Biological organisms sense their environment, process information, and continuously react to both internal and external stimuli. We can now harness organisms as computational substrates, and extend their behavior by embedding biochemical logic circuitry that controls intra- and inter-cellular processes. The engineering and construction of reliable logic circuitry enables a wide range of programmed applications. The application areas include drug and biomaterial manufacturing, programmed therapeutics, embedded intelligence in materials, sensor/effector arrays, gene therapy, and nanoscale fabrication.

In this talk, I will describe my research that uses computer engineering principles of abstraction, composition, and interface specifications to build programmable bio-organisms with sensors and actuators precisely controlled by logic circuitry. Here, recombinant DNA-binding proteins represent signals, and recombinant genes perform the computation by regulating protein expression. To demonstrate basic cellular computation and intercellular communication, I will describe the construction and testing of biochemical gates in Escherichiac that implement the and logic operations. After measuring and modifying the "device physics" of these gates, I combined matching gates to implement several small circuits. To aid in this biocircuit design process I implemented BioSpice, a prototype genetic circuit simulation and verification tool.

Finally, I will describe the Microbial Colony Language (MCL), a simple programming paradigm that could be instantiated with small circuits and intercellular communications. This intermediate-level programming language is used to explore how to achieve globally coordinated behavior (e.g. pattern formation) from a large number of unreliable computing elements such as programmed cells that are constrained to communicate locally.