Suppose, if you will, that alien scientists came down to Earth and began to study the local lifeforms. But let's suppose that these aliens arrive by the side of a busy expressway, and stay there. Our extraterrestrials might conclude that cars are the dominant inhabitants of Earth.
Cars clearly exhibit intelligent behaviour, being able to navigate around obstacles and follow complex instructions on road signs. How, the aliens may wonder, do the cars manage this? What is the seat of car intelligence? After some experimentation, the aliens would eventually work out that it is a carbon-based organ inside the car - aka the driver - that is controlling the vehicle. The driver is the one making the decisions, and the rest of the car is just following its commands. The proof of this is that if the aliens remove a car's driver, it stops moving. Experiments could be conducted to find out the function of different parts of the driver. Lesion the driver's feet, for instance, and the car would have trouble braking and accelerating, while arm damage would produce selective deficits in turning. These lesion experiments could be supplemented with imaging studies, in which aliens scan the car and record the activity in the different parts of the driver. Just as lesion studies predicted, the feet would be more active when braking, while arm movements would predict turns.
Eventually, "driverscience" - the study of the driver and its function - would become a well-developed field of alien research. Everyalien would know that the arms are responsible for steering while the feet control speed, and so on.
I hope it's obvious that in this scenario I'm drawing an analogy between the driver, as controller of the car, and the brain as the controller of the body. The aliens have concluded that the human driver is the "brain" of the car.
Knowing neuroscience as we do, we might be tempted to say that the aliens are mistaken, and that only the driver's brain is actually responsible for controlling the car. The aliens are wrong in thinking that hands or feet or other body-parts have anything to do with intelligence, we think. The brain is the driver of the driver.
Yet who is to say that we are not falling into the same trap as the aliens, when we attribute intelligence to particular brain regions? If we talk about the amygdala (say) "recognising a threat", we imply that this region, by itself, is carrying out an intelligent function; but this might be as mistaken as to say that the feet "recognize" that the car is going too fast.