Scientists, inasmuch as they are focused on the observable/measurable, are concerned with actions, with dispositions to action, and with characteristics that distinguish things with one kind of disposition from those with other characteristics. This range of concerns is narrower than a philosopher might have: it tends to exclude concern with that in virtue of which a thing having many characteristic parts is one being rather than a composite of those parts. This narrow focus likewise bears upon our knowledge of a thing's substantial form, i.e. that in virtue of which it is one whole being rather than a composite of many beings. In the case of living things it bears upon the soul, for it is the form that gives unity to the parts, duration through time and a kind of impetus to life acts. The substantial form can be defined as the first act of a body, in virtue of which it acts as it does, while the soul gets a more specific definition the first act of a body disposed toward life, in virtue of which it engages in life acts. If there is a soul/substantial form, then science as practiced today is systematically blind to both of them. For scientists distinguish different kinds of things in virtue of the differences in their parts, and this focus leaves aside the question of why either of these types of components is one whole being or just part of a whole; it leaves aside the question of whether each of these components is likewise a whole being or a composite of even smaller parts. Cells consist of organelles, which consist of molecules, which consist of atoms, which consist of particles, etc. That's all a scientist needs to think of. At each level, the very method used to distinguish one type of individual from others defines eachtype in terms of its parts. It never considers whether one of these wholes is more genuinely a whole than the others.
That is not to say that this method obviates the need to consider whether such unifying forms/activities exist in nature. For this methodological setting aside of such questions is a kind of naivete that would run aground if we were to make it into an ontological claim. For if there is no such thing as one whole atom but rather only the collection of its parts, then we can say the same thing of each of the parts, and of the parts of the parts, etc., ad infinitum. What we would be left with an infinite number of infinitely small parts... something like Leibnitzian monads... If such a consequence is absurd, then we need to reject the claim that every whole is nothing other than the sum of its parts.
One bit of support for this rejection might come from the notion of emergent properties. They are more than the sum of the properties of their parts. To affirm the existence of emergent properties is to open oneself to the possibilities that there is something like a substantial form/ soul. One need only add the claim that such properties are the properties are the properties of beings. Properties emerge because levels of being emerge. An organism is such a being and the soulis nothing other than the most basic activity of the organic body: you might call it the organism's very act of being.
More to consider: whether it is systems rather than beings that exist and have emergent properties... can't do that now, as I gotta cook supper.
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