Information in Biology


Roy Bar-Ziv and Elisha Moses, Academic Year 2008-09

The course examines the role that Information Theory plays in Biology, viewed from the perspective of Physics and of physicists. The course will be conducted in the form of student lectures, with one or two lectures per student. Grading will be based mostly on this lecture, as well as on participation and a surprise quiz. Topics will include:



Information in Biology - Papers




    Physics of information


  1. L. Szilard, On the decrease of entropy, Z. fur Physik 1929 (German version).


  2. R.P. Feynman, Ratchet and pawl, Feynman Lectures on Physics, Vol. I, Ch. 46.


  3. M.O. Magnasco, Forced thermal ratchets , PRL 1993.
    A. Ajdari and J. Prost, Drift induced by a spatially periodic potential of low symmetry: Pulsed die1ectrophoresis, C. R. Acad. Sci. Paris, t. 315, Serie II, p. 1635-1639 1992.
    F. Julicher, A. Ajdari, and J. Prost, Modeling molecular motors, Rev. Mod. Phys., Vol. 69, No. 4 1997.


  4. L.P. Faucheux, L.S. Bourdieu, P.D. Kaplan, and A.J. Libchaber, Optical thermal ratchet, PRL 1994.


    5. Presentation: Yovav Kalifon

  5. F. Attneave, Some informational aspects of visual perception, Psychological Review 1954.


  6. C.E. Shannon, Communication in the presence of noise, Proceedings of the IEEE 1948.

    Presentation: Ori Katz

    7. Related Videos: First Vocoder Human Organ, The Shannon Juggler.




    Information and Computation


  7. C.H. Bennet, Logical reversibility of computation, IBM Journal of Research and Development 1973


  8. R. Landauer, Computation: a fundamental physical view, Physica Scripta 1987.
    R. Landauer, Irreversibility and heat generation in the computing process, IBM J. Res. Develop. Vol. 5 No. 3 1961.


    9. Presentation: Avraham Guttman

  9. A. Turing, Computing Machinery and Intelligence , Mind 49: 433-460 1950.


  10. J. von Neumann, The general and logical theory of automata, Hixon Symp. on Cerebral Mechanisms in Behavior 1951.

    Presentation: Adam Lampert





    11. Biological Computation


  11. L.M. Adleman, Molecular Computation of Solutions to Combinatorial Problems, Science 1994.


  12. M. Ptashne and A. Gann, Imposing specificity by localization: mechanism and evolvability, Current Biology 1998.


    13. Presentation: Michal Levo
    Related Videos: PCR1, PCR2, Transcription To Dance By, Virus Invades Cell (bacteriophage T4).

  13. N. Barkai and S. Leibler, Robustness in simple biochemical networks, Nature 1997.
    See also W. Bialek and S. Setayeshgar, Physical limits to biochemical signaling, PNAS 2005.


    14. Presentation: Oren Shoval
    Related Video: Swimming E. coli

  14. E. Winfree, X. Yang and N.C. Seeman, Universal Computation via Self-assembly of DNA: Some Theory and Experiments, in DNA Based Computers II: DIMACS Workshop, June 10-12, 1996 Ed. by L.F. Landweber and E.B. Baum 1999.
    E. Winfree, F. Liu, L.A. Wenzler and N.C. Seeman, Design and self-assembly of two-dimensional DNA crystals, Nature 1998.


    15. Presentation: Benny Gil




    Coding and Error Correction


  15. C.E. Shannon, A universal Turing machine with two internal states, Automata Studies 1956.


  16. G.A. Miller, The magical number seven, plus or minus two: some limits on our capacity for processing informatio, Psychological Review 1956.


    17. Presentation: Adina Lederhendler

  17. T. Tlusty, A simple model for the evolution of molecular codes driven by the interplay of accuracy, diversity and cost, Physical Biology 2008.


    18. Presentation: Gidi Lazovsky

  18. R.W. Hamming, Error detection and error correction codes, Bell Syst. Tech. J. 1950.
    See also Hamming's later comments on this paper.


    19. Presentation: Rami Pugatch

  19. J.J. Hopfield, Kinetic Proofreading: A New Mechanism for Reducing Errors in Biosynthetic Processes Requiring High Specificity, PNAS 1974.
    See an experimental verification in J.J. Hopfield et al., Direct experimental evidence for kinetic proofreading in amino acylation of tRNA, PNAS 1976


  20. R. Bar-Ziv, T. Tlusty, and A.J. Libchaber, Protein-DNA computation by stochastic assembly cascade, PNAS 2002.


    21. Presentation: Yarden Cohen
    Related Video: Price of Making Errors

  21. MacKay and McCulloch, The limiting information capacity of a neuronal link, Bulletin of Mathematical Biology 1952.





    22. Genetic Information


  22. G.M. Rubin et al., Comparative genomics of the eukaryotes, Science 2000.


    23. Presentation: Ishay Ben Zion

  23. J.-M. Claverie, What if there are only 30,000 human genes, Science 2001.
    This discusses some consequences of the huge human genome sequencing project by J.C. Venter et al., The Sequence of the Human Genome, Science 2001.


    24. Presentation: Yoni Toker


  24. H.J. Bussemaker, H. Li, and E.D. Siggia, Building a dictionary for genomes: Identification of presumptive regulatory sites by statistical analysis, PNAS 2000.


    25. Presentation: Tal Frank

  25. N.S. Holter, A. Maritan, M. Cieplak, N.V. Fedoroff, and J.R. Banavar, Fundamental patterns underlying gene expression profiless, PNAS 2001.


    26. Presentation: Effi Kenigsberg
    Related Video: Wild-Type Yeast Mitosis


    Language


  26. C.E. Shannon, Prediction and entropy of printed English, Bell System Technical Journal 1951.


    27. Presentation: David Gelbwaser

  27. W. Enard, M. Przeworski, S.E. Fisher, C.S.L. Lai, V. Wiebe, T. Kitano, A.P. Monaco and S. Paabo, Molecular evolution of FOXP2, a gene involved in speech and language, Nature 2002.
    C.S.L. Lai, S.E. Fisher, J.A. Hurst, F. Vargha-Khadem and A.P. Monaco, A forkhead-domain gene is mutated in a severe speech and language disorder, Nature 2001.

    Presentation: Lilach Goren

    See also:
    H.H. Stedman, B.W. Kozyak, A. Nelson, D.M. Thesier, L.T. Su, D.W. Low, C.R. Bridges, J.B. Shrager, N. Minugh-Purvis and M.A. Mitchell, Myosin gene mutation correlates with anatomical changes in the human lineage, Nature 2004, and the related News&Views.





    28. Organization of Information - Networks


  28. J.G. White, E. Southgate, J.N. Thomson and S. Brenner , The Structure of the Nervous System of the Nematode Caenorhabditis elegans, Trans. R. Soc. Lond. B Biol. Sci. 1986 (This is a hefty file - about 340 pages in 30Mbyte).


  29. P. Uetz et al., A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae, Nature 2000.


  30. M. Chee, R. Yang, E. Hubbell, A. Berno, X.C. Huang, D. Stern, J. Winkler, D.J. Lockhart, M.S. Morris, S.P.A. Fodor, Accessing Genetic Information with High-Density DNA Arrays, Science 1996.
    See also:
    S.P.A. Fodor, J.L. Read, M.C. Pirrung,L. Stryer, A.T. Lu and D. Solas, Light-Directed, Spatially Addressable Parallel Chemical Synthesis, Science 1991.
    As well as:
    M. Schena, D. Shalon, R. Heller, A. Chai, P.0. Brown, and R.W. Davis, Parallel human genome analysis: Microarray-based expression monitoring of 1000 genes, PNAS 1996.


  31. A.-L. Barabasi and R. Albert, Emergence of Scaling in Random Networks, Science 1999.


    32. Presentation: Michael Klots

  32. R. Milo, S. Shen-Orr, S. Itzkovitz, N. Kashtan, D. Chklovskii, U. Alon, Network Motifs: Simple Building Blocks of Complex Networks, Science 2002.
    S. Kalir, J. McClure, K. Pabbaraju, C. Southward, M. Ronen, S. Leibler, M.G. Surette, U. Alon, Ordering Genes in a Flagella Pathway by Analysis of Expression Kinetics from Living Bacteria, Science 2001.


    33. Presentation: Yoav Lahini




    Synthetic Biology


  33. M.B. Elowitz and S. Leibler, A synthetic oscillatory network of transcriptional regulators, Nature 2000.


  34. S.-H. Park, A. Zarrinpar, W.A. Lim, Rewiring MAP Kinase Pathways Using Alternative Scaffold Assembly Mechanisms, Science 2003.


    35. Presentation: Mati Cohen

  35. H. Kobayashi, M. Kaern, M. Araki, K. Chung, T.S. Gardner, C.R. Cantor and J.J. Collins, Programmable cells: Interfacing natural and engineered gene networks, PNAS 2004.


  36. L. You, R.S. Cox III, R. Weiss and F.H. Arnold Programmed population control by cell-cell communication and regulated killing, Nature 2004.


    37. Presentation: Noam Vardi




    Information in Biology - Good books for background:


    1. Sneppen and Zocchi: Physics in Molecular Biology.

    2. Feynman: Lectures on Computation.

    3. Nelson: Biological Physics - Energy, Information, Life.

    4. Leff and Rex: Maxwell's Demon - Entropy, Information, Computing.





    Information in Biology - Additional papers on Maximal Entropy and Information Theory:


    1. E.T. Jaynes Information theory and statistical mechanics, in Brandeis University Summer Institute Lectures in Theoretical Physics 1963, Ed. by K.W. Ford.
      E.T. Jaynes The Gibbs Paradox, in Maximum Entropy and Bayesian Methods 1992, Ed. by C.R. Smith, G.J. Erickson and P.O. Neudorfer.
      E.T. Jaynes Information Theory and Statistical Mechanics, Phys. Rev. 1957.
      E.T. Jaynes Where do we stand on Maximal Entropy?, presented at the Maximum Entropy Formalism Conference, MIT 1978.


    2. T.D. Schneider Theory of Molecular Machines. I. Channel Capacity of Molecular Machines, J. Theoretical Biol. 1991.






      3. Organization