Skip to main content Accessibility help

We use cookies to distinguish you from other users and to provide you with a better experience on our websites. Close this message to accept cookies or find out how to manage your cookie settings.

Close cookie message
×
Hostname: page-component-76fb5796d-vfjqv Total loading time: 0 Render date: 2024-04-27T06:52:22.664Z Has data issue: false hasContentIssue false

General Reading and Bibliography

Published online by Cambridge University Press:  05 May 2022

Andrew Travers
Andrew Travers
Affiliation:
University of Cambridge
Get access

Summary

A summary is not available for this content so a preview has been provided. Please use the Get access link above for information on how to access this content.
Image of the first page of this content. For PDF version, please use the ‘Save PDF’ preceeding this image.'
Type
Chapter
Information
Why DNA?
From DNA Sequence to Biological Complexity
 , pp. 192 - 208
Publisher: Cambridge University Press
Print publication year: 2022

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Primary Sources

Bonner, J. (1988) The evolution of complexity by means of natural selection. Princeton University Press, Princeton, NJ.Google Scholar
Calladine, C.R., Drew, H.R., Luisi, B.F, Travers, A.A. (2004) Understanding DNA and how it works. Elsevier, San Francisco, CA.Google Scholar
Coyne, J.A. (2009) Why evolution is true. Oxford University Press, Oxford, UK.Google Scholar
Darwin, C. (1859) On the origin of species by means of natural selection, or the preservation of favoured races in the struggle for life. John Murray, London, UK.Google Scholar
Dawkins, R. (1976) The selfish gene. Oxford University Press, Oxford, UK.Google Scholar
Dawkins, R. (1982) The extended phenotype. Oxford University Press, Oxford, UK.Google Scholar
Dawkins, R. (2004) The ancestor’s tale. Weidenfeld and Nicholson, London, UK.Google Scholar
Dawkins, R. (2009) The greatest show on Earth. Bantam Press, London, UK.Google Scholar
Greaves, M. (2000) Cancer. The evolutionary legacy. Oxford University Press, Oxford, UK.Google Scholar
Jencks, C. (1995) The architecture of the jumping universe. Academy Editions, London.Google Scholar
Jones, S. (1999) Almost like a whale. Transworld Publishers, London, UK.Google Scholar
Jukes, T.H. (1963) Observations on the possible nature of the genetic code. Biochemical and Biophysical Research Communications 10, 155–159.Google Scholar
Kauffman, S.A. (1993) The origins of order. Oxford University Press, Oxford, UK.Google Scholar
Koonin, E.V. (2012) The logic of chance: The nature and origin of biological evolution. Pearson Education Inc., Upper Saddle River, NJ.Google Scholar
Lane, N. (2015) The vital question. Profile Books, London, UK.Google Scholar
Lineweaver, C., Davies, P., Ruse, M. (Eds.) (2013) Complexity and the arrow of time. Cambridge University Press, Cambridge, UK.Google Scholar
Mayr, E. (1963) Animal species and evolution. Belknap Press, Cambridge, MA.Google Scholar
Muskhelishvili, G. (2015) DNA information: Laws of perception. Springer, Dordrecht, Germany.Google Scholar
Papineau, D. (2018) Thomas Bayes and the crisis in science. Times Literary Supplement, 28 June.Google Scholar
Renfrew, C. (1987) Archaeology and language: The puzzle of Indo–European origins, Pimlico, London, UK.Google Scholar
Schrödinger, E. (1944) What is life? Cambridge University Press, Cambridge, UK.Google Scholar
Smith, E., Morowitz, H.J. (2016) The origin and nature of life on earth. Cambridge University Press, Cambridge, UK.Google Scholar
Tainter, J.A. (1988) The collapse of complex societies. Cambridge University Press, Cambridge, UK.Google Scholar
Vologodskii, A. (2015) Biophysics of DNA. Cambridge University Press, Cambridge, UK, 2015.Google Scholar
von Neumann, J. (1958) The computer and the brain. Yale University Press, New Haven, CT.Google Scholar
Wilson, E.O. (1992) The diversity of life. Allen Lane, London, UK.Google Scholar

Secondary Sources

Boltzmann, L. (1886) Der zweite Hauptsatz der mechanischen Warmetheorie. Vienna: Gerold, p. 21.Google Scholar
Lewis, G.N. (1930) From a letter to Irving Langmuir, 5 August 1930. Quoted in Reingold, N. (1981) Science in America: A documentary history 1900–1939. University of Chicago Press, Chicago, IL, 400.Google Scholar
Landauer, R. (1991) The physical nature of information. Physics Letters, 217, 188–193.Google Scholar
Maxwell, J.C. (1850) In Maxwell, J.C., Harman, P.M. (Eds.) (1990) The scientific letters and papers of James Clerk Maxwell, Vol. 1, 1846–1862, p. 197. Cambridge University Press, Cambridge, UK.Google Scholar
Monod, J. (1970) Le Hasard et la Nécessité: Essai sur la philosophie naturelle de la biologie moderne. Paris: Éditions du Seuil.Google Scholar
Szilard, L. (1929) In Über die Entropieverminderung in einem thermodynamischen System bei Eingriffen intelligenter Wesen (On the reduction of entropy in a thermodynamic system by the intervention of intelligent beings). Zeitschrift für Physik 53, 840–856.Google Scholar
Monod, J. (1970) Le Hasard et la Nécessité: Essai sur la philosophie naturelle de la biologie moderne. Paris: Éditions du Seuil.Google Scholar
Boltzmann, L. (1905) Populäre Schriften, 1905. Leipzig: Verlag von Johann Ambrosius Barth, p. 396.Google Scholar
Luhmann, N. (1984) Soziale Systeme: Grundriß einer allegemeinen Theorie. Surkamp Verlag, Frankfurt-am-Main, Germany.Google Scholar
English edition: translated by Bednarz, J. Jr. (1995) Social systems, Stanford University Press, Stanford, CA.Google Scholar
Dawkins, R. (1982) The extended phenotype. Oxford University Press, Oxford, UK.Google Scholar
Mayr, E. (1963) Animal species and evolution. Belknap Press, Cambridge, MA.Google Scholar
Darwin, C. (1871) From a letter to J.D. Hooker, 1 February 1871.Google Scholar
Mayr, E. (1963) Animal species and evolution. Belknap Press, Cambridge, MA.Google Scholar
Bateson, W. (1894) Materials for the study of variation treated with especial regard to discontinuity in the origin of species. Macmillan, London, UK.Google Scholar
Boltzmann, L. (1886) Der zweite Hauptsatz der mechanischen Warmetheorie. Vienna: Gerold, p. 21.Google Scholar
Lewis, G.N. (1930) From a letter to Irving Langmuir, 5 August 1930. Quoted in Reingold, N. (1981) Science in America: A documentary history 1900–1939. University of Chicago Press, Chicago, IL, 400.Google Scholar
Landauer, R. (1991) The physical nature of information. Physics Letters, 217, 188–193.Google Scholar
Maxwell, J.C. (1850) In Maxwell, J.C., Harman, P.M. (Eds.) (1990) The scientific letters and papers of James Clerk Maxwell, Vol. 1, 1846–1862, p. 197. Cambridge University Press, Cambridge, UK.Google Scholar
Monod, J. (1970) Le Hasard et la Nécessité: Essai sur la philosophie naturelle de la biologie moderne. Paris: Éditions du Seuil.Google Scholar
Szilard, L. (1929) In Über die Entropieverminderung in einem thermodynamischen System bei Eingriffen intelligenter Wesen (On the reduction of entropy in a thermodynamic system by the intervention of intelligent beings). Zeitschrift für Physik 53, 840–856.Google Scholar
Monod, J. (1970) Le Hasard et la Nécessité: Essai sur la philosophie naturelle de la biologie moderne. Paris: Éditions du Seuil.Google Scholar
Boltzmann, L. (1905) Populäre Schriften, 1905. Leipzig: Verlag von Johann Ambrosius Barth, p. 396.Google Scholar
Luhmann, N. (1984) Soziale Systeme: Grundriß einer allegemeinen Theorie. Surkamp Verlag, Frankfurt-am-Main, Germany.Google Scholar
English edition: translated by Bednarz, J. Jr. (1995) Social systems, Stanford University Press, Stanford, CA.Google Scholar
Dawkins, R. (1982) The extended phenotype. Oxford University Press, Oxford, UK.Google Scholar
Mayr, E. (1963) Animal species and evolution. Belknap Press, Cambridge, MA.Google Scholar
Darwin, C. (1871) From a letter to J.D. Hooker, 1 February 1871.Google Scholar
Mayr, E. (1963) Animal species and evolution. Belknap Press, Cambridge, MA.Google Scholar
Bateson, W. (1894) Materials for the study of variation treated with especial regard to discontinuity in the origin of species. Macmillan, London, UK.Google Scholar
Adam, P.S., Borrel, G., Gribaldo, S. (2018) Evolutionary history of carbon monoxide dehydrogenase/acetyl-CoA synthase, one of the oldest enzymatic complexes. Proceedings of the National Academy of Sciences of the USA 115, E1166–E1173.Google Scholar
Adam, P.S., Borrel, G., Gribaldo, S. (2019) An archaeal origin of the Wood–Ljungdahl H4MPT branch and the emergence of bacterial methylotrophy. Nature Microbiology 4, 2155–2163.Google Scholar
Adami, C. (2002) What is complexity? Bioessays 24, 12, 1085–1094.Google Scholar
Adami, C., Ofria, C., Collier, T.C. (2000) Evolution of biological complexity. Proceedings of the National Academy of Sciences of the USA 97, 9, 4463–4468.Google Scholar
Allman, S., Baldwin, I.T. (2010) Insects betray themselves in nature to predators by the rapid isomerization of green leaf volatiles. Science 329, 1075–1078.Google Scholar
Amouyal, M., Buc, H. (1987) Topological unwinding at strong and weak promoters by RNA polymerase. A comparison between the lac wild type and the UV5 sites of Escherichia coli. Journal of Molecular Biology 195, 795–808.Google Scholar
Anderson, P., Bauer, W. (1978) Supercoiling in closed circular DNA: Dependence upon ion type and concentration. Biochemistry 17, 594–601.Google Scholar
Aragão, L.E.O.C. (2012) The rainforest’s water pump. Nature 489, 217–218.Google Scholar
Arnott, S. (2006) Historical article: DNA polymorphism and the early history of the double helix. Trends in Biochemical Sciences 31, 349–354.Google Scholar
Avery, O.T., Macleod, C.M., McCarty, M. (1944) 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. Journal of Experimental Medicine. 79, 137–158.Google Scholar
Baldwin, G.S., Brooks, N.J., Robson, R.E., Wynveen, A., Goldar, A., Leikin, S., Seddon, J.M., Kornyshev, A.A. (2008) DNA double helices recognize mutual sequence homology in a protein free environment. The Journal of Physical Chemistry B 112, 1060–1064.Google Scholar
Barbieri, M. (2016) What is information? Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences 374, pii, 20150060.Google Scholar
Barrangou, R., Fremaux, C., Deveau, H., Richards, M., Boyaval, P., Moineau, S., Romero, D.A., Horvath, P. (2007) CRISPR provides acquired resistance against viruses in prokaryotes. Science 315, 1709–1712.Google Scholar
Bateson, W. (1894) Materials for the study of variation treated with especial regard to discontinuity in the origin of species. Macmillan, London, UK.Google Scholar
Bayes, T. (1763) An essay toward solving a problem of the doctrine of chances. Philosophical Transactions, 307–418.Google Scholar
Bérut, A., Arakelyan, A., Petrosyan, A., Ciliberto, S., Dillenschneider, R., Lutz, E. (2012) Experimental verification of Landauer’s principle linking information and thermodynamics. Nature 483, 187–189.Google Scholar
Bird, A. (2007) Perceptions of epigenetics. Nature, 447, 396–398.Google Scholar
Boehnke, P., Bell, E.A., Stephan, T., Trappitsch, R., Keller, C.B., Pardo, O.S., Davis, A.M., Harrison, T.M., Pellin, M.J. (2018) Potassic, high-silica Hadean crust. Proceedings of the National Academy of Sciences of the USA 115, 6353–6356.Google Scholar
Böhle, U.-R., Hilger, H.H., Martin, W.F. (1996) Island colonization and evolution of the insular woody habit in Echium L. (Boraginaceae). Proceedings of the National Academy of Sciences of the USA 93, 11740–11745.Google Scholar
Brillouin, L. (1953) Negentropy principle of information. Journal of Applied Physics 24, 1152–1163.Google Scholar
Brillouin, L. (1956) Science and information theory. Academic Press, New York, NY.Google Scholar
Brouns, S.J., Jore, M.M., Lundgren, M., Westra, E.R., Slijkhuis, R.J., Snijders, A.P., Dickman, M.J., Makarova, K.S., Koonin, E.V., van der Oost, J. (2008) Small CRISPR RNAs guide antiviral defense in prokaryotes. Science 321, 960–964.Google Scholar
Buchner, P. (1965) Endosymbiosis of animals with plant microorganisms (English translation by Müller, Bertha). Interscience, New York, NY.Google Scholar
Cech, T.R., Zaug, A.J., Grabowski, P.J. (1981) In vitro splicing of a ribosomal RNA of Tetrahymena: Involvement of a guanosine nucleotide in the excision of the intervening sequence. Cell 27, 487–496.Google Scholar
Chaisson, E.J. (2011) Energy rate density as a complexity metric and evolutionary driver. Complexity 16, 27–40.Google Scholar
Chaisson, E.J. (2013) Using complexity science to search for unity in the natural sciences. In Complexity and the arrow of time (ed. Lineweaver, C., Davies, P., Ruse, M.). Cambridge University Press, Cambridge, UK.Google Scholar
Chaisson, E.J. (2015) Energy flows in low-entropy complex systems. Entropy 17, 8007–8018.Google Scholar
Church, R., McCarthy, B.J. (1967) Changes in nuclear and cytoplasmic RNA in regenerating mouse liver. Proceedings of the National Academy of Sciences of the USA 58, 1548–1555.Google Scholar
Ciciriello, F., Costanzo, G., Pino, S., Crestini, C., Saladino, R. & Di Mauro, E. (2008) Molecular complexity favors the evolution of ribopolymers. Biochemistry 47, 2732–2742.Google Scholar
Cleveland, L.R., Grimstone, A.V. (1964) The fine structure of the flagellate Mixotricha paradoxa and its associated micro-organisms. Proceedings of the Royal Society B: Biological Sciences, 159, 668–686.Google Scholar
Cobb, M. (2017) 60 years ago Francis Crick changed the logic of biology. PLoS Biology 15(9), e2003243.Google Scholar
Coen, E. (2001) Goethe and the ABC model of flower development. Comptes Rendus de l'Académie des Sciences – Series III 324, 523–530.Google Scholar
Cozzarelli, N.R., Boles, T.C., White, J.H. (1990) Primer on the topology and geometry of DNA supercoiling. In DNA topology and its biological effects (eds. Cozzarelli, N.R., Wang, J.C.), pp. 139–184. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.Google Scholar
Crawford, J.L., Kolpak, F.J., Wang, A.H., Quigley, G.J., van Boom, J.H., van der Marel, G., Rich, A. (1980) The tetramer d(CpGpCpGp) crystallizes as a left-handed double helix. Proceedings of the National Academy of Sciences of the USA 77, 4016–4020.Google Scholar
Crick, F.H.C. (1958) On protein synthesis. Symposia of the Society for Experimental Biology 12, 138–163.Google Scholar
Crick, F.H.C. (1966) Codon-anticodon pairing: the wobble hypothesis. Journal of Molecular Biology 19, 548–555.Google Scholar
Crick, F.H.C. (1968) The origin of the genetic code. Journal of Molecular Biology 38, 367–379.Google Scholar
Cubas, P., Vincent, C., Coen, E. (1999) An epigenetic mutation responsible for natural variation in floral symmetry. Nature 401, 157–161 (1999).Google Scholar
Danchin, A., Nikel, P.I. (2019) Why nature chose potassium. Journal of Molecular Evolution 87, 271–288.Google Scholar
Darwin, C. (1842) Essays of 1842 and 1844. http://darwin-online.org.uk/converted/pdf/1909_Foundations_F1556.pdfGoogle Scholar
Dawkins, R. (1976) The selfish gene. Oxford University Press, Oxford, UK.Google Scholar
de Frutos, M., Leforestier, A., Livolant, F. (2014) Relationship between the genome packing in the bacteriophage capsid and the kinetics of DNA ejection. Biophysical Reviews and Letters 9, 81–104.Google Scholar
Dibrova, D.V., Galperin, M.Y., Koonin, E.V., Mulkidjanian, A.Y. (2015) Ancient systems of sodium/potassium homeostasis as precursors of membrane energetics. Biochemistry (Moscow) 80, 495–516.Google Scholar
DiMaio, F., Yu, X., Rensen, E., Krupovic, M., Prangishvili, D., Egelman, E.H. (2015) A virus that infects a hyperthermophile encapsidates A-form DNA. Science 348, 914–917.Google Scholar
Doolittle, W.F., Sapienza, C. (1980) Selfish genes, the phenotype paradigm and genome evolution. Nature 284, 601–603.Google Scholar
Eddington, A.S. (1928) Quote from The Nature of the Physical World. Cambridge University Press, Cambridge, UK, 1928.Google Scholar
El Hassan, M.A., Calladine, C.R. (1997) Conformational characteristics of DNA: Empirical classifications and a hypothesis for the conformational behaviour of dinucleotide steps. Philosophical Transactions of the Royal Society A: 355, 43–100.Google Scholar
Francis, R., Read, D.J. (1984) Direct transfer of carbon between plants connected by vesicular arbuscular mycorrhizal mycelium. Nature 307, 53–56.Google Scholar
Gilbert, N., Allan, J. (2014) Supercoiling in DNA and chromatin. Current Opinion in Genetics and Development 25, 15–21.Google Scholar
Glaab, F., Kellermeier, M., Kunz, W., Morallon, M., Garciá-Ruiz, . (2012) Formation and evolution of chemical gradients and potential differences across self-assembling inorganic membranes. Angewandte Chemie International Edition 51, 4317–4321.Google Scholar
Goldstein, E., Drlica, K. (1984) Regulation of bacterial DNA supercoiling: Plasmid linking numbers vary with growth temperature. Proceedings of the National Academy of Sciences of the USA 81, 4046–4050.Google Scholar
Gorin, A.A., Zhurkin, V.B., Olson, W.K. (1995) B-DNA twisting correlates with base-pair morphology. Journal of Molecular Biology 247, 34–48.Google Scholar
Greaves, M. (2000) Cancer. The evolutionary legacy. Oxford University Press, Oxford, UK.Google Scholar
Guerrier-Takada, C., Gardiner, K., Marsh, T., Pace, N, Altman, S. (1983) The RNA moiety is the catalytic subunit of the enzyme. Cell 35, 849–857.Google Scholar
Hamilton, W. (1964) The genetical evolution of social behaviour. Journal of Theoretical Biology 7, 1–16, 17–52.Google Scholar
Hemmo, M., Shenker, O.R. (2012) The road to Maxwell’s demon. Cambridge University Press, Cambridge, UK.Google Scholar
Holland, T. (2005) Persian fire: The first world empire and the battle for the west. Random House, New York, NY.Google Scholar
Hsieh, L.S., Rouvière-Yaniv, J., Drlica, K. (1991) Bacterial DNA supercoiling and [ATP]/[ADP] ratio: Changes associated with salt shock. Journal of Bacteriology 173, 3914–3917.Google Scholar
Hunter, C.A. (1993) Sequence-dependent DNA structure. The role of base stacking interactions. Journal of Molecular Biology 230, 1025–1054.Google Scholar
Hunter, C.A. (1996) Sequence-dependent DNA structure. Bioessays 18, 157–162.Google Scholar
Huxley, J. (1959) Introduction. In de Chardin, P.T. The phenomenon of man. Harper, New York, NY.Google Scholar
Hyman, A.A., Weber, C.A., Jülicher, F. (2014) Liquid-liquid phase separation in biology. Annual Review of Cell and Developmental Biology 30, 39–58.Google Scholar
Inoue, S., Sugiyama, S., Travers, A.A., Ohyama, T. (2007) Self-assembly of double-stranded DNA molecules at nanomolar concentrations. Biochemistry 46, 164–171.Google Scholar
Jaynes, E.T. (2003) Probability theory: The logic of science. Cambridge University Press, Cambridge, UK. See Chapter 22 for quote.Google Scholar
Johnson, R.E., Prakash, L., Prakash, S. (2005) Biochemical evidence for the requirement of Hoogsteen base pairing for replication by human DNA polymerase I. Proceedings of the National Academy of Sciences of the USA 102, 10466–10471.Google Scholar
Kato, J., Misra, T.K., Chakrabarty, A.M. (1990) AlgR3, a protein resembling eukaryotic histone H1, regulates alginate synthesis in Pseudomonas aeruginosa. Proceedings of the National Academy of Sciences of the USA 87, 2887–2891.Google Scholar
Koonin, E.V. (2009) Darwinian evolution in the light of genomics. Nucleic Acids Research 37, 111–1034.Google Scholar
Koonin, E.V., Wolf, Y.I. (2009) Is evolution Darwinian and/or Lamarckian? Biology Direct 4, 42.Google Scholar
Koski, J.V., Maisi, V.F., Pekola, J.P., Averin, D.V. (2014) Experimental realization of a Szilard engine with a single electron. Proceedings of the National Academy of Sciences of the USA 111, 13786–13789.Google Scholar
Lane, N., Allen, J.F., Martin, W. (2010) How did LUCA make a living? Chemiosmosis in the origin of life. Bioessays 32(4), 271–280.Google Scholar
Larson, A.G., Elnatan, D., Keenen, M.M., Trnka, M.J., Johnston, J.B., Burlingame, A.L., Agard, D.A., Redding, S., Narlikar, G.J. (2017) Liquid droplet formation by HP1α suggests a role for phase separation in heterochromatin. Nature 547, 236–240.Google Scholar
Laundon, C.H., Griffith, J.D. (1988). Curved helix segments can uniquely orient the topology of supertwisted DNA. Cell 52, 545–549.Google Scholar
Lazcano, A. (2010) Historical development of origins research. Cold Spring Harbor Perspectives in Biology 2, a002089.Google Scholar
Lee, K.S., Bumbaca, D., Kosman, J., Setlow, P., Jedrzejas, M.J. (2008) Structure of a DNA-protein complex essential for protection in spores of Bacillus species. Proceedings of the National Academy of Sciences of the USA 105, 2806–2811.Google Scholar
Leforestier, A., Livolant, F. (2009). Structure of toroidal DNA collapsed inside the phage capsid. Proceedings of the National Academy of Sciences of the USA 106, 9157–9162.Google Scholar
Leforestier, A., Livolant, F. (2010) The bacteriophage genome undergoes a succession of intracapsid phase transitions upon DNA ejection. Journal of Molecular Biology 396, 384–395.Google Scholar
Lewis, G.N. (1926) quote from pp. 158–159 of The Anatomy of Science. Yale University Press, New Haven, CT.Google Scholar
Lilley, D.M.J. (1980) The inverted repeat as a recognisable structural feature in supercoiled DNA molecules. Proceedings of the National Academy of Sciences of the USA 77, 6468–6472.Google Scholar
Linnaeus, C. (1749) De Peloria. Diss. Ac. Amoenitates Academicae III, Uppsala.Google Scholar
Liu, L.F., Wang, J.C. (1987) Supercoiling of the DNA template during transcription. Proceedings of the National Academy of Sciences of the USA 84, 7024–7027.Google Scholar
Lotka, A.J. (1922a) Contributions to energetics of evolution. Proceedings of the National Academy of Sciences of the USA 8, 147–151.Google Scholar
Lotka, A.J. (1922b) Natural selection as a physical principle. Proceedings of the National Academy of Sciences of the USA 8, 151–154.Google Scholar
Luger, K., Mäder, A.W., Richmond, R.K., Sargent, D.F., Richmond, T.J. (1997) Crystal structure of the nucleosome core particle at 2.8 Å resolution. Nature 389, 251–260.Google Scholar
Macallum, A.B. (1926) The paleochemistry of the body fluids and tissues. Physiological Reviews 6, 316–357.Google Scholar
Mace, H.A., Pelham, H.R., Travers, A.A. (1983) Association of an S1 nuclease-sensitive structure with short direct repeats 5’ of Drosophila heat shock genes. Nature 304, 555–557.Google Scholar
MacFarlane, R. (2019) Underland. Hamish Hamilton, London, UK.Google Scholar
Margulis, L. (1991) Symbiosis and symbioticism. In Symbiosis as a source of evolutionary innovation: speciation and morphogenesis (ed. Margulis, L.), pp. 1–13, MIT Press, Boston, MA.Google Scholar
Marr, C., Geertz, M., Hütt, M.T., Muskhelishvili, G. (2008) Dissecting the logical types of network control in gene expression profiles. BMC Systems Biology. 2, 18.Google Scholar
Martin, W., Kowallik, K.V. (1999) Annotated English translation of Mereschkowsky’s 1905 paper ‘Über Natur und Ursprung der Chromatophoren im Pflanzenreiche’. European Journal of Phycology 34, 287–295.Google Scholar
Maurer, S., Fritz, J., Muskhelishvili, G., Travers, A. (2006) RNA polymerase and an activator form discrete subcomplexes in a transcription initiation complex. EMBO Journal 25, 3784–3790.Google Scholar
Mayr, E. (1963) Animal species and evolution. Belknap Press, Cambridge, MA.Google Scholar
McClellan, J.A., Boublíková, P., Paleček, E., Lilley, D.M.J. (1990) Superhelical torsion in cellular DNA responds directly to environmental and genetic factors. Proceedings of the National Academy of Sciences of the USA 87, 8373–8377.Google Scholar
McClintock, B. (1950) The origin and behavior of mutable loci in maize. Proceedings of the National Academy of Sciences of the USA 36, 344–355.Google Scholar
Medvedkin, V.N., Permyakov, E.A., Klimenko, L.V., Mitin, Y.V., Matsushima, N., Nakayama, S., Kretsinger, R.H. (1995) Interactions of (Ala*Ala*Lys*Pro)n and (Lys*Lys*Ser*Pro)n with DNA. Proposed coiled-coil structure of AlgR3 and AlgP from Pseudomonas aeruginosa. Protein Engineering, Design and Selection 8, 63–70.Google Scholar
Melis, P. (2003) The Nuragic civilization. Carlo Delfino editore, Sassari, Italy.Google Scholar
Mereschkowsky, C. (1905). Über Natur und Ursprung der Chromatophoren im Pflanzenreiche. Biologisches Centralblatt 25, 593–604.Google Scholar
Mereschkowsky, C. (1910). Theorie der zwei Plasmaarten als Grundlage der Symbiogenesis, einer neuen Lehre von der Entstehung der Organismen. Biologisches Centralblatt 30, 278–288, 289–303, 321–347, 353–367.Google Scholar
Miller, S.L. (1953) A production of amino acids under possible primitive Earth conditions. Science 117, 528–529.Google Scholar
Miller, S.L., Urey, H.C. (1959) Organic compound synthesis on the primitive earth. Science 130, 245–251.Google Scholar
Minyat, E.E., Khomyakova, E.B., Petrova, M.V., Zdobnov, E.M., Ivanov, V.I. (1995) Experimental evidence for slipped loop DNA, a novel folding type for polynucleotide chain. Journal of Biomolecular Structural and Dynamics 13, 523–527.Google Scholar
Mizuno, T., Chou, M.-Y., Inouye, M. (1984) A unique mechanism regulating gene expression: Translational inhibition by a complementary RNA transcript. Proceedings of the National Academy of Sciences of the USA 81, 1966–1970.Google Scholar
Molina, E.C. (1963) Two papers by Bayes with commentaries. Hafner Publishing Co., New York, NY.Google Scholar
Morowitz, H.J. (1978) Foundations of bioenergetics. Academic Press, New York, NY.Google Scholar
Moyroud, E., Wenzel, T., Middleton, R., Rudall, P.J., Banks, H., Reed, A., Mellers, G., Killoran, P., Westwood, M.M., Steiner, U., Vignolini, S., Glover, B.J. (2017) Disorder in convergent floral nanostructures enhances signalling to bees. Nature 550, 469–474.Google Scholar
Mulkidjanian, A.Y., Bychkov, A.Y., Dibrova, D.V., Galperin, M.Y., Koonin, E.V. (2012) Origin of first cells at terrestrial, anoxic geothermal fields. Proceedings of the National Academy of Sciences of the USA 109, E821–E830.Google Scholar
Muskhelishvili, G., Travers, A. (1997) The stabilisation of DNA microloops by FIS – a mechanism for torsional transmission in transcription activation and DNA inversion. Nucleic Acids and Molecular Biology 11, 179–190.Google Scholar
Nigatu, D., Henkel, W., Sobetzko, P., Muskhelishvili, G. (2016) Relationship between digital information and thermodynamic stability in bacterial genomes. EURASIP Journal on Bioinformatics and Systems Biology, 4.Google Scholar
Niklas, K.J. (1986) Large-scale changes in plant and animal terrestrial communities. In Patterns and processes in the history of life (eds. Raup, D.M., Jablonski, D.), pp. 383–405, Springer, Berlin, Germany.Google Scholar
Nowak, M.A., Tarnita, C.E., Wilson, E.O. (2010) The evolution of eusociality. Nature 466, 1057–1062.Google Scholar
Olson, W.K., Gorin, A.A., Lu, X.-J., Hock, L.M., Zhurkin, V.B. (1998) DNA sequence-dependent deformability deduced from protein-DNA crystal complexes. Proceedings of the National Academy of Sciences of the USA 95, 11163–11168.Google Scholar
Oparin, A.I. (1936) Vozniknovenie zhizni na zemle. Moscow: Izd. Akad. Nauk SSSR. (English translation with annotations by Morgulis, S., Oparin, A.I. (1938) The origin of life. New York: Macmillan.)Google Scholar
Orgel, L.E. (1968) Evolution of the genetic apparatus. Journal of Molecular Biology 38, 381–393.Google Scholar
Orgel, L.E., Crick, F.H.C. (1980) Selfish DNA: The ultimate parasite. Nature, 284 604–607.Google Scholar
Owen, D.J., Ornaghi, P., Yang, J.-C., Lowe, N., Evans, P.R., Ballario, P., Filetici, P., Travers, A.A. (2000) The structural basis for the recognition of acetylated histone H4 by the bromodomain of histone acetyltransferase Gcn5p. EMBO Journal 19, 6141–6149.Google Scholar
Parrondo, J.M.R., Horowitz, J.M., Sagawa, T. (2015) Thermodynamics of information. Nature Physics 11, 131–139.Google Scholar
Pearce, B.K.D., Pudritz, R.E., Semenov, D.A., Henning, T.K. (2017) Origin of the RNA world. The fate of nucleobases in warm little ponds. Proceedings of the National Academy of Sciences of the USA 114, 11327–11332.Google Scholar
Pennisi, E. (2013) The CRISPR craze. Science 341, 833–836.Google Scholar
Pennisi, E. (2016) A lichen ménage à trois. Science 353, 337.Google Scholar
Penrose, R. (2010) Cycles of time. The Bodley Head, London, UK.Google Scholar
Petrov, A.S., Gulen, B., Norris, A.M., Kovacs, N.A., Bernier, C.R, Lanier, K.A., Fox, G.E., Harvey, S.C., Wartell, R.M., Hud, N.V., Williams, L.D. (2015) History of the ribosome and the origin of translation. Proceedings of the National Academy of Sciences of the USA 112, 15396–15401.Google Scholar
Portier, P. (1918) Les symbiotes. Masson, Paris, France.Google Scholar
Protozanova, E., Yakovchuk, P., Frank-Kamenetskii, M. (2004) Stacked-unstacked equilibrium at the nick site of DNA. Journal of Molecular Biology 342, 775–785.Google Scholar
Raff, R.A., Kaufmann, T.C. (1983) Embryos, genes and evolution. Macmillan, New York, NY.Google Scholar
Reiter, N.J., Osterman, A., Torres-Larios, A., Swinger, K.K., Pan, T., Mondragón, A. (2010) Structure of a bacterial ribonuclease P holoenzyme in complex with tRNA. Nature 468, 784–789.Google Scholar
Renfrew, C. (1987) Archaeology and language: The puzzle of Indo-European origins, Pimlico, London, UK.Google Scholar
Rhodes, D., Klug, A. (1980) Helical periodicity of DNA determined by enzyme digestion. Nature 286, 573–578.Google Scholar
Roach, J.C., Glusman, G., Smit, A.F.A., Huff, C. D., Hubley, R., Shannon, P.T., Rowen, L., Pant, K.P., Goodman, N., Bamshad, M., Shendure, J., Drmanac, R., Jorde, L.B., Hood, L., Galas, D.J. (2010) Analysis of genetic inheritance in a family quartet by whole-genome sequencing. Science 328, 636–639.Google Scholar
Rosenberg, E., Koren, O., Reshef, L., Efrony, R., Zilber-Rosenberg, I. (2007) The role of microorganisms in coral health, disease and evolution. Nature Reviews Microbiology 5, 355–362.Google Scholar
Saladino, R., Botta, G., Bizzarri, B.M., Di Mauro, E., Garciá Ruiz, J.M. (2016) A global scale scenario for prebiotic chemistry: Silica-based self-assembled mineral structures and formamide. Biochemistry 55, 2806–2811.Google Scholar
Saladino, R., Di Mauro, E., Garciá-Ruiz, J.M. (2019) A universal geochemical scenario for formamide condensation and prebiotic chemistry. Chemistry, 25, 3181–3189.Google Scholar
Satchwell, S.C., Drew, H.R., Travers, A.A (1986) Sequence periodicities in chicken nucleosome core DNA. Journal of Molecular Biology 191, 659–675.Google Scholar
Schimper, A.F.W. (1883) Über die Entwicklung der Chorophyllkörner und Farbkörper. Botanische Zeitung 41, 105–114.Google Scholar
Schneider, T.D. (1997) Information content of individual genetic sequences. Journal of Theoretical Biology 189, 427–441.Google Scholar
Schwendener, S. (1867). Über die wahre Natur der Flechten. Verhandlungen der Schweizerischen Naturforschenden Gesellschaft in Rheinfelden 51, 88–90.Google Scholar
Shannon, C. (1948) A mathematical theory of communication. Bell System Technical Journal 27, 379–423.Google Scholar
Sharov, A.A. (2016 ) Coenzyme world model of the origin of life. Biosystems 144, 8–17.Google Scholar
Simard, S.W., Perry, D.A., Jones, M.D., Myrold, D.D., Durall, D.M., Molina, R. (1997) Net transfer of carbon between ectomycorrhizal tree species in the field. Nature 388, 579–582.Google Scholar
Simon, H.A. (1962) The architecture of complexity. Proceedings of the American Philosophical Society 106, 467–482.Google Scholar
Spracklen, D.V., Arnold, S.R., Taylor, C.M. (2012) Observations of increased tropical rainfall preceded by air passage over forests. Nature 482, 282–285.Google Scholar
Strom, A.R., Emelyanov, A.V., Mir, M., Fyodorov, D.V., Darzacq, X., Karpen, G.H. (2017) Phase separation drives heterochromatin domain formation. Nature 547, 241–245.Google Scholar
Sundquist, W.I., Klug, A. (1989) Telomeric DNA dimerizes by formation of guanine tetrads between hairpin loops. Nature 342, 825–829.Google Scholar
Sutherland, J.D. (2016) The origin of life – out of the blue. Angewandte Chemie International Edition 55, 104–121.Google Scholar
Tainter, J.A. (1988) The collapse of complex societies. Cambridge University Press, Cambridge, UK.Google Scholar
Thomson, W. (Lord Kelvin) (1879) The sorting demon of Maxwell. Nature 20, 126.Google Scholar
Toyabe, S., Sagawa, T., Ueda, M., Muneyuki, E., Sano, M. (2010 ) Experimental demonstration of information-to-energy conversion and validation of the generalized Jarzynski equality. Nature Physics 6, 988–992.Google Scholar
Travers, A. (2006) The evolution of the genetic code revisited. Origins of Life and Evolution of Biospheres 36, 549–555.Google Scholar
Travers, A., Muskhelishvili, G. (2020) Chromosomal organisation and regulation of genetic function in Escherichia coli integrates the DNA analog and digital information. EcoSal Plus 9(1). doi: 10.1128/ecosalplus.ESP-0016-2019.Google Scholar
Tuovinen, V., Ekman, S., Thor, G., Vanderpool, D., Spribille, T., Johannesson, H. (2019) Two basidiomycete fungi in the cortex of wolf lichens. Current Biology 29, 476–483.Google Scholar
Turner, A.L., Watson, M., Wilkins, O.G., Cato, L., Travers, A., Thomas, J.O., Stott, K. (2018) Highly disordered histone H1-DNA model complexes and their condensates. Proceedings of the National Academy of Sciences of the USA 115, 11964–11969.Google Scholar
Van Roey, K., Uyar, B., Davey, N. (2014) Short linear motifs: Ubiquitous and functionally diverse protein interaction modules directing cell regulation. Chemical Reviews 114, 6733–6778.Google Scholar
Wang, J.C. (1979) Helical repeat of DNA in solution. Proceedings of the National Academy of Sciences of the USA 76, 200–203.Google Scholar
Watson, J.D., Crick, F.H.C. (1953) Molecular structure of nucleic acids: A structure for deoxyribonucleic acid. Nature 171, 737–738.Google Scholar
Watson, M., Stott, K. (2019) Disordered domains in chromatin binding proteins. Essays in Biochemistry 63, 147–156.Google Scholar
Weiss, M.C., Sousa, F.L, Mrnjavac, N., Neukirchen, S., Roettger, M., Nelson-Sathi, S., Martin, W.F. (2016). The physiology and habitat of the last universal common ancestor. Nature Microbiology 1(9), 16116.Google Scholar
Williams, T.A., Szöllősi, G.J., Spang, A., Foster, P.G., Heaps, S.E., Boussau, B., Ettema, T.J.G., Embley, T.M. (2017) Integrative modeling of gene and genome evolution roots the archaeal tree of life. Proceedings of the National Academy of Sciences of the USA 114, E4602–E4611.Google Scholar
Wilson, E.B. (1899) The structure of protoplasm. Science 10, 33–45.Google Scholar
Woese, C.R. (1968) The fundamental nature of the genetic code: Prebiotic interactions between polynucleotides and polyaminoacids and their derivatives. Proceedings of the National Academy of Sciences of the USA 59, 110–117.Google Scholar
Wright, P.E., Dyson, H.J. (1999) Intrinsically unstructured proteins: Re-assessing the protein structure-function paradigm. Journal of Molecular Biology 293, 321–331.Google Scholar
Wu, C.-Y., Travers, A. (2019) Modelling and DNA topology of compact 2-start and 1-start chromatin fibres. Nucleic Acids Research 47, 9902–9924.Google Scholar
Zamenhof, S., Shettles, L.B., Chargaff, E. (1950) Human deoxypentose nucleic acid. Nature 165, 756–757.Google Scholar
Zuo, Y., Steitz, T.A. (2015) Crystal structures of the E. coli transcription initiation complexes with a complete bubble. Molecular Cell 58, 534–540.Google Scholar

Save book to Kindle

To save this book to your Kindle, first ensure coreplatform@cambridge.org is added to your Approved Personal Document E-mail List under your Personal Document Settings on the Manage Your Content and Devices page of your Amazon account. Then enter the ‘name’ part of your Kindle email address below. Find out more about saving to your Kindle.

Note you can select to save to either the @free.kindle.com or @kindle.com variations. ‘@free.kindle.com’ emails are free but can only be saved to your device when it is connected to wi-fi. ‘@kindle.com’ emails can be delivered even when you are not connected to wi-fi, but note that service fees apply.

Find out more about the Kindle Personal Document Service.

Available formats
×

Save book to Dropbox

To save content items to your account, please confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your account. Find out more about saving content to Dropbox.

Available formats
×

Save book to Google Drive

To save content items to your account, please confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your account. Find out more about saving content to Google Drive.

Available formats
×