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I think the issue here is less the fact that the model is wrong, and more that it just doesn't go into enough detail....which is understandable considering the mechanisms behind phantom limbs and phantom limb pain is not completely understood.

When there is pain sensation from a limb that is no longer there, it is due to the fact that the nociceptors and the synapses that carry their signals to the brain have had an afferent barrage (usually) and the functioning of the sensory nerves and their pathways have so messed up that there is continual abnormal firing, resulting in pain. This is why when patients have a limb amputated in the hospital they give a nerve block and use anesthetic, as well as why there is evidence that shows patients who had no pain in limbs before they were amputated do not usually have phantom limb pain, but people who had horrible pain in their limb (ie the reason why it had to be amputated) did. [Also if your wondering how they got data on people who didn't have pain in limbs that were amputated, it was from an area in Africa where healthy people were dragged from their houses at night and their limbs were cut off by another group.]

Phantom limb pain is an issue that deals with the spinal cord and the associated nerves, which is why I don’t think it’s an error in the model, but merely details an area where more detail is needed. However, this detail is needed not only in the model, but in real life as well, since the mechanism underlying this problem is not well understood.

 In fact, I think the model does a rather nice job of summarizing the observations we have on phantom limb pain. We have shown now that input can affect boxes, which can then modify/amplify/etc the signal and send it to the brain. These inner boxes obviously have a malfunction, and continually send information that is not accounted for by the input, something out new model allows us to show.