By birth, I specifically mean when the Winnower entered
this universe. What if there species were the first to see the might of the light and darkness, maybe some cataclysmic event transpires, and the being that would become the Witness has to turn to the Winnower for aid, where they then becomes its avatar.
That would first off explain there name, but also possibly explain why they are so high up in the food chain.
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I think the Witness was one of the creatures in the garden and "Witnessed" the gardener and winnower fighting as well as their power. And by watching the winnower, it learned how to use the powers of the dark.