Transfiguration magic doesn't allow "part of an object" to be transfigured, and that's linked to what you consider to be an "object". So wizards can't transfigure "part of an object" because to them, an eraser is definitely a "whole object". Harry tries to transfigure part of it by reasoning that the "whole" eraser is made up of tiny atoms and quarks (panels 2 and 3) that are definitely separate objects. When that doesn't work, he realizes that quarks and atoms are just things reasoned out by scientists to explain how matter is formed. His next try is more abstract. He visualizes the universe as hazy, undefined waves of matter that sometimes bunch together into what normal wizards call "whole objects", but can come apart just as easily, so really nothing is a whole object. (panel 4) That's when it works.