The question isn't stupid at all! There are many idioms in every language that native speakers take for granted, but are not clear at all to people who don't possess the same degree of familiarity. You are correct about your assumptions....the phrase has its origins in the urges that come from natural body function, thus "Nature is calling." There are references to that behavior in the forums, but they typically are phrased differently, using terms such as "peeing!"