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Descartes deduced his scientific theories about the natural world from a metaphysical foundation, in turn deduced by the application of his rationalist methodology. He wrote that "the whole of philosophy is like a tree. The roots are metaphysics, the trunk is physics, and the branches emerging from the trunk are all the other sciences, which may be reduced to three principle ones, namely medicine, mechanics, and morals".[[CiteRef::Clarke (1992)|p. 271]] One ought to construct a metaphysics first, based on criteria independent of observation, and subsequently consider physical theories consistent with the metaphysical foundation. His natural philosophy was in stark contrast to the accepted Aristotelianism, which emphasizes experience and intuition as routes to knowledge, rather than reason. In Aristotelian natural philosophy all objects were a compound of form and matter, a concept called hylomorphism. Form gives material bodies their distinctive properties, and makes them different from one another. It explains why fire rises and stones fall. Matter is what all material bodies share in common. All things have teleological goals or purposes [[CiteRef::Shields (2016)]].
In Descartes' mechanical corpuscular natural philosophy, by contrast, there are just two kinds of substance that are entirely different from each other in kind: mental substance and physical substance. The fundamental property of '''mental substance''' was thought, and Descartes equated it with the rational soul of God and humans. The fundamental feature of '''physical substance''' was extension in space. He rejected Aristotle's distinction between form and matter, including Aristotle's four elements. [[CiteRef::Ariew (1992)]] Cartesian mechanics rejects the void posited by atomists; instead matter fills the universe as a plenum. If all matter is extended, Descartes reasoned that there can be no space without extended matter. Also unlike atomism, matter is infinitely divisible, though visible things are composed of tiny corpuscles that interact with one another by physical contact. The corpuscular composition of a material body, rather than form, determines its properties. Since corpuscles are too small to be directly observed, their size and shape must be hypothesized, though observation can allow us to infer the plausibility of our guesswork. Our senses, Descartes maintained, do not inform us of the mechanical world as it is, but provide us with sensations which are mere signs of their objective causes. Only extended matter and motion exist apart from our minds. Secondary qualities, such as colors, are created in our minds in response to mechanical stimuli. [[CiteRef::Clarke (1992)]] Descartes completed a manuscript that was to be a comprehensive expression of his mechanical natural philosophy, called ''The World''. He withdrew his plans to publish it upon learning of the condemnation of Galileo in Rome in 1633. The work never appeared during his lifetime, but two major fragments, the ''Treatise on Light'', and the ''Treatise on Man'' were published posthumously. The first dealt with physics, and the second put forward a theory of physiology, nervous system function, and the mind/brain relationship. [[CiteRef::Garber (1992)]][[CiteRef::Descartes (1664/2003)]]
In Descartes cosmology, the universe is essentially mechanical in character. Copernican heliocentrism is accepted, and planetary motion is explained in terms of a swirling '''vortex''' of material particles. Earth, as a moving planet, is the center of its own smaller vortex. The particles of the vortex push larger bodies towards its center and this explains gravity without supposing, as did Aristotle, that the sphere of earth was at rest in its natural place; the center of the universe. It also made it reasonable to suppose that other planets had their own attractive vorticies, and were thus other worlds. [[CiteRef::Garber (1992)]]
Another sort of objection raised in commentaries on Descartes had to do with the fact that corpuscular explanation involved hypothetical unobservable entities, and the supposition that this invisibly small world could be understood by analogy with larger objects. Descartes countered that "there is nothing more in keeping with reason that we judge about those things that we do not perceive, because of their small size, by comparison and contrast with those that we see" [[CiteRef::Clarke (1992)|p. 267]] He felt that a plausible model, though potentially incorrect due to the unobservability of its fundamental parts, was better than none at all. The role of unobservable entities and metaphysics in the physical sciences was to remain a matter of prolonged debate. The positing of unobservably small entities in explanations of observable phenomena has become an accepted and central practice of modern physics and also modern biology which places a strong emphasis on the molecular basis of biological phenomena.
One particularly notable objection came from Princess Elizabeth of Bohemia (1618-1680), who questioned Descartes’ theory of substance in a letter dated the tenth of May, 1643. In it, she asks “Given that the soul of a human being is only a thinking substance, how can it affect the bodily spirits, in order to bring about voluntary actions?”[[CiteRef::Descartes (2009)]] Descartes would never gives a satisfactory answer to this central question over the course of the correspondence. In 1747, in his ''L'Homme machine''(''Machine Man'') Julien Offray de La Mettrie (1709-1751) raised another simple, but devastating objection to Descartes' supposition that human reason must be due to an immaterial mental substance. He noted that reason can become impaired by material causes such as drunkenness and fever. [[CiteRef::De La Mettrie (1747/1996)]]. In the nineteenth century, Princess Elizabeth's objection became far more poignant with the formulation of the law of the conservation of energy which implied causal closure of the physical world to influence by a mental substance. In the early twentieth century, the mathematician Alan Turing (1912-1954) showed that it was possible to construct a general purpose machine capable of performing any possible mathematical computation, thereby demonstrating that a general purpose machine was possible and refuting Descartes' core argument against a mechanical understanding of human reason. By the end of the twentieth century, the relevant scientific communities of neuroscience and cognitive science had rejected the idea of a mental substance and sought a mechanistic physical explanation for the mind [[CiteRef::Bechtel (2008)]], though there was still no agreement as to whether consciousness could be explained in this fashion. [[CiteRef::Chalmers (1996)]]
Descartes' physical natural philosophy did not fare nearly so well. Within fifty years, Issac Newton (1642-1726) formulated a more mathematically precise and explanatorily powerful physical theory, which became the accepted theory of the physical world. It rejected a major tenet of Descartes' corpuscularism by positing a gravitational force that acted at a distance. Newton's laws of motion, however, bore important similarities to those formulated earlier by Descartes. [[CiteRef::Clarke (1992)]]
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