In order to avoid all types of Pantheism, New Age Monism and Neo-Gnosticism, it is necessary to emphasize the purely and strictly material-physical nature of the inanimate form of the Body of the Universe and the material physical nature of the animate, vegetative plant and sensitive animal "souls" or principles, especially as contrasting with the rational-spiritual-immortal human soul of man.
Perhaps the best way to approach this subject is in connection with the transubstantiation of the bread and wine into the Body and Blood of Our Lord Jesus Christ in the Holy Sacrifice of the Mass, the Eucharistic Sacrifice. The substance of any being is that which causes it to exist. Another word for substance is form. In fact, it is the substantial form that is changed in the Consecration of the Mass. Bread and wine - in their very substance are changed into the Body and Blood of Christ. But substances have accidents, or properties, perceived by our five senses. These properties of color, taste, texture (feeling), smell and sound are not changed in the Consecration, and this is what makes transubstantiation a miracle.....something that temporarily suspends the Created Order of Nature. Therefore, even though the substance of the bread and wine have been changed into the Body and Blood of Jesus Christ, the glorified but also the immolated God-Man and even though our senses still perceive only the accidental properties of white bread and red or white wine, faith tells us that this bread and wine are really and truly, thus substantially, the whole Being of the Divine Person, Our Lord Jesus Christ!
We cannot go beyond this kind of explanation, and most of us do not need to go even this far. On the other hand, however, today we live in an age of domination by technology and the wonders performed by the sciences of chemistry and physics. Any high school teacher of chemistry could give us the chemical formula for the bread and the wine. It is precisely these chemical elements in their form as bread and wine, that are changed - not in their formulas - because these are the accidents, but in their invisible form of substance. The great difference between this substantial change of transubstantiation in the Consecration of the Mass, is that this is the one and only substantial change that issues in life instead of death. This difference cannot be emphasized too much. It involves the great error - approaching heresy - of the Neo-Scholastic, every single one of them, even the greatest one, Rev. Reginald Garigou-Lagrange, O.P.
The mistake they all made was to assert that the atomic elements, such as hydrogen and oxygen, were subsstances; whereas actually they are accidents of the greater substance, which is the Body of the Universe, created ex nihilo and in toto on Day One of the First Week of the World. This they did not see! This writer did a thorough study of this subject in response to a challenge by Dr. Dennis McInerny some years ago. My conclusions were rejected by him but he has never, to my knowledge, put forth any kind of objections to my work. He has only rejected it as of no account. It is therefore up to the church, in the person of her theologians yet to be, to settle this problem which is of paramount importance for theology and all the lower sciences.
All changes in atomic structure, - changes going on constantly in all areas of inanimate and animate being, are changes in the accidental properties of the greatest substance, which is the Body of the Universe - a body with no "soul", but with material-formal causes or principles, which determine both the possibilities and the limitations of all changes in the universe. One can hardly overestimate the importance of the correct identification of this first of all substantial forms and also, the first of all secondary causes created on Day One. Only when an individual plant, or animal, or human being dies, does a substantial change take place. Even when individual plants, animals and humans reproduce their kind in the Order of Generation, there is no substantial nor accidental change, but a pro-creation or re-production by means of the secondary causes given their powers of agency with their substantial forms in the Order of Creation.
All of this greatly highlights and enhances our appreciation in contemplation of the one unique and only substantial change that produces life instead of death - the reproduction and representation of the Sacrificial death of Jesus Christ on the cross and its repitition in the Eucharistic Sacrifice of the Mass. Let the theologians and mystics elaborate upon this unique salvific event!!