Did you not read the paper? The whole point is that "all is material". But causality is both micro and macro when it comes to complexity.I'm guessing these authors would ask: What is Pattee's definition of "material"?
So to use the Aristotelean frame, material and effective cause are "down there" at the level of micro-physics. But formal and final cause are the "up there" as the global material constraints.
Pattee defines the bit you mean as material as "the rate dependent dynamics of construction". It is what reductionists would like to believe is the whole of materiality. But Pattee shows how non-holonomic constraints are also part of material reality.
This is important because the conventional computational view of symbols is "physics-free" as Pattee says. There is something obviously right about computationalism (which is why it seems central to scientific theories of mind), but as a discourse it is not actually grounded in the physical, in the material. Instead it floats free in a rather Platonic fashion that leads to all kinds of familiar philosophical problems (like Searle's chinese box).
So that is why I single Pattee out here. He is a strict materialist (though his background in QM would already make him say the material is not so simple). And he shows how more is different. Materiality has this hidden face of semiotic control lurking within it.
You can see Pattee arguing against the other side - those who fail to ground the computational in the material - in his paper, Artificial life needs a real epistemology.