William, the 'problem' is that we do not perceive the phenomenal universe directly. Our senses input data to the brain which interprets it and produces a 'best guess' ... but the doubt is because we therefore perceive ourselves as separate from the universe, from what we perceive, that there is a 'me' and a 'that' - we are ego led - but this is a delusion - we are an unseparated part of the entire universe and can never be separate - there is only 'one thing'.
Once this is realised the doubt (and questions) disappear - this is the state known as enlightenment - a sudden moment when one becomes what one actually is, a conscious and aware being in oneness with everything else ... that awareness, that state of mind, that perception, has been described by a medieval Zen master as "not one, not two"
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