The Great Chain of Being is a traditional map that starts from God and arranges inferior beings in a hierarchy below. Following the move to centering meaning, the third phase of sign action, interpretation and particularly the perspective of a community of linguistic beings doing the work of discovery and interpretation.
If we invert the traditional map and start from the smallest most numerous existing entities and describe the stacks of emergent systems that occur in experience, we have a very different project. The top down analysis is useful, but if it does not connect to actual bottom up structures, the lack of grounding can become a critical flaw. In terms of physical theories, the goal is to connect existential entinties at any organizational level with physical processes. The central claim of this work is that a Peircean grounding of an appropriate physical sign based interpretation of the physical theories themselves is the necessary philosophical grounding for any theory of everything that can be taken seriously. This thesis, at least up to the mathematics that is a bit beyond me much of the time, provides some key frameworks for talking about the important topics.
Turing anticipates that the question of whether intelligence is a computable function is a key question, and wants to give the automated intelligences every chance of hiding its differences in a simple teletype interface. He may or may not have anticipated that the simple tasks of conversing in natural language text would be so difficult, and then that cognitive tasks that are mastered and/or instinctual in many living systems would likewise be extremely challenging. I suggest that it may be that living systems have evolved many systems, so would it be surprising that they might take advantage of what might be catagorized as quantum computation? Can we not name the hypothesis that physical systems are constructed primarily of physical quantum information processors, and that the best way to understand inteligent organisms (i.e. the entire network of living things in whole and in parts) is as the operation of semiotic systems composed of these information processes.
The Ground of Being
It turns out that the bottom of the chain is just as mysterious as the top. Physically the bottom end of the size scale in time and space terminates when the mathematical models break down in infinities. Below a certain scale the energy of entire universes is available; one could say that math has broken down, that the models are no longer descriptive. Could it be that this is a demonstration of "As Above, so Below", that the ground and the source are connected? The chain is more of a loop, and the Hermetic maxim suggests a way out. How is it that the different levels of reality corespond to one another? I would suggest that the unity can be found in the way signs and signals are both part of the organization within levels, and the connection between levels. If signs have such a central role in existence, then some kind of primordial awareness permiates the world. From the smallest particles to living organisms and to all corners of the known universe. Awareness may be the wrong word, we don't want or need anything more than the connections implied by the physical models and the ability to relate parts to wholes.
There are many deep and interesting questions in cosmology and philosophy that might be better answered with semiotics more central in our thinking, but we can start with just mapping the territory as it is known from the bottom of the scale to the top.
The Four Forces
At the smallest scale, the current science is quantum mechanics. That program has been extremely successful and we have a very accurate integrated model for three of the four forces. The odd man out is gravity, which is most important at the largest scales because it is universally attractive. The weak and strong nuclear forces account for what kind of matter there is. We can sum this up as how many atomic nuclei of each type, the major types are all on the periodic table of elements, plus variations (isotopes, plus free neutrons), and then there will be enough eletrons to balance all the protons.
The strong force holds the nuclei together, so except inside stars or atomic bombs, they don't change much. The exception for alpha and beta decay and similar processes involving the weak force. This is the source of most nuclear radiation. Neutrons on their own decay slowly, splitting into a proton and an electron (plus a weak force carier, some form of neutrino), and in similar ways this sort of change happening in a larger nucleus would change the atomic number and maybe emit stable 'parts', typically a hellium nucleus with two neutrons and two protons. So, most everything in our local experience is stable at the lowest levels of organization. The Sun is fusing hydrogen into helium and bathing us in energy, and isotopes are slowly decaring in the earth. We've mined some of the unstable elements to exploit nuclear energy, but our main experience of the nuclear forces is in how stable the mix of elements is locally.
The force that dominates our immediate world is the electromagnetic force. The atomic number of each atom determines the number of electrons that it will attract. Chemistry is all about how the electron clouds of atoms interact and form more or less stable arrangements. When atoms collide kinetically, it is their electron clouds that bounce off of each other an send them each flying in another direction, maybe with other changes to states of angular momentum or arrangement.
The Scale from the Bottom Up
Zero - Below the Planck scale, we don't really have a theory that works. Maybe what's down there, to the extent that we can see anything, is just a reflection of the outer universe. In any case it is all speculative, and probably science isn't going to be that much help at the current level of development.
One - The Standard Partical Model particles:
Two - The Chemical Elements
Three - Molecules and Chemical Interactions
Four - (Energy scale) Temperature and Pressure - Substances and Phases
Five - (Structure and Organization) - Processes, Information and Evolution
Six - (Context and Environment) - Planet, Solar System, Galaxy, Group, Universe, God
The Physical Sign Hypothesis
Coming back to what was hinted in the chapter introduction, we name this idea. Fundamental to this hypothesis is Peirce's irreducably triadic theory of Signs. The hypothesis is that by identifying the triadic sign relationships and elements that are already present in modern physical theories and their models of the world, we will finally be ready to found a mature theory of cognitive processes and intelligence. The conjecture is that many forms of quantum computation are involved in the realization of these processes in nature. It may, in fact, be very difficult in practice to determine the truth of this conjecture in the every-day experiences that they are necessary to. The complexity and subtlety of the systems involved may even make it impossible as any attempt to observe them destroys the coherence necessary for function. I suspect that Peirce was trying to grasp at this hypothesis, but it was too far ahead of when the other necessary ideas would emerge. It is just beyond my grasp to express it, and well beyond by ability to confirm even the smallest parts of the math required, but I just know there is a comprehensive theory that uses Semiotics and Quantum Information Theory to make sense of the Physical ToEs and ground them in philosophy.