The phrase "by the waters of Babylon" is an allusion to Psalm 137, in which the Israelites mourn their exile from Jerusalem and weep over their memory of their lost homeland. The waters of Babylon are not where they belong. They long to be back in Israel.
Likewise, John would like to return to the former glory of the civilization he realizes his people were once a part of. When he travels to the Place of the Gods, which we as readers recognize as New York City, he realizes it was built by human beings like his people, not by Gods. Like the Israelites, he laments over what was lost and holds the hope his people can return to it.
The title is an example of dramatic irony, which occurs when the reader knows what characters in a story do not. Because they have lost so much knowledge, the Hill People cannot know of their heritage in the Judeo-Christian tradition, just as they cannot recognize the Place of the Gods as Manhattan.
John contrasts his own people, the Hill People, to the Forest People. His own people have made advances the Forest People have not. As John notes:
We are not ignorant like the Forest People—our women spin wool on the wheel, our priests wear a white robe. We do not eat grubs from the trees, we have not forgotten the old writings, although they are hard to understand.
The Hill People are better positioned to begin relearning the old knowledge. The title is important because it suggests the hope that, like the Israelites, the Hill People will return one day to the Promised Land of their former civilization.
The title of the story is an interesting choice by the author because "Babylon" is not ever mentioned in the story. Benét is counting on readers knowing that the title alludes to a passage of scripture from the bible. That passage is the opening lines of Psalm 137:
By the rivers of Babylon we sat and weptwhen we remembered Zion.
Psalm 137 is not a happy, praise filled Psalm. Instead it is a lament by the people of Israel. Looking back at that time in history, the people of Israel had a great deal to be sad over. They had been captured and removed from Jerusalem/Zion which was their promised holy land. It's important to know that Israel was a great nation at that time, and Jerusalem was a center for knowledge and learning. Unfortunately, all of that knowledge and power couldn't protect the people from their eventual fall at the hands of the Babylonians.
Knowing this should immediately clue readers into why the title's allusion is important to the story. New York City was that place of power and knowledge, yet all of that learning couldn't protect the people from their future destruction. John eventually learns that the Place of the Gods wasn't filled with gods. It was filled with people who had great knowledge, but they lost it...
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all. John will stand at the river bank with this knowledge, and that is likely similar to the people of Israel standing by the rivers of Babylon and remembering the loss of their previous knowledge, power, and greatness.
Further Reading
The allusion in the title is to the 137th Psalm. This psalm describes the despair of the exiled Israelites after Nebuchadnezzar II deported them from their lands in Babylon, after which he had the temple in Jerusalem destroyed. This allusion is symbolic because the despair of the Israelites is now being felt by the survivors of the Great Burning, who also live in exile. Like the Jews' continued desire to return to Jerusalem, John in the novel states a desire to return to, and rebuild, their ruined cities.
The Forest People are something of a cautionary tale. They are ignorant, and they fight against the more civilised people who, like John, regret the destruction of their great society and seek a return to that greatness. They indicate that human civilisation may advance to a very high level, only to be reduced to barbarism by the vicissitudes of such events as the Burnings.
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.