To get knowledge from scratch there really is only observation. We are pretty limited as human beings, we can only take in information about things we can directly sense, we can sense through indirect observation, or that we can build instruments to sense for us. After that its the same thing I mentioned above, use some method to refine that observation into a repeatable, testable theory.

The bad science that many people try to do is to start with a theory, usually with some social or political agenda attached, and work backward collecting evidence that “supports” it. That’s not a way of gaining knowledge though, it’s just a way of emulating the look and feel of science.