As David Kolb puts it, the key to using hypertext to show logical structure is to be willing to mix presentation of structure within a single writing space, and hypertext links to other writing spaces.
Let single writing spaces present passages of argument, diagrammed or analyzed however is convenient. Let hypertext links take the reader to the arguments that support the parts of the argument presented on the page. Don't try to show all the structure either on the page or in the hypertext links. The single writing space would show fine structure where individual propositions relate to one another over a relatively small span that does not tax the reader's short-term memory. The hypertext links would show how larger blocks of argument relate to one another. Such a mixed presentation would take advantage of the power of prose paragraphs to present fine structure, and also of hypertext's ability to lay out typed relations between blocks of prose.
By not using hypertext to model every move, we would assist perception rather than burdening it. (from Socrates In the Labyrinth).
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