Error Detection & Correction in Replicating Machines

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(Next Meeting)
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===Next Meeting===
===Next Meeting===
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*'''PROPOSED''' 4-6p on Tuesday August 30 Room TBA
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*'''PROPOSED''' TBA
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**DE, JG, AL, [[User:Bcanton|BC]], [[Jason Kelly|JK]], AC, GJS are OK
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**OK
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**TK are pending
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**DE, JG, AL, [[User:Bcanton|BC]], [[Jason Kelly|JK]], AC, GJS and TK are pending
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====Assignments====
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====Proposed Assignments====
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#Read/skim Haussler papers
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#Read/skim phage variation mechanism papers
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##[http://www.sciencemag.org/cgi/content/full/304/5675/1321 Ultraconserved Elements in the Human Genome]
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##[http://www.nature.com/nsmb/journal/vaop/ncurrent/abs/nsmb992.html The C-type lectin fold as an evolutionary solution for massive sequence variation]
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##[http://www.genome.org/cgi/content/full/15/8/1034 Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes]
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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]
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#Read/skim Kelly thesis proposal
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##[http://www.sciencemag.org/cgi/content/full/295/5562/2091 Reverse Transcriptase-Mediated Tropism Switching in Bordetella Bacteriophage]
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##Entire proposal [http://hdl.handle.net/1721.1/21169 here], relevant sections are 3.5 and 4.3.
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##Also, in wiki format and slightly updated [[Evolutionary Stability|here]].
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#Read/skim Alon paper
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##[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]
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===Suggested Folks (not yet contacted/signed up)===
===Suggested Folks (not yet contacted/signed up)===

Revision as of 16:28, 20 September 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 TBA
    • OK
    • DE, JG, AL, BC, JK, AC, GJS and TK are pending

Proposed Assignments

  1. Read/skim phage variation mechanism papers
    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

Suggested Folks (not yet contacted/signed up)

Background Reading & External Links

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