This work uses an ALife simulation to explore the implementation of embodied reaction logic in a chemical computer. Chemical systems have potential for computation. There are properties of a logical system that are desirable in any computational system, such as the ability of the system to change state in response to some input. An issue in chemistry is that the molecules must have some physical embodiment, which must somehow represent state; state is then interpreted as the presence or absence

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... of certain molecular configurations in the system. The design of a chemical logic gate is a means of showing that a chemical system can change state appropriately and that the information encoded in the molecules is available to be processed as information. This paper compares two simulated chemical computing systems: Bindworld (a simple illustrative example) and Stringmol, (a fully implemented complex DNA-inspired evolutionary computing framework). The problems and design decisions involved in creating a NOT gate in each system are compared, showing that designed computational systems require a certain complexity and flexibility to be useful to human operators. Finally we discuss general extensions to the Stringmol reaction chemistry that would simplify the process of information processing in embodied systems.