[BBF Standards] BioHackathon, or Characterization Challenge

[Drew Endy]

First, let me point out to the list who's versus whose:
http://www.wsu.edu/~brians/errors/who's.html

Meanwhile, Bryan, your comment might be well connected to something I  
was struggling to say...

On Feb 11, 2008, at 9:35 PM, Bryan Bishop wrote:
> I would like to point out to the list that doubling rate is strongly
> linked to development cycle time in terms of biobricks and the
> standards. It seems to be nearly equivalent to waiting for the  
> compiler
> to finish (except, biobricks are like precompiled bytecode).


As soon as we start working with doubling times below 40 minutes, for  
many of our systems, the debugging time constant for system  
performance is limited not by cell growth rate, but rather by the time  
it takes for protein (and other molecular) levels to rise and fall.  
Some of the fastest protein production systems around are found in  
phage, the best of which can produce convert most of E.coli into phage  
specific proteins by 10-20 minutes post infection.  Faster than this  
and we have to start thinking carefully about how cell doubling time  
is driving the reset of system state to ground.

Meanwhile, note that we should be able to deploy active mRNA and  
protein degradation systems (e.g., ClpX) to push faster reset times  
independent of the cell growth rate (c/o Bob Sauer et al.).

So, eventually, my guess would be that we want to consider cell  
doubling times for specific purposes (i.e., production of DNA, cells,  
or other objects), but otherwise figure out how to decouple the  
operation of our engineered biological systems from cell doubling time.