The first programs he wrote for the Atlas and the Mark II ("the Baby"), seem to have been focused on a theory he had around how animals got their markings.

They look a little to me (as a non-expert in these areas, and reading them in a museum over about 15 minutes, not doing a deep analysis), like a primitive form of cellular automata algorithm. From the scrawls on the print outs, it's possible that he was playing with the space of algorithms not just the algorithms themselves.

It might be worth going back and looking at that early work he did and seeing it through this lens.

This makes ruliology an invaluable cartography of the computational landscape, but not a foundation. It maps the territory without explaining what the territory is made of.

https://en.wikipedia.org/wiki/A_New_Kind_of_Science

But exactly what is the problem here? Other than perhaps a very mechanical view of the universe (which he shares with many other authors) where it is hard to explain things like consciousness and other complex behaviors.