The author learned about or was reminded of Punnett squares, either from a biology student friend or Wikipedia, and decided to make a humorous comic strip on the subject. The format he eventually landed on was of the “improbable human interaction” variety, wherein the humor is derived from two-to-three people doing or saying something unrealistic.
This particular interaction involves two biologists on a first date who find themselves creating Punnett squares in order to determine the genetic traits of any children they would have if they were to mate. This is funny because you would not expect two adults on a first date to discuss having children, especially in such a clinical fashion.
Trivia: 97% of sex can be made more comfortable for geeks to discuss in the context of a science-related joke.