I believe the reason why the scientists used religion as a means to make the perfect society is because they are less likely to question it. When you have a religion, things are what they appear to be and hardly anyone gives a second thought about it. Anyone who breaks away from the norm is weeded out like the plague.
I think the scientists are still in charge, as leaders in the society, the system doesn't look self sustainable as with evidence of so many people vanishing.
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