If we take the -nomos suffix as “law” then theonomy is good and autonomy is evil, because one should submit to God’s law rather than be a law to oneself.
But being “autonomous” does not typically mean being a law unto oneself in all contexts. It can means simply being self-governed. A child becomes “autonomous” to a degree at the age of eighteen because the child becomes an adult and is permitted to make choices for him- or herself. One becomes “autonomous” when one is given space and time to make one’s own decisions without immediate supervision.
In other words, you are autonomous when you are expected to supervise yourself rather than be supervised by someone else.
Autonomy can be a matter of degree: you can be told to report back in two weeks or six months on a project. You are autonomous in that you are “on your own” until the appointed time of review. Or you can be given a mission without being given minute instructions on how to succeed at the mission. Determining your best strategy to complete the mission is part of the mission itself. So in both cases you have a lesser or greater degree of autonomy without denying a higher authority.
So God has left us largely autonomous, or rather, with the charge to become autonomous and thus complete his mission for us.
But to what end? If we don’t have at least an overarching plan for human beings in mind, then how can we unify our desires, perceptions, and impulses toward an intelligible goal? With no goal, we become slaves to vices. With a false goal, we will eventually find that our “autonomy” is actually slavery to some principle that doesn’t truly suit us.
If God is truly the Father, Son, and Holy Spirit revealed in the Bible and in the Gospel of Jesus Christ, then only by governing ourselves to serve him and model ourselves on him can we be truly self-integrated and self-governing.
So, this is the conclusion of the matter: The only real autonomy is found in theonomy.
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