I apologize for the huge delays in posting, but I promise that it hasn't been in vain.
For the past five months, I've been going back and forth between a wet and dry lab, continuing to develop new stochastic numerical methods while helping to build a gene network in E. coli. I started my graduate studies in the computational area of systems / synthetic biology and moving into the experimental side has certainly been a change of pace. Some of the other bio people are pretty shocked to find me pipetting. When they ask why, I usually say something glib like "What use is designing something if you never build it?" Which is more or less true. However, in between experiments, I've been designing new networks and developing new stochastic methods. The work is going well. I (and my advisor, of course) have two papers in the review process and two more being written. I'll wait until they're published online before blogging about them (probably safer that way, heh).
I still believe that synthetic biology will never mature into an engineering science unless we use computational tools to quantitatively predict the behavior of a biological system. We need to create the same sort of tools, like CAD, that the auto industry uses to design cars. They spend 95% of their time on the computer, testing new hypothetical designs, and they only build prototypes when they see something work well. The same can be said for other industries, including building chemical or pharma plants and computer chips. The same process must develop for synthetic bio. We need more experiments to determine how simple biological systems work, but then we must incorporate that information into realistic models, powered by sophisticated mathematics. Without the combination of both, we'll be flailing in the dark, using the trial and error system that is rarely productive, often boring, and never generalizable.
I also have some thoughts on the differences between wet and dry lab experiments. I'll save that for a future post, I think.
I recently received a bunch of questions about stochastic methods from Dr. Herbert Sauro, who (like me) is a member of the sbml-discuss mailing list. They were very good questions and I think I did a decent job of answering them so I think I'll link them here
Ok, that's all for now (I so suck at blogging).