I've learned for so many years how to live by the scientific method, but what happens when the conclusions gathered from our observations of natural data don't line up with the conclusions offered us by Holy Spirit? What do we do when Holy Spirit is telling us to do something that seems to contradict our much valued 'common sense?' For example, when Peter saw Jesus walking on water, what would possess him to think he should walk on water. Everyone knows you can't walk on water!
As Jesus says in the above passage, I am guilty of living much of my Christian life reacting to my observations of the world, not Holy Spirit's revelation within me. My M.O. is to observe the world around me (I learned this in seminary), then to figure out a 'Christian' or 'spiritual' response (WWJD), then I ask God to help me pull it off. My problem, as the Lord is revealing it to me, is that I bring Holy Spirit into the process too late. Holy Spirit is teaching me that I can't even make healthy observations without him. It is Holy Spirit's job is to illumine the spiritual, which is superior to the natural. With spiritual eyes, ears, etc., we learn to see both the natural and spiritual. The challenge can be choosing the spiritual over the natural!
For example, in 2 Kings 6, Elisha and his servant are surrounded by "strong force" of the Aramean army. Elisha's servant, understandably concerned considering the odds (2 vs. hundreds, maybe thousands), responds in fear - "Oh, my master, what shall we do?" Elisha, who was learning to see the spiritual realm as well as the natural, says to his servant - "Don't be afraid...those who are with us are more than those who are with them." Elisha goes on to pray for the servant's 'eyes' to be opened. "Then the Lord opened the servant's eyes, and he looked and saw the hills full of horses and chariots of fire all around Elisha (vv.14, 16, 17)." We can either live as Elisha, with spiritual eyes and faith for the supernatural, or the servant, with natural eyes and fear.
Jesus himself says he only does and says what he sees and hears the Father doing (John 5:19, 12:49). Jesus lived every moment of his earthly ministry according to spiritual sense. In other words, Jesus lived the same life he calls us to- a life of simple obedience to what Holy Spirit tells or shows us. This life rises up within us, not from outside of us. We don't get this life by listening to enough sermons, or reading enough books, or attending enough conferences, or even by attending enough prayer meetings. We get this life when we acknowledge the kingdom of God IS WITHIN US! We're free from looking to the religious professionals, or anyone else to get it for us. Every spirit-filled Christian has the right and privilege of learning to walk in Jesus' footsteps, which is to simply obey what Holy Spirit is telling and showing you.
With Holy Spirit living inside us, we have access to the kingdom of God (on earth as it is in heaven) for every bit of our lives! Holy Spirit will show us the Jesus' heart for every matter. Like Jesus, we'll begin to live according to what we see in the Spirit. Like Elisha, we'll stand confident in the face of every adversary, seeing in the Spirit the incredible resources God enlists on our behalf as we obey Him.
Learning to see with Spiritual eyes isn't an overnight deal. We learn each day to turn inward, to Holy Spirit within us, listening and responding to His voice, until our natural way of living is supernatural. This is living by faith; not hoping God will do something for us because someone else said so, but because Holy Spirit within us speaks to us, reveals to us, and confirms for us the Lord's desire for every situation we'll submit to Him.
(Everything I just wrote feels pretty pathetic compared to how Holy Spirit is revealing it to me in my spirit, but this is my best attempt to communicate it. Forgive me if it sounds preachy, teachy, or anything but my own journey!)

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