The word "theory" has a number of distinct meanings in different fields of knowledge, depending on the context and their methodologies. In common usage, people use the word "theory" to signify "conjecture", "speculation", or "opinion." In this sense, "theories" are opposed to "facts" — parts of the world, or claims about the world, that are real or true regardless of what people think.
In science, a theory is a proposed description, explanation, or model of the manner of interaction of a set of natural phenomena, capable of predicting future occurrences or observations of the same kind, and capable of being tested through experiment or otherwise falsified through empirical observation. It follows from this that for scientists "theory" and "fact" do not necessarily stand in opposition. For example, it is a fact that an apple dropped on earth has been observed to fall towards the center of the planet, and the theory which explains why the apple behaves so is the current theory of gravitation.
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