Just for clarification: the Matrix is the same as the Chicken Coop in the novel, White Tiger…
As a mad scientist, my job is to distinguish the “things” that are in your way of direction, in your way of clarity, and to devise ways for you to go around them or through them.
One tool that has proven invaluable is isolation. Isolating what you want to see. Seeing it by itself. So you can see it for what it is, in all its glory…
In nature, to our eyes, things are grouped, things are undifferentiated and solid.
Your language supports that too… everything is the same as everything else, except not always. That is how we see. We don’t see boundaries, we don’t separate out what we want to see, we always see things together. We say: it IS… but there is no “it” and therefore there is no “is”. If we said: It seems that … then we would be closer to reality… but we don’t say that. That would require humility.