I read Imtiaz's post The Ultimate Framework of Religion. In this post he says "The most fundamental difference between religion and science is the capacity for allegorical interpretation. It is very difficult to interpret scientific texts allegorically whereas most of the literature in religious texts has an allegorical meaning attached to it." For the most part I agree with this. However, I would like to point out that there is still allegory in Science, and especially in modern physics.
We understand the world as it is in terms of classical principles, but when we move into the world of the very small these fundamental laws break down. We can see this through experinment. We are thus forced to use allegory to explain theories for how things exist in the quantum world because we cannot observe them directly. Science does not use allegory often, but many times it is a useful tool in understanding those things that are beyond our direct human observation.
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