Is the the theme of "By the Waters of Babylon" about your spirit and seeking out knowledge and that there is always more to learn?
That is definitely one possible theme of this story, and that theme is best exemplified by the main character, John, as he seeks knowledge. Despite the traditional rules forbidding going to the "place of the gods," and many warnings against it, John trusts his intuition, his spirit, and goes on to discover astounding truths that will change his life, and the life of his tribe, forever. If this is a theme that you want to show as dominant in the story, using John as the example of it will work very well. So, a theme of inquisition, and seeking knowledge, can definitely be supported in this story.
However, as in many stories, there is not just one theme--this story is rich with potential lessons to be learned, and themes that are also valid. I have provided a link below that discusses a few of them. I also see a theme of history hopefully not repeating itself, of being careful and wise with knowledge given, of growth, of initiation rites, of human destruction, of progression, hope and truth. I hope that these thoughts help a bit; good luck!