A critical challenge for the design of embedded controllers is incorporating desirable qualities such as robustness, fault tolerance, and adaptability into the control process in order to respond to dynamic environmental conditions. An embedded controller governs the execution of a task-specific system by monitoring information from its environment via sensors and producing an appropriate response through the system's actuators, often independent of any supervisory control. For a human developer, identifying the set of all possible combinations of conditions a system might experience and designing a solution to accommodate this set is burdensome, costly, and often, infeasible. To alleviate this burden, a variety of techniques have been explored to automate the generation of embedded controller solutions. In this dissertation, we focus on the bio-inspired technique referred to as evolutionary computation where we harness evolution's power as a population-based, global search technique to build up good behavioral components. In this way, evolution naturally selects for these desirable qualities in order for a solution to remain competitive over time in the population. Often, these search techniques operate in the context of uncertainty where aspects of the (1) problem domain, (2) solution space, and (3) search process itself are subject to variation and change. To mitigate issues associated with uncertainty in the problem domain, we propose the digital enzyme, a biologically-inspired model that maps the complexity of both the environment and the system into the space of values rather than instructions. To address uncertainty in the solution space, we remove constraints in our initial digital enzyme model to allow the genome structure to be dynamic and open-ended, accommodating a wider range of evolved solution designs. Finally, to help explore the inherent uncertainty that exists in the search process, we uncover a hidden feature interaction present between the diversity-preserving search operator of a popular evolutionary algorithm and propose a new way to use niching as a means to mitigate its unwanted effects and bias on search.
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