What is the distinction between the the Metaphysical Stage and the Scientific Phase in Aguste Comte's Three Stage theory regarding Epistemology and how did these two theories affect society differently? Examples supporting the differences in their method and function would be greatly appreciated. I'm reading this text.

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The Metaphysical Stage of Comte's argument focuses on the introduction of scientific thought into the general consciousness.  There are still many beliefs about God(s) and how such entities influence the world.  For example, the planets moved from being Gods to being objects which still influence people's behavior.  This was viewed by Comte as moving in the right direction, away from theism and toward actualization.  The benefit of the metaphysical stage, 1300-1800 (approximately), was the creative thinking brought on by science.  Natural phenomenon were observed and tested to find the cause.  The downside was people tended to still lay the cause on the divine if it was outside the realm of current scientific knowledge. 

The Scientific Stage represents the ideal for Comte.  In this stage people begin to experience the world solely through scientific explanation and abandon the idea of God(s) altogether.  This stage of reason and thought Comte believed would allow man to truly understand the world and conquer it without the limitations of theism.  The benefit is the advancements of science and social changes no longer hampered by strict theological demands.  The issues of women's rights, civil rights and current ones such as gay marriage would not be possible in the Metaphysical stage due to science wanting to concur with theology.  One downside is the introduction of conflict as some people still have theistic believes which conflict with social changes.  Another con is the advancements are so rapid and often contradicting it destabilizes society.    

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