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Biosystems are unitary entities that are alive to some degree as a system. They occur at scales ranging from the molecular to the biospheric, and can be of natural, artificial or combined origin. The engineering of biosystems involves one or more of the activities of design, construction, operation, maintenance, repair, and upgrading. Engineering is usually done in order to achieve certain preconceived objectives by ensuring that the resultant systems possess particular features. This article concerns the engineering of biosystems so that they will be somewhat autonomous, or able to pursue their own goals in a dynamic environment. Central themes include: the computational abilities of a system; the virtual machinery, such as algorithms, that underlie these abilities (mind); and the actual computation that is performed (mentation). A significantly autonomous biosystem must be engineered to possess particular sets of computational abilities (faculties). These must be of sufficient sophistication (intelligence) to support the maintenance and use of a self-referencing internal model (consciousness), thereby increasing the potential for autonomy. Examples refer primarily to engineered ecosystems combined with technological control networks (ecocyborgs). The discussion is focused on clear working definitions of these concepts, and their integration into a coherent lexicon, which has been lacking until now, and the exposition of an accompanying philosophy that is relevant to the engineering of the virtual aspects of biosystems.