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Descartes concluded that if his goal was to attain certain knowledge about the world,the accepted methodology for doing so must be rejected, and a new one would be required. Methodology held a central place in his epistemology; in fact, one of Descartes’ criticisms of Galileo was that he failed to produce a fully developed methodology to justify his discoveries, and had simply explained particular physical phenomena.[[CiteRef::Ariew (1986)]] Rather than experience and intuition, Descartes new methodology, '''methodological skepticism'''was based on reason and on embracing his skeptical doubtsthe capacity to doubt. The harder a proposition was to doubt, the greater its certainty. This was an epistemological innovation. His strategy was first, to reject all knowledge that he cannot be certain of, and accept only those propositions of which he can accept as is certain, and proceed deductively . He would deduce other knowledge from those such axioms according to using reason. By this method Descartes hoped to produce a kind of systematized knowledge that, he believed, could be universally acceptableaccepted. In his 'Meditations on First Philosophy', [[CiteRef::Descartes (2004)]] Descartes identified the sole indubitable proposition upon which he would build his entire philosophical system : he was certain of his own existence as his famous a thinking being, or in latin, '''‘Cogito, Ergo Sum’''' (also styled ‘Dubito, Ergo Cogito, Ergo Sum’ or simply as ‘the Cogito’); “I think, therefore I am.” He concluded that From the one thing he could be certain foundation of was his own existence as a thinking being. From this foundation , Descartes deduced that he was that he must be a created thingbeing, his requiring that this requires a creator, that creator being God, the benevolent nature of God, and the consequent reliability of his God-given senses and reason, that were . It was therefore useful possible to use his senses and reason to gain knowledge of an external world. This reasoning formed the foundation of his systematized scientific worldview.[[CiteRef::Newman (2014)]]

Although Descartes maintained some methodological aspects of the Scholastic-Aristotelian mosaic methodology – namely the an axiomatic-deductive, epistemic-foundationalist structure of investigation – one . But the critical difference in his methodology was the shift in the method of theory choice. It jettisoned the Aristotelian expectation that a theory must be experientially based and intuitively obvious for it to be acceptable, and although his system, as it ended up, allowed for knowledge that was both experiential and intuited,[[CiteRef::Newman (2014)]] the ultimate justification for knowledge claims was human reasonand the absence of doubt. Descartes was both a '''rationalist''' and an ''a priorist'', in that his epistemology and metaphysics allows for the existence of synthetic a priori propositions.

Descartes deduced his scientific theories about the natural world from were grounded in 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 (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 particlesaround the central sun. 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)]]

Descartes also challenged Aristotelian physiology. Aristotle's theory of physiology posited three souls or vital principles, ; the nutritive soul, responsible for nutrition and reproduction, and comprising comprised the entirety of the soul in plants, the . The sensitive soul, responsible for perception, locomotion, imagination, and desire, was added to the sensitive soul in animals. A third component, the intellectual soul , was found uniquely in human beings. [[CiteRef::Shields (2016b)]][[CiteRef::Van der Eijk (2000)]] Descartes rejected the nutritive and sensitive souls, supposing their functions were instead performed by corpuscular mechanisms, the nature of which he outlined in his ''Treatise on Man''. [[CiteRef::Descartes (2007)]] Descartes' mental substance served roughly the same role as Aristotles' intellectual soul. Animals, according to Descartes, are complex automata composed of physical substance only and cannot be said to think or feel in the way that human beings or God can; these properties being made possible by mental substance. [[CiteRef::Des Chene (2001)]][[CiteRef::Clarke (1992)]][[CiteRef::Descartes (2007)]] Descartes posited a mental substance for theological, metaphysical, and scientific reasons. He supposed that thought could not be mechanized, since all the machines known to him were specialized to perform one particular function, but human reason was a general purpose instrument.[[CiteRef::Hatfield (1992)]][[CiteRef::Cottingham (1992)]]

  Part Descartes mechanical natural philosophy fostered a radical change in how natural philosophers gained new knowledge. The Aristotelian-medieval methodology accorded a very limited role for experiments in scientific investigation. This is because a strict distinction is made between natural and artificial things. Every natural thing behaved in accordance with its nature; acorns grow on oak trees, because that is what their nature dictates. Artificial things have an external source of change. The cogs and springs of a clock are constructed so that they no longer behave according to their respective natures (which is simply to fall towards their natural place at the center of the universe, rather than function as parts of a machine that tells time for humans). A thing cannot reveal its true nature under the artificial conditions of experimentation, because the experimental set up necessarily puts things under artificial conditions. To gain knowledge, things must be observed in their natural undisturbed state. Descartes' mechanical natural philosophy rejected the natural/artificial distinction along with its rejection of forms and teleology. Matter always obeyed the same set of mechanical laws regardless of its situation. Thus,under the mechanical natural philosophy experimentation was often a good source of knowledge about experimental method goes here nature, and its adherents often became practitioners. [[CiteRef::Barseghyan (2015)|p. 181 Barseghyan-182]]

The overthrow of the Aristotelian tradition, even in places where Cartesianism was rejected and the community maintained Aristotelianism, forced the academic community in Europe to reconsider and defend the Aristotelian mosaic in ways that had never before been encountered. Though the dialectical approach to scholarship throughout the medieval period saw scholars constantly questioning various aspects of the Aristotelian worldview, Descartes’ wholesale rejection of huge swaths of the mosaic and its central concepts were unprecedented. Theories like hylomorphism, which had been a given in the mosaic of the sixteenth and early seventeenth centuries , and had endured through multitudes of adjustments, reconciliations and dialectic criticism had never before faced complete overhaul as that Descartes 's mechanical natural philosophy threatened. Although Descartes theories would eventually be supplanted by those of Newton, he made the critical first steps to replacing the Aristotelian-scholastic mosaic.[[CiteRef::Hatfield (2016)]]