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In common parlance, a theory is a hunch or guess about something (e.g., "I have a theory that my teacher is an alien"). In science, however, a theory is an explanation of a set of observations that has been tested and found to be well-supported by evidence (e.g., "the theory of relativity"). The common usage of the word theory is closer in meaning to hypothesis in science: a plausible (or possible) explanation.

The distinction between a theory and a hypothesis (or even a guess) is an important one, and ignoring it leads to the kind of equivocation in apologetics exemplified by the claim that "evolution is only a theory".

As defined by Kevin Padian in his testimony in the Kitzmiller v. Dover Area School District trial:

"A theory, in science, [is] a very large body of information that's withstood a lot of testing. It probably consists of a number of different hypotheses, many different lines of evidence. And it's something that is very difficult to slay with an ugly fact, as Huxley once put it, because it's just a complex body of work that's been worked on through time."

Kitzmiller v. Dover trial transcript, day 9, a.m. session

v · d Science
v · d General science
Scientific method   Scientific theory · Hypothesis · Evidence · Examining claims · Skepticism
Scientific Disciplines   Physics · Biology · Chemistry · Psychology · Medical Science · Mathematics
History of science   Heliocentrism · Quantum mechanics
Champions of reason   Carl Sagan · James Randi

v · d Biology
Evolution   Natural selection
Abiogenesis   The Urey-Miller experiment
Evolutionary straw men   Life just exploded from nothing · So you think we came from monkeys · How did the first dog find a mate · Crocoducks · Banana argument · 747 Junkyard argument · Irreducible complexity · Chuck Missler's jar of peanut butter · What good is half a wing?
Notable Biologists   Charles Darwin · Richard Dawkins · PZ Myers
Notable quacks   William Dembski · Michael Behe · Geoffrey Simmons · Ken Ham · Michael Cremo

v · d Physics
Concepts   Cosmology · Big bang · Relativity theory · Black holes · Quantum mechanics
Physics straw men   Fine-tuning argument · Anthropic principle
Notable Physicists   Isaac Newton · Albert Einstein · Richard Feynman · Stephen Hawking
Notable Quacks   Dinesh D'Souza · Ray Comfort

v · d Mathematics
Statistics   Sample size · Selection bias · Standard deviation · Statistical significance · Statistical probability · Meta probability · Gambler's fallacy
Mathematics and religion   Biblical value of pi