Skip to main content
SpringerLink
Log in

Biology

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

  • 1427 Accesses

Abstract

As already alluded to in Preface, the American paleontologist Gaylord Simpson (1964) made a statement to the effect that Physicists study the principles that apply to all phenomena; biologists study phenomena to which all principles apply.

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

Access this chapter

Log in via an institution
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

  • Abbott, D., Davies, P.C., Pati, A.K.: Quantum Aspects of Life, pp. 349–380. Imperial College Press, London (2009)

    Google Scholar 

  • Alberts, B.: The cell as a collection of protein machines: preparing the next generation of molecular biologists. Cell 92, 291–294 (1998)

    Article  Google Scholar 

  • Aloy, P., Russell, R.B.: Ten thousand interactions for the molecular biologist. Nat. Biotechnol. 22(10), 1317–1321 (2004)

    Article  Google Scholar 

  • Atkins, P.: Four Laws that Drive the Universe. Oxford Univeristy Press, Oxford (2007)

    Google Scholar 

  • Bacciagaluppi, G., Valenti, A.: Quantum Theory at the Crossroads: Reconsidering the 1927 Solvay Conference. Cambridge University Press, Cambridge (2009)

    MATH  Google Scholar 

  • Bellomo, N., Bellouquid, A., Harrero, M.A.: From microscopic to macroscopic descriptions of multicellular systems and biological growing tissues. Comput. Math. Appl. 53, 647–663 (2007)

    Article  MathSciNet  MATH  Google Scholar 

  • Benham, C.J.: Duplex destabilization in supercoiled DNA is predicted to occur at specific transcriptional regulatory regions. J. Mol. Biol. 255, 425–434 (1996a)

    Article  Google Scholar 

  • Benham, C.J.: Computation of DNA structural variability – a new predictor of DNA regulatory regions. Comput. Appl. Biosci. 12(5), 375–381 (1996b)

    Google Scholar 

  • Benham, C.J., Bi, C.: The analysis of stress-induced duplex destabilization in long genomic DNA sequences. J. Comput. Biol. 11(4), 519–543 (2004)

    Article  Google Scholar 

  • Bennett, C.H.: Thermodynamics of computation - a review. Int. J. Theor.Phys. 21(12), 905–940 (1991)

    Article  Google Scholar 

  • Blobel, G.: Nuclear-cytoplasmic transport, The 4th Morris Lecture, Robert Wood Johnosn Medical School, UMDNJ, Picataway, N.J, 4 Nov 2007

    Google Scholar 

  • Bohm, D., Hiley, B.J.: The Undivided Universe. Routledge, London (1993)

    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 

  • Cahay, M.: Quantum confinement VI: Nanostructured materials and devices: Proceedings of the International Symposium, The Electrochemical Society (ECS) Pennington, NJ 08534, USA 2001

    Google Scholar 

  • Collier, J.: Causation is the transfer of information. In: Sankey, H. (ed.) Causation, Natural Laws and Explanation. Kluwer, Dordrecht (1999)

    Google Scholar 

  • Culler, J.: Ferdinand de Saussure. Cornell University Press, Ithaca (1991). Revised Edition

    Google Scholar 

  • Curley, E.: A Spinoza Reader: The Ethics and Other Works, pp. 67–70. Princeton University Press, Princeton (1994)

    Google Scholar 

  • Davies, P., Gregersen, N.H. (eds.): Information and the Nature of Reality: From Physics to Metaphysics. Cambridge University Press, New York (2010)

    Google Scholar 

  • Dellaire, G.: Nuclear compartment: Nuclear pore. http://npd.hgu.mrc.ac.uk/compartments/nuc_pore.html (2007)

  • Dillon, M.C.: Merleau-Ponty's Ontology. Northwestern University Press, Evanston (1997)

    Google Scholar 

  • Dundr, M., Misteli, T.: Functional architecture in the cell nucleus. Biochem. J. 356, 297–310 (2001)

    Article  Google Scholar 

  • Gilson, J.G., McPherson, R.: Quantization of Boltzmann’s Gas Constant. Downloaded from the Internet through Google on 3/18/2011. No reference was given in the document (2011)

    Google Scholar 

  • Green, D.E., Ji, S.: The electromechanochemical model of mitochondrial strucutre and funciton. In: Schulz, J., Cameron, B.F. (eds.) Molecular Basis of Electron Transport, pp. 1–44. Academic Press, New York (1972a)

    Google Scholar 

  • Green, D.E., Ji, S.: Electromechanochemical model of mitochondrial structure and function. Proc. Natl. Acad. Sci. U. S. A. 69, 726–729 (1972b)

    Article  ADS  Google Scholar 

  • Halle, J.-P., Meisterernst, M.: Gene expression: increasing evidence for a transcriptosome. Trends Genet. 12(5), 161–163 (1996)

    Article  Google Scholar 

  • Hartwell, L.H., Hopfield, J.J., Liebler, S., Murray, A.W.: From molecules to modular cell biology. Nature 402(Suppl. 6761), C47–C52 (1999)

    Article  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 

  • 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 

  • Ishii, Y., Yangida, T.: Single molecule detection in life science. Single Mol. 1(1), 5–16 (2000)

    Article  ADS  Google Scholar 

  • Ishii, Y., Yanagida, T.: How single molecule detection measures th dynamics of life. HFSP J. 1(1), 15–29 (2007)

    Article  Google Scholar 

  • Ji, S.: Energy and negentropy in enzymic catalysis. Ann. N. Y. Acad. Sci. 227, 419–437 (1974a)

    Article  ADS  Google Scholar 

  • Ji, S.: A general theory of ATP synthesis and utilization. Ann. N. Y. Acad. Sci. 227, 211–226 (1974b)

    Article  ADS  Google Scholar 

  • Ji, S.: The principles of ligand-protein interactions and their application to the mechanism of oxidative phosphorylation. In: Yagi, K. (ed.) Structure and Function of Biomembranes, pp. 25–37. Japan Scientific Societies Press, Tokyo (1979)

    Google Scholar 

  • Ji, S.: Watson-crick and prigoginian forms of genetic information. J. Theor. Biol. 130, 239–245 (1988)

    Article  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.: Complementarism: A new dialogue between science and religion based on modern biology, In: Proceedings of the Fourth KSEA (Korean Scientists and Engineers Association in America) Northeast Regional Conference, pp. 319–328. Stevens Institute of Technology, Hoboken, N.J (1993)

    Google Scholar 

  • Ji, S.: Complementarism: a biology-based philosophical framework to integrate western science and eastern tao, in Psychotherapy East and West: Integration of Psychotherapies, pp. 517–548. Korean Academy of Psychotherapists, 178–23 Sungbuk-dong, Songbuk-ku, Seoul 136–020, Korea (1995)

    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 linguistics of DNA: words, sentences, grammar, phonetics, and semantics. Ann. N. Y. Acad. Sci. 870, 411–417 (1999b)

    Article  ADS  Google Scholar 

  • Ji, S.: Free energy and information contents of Conformons in proteins and DNA. Biosystems 54, 107–130 (2000)

    Article  Google Scholar 

  • Ji, S.: Molecular information theory: solving the mysteries of DNA. In: Ciobanu, G., Rozenberg, G. (eds.) Modeling in Molecular Biology, Natural Computing Series, pp. 141–150. Springer, Berlin (2004a)

    Chapter  Google Scholar 

  • Ji, S.: First, second and third articulations in molecular Ccmputing in the cell. In: Abstracts, 2005 World DNA and Genome Day, Dalian, China, 25–29 April 2005, p. 77

    Google Scholar 

  • Ji, S.: Info-statistical mechanics of cell metabolism. In Abstract, 56th Statistical Mechanics Conference, Rutgers University, Piscataway, 17–19 Dec 2006, p. 6.. Available at http://www.math.rutgers.edu/events/smm/smm96_shorttlks.abs.html (2006a)

  • Ji, S.: SOWAWN machines and life. http://necsi.org:8100/Lists/complex-science/Message/8370.html (2006b)

  • Ji, S.: S- and H-categories of entropies. Mailing List complex- science@necsi.org Message #8861 (2006d)

    Google Scholar 

  • 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.: The Cell Language Theory: Decoding RNA Waves, the Sound of Cell Langauge. Imperial College Press, London (2012) (to appear)

    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 

  • Ji, S., So, K.: The universal law of thermal transitions applicable to blackbody radiation, single-molecule enzymology and whole-cell metabolism. In: Abstract B1, The 102nd Statistical Mechanics Conference, Rutgers University, Piscataway, N.J, 13–15 Dec (2009d)

    Google Scholar 

  • Jin, T., Sasaki, A., Kinjo, M., Miyazaki, J.: A quantum dot-based ratiometric pH sensor. Chem. Commun. 46, 2408–24510 (2010)

    Article  Google Scholar 

  • Klir, G.J.: Developments in uncertainty-based information. Adv. Comput. 36, 255–332 (1993)

    Article  Google Scholar 

  • Kragh, H.: Max Planck: the reluctant revolutionary. From Physics World Dec 2000. Available at http://www.physicsworldarchive.iop.org (2000)

  • Laszlo, E.: The Connectivity Hypothesis: Foundation of an Integral Science of Quantum, Cosmos, Life, and Consciousness. State University of New York Press, Albany (2003)

    Google Scholar 

  • Layzer, D.: The arrow of time. Sci. Am. 233, 56–69 (1975)

    Article  ADS  Google Scholar 

  • Leff, H., Rex, A.: Maxwell’s Demon: Entropy. Computing, Princeton University Press, Princeton, Information (1962)

    Google Scholar 

  • Lloyd, S.: Programming the Universe: A Quantum Computer Scientist Takes on the Cosmos. Alfred A Knopf, New York (2006)

    Google Scholar 

  • Lockless, S.W., Ranganathan, R.: Evolutionarily conserved pathways of energetic connectivity in protein families. Science 286, 295–299 (1999)

    Article  Google Scholar 

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

    Article  ADS  Google Scholar 

  • Mamontov, E., Psiuk-Maksymowitcz, K., Koptioug, A.: Stochastic mechanics in the context of the properties of living systems. Math. Comp. Modeling 44(7–8), 595–607 (2006)

    Article  MATH  Google Scholar 

  • McClare, C.W.F.: Chemical machines, maxwell's demon and living organisms. J. theoret. Biol. 30, 1–34 (1971)

    Article  Google Scholar 

  • McKaughan, D.J.: The influence of Niels Bohr on max delbrück. Isis 96, 507–529 (2005)

    Article  MathSciNet  MATH  Google Scholar 

  • Mikula, S., Niebur, E.: The effects of input rate and synchrony on a coincidence detector - analytical solution. Neural Computat. 5(3), 539–547 (2003)

    Article  Google Scholar 

  • Morrison, M.A.: Understanding Quantum Physics: A User’s Manual, p. 169. Prentice Hall, Englewood (1990)

    Google Scholar 

  • Murdoch, D.: Niels Bohr’s Philosophy of Physics. Cambridge University Press, Cambridge (1987)

    Book  Google Scholar 

  • Nave, R.: Blackbody radiation. http://hyperphysics.phys-astr.gsu.edu/ hbase/mod6.html (2009)

  • Norris, V., et al.: Hypothesis: hyperstructures regulate bacterial structure and the cell cycle. Biochimie 81, 915–920 (1999)

    Article  Google Scholar 

  • Norris, V., den Blaauwen, T., Cabin-Flaman, A., Doi, R.H., Harshey, R., Janniere, L., Jimenez-Sanchez, A., Jin, D.J., Levin, P.A., Mileykovskaya, E., Minsky, A., Saier Jr., M., Skarstad, K.: Functional taxonomy of bacterial hyperstructures. Microbiol. Mol. Biol. Rev. 71(1), 230–253 (2007a)

    Article  Google Scholar 

  • Norris, V., den Blaauwen, T., Doi, R.H., Harshey, R.M., Janniere, L., Jimenez-Sanchez, A., Jin, D.J., Levin, P.A., Mileyknovskaya, E., Minsky, A., Misevic, G., Ripoll, C., Saier Jr., M., Skarstad, K., Thellier, M.: Toward a hyperstructure taxanomy. Annu. Rev. Microbiol. 61, 309–329 (2007b)

    Article  Google Scholar 

  • Pais, A.: Niels Bohrs’ Times, in Physics, Philosophy, and Polity, pp. 438–447. Clarendon Press, Oxford (1991)

    Google Scholar 

  • Peirce, C.S.: The categories defined. In: Houser, N. (ed.) The Essential Peirce: Selected Philosophical Writings, Volume 2 (1893–1913), pp. 160–178. Indiana University Press, Bloomington (1903)

    Google Scholar 

  • Pierce, J.R.: Introduction to Information Theory. Second, Revised Edition. Dover Publications, New York (1980)

    MATH  Google Scholar 

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

    MATH  Google Scholar 

  • Poole, A.M., Ranganathan, R.: Knowledge-based potentials in protein design. Curr. Opin. Struct. Biol. 16, 508–513 (2006)

    Article  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 

  • Prigogine, I.: Schrödinger and the riddle of life. In: Ji, S. (ed.) Molecular Theories of Cell Life and Death, pp. 239–242. Rutgers University Press, New Brunswick (1991)

    Google Scholar 

  • Roederer, J.G.: On the concept of information and its role in nature. Entropy 5, 3–33 (2003)

    Article  ADS  MATH  Google Scholar 

  • Roederer, J.G.: When and where did information first appear in the universe? In: Seckbach, J. (ed.) Bioinformatics. Kluwer Academic Publ, Dordrecht, The Netherlands (2004)

    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 

  • Scruton, R.: Spinoza, p. 16. Routledge, New York (1999)

    Google Scholar 

  • Seife, C.: Decoding the Universe: How the New Science of Information Is Explaining Everything in the Cosmos, from Our Brain to Balck Holes. Viking, New York (2006)

    Google Scholar 

  • Shannon, C.E., Weaver, W.: The Mathematical Theory of Communication. University of Illinois, Urbana (1949)

    MATH  Google Scholar 

  • Simpson, G.G.: This View of Life, Harcourt. Brace & World, New York (1964)

    Google Scholar 

  • Smith, H.A., Welch, G.R.: Cytosociology: a field-theoretic view of cell metabolism. In: Ji, S. (ed.) Molecular Theories of Cell Life and Death, pp. 282–323. Rutgers University Press, New Brunswick (1991)

    Google Scholar 

  • Socolich, M., Lockless, S.W., Russ, W.P., Lee, H., Gardneer, K.H., Ranganathan, R.: Evolutionary information for specifying a protein fold. Nature 437, 512–518 (2005)

    Article  ADS  Google Scholar 

  • Srere, P.A.: Complexes of sequential metabolic enzymes. Ann. Rev. Biochem. 56, 89–124 (1987)

    Article  Google Scholar 

  • Süel, G.M., Lockless, S.W., Wall, M.A., Ranganathan, R.: Evolutionarily conserved networks of residues mediate allosteric communication in proteins. Nat. Struct. Biol. 10(1), 59–69 (2003)

    Article  Google Scholar 

  • Tolman, R.C.: The Principles of Statistical Mechanics, pp. 42–46. Dover Publications, New York (1979)

    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, S.J., Akil, U.: Gene chips and arrays revealed: a primer on their power and their uses. Biol. Psychiatry 45, 533–43 (1999)

    Article  Google Scholar 

  • Wheeler, J.A.: Information, physics, quantum: the seaerch for links. In: Zurek, W.H. (ed.) Complexity, Entropy and the Physics of Information, pp. 3–28. Addison- Wesley Publishing Company, Redwood City (1990)

    Google Scholar 

  • Wheeler, J.A.: Geons, Black Holes & Quantum Foam: A Life in Physics, pp. 340–341. W.W. Norton & Company, New York (1998)

    MATH  Google Scholar 

  • Wicken, J.S.: Entropy and information: suggestions for common language. Phil. Sci. 54, 176–193 (1987)

    Article  MathSciNet  Google Scholar 

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

    MATH  Google Scholar 

  • Xie, X.S., Lu, P.H.: Single-molecule enzymology. J. Biol. Chem. 274(23), 15967–15970 (1999)

    Article  Google Scholar 

  • Xie, X.S.: Single-molecule approach to enzymology. Single Mol. 2(4), 229–239 (2001)

    Article  ADS  Google Scholar 

  • Zwanzig, R.: Rate processes with dynamic disorder. Acc. Chem. Res. 23, 148–152 (1990)

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Dept. of Pharmacol. & Toxicol. Ernest Mario School of Pharmacy, Rutgers University, Piscataway, NJ, 08854, USA

    Sungchul Ji PhD

Authors
  1. Sungchul Ji PhD
    View author publications

    You can also search for this author in PubMed Google Scholar

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). Biology. In: Molecular Theory of the Living Cell. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-2152-8_4

Download citation

  • DOI: https://doi.org/10.1007/978-1-4614-2152-8_4

  • 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

Search

Navigation