Musings on the Soul

From the catholic tradition we know that man not only exists out of a material body and a non-material spirit, but also out of a soul and so is a trinitarian being created in the image of the Trinity [NB a complementary representation of the Trinity is man as created male ánd female (Gen 1:27) and from whose mutual love are born children cf. the Holy Spirit progressing from the Father ánd the Son, the well known filioque from the Credo]. Nevertheless, the soul is a somewhat obscure entity.
Of material bodies we know well what they are, namely the stuff that natural sciences study and which behaves according to the laws of nature. The human spirit (Greek pneuma, Latin spiritus, possibly also animus mind, Hebrew ruach) is already a bit more difficult to imagine. On one hand it differentiates us from the rest of material creation, on the other hand we share it with the supernatural beings like the angels. Our spirit makes that we are immortal, rational, creative(!) and free [NB not almighty or non-influenciable! see the blog post on Quantum Free Will]; and so we are moral beings and responsible for ourselves. Our spirit we got directly from the Trinity and does not undergo change (because that is connected to time, a central part of the laws of nature, right?). Rationality needs knowledge and ours is very limited in contrast to those of the angels; because of that I doubt whether our spirit is also the seat of our knowledge / memory (think about Alzheimer, which makes us loose a lot of it, right?).
What is then lacking if we already have a body and a spirit? Which 'place' is there for our soul (Greek psyche, Latin anima, Hebrew nephesh), especially from the viewpoint of a scientist? Consequently soul and spirit are often seen as synonymous, or else to the soul apparently contradictory meanings are ascribed. Returning to the image of the Trinity, similarly as the Holy Spirit is Love, the connection between the Father and the Son (so much so that we say that the Trinity IS Love), so our soul connects our spirit with our body, unites them (so much so that we say that we ARE a soul while we HAVE a body and a spirit) [NB see e.g. Oehler Old testament Theology I, 217: "man has spirit but he is soul ... In the soul which sprang from the spirit and exists continually through it, lies the individuality -- in the case of man his personality, his self, his ego." Nevertheless, animals have (mortal) souls without spirit]. Various expressions of speech equally indicate this truth: 'the eyes are the mirrors of the soul' (of who you really are), 'to sell his soul and sanctity' (really everything), 'that cuts me through the soul' (through my innermost being), 'the more souls the more joy' (persons), 'to give someone on his soul' (a severe beating), 'being soul companions' (connected, with comparable personality), 'may God have her soul' (herself), 'to be happy in your soul' (profoundly), 'to do something with your heart and soul' (with your whole being) [NB some expressions may only exist in Dutch;)]. By the way, the concept of the heart is quite comparable to that of the soul since both refer to the identity and also have material as well as spiritual aspects. 
Since the soul is the connection between body and spirit, makes us one, and the body is in a continual state of formation (not only in the womb), the soul must also be in a continual state of formation. Our body behaves according to the laws of physics, and our DNA (the blueprint of our body) was given to us by God through our parents; yet we still have quite some influence on our bodies: we can cut our nails, paint our hair and what we eat and how we behave strongly influence how our body develops (e.g. training or a beer belly?!). Such it must also be with our soul: she partly comes from God (either directly or indirectly via the laws of nature or our parents) and we partly form her ourselves into our fully own personality (by our free decisions coming from our spirit). Psychology ('science of the soul') studies our personality, our habits in reacting and acting, our emotions, feelings, desires (our passive emotions) and also our unconscious deeds. Many of these habits we received (namely in our infancy from our parents) or are predestined ('it's in our genes') and therefore are not our responsibility; nevertheless, while our life progresses they become more and more our responsibility in sofar as we formed them by our (conscious) choices, or we could have done and didn't. In other words, our responsibility for our souls increases with our influence on and responsability for our bodies; and so the forming of our soul must have started at conception together with that of our body (with which she forms a unity). 
Somewhat surprising is that the Church does not take a stand on when exactly the human ensoulment takes place. There are good indications that in the earliest church the view of Pythagoras dominated that the ensoulment takes place at conception. Only from the time of St Augustine discussions on this point and shifts in the point of view became more general under influence of other Greek views, especially that of Aristotle at the time of St Thomas Aquinas. Aristotle thought that first an (exclusive) vegetative soul was formed in the human embryo, then an animal soul and only later the rational/spiritual soul that is unique for man. That's why only after 40 days (or more for girls?!) an embryo would really be human, have a human soul. This conviction was closely related to the concept of the soul as 'form of the body'; 40 days then was the time after which the form of the embryo was recognisable as human (and apparently that took longer for girls...). Nowadays, by means of DNA techniques human embryos can be distinguished from animal ones already at conception.
And despite that the Church never took a stand regarding the human ensoulment, yet she has always defended the sanctity of human life from conception. One argument is prudence: there is no guarantee that at any moment after conception the embryo does NOT yet have a human soul; another argument is that even if the embryo does not yet have a (human) soul, it is still a developing human life that is wanted by God and only needs time to come to full fruition. The situation can be compared to that of a vegetative person: since he/she only lives a vegetative life, it seems that only the vegetative part of the soul is left (although the form of the body didn't change in becoming vegetative?!). Yet he/she still is a (fully) human person, much like that a handicap doesn't make a person less human.
The apparently contradictory views on the ensoulment at conception seem to reconcile via the concept of the soul that forms in parallel and unity with our body. Although our body only starts to form at our conception, it is still fully human; in the same way our developing soul is still human although then only vegetative (or not even). The collaboration between nature and our spirit in the forming of our soul (and body?!) is present from the beginning, it just starts out quite one sided...
A remarkable confirmation gives Ps 51:5: "I was formed in guilt and guilty my mother received me;" this expresses that I have been a sinner from conception; and that is only possible if I was human, not just body or vegetative soul. Also, the expression 'receive and carry a son' is used throughout the Bible and indicates that the human person (the son) starts at conception (not just his body that later becomes the son at birth or so).
In the stressing of the unity of body and soul and their parallel formation, their distinction can fade (cf. Isa 10:18, Deut 12:23, Ps 30:10) and so also the image of what the soul is. The earlier concept of the soul as the 'form of the body' is not very useful if by that we only mean an external form. However, in the sense of 'abstract organisation' (complexity) refering to the body  functioning as one whole, the concept IS very meaningful. The clearest complexity is found in our neurological patterns (our brain) and those certainly are related to the seat of our passions and subconscious (instincts or habits), the stuff that psychology studies. But it is too simple to equal our soul to the complexity of our brain (like software on a computer) since already every cel of our body contains a very high level of complexity, not just the brain. Moreover our brain is intimately connected with the rest of the body via our nerve system and so one cannot really say where the brain ends and the 'rest' begins. A good example is the phantom pain of amputated limbs that are still there for us (in our soul?!). By means of quantum effects in our brain we can express our free will via our body [NB see again the blog post on Quantum Free Will]. Then it seems obvious if (non-local) quantum-correlations play a role in this as well, possibly even connect our whole body via the nervous system? And so it follows that a meaningful soul can only refer to the functional whole of the body.
Further, the soul as 'life-principle' (another often used concept) could well be an inseparable part of our human soul (the 'lowest'), that which is comparable to the souls of other living beings. The concept 'vegetative soul' was used for this before; in computer language it would refer to the operating system (but beware the earlier warning on the comparison with computer software). The expression 'to keep one's body and soul together' after all means to stay alive.
With death this type of soul obviously ends. The human soul yet is a spiritual one [NB immortal cf. Rev 6:9 & 20:4], "a life-giving, separable, surviving entity, the medium of one's own personal existence" [NB according to the 19th century anthropologist Edward Burnett Tyler from Oxford]; to call her a spiritual body (or possibly a bodily spirit?) could well be the most concise way to express both her connection as difference with our other parts.
To conclude, it is educational to look at the distinction between soul and spirit in the context of redemption in the gospel: Jesus gave up his "psyche for the sheep" (John 10:15) and He gave his "psyche as ransom" (Mat 20:28); that is after all man's own property, and that what is redeemed [NB cf. Heb 10:39, Jam 1:21, Ps 48:9, Acts 2:27, namely of the power of the Sheol]. But "Jesus gave up his pneuma to the Father" (John 19:30) because this was a gift of God, "His breath" (cf. Gen 35:18, Jer 15:2).

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