A Standard Parts List for Biological Circuitry
Author(s)Arkin, Adam P; Endy, Drew
One of the hallmarks of biochemical circuits found in nature is analog, asymmetric, asynchronous design. That is, there is little standardization of parts, e.g. all the promoters have different strengths and kinetics, transcription factors are designed to have different effects at different loci, and each enzymatic reaction has its own idiosyncratic mechanism and rates. In addition, all of the heterogeneous circuit elements are executing their functions concurrently and asynchronously. Biological circuits are seemingly designed to deal with the fluctuating delays, different time-scales and energy requirements associated with each component process of the overall network. These factors also make design of novel biochemical circuitry from existent parts difficult to achieve. Without standardization, the qualitative design methods used in other engineering fields are simply inapplicable. The de facto design methodology for biological circuitry is natural selection. Rational design of biological systems by humans has remained restricted to rather small or hit-or-miss efforts and has often relied on the ability to "select" for biochemical parts that fulfill some criteria. In practice however biological-designers are rare, and solutions are usually realized through an expensive stepwise trial and error approach or through mutation and selection. Furthermore, these otherwise practical approaches are limited in terms of the problems they can solve. We believe that implementation of designed biological circuitry is limited by issues of practice.
DARPA White Paper
standard, biological parts
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