Endy:Measkit PLO/v2

Overal

Important points

1. PoPS is an appropriate unit for promoter activity
   • Promoter activity is sensitive to experimental conditions
   • Promoter activity may be effected equivalently across different promoters when they are placed in different conditions
   • Relative promoter activity measured in SPUs by normalizing to a reference standard may allow for the specification of a range of promoters and a range of conditions where relative promoter activity is predictable.

Leave out

1. Calibration of instruments to make PoPS measurement.
2. Reporting our measurements in PoPS. We didn't seriously determine the values of parameters in our GFP->PoPS model for any of the different conditions. We can say that this is significant work and in general is a strike against measurement in PoPS.
3. RBS measurements - The only RBS measurements were taken in the Endy lab and we lack the significant multi-condition data and the lab-lab data that the promoters have. Also it requires a separate run through of the model and presents a more challenging set of issues with canceling some parameters since different RBS = different mRNAs. My main concern is that it distracts from the overall story. We could mention, but i'd rather see it in the Supplementary materials with a mention in the discussion?

Introduction

1. Engineering many-component systems is made easier by developing collections of standard parts that can be reused.
2. It is easier still to predict the behavior of engineered biological systems assembled from standard parts if the component parts themselves were well characterized.
   • be scholarly here, making reference to current parts collections, and lack of characterization thereof.
     • For example the registry of biological parts contains X promoters and Y RBSs Z of which have been measured.
3. Measurement of physical objects is well understood and has been successfully developed and applied in other domains (e.g., principle of correlation, et cetera). A couple lessons:
   1. In order to make a measurement we need (1) a method of measurement and (2) a principle of correlation. For example... in measuring length...
   2. In order to control for the effect of conditions on the object being measured, we can (a) hold the conditions constant, (b) measure objects that are insensitive to conditions (c) Specify models that predict activity across different conditions.
4. Measuring biological parts consistently has proven challenging, and may be unlike past experiences
   • It is unrealistic to expect that researchers will be able to use standard conditions in the short term. This is both due to practical constraints of replicating the exact media, cells, growth conditions, etc, in independent laboratories as well as due to engineering constrains where different applications simply require different operating conditions (much as cars must drive in different temperature and weather).
   • The property we are measuring, promoter activity, is sensitive to experimental conditions.
   • Our models for promoter activity in different conditions are incomplete / non-existent.
   • "There is no such thing as a standard component, because even a standard component works differently depending on the environment." -- New York Times, Tuesday, Jan 17, 2006, Custom-Made Microbes, at Your Service