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Just because the science faction are in control does not mean they cannot use religion as a tool to shape society, at least for a period of time. That's precisely what the foundation did during the early rise out of the dark ages to control the warlord systems near Terminus.
There are no other faction that can apply genetic manipulation to introduce the wolf trait as well shame to death trait. The fact that the kids and the monk are still under the effect of these genetic modification is one sign that the scientist are still on control.
The school and the social control that removes trouble some kids is another sign. It takes knowledge and training in psycho analysis to accurately predict the correct candidates to be eliminated. The system being used in the school, family and the 'religion' are psychological conditioning that would require science faction to maintain.
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