Wikipedia describes phantom limb pain thusly (I am removing references in the quote for your reading convenience. If you want the references, click on the Wikipedia link):
A phantom limb is the sensation that an amputated or missing limb is still attached to the body and is moving appropriately with other body parts. Approximately 50 to 80% of amputees experience these phantom sensations in their amputated limb, and the majority of these people report that the sensations are painful. Phantom sensations and phantom pain may also occur after the removal of body parts other than the limbs, e.g. after amputation of the breast, extraction of a tooth (phantom tooth pain) or removal of an eye (phantom eye syndrome).
Phantom pains can also occur in people who are born without limbs and people who are paralyzed. Phantom pains occur when the missing limb causes discomfort. Other induced sensations include warmth, cold, itching, squeezing and burning. The missing limb often feels shorter and may feel as if it is in a distorted and painful position. Occasionally, the pain can be made worse by stress, anxiety and weather changes.
For afterlife-scoffing materialists such as myself, phantom limb pain causes no controversy, and creates no explanatory problems:
Some people with phantom limbs find that the limb will gesticulate as they talk. Given the way that the hands and arms are represented on the motor cortex and language centers, this is not surprising. Some people find that their phantom limbs feels and behaves as though it is still there, others find that it begins to take on a life of its own, and doesn't obey their commands.
In the early 1990s, Tim Pons, at the National Institutes of Health (NIH), showed that the brain can reorganize if sensory input is cut off. Hearing about these results. S. Ramachandran realized that phantom limb sensations could be due to "crosswiring" in the somatosenory cortex, which is located in the postcentral gyrus, and which receives input from the limbs and body. Input from the left side of the body goes to the right hemisphere and vice versa. The input from extremities comes into the somatosensory cortex in an ordered way, the representation of which is referred to as the somatosensory homonculus. Input from the hand is located next to the input from the arm, input from the foot is located next to input from the hand, and so on. One oddity is input from the face is located next to input from the hand.
Ramachandran reasoned that if someone were to lose their right hand in an accident, they may then have the feelings of a phantom limb because the input that normally would go from their hand to the left somatosensory cortex would be stopped. The areas in the somatosensory cortex that are near to the ones of the hand (the arm and face) will take over (or "remap") this cortical region that no longer has input. Ramachandran and colleagues first demonstrated this remapping by showing that stroking different parts of the face led to perceptions of being touched on different parts of the missing limb and subsequently demonstrated that the somatosensory cortex reorganizes using magnetoencephalography (MEG) which permits visualization of activity in the human brain.
But what about the afterlife-believing immaterialist? Does phantom limb pain create problems for such a worldview? Well, I believe that it depends on the immaterialist in question.
Some immaterialists may accept the above quoted materialistic explanation for phantom limb pain. This is all well and good, and I would indeed applaud any immaterialist who adopts such a materialistic explanation. But if the immaterialist accepts such a material explanation for phantom limb pain, then why not also accept a material explanation for near-death experiences, or even death itself (in other words, no afterlife and no immaterial consciousness or soul)?
But let's move on to the immaterialist who believes that phantom limb pain is the result of that part of one's spirit or soul continuing to be attached to one's body, while the corresponding physical body part is missing (By the way, the reason I'm bringing this whole topic up in the first place is because I recently had a discussion about phantom limb pain with an afterlife-believing immaterialist).
Why, if the immaterial spirit portion of the amputated limb is still "attached" to one's soul, is it uncontrollable? Shouldn't one be able to still control one's spirit limb just like one can control their own thoughts? Or why wouldn't the spirit limb disappear into the immaterial afterlife dimension and wait for the rest of one's soul to arrive upon their death? Why would a material tool such as a mirror box be so helpful in relieving the phantom limb pain if the cause of the pain is the immaterial and disembodied spiritual portion of the limb?
At one point while discussing phantom limb pain with my immaterialist friend, I took the conversation one step further. I asked, "What if one's head is amputated instead of an arm? Would the person feel phantom head pain?" To this he only laughed, as if my question was totally absurd. I considered his laugh a victory on my part. Why? Because in his laughing dismissal of my question, he revealed that he believed the soul or spirit to be materially limited to the head, and that he was assigning a spiritual-physical disconnect or independence in an arbitrary fashion.
If one's spirit exists in one's arm and one's head, than isn't it logical to conclude that one's spirit exists in the entire body? Why would a spirit be able to control a physical body that is missing an arm, but not a body that is missing a head? Why would a person's immaterial spirit or consciousness experience phantom pain when an arm is severed, but not when one's head is severed?
Isn't the immaterialist's assumption that a severed head results in death some kind of concession to the materialist position? Why can't I just cut off my head and continue to live while experiencing phantom head pain? Isn't the immaterialist's assertions regarding the spirit and various severed body parts totally arbitrary?
If I lose my hand, and I still "sense" it's existence, then why don't I still "sense" the existence of my complete and intact mental facilities when I get a frontal lobotomy? Why don't I still "sense" the existence of my head when it gets blown off? Why do I instead die and (presumably) move on to the afterlife once my head is blasted to bits?
If the destruction of my head but the preservation of the rest of my body results in ascension to the afterlife, then does only my "head" portion of the spirit ascend while my "spiritual" arms and legs remain on Earth? I doubt that any immaterialist would agree with that proposition! So why should my spiritual arm remain with me after physical amputation, if my spirit in its entirety will ascend to Heaven when something as simple as a .22 caliber bullet pierces my brain stem?
As you can see, many unusual questions arise when immaterialism is combined with phantom limb pain (or any biological phenomenon for that matter). When biological hairs are split, such as in the case of phantom limb pain, only the materialist explanation makes any sense at all.