In thinking about how protoglyphs might form in the mind, here are some 'first thoughts' (recently resurrected from old memories). What follows below is a very rough draft as I work through this sequence.
1. In the earliest stages of development, the brain has a set of hard-wired patterns that are innate and common to all people (phosphenes may be examples of these patterns). Exactly what these patterns look like is still unknown. They need to be identified. The patterns are represented in the brain by neural receptors that are sensitized or physically receptivity to external stimuli for these patterns.
2. As development and learning continues, the brain is exposed to pattern instances experienced in the external environment. Samples of fuzzy data are pieced together, and the pattern becomes 'activated' and robust in the brain. Over time, the pattern becomes 'averaged' into a geometric prototype of the pattern. The brain has now learned the pattern and it can be reliably recalled when an instance is presented in the environment. The interesting thing here is that the presentation of the pattern (in the external environment) can stimulate recall for one or more instances, one or more instances can recall the pattern from memory, or a single instance can recall another instance. I think an advanced mind may lose its ability to recall these lower order patterns, and only be able to recall specific instances. I think protoglyphs may lie just at the border of consciousness or may even be subconscious for some people. For people who aren't 'visual thinkers', it is quite likely that their prototypes reside below the level of conscious thought.
3. More data is presented through multisensory 'enforcing instances'. Each instance that is encountered is mapped onto the geometric prototype. This is a protoglyph. A protoglyph is both the pattern itself, the 'sacred geometry' and all corrollated instances associated to it. Imagine a circle (to represent a pattern) and an array of fuzzier misshapen circles superimposed over the 'perfect' circle as messy data. Each instance now mapped in the mind now also has associated with it all other instances that share this particular pattern/structure.
4. The protoglyphs can combine in ways to create 'compound protoglyphs' or compound patterns.