Just thought I'd drop off some thoughts..
I'm currently doing my certificate III in non-emergency patient transport and this entire week we've been looking at brain function and deterioration. Mostly to do with Alzhiemer's and Dementia.
What I found most interesting is that Brain Neuro patterns look amazingly similiar to this...

And, in fact.. Act to work together by "synthesizing" with each other to gain logical throught processes and movements. Now, this is the first dream sequence...
Now, notice the second dream sequence.

They are significantly blurred and distorted...
Now look at what happens with proper brain function..

And now with a dementia affected neurological Pathway

Some "circuits" are greyed out as the dementia deteriorates the brain function. Now compare this to the "trees" from the dream sequences....
Now, lastly, in the 3rd dream sequence it starts off with the kid and no trees. Which could only stand to reason (according to this theory) that the "indoctrinated" part of the brain has totally taken over and started burning holes in Shepard's actual brain... Evidenced by this...

Oh and, for the record, this is what the "synthesis" refers to between neurological co-operation.

Which you can also see occuring in the previous picture of normal brain function also.