Error Detection & Correction in Replicating Machines: Difference between revisions

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*[[Jeff Gritton]]
*[[Jeff Gritton]]
*[[Jason Kelly]]
*[[Jason Kelly]]
*[[Sri Kosuri]]
*[[Tom Knight]]
*[[Tom Knight]]
*[[User:labnoa|Ania Labno]]
*[[User:labnoa|Ania Labno]]
*[[Gerry Sussman]]
*[[Gerry Sussman]]
*[[Reshma Shetty]]
*[[Julie Norville]]


===Meeting Archive===
===Meeting Archive===
*[[RWE072605]]
*[[RWE072605]]
*[[RWE083005]]


===Next Meeting===
===Next Meeting===
*'''PROPOSED''' 4-6p on Tuesday August 30 Room TBA
*'''PROPOSED''' TBA
**DE, JG, AL, [[User:Bcanton|BC]], [[Jason Kelly|JK]], AC are OK
**nobody is yet OK
**TK, GJS are pending
**DE, JG, AL, [[User:Bcanton|BC]], [[Jason Kelly|JK]], AC, GJS and TK are pending


====Assignments====
====Proposed Assignments====
#Read/skim Haussler papers
#Read/skim phage variation mechanism papers (we need to decide if we want to explore these, [[User:Endy|Endy]] 16:32, 20 Sep 2005 (EDT))
##[http://www.sciencemag.org/cgi/content/full/304/5675/1321 Ultraconserved Elements in the Human Genome]
##[http://www.nature.com/nsmb/journal/vaop/ncurrent/abs/nsmb992.html The C-type lectin fold as an evolutionary solution for massive sequence variation]
##[http://www.genome.org/cgi/content/full/15/8/1034 Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes]
##[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]
#Read/skim Kelly thesis proposal
##[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]
##Kelly to provide PDF and point out relevant sections
 
#Read/skim Alon paper
##[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16049495&query_hl=1 Optimality and evolutionary tuning of the expression level of a protein]


===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===
Line 43: Line 45:
*[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]
===Ideas & Links===
*[[Codon_Optimized_for_Failure]]
*[https://dspace.mit.edu/handle/1721.1/21169 Design and Evolution of Engineered Biological Systems]

Latest revision as of 18:51, 21 May 2007

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

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