In order to avoid all forms of Pantheism and New Age Gnosticism, it is necessary to understand that the Substance, better termed the Substantial Form of the elements, of plants and of animals, is each one entirely material, physical and in no way spiritual. Perhaps this is best understood today by Catholics in connection with the transubstantiation of the bread and wine into the Body-Blood-Soul and Divinity of Jesus Christ in the Holy Sacrifice of the Mass. The substance of the bread and wine is material and specifically elemental, or of the material elements. To be more specific, I would need the chemical formula for the bread and wine. Any high school teacher of chemistry can provide these formulas. And it is these chemical elements that change their invisible, but material substantial form, from bread and wine into the Body and Blood of the God-Man.
The substance of God's Body & Blood is entirely spiritual. This is the one exception in the non-human domain, because the soul of man is spiritual. The eucharistic transubstantiation alone is from inanimate-physical-elemental to divinely spiritual and immaterial substance. The elements in transubstantiation retain their accidental-physical properties of visibility, taste, etc. but have transferred their elemental obedience from the inanimate body of the universe to the sacred humanity of the God-Man in His Glorified, but also still-and-ever immolated state of the slain Lamb of the Apocalypse.
The real miracle is that these elements - (hydrogen, oxygen, carbon, etc.) in their very specific arrangement/form/structure, do not burst forth out of their physical-material forms and manifest the glorified Humanity of the God-Man. Their change of obedience from the physical-elemental to the Divine Form remains hidden from the human senses. Even in those "miraculous" occurrences wherein the Body & Blood are seen, their form is not glorified as it should be in reality. God is simply allowing the senses to receive some sort of satisfaction when confronted with the real miracle of tran-substance or change of substantial form. To understand this in the most elementary way, one must understand that the substance or substantial form is that cause which guarantees that the being of a thing is one-good-true to its created nature. Everything presupposes Creation.
God created the form (formula) for the bread and for the wine on Day Three of Creation Week. These two formulas, spiritually merging into One Form for the Consecration/Transubstantiation, remain with their physical manifestations perceived by our senses, BUT, the substance underlying these physical properties and giving them their Form or Being, has changed from that of the bread and wine to that of the Glorified-Immolated Humanity of Jesus Christ. We cannot go beyond that and most need not go even that far!
"Jesus, My Lord, My God, My All - How Can I Love Thee As I Ought, - And How Revere This Wondrous Gift, - So Far Surpassing Hope or Thought? Sweet Sacrament - We Thee Adore! Oh Make Us Love Thee More and More - Oh Make us Love Thee More and More!