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"Incongruity" refers to things that aren't related to each other. There are many examples of incongruous illustrations and points throughout Allen's speech. As is typical with much of his work, his irreverence for all serious topics encourages Allen to create incongruous situations and explanations whenever and however possible.
As a "Speech to the Graduates," Allen addresses a very serious topic - the meaning of life. The most basic way to express this question is to ask"How is it possible to find meaning in a finite world given my waist and shirt size?" Allen's personal measurements, such as his waist or shirt, have no relationship with any meaning hidden in the finite world.
Venturing further in his search, Allen asks,
can the human soul be glimpsed through a microscope? Maybe-but you'd definitely need one of those very good ones with two eyepieces.
Again, the incongruity is found in the idea of using any microscope, even a "very good one with two eyepieces" to be able to visualize the human soul. Even the suggestion that it would be possible to see a soul is incongruous.
In the same way, Allen explains the "crisis of faith" in which modern man finds himself by considering experiences that have disturbed his faith in life. "He has seen the ravages of war, he has known natural catastrophes, he has been to singles bars." The last is hardly of the same importance or influence as the first two events.