Of course we fully renounce any unmanageable proliferation of the wholeness view such as "wholeness of human fates or destinies", "wholeness of terrestrial landscapes", etc. After having well and unequivocally established wholeness (see further down), we can and must also renounce the concept of super-ordinate wholeness (as well as of sub-ordinate wholeness, or of partial wholeness (being wholly absurd)). In both directions there either are new wholenesses or none at all [We may think of the supposed fact that all true beings (living or non-living) are Substances in the metaphysical sense, and these Substances are true wholes.].
[We [JB] assume every molecule (living or non-living) to be a single Substance in the metaphysical sense, that is, in the sense of it to be one single subsistent true being. This "to be one single being" is accomplished by the supposed fact that in the molecule the constituent atoms, as constituent particles, exist only virtually in the molecule. All conserved properties of these atoms are now properties of the one molecule, i.e. of the one Substance. This, then, is the supposed holism of the molecule. But these properties (qualities) are spatially adjacent or separated from one another in the molecule. The molecule is a spatial mozaic of its qualities. The location in the molecule of these conserved atomic qualities corresponds with the location of the virtual atoms in the molecule. How, then, in the molecule, true holism is attained apart from the fact that it is taken to be one single Substance? If the molecule is one single Substance, it must have one single substantial form (in-forming prime matter). This one form represents in some way the overall totality of the molecule's qualities (i.e. of the molecule's properties of content). And this is precisely the holism of the molecule : All the qualities of the molecule, apparently, together result, not by simple addition or summation (because that doesn't result in true unity) in one single intelligible content, the substantial form, of the molecule, but in some other way. The unity of the substantial form, accomplished by the togetherness of the mentioned qualities, may be compared to a piece of music consisting of a harmony of discrete musical notes. It is clear that the assumed true holistic unity of the substantial form (and with it that of the Substance) cannot be demonstrated or deduced by natural science. It is assumed by natural philosophy by taking Substance as a true being [i.e. the primary instance of Being] and the substantial form as the primary instance of Substance (secondary instances of it are its prime matter, and the matter-form composite). So it is from the philosophical doctrine of Being that holism is defined and as such found in true Substances. The metaphysical basis of the holism of a given thing is its being one single being. In molecules and organisms the physical basis of their holism is the chemical bonding of their atomic constituents.
We may express these things also in a more or less different way :
A true aggregate of constituents is not an intrinsic but an extrinsic whole (i.e. a whole, generated by extrinsic causes), and thus not in fact a whole at all. It is not a Substance, because its constituents are (as to their beingness) prior to the aggregate. Because the constituents of the aggregate are still subsistent beings (ultimately Substances) the aggregate itself cannot be such a being. It IS its constituents. And if there is, in an aggregate, any connection at all between its constituents, it is not stoichiometric, i.e. there is in an aggregate no constant and repeatable proportion between the several components.
On the contrary, a molecule is an intrinsic being, and therefore it is, metaphysically taken, a true Substance. This is because its atomic constituents are no longer in themselves subsistent beings, but are such beings only through their common substrate (i.e. through the molecule). They are no longer subsistent parts of an aggregate but inhere a common substrate as their carrier. They have become properties (or, more generally, determinations) of the molecule. And so, because the constituents have given up their status as subsistent beings, the "aggregate" of them can now be a subsistent being itself, in fact it now is the only subsistent being. It is (as to its beingness) prior to its constituents, it is a true Substance, a primary instance of Being.
In the foregoing Series of documents, especially in its parts XVe and XVf, we established (following Hoenen) that natural science methodically cannot distinguish between the molecule-consisting-of-actual-atoms and the molecule-consisting-of-virtual-atoms. It cannot decide upon what's really the case as to molecules. It contains, however, one indication that indeed the molecule is not a mere aggregate (i.e. that it must be taken holistically instead of reductionistically) : A molecule consists of constituents, atoms, that are c h e m i c a l l y bonded to one another. This means that the proportions of constituents are constant, i.e. that their connection is stoichiometric. But more importantly, all chemical bonds do necessarily involve quantum conditions rendering the chemical bond not to be a mere mechanical connection. So the molecule is not a mechanical aggregate of atoms. Whether this necessarily implies that then the atoms of the molecule are only virtually present in it, that these atoms are (as to their beingness) not prior to the aggregate anymore, that the aggregate has become a true Substance in the metaphysical sense, natural science cannot decide upon, because that isn't a scientific question but one of natural philosophy. And it is the holistic properties evident in crystals (which are, in fact, molecules), and almost certainly present in atoms and in all molecules (such as proteins), and evident in organisms, that convinces me [JB], as natural philospher, that not only free atoms (or 'fundamental particles' for that matter) are true metaphysical Substances (but cease to be so when taken up into a molecule), but that being a Substance does occur also in entities above the atomic level (or, generally, above the micro-physical level), that is, also in all molecules and organisms. The fact that at least already things like molecules are true beings of their own, that they are not, qua beingness, reducible to their atomic constituents, demonstrates that material reality is not exclusively constituted reductionistically. At different levels of size and complexity there do exist true wholes. And this further means that natural science cannot, even in principle, exhaustively explain material reality.]