The first was the church of his time which, to put it lightly, was not a fan of science and even felt threatened by its exploration of the natural world. And second, Descartes had to prove, before he put forth his method, that there was a reason to have a method in the first place. In other words, Descartes had to prove that there was a solid truth to search for. He found his way around these obstacles through his use of his method to "prove" the existence of God.
With God he found his salvation, the way around these two issues that plagued his time. Descartes proved that he "was certain that I am a thinking" and that he was unable to exist in the sense that he couldn't doubt his existence, for to do so was a thought and thus existence in and of itself. However, while Descartes could prove he existed he had to prove that something other then him existed also. This was necessary because if he could not prove this his logic would falter and his method could be seen as pointless as it searched for truth where none potentially existed. However, through much deliberation and thought Descartes determined that because he had an impression of God, an idea of an all powerful deity, that this idea must have come from somewhere. It couldn't be him, since he was imperfect and was thus unable to grasp the perfection of which he was thinking. Thus, the perfection that so impressed his mind must exist for it would have to exist in order for Descartes to have a thoughtful impression of it. From here Descartes was able to follow his logic through and deduce that since he existed as a thinking thing, and that God existed as a perfect all good being, then the things which Descartes saw clearly could be held as true if seen with reason. This was due to the fact that God was not a deceiver and gave Descartes the faculty of understanding which when used properly could enable him to arrive at truth. "But once I perceived there was a God, and I also understood at the same time that everything else depends on him, and that he is not a deceiver, I then concluded that everything I clearly and distinctly perceive is necessarily true." (p131/70)
This argument solved the two issues Descartes faced and showed why he presented the Meditations in the manner that he did. First, his proof for God is rather compelling and showed the church of his time that his scientific method could live in harmony with religious belief, and even in some cases aid in its understanding. In addition, by proving that God exists Descartes had the ability to ascertain that the physical world, created by a benevolent God, was able to be examined in a truthful and right manner. Thus Descartes showed how science and religion could coexist and also established a reason to pursuing scientific truth by attempting to prove that there is an honest truth to be discovered should we precede with good faith and reason.
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