Skip to main content

Principles and Mechanisms of Biological Evolution

  • Chapter
  • First Online:
Molecular Theory of the Living Cell
  • 1378 Accesses

Abstract

The year 2010 marked the 150th anniversary of the historic publication of Darwin’s (1809–1882) “Origin of Species” in which he proposed his theory of evolution by natural selection (Darwin 1859). Evolution (to be defined below) is a controversial topic (Miller 2008; Carroll 2006) and has been attracting the interest of both scientists and lay public, ranking among the most widely discussed subjects on the Internet (see Table 14.1). For example, evolution theory has been visited by more people than Einstein’s relativity theory as of August 2009 and is comparable to the topic of Obama’s cabinet in the number of visitors.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 169.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 219.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 219.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Agarwal, B.K.: Quantum Mechanics and Field Theory. Asia Publications, New York (1977)

    Google Scholar 

  • Anderson, P.W.: More is different. Science 177, 393–396 (1972)

    Article  ADS  Google Scholar 

  • Avery, O., MacLeod, C.M., McCarty, M.: Studies on the chemical nature of the substance inducing transformation of pneumococcal types: induction of transformation by a desoxyribonucleia acid fraction isolated from pneumococcal type III. J. Exp. Med. 79(2), 137–158 (1944)

    Article  Google Scholar 

  • Brillouin, L.: Negentropy principle of information. J. Appl. Phys. 24(9), 1152–1163 (1953)

    Article  ADS  MATH  Google Scholar 

  • Brillouin, L.: Science and Information Theory, pp. 152–156. Academic Press, New York (1956)

    MATH  Google Scholar 

  • Brooks, D.R., Wiley, E.O.: Evolution as Entropy. The University of Chicago Press, Chicago (1986)

    Google Scholar 

  • Carroll, S.: Endless Forms Most Beautiful: The New Science of Evo Devo. W. W. Norton & Co, New York (2006)

    Google Scholar 

  • Chothia, C.: One thousand families for the molecular biologist. Nature 357, 543–544 (1992)

    Article  ADS  Google Scholar 

  • Darwin, C.: On the Origin of Species by Means of Natural Selection, or the Preservation of Favored Races in the Struggle for Life. John Murray, London (1859)

    Google Scholar 

  • Dobzhansky, T.: Nothing in biology makes sense except in the light of evolution. Am. Biol. Teach. 35(March), 125–129 (1973)

    Article  Google Scholar 

  • Eldredge, N., Gould, S.J.: Punctuated equilibria: an alternative to phyletic gradualism. In: Schopf, r.J.M. (ed.) Models in Paleobiology, pp. 82–115. Freeman Cooper, San Francisco (1972)

    Google Scholar 

  • Fodor, J.A., Piattelli-Palmarini, M.: What Darwin Got Wrong. Profile Books, London (2010)

    Google Scholar 

  • Garcia-Martinez, J., Aranda, A., Perez-Ortin, J.E.: Genomic run-on evaluates transcription rates for all yeast genes and identifies gene regulatory mechanisms. Mol. Cell 15, 303–313 (2004)

    Article  Google Scholar 

  • Gerhart, J., Kirschner, M.: Cells, Embryos and Evolution. Blackwell, Oxford (1997)

    Google Scholar 

  • Gurzadyan, V.G., Penrose, R.: Concentric circles in WMAP data may provide evidence of violent pre-Big-Bang activity, arXiv:1011.3706v1 [astro- ph.CO] (2010)

  • Haken, H.: Synergetics, an Introduction: Nonequilibrium Phase Transitions and Self-Organization in Physics, Chemistry, and Biology, 3 (rev. enl)th edn. Springer-Verlag, New York (1983)

    MATH  Google Scholar 

  • Han, M.Y.: Quarks and Gluons: A Century of Particle Charges. World Scientific, Singapore (1999)

    Book  Google Scholar 

  • Herbert, N.: Quantum Reality: Beyond the New Physics, An Excursion into Metaphysics, p. 64. Anchor Books, Garden City (1987)

    Google Scholar 

  • Heylighen, F., Joslyn, C.: Cybernetics and second-order cybernetics. In: Meyers, R.A. (ed.) Encyclopedia of Physical Science & Technology, 3rd edn, pp. 1–24. Academic Press, New York (2001)

    Google Scholar 

  • Huynen, M.A., van Nimwegen, E.: The frequency distribution of gene family sizes in complete genomes. Mol. Biol. Evol. 15(5), 583–589 (1998)

    Article  Google Scholar 

  • Huxley, A.F., Hanson, J.: In: Bourne, G.H. (ed.) The Structure and Function of Muscle, vol. I, pp. 183–227. (1960)

    Google Scholar 

  • Ishijima, A., Kojima, H., Higuchi, H., Harada, Y., Funatsu, T., Yanagida, T.: Simultaneous measurement of chemical and mechanical reaction. Cell 70, 161–171 (1998)

    Article  Google Scholar 

  • Jaynes, E.T.: Information theory and statistical mechanics. Phys. Rev. 106, 620–630 (1957a)

    Article  MathSciNet  ADS  MATH  Google Scholar 

  • Jaynes, E.T.: Information theory and statistical mechanics II. Phys. Rev. 108, 171–190 (1957b)

    Article  MathSciNet  ADS  Google Scholar 

  • Ji, S.: The bhopalator – a molecular model of the living cell based on the concepts of conformons and dissipative structures. J. Theor. Biol. 116, 399–426 (1985a)

    Article  Google Scholar 

  • Ji, S.: The Bhopalator: a molecular model of the living cell. Asian J. Exp. Sci 1, 1–33 (1985b)

    Google Scholar 

  • Ji, S.: Biocybernetics: a machine theory of biology. In: Ji, S. (ed.) Molecular Theories of Cell Life and Death, pp. 1–237. Rutgers University Press, New Brunswick (1991)

    Google Scholar 

  • Ji, S.: Isomorphism between cell and human languages: molecular biological, bioinformatics and linguistic implications. Biosystems 44, 17–39 (1997a)

    Article  Google Scholar 

  • Ji, S.: The cell as the smallest DNA-based molecular computer. Biosystems 52, 123–133 (1999a)

    Article  Google Scholar 

  • Ji, S.: The Bhopalator: an information/energy dual model of the living cell (II). Fundam. Inform. 49(1–3), 147–165 (2002b)

    MATH  Google Scholar 

  • Ji, S. (2004b).: Semiotics of life: a unified theory of molecular machines, cells, the mind, peircean signs, and the universe based on the principle of information- energy complementarity. In: Reports, Research Group on Mathematical Linguistics, XVII Tarragona Seminar on Formal Syntax and Semantics, Rovira i Virgili University, Tarragona, Spain, 23–27 April 2003. Available at Google and at http://grammars.grlmc.com/GRLMC/reports/SOLManuscriptsubmitted_final.doc

  • Ji, S.: Modeling the single-molecule enzyme kinetics of cholesterol oxidase based on Planck's radiation formula and the principle of enthalpy-entropy compensation. In: Short Talk Abstracts The 100th Statistical Mechanics Conference, Rutgers University, Piscataway, N.J, 13–16 Dec (2008b)

    Google Scholar 

  • Ji, S., Chaovalitwongse, A., Fefferman, N., Yoo, W., Perez-Ortin, J.E.: Mechanism-based clustering of genome-wide mRNA levels: roles of transcription and transcript-degradation rates. In: Butenko, S., Chaovalitwongse, A., Pardalos, P. (eds.) Clustering Challenges in Biological Networks, pp. 237–255. World Scientific Publishing Co, Singapore (2009a)

    Chapter  Google Scholar 

  • Kelso, J.A.S.: Dynamic Patterns: Self-Organization in Brain Science and Behaviors. The MIT Press, Cambridge (1995)

    Google Scholar 

  • Kirschner, M., Gerhart, J.: Evolvability. Proc. Natl. Acad. Sci. U. S. A. 95, 8420–8427 (1998)

    Article  ADS  Google Scholar 

  • Kirschner, M.W., Gerhart, J.C.: The Plausibility of Life: Resolving Darwin’s Dilemma. Yale University Press, New Haven (2005)

    Google Scholar 

  • Kondepudi, D., Prigogine, I.: Modern Thermodynamics: From Heat Engine to Dissipative Structures. Wiley, Chichester (1998)

    Google Scholar 

  • Koomin, E.V., Wolf, Y.I., Karev, G.P.: The structure of the protein universe and genome evolution. Nature 420, 218–223 (2002)

    Article  ADS  Google Scholar 

  • Laughlin, R.: A Different Universe: Reinventing Physics from the Bottom Down. Basic Books, New York (2005)

    Google Scholar 

  • Lloyd, S.: Quantum mechanics and emergence. In: Abbott, D., Davies, P.C., Pati, A.K. (eds.) Quantum Aspects of Life, pp. 19–30. Imperial College Press, London (2009)

    Google Scholar 

  • Lu, H.P., Xun, L., Xie, X.S.: Single-molecule enzymatic dynamics. Science 282, 1877–1882 (1998)

    Article  ADS  Google Scholar 

  • Mayr, E.: One Long Argument: Charles Darwin and the Genesis of Modern Evolutionary Thought. Harvard University Press, Cambridge (1991)

    Google Scholar 

  • Michaelis, L., Menten, M.L.: Die kinetik der invertinwirkung. Biochem. Z. 49, 333–369 (1913)

    Google Scholar 

  • Miller, K.R.: Only A Theory: Evolution and the Battle for America’s Soul. Viking, New York (2008)

    Google Scholar 

  • Miyazawa, S.A., Jernigan, R.L.: Residue-residue potentials with a favourable contact pair term and an unfavourable high packing density term, for simulation and threading. J. Mol. Biol. 256, 623–644 (1996)

    Article  Google Scholar 

  • Planck, M.: On an improvement of Wien’s equation for the spectrum. Verhandl. Dtsch. phys. Ges 2, 202 (1900)

    Google Scholar 

  • Plotnitsky, A.: Reading Bohr: Physics and Philosophy. Springer, Kindle Edition (2006)

    MATH  Google Scholar 

  • Prigogine, I.: Dissipative structures and biological order. Adv. Biol. Med. Phys. 16, 99–113 (1977)

    MathSciNet  Google Scholar 

  • Prigogine, I.: From Being To Becoming: Time and complexity in Physical Sciences, pp. 19–26. W. H. Freeman and Company, San Francisco (1980)

    Google Scholar 

  • Ramond, P.: Field Theory: A Modern Primer. Benjamin, Reading, Massachusetts (1981)

    Google Scholar 

  • Ryder, L.H.: Quantum Field Theory. Cambridge University Press, Cambridge (1985)

    MATH  Google Scholar 

  • Salthe, S.N.: Development and Evolution. MIT Press, Cambridge (1993)

    Google Scholar 

  • Salthe, S.N.: Development and Evolution: Complexity and Change in Biology, pp. 5–10, 20–25, and 131–136.The MIT Press, Cambridge, Mass (1996) Salthe, S. N. (2009). Personal communication.

    Google Scholar 

  • Swanson, C.P.: The Cell, 2nd edn. Prentice-Hall, Englewood Cliffs (1964)

    Google Scholar 

  • Turvey, M.T., Kugler, P.N.: A comment on equating information with symbol strings. Am. J. Physiol. 246, R925–R927 (1984) (Regulatory Integrative Comp. Physiol. 15)

    Google Scholar 

  • Volkenstein, M.V.: Entropy and Information. Birkhäuser, Basel (2009)

    Book  MATH  Google Scholar 

  • Watson, J.D., Crick, F.H.C.: Molecular structure of nucleic acid. Nature 171, 737–738 (1953)

    Article  ADS  Google Scholar 

  • West-Eberhard, M.J.: Evolution in the light of developmental and cell biology, and vice versa. Proc. Nat. Acad. Sci. USA 95, 8417–8419 (1998)

    Article  ADS  Google Scholar 

  • Wes-Eberhard, M.J.: Developmental Plasticity and Evolution. Oxford University Press, Oxford (2003)

    Google Scholar 

  • Wolfram, S.: A New Kind of Science. Wolfram Media, Champaign (2002)

    MATH  Google Scholar 

  • Zeldovich, K.B., Chen, P., Shakhnovich, B.E., Shakhnovich, E.I.: A first- principles model of early evolution: emergence of gene families, species, and preferred protein folds. PLoS Comput. Biol. 3(7), e139 (2007a). doi:10.1371 /journal.pcbi.0030139

    Article  ADS  Google Scholar 

  • Zeldovich, K.B., Chen, P., Shakhnovich, E.I.: Protein stability imposes limits on organism complexity and speed of molecular evolution. Proc. Nat. Acad. Sci. USA 104(41), 16152–16157 (2007b)

    Article  ADS  Google Scholar 

  • Zeldovich, K.B., Shakhnovich, E.I.: Understanding protein evolution: from proteins physics to Darwinian selection. Ann. Rev. Phys. Chem. 59, 105–127 (2008)

    Article  ADS  Google Scholar 

  • Zimmer, C.: Evolving Darwin. Time p. 51. 23 Feb 2009

    Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Sungchul Ji PhD .

Rights and permissions

Reprints and permissions

Copyright information

© 2012 Springer Science+Business Media, LLC

About this chapter

Cite this chapter

Ji, S. (2012). Principles and Mechanisms of Biological Evolution. In: Molecular Theory of the Living Cell. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-2152-8_14

Download citation

  • DOI: https://doi.org/10.1007/978-1-4614-2152-8_14

  • Published:

  • Publisher Name: Springer, New York, NY

  • Print ISBN: 978-1-4614-2151-1

  • Online ISBN: 978-1-4614-2152-8

  • eBook Packages: Physics and AstronomyPhysics and Astronomy (R0)

Publish with us

Policies and ethics