Error Detection & Correction in Replicating Machines

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(Participating Folks)
(Suggested Folks (not yet contacted/signed up))
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===Suggested Folks (not yet contacted/signed up)===
===Suggested Folks (not yet contacted/signed up)===
 +
*Eric Alm
*Norm Margolus
*Norm Margolus
*Jonathan Rees
*Jonathan Rees
 +
*[http://www.cs.washington.edu/homes/weise/ Daniel Weise]
===Background Reading & External Links===
===Background Reading & External Links===

Revision as of 03:19, 31 August 2005

Contents

Replication with Error Working Group

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

Meeting Archive

Next Meeting

  • PROPOSED 4-6p on Tuesday August 30 Room TBA
    • DE, JG, AL, BC, JK, AC, GJS are OK
    • TK are pending

Assignments

  1. Read/skim Haussler papers
    1. Ultraconserved Elements in the Human Genome
    2. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
  1. Read/skim Kelly thesis proposal
    1. Entire proposal here, relevant sections are 3.5 and 4.3.
    2. Also, in wiki format and slightly updated here.
  1. Read/skim Alon paper
    1. Optimality and evolutionary tuning of the expression level of a protein

Suggested Folks (not yet contacted/signed up)

Background Reading & External Links

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