Gravity is just a theory. Evolution is just a theory. Yet K-12 students are given both as "facts," which leads some parents to scratch their protruding foreheads and conclude science doesn't know anything and thus religion should replace it.
One of the most popular examples of science "changing its mind" came over the last generation, with a growing realization that dinosaurs and birds have a lot in common.
Thus the chicken on your plate must be related to Tyrannosaurus Rex, just as you are related to the monkey.
Now that theory is being replaced. A growing body of evidence indicates birds and dinosaurs had a common ancestor, but that their evolution diverged. Raptors may be a bird-like descendant of a different genealogical family from dinosaurs.
A lot of this work is coming from John Ruben, a zoologist at Oregon State University. (Go Beavers.)
One of Ruben's key findings involves a bird's thigh (above, from ScienceDaily), which is fixed in place and allows it the lung capacity to fly. Like people, dinosaurs had a thigh bone that moved as it crossed the ground. In other words birds run from their knees, dinosaurs ran from their hips.
You can taste this evolution in action. Try cooking a duck, a bird that flies. Notice how the breast is dark meat, and the thigh is tucked right into it? Now cook a chicken, a bird that mainly glides and runs. The breast is light, the thigh easier to separate at the hip and darker, because it gets more use.
This does not mean that bird-like dinosaurs such as the feathered Anchiornis huxleyi found last year in China, are unrelated to modern birds. But it could have been a transitional creature on a separate, but related evolutionary path. Feathers may have evolved twice.
Yes, it's complicated.
Ruben's theories raise many more questions than they answer. That's the point.
Science is not, and never really has been, about answers. If you want answers talk to an engineer. Science is about questions. The best theories ask the best questions, leading us to new avenues of discovery.
What Ruben has shown us, once again, is not just that science can change its mind, but that science and religion are fundamentally different and should never be confused even though, as is the case of birds and dinosaurs, confusion may seem the easier way to go.