Science Ch.17 - What Does the Human Spirit Do?

What is the difference between the human spirit and soul? Neurologists and philosophers ask a similar question about the mind and brain.

A bizarre experiment took place in 1907 when an American doctor, Duncan MacDougall, tried to measure the weight of the human spirit. He put the beds of six dying men on an industrial weighing machine and found that one of them lost three-quarters of an ounce when he died. The other five results gave the “wrong” answer, so they were dismissed as faulty. You won’t be surprised to hear that more accurate equipment under controlled conditions has failed to replicate this experiment.1

       Almost all human functions can now be traced to physical impulses from the brain, hormones, social interactions, and learning. In the previous chapter we saw that very few abilities are unique to our species, and some of these are merely due to our larger brains. That’s why the Bible speaks of a “soul” (our emotions, personality, and life) as residing in animals as well as humans. But the Bible also refers to another component that is separate from our bodies – our “spirit” – and it uses the words for “spirit” only with regard to God, angels, and humans, but not animals.

       The Bible uses “soul” (Hebrew nephesh and Greek psuchÄ“) as a word for part of the body. It is used when counting numbers, because the soul is part of the visible body (e.g., Gen 46:18, 22, 25, 26, 27, where each number is followed in the Hebrew by “souls”). It is even used when “soul” means a corpse – for example, in the laws about touching a dead person (Num 5:2; 6:6, 11; 9:6, 7, 10; 19:11, 13). In contrast, a “spirit” (Hebrew ruach and Greek pneuma) is described as something that isn’t seen and can’t be grasped in your hand – like the wind (John 3:8).

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Spirit and body

The Bible regards the spirit as being within the body but not part of it. While a fetus is growing, “the spirit comes to the bones in the womb” (Eccl 11:5 ESV) just as God originally “formed the spirit of man within him” (Zech 12:1 ESV). Then, at death, “the spirit returns to God who gave it” (Eccl 12:7): so the psalmist says, “into your hands I commit my spirit” (Ps 31:5) – which Jesus quoted when he “gave up his spirit” (Matt 27:50; Luke 23:46; John 19:30) – and Stephen said, “Receive my spirit” (Acts 7:59). When someone was brought back from death, “her spirit returned” (Luke 8:55). After death, the flesh is destroyed, but the “spirit” survives (1 Cor 5:5; 1 Pet 3:18), and God determines how good this spirit is (Prov 16:2) – though the “spirits” of believers are made righteous by God himself (Heb 12:23). It appears, therefore, that a human spirit can live without a body, but a body without a spirit is dead (Jas 2:26). However, we are promised a new body for our spirits (1 Cor 15:35-49), like Jesus, who rose with his new body as the “firstborn from among dead” (Col 1:18; Rev 1:5). He was not merely a spirit because “a spirit does not have flesh and bones as you see that I have” (Luke 24:39 ESV).

       The Bible also describes the spirit as the part of us that makes decisions. When God caused someone to be obstinate, God made his “spirit” stubborn (Deut 2:30), and people have “no spirit left” (Josh 2:11 ESV) in situations of extreme fear and helplessness (Josh 2:11; 5:1; Ps 142:3). When tempted, “the spirit is willing,” but “the flesh is weak” (Mark 14:38 = Matt 26:41). God “stirred up the spirit of Cyrus king of Persia” to make him decide to release Israel from their exile (2 Chr 36:22; Ezra 1:1 ESV), then stirred the spirits of individual Jews to go and rebuild the Temple (Ezra 1:5; Hag 1:14). When humans rebel against God, it is their “spirit” that turns against him (Job 15:13; Ps 78:8), and when they decide to follow him they are “contrite … in spirit” (Isa 57:15; 66:2; also 1 John 4:3). It is the “spirit” that is born again and renewed when someone turns to God (John 3:6; Ps 51:10; Ezek 11:19; 18:31; 36:26).

Spirits communicate

We communicate with God through the Holy Spirit, who speaks to our spirit and teaches our spirit how to pray (Rom 8:16, 27; 1 Cor 14:14), because these things are “spiritually discerned” (1 Cor 2:14 ESV). We can pray with our minds, but this is different from praying with our spirit (1 Cor 14:15). Only a person’s own spirit really knows their inner thoughts – other than God himself (1 Cor 2:11).

       Therefore, “spirit” is not just another word for “soul.” Paul makes it very clear that they are different when he refers to our “whole spirit, soul and body” (1 Thess 5:23; also Heb 4:12). The soul is part of the human body (and part of an animal’s body), whereas a spirit can exist independently of the body, though it may feel somewhat naked till it can “clothe itself with the imperishable” – the new body (1 Cor 15:50-54).

       One way to think about our spirit is to imagine trying to connect to the internet. Our brain is like a computer suffused with the information signals from the internet, but we can’t read anything online or talk to anyone with it unless we have a router to communicate. Our spirit can intercept and understand things on a spiritual level, which we may be completely unaware of even with our minds. Likewise, an animal can’t communicate on a spiritual level because it doesn’t have a spirit and isn’t even aware that anything exists to communicate with.

       And to take the analogy further, a computer connected to the internet only becomes useful when we have a keyboard to interact with it. Without that, the computer would just be inactive, waiting for instructions, and we wouldn’t be aware that it was connected to the internet. This implies that having a spirit is not enough: there must be some component in our brain that acts like that keyboard for interacting with it. This suggests that even if an ape had a spirit, the ape’s brain wouldn’t be able to connect with it. But our brains have developed differently, so that when God implanted a spirit in humans, our brains were able to interact with it – though we don’t yet know how. The result is that we are no longer just animals interacting with the physical world; we are also open to the whole spiritual world – whether we take time to explore it or not.

       What is it in our brains that is different – that allows us to connect on a spiritual level? We cannot answer this question because it is difficult for any kind of science to investigate something that is completely immaterial; by its nature, our spirit will not interact with any instruments or photographic chemicals.

       What about interactions in the other direction, from our spirit to our body? If a spirit can’t interact with matter, then it can’t move a limb, or influence emotions via chemicals (such as adrenalin), or create even the merest spark of thought in the brain. If it cannot interact with anything physical, it can only observe. Our human bodies would get on with life by means of animal reflexes: eating, growing, having temper tantrums, learning to speak, having children, getting ill, and dying. If our spirit cannot interact with the brain, it can never prompt us to do anything “spiritual,” or even to show kindness to someone; we would merely act like clever animals, and our spirit would be a voiceless onlooker.

       This problem is related to that of free will: we all feel as though we can freely make moral decisions, many of us feel as though we can communicate with God, and almost all of us feel as though we are a “person” who should be able to survive death – but this might all be an illusion. Theologians talk about the spirit, while philosophers and neuroscientists talk about the mind, but neither has any way to describe it in a way that can be tested. On their own, neither the Bible nor science helps us to define or discover what a spirit or mind is. However, together, the two areas of knowledge may bring us a little closer to doing so.

       The various sciences have led us to regard the world like a complex billiard table, where hitting one ball inevitably results in movements by other balls in a predictable way. In that case, if we had a computer big enough to record the position and movement of every atom, then in theory we could predict exactly what would happen at any point in the future. Just as we can wind forward the mechanism of a planetarium to see when the next solar eclipse will happen, we could theoretically examine a person and the whole world around them to predict when he would next lose their temper.

Quantum connection

However, this is only true up to a certain point because predictability doesn’t extend to the subatomic world, where quantum uncertainty takes over. On a billiard table we can measure exactly where a stationary ball is, but if it were as small as an electron we’d only be able to measure its stationary position to the nearest 10−35 meters.2 This Heisenberg uncertainty principle is not due to the limitations of our measuring instruments but is part of the fundamental nature of matter itself. It means that when, for example, two neutrons collide, one of them may split into a proton and electron, or it may not – and it is impossible to predict with certainty whether it will happen even under identical circumstances. When this uncertainty was first discovered, there were many skeptics – including Albert Einstein – but all the experiments at institutions such as the CERN (the European Organization for Nuclear Research) continue to confirm it.

       Quantum uncertainty does not mean that the universe is unpredictable, because these uncertainties only occur at the subatomic level and average themselves out at larger scales. These tiny particles are like mayflies hovering over a lake. They could conceivably cause a ripple in the water if they all gathered in one small spot and all flew in the same direction, but because they all fly randomly in different directions, their movements cancel each other out. However, this tiny area of uncertainty may also be influenced by spiritual forces in ways we don’t understand and can’t measure. Of course, we can’t know this for certain, but we also can’t rule it out.

       Academics have seriously considered the possibility that our spirit could interact with our brains at the quantum level, below the threshold of quantum uncertainty. For example, Peter Clarke, a neurologist who happens to be a Christian, has done the math to see whether this would allow the spirit to fire an individual neuron. Unfortunately, the calculations don’t add up: the amount of action that could be performed in this tiny area of unpredictability is not enough to make even a single neuron fire.3 This is an ongoing area of research, and Clarke has indicated some currently insurmountable problems, though he didn’t take into account cascade reactions, where tiny causes can result in larger effects. Quantum effects have now been found to trigger our sense of smell, which makes it more reasonable that quantum fluctuations may trigger thoughts, too; however, this kind of research is in its infancy.4

No conflict

It is therefore reasonable to suppose that an immaterial spirit, which cannot be measured or contained, can nevertheless interact with human thought without being detectable by any possible machine or other person. That is, although we cannot yet demonstrate this, it is not contrary to reason or to what we do already know. Our spirit may indeed act as a “ghost in the machine” by making decisions that are communicated to our brain and thereby turned into thought and action. Of course, I am not concluding that this is definitely the way that a spirit inhabits and influences a body. At present we can only conclude that it could be, though this is sufficient to show that there is no necessary conflict between the science of neurology, the philosophy of mind, and the theology of an immaterial human spirit.

       This spirit enables us to know that there is something “out there” that we can communicate with. Returning to the analogy of our spirit being like a router installed in our computer brain, prayer is like a computer microphone to enable communication with God. Most of us don’t have anything equivalent to a screen or headphones on this equipment because we don’t see visions of God or hear his voice. However, that we aren’t conscious of hearing him in the same way that we hear from other people doesn’t mean that we don’t hear him at all. Most of what happens in our brains occurs subconsciously, so why should our interactions with God be any different? Just as some people can learn to control their heart rate (which is normally done subconsciously), some individuals (called “prophets” in the Bible) are able to audibly hear and sometimes see things from God.

       One consequence of having a spirit is that God’s Holy Spirit can interact with us. This makes us truly different from animals, and explains why humans are alone in their wish to worship and pray to God. It also helps to explain why every one of us is so important to him.


• The Bible uses “spirit” for the nonphysical part of us that communicates with God.
• In that case, our physical brain has to interact with something instruments can’t measure.
• Biological functions such as smell occur as quantum-level interactions.
• Proposal: The brain and spirit may interact at a level of quantum uncertainty.

1^ See Wikipedia, “21 Grams Experiment” (
2^ See chap. 2, “God Does Work in the Gaps.”
3^ Peter G. H. Clarke, “Determinism, Brain Function and Free Will,” Science and Christian Belief 22 (2010) (
4^ See Jason Palmer, “‘Quantum Smell’ Idea Gains Ground,” BBC News, January 28, 2013 (

This was previously published in a similar form in Christianity magazine

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