Error Detection & Correction in Replicating Machines

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(Participating Folks)
Current revision (21:51, 21 May 2007) (view source)
(Participating Folks)
 
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*[[Gerry Sussman]]
*[[Gerry Sussman]]
*[[Reshma Shetty]]
*[[Reshma Shetty]]
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*[[Julie Norville]]
===Meeting Archive===
===Meeting Archive===
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##[http://www.nature.com/nature/journal/v431/n7007/abs/nature02833.html Tropism switching in Bordetella bacteriophage defines a family of diversity-generating retroelements]
##[http://www.nature.com/nature/journal/v431/n7007/abs/nature02833.html Tropism switching in Bordetella bacteriophage defines a family of diversity-generating retroelements]
##[http://www.sciencemag.org/cgi/content/full/295/5562/2091 Reverse Transcriptase-Mediated Tropism Switching in Bordetella Bacteriophage]
##[http://www.sciencemag.org/cgi/content/full/295/5562/2091 Reverse Transcriptase-Mediated Tropism Switching in Bordetella Bacteriophage]
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##[http://www.nature.com/nature/journal/v438/n7065/abs/nature04114.html A mutation accumulation assay reveals a broad capacity for rapid evolution of gene expression]
===Suggested Folks (not yet contacted/signed up)===
===Suggested Folks (not yet contacted/signed up)===
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*[http://www.cs.washington.edu/homes/weise/ Daniel Weise @ UW CS]
*[http://www.cs.washington.edu/homes/weise/ Daniel Weise @ UW CS]
**[http://www.cs.washington.edu/homes/weise/590ce.html Dan's summary course]
**[http://www.cs.washington.edu/homes/weise/590ce.html Dan's summary course]
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===Ideas & Links===
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*[[Codon_Optimized_for_Failure]]
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*[https://dspace.mit.edu/handle/1721.1/21169 Design and Evolution of Engineered Biological Systems]

Current revision

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 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))
    1. The C-type lectin fold as an evolutionary solution for massive sequence variation
    2. Tropism switching in Bordetella bacteriophage defines a family of diversity-generating retroelements
    3. Reverse Transcriptase-Mediated Tropism Switching in Bordetella Bacteriophage
    4. A mutation accumulation assay reveals a broad capacity for rapid evolution of gene expression

Suggested Folks (not yet contacted/signed up)

Background Reading & External Links

Ideas & Links

Personal tools