Take notes -- preferably as a mind map or a concept map. Initially on paper or in software, but eventually in your mind.

They connect different ideas: because, as a result of, in conclusion, etc. Relationships answer why and how questions.

Read for Ideas -- not one word at a time or one sentence at a time. Each idea is one Myndbit describing what, when, where, and who.

Organize your ideas on your mind map. Parallel, sequential, radial, cause and effect, unconnected, etc.

Is an idea fact or opinion? Is a relationship between two ideas fact or opinion? How strong is the relationship? How strong is an argument?