Error Detection & Correction in Replicating Machines

Introduction
Biological systems are replicating machines that make (a small number of) errors during the machine replication process. From a practical engineering standpoint, we need to understand how to design biological systems that perform as expected. We can imagine that a future biological engineer might be called upon to design an 8-bit counter that has a p(working) > 0.99 upto 256 doubling events. Or, we can imagine needing to design a metabolic pathway that has a p(failure) > 0.99 after 3000 doubling events. And so on. In other words, the evolutionary stability, or lack thereof, for our engineering biological systems should become part of the initial system specification, and our designs should be able to meet these specifications. From a scientific perspective, we suspect that learning how to solve questions of error detection and correction in replicating machines will lead to a better understanding of biological evolution.

Participating Folks

 * Barry Canton
 * Austin Che
 * Drew Endy
 * Jeff Gritton
 * Jason Kelly
 * Sri Kosuri
 * Tom Knight
 * Ania Labno
 * Gerry Sussman
 * Reshma Shetty
 * Julie Norville

Meeting Archive

 * RWE072605
 * RWE083005

Next Meeting

 * PROPOSED TBA
 * nobody is yet OK
 * DE, JG, AL, BC, JK, AC, GJS and TK are pending

Proposed Assignments

 * 1) Read/skim phage variation mechanism papers (we need to decide if we want to explore these, Endy 16:32, 20 Sep 2005 (EDT))
 * 2) The C-type lectin fold as an evolutionary solution for massive sequence variation
 * 3) Tropism switching in Bordetella bacteriophage defines a family of diversity-generating retroelements
 * 4) Reverse Transcriptase-Mediated Tropism Switching in Bordetella Bacteriophage
 * 5) A mutation accumulation assay reveals a broad capacity for rapid evolution of gene expression

Suggested Folks (not yet contacted/signed up)

 * Eric Alm
 * Norm Margolus
 * Jonathan Rees
 * Daniel Weise

Background Reading & External Links

 * Theory of Self-Reproducing Automata, John von Neumann
 * Drew has a copy of this if anybody wants to read it.
 * html version
 * Daniel Weise @ UW CS
 * Dan's summary course

Ideas & Links

 * Codon_Optimized_for_Failure
 * Design and Evolution of Engineered Biological Systems