BMCB625:Mathematics in Biology
Overview of Topic
1.) Take Home Message (Big Picture / Themes):
- A.) Common Languages for Quantitative Biology
- B.) Probability in Gene Expression
2.) Important Experimental Details
Papers
Outline of Talk and Discussion
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- Introduction: Perspectives between disciplines and the Language of Biology
- Can we develop a common language? Is it mathematics? Should it be? In what cases?
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- Classic Biological Underpinning by Mathematical (Statistical) Arguments
- Luria-Delbrück Fluctuation Analysis
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- Static Picture of Dynamic Pathways
- The Lac Operon as a Model of Bistability and Stochastic Events
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- Discussion
PAPERS:
- MAIN PAPER: "Multistability in the lactose utilization network of Escherichia coli"
- EM Ozbudak, et al, Nature 427, 737-740 (19 February 2004)
- CLASSIC: "Mutations of Bacteria from Virus Sensitivity to Virus Resistance"
- S. E. Luria and M. Delbrück, Genetics. 1943 November; 28(6): 491–511
[| Classic Paper 1943 Luria & Delbruck]
- See Below: [| "Biologists Fixing Radios"]
Chris - Bonus Materials
Ranking:
- Critical Read/of Outstanding Interest (oo)
- Importand Read (o)
- Of Interest (no label)
- (o) A good primer on how biologists and engineers look at a problem in different ways; while many comments do not address the complexity of biochemistry and genetics, it does provide an interesting perspective on what we consider "important." Also, of importance, in my opinion, is developing a common language by which numerous disciplines can communicate. I'll touch more on this particular topic during my talk.
Y. Lazebnik, "Can a Biologist Fix a Radio? or, What I Learned while Studying Apoptosis" [| "Biologists Fixing Radios"]
Unresolved Questions for Followup
Discussion/Homework Questions
Mahta
Larry
1. As a reductionist, I would attempt to explain the behavior of such circuits in terms of the behavior of the components, what are the limitations of this approach (reductionist view)?
2. "Despite many molecular components of biological organisms being identified and characterized using genetic and biochemical techniques, it is still not possible to predict system behavior except in the simplest systems."( pmid=17170763 ) What needs to happen in the field in order to be able to model more complex systems?
Chayne
Jon
The author's state: "The discontinuous transition from low to high induction is analogous to a first-order phase transition such as evaporation in a liquid-gas system, with chemical noise instead of thermal noise driving stochastic transition between these states"
Q: What is chemical noise and how is diffrent than thermal noise?
A: I think they mean the sugar - promoter interaction is "chemical noise" and it is analagous to the phase transition due to thermal noise.
Q:
