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A biological science that acknowledges soul. 
Let us now consider how the idea of ‘soul’ might be fitted in the narrative proposed by modern evolutionary biology. This science teaches us that sensory perception was a product of evolution. Moreover, the sense of sight evolved relatively suddenly (at the beginning of the Cambrian Explosion, which it effectively caused), whereas the other senses (sound, smell, taste, touch) evolved more gradually. We have much to learn from these findings[1].
In early life forms, which were unicellular (i.e. consisted of a single cell), there might have been simple ‘perception’ of light, in the sense of an ability to ‘detect’ the presence or absence of light, or different intensities of light, or the direction of light; but there was no true ‘sight’ until the eye evolved as a distinct, specialized organ. Similarly for mechanical vibrations, temperature variations, chemicals, and so forth. I have put the terms ‘perception’ and ‘detection’ in inverted commas, because it is not sure that what occurred at that stage could be called cognition – it could well have simply consisted of mechanical responses to physical stimuli, which could only be likened to cognition metaphorically.
When life forms became multicellular, true perception could emerge, with some cells specializing as a nervous system and others as sense organs. But such more complex systems could also have involved mechanical responses to stimuli, similar to what a well-programmed complex robot might perform, without actual cognition taking place. It is only as of the moment that certain select organisms acquired a ‘self’, over and above the physical cells making up their bodies, that they acquired minds (i.e. mental experiences by the self, in addition to physical ones) and cognitive powers (and inevitably volitional and valuative powers too).
It may alternatively be that selfhood (i.e. soul), and minimal degrees of the powers associated with it, were present from the start, even in unicellular organisms. When unicellular organisms joined together to form more complex multicellular ones, in which individual cells became specialized, they collectively acquired a single self, with probably increased collective powers of cognition, volition, and valuation. If that was the case, the evolution of ever more complex multicellular organisms would have merely broadened and sharpened the cognitive and volitional and valuative powers of the self that were inherent in life as such. The eye made possible more precise vision, the ear more precise hearing, smell and taste more precise detection of chemical composition, the sense-organs of touch finer touch sensations, our feet better mobility, our hands better prehension, and the central nervous system provided more varied and efficient integrative potentials.
The self might perhaps be viewed as the unifying force of the body, that which literally integrates its material components (whether the molecules composing a cell, or the cells constituting a larger entity) and gives them a single and common identity; but it certainly cannot be viewed as itself a physical element of the body, or as a mental substance, or as an abstraction or essence, or as an idea or concept. It must be viewed as something concrete (i.e. not abstract) yet distinct from matter or mind, because only thus could it have the exceptional powers attributed to it, namely consciousness, free will and value-judgment, and those relative to both matter and mind.
It is certainly not some physical stuff lodged somewhere in the body (e.g. the brain) that has these powers, nor any mental stuff; it must be something else entirely, capable of interaction with the phenomena of matter and mind, yet quite distinct from them. As I have argued elsewhere, we might metaphorically refer to the spiritual realm as a dimension perpendicular to the two dimensions of matter and mind. But this cannot be taken literally, because the very notion of dimensions is a spatial one and we have no basis for claiming that soul has spatial extension or location. All we can say for sure is that a soul is somehow associated with the body and mind of the living organism concerned for the duration of its life.
Note well that I am not advocating all living things as having a single kind of soul, with the same powers of cognition, volition, and valuation. What I have said is that each species of organism that has a soul, has one with a naturally determined range of cognitive, volitional and valuative, powers specific to it. And indeed, individuals within a given species are naturally endowed with different ranges of cognitive, volitional, and valuative, powers; and they may even lose some of these powers through some physical mishap in the course of their lives if at all born with them. Moreover, to say that an organism has a soul is not necessarily to claim that its soul can or does exist without its body, as a sort of ghost, before it is born or after its death. This issue is left open for lack of evidence one way or the other. All we need claim is that during their lifetime (certain or all) organisms have a single ongoing soul.
Having said that souls in different species (among those which have soul, if not all of them do), and in different individuals within them, have different scopes and degrees of cognitive, volitional, and valuative, powers, it occurs to me that there might be something, after all, in the Aristotelian idea, which was widely believed until the advent of modern biology, that there are three kinds of soul – the vegetative, the animal, and the human[2]. This doctrine claims a hierarchy of increasing powers (very roughly stated): the vegetative being limited to the powers of growth and reproduction, the animal additionally involving the powers of sense-perception and mobility, and the human adding the power of rationality. I do not here advocate it, but I can see that some such doctrine could reasonably be revived: considering that as organisms become more complex, they acquire souls with increasing powers, it is conceivable that three (or more or less) classes of soul might be defined (assuming such clear lines can be drawn and that all organisms can be fitted in these three classes).
In any case, it is certainly possible to formulate a narrative of life’s evolution which includes the emergence (either from the start of life on earth and generally – or alternatively, eventually and particularly) of the soul and its essential powers (including mental experience). Contrary to what many people think and claim, the theory of evolution is not, logically, inherently materialist. It can and should be fully adapted to include mind and soul. The important point to note is that an account of this sort (whichever it is) must be true, since we (people) are here to prove the fact with our phenomenological experience of matter, mind, and self, implying powers of cognition, volition, and valuation. Introspective experiences cannot just be dismissed and ignored, as some people try to do; it is not scientific to do that. All evident facts must be acknowledged and seriously taken into consideration in scientific discourse; we cannot pick and choose, simplifying things as convenient. All complexities must be acknowledged and taken into consideration.
A pertinent question in this context is: as of when in its development does an individual organism’s soul come into being? As regards humans, this question is politically charged nowadays, since the answer is relevant to the controversial issue of abortion. The logical answer would seem to me, in view of the above reflections, to be that a human being may be said to have a soul, before birth, at least as of when it evidently has some degree of consciousness and volition. This means: when a fetus has evidently developed sensory and motor faculties, since it responds to perceivable sensory stimuli with voluntary motor responses. After exactly how many days, weeks, or months, that behavior pattern first manifestly occurs is up to medical science to determine.[3]
It might be argued that such sensory-motor behavior is only indicative of an ‘animal’ soul, not a ‘human’ soul, since presumably a fetus does not yet show signs of rationality (conceptualization, classification, verbalization, logic, memory, imagination, anticipation, and the like) any more than a recently born baby does (correct me if I am wrong). But surely, the brain and nervous system of a human fetus (and all the more so that of a newly born baby) are at some point all set for rational functioning, so that we can as of that point at least say that the fetus (and a fortiori the subsequent baby) has rational potential. Perhaps this point, if it can be identified, should be viewed as the true threshold for specifically human identity.
 

[1]              Read for instance the works of Andrew Parker, notably In the Blink of an Eye (Sydney, Australia, The Free Press, 2003).
[2]              Aristotle, I gather, did not view ‘souls’ as distinct substances inhabiting physical bodies (as Plato did), but rather as the organizing principles of living organisms, their physical structures and processes. Both these views are very different, note, from my notion of soul as self. Plato’s soul is a concrete spiritual stuff; Aristotle’s is an essence, an abstraction; whereas mine is something else again, undefinable even by analogy because it is so sui generis.
[3]              As of then, therefore, deliberately killing the fetus (voluntary abortion) could well be considered as murder of a defenseless creature, albeit one residing within the body of another (the mother) and still in need of the hospitality of that host to fully develop. Women with unwanted pregnancies argue that they have the right to freely choose to rid their sovereign body of the unwelcome guest. This is obviously a complex ethical issue, pitting the interests of two creatures against each other. It cannot be adequately dealt with in a mere footnote; but my opinion is, briefly put, as follows. How did the ‘guest’ get into the ‘host’? If the woman is pregnant through voluntary sexual intercourse, she is morally responsible for the consequences; if she foolishly allows the fetus time enough to develop a soul, she cannot thereafter kill it at will on the ground that it is something found within her body against her will. However, if she was raped, she is of course free to rid herself of the foreign body forcibly injected into hers by some rapist, even if she discovers her pregnancy after the fetus has developed a soul. Abortion would also be quite ethical, if the mother is seriously physically endangered by the pregnancy or if the fetus is tragically very abnormal – though in such cases doctors and judges would have to be consulted to estimate whether interruption of pregnancy is reasonably necessary or at least recommended.
 

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