Much of my thought on the practice of, and relationship between, theory and analysis is influenced by my science background and my continuing involvement in amateur astronomy. However, I am beginning to believe that my views (in the application to music) may be flawed. While Melissa is correct in suggesting that science often has an agenda in the application of a theory, (particularly when commerce in involved) pure science is as interested in refuting theory as it is in supporting it. Carl Sagen points out that in science a theory is never proved "right": A theory describes the observed and makes predictions on the unobserved. At any point a single observation may throw into doubt the validity of any theory, even one that has been undisputed for decades. The history of science is strewn with the corpses of theory.
 So, what does this have to do with music? Much of the debate in music focuses on what Kerman calls the "empiricism" and "formalism" of musical theory and analysis. (Kerman, Contemplating Music) I believe that this stems from a desire on the part of some analysts to establish the discipline as a "real" science, dedicated to the pursuit of truth through the use of disinterested analytical technique. However, the end goal of science is (or should be) very different from that of music. The scientist is interested in the systems that govern a given phenomena -gravity, the common cold, global warming, etc. - problems which have, at their core, a single correct solution. It is this single solution that the scientific method is designed to reveal: To apply the scientific method to music is to imply that there is a correct solution to every musical "problem", an assumption that most would find unpalatable due to the subjective nature of art. This also has the effect of drawing competing theories into hierarchical conflict as one tries to refute the next (as in the century long debate over the correct function of Wagner's Tristan chord).
 This issue is addressed by Kofi Agawu in his MTO article Analyzing music under the new musicological regime. Given the perceived formalist nature of music analysis, Agawu states "it would seem that the aims of theory and the new musicology are fundamentally incompatible". The anti-formalist nature of post-modern thought, demands that it treat the results of analysis with some suspicion, if not ignoring those results altogether. However, if we reverse the mantra of science and use analysis to produce a multiplicity of equally valid results (what Agawu describes as the "New Theory," a partner of the "New Musicology") the practice of theory and analysis will be well on the way to becoming a powerful ally of the musicologist and music critic.
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