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I nterms of classical conditioning, a phobia is a conditioned response of intense fear to a conditioned stimulus of the phobia trigger. This association was most likely made while the person was still developing physically and mentally and the brain had not finished growing and wiring itself. Something happened that strongly associated pain with the conditioned stimulus.
This event could have been a fall from a ladder that generated a fear of heights, or an relatively serious injury that occured at the same time that the unconditioned stimulus was introduced. It could also be a "crossed wire" in the brain, where the phobia has no discernable cause.
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