In Flowers for Algernon, both Charlie Gordon and Algernon the mouse are subjected to the same tests because they are both a part of the same experiment. First, the doctors do the experiment on Algernon to see if they can increase his intelligence. When they find out that it is possible, they want to see if they can replicate these same results on a human being.
Charlie is a great candidate for this study, due to the fact that he begins the story with a low IQ of just 68. He wants to learn, though, and to improve himself, so in the novel (if you are reading the short story, this part may be slightly different), he takes classes at a college for mentally challenged individuals. While there, his teacher sees potential in him and recommends him as a subject for the experiment she knows the doctors are conducting.
After having a risky surgery, Charlie's intelligence increases just like Algernon's. They are both then tested with similar exams to check the rate at which their intelligence is growing.
However, after a certain point, Algernon's intelligence begins to decline. The doctors then must continue to test both subjects of this experiment to try to find out why this is happening and if it will happen to Charlie, as well. Since the same surgery was conducted on both, researchers perform the same tests to see if both Algernon and Charlie are experiencing the same effects.
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