He compares it to rebuilding a city guided by reason. This reliance on reason was important. This was only in philosophy. He tries to isolate rules of reason that make mathematical reasons solid. Only use things that are clear and distinct in our minds. Analyze things in their simplest elements. Build up step by step. Analysis and synthesis. Check your work to make sure you do things correctly. By following these rules. In his effort to find what is really true he applied his own beliefs. Anything he can doubt he will throw it out. He is trying to defeat skepticism but using the rules of skepticism. Lets try to doubt everything and see what were left with. Even the usual reasoning he questions, maybe his memories wrong, maybe mixed up? He says can i doubt that I'm thinking, he's thinking! He says I think therefor I am. By the fact that he's thinking he must exist.
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