Radical skepticism was just a tool in the rationalist philosophy of Rene Descartes, since he wanted to establish clear and distinct proof for the existence of minds and bodies, and found that ultimately he was unable to doubt his own existence. From this he derived the fundamental precept of Cogito ergo sum (I think therefore I exist) and from this went on to affirm the existence of God and the physical universe. No sane or rational person could seriously doubt their own existence or the reality of physical objects outside of themselves, no matter how flawed or imperfect human perceptions might be. We may be deceived on details or specific perceptions, but not on the basic fact that minds and material substances actually exist.
In his first three Meditations, Rene Descartes did not intend to disprove the existence of God, the soul, matter and physical bodies. Just the opposite, as he says in his title he was searching for the right methods that would yield clear and distinct proof for the existence of God, minds and bodies. Descartes took it as a matter of faith that God and the soul really existed and that the Bible was true, but went on to state that he could prove this through science and natural reason. Like Galileo and William Harvey, at the dawn of what would later be called the Scientific Revolution, he was breaking with the older concepts of nature and physics based on the science of Aristotle and moving in the direction of what would eventually be described as the modern scientific method. His doubt and skepticism has a clear an distinct purpose in his analytic philosophy, as he breaks down every common belief and assumption, subjecting then to merciless skepticism, until he arrives at what he considers to be the core of absolute truth that cannot be doubted—the existence of his own minds and thoughts. From there he goes on to create a new synthesis by offering proof that God exists, and then that matter, bodies and the physical universe also exist. After that, he goes on to describe the nature of that physical reality, although he should be granted considerable leeway in this area given the severe limitations of 17th Century science and technology. He refrained from discussing final or ultimate causes, except for the implication that God was probably the First Cause and Prime Mover of everything else, and he could not have known about the Big Bang theory and evolution. By modern standards, of course, the existence of God and the immortal soul that Descartes claimed to have proven are subject to debate, but that was much less true of the 17th Century.
Descartes was not a nihilist or solipsist who truly doubted the existence of anything outside his own mind, and only used skepticism to arrive at clear and distinct ideas. He wanted to prove that God existed as well as thinking, rational beings, but his first step in the process was to radically doubt everything. In the First and Second Meditations, he considers perhaps God, the body and the whole physical universe were dreams or hallucinations, or that his thoughts and perceptions were being manipulated by some evil being (Descartes, 1968, p. 33). Ultimately, though, he states in Meditation Two that he cannot sincerely doubt his own thoughts and comes to the famous conclusion of Cogito ergo sum—I think therefore I am. This particularly proposition seems all but impossible to refute, at least for a sane person (Descartes, p. 35).
Given the limits of 17th Century science, Descartes would not have known about subatomic particles, chemical reactions, evolution and nuclear physics, so his discussion of matter and physical properties will naturally seem archaic. He understood that physical qualities are subject to change, but maintained that some type of basic substance underlay all forms of matter. This substance remained the same no matter how much the accidental or contingent qualities changed. For example, a piece of wax that he discusses in Meditation Two, freshly taken from the honeycomb still had a honey flavor, as well as a scent, color, shape and size, hardness and coldness, some tactile quality, and so on. When brought close to the fire, though, all these qualities changed, including flavor, flower scent, color, original shape, size, coldness as the substance became hot and liquid. Descartes wondered whether this material was still the same wax and if so, what constituted its identity, substance and essential quality (Descartes, p. 38).
In Meditation Three, Descartes concurs with Aristotle and Thomas Aquinas that God is the First Cause and Prime Mover in nature, but he preferred to concentrate on physical, material and efficient causes. Once again, he did not doubt that God existed, and stated that he was perfect and eternal, but also that God had given human beings minds, senses and judgment through which they could comprehend the natural world. God did not create humanity to be all-knowing and all-powerful, or ensure that people would never be mistaken. Descartes also thought that because of these limitations, any attempts to know about the ends or final causes in the mind of God would be presumptuous and doomed to failure (Descartes, p. 45). Physics could only discern efficient and limited causes in the physical universe, but would never be able to discern the ultimate truths. These ideas and sensations must come from a source outside of his mind, just as his understanding of geometry and mathematics. He claims that his ideas come either from God or from the faculties of his mind that have clear ideas about physical bodies and objects.
Descartes probably could have made same arguments about the existence of minds and bodies without introducing God into the discussion at all. Some of the objections raised to his work included doubts about whether the mind has and clear or distinct ideas about God and the soul, or whether these came from God. Even so, this was the 17th Century, when religious wars were still going on and the Inquisition was still active. He was a prudent philosopher who wished to survive and continuing publishing, and although he probably realized that God’s existence or nonexistence can only be a matter of faith, not scientific proof, it would not have been wise to openly raise the possibility of God’s possible nonexistence at the time. Descartes asserts that all humans had both a body and mind (soul), and that the mind was eternal while the body was subject to physical and material laws. Thus the universe was divided between the mind and matter, and the physical world could be explained by mathematical and scientific laws. Once again, such a proposition can be a matter of faith but reasonable people can (and do) dispute these questions, at least in environments where disputes and debates are permitted. For the most part they simply were not in the world that Descartes knew.
Even without the aid of electron microscopes and modern knowledge of chemistry and physics, obviously some type of material substance still exists in this new form. That would also be true of the ashes remaining when a piece of wood was burned in a fire, or many other similar examples that might come to mind. This argument seems to be a valid proof that some type of matter or physical substance does exist outside of the human mind or imagination, even though its condition and appearance is being altered all the time. Nor does it seem possible that the mind could really be aware of this without some type of senses or images from direct experience. Science in the modern sense could hardly function without a fundamental assumption like this, or without the tool of radical skepticism that Descartes applied to the older scientific ‘truths’ or Aristotle, Aquinas and the Scholastics. Like Galileo, of course, he found it necessary to be prudent about the truly radical implications of this new science, such as the questions it raised about the existence of God, the immortal soul and an unseen realm that was spiritual and eternal. Descartes attempted to resolve this problem with dualism that still had a place for God and the soul as the most important items that existed.
Descartes, R. (1968). Meditations. Harmondsworth: Penguin.