An interpretation (spoilers)
Spoilers
There is a natural order to the universe that Janos describes in the opening description of the solar system. Sometimes the natural order doesn't seem to be the best for humans such as when an eclipse occurs that deprives us of light. Humans get scared by this but if we wait it out, we discover that it is only momentary and the natural order is the best after all. If we had tried to somehow tamper with the natural order of the solar system to avoid eclipse we could make it worse. The same principle applies to the musical scale. Werckmeister invented the current unnatural musical scale since the natural ratio of the sound frequencies didn't seem to tune an organ properly. The professor in the movie believes that it produces awful music. The third system in the movie is the social-political system of the country that also has a natural order that currently seems not to work. There are shortages of coal and fuel and work and and phones are not working for a long time. The common men in the area are getting very agitated with the seeming failure of the system especially now in the cold winter. The Prince is fomenting anarchy by saying that the current "whole is nothing", "nothing counts" . The angry men gather in towns led by the Prince and take their anger out on the stores and shops and hospitals and post offices. In her own way, the professors wife also feels the natural social order is not right mainly because she has lost her high role as wife and town leader. She sees the discontent as a way of re-gaining her stature. Her plan is to have the violent mob destroy the current town government, cause chaos, and then align with the police and the military to form a new government and a new order where she is the leader. Her plan seems to succeed but causes disaster for the town. The mob destroys the hospital but leaves a fragile naked old man alone since possibly the men know that his condition is inevitable for all of humankind and can't be "wrong". Innocent Janos is caught up in the middle of this plot and eventually the new social order shocks and ruins his inner stability, and causes him a nervous breakdown. At the end the whale represents how far from the natural order of life things have gotten, that now a whale sits in the middle of a town in Hungary.
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