Error Detection & Correction in Replicating Machines: Difference between revisions
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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. | 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]] | *[[Drew Endy]] | ||
*[[Jeff Gritton]] | |||
*[[Jason Kelly]] | |||
*[[Sri Kosuri]] | |||
*[[Tom Knight]] | *[[Tom Knight]] | ||
*[[User:labnoa|Ania Labno]] | |||
*[[Gerry Sussman]] | *[[Gerry Sussman]] | ||
*[[ | *[[Reshma Shetty]] | ||
*[[ | *[[Julie Norville]] | ||
===Meeting Archive=== | |||
*[[RWE072605]] | |||
*[[RWE083005]] | |||
===Next Meeting=== | ===Next Meeting=== | ||
* | *'''PROPOSED''' TBA | ||
** | **nobody is yet OK | ||
**GJS. | **DE, JG, AL, [[User:Bcanton|BC]], [[Jason Kelly|JK]], AC, GJS and TK are pending | ||
====Proposed Assignments==== | |||
#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.nature.com/nsmb/journal/vaop/ncurrent/abs/nsmb992.html The C-type lectin fold as an evolutionary solution for massive sequence variation] | |||
##[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.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)=== | ||
*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=== | ||
*Theory of Self-Reproducing Automata, John von Neumann | *Theory of Self-Reproducing Automata, John von Neumann | ||
**Drew has a copy of this if anybody wants to read it. | **Drew has a copy of this if anybody wants to read it. | ||
**[http://www.walenz.org/vonNeumann/index.html html version] | |||
*[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
- Barry Canton
- Austin Che
- Drew Endy
- Jeff Gritton
- Jason Kelly
- Sri Kosuri
- Tom Knight
- Ania Labno
- Gerry Sussman
- Reshma Shetty
- Julie Norville
Meeting Archive
Next Meeting
Proposed Assignments
- Read/skim phage variation mechanism papers (we need to decide if we want to explore these, Endy 16:32, 20 Sep 2005 (EDT))
- The C-type lectin fold as an evolutionary solution for massive sequence variation
- Tropism switching in Bordetella bacteriophage defines a family of diversity-generating retroelements
- Reverse Transcriptase-Mediated Tropism Switching in Bordetella Bacteriophage
- 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
