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I think the movie was a commentary on how prevalent violence was destined to become. The rapes were there for shock value - to desensitize the audience. It works: through the use of gratuitous violence, we become more accepting of violence. We learn that with certain triggers we are just as capable of similar violence. When he is put into the system and brainwashed, we sympathize and begin to view Alex as a perverse hero, (Tony Soprano?) someone who remains true to their identity and unbroken by the system.
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