In response to the subject of the polarities of theory vs.analysis as the major philosophical premise of the course I did some reading which will hopefully add some to our previous discussion.
In his book Analysis, Ian Bent suggests that "analysis is the part of the study of music which takes as its starting point the music itself, rather than extreme factors." (pg. 1) Here is our first polarity according to Bent: the work vs. extreme factors. This is where I believe theory offers a hand to analysis. Even in the outside world (Bent's extreme factors) I believe we can find structures which can be applied through analysis.
Bent outlines many other polarities within the field of theory/analysis. They are: music aesthetics vs. compositional theory, philosophical vs. technical, analyst vs. historian, descriptive vs.judicial, and objective vs. subjective.
Take for example the polarity philosophical vs. technical. The analyst works as a scientist and the aesthetician works as a philosopher. The analyst is concerned with the music itself and the structures within that music, whereas the aesthetician looks at the nature of music and its place among the arts, life and reality. The analyst works empirically and comes to grips with the piece of music on its own terms, whereas the aesthetician will look at the musical work in terms of other things.
Bent paints the picture of the analyst as an objective scientist. However, not even a scientist is completely objective, they too set up there experiments with the subjective hypothesis.
In his book, Analysis and Value Judgement, Carl Dalhaus sets up his major polarity as subjective vs. objective. Dalhaus suggests that the two complement each other. Dalhaus suggests (as did I) that "subjective judgement provides the psychological premise and point of departure for the discovery of rational explanations." (pg. 3) As Dalhaus points out aesthetic judgements can only be sustained by factual judgements which depend on analytical methods - even the analytical methods subjectively demonstrate the musical attitudes of the period.