You are approaching a metaphysical problem from an empirical perspective. It is true all learning starts with the senses, and all that you stated lies In the material or physical world although empirical scientists use measurement (math)and scientific principles in their experiments which deals with the second degree of abstraction which you do not seem to understand.
You seem to be telling Aristotle, Aquinas, Locke, etc. that they can’t do metaphysics. Aristotle, for instance, held that the mind starts as tabula rasa, a blank slate. Therefore abstractions are not innate, they are abstracted from learning, and so must also start with the senses as there was nothing else on the blank slate.
The five senses are receptors that transmit electrical impulses to the brain via the nervous system. If you observe, change always takes place in a physical medium, eg sound waves, light waves, pressure, and chemical reaction, what the brain does it records these sense impressions which are giving the mind sense data. It is the mind that interprets the data, it gives the data meaning. eg words made up of vowels and consonants which are sounds given meanings. Because the soul is united to the body, the intellect, a power of the soul depends “extrinsically” on the physical for sense data. It is the power of “abstraction” that makes it possible to gain knowledge which is of an non-material nature. You missed this in your reference to the teachings of St.Thomas
As I said, thoughts don’t have mass, they are instead about structure and form, therefore the soul is the form of the body. That is exactly, precisely, what the CCC says.
St.Thomas recognizes the spirituality of the soul by it’s powers, intelligence and volition. Every power has a source, and he reasons that that power is the soul, the form and immanent, animating force of life in the human body. That force, or soul makes man a rational animal, a homo sapien (a knowing man) He also speaks of the 'phantom", an image that forms in the brain from which by the intellectual power of the soul abstracts the idea. This image or phantom Is made up of sense data it seems much like the electrical transmissions and frequencies that form a TV image. By touching the brain with electrodes music was heard. As Thomas might say the brain is like a " tableau raza" (spelling?) meaning “a blank page” eg a blank CD
If you agree with the mind starting as tabula rasa then I don’t understand why you said metaphysics is prohibited from empirical reasoning, since on an empty slate the starting point for all thought cannot be other that sense data.
Whether the mind of a new born is totally tabula rasa is of course controversial. Talk of the soul as the animating force of life also needs dealing with carefully, as we are not animists and generally we believe in metabolism rather than élan vital.
Also there is a fallacy, known as the homunculus fallacy, which supposes a viewer inside our mind who views an internal TV picture. It’s a fallacy because it doesn’t explain how the homunculus sees the internal TV, except by another homunculus inside it’s mind leading to an infinite regress.
Innocente:
The scientific world is under the spell of that nineteenth century mode of thinking originated by Auguste Comte a French philosopher, known as “Positivism” which eliminates all metaphysics from philosophy and restricts scientific knowledge to facts and relations between facts. They say that the scientific method is one of exact mathematical measurement, but things like ontology are of no consequence. Positivism confines itself to the data of experience and it excludes apriori or metaphysical speculations and emphasizes the achievements of science. Positivism is closely connected to empiricism, pragmatism. Auguste Comte deified man as the “Be all, and End all” and denies a personal God. It smacks of humanism,a modern nontheistic, rationalist movement that hold man is capable of self-fulfillment, ethical conduct without recourse to supernaturalism.
Positivism was disproved long ago. If one Catholic in every thousand is a scientist, there are a million Catholic scientists in the world. So forget those on this forum who say we must choose between Christianity and science. As I said, I imagine a Catholic neuroscientist would find her science completely compatible with the bible and Aquinas.