For centuries, philosophers argued about the existence of the soul, but the Bible makes it clear that there is one given to each human that has been conceived. In addition, for those who have accepted Christ as their Savior, the Holy Spirit comes to reside within them. Wherein lies the soul and Spirit in the body, and when do they enter, and when do they depart?
The ancients at times believed the soul lay hidden in the heart, and sometimes even the liver was suspected of being a residence. The Christian view is that the soul does not have its existence dependent on the corporeal body, and in fact survives when the body dies. The soul is thought to enter the human body at conception, and depart upon death. From a medical standpoint, we know that the soul does not reside in the arms or legs, for they can be lost. From a cardiac surgeon's standpoint, the soul is not in the heart; I have taken the heart from a deceased person and transplanted it into another living person, but the recipient's mind and soul remained their own. It would seem, however, that although the soul can exist apart from the body, it manifests its presence in the brain. I believe a mind is a prerequisite for having a soul.
A dead person has neither soul nor can be indwelt by the Holy Spirit. The only thing that remains is the deteriorating flesh of what was once a vital person. The soul does not live in a woman's eggs or a man's sperm, but once life is created, enters within. Although the brain does not yet exist in reality in the embryo, with thoughts and consciousness, there is the full potential for a functioning, thinking, rational human being, and the soul awaits the blossoming of brain waves, then conscious thought, birth, and speech.
I can think of two cases where a body is alive, but there is no functioning brain, thought, or consciousness. The most obvious is the brain-dead patient, from whence we obtain those organs for transplantation mentioned earlier. I have been called upon in my career to make brain death determinations. There is often a quite detailed list of assessments that must be made. The first is an apnea test, to see if the patient will breathe on their own, without a respirator; they usually must be disconnected for ten minutes to see if they will draw a breath. Another is to do an EEG or electroencephalogram, to see if any brain waves are present. There is the test for reflexes, usually the last of the signs of physical life to leave, such as stroking the corneas with a cotton swab to see if there is blinking, or even putting cold water into the ear canal to see if the eyes will twitch. The back of the throat is stimulated, to see if there is any gagging. If the body makes no attempt to breathe, has a flat EEG, and has no reflexes, they are declared brain dead. They are simply a body of flesh with some functioning organs that is kept alive by machines. Whatever made them a person is gone. I feel fairly confident that their soul has departed and the Holy Spirit does not reside within.
The second instance is an infant born with anencephaly. This is a catastrophic birth defect where a child is born essentially without a major portion of their brain. In particular, the cerebrum and the skull are absent, and this is where thinking and consciousness occur. These unfortunate infants have a lower brain portion and spinal column, and may have some reflexes, but will die within a few hours or days without ever having a conscious thought. Their appearance can be quite distressing, but here is an illustration that is not unduly gruesome and gives you the general idea:
It would seem to me that with no consciousness and no potential for consciousness, a soul would never be able to be manifest, and God only knows if there was one from conception until death.
Where we run into real problems, from the anencephalic at conception to the brain-dead at death, is all the cases in between. Does a severely mentally disabled child have a soul? It think so. However, I have seen someone that for all intents and purposes was brain dead, with no spontaneous breathing, no brain-waves on EEG, and all reflexes gone except the blink reflex in one eye when the cornea was stroked. Is there still a soul in that body? I doubt it, and indeed in that person event the blink reflex eventually disappeared. And what about those in comas, or vegetative states, do they still have souls? In that case, I think they still do. And those at the other end of life with severe dementia, I certainly believe that they still have a soul residing within.
I do not have the ability or the authority from God to make these determinations in all cases. Life belongs to Him. The anencephalic child will die according to His will; the mentally disabled, comatose, and demented will live and struggle according to His plans, and for His purposes. For those who accepted Christ before their coma, dementia, or brain-death, I think they are indwelt by the Holy Spirit and will receive eternal life. For those who are born without the ability to rationally understand or accept Jesus, I believe God will have a dispensation of mercy, as it is thought by many that He does when a young normal child dies.
To make matters even more difficult, there is the question of all those embryos. There are a lot more of them out there than you think there are. Depending on whose statistics you believe, it is possible that there are up to three times as many embryos created that will not make it to a functional pregnancy as those that will, and of the confirmed pregnancies, fifteen to thirty per cent will have a miscarriage. It is also felt that of all these embryos that do not make it to a live birth, sixty per cent were defective in some form, in a way that would have precluded them from drawing a breath outside the womb. Though somehow deformed in their development, and with God's sovereign will declaring their death before life, from a Christian standpoint, each was endowed with a soul at conception. Many also believe that God will grant mercy to these unborn children as well as the born, and entry into heaven will be allowed. Then there are the million babies deliberately sacrificed in the womb with legalized abortion. They have souls, and in their innocence, I believe God will spare them, too. If you think the world is full of strangers now, it is possible that heaven will be filled with three times as many people that never saw the light of day.
In vitro fertilization is a sensitive subject, but it needs to be brought up. In this process, eggs are harvested from the woman and combined with the man's sperm. Several embryos are created. Some will die in the culture dish, and of those that survive, the best-looking specimens under the microscope will be implanted, in hopes of a pregnancy. Only thirty per cent of in vitro procedures will result in a pregnancy, so seventy per cent of the implanted embryos will die of a miscarriage. The ones that are not implanted will be destroyed, which is essentially the same as an abortion. My wife and I, who are childless, could not allow ourselves to participate in this process and create embryos that would be potentially destroyed. Embryos apparently can be adopted out; they can also be stored. This means frozen.
We see in the news that a well known actress and her husband created a bunch of embryos (I would call them people), then froze them for later use. They since have divorced, and are now fighting over their embryos or property (I would call them people). These embryos, the first stage of life, who in the womb would continuously grow and develop until leaving the mother's birth canal to draw breath, learn to speak, take steps, go to school, learn and play, are now in a freezer. And what of their souls? I assume the souls entered into the embryos at conception, and since they are not dead, still reside there. What does a soul do in a freezer? Are God's purposes for the life He created fulfilled in sub-zero storage? How arrogant of man (and woman) to do this with a life, when all life belongs to Him.
Those of us who are Calvinists believe that God choses His elect. And we jokingly refer to those who have accepted Christ yet seem to lack fervor as the "frozen chosen". Some of those embryos were ordained by God before the beginning of time to be born and grow to love His Son Christ and receive Him as their Savior, destined to be indwelled by the Holy Spirit. They were chosen by Him as His own, and now they are frozen. They lie in suspended animation, awaiting to be born, and just as the aborted fetus cries not to be put to death, the frozen embryo cries to be put to birth. For this, they must be thawed, just as God needs to thaw the glacial hearts of those who put them into the icebox.