The role of theory in science is discussed in the context of understanding brain function. Historically, theories of brain functions have oscillated between localization and anti-localization beliefs. In the last 50 years, the important discoveries of the ascending reticular activating system (ARAS), feature extracting neurons and synaptic growth led many to orthodoxy. Research became more and more focused upon the elements comprising the nervous system and their interconnections. The mainstream belief became that many brain functions including consciousness were localized, certain kinds of brain injuries produced irreversible functional deficits. Contrary scientific challenges were discouraged by the omnipresence of such theory. Examples of theoretical "Einstellungen" in the areas of ARAS, coma, treatment of brain injuries and consciousness are given, as well as signs that the pendulum is swinging back to an approach to the system as a whole rather than a focus on its parts.