I'm not entirely sure of the meaning of the title,'Lord of the Flies'.
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On a literal level, "the Lord of the Flies" is what Simon ends up calling the severed pig's head, which is covered with flies. On a figurative level, the word "Lord" implies power and the "flies" imply decay. Put them together and you have something dark and ghastly that lies within the hearts of men, or boys in this case, that craves power and feeds on itself.