As a planet we tend to treat them rather differently. Philosophy is significantly more embedded within governments, even more so than religion. The difference is that religion, being "separate" from the government, tends to get much more buzz, simply due to its nature. However, philosophy is nowadays (and previously) just the nature of social conformism, and the general populace tend to deviate very little from it. Point is, religion and philosophy, while really similar to one another, are treated very differently by society, and wont be in too much conflict with one another if it stays that way. Once philosophical doctrine is taken more prominently than religion, which I suspect it may eventually (and has in the past), religion will likely fight back, for religion is just a branch of philosophy.
The God Paradox states asked, "Can God make a rock he can't lift?" The answer is of course yes. He is God and can do everything but no he can't because if he can't lift it he is not all mighty. This shows that Philosophy and Religion can and have worked as one however many thinkers challenged their own faith.
Religion is just resignation when faced with the horrors of the world. Instead of solutions, religion just says "life after death". Philosophy seeks first to understand, and then to propose any needed solutions. The religious demand acceptance of their beliefs without questions. Philosophers welcome dissent and questioning. Religion seeks to declare dissent a thought crime, Philosophy calls dissent the jewel of Liberty.
There is a reason why a PHD is a doctorate in the philosophy of a field. Philosophy is about critical thinking, logic. Regardless of what the colloquial usage has become, the actual field breaks down into how and why we consider things the way that we do. So, given that religion is a faith based position, not a reasoned one, they are necessarily in conflict.
Philosophy and religion both ask the big questions; is there a God? Is there a life after death? What is human nature? How are we to live our lives? What differs is their method of finding the answers; philosophy uses reason and religion relies on faith. Thomas Aquinas said that faith and reason never contradict each other when both faith and reason are used properly, the result is truth, and truth can never contradict truth.
Philosophy in my book, is critical thinking and deriving a explanation through logic. A persons logic can be based on religion, so their explanations can be supported by religion. Therefore religion is a way of thinking, making it a philosophy. Praying five times a day may not make sense to a atheist, but for a religious person it makes sense, because it is common knowledge that there is a life after death. Of course there is also philosophy in conflict with religion, but to say philosophy is directly in conflict with religion, is wrong. If in doubt I will refer to some of the works of Pascal.
Philosophy can and is commonly used to justify and reason through religious belief. Arguments like the Kalam, the argument from contingency, and the ontological argument are all philosophical in nature but they answer questions that are inherently religious, so no, philosophy and religion do not come into conflict with one another.
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