Physics 434, 2012: Lecture 1

From Ilya Nemenman: Theoretical Biophysics @ Emory
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Back to Physics 434, 2012: Information Processing in Biology.

  • Welcome
  • Details and expectations
    • We will schedule a 2-hour office hour/supplementary instruction sections
    • Very mathematical course, but we will create an infrastructure for you to succeed
    • Starting end of October, we will be devoting about one class every two weeks to students presenting journal papers. I will provide you with a list of papers to choose from by mid-September.
    • Homeworks will be due by end of the day on Fridays.
  • The main questions to be asked in the whole course (not necessarily in this order):
    • How well, in objective terms, do various biological systems transduce available sensory information?
    • What stays in the way of their performance?
    • Which strategies can be used by the systems to improve the quality of processing?
  • Intro to E. coli chemosensing
    • E. coli is small -- natural measuring stick. See Sizing up E coli section in Physical Biology of the Cell -- see below.
    • Can have as few as one or even less of molecules of a chemoattractant in a volume the size of E. coli. 1 nM concentration is about 1 molecule per E. coli volume
    • Still, even with these concentrations, E. coli can follow chemoattractants (Adler 1975, Budrene and Berg, 1991, 1995)
    • The flagella and the run/tumble strategy of E. coli motion. See movies at http://www.rowland.harvard.edu/labs/bacteria/movies_ecoli.html
    • The reason the bacterium does runs is to outrun diffusion: the ability to measure the concentration of a chemical around oneself is limited in accuracy by , where is the concentration, is the linear size of the detecting cell, is the diffusion coefficient, and is the observation time.
    • The E. coli behavioral strategy is fully dictated by the physical structure of the world it leaves in: small size that limits total number of molecules in the cell volume, diffusion that takes molecules to and away from the cell and prevents the bacterium from keeping moving in a straight line, and the need to go to greener pastures.
    • The basic structure of the E. coli chemotaxis signaling pathway. See http://www.rowland.harvard.edu/labs/bacteria/projects_fret.html
  • Intro to neural computation
    • Neurons communicate with spikes (see Dayan and Abbott, 2005)
    • Spikes occur at random times, and it takes only a handful of spikes for a system to make a decision (Rieke et al, 1999)
  • Intro to decision making processes
    • Behavioral changes in rodents happen on the time scales of only very few observations (Gallistel et al, 2001)
  • Main point to carry out: Biological signal processing is not deterministic, hence we will spend the next lectures on some basic probabilistic concepts