Like several others before I would like to refer to Thomas Kuhn and his book “The Structure of Scientific Revolutions”.
Kuhn discriminates between two phases of scientific work:
- Normal science: Working within a given theory, applying the theory to
elaborate on phenomena covered by the theory.
As examples I
consider: Calculating the motions of the planets by solving Newton’s
equations. Solving questions about electromagnetism by applying
Maxwell’s equation. Calculation the spectra of atoms by solving the
Schroedinger or Dirac equation. Scientific research is guided by the theory which is accepted in this field.
- Scientific revolutions: Changing the paradigm, breaking with the
previously accepted theory. Introducing new concepts.
As examples I
consider: Breaking with the geocentric model, breaking with the
concept of absolute space and absolute time (theory of relativity),
breaking with the concept of action at a distance by introducing the
concept of waves, breaking with the concept of determinism for the
microcosmos (quantum theory).
Developing a new theory based on a
different fundamental principle, because important problems cannot be
explained on the basis of the accepted theory.
Note. My answer only deals with the first part of your question. I am not able to contribute to answers about the syntax, semantics and pragmatics of scientific theories.
Added: During the phase of normal science the dominant paradigm can restrict the generation of hypotheses.
Maxwell’s theory of electromagnetism, based on his fundamental equations, predicts that accelerated charges generate electromagnetic radiation. And the latter reduces the energy of the charged sources.
Applied to the model of atoms with their circulating electrons, the electrons should radiate on their circular orbits, lose energy and fall into the nucleus of the atom within a short period. As a consequence, matter cannot be stable according to Maxwell theory.
Nobody could create a hypothesis to explain stability of matter as long as he/she follows the Maxwell theory.