There are two nerve pathways going from your skin to the spinal cord: touch and pain. From the spinal cord, they go up to the brain where they activate emotion and fear centres etc. At the spinal cord, the touch pathways inhibits the pain pathway and according to the Gate Theory of Pain, rubbing the hurt area causes the touch pathway to inhibit the pain pathway at the spinal cord so it does not go up to the brain and that is why there is some analgesia when you touch the hurt area. After a while though, the pain pathway from the hurt area becomes sensitized and touch becomes a pain signal (i.e. inflamed skin).
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