In studying brain activity during the behavior of living animals, it is not possible simultaneously to analyze all levels of control from molecular events to motor responses. To provide insights into how levels of control interact, we have carried out synthetic neural modeling using a brain-based real-world device. We describe here the design and performance of such a device, designated Darwin VII, which is guided by computer-simulated analogues of cortical and subcortical structures. All levels of Darwin VII's neural architecture can be examined simultaneously as the device behaves in a real environment. Analysis of its neural activity during perceptual categorization and conditioned behavior suggests neural mechanisms for invariant object recognition, experience-dependent perceptual categorization, first-order and second-order conditioning, and the effects of different learning rates on responses to appetitive and aversive events. While individual Darwin VII exemplars developed similar categorical responses that depended on exploration of the environment and sensorimotor adaptation, each showed highly individual patterns of changes in synaptic strengths. By allowing exhaustive analysis and manipulation of neuroanatomy and large-scale neural dynamics, such brain-based devices provide valuable heuristics for understanding cortical interactions. These devices also provide the groundwork for the development of intelligent machines that follow neurobiological rather than computational principles in their construction.