To add a little more background on the nature of what is being encoded:
I believe that everything that you learn is framed and parsed in terms of what you have learned before; you learn delta coding based on your prior life experiences. If you extend this all the way back you build on your innate built-in instinctive and emotional wiring as dictated by your genetics. It is nature first, then nurture.
To flesh this out - as you experience the world prior memories are being recalled as part of your predictive process; this is exactly what HTM proposes and there is nothing new in what I am saying. Perception is a process of active recall of prior memories. To the degree that you recognize what you are seeing - there is nothing novel so no learning is being triggered. But nothing is ever really exactly this same - there are always differences. Some examples might be different viewing angles or different contexts.
These differences are triggering your novelty detectors (Surprise!) - the most basic feature of the HTM canon. This novelty triggers learning throughout the hierarchy of connected maps everywhere that novelty is detected. We are always refining our inner models with these new perceptions.
This novelty/surprise based learning seems to be at different rates in the cortex vs the hippocampus. There is considerable research that shows that the learning rate can also be modified by chemicals released by the limbic system. It is very likely that different emotions generate more rapid learning in the hippocampus; perhaps differently based on the type of recognition in the amygdala.
Here is where I will strike out on my own with a proposal based on various hints I have seen in the literature; as the learning occurs I propose that the metabolites accumulate in the cell body, more than likely in the dendrite. This is what I call the ROE (residue of experience) - or a chemical memory independent of direct modifications of the synaptic connection nodes. This is not essential to the proposed process but a possible enhancement. More on this later.
When the brain switches to sleep mode it is time to take the more rapidly/deeply learned new engrams in the hippocampus which are themselves changes (delta) generated when recalling older prior memories in the cortex and push them onto the cortex. This clears these new memories from the hippocampus and prepares the system to start over with a fresh slate when you wake up.
One of the slippery parts of this (to me anyway) is that we remember patterns WHICH INCLUDE FRAGMENTS OF SEQUENCES as part of our memories; we learn transitions. Part of what will be added onto our prior learned patterns will be collections of transitions in the context of older recalled patterns. (I can easily see how patterns can be held and added up because my thinking is a form of 2D pattern manipulation - I don’t inherently see sequences of transitions so this is very hard for me to visualize but it must be happening!)
I have been looking for research that shows that some sorts of memory enhancement chemical are circulated during the dreaming process to enhance the transfer of memories. I do think that I will find them as there are several lines I have seen that indicate that the learning rate is being modified during spindle waveforms. I think that this interacts with the aforementioned “residue of experience” to help modify the generation of new connections.
Even if the ROE theory has no foundation “spindle” brain wave are known to excite the hippocampus in dreaming - driving a recall in both the cortex and hippocampus at the same time. If the hippocampus has leaned a response that makes it fire faster from new learning (using the “standard” spike timing learning ) this could trigger learning in the related cortex. This excitation sweeps through again and again as long as there are significant phase differences in response between the two areas.
Dreams? What to make of them. They are always personal and often filled with all sorts of deep meaning and connections. I am not surprised. As I indicated - your daily learning is based on personal recall of prior memories. Some of this may require that pools of previously un-related material be recalled to match what you are perceiving. As closely related parts of the prior learning are modified in the dreaming state you may be making new connections that “finally” connect partial patterns that have been building up. Part of very old memories may end up being reinforced to the point where they go from almost forgotten to being closer to the surface.
What is the episodic part of our neural mechanism supposed to make of our mental furniture being shifted around and modified while these little bits of new learning is being consolidated? Perceiving these recalled patterns as they are being recalled and reinforced is what we call “dreaming.”
Dreams are made of the stuff of our prior experience being modified on the fly so it is likely to pull up the emotional freighting that is associated with the recall of the original, somewhat unrelated, old memories that are being are pressed into service. As I said - I am not surprised that these are perceived as having deeply personal meanings that you may not be able to recognize as they really are novel synthesis of your prior experiences.
I may come back to this post and tune it up but this is a good start on getting out some ideas that I have been harboring for a long time.