I am confused now over scientific method. Do we have physical examples of the tight junction theory within PWP or Alzheimer's? Is this done upon autopsy?

I thought in scientific research we start with an idea or theory; becomes a hypothesis or many hypotheses; we test them with scientific measure...only then after we have evidence does the theory become codified in print within a book. Aren't some key research pieces substantiating the theory (after the fact, not supporting it) essential?

Maybe i am missing something; it just seems like a rather large leap is being made over the method. Not that I am at all questioning theory. Anyone wondering this too?

Laura