One theme of "Flowers for Algernon" is the cruelty in taking advantage of the mentally challenged. Before the surgery, Charlie is a happy man, and he believes that he has friends. Frank Reilly and Joe Carp often laugh at Charlie and use him for a laugh, but Charlie interprets this laughter as genuine friendship. Since he doesn't understand the difference between laughing with them and being the target of the joke, the ways they take advantage of Charlie for their own amusement is noticeably cruel.
There is also the experiment itself. Charlie is sought out because of his low intelligence. The implication is that his intelligence is not good enough and somehow weaker compared to "average" society. While Charlie himself does express a desire to be smart, in his initial understandings, he did not grasp the risks of the surgery. He was only able to see a potential path to the goals he had always had, but he didn't have a real advocate to explain to him what he could possibly lose. When Charlie loses his intelligence, there is a sense of shame in returning to the "below average" levels of intelligence where he started. Instead of being able to enjoy his life, he is miserable, being able to now recall parts of what he has lost.
The story shows that those with mental challenges need strong advocates who can work to help them make sound decisions regarding their medical care and to help shield them from those who may seek to take advantage of them to further their own ambitions.
A major theme of "Flowers for Algernon" is the cruelty of using a human being as an experimental "lab rat" to advance medical science before the science is ready for human testing.
Charlie, who doesn't have the intellectual capacity to give informed consent, is urged into experimental surgery to improve his intellect. Unfortunately, one of the key figures behind the experiment, Dr. Nemur, is aging and wants one last great success before his retirement. Therefore, he rushes forward with the surgery before he has sufficiently tested the data, not taking into account the degree to which his career ambitions could do harm to a human life.
At first, the surgery is a success, and Charlie's intellect rapidly increases until he is a genius. At this point, however, he analyzes the experimental data and realizes his intellect will decline back to a mentally disabled state equally rapidly. So will the intellect of the lab mouse Algernon, whose intelligence was also enhanced by the surgery. Charlie realizes too late that he mattered no more to the architects of the experiment than a lab animal would.
Through reading the story from Charlie's first-person point of view, we identify strongly with his yearning desire to be intelligent and the joy that comes into his life as his horizons expand. We then feel the failure of the experiment as a crushing blow, just as he does. To us, he is fully human, and we...
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therefore feel the cruelty of what was done to him.
The story is a warning to science not to get ahead of itself, written in an era when surgeries such as frontal lobotomies were done without a full understanding of their devastating impacts.
There are a number of major themes present in Daniel Keyes's novel Flowers for Algernon. One of the most thought-provoking is the nature of happiness. Before Charlie undergoes his experiment, a strong argument can be made that he is happy. He has a job in a bakery that he enjoys. He has what he sees as pleasant interactions with his coworkers and friends. He values the education he receives from his teacher, Alice.
Then he becomes smart. He undergoes an operation that causes a huge increase in his IQ, and he realizes the reality of his situation—that he was looked down upon by the people around him. As his intelligence grows, he alienates those he cares about. In both situations, Charlie is exceptional. At the beginning of the novel, he is exceptional due to his lack of understanding. He then becomes exceptional because he gains so much understanding. He is not, however, happier with this increased intellectual ability.
It would seem that Charlie is happier at the beginning of the text—happy to be in Alice's class, happy to laugh along with his coworkers as they make fun of him. Once he gains understanding, he drinks, gets in fights, and becomes incredibly depressed. When Charlie begins to revert to his former state of intellect, it may seem at first to be a positive thing. But because he remembers his genius, he feels shame at the idea of being pitied. He cannot revert to his former state of joy.
This text almost seems to be a biblical allegory for the story of the Tree of Knowledge from Genesis. Much like when Adam and Eve eat from the forbidden Tree, Charlie is cast out of Eden—he loses his innocence. Even though he tries, he can't regain that simple happiness he once had. This text asks us to question, using the extreme example of Charlie, the extent to which knowledge can give us joy. For Charlie, it can't; it only brings him misery.