For Aristotle a substance is an individual thing. For Descartes substance is a distinct thing, known conceptually. His new standard for ontology is how doubtable it is as something existing independently. And so substances are designated by innate ideas. What always accompanies my perception of material objects is what reflects their true and distinct nature, which is spatial extension. Whatever I can doubt about the reality of my thoughts, there is always thinking and its modes willing, feeling, affirming, denying. Only those objects of either these two substances, matter and mind, exist.
This was intended to a be a textbook to replace the Aristotelean/Scholastic curriculum in schools. The very way it was written shows. It is written in a fairly subjective way almost without reference to anybody else except the thoughts and musings of the author. Everything in the book is quite parsimonious, following from what is said in the first half of Book I. He even says in Book IV that "there is no phenomenon of nature whose explanation has been omitted in this treatise." A bold claim. I think he is right, if you accept his foundational presuppositions. Overall it reads like a synthesis of Scholastic/Medieval philosophy and materialism. He acknowledges that he "made no use of any principle which was not received and approved by Aristotle." And to today's readers I think he is right. The language he used seems archaic today. Offering a proof of God and talking about substance for instance. He briefly mentions Democritus, mostly to deny more influence from him than anybody else. He was probably talking like this to avoid conflict with Catholicism and avoid charges of atheism because he is in retrospect key to the materialist, mechanistic conception of the universe. Nonetheless I see a synthesis between the old and emerging "corpuscular" or atomistic views of the universe which reigned until around the 20th century.
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