i love me some graph theory, but this huge Wolfram post about his idea for a "fundamental theory of physics" seems like he got carried away with it.
A lot of emphasis is placed on the visual representations of graphs resembling structures, like this.
This seems like an error to me - a graph in its abstract form has no defined spatial layout, and creating one for the sake of understanding is an artifact of human perception.
I've thought for a while now that huge, complex graph visuals like these are not that helpful for human understanding of what they represent.

People really like to recognize patterns in the visual representation, but a visual pattern may just be an artifact of how it was drawn
We are literally wired for pattern recognition, and it certainly feels smart to look at a giant graph and pretend that i've understood what it represents.

but if your graphs look like this it may be time to focus on a subset, or put down the graph theory book.
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