The title "By the Waters of Babylon" is a clear allusion to Psalm 137 of the Bible, which begins "By the Waters of Babylon I sat down and wept." This Psalm is a lament of the Israelites for their lost "promised land" of Israel from which they have been exiled. Their homeland was destroyed and its people scattered. There is a clear parallel therefore between the lament of the Psalmist for his home and the realisation of John of what has happened and his sadness at what has been lost. Using this allusion therefore reinforces the message of the short story: the eventual threat of self-destruction if we are unable to curb our thirst for knowledge - and not "eat it too fast."
The problem with the Forest people demonstrates the kind of primal, savage society that John and his tribe live in. Despite the incredible advances that man made, the resulting cataclysm reduced mankind to a neanderthal-like state, robbing him of ideals such as the capacity for mutual understanding and the ability to co-exist with different people and replacing them with a Darwinian survival of the fittest code of law. This likewise reinforces the dangers of knowledge by showing us that any future man could have after such a cataclysm can only be bleak, barbaric and bellicose.