Categorical Ontology of Complex Systems, Meta-Systems and Theory of Levels: The Emergence of Life, Human Consciousness and Society

Single cell interactomics in simpler organisms, as well as somatic cell interactomics in multicellular organisms, involve biomolecular interactions in complex signalling pathways that were recently represented in modular terms by quantum automata with ‘reversible behavior’ representing normal cell cycling and division. Other implications of such quantum automata, modular modeling of signaling pathways and cell differentiation during development are in the fields of neural plasticity and brain development leading to quantum-weave dynamic patterns and specific molecular processes underlying extensive memory, learning, anticipation mechanisms and the emergence of human consciousness during the early brain development in children. Cell interactomics is here represented for the first time as a mixture of ‘classical’ states that determine molecular dynamics subject to Boltzmann statistics and ‘steady-state’, metabolic (multi-stable) manifolds, together with ‘configuration’ spaces of metastable quantum states emerging from complex quantum dynamics of interacting networks of biomolecules, such as proteins and nucleic acids that are now collectively defined as quantum interactomics. On the other hand, the time dependent evolution over several generations of cancer cells --that are generally known to undergo frequent and extensive genetic mutations and, indeed, suffer genomic transformations at the chromosome level (such as extensive chromosomal aberrations found in many colon cancers)-- cannot be correctly represented in the ‘standard’ terms of quantum automaton modules, as the normal somatic cells can. This significant difference at the cancer cell genomic level is therefore reflected in major changes in cancer cell interactomics often from one cancer cell ‘cycle’ to the next, and thus it requires substantial changes in the modeling strategies, mathematical tools and experimental designs aimed at understanding cancer mechanisms. Novel solutions to this important problem in carcinogenesis are proposed and experimental validation procedures are suggested. From a medical research and clinical standpoint, this approach has important consequences for addressing and preventing the development of cancer resistance to medical therapy in ongoing clinical trials involving stage III cancer patients, as well as improving the designs of future clinical trials for cancer treatments.\ud \ud \ud KEYWORDS: Emergence of Life and Human Consciousness;\ud Proteomics; Artificial Intelligence; Complex Systems Dynamics; Quantum Automata models and Quantum Interactomics; quantum-weave dynamic patterns underlying human consciousness; specific molecular processes underlying extensive memory, learning, anticipation mechanisms and human consciousness; emergence of human consciousness during the early brain development in children; Cancer cell ‘cycling’; interacting networks of proteins and nucleic acids; genetic mutations and chromosomal aberrations in cancers, such as colon cancer; development of cancer resistance to therapy; ongoing clinical trials involving stage III cancer patients’ possible improvements of the designs for future clinical trials and cancer treatments. \ud \u

From Simple to Complex and Ultra-complex Systems:\ud A Paradigm Shift Towards Non-Abelian Systems Dynamics

Atoms, molecules, organisms distinguish layers of reality because of the causal links that govern their behavior, both horizontally (atom-atom, molecule-molecule, organism-organism) and vertically (atom-molecule-organism). This is the first intuition of the theory of levels. Even if the further development of the theory will require imposing a number of qualifications to this initial intuition, the idea of a series of entities organized on different levels of complexity will prove correct. Living systems as well as social systems and the human mind present features remarkably different from those characterizing non-living, simple physical and chemical systems. We propose that super-complexity requires at least four different categorical frameworks, provided by the theories of levels of reality, chronotopoids, (generalized) interactions, and anticipation

From Simple to Complex and Ultra-complex Systems:\ud A Paradigm Shift Towards Non-Abelian Systems Dynamics

Atoms, molecules, organisms distinguish layers of reality because of the causal links that govern their behavior, both horizontally (atom-atom, molecule-molecule, organism-organism) and vertically (atom-molecule-organism). This is the first intuition of the theory of levels. Even if the further development of the theory will require imposing a number of qualifications to this initial intuition, the idea of a series of entities organized on different levels of complexity will prove correct. Living systems as well as social systems and the human mind present features remarkably different from those characterizing non-living, simple physical and chemical systems. We propose that super-complexity requires at least four different categorical frameworks, provided by the theories of levels of reality, chronotopoids, (generalized) interactions, and anticipation

Three-slit experiments and quantum nonlocality

An interesting link between two very different physical aspects of quantum mechanics is revealed; these are the absence of third-order interference and Tsirelson's bound for the nonlocal correlations. Considering multiple-slit experiments - not only the traditional configuration with two slits, but also configurations with three and more slits - Sorkin detected that third-order (and higher-order) interference is not possible in quantum mechanics. The EPR experiments show that quantum mechanics involves nonlocal correlations which are demonstrated in a violation of the Bell or CHSH inequality, but are still limited by a bound discovered by Tsirelson. It now turns out that Tsirelson's bound holds in a broad class of probabilistic theories provided that they rule out third-order interference. A major characteristic of this class is the existence of a reasonable calculus of conditional probability or, phrased more physically, of a reasonable model for the quantum measurement process.Comment: 9 pages, no figur

Barrel Shifter Physical Unclonable Function Based Encryption

Physical Unclonable Functions (PUFs) are circuits designed to extract physical randomness from the underlying circuit. This randomness depends on the manufacturing process. It differs for each device enabling chip-level authentication and key generation applications. We present a protocol utilizing a PUF for secure data transmission. Parties each have a PUF used for encryption and decryption; this is facilitated by constraining the PUF to be commutative. This framework is evaluated with a primitive permutation network - a barrel shifter. Physical randomness is derived from the delay of different shift paths. Barrel shifter (BS) PUF captures the delay of different shift paths. This delay is entangled with message bits before they are sent across an insecure channel. BS-PUF is implemented using transmission gates; their characteristics ensure same-chip reproducibility, a necessary property of PUFs. Post-layout simulations of a common centroid layout 8-level barrel shifter in 0.13 {\mu}m technology assess uniqueness, stability and randomness properties. BS-PUFs pass all selected NIST statistical randomness tests. Stability similar to Ring Oscillator (RO) PUFs under environment variation is shown. Logistic regression of 100,000 plaintext-ciphertext pairs (PCPs) failed to successfully model BS- PUF behavior