First let's talk about
Some people use the existence of phantom limbs as evidence for a soul, fortunately there is an alternate explanation involving the physiology of the brain. It is possible to stimulate specific neurons in a patient's brain and ask them what they feel, if you touch the right spot, they will feel it in various parts of their body. If we draw the corresponding body parts over the brain we get the brain map below. Obviously certain parts of our body are more sensitive than others and therefore take up more real estate, if we draw a person with these distortions we get the homunculus, also pictured below (pictures taken from mm-theory.com)
One explanation of what is going on here is that there is much redundancy in the signals that are sent to the brain. When we scratch our cheek, our brain gets the signal that our hand is being scratched in addition to the correct signal about our cheek. But since our real hand is also sending a signal that nothing is going on, the errant signal is ignored. However, once the hand is gone the overactive signal is allowed to run wild. Once Ramachandran first published this idea he got a number of calls from amputees with stories of their own to tell. One man in particular who had his leg amputated said that he felt orgasms in his phantom foot, notice that the feet and genitals are next to each other on the brain map. This could even be the origin of the foot fetish!
In addition to the redundancy of the brain map, it seems that after an amputation the brain is able to create new pathways, Ramachandran suggests that perhaps there are times when a connection is made incorrectly. For example, perhaps a touch sensor is connected to a pain receptor, in this case a touch on the cheek could trigger pain in the phantom hand. It would even be possible that every time an amputee made a certain facial expression it would cause a phantom pain, diagnosing such a thing would be a nightmare.
Phantom limbs themselves being a result of redundant wiring but phantom pain being result of rewiring would explain why the phantom limbs often show up right away, and yet the phantom pain usually starts months later. Unfortunately, while this does explain things a bit, it doesn't necessarily help patients who have phantom limb pain. Although, if I recall correctly from the last time I read this (13 years ago), there were at least some cases in which he was able to help people with their phantom pain. I think we will get to it in the next chapter.