Although the word is never stated in the film (as far as I know), perception is a key word in regards to Being John Malkovich. Craig enjoys the experiences of being inside Malkovich, as well as being a common puppeteer, because they allow him to experience what it's like to be in someone else's skin, see what someone else sees, and feel what someone else feels. People who "are" John Malkovich, are able to percieve what it's like to experience life as someone else. They aren't physically John Malkovich, they are experiencing life by way of perception. This movie calls into question the relationship between body and mind. It also forces us to wonder who we are and what governs and controls our actions.
Perception is defined by the OED as "1. a. The process of becoming aware or conscious of a thing or things in general; the state of being aware; consciousness." I think this definition accuretely defines what the people who entered John Malkovich experienced. These people were conscious inside of his head (i.e. they still had their own sense of self; memories, ideas, etc.)
However, the definition gets muddy in terms of the film because the film seems to question ideas about perception by depicting one individual as being inside and controlling the actions of another individual, while still having his own sense of self. Craig demonstrates this when he begins to control Malkovich and chooses to live vicariously through him. Craig knows he is merely the puppeteer of Malkovich and he still is conscious of his own being. All this being said, the film really makes one think about his/her own consciousness. Is someone else implanting ideas and thoughts into our heads? How can we trust our perceptions?
2 years ago