoS One 2011; 6: e20234.
Early modern human migration into Asia: Brown, P. “Recent human evolution in East Asia and Australasia.” Phil Trans Roy Soc Lon Bio Sci 1992; 337: 235–42.
Aggressive symbiont: I have explained and defined what a viral aggressive symbiont comprises in three books, Virus X, Darwin's Blind Spot, and Virolution, as well as in many scientific papers.
Chapter 16: The Great Wilderness of Prehistory
Epigraph: taken from Libby's Nobel lecture.
The timing of early modern humans entering Asia: Mellars, P. “Why did modern human populations disperse from Africa ca. 60,000 years ago? A new model.” PNAS 2006; 103(25): 9381–86.
Douka, K. “Exploring ‘the great wilderness of prehistory’: the chronology of the Middle to the Upper Paleolithic transition in the Northern Levant.” Mitteilungen der Gesellschaft für Urgeschichte 2013; 22: 11–40.
Douka, K., Bergman, C. A., et al. “Chronology of Ksar Akil (Lebanon) and implications for the colonization of Europe by anatomically modern humans.” PLoS One 2013; 8(9): e72931: 1–10.
Mellars, P., and French, J. C. “Tenfold population increase in Western Europe at the Neanderthal-to-modern human transition.” Science 2011; 333: 623–27.
Evidence for widespread recent evolutionary change in the human genome: Wang, E. T., Kidama, G., et al. “Global landscape of recent inferred Darwinian selection for Homo sapiens.” PNAS 2006; 103: 135–40.
Chapter 17: Our Human Relatives
Epigraph: from “A conversation with Svante Pääbo.” Edge.org, April 7, 2009.
Sequencing genomes of animals and plants:
Miller, W., Drautz, D. I., et al. “Sequencing the nuclear genome of the extinct woolly mammoth.” Nature 2008; 456: 387–90.
Dabney, J., Knapp, M., et al. “Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments.” PNAS 2013; doi/10.1073/pnas.1314445110.
Amemiya, C. T., Alföldi, J., et al. “The African coelacanth genome provides insights into tetrapod evolution.” Nature 2013; 496: 311–16.
For Neanderthal fossils and appearances: Stringer, C., and Gamble, C., 1994.
Neanderthals and art: Abadía, O. M., and González Morales, M. “Redefining Neanderthals and art: an alternative interpretation of the multiple species model for the origin of behavioural modernity.” Oxford J Archaeology 2010; 29(3): 229–43. See also, Zilhão, J. “Symbolic use of marine shells and mineral pigments by Iberian Neanderthals.” PNAS 2010; 107: 1023–28.
Superiority complex with regard to Neanderthals: Villa, P., and Roebroeks, W. “Neanderthal demise: an archaeological analysis of the modern human superiority complex.” PLoS One 2014; 9 (4): e96424.
Chapter 18: The Fate of the Neanderthals
Epigraph: from Zilhão, J., and Trinkaus, E. Eds. “Portrait of the Artist as a Child: The Gravettian Human Skeleton from the Abrigo do Lagar Velho and its Archeological Context.” Trabalhos de Arquelogia 2002; 22: 9.
Neanderthal mitochondrial draft genome: Green, R. E., Malaspinas, A. S., et al. “A complete Neanderthal mitochondrial genome sequence determined by high-throughput sequencing.” Cell 2008; 134: 416–26.
First draft Neanderthal nuclear genome: Green, R. E., Krause, J., et al. “A draft sequence of the Neanderthal Genome.” Science 2010; 328: 710–22.
ABO blood group: Lalueza-Fox, C. “Genetic characterization of the ABO blood group in Neandertals.” BMC Evolutionary Biology 2008; 8: 342.
Neanderthals and modern humans share the same variant of the language gene: Krause, J., et al. “The derived FOXP2 variant of modern humans was shared with Neandertals.” Curr Biol 2007; 17: 1908–12.
Neanderthals found to have red hair and fair skin: Lalueza-Fox, C., Rompler, H., et al. “A malocortin 1 receptor allele suggests varying pigmentation among Neanderthals.” Science 2007; 318: 1453–55.
Neanderthal ancestry in Asians: Wall, J. D., Yang, M. A., et al. “Higher levels of Neanderthal ancestry in East Asians than in Europeans.” Genetics 2013; 194: 199–209.
The reappraisal of Neanderthal culture and society: Abadía, O. M., and Morales, R. G. “Redefining Neanderthals and art: an alternative interpretation of the multiple species model for the origin of behavioural modernity.” Oxford J Archaeol 2010; 29(3): 229–43.
Teaching Neanderthal children: Spikins, P., Hitchens, G., et al. “The cradle of thought: growth, learning, play and attachment in Neanderthal children.” Oxford J Archaeol 2014; 33(2): 1
11–34.
Compassion, culture of Neanderthals: Spikins, P. A., Rutherford, H. E., and Needham, A. P. “From homininity to humanity: compassion from the earliest archaics to modern humans.” Time and Mind: The J of Archaeology, Consciousness and Culture 2010; 3(3): 303–26.
The complete Neanderthal genome from the Altai Cave: Prufer, K., Racimo, F., et al. “The complete genome sequence of a Neanderthal from the Altai Mountains.” Nature 2014; 505: 43–49.
Genomic contribution of Neanderthals to present-day humans: Sankararaman, S., Mallick, S., et al. “The genomic landscape of Neanderthal ancestry in present-day humans.” Nature 2014; 507: 354–57.
Neanderthal legacy in terms of disease: Leake, J. “Neanderthals’ revenge: the gift of deadly genes.” Sunday Times, 26.01.14: 19.
Disparity in human to Neanderthal populations when they met: Mellars, P., and French, J. C. “Tenfold population increase in Western Europe at the Neanderthal-to-modern human transition.” Science 2011; 333: 623–27.
Discovery of the Denisovan genome. Marshall, M. “Mystery Relations.” New Scientist: April 5, 2014; 34–38.
Denisovan mitochondrial genome: Krause, J., Fu, Q., et al. “The complete mitochondrial DNA genome of an unknown hominin from southern Siberia.” Nature 2010; 464: 894–97.
The Denisovan nuclear genome: Reich, D., Green, R. E., et al. “Genetic history of an archaic hominin group from the Denisova cave in Siberia.” Nature 2010; 468: 1053–60.
Tibetan inheritance from the Denisovans: Huerta-Sánchez, E., Jin, X., et al. “Altitude adaptations in Tibetans caused by introgression of Denisoval-like DNA.” Nature 2014; doi:10.1038/nature13408.
DNA from Sima de los Huesos: The genome of a fossil from the Sima de los Huesos: Meyer, M., Fu, Q., et al. “A mitochondrial sequence of a hominin from Sima de los Huesos.” Nature 2014; 505: 403–36.
Chapter 19: What Makes You Unique
Epigraph: Darwin, C., 1859. Chapter IV: Natural Selection: 131.
Jeffreys’ discovery of DNA fingerprinting: Jeffreys, A. J., Wilson, V., et al. “Hypervariable ‘minisatellite’ regions in human DNA.” Nature 1984; 314: 67–73.
Our oneness as a species: Cavalli-Sforza, L. L., 2001.
References to haplogroup differences between the sexes, in Europe and in Western Europe, including the British Isles: Wilson, J. F., Weiss, D. A., et al. “Genetic evidence for different male and female roles during cultural transitions in the British Isles.” PNAS 2001; 98: 5078–83. See also, Capelli, C., Redhead, N., et al. “A Y chromosome census of the British Isles.” Curr Biol 2003; 13: 979–84.
Venter and Watson more similar to Korean genome: Barbujani, G., et al. “Human races.” Curr Biol 2013; 23(5): R185–R187. See also, Ahn, S.-M., Kim, T.-H., et al. “The first Korean genome sequence and analysis: full genome sequencing for a socio-ethnic group.” Genome Research 2009; 19:1622–29.
Öetzi the Iceman: Ermini, L., Olivieri, C., et al. “Complete mitochondrial genome sequence of the Tyrolean Iceman.” Curr Biol 2008; 18: 1687–93. See also, Keller, A., Graefens, A., et al. “New insights into the Tyrolean iceman's origin and phenotype as inferred by whole-genome sequencing.” Nature Communications 2012: doi: 2-.1038/ncomms1701|www.nature.com/naturecommunications.
The origins of different sections of the human genome: Pääbo, S.: 186–87.
Chapter 20: The Fifth Element
Epigraph: Venter, J. C.: 110.
For more lay-directed discussion of scientists and ethics involved see Duncan, D. E., 2006.
Adverse drug reactions: Thiesen, S., Conroy, E. J., et al. “Incidence, characteristics and risk factors of adverse drug reactions in hospitalized children—a prospective observational cohort study of 6,601 admissions.” BMC Medicine 2013; 11: 237. http://www.biomedcentral.com/1741-7015/11/237.
Chen, R., Mias, G. I., et al. “Personal Omics profiling reveals dynamic molecular and medical phenotypes.” Cell 2012; 148: 1293–307.
Regulation of GM crops: see Wikipedia article, “Genetically modified organism containment and escape.”
Wild canola found to contain genetically modified genes: ibid.
We are still evolving: Voight, B. F., Kudaravalli, S., et al. “A map of recent positive selection in the human genome.” PLoS Biology 2006; 4(3): e72, 0446–58.
Constructing the first artificial genome: Gibson, D. G., Glass, J. I., et al. “Creation of a bacterial cell controlled by a chemically synthesized genome.” Science 2010; 329: 52–56.
Human embryo deliberately engineered in a scientific experiment: Liang, P., Xu, Y., Zhang, X., et al. “CRISPR/Cas9-mediated gene editing in human tripronuclear zygotes.” Protein Cell 2015 doi 10.1007/s13238-015-0153-5.
ΦX174 (bacteriophage virus) 121
Acheulean (Middle Stone Age) stone tools 220, 249
achondroplasia 109
adenine 17–18, 69, 77, 80, 81, 87, 94, 102, 107, 142, 199
adeno-virus 2, 131
“adjuvant” 13
Africa: human ancestry/migration patterns 211–12, 214–24, 226–42, 249–50, 256, 259, 260, 261, 267, 276, 288, 290, 301
Agassiz, Jean Louis Rodolphe 138
AIDS 159, 162, 223, 301
Air (long non-coding RNA) 192
alkaptonuria 93
Alloway, J. L. 16–17
alpha helix, protein 56–7, 64, 65, 68–9, 81
Altai Mountains, Siberia 202, 267–8, 270–1, 273–6
Altmann, Richard 17
Ambros, Victor 185
American Association for the Advancement of Science 260
amino acids 18, 28, 53, 68, 79, 93, 95–6, 97, 98, 107, 131, 158, 181, 187
Angelman syndrome 192, 194
antibiotics 6, 19, 20, 32, 48, 128, 316
anti-sense DNA 105–6, 177, 194, 199
Anzick-1 198, 202–3, 207
apoptosis (programmed cell death) 153, 185–9
Arabian Peninsula 212, 217, 233, 236
archaea 151–2
archeogenetics 219, 240
Archaeological Museum of Lebanon 232
Aristotle 147
Arkwright, J. A. 12
art, Neanderthal production of 254–6
Asia: human ancestry/migration patterns 143, 197–8, 201, 202, 203, 211, 212, 214, 217, 218, 222, 224, 226, 228, 229, 230, 233, 234, 235, 236, 237, 238, 239, 240, 241, 248, 249, 261, 277, 288, 301
Astbury, William 46, 68
astrocyte 169–70
Atapuerca Mountains, Burgos, Spain 278–9
Atlantic Ocean 198, 271
Australia
human ancestry in 249, 255, 277
Human Genome Project and 123
koala retrovirus epidemic in 161–2, 223
autosomes 107, 108, 114, 189, 212, 241
Avery, Professor Oswald Theodore
Alloway and 16
character 10, 25, 30–5
Chargaff and 79, 92
classification of TB germ and 10
Copley Medal, Royal Society, awarded 32
cranberry bog bacillus and 19
Crick and 53
Dawson and 15–16
DNA discovery 13, 14, 15–17, 19, 21, 22–3, 24, 25–7, 29–35, 36, 40, 43–4, 53, 79, 92
DNA discovery disputed 25–7, 29, 34–5, 79, 179
Dubos and 6–7, 10, 17, 19, 20, 29–30, 31, 32, 33, 34
“Fess” 10, 41
Griffith's experiments and 13, 14
health 19–20, 21
honorary degree, Cambridge University 32–3
Koch and 10, 14
Luria and 43–4
recognition of achievement, lack of 29–30, 31, 33, 34–5
“Studies on the chemical nature of the substance-inducing transformation of pneumococcal types: induction of transformation by a desoxyribonucleic acid fraction isolated from pneumococcus type III” 22–3, 24, 29, 34–5
Watson and 40, 43–4
bacteria 5
adaptation 11–12
archaea and 151–2
autotrop
hic 158
Avery's discovery of DNA and 13–17, 23, 36, 44, 92
bacteriophages/phages and see bacteriophages/phages
classification of 9–10, 25, 29
“coitus” and chromosome 99–100
cyanobacteria 151–2, 206, 282
definition of virus and 156–7
DNA sequencing and 121
heredity 10–17, 41, 42
Dubos and 5, 10, 15, 16
first completely sequenced genome of a bacterium 126
killing of 157
Koch's postulates 10–11
as living organisms 10
mitochondrial genome and 154, 204, 205–6
“more virulent” or “attenuated” 11, 12
nitrogen cycle and 150
oxygen breathing, first 152
pathogenic (disease-causing) 10–11, 12–13
polysaccharide and 13–14, 17, 19, 21, 22, 25, 33
prokaryotes 9–10
rhizobia 150
serotypes 12, 13
Smooth and Rough (S and R) 12–14, 15, 16
symbiotic union and 149, 150, 151–2, 153
Venter's group create a living bacterial cell 304
Venter synthesizes the Mycoplasma genitalium genome 303–4
bacteriophages/phages 56, 96
discovery of DNA structure and 41–4
evolution out of exceedingly ancient viral lineages 158–9
first complete genome determined (ΦX174) 121, 132, 158–9
genetic information passed from one to another, process of 99–100
Hershey and Chase confirm discovery of DNA with experiment with 27–9, 36
Luria and Delbruck investigate interplay with host bacteria 41–3, 63, 92
phage group 41–5, 57, 97, 99
Watson and 41, 44, 45
Bailey, Bill 269–70
Bailey, Shara 252
Bary, Professor Anton de 147
Bateson, William 8
Baulcombe, David 186
Bayer Company, Elberfield, Germany 20
Bayesian modeling 232–3
Beadle, George W. 93, 130
Becker and Duchenne muscular dystrophies 134–5
Berg, Paul 294
Bergman, Dr. Christopher H. 231–2
Bergström, Karl Sune Detlof 243