As an atheism-leaning agnostic, I'll throw some light on this from a different angle. I believe that many things are explained in different ways and labelled differently by those of different schools of thought. I feel that what theists describe ase the "Holy Spirit" is a state of self-actualization. For those who believe in a supreme being, it can be through the fulrillment of your own spiritual needs and getting as close as humanly possible to God. For those who practice Eastern religions, it can be achieved through the triumph of self-control over negative instincts and emotions. For an atheist, it can be achieved by becoming the best person you can be. In all cases, it represents the pinnacle of human achievement and the resulting state of mind in which we feel complete.
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