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We've discussed how the nervous system is very flexible and adaptive, but I think this is one of the areas where we see it has a very hard time adjusting. Phantom Limb Syndrome is very common, which someone might imagine when you think of how traumatic it must be to lose a limb.

The way the body is wired, the brain doesn't just "forget" the limb is there. After receiving input from it for so long, it has become accustomed to it. One of the problems is the periphery, the nerve endings that have been severed try to re-grow, but they re-grow abnormally, giving the brain varied and strange input.

There are also changes in the CNS. The loss of normal sensory input can cause the brain to try to accommodate for this by increasing the input it receives or even "making it up." If a limb exhibited a certain pattern of input previously to the limb amputation (for example, a lot of pain from a traumatic injury), the brain may "feel" this, because it doesn't know what else to feel.

There have been cases where people have had a sliver of metal under their nail before their arm was amputated. After their limb was cut off, they felt that same pain in their phantom limb.