Autonomous systems have the capability to independently (and successfully) perform complex tasks. Consumer and governmental demands for such systems are frequently forcing engineers to push many functions normally performed by humans into machines. s a functional architecture for an intelligent autonomous controller with an interface to the process involving sensing (e.g., via conventional sensing technology, vision, touch, smell, etc.), actuation (e.g., via hydraulics, robotics, motors, etc.), and an interface to humans (e.g., a driver, pilot, crew, etc.) and other systems. The “execution level” has low-level numeric signal processing and control algorithms (e.g., PID, optimal, adaptive, or intelligent control; parameter estimators, failure detection and identification (FDI) algorithms). The “coordination level” provides for tuning, scheduling, supervision, and redesign of the execution-level algorithms, crisis management, planning and learning capabilities for the coordination of execution-level tasks, and higher-level symbolic decision making for FDI and control algorithm management. The “management level” provides for the supervision of lower-level functions and for managing the interface to the human(s) and other systems.