What is the main theme in "By the Waters of Babylon"?

The main theme of "By the Waters of Babylon" is that knowledge is important. However, the improvements that knowledge can bring must be introduced slowly, as too much change all at once is destabilizing.

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I would argue that the main theme in "By the Waters of Babylon" is the thirst for knowledge. Unlike other members of the Hill People community, our protagonist, John, is dissatisfied with the rule that tribe members are forbidden to go east and to cross the great river.

As soon as he realizes that there is a lost civilization in the east, his desire is not for wealth or fame, but for knowledge. When he experiences what was once New York City, his thirst for the knowledge of those who lived in the city intensifies. He becomes determined to use his priesthood to help his people integrate all the knowledge that awaits into their way of life.

Understanding and knowledge cast out fear, and as John's knowledge grows, so his fear diminishes. The east is not, as his people had always told him, filled with magical mists or ever-burning flames. There are no spirits or demons, just an assortment of ruined buildings and a burning curiosity to know more.

John acknowledges that knowledge has not always been used well, which resulted in the destruction of the city. He also realizes that what he and the other Hill People have presumed to be gods were actually just people from an earlier society.

He returns home inspired by everything that he has learned and excited to share everything with his people.

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The main theme of "By the Waters of Babylon" is the importance of knowledge as a route to social advancement. Alongside this runs the idea that change based on new forms of knowledge is best introduced gradually.

John travels to the Place of the Gods and investigates it for himself instead of relying on traditional teaching. While there, he learns the important truth that it was built by humans, not gods. From that piece of information, he realizes that his people, too, can attain knowledge that was once believed to be godlike and out of reach.

This knowledge animates and excites him. He is eager to return to his village to spread a revelation that he believes will radically change his people for the better. However, when he gets back, his father says to him that

If you eat too much truth at once, you may die of the truth.

This cautions John to take care and slow down. He understands that the knowledge that his society can improve itself is important, but he also perceives that he could tear his society apart by shocking it with too much information all at once.

The story is a period piece, reflecting a time in which technological progress was seen wholly as a good. John never questions why the former, more advanced society he wants to emulate might have destroyed itself. Today, we might see more value in a hybridization of the ecological "primitivism" that John wants to abandon and technology.

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I would say that the theme of the story is the difference between knowledge and truth. The son longs to learn the secrets of the “dead places.” His journey to the bombed out city is forbidden by the laws of his people, but he is compelled to go nevertheless. What he discovers is that the “gods” of this place were not gods at all — they were humans like himself. While their technological achievements were very great, the “gods” were most definitely fallible, as the ruins of the great city attest. 

The son’s thirst to know is distinguished from the laws of the priesthood and of his society, which forbids travel to the dead places. The “truth” about these places, as he has learned it from his father, is that they are dangerous, poisonous places, and that the ways of the gods are an unsolvable mystery. These rules are in place in part to protect the hill people from making the same mistakes the “gods” made. As his father puts it after the son tells him what he has learned, “If you eat too much truth at once, you may die of the truth,” meaning that sometimes people are not ready to know everything. Although the son was compelled to break the law and visit the city to see things for himself, afterwards he comes to understand why the law existed in the first place — to prevent the people from “eating knowledge too fast.”

The story ends with the son deciding that once he becomes priest his people must return to the dead places to “rebuild.” The presumption is that their relearning of the old knowledge will be tempered by the truth that great knowledge does not make one infallible.

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I think the main theme of "By the Waters of Babylon" is the importance of knowledge.  That theme is a double edged sword though.  Knowledge is important to have and not lose, but it is equally important to not abuse.  

Throughout the story, the reader is learning about the world through the limited view of John.  Things seem vaguely familiar, but completely different.  Eventually the reader learns that the story is taking place in a far off future in a world that has been destroyed by nuclear war.  All of the technology and learning of hundreds of years before has been lost, and the world has reverted to tribal origins and deep superstitions.  The story ends with John vowing to bring back the lost knowledge to his people, so that they can once again be great.  

The other side of the importance of knowledge though comes as a warning from Benet.  John tells his readers that the "gods" had gotten too powerful in their knowledge.  Their learning accelerated beyond their ability to control it and its technologies.  The consequence was the destruction of the world.  

I saw them with wisdom beyond wisdom and knowledge beyond knowledge. And yet not all they did was well done—even I could see that, and yet their wisdom could not but grow until all was peace

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