John 3:3-6 Jesus answered and said unto him, Verily, verily, I say unto thee, Except a man be born again, he cannot see the kingdom of God. Nicodemus saith unto him, How can a man be born when he is old? can he enter the second time into his mother’s womb, and be born? Jesus answered, Verily, verily, I say unto thee, Except a man be born of water and of the Spirit, he cannot enter into the kingdom of God. That which is born of the flesh is flesh; and that which is born of the Spirit is spirit.
The most complicated and misunderstood issues in the intended design is the third part, the spirit. The reason is both simple and complicated. Up until the time we are reborn in the spirit, we have had years of nothing but the two parts of the intended design, the body and soul. During this period of time the body and soul have been cooperating with selfish interests. The body wants what it wants to satisfy its design, the soul is ever searching to satisfy those needs with a vested interest in interacting with the environment to meet those needs and hoping to satisfy those needs with a sense of accomplishment.
Now the Spirit which is God takes up residence within the body. The Spirit is perfect in performance of design, He has to be, He is God. The role of the Spirit is to communicate with the soul all that Jesus Christ is and does in accomplishing the promises of His New Covenant. As God He has the power to enforce the will of God the Father. This includes having power to act as God without permission of the body and soul. The body and soul have no power over the Spirit.
Here in lies the battlefield of living a life in Christ, for the Spirit does not interfere with free will. The soul must choose to love God, Jesus Christ and act in accordance with original design to access all the promises of the New Covenant. That is obedience of faith.
Next is the issue of living by design, as God intended.
Genesis 2:7 And the Lord God formed man of the dust of the ground, and breathed into his nostrils the breath of life; and man became a living soul.
A living soul is that animation force in which the body moves and is directed to act in response to observation, understanding, reasoning, and desire. All living animals have a soul if they have a developed central nervous system. We can observe that in the actions of animals, and prolonged observation which bring about understanding to their particular nature, design and capability.
Animals can be singular in action, loners who have the highest level of selfish interests. Others can and do take on a communal personality, finding survival is served best in cooperative efforts. These animals have a form of communication which is not always understood by speech, but by posture, and actions. Some species develop complex communication skills which we can observe but only have an observers understanding.
Still other pack animals seem to be able to find a roll within the unit to serve the pack and seem to silently move in unison with the whole without any communication, as if they have a knowing which we have a hard time understanding.
Man however has developed the most complex soul functions. The mind of man, a function of the physical body, has developed the highest degree of complexity in observation and reasoning skills. The soul of man makes one distinction above that of animal and that is awareness of things greater than self-awareness. We seek our creator.
Now the soul is physically tied to the body in design. Without the living brain, the soul has no connection to the body. The soul is subject to the workings of the body, is aware of the bodies needs and desires, which are natural and without flaw. How the soul chooses to satisfy those needs and desires is however not determined by design intent but rather by selfish interests of the soul in reason and interests.
The body needs fuel but a steady diet of ice cream is not by design but rather selfish desire.