Although Bourne's amnesia at the start of the first film in the series is profound (and profoundly important to the unfolding story), we quickly learn that there are some things Bourne does remember from his past. For example, how to speak multiple languages, how to drive and how to fight. All of these are complex motor tasks that he learned before he was shot and fell in to the water.
This aspect of Bourne's amnesia is actually quite accurate. For people with “organic” amnesia (where neurological memory loss is typically due to damage to the medial temporal lobes in the brain), memory for skills and habits is intact, even though other memories are lost. There is truth to the cliché that you never forget how to ride a bicycle.
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