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Contrary to popular belief, when scientists use the word "theory", they are not referring to conjectures that they have pulled out of thin air and have no data to support such claims. The scientific use of the word "theory" is much different than the colloquial use.

In science, a theory refers to an integrated set of principles that explain and predict events that are observed in the natural world. Theories, in the scientific sense, summarize and explain facts, and imply testable predictions that allow for the falsification of the theory. Theory is vital to scientific endeavour, as it generates hypotheses to be tested, gives direction to research (and even suggests new areas for research), and, if the theory is good, has a high amount of explanatory power without requiring extensive modification to the theory. Theory without data is just conjecture, but data without a theoretical explanation is as good as meaningless to scientific practice.
An example of a scientific theory that is often mistaken as just a "theory" is the theory of evolution. Contrary to common misconceptions, evolutionary biology is one of the most prolific fields in science, with hundreds of thousands of peer-reviewed papers attesting to the theory's veracity, and an ever-increasing body of research.

Other examples include general relativity (yes, gravity is technically "only" a theory), special relativity, atomic theory (yes, atoms are "only" a theory too), and germ theory (the theory that small microscopic organisms are the cause of many illnesses).
by Amygdala May 05, 2011
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