Physics 380, 2011: Lecture 1

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Back to Physics 380, 2011: 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 $\delta C/C\sim 1/{\sqrt {CaDt}}$, where $C$ is the concentration, $a$ is the linear size of the detecting cell, $D$ is the diffusion coefficient, and $t$ 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