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A scientific theory is a series of statements about the causal elements for observed phenomena. A critical component of a scientific theory is that it provides explanations and predictions that can be tested.
Usually, theories (in the scientific sense) are large bodies of work that are a composite of the products of many contributors over time and are substantiated by vast bodies of converging evidence. They unify and synchronize the scientific community's view and approach to a particular scientific field. For example, biology has the theory of evolution and cell theory, geology has plate tectonic theory and cosmology has the Big Bang. The development of theories is a key element of the scientific method as they are used to make predictions about the world; if these predictions fail, the theory is revised. Theories are the main goal in science and no explanation can achieve a higher "rank" (contrary to the belief that "theories" become "laws" or "facts" over time).
"Theory" is a Jekyll-and-Hyde term that means different things depending on the context and who is using it. While in everyday speech anything that attempts to provide an explanation for a cause can be dubbed a "theory", a scientific theory has a much more specific meaning. Scientific theory is far more than just a casual conjecture or some Joe's guesswork. A theory in this context is a well-substantiated explanation for a series of facts and observations that is testable and can be used to predict future observations.
 Common misconceptions about theories
 "Just" a theory
“”Creationists make it sound as though a 'theory' is something you dreamt up after being drunk all night.
Creationist and Intelligent design proponents often like to describe the theory of evolution as just a theory. This relies on equivocating the common usage of the term theory (meaning "idea" or "guess" - more literally speaking, "hypothesis" or "conjecture") with the scientific meaning. Theories are the single highest level of scientific achievement and nothing is just a theory - that would be like saying Bill Gates is just a multibillionaire. Additionally, one might say that the notion of evolution is "just a theory" in the same way that Cell Theory and the Gravity (fundamental principles of biology and physics, respectively) are "just theories."
This argument played out with hilarious ramifications in the recent decision of the Florida State Board of Education to teach evolution as a "scientific theory". Apparently, the creationists on the Florida SBOE thought that this was a "compromise" — by making evolution a "scientific theory" at law, they thought, it would weaken the position of evolution. After all, then it would be "just a theory," right? Wrong! This "compromise" actually puts evolution on the exactly right footing — at the highest tier of science — and ensures that students will be taught about what the term "scientific theory" really means, hopefully eventually drawing the sting of the colloquial meaning confusion.
To quickly counter this argument, you can say "Gravity is just a theory too", and they will be forced to turn to some other argument.
 Theories and laws
Another common misconception is that a theory is the step you go through while on your way to a law of science. Scientific laws and theories are two very different things and, despite what it may seem, one never becomes the other. Scientific laws are factual observations usually derived from mathematical modeling; they merely distill empirical results into concise verbal or mathematical statements that express a fundamental principle of science - for example, gravity attracts, force equals mass times acceleration and so on. Theories are the causal explanations behind what creates these laws and observations of nature. Theories also combine laws into a framework that is greater than the sum of its parts. In genetics, many different laws describe how genes interact in different combinations to influence heredity - work done principally by Gregor Mendel. Genetic theory combines these laws into a unified framework that can be used as an explanation and to make predictions. Evolutionary theory then combines genetic theory, the theory of natural selection and other theories with the various laws with which they are associated into a complex framework that forms the basis of much research in the field of biology.
Even superb theories, or laws, can be superseded by more successful theories. For instance, Newton's "Law" of gravitation is superb at predicting the path of a spacecraft among the outer planets of the Solar system, but it breaks down when large masses are involved, such as that of the sun. The precession of the aphelion of Mercury can only be explained by Einstein's general relativity, which is a refinement of Newton's Law taking into account the slight bending of spacetime near the sun.
 Falsified theories
Clearly, if a theory has been falsified it no longer fulfills the definitions at the start of the article. It may well still be a "theory" in the sense of the common usage, but in scientific terms it has become a superseded theory. For example, geocentrism was a theory, as was the concept of four elements (Earth, Fire, Wind and Water) and Larmarckian evolution which turned out to be less than accurate. These have been disproved conclusively enough (although some will beg to differ).
Because of the ability for good theories to make predictions, even if they are shown to be false (or more specifically, inaccurate in certain conditions) they can still be used to make predictions that are useful approximations. Newtonian mechanics may well be total nonsense in the light of 20th Century physics pioneered by Einstein, but no one uses Special Relativity to work out the momentum of an automobile. And while Quantum mechanics may, in principle, be completely replaced by something else, nothing is going to change the fact that the Schrodinger Equation predicts the spectroscopic features of the hydrogen atom perfectly. Even some of the more "silly" theories of old may have some use because of how they work, the classic example being that of a flat Earth. While everyone knows that the Earth isn't flat, someone building a shed in their garden doesn't need to allow for the curvature of the Earth.
 Developing theories
Science's understanding of the universe is indeed subject to change - otherwise it would be incapable of making any use of new technology and would be pointless. While people often say that this means all current scientific knowledge is "wrong", this is far from the right way of describing it. If a theory produces good results, it is right, but when it doesn't, it's best described as inaccurate. Theories will usually evolve from a less accurate to a more accurate version of reality. One of the major misconception that when theories change the change is massive and total. When discussing the "Relativity of Wrong", Isaac Asimov quipped that someone "living in a mental world of absolute rights and wrongs, may be imagining that because all theories are wrong, the earth may be thought spherical now, but cubical next century, and a hollow icosahedron the next, and a doughnut shape the one after." But this is clearly not the case, and applies as much to the microscopic, nuanced worlds of atomic theory and theoretical physics as it does to more obvious examples such as the shape of the Earth.
Many people believe that Einstein came along and made all of Newton's theories redundant (some will also say that quantum theory usurped relativity and that string theory in turn usurped quantum theory and so on). This is not the case, as even the largest changes to our understanding are relatively small. Theories are changed by small steps and new ones will usually consist of the old one with a bit added. For example, one can formally show that Newton's laws are an approximation to special relativity that applies when velocities are small compared to the speed of light. A "Theory of Everything" that combines quantum mechanics and gravity will still resemble quantum mechanics. The Schrodinger Equation, Hartree-Fock theory, spin dynamics and particle-wave duality, fundamental components of quantum mechanics will all still be there, as useful and accurate as ever.
 Theory and hypothesis
One common misconception is that scientific theories are derived from hypotheses that have met with confirming experimental evidence - and that there is a hierarchy of science starting with the hypothesis that reaches theory and eventually reaches law. This is in fact wrong, as theories are completely separate from hypotheses - a hypothesis does not become a theory, and if experimental evidence contradicts a theory it is not downgraded to a hypothesis.
A theory is a fully working model, supported by evidence and accepted as valid and accurate at predicting and testing observations. A hypothesis tends to be a bit smaller, a guess or conjecture about how something might work - a "working hypothesis" is something with good enough supporting evidence that an individual will accept as true for the sake of furthering their research. Importantly, a hypothesis is a testable statement and unlike a theory it might well be proved to be "right" or "wrong" without causing any major problems for established science. It is a hypothesis that leads to experiment and it is many of these factors - ideas, concepts, experiments, evidence and so on - working together that theories emerge from.
 See also
- Theories Guide, Wikipedia on Theories
- 5 Ws, Wikipedia on Who, What, Where, When, Why, How
- Introduction to the Scientific Method, an important site
- ISCID.org William A. Dembski on providing details about the mechanism of ID
- The Measure of Design Touchstone magazine, July/August 2004. Paul Nelson: "... the biggest challenge facing the ID community is to develop a full-fledged theory of biological design."
- Reply to Shanks and Joplin Michael Behe, "Reply to Shanks and Joplin", Reports of the National Center for Science Education, volume 21 number 3-4 (May-August 2001), page 15 ID "says nothing directly about how biological design was produced ... or other such questions"
- Just a Theory, SMBC Theater
- If You Want a Good Story, Look to Darwinian Evolution, Not Intelligent Design by David Klinghoffer of the Discovery Institute