Imagine: a mad scientist with a ray gun shoots at a neuron somewhere in cortical layer IV of your visual area MT, burning it up in a matter of microseconds (just for fun, imagine also that the ray gun leaves everything else intact).
With one neuron missing, you probably won't notice any perceptual change. But what if, one by one, all neurons in are MT went AWOL? You'd be stuck with an annoying inability to visually detect motion.
Now imagine that for every cell that our fancy ray gun hits, it replaces it with a magical transistor equivalent. These magical transistors have wires in place of each and every dendrite, a processing core, and some wires in place of axon(s). Naturally, the computational core analyzes the sum of all inputs and instructs the axon to "fire" accordingly. Given any set of inputs to the dendrite wires, the output of the axon wires is indistinguishable from that of the deceased neuron.
We can still imagine that with one neuron replaced with one magical transistor, there wouldn't be any perceptual change. But what happens when more and more cells are replaced with transistors? Does perception change? Will our subject become blind to motion, as if area MT weren't there? Or will motion detection be just as good as with the real neurons? I am tempted to vote in favor of "No change [we can believe in]," but have to remain skeptical: there is simply no direct evidence for either stance.
Ray guns aside, it is not hard to see that a computational model of a brain circuit may be a candidate replacement of real brain parts (this is especially true considering the computational success of the Blue Brain Project's cortical column, which comprises 10,000 neurons and many more connections among them). For example, we can imagine thousands of electrodes in place of inputs to area MT that connect to a computer model (instead of to MT neurons); the model's outputs are then connected, via other electrodes, to the real MT's outputs, and ta-da! Not so fast. This version of the upgrade doesn't shed any more light on the problem than the first, but it does raise some questions: do the neurons in a circuit have to be connected in one specific way in order for the circuit to support perception? Or is it sufficient simply for the outputs of the substitute to match those of the real circuit, given any set of inputs? And, what if the whole brain were replaced with something that produced the same outputs (i.e. behavior) given a set of sensory inputs - would that "brain" still produce perception?