expand_less Given that a System is an information structure, we can proceed to analyze the world in terms of its nested information structures or subsystems. All of the dynamics of complex systems can be realized in theory and observation by decomposing natural systems along emergent information flow boundaries. In biological cybernetics and cognitive sciences, we can analyze living organisms as self-producing and maintaining networks of processes that are open to the environment and the other beings coexisting therein. With the development of symbolic language in the homo line, the stage was set for developing extended phenotypes in material culture. With homo sapiens and the Neolithic Age this kicks into high gear, first accellerating slowly but the pace of change is ramping up the whole time.
This is how we find ourselves in the age of disruptive change where we either wise up fast or get kicked off the planet by our own actions. Much of the change is in the technology of information systems, but even more significant is the evolution of material culture noted above. The ability to not just use tools but to invent them requires an interruption in the normal uses of language that give only the capacity to use language within the given framework. To invent a new tool the individual must first imagine using that tool. A tool might be modified and made better within a space of variation already given, but a new category of tools for a new food source. First the new action including possible invention has to be imagined, the tools fashioned and use attempted. Failure reveals more of the world and now more people engage and play and experiment until sucess. When cognition can go beyond the manipulation of a world given and think about the experience outside the fishbowl of a given life-world embedded necessarily in learned habits of perception and responding active rituals.
Initially, this process might be largely pre-linguistic and take place only within the mind of one or more bright individuals manipulating, making and trying different use patterns. It would not need extensive verbal language and could be done completely in the hands-on process of doing things, maybe first as an individual and then showing how it works and others picking it up directly from watching other individuals in action. Verbal cues need not be any more or less than what is already in use before the new invention is introduced. The special cognitive mode of stepping back and considering is only required in the initial stages when the invention is new and and use is novel. Smaller adjustments can now evolve on top of the initial innovation with more ordinary thinking prompted by limitations revealed in use and further trial and error.
The break from life as given to the examined life of awareness is deep and wide and in general not of much survival value within a given way of living. On the other hand, for creating new ways of living and responding adaptively to a changing situation, it is obvious how thinking outside the box might save the day not only for the wise guy with a crazy plan but the whole social group. Inventions of new tools and even ephemeral ways of thinking and doing things almost require trade to develop in parallel with new lingustic modes of dissemination of new tools and culture.
Anthropologists can trace the development and dissemination of culture in a number of ways, and one of them is the way that different tools and technique appear and spread over time and place. Many of the sites producing data are relatively recent discoveries, yet another indicator of disruptive change. We now have so many well-educated specialists that all fields are accellerating as more trained field workers spread about the world and are recruited from more diverse places and cultures. However this capacity originated, once established, it feeds back and accellerates the pace of change. Language goes back to a number of our homonid ancestors although we can only speculate about the language use and cultural possibilities of extinct relatives. Some tools and material culture were alreacy present, but the record shows only very limited development over long histories before the recent period of accellerated growth.
Another aspect that none can ignore is the pace of change in digital technologies. Moore's law will not go on forever, but it has not bottomed out yet. This field was primative when I was born, and at a price that I built a kit computer in high school. Today's youth have what would have been a supercomputer then in the palm of their hands. This means that all the sciences can gather, store and process ever more data. We can also process the data in many ways that seem to magically extract knowledge and use learning processes to teach machines to do what used to require a human. The information technologies of speech, writing and numbers start the ball rolling and now it just shifted into a new much higher gear with a whole new set of gears we don't even know how to access yet.
This brief outline goes a long way to justifying the need for systems theory as a foundational component of any theory of everything (ToE). It should also make clear why any ToE is necessarily incomplete in some very deep ways. The formalities of theory can never fully capture the actuality of emegent systems of natural science. We have special sciences of each level of organization of reductionist models of natural s;ystem dynamics, and they can only be joined into a coherent picture with system theory. To develop a theory, we will need to define the elemental objects and their properties, but we must resist finally settling on particular definitions so that our theory will remain open to modified definitions that better match working practices. Ultimately this work should be grounded in pragmatic philosophy where knowledge is the result of experience in the practices in one or more fields of inquiry. This is also postmodernist in that no tradition is privileged and the truth will be multiple in the sense that some traditions will likely have conflicting truths. We can work to resolve such conflicts, but only by constructing spaces where meanings can be translated and considered outside any traditoin.
The success of the reductionist, objectivist epistemologies is that none can really seriously deny their import whenever their application is successful. The failure is to not recognize that this doesn't complete the picture. Systems theory can be used as a bridge. Understanding that Plato's eternal forms of mathematics are just that, patterns of relating that are independent of time, place and context, but that also leaves an enormous space for the contingent, historical or as the economists say, "path dependent". This is not only the path into the world for meaning and aesthetics, but it is the cure for self-importance. It could have been otherwise. The past does not fully determine the future. This is an informational property of the Universe, information can and is created and destroyed and that is the source of all asymetries in time and the difference between time an space.
I'd have to check this fully with the philosophical physicists, but if your theory has observation and the collapse of the wave function as real and significant to what exists, then information is created and destroyed in time. Therefore, nothing is time reversable, but it leaves open a lot more possibility of significant (meaningful) connections between past, present and future. Consciousness, if essentially quantum based, might be able to navigate time in some causal (intentional?) ways.
-> Integral because integration of parts into wholes is a more important distinction. Of course it is universal. Integral also good in that it refers to wholeness which ties to whole numbers, zero, one and the rest generated from relations of these two. 
Strong advocates of reductionism and in general philosophers of science who focus to closely on foundations, what is the most basic stuff that everything else is made of only consider analysis and require that emergent systems levels must be fully determined by the actions and elements of the foundational elements are making a huge error. It isn't just the kind of whole systems behavior observed in many simple dynamic system that exhibit complex emergent processes that are inherently unpredictable. That is one aspect of this principle, but more important is what it means for the behavioral aspects of living systems. The high level behavior of people in culture.
Principle of threes: refer to Peirce and his demonstrations that two elements are insufficient and any more complex can be build from them. {0, 1, (0, 1)} or maybe this way too: {, 0, 1} as nothing, none (of x) and some.
Minsky says: the evolution just forgets its mistakes, but I think we must trouble this claim. If an information system can save traces of what didn't work, then it can retain some ability to respond in yet anther way to stress or threat of extenction. Darwin and much after ignores the social aspects of information systems. What travels with what. It is sometimes said that most DNA coding seems to be just junk, random information that codes for nothing. By Turing and related proofs, you can't say anything like that. If you start asking how might it do that, and know how creative evolutionary search processes are, you would not say that anything is fogotten. Archived in the Akashic records outside of time and space.
Stuff vs. Structure: things, matter, fermions, patterns, energy, bosons: Everything has both aspects, and each phenomemal event bridges between them to the extent that we can't really separate them. The claim that the world is just mathematical, ideas says that it is just structure, no stuff, and in some ultimate sense this can be true. If you think the world is just a simulation, you don't believe in any reality, but if you go the other way you may be forced to believe (positively) in any reality or all possible reality. If we are truly a skeptic, we cannot take either of these as conclusive. Personally the latter is much more attractive and horrifying as well.
In physics: to get exact answer, you need infinite number of measurements by an infinitely large aperatus. This will be important for understanding systems and emergence.
Related is concept of using principles of minimizing the action. Implied in a sense that the particle knows where it is going so it can select its path. You have to have the start and end states to know it.
Difference between the system itself and the description of it. All the models for each subsystem and their relationships are also extracted from the world with experiments and measurements, always finite measurement with finite systems doing the measurements, therefore only partial precision and in fact the model itself and the system relations for emergent systems are underdetermined themselves. By this I mean that the models of the parts of the world involved in the measuring, the objects of study and the instruments and scientists are necessarily partial and tentative. This is just to say that the work is incomplete, but given the infinities involved in complete precision implied an even more radical incompleteness. The distance from the finite to the infinite is beyond any measure, and the complete model necessary to understand may be well off into the infinite reaches of very real possibility.
Arkani-Hamed at about 1:00 in he reduces all possible Feynman diagrams to combinations of two basic element which look remarkably like an icon for a triadic sign. A node with three edges with either a black or white node. The leaves are labelled labels, which must be just quantum states of simple standard model particles. So for interactions with more than three elements you can just do permutation at the leaves and sum up to get answers for complex Feynman diagrams. This math move actually makes it possible to calculate Feynman diagrams that are far to complex to manage even with the brightest graduate students and the biggest computers.
Leading up to this point he references the history of QM being emergent as a limit in the QM model and a more simple intuitive law that was derived classically. We are talking here about the equivalence of Schnell's law using refractive indexes and the method of minimizing action which is mathematically isomorphic to QM.
Gerald Joyce This work is brilliant on early evolution. Can we develop a language and logic of integral systems that supports this work? Work on autopeotics in systems biology is another aspect of the same thing. In the RNA work, you see several clear indications of the importance of concpets we are developing here. First, information is present but not fully accounted for in an end to end, or full cycle sense. Free energy is flowing through the system, mostly as triphosphates that are part of the individual nucleotide bases, the building blocks of the RNA chains. DNA are another building block for different chains, but that comes later in the story. Free energy is thermodynamic energy, from statistical mechanics, Boltzman, and we also have digital information in the one of four different bases that occur at each location in an RNA macromolecule, two bits per base, and DNA will have this same coding structure.
The rybosome is the cells machinery for making protiens, but it is embeddedd in a much more complex replecation system with many autocatalitic loops and feedback relationships throughout, but if you can show that significant parts and subunits of systems componets, in this case the rybosome, you are starting to demonstrate the plausability the living systems we see today emerging spontaneously over a long history of evolving forms. Joyce seems to have a hypothesis that a complete self-replicating life form based on RNA only would have to precede DNA/RNA life we see, but that may not be the case. In other words, he could be substantially right, but historically a fully autopoetic form of RNA/protein system may never  have completely emerged. Or, from another perspective, the DNA systems may have been there much earlier, side by side with the livelier and volitile RNA a more slowly evolving DNA system. They are already looking at cycles of information transfer from RNA to DNA and back again, and the question is only when does this become significant at the whole systems level. Maybe we need to think in terms of open loop and closed loop systems and replication.
He is asked about viruses, and I really wonder about his answer that there are just parasitic. One systems parasite is anothers mainstay. Margullis already showed us how multiple independent self-replicators must have joined forces to create the eukariotic cell, and this begs the question about when, if ever, the simple components would have been independently autopoetic. System boundaries imposed arbitrarily by analysis have no reality, only real barriers to flows of information, energy and macromolecules. Joyce and his colleagues are just studying a small part of the whole system. Given this picture, how can any given autopoetic organism be fully separated from the whole system, from Gaia. The whole planet is alive, not just the individual bits of it. The ego perspective is an illusion created by evolution to serve or autopoetic continuation. No gods are necessary to create this awsome mysterious place we find ourselves, our Garden of Eden. We are arrogant to think our small brains can comprehend it all, and should be content that we understand as much as we do. The old books are koans to spur our imaginations, not maps of the real world. Even Good and Evil are myths of perspective. What purposes are you aligned with? The sin of pride is to think we can know the difference. Even if we can, do we have the power of mind not to deceive ourselves and follow instinctive purpose and give a clever rationalization?
Speaking of systems, what about membranes and sugars? Photosynthesis is maybe way off as an organized system
Could the phenominal world be the equivalent of Leibniz' God? For some reason I have hesitated to dig into Leibniz Monadology as a bit of a reactionary implulse as we have in Newton's odd spiritual writings. I've suspected that maybe monads could be an elemental foundation of a deeper theory. Tim  Maudlin's thoughts about the meaning of QM and more, and the way his philosopic thoughts reach beyond the boundaries of physics in a clear thinking way are more the kind of metaphisical grounding that I find necessary for any competent philosophy is heartening, and this is what is guiding my inquiry at this point. https://www.youtube.com/watch?v=mJYgRRHL6_A Was helpful to get starting thinking about monads. I've long had an insight about the Pauli Exclusion principle, that it is very odd and deep. It must relate to the whole (emergent) vs. the parts (elements/parts at the next lower level) because it is a principle that says something about the quantum states of each part being necessarily different than all the other parts of the whole. Well, the formulations probably don't say whole and parts, but maybe that is fundamental. Plus a principle that any whole is another unique quantum state for the object emergent at the next level.
Hence, all atoms of a crystal, or a macromolecule or a simple molecule will be in a unique (micro)state with respect to any system of which it is a subpart. It begs the question of what makes a bag of parts a whole system, but perhaps this is discoverable with good experiments. The Pauli Exclusion seems a good equivalent for Leibniz' requirement that each monad of a system and therefore the universe must always be in a unique state. How could such a condition be understood accept as a decree of the God that is a necessary condition for the Universe to exist. If you get mathematical and think universally, the number of monads is the power set of all the fundamental subunits. This set is finite for a finite universe. The power set is also finite, but enormous. Two to the power of the number of standard model fermion parts (parts that Pauli excusion principle applies to). This principle allows for the sorts of large scale demonstrations using some variant of the pidgeon hole argument to predict Bolzman's brains in an infinite universe.
However, it may be the the continuum conceived of by Leibniz and taken up in his own way by Peirce are something that makes an important difference in the applicability of such arguments. We might also bring in George Elis and the consideration of the existence of absolute infinities and if potential infinities are enough for a continuum? Does this also once and for all answer Zeno and many paradoxes of infinities. Curiouser and curiouser the worm turns and clarity excapes us.
{\displaystyle \varnothing }