The central theme in Flowers for Algernon is Man Playing God. The basic structural layout of the novel supports this theme. The novel's chronological timeline begins March 3 and ends November 21. The seasonal interpretation is obvious. Charlie's surgery takes place in the spring, a time of new beginnings, new growth, and re-birth. The progress reports, and our journey with Charlie, come to an end in the heart of autumn. Autumn is the season that displays nature's decline. Autumn isn't death as symbolized by winter, but it is the loss of new growth and the beginning of regression. A synonym for autumn is "fall," and that word, in the verb form, is what we witness in Charlie.
Charlie's personal odyssey spans a period of nine months, which is both a plot technique and a representation of the human gestation period (a period in which new life is developed and nurtured, culminating in the birth of a new individual). At the conclusion of Charlie's nine-month development, however, no new individual is born. Rather, readers witness the rebirth of the original Charlie. This "failure" symbolizes the ultimate failure in the concept of Man Playing God.
Many overt references to this theme run throughout the novel. Many people, including Charlie, discuss tampering with man's intelligence. The first nurse Charlie encounters after his surgery introduces this theme. She tells Charlie that if God had wanted Charlie to be smart, God would have made him that way. Charlie also remembers his mother telling him about God, and that they were to pray to God to make Charlie smart. Even Dr. Guarino, "with the Lord's help," might be able to make Charlie like other children. Finally, Professor Nemur admits this ambition in his speech at the International Psychological Association presentation when he says, "We have taken one of nature's mistakes and by our new technique have created a superior human being."
Another theme that is essential to Flowers for Algernon is one of friendship. This theme encompasses all aspects of friendship: expectations, perceptions, and the importance of it. Charlie's friends at the bakery — Gimpy, Frank, and Joe — are the ideal studies in the perception of friendship. Before the surgery, these men were Charlie's best friends. He loved their company and looked forward to spending time with them. After the surgery, Charlie is able to view their relationship in a different light and comes to realize is that these men were not friends. They not only made fun of him, but he was also often used solely for their entertainment. As he recognizes that, so ends their friendships. However, as Charlie is failing intellectually, he returns to the bakery, and it is these "friends" who welcome him back, having accepted him for who he again is.
The first book that Charlie reads after his surgery foreshadows the friendship struggles that he will encounter. Miss Kinnian has Charlie read Robinson Crusoe. As Charlie interprets it, the book is about a very smart man marooned on a desert island. Charlie feels very sorry for Robinson Crusoe because he is all alone and has no friends.
The strength of friendship is examined in Charlie's relation-ship with Algernon. The white mouse offers Charlie what he needs most in this world: unconditional friendship. Charlie shares the experience of the experimental surgery with Algernon, and Charlie discovers his own fate through Algernon. When Charlie has regressed to a point that is below where he began, we see the strength of friendship, not only in the friendship that existed between Algernon and Charlie, but also in the friendship that Charlie offers to those around him. At the conclusion of the novel, Charlie is unable to remember many things from his past, but he is aware that his regression is upsetting to others, especially to Miss Kinnian, whom he considers a friend. He chooses to move to the Warren State Home out of consideration for his friends. And, truly a loyal friend himself, Charlie's final entry in his progress report requests that someone please remember to put flowers on Algernon's grave.
A third pervasive theme in the novel is the role of intelligence in human relationships. Charlie's social self suffers both as an individual of low intelligence and one of high intelligence. Charlie expects that increased intelligence will please his friends and increase the number of friends that he has. He is not prepared for the change in his relationships with his friends brought about by his new intelligence, nor is he prepared for the changes in himself. As a genius, he joins in with people who condescend to people who know less than they and becomes even less able to make and maintain friendships than he was as the original Charlie.
Does Charlie regret his brief flirtation with genius? Would he have been better off without the experiment? Charlie tells Alice that he does not regret being part of the experiment. "Im glad I got a second chanse in life . . . because I lernd alot of things that I never even new were in this werld and Im grateful I saw it all even for a littel bit." He also notes that he's probably the first "dumb persen in the world who found out some thing importent for siense." As Charlie notes in Progress Report 16, "intelligence and education that hasn't been tempered by human affection isn't worth a damn." The difficulties faced by the intelligent person who often lacks good social skills persist even today as "nerds" are made fun of by the "in," crowd and as introverts are often treated as "flawed" because of their more private personalities.