Fundamental limits of biological measurement
(BE.481J, 7.86J, MAS.866)

Spring 2005

Scott Manalis E15-422
Peter Sorger 68-371
Teaching Assistants:
Ben Zeskind WI-639
Craig Forest 3-147
Laboratory Instructor:
Maxim Shusteff E15-420
Tuesday and Thursday, 1 - 2:30 pm
Credit hours:
3 - 3 - 6
Graduate or senior undergraduate


This course explores the need for quantitative measurement in biology using particular biological systems as case studies. The class discusses both conventional and emerging measurement techniques and devices in coordination with principles of interpretation. Biological topics include apoptosis signaling and biological networks, and engineering topics include microsystems and automation, imaging and diffraction. The course introduces the mathematical and experimental methodologies necessary for quantitative measurement, such as wave theory, fourier transform, and noise theory. An essential aspect of measurement emphasized in the course is understanding the physical limits and interpretation of data obtained with advanced technologies. Homework assignments aid in helping students to understand the theories and limitations and enable them to be applied in real biological problems. At the conclusion of the course, the class uses home-built atomic force microscopes to explore the principles taught during the course.


Reading and Assignments



Feb 1 |
Systems Biology and Measurement: The Data Drought (Sorger)
Feb 3 |
Laboratory measurement today: Lab in a room (Sorger)
Feb 8 |
Laboratory measurement tomorrow: Lab on a chip (Manalis)
Feb 10 |
Solid-liquid interface: the electrical double layer (Manalis)
Feb 15 |
Molecular recognition: binding affinity and thermodynamics (Sorger)
Feb 17 |
Affinity detection: microarray, Elisa, phosphor affinity chromotography (student presentation)
Feb 22 |
-no class- (Monday schedule)
Feb 24 |
Measurement in nature I: Physics of chemoreception (Manalis)
March 1 |
Measurement in nature II: Mammalian signal transduction (Sorger)
  Time Varying Data (Manalis)
Measurement in the time and frequency domain
March 3 |
Signal analysis I: Fourier transforms
March 8 |
Signal analysis II: Correlation, convolution, and filters
March 10 |
Forces and biological systems (student presentations)
March 15 |
Noise, mechanical systems, and ultimate limits of position and force detection
March 17 |
Random processes and the fluctuation dissipation theorem
spring break

Spatially Resolved Data (Sorger)
Measurement in the spatial domain

March 29 |
Microscopy and biological systems (student presentations)
March 31 |
Introduction to imaging, microscopes diffraction
April 5 |
Diffraction and Fourier approaches to imaging
April 7 |
Resolution and detectability
April 12 |
Diffraction methods in biological measurement (student presentations)
April 14 |
Crystallography and X-Ray Diffraction (Harrison)
April 19 |
-no class-
April 21 |
EM and electron diffraction (Harrison)
April 26 |
5D data-space and time: super-resolution
  Force Measurement Laboratory (Manalis)
April 28 |
Instrumentation: filters, amplifiers, data acquisition and signal processing
May 3 |
Microcantilevers and thermomechanical noise
May 5 |
Atomic force microscopy: imaging and applications
May 10 |
Optical trap I: bead manipulation and calibration (Lang)
May 12 |
Optical trap II: e-coli flagellum (Lang)