One difficult question raised by Daniel Keyes's Flowers for Algernon with respect to whether or not Charlie should take part in the experiment concerns any possible ramifications. In other words, will the experiment cause Charlie more harm than good? As we learn in chapter 5, Professor Nemur feels certain that the experiment will not put him in physical danger. However, he is also afraid of the potential side effects of raising an IQ as low as Charlie's to a high IQ; he feels it may overwhelm Charlie, and in Charlie's words, that Charlie "would get sick from it." Professor Nemur further points out that, while the experiment may succeed, it's also possible that the success would only be temporary, and his intelligence may deteriorate after being raised. If his intelligence deteriorated, he could be even worse off than he is now and need living assistance.

A second question raised by the experiment concerns the experiment's ethics. The scientists had intended to create a new kind of human intellect, to create a "superman"; however, their desires raises the question, is it really ethical to want to create something new out of what already exists? The scientists treated Charlie as if he was subhuman because he was mentally handicapped; they further acted on the belief that they could make him human by raising his intellect. Yet, Charlie was of course already human, and their experiment was inhumane because it treated him as subhuman. Hence, rather than wanting to create a new race of intellect out of already existing intellect, they should have been willing to accept Charlie's intellect as it was.