Sentence:  If , as I suspect , the problem is largely of the second sort , then development of a theory better able to handle tone will result automatically in better <WSD>theory</WSD> for all phonologic subsystems . 
Meaning of the word marked with <WSD> tags:  a well-substantiated explanation of some aspect of the natural world; an organized system of accepted knowledge that applies in a variety of circumstances to explain a specific set of phenomena