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

Emerging solutions from the battle of defensive alliances

Competing strategies in an evolutionary game model, or species in a biosystem, can easily form a larger unit which protects them from the invasion of an external actor. Such a defensive alliance may have two, three, four or even more members. But how effective can be such formation against an alternative group composed by other competitors? To address this question we study a minimal model where a two-member and a four-member alliances fight in a symmetric and balanced way. By presenting representative phase diagrams, we systematically explore the whole parameter range which characterizes the inner dynamics of the alliances and the intensity of their interactions. The group formed by a pair, who can exchange their neighboring positions, prevail in the majority of the parameter region. The rival quartet can only win if their inner cyclic invasion rate is significant while the mixing rate of the pair is extremely low. At specific parameter values, when neither of the alliances is strong enough, new four-member solutions emerge where a rock-paper-scissors-like trio is extended by the other member of the pair. These new solutions coexist hence all six competitors can survive. The evolutionary process is accompanied by serious finite-size effects which can be mitigated by appropriately chosen prepared initial states.Comment: 11 pages, 8 figures, accepted for publication in Scientific Report

Interference competition and invasion: spatial structure, novel weapons and resistance zones

Certain invasive plants may rely on interference mechanisms (allelopathy, e.g.) to gain competitive superiority over native species. But expending resources on interference presumably exacts a cost in another life-history trait, so that the significance of interference competition for invasion ecology remains uncertain. We model ecological invasion when combined effects of preemptive and interference competition govern interactions at the neighborhood scale. We consider three cases. Under "novel weapons," only the initially rare invader exercises interference. For "resistance zones" only the resident species interferes, and finally we take both species as interference competitors. Interference increases the other species' mortality, opening space for colonization. However, a species exercising greater interference has reduced propagation, which can hinder its colonization of open sites. Interference never enhances a rare invader's growth in the homogeneously mixing approximation to our model. But interference can significantly increase an invader's competitiveness, and its growth when rare, if interactions are structured spatially. That is, interference can increase an invader's success when colonization of open sites depends on local, rather than global, species densities. In contrast, interference enhances the common, resident species' resistance to invasion independently of spatial structure, unless the propagation-cost is too great. Increases in background mortality (i.e., mortality not due to interference) always reduce the effectiveness of interference competition

Rhythms and Evolution: Effects of Timing on Survival

The evolution of metabolism regulation is an intertwined process, where different strategies are constantly being developed towards a cognitive ability to perceive and respond to an environment. Organisms depend on an orchestration of a complex set of chemical reactions: maintaining homeostasis with a changing environment, while simultaneously sending material and energetic resources to where they are needed. The success of an organism requires efficient metabolic regulation, highlighting the connection between evolution, population dynamics and the underlying biochemistry. In this work, I represent organisms as coupled information-processing networks, that is, gene-regulatory networks receiving signals from the environment and acting on chemical reactions, eventually affecting material flows. I discuss the mechanisms through which metabolism control is improved during evolution and how the nonlinearities of competition influence this solution-searching process. The propagation of the populations through the resulting landscapes generally point to the role of the rhythm of cell division as an essential phenotypic feature driving evolution. Subsequently, as it naturally follows, different representations of organisms as oscillators are constructed to indicate more precisely how the interplay between competition, maturation timing and cell-division synchronisation affects the expected evolutionary outcomes, not always leading to the \"survival of the fastest\"

Competitive exclusion and Hebbian couplings in random generalised Lotka-Volterra systems

We study communities emerging from generalised random Lotka--Volterra dynamics with a large number of species with interactions determined by the degree of niche overlap. Each species is endowed with a number of traits, and competition between pairs of species increases with their similarity in trait space. This leads to a model with random Hopfield-like interactions. We use tools from the theory of disordered systems, notably dynamic mean field theory, to characterise the statistics of the resulting communities at stable fixed points and determine analytically when stability breaks down. Two distinct types of transition are identified in this way, both marked by diverging abundances, but differing in the behaviour of the integrated response function. At fixed points only a fraction of the initial pool of species survives. We numerically study the eigenvalue spectra of the interaction matrix between extant species. We find evidence that the two types of dynamical transition are, respectively, associated with the bulk spectrum or an outlier eigenvalue crossing into the right half of the complex plane.Comment: 14 pages, 9 figures + Supplemen

Embodied creativity: a process continuum from artistic creation to creative participation

This thesis breaks new ground by attending to two contemporary developments in art and science. In art, computer-mediated interactive artworks comprise creative engagement between collaborating practitioners and a creatively participating audience, erasing all notions of a dividing line between them. The procedural character of this type of communicative real-time interaction replaces the concept of a finished artwork with a ‘field of artistic communication’. In science, the field of creativity research investigates creative thought as mental operations that combine and reorganise extant knowledge structures. A recent paradigm shift in cognition research acknowledges that cognition is embodied. Neither embodiment in cognition nor the ‘field of artistic communication’ in interactive art have been assimilated by creativity research. This thesis takes an interdisciplinary approach to examine the embodied cognitive processes in a ‘field of artistic communication’ using a media artwork called Sim-Suite as a case study research strategy. This interactive installation, created and exhibited in an authentic real-world context, engages three people to play on wobble-boards. The thesis argues that creative processes related to Sim-Suite operate within a continuum, encompassing collaborative artistic creation and cooperative creative participation. This continuum is investigated via mixed methods, conducting studies with qualitative and quantitative analysis. These are interpreted through a theoretical lens of embodied cognition principles, the 4E approaches. The results obtained demonstrate that embodied cognitive processes in Sim-Suite’s ‘field of artistic communication’ function on a continuum. We give an account of the creative process continuum relating our findings to the ‘embedded-extended-enactive lens’, empirical studies in embodied cognition and creativity research. Within this context a number of topics and sub-themes are identified. We discuss embodied communication, aspects of agency, forms of coordination, levels of evaluative processes and empathetic foundation. The thesis makes conceptual, empirical and methodological contributions to creativity research

The ornamentation of Brunelleschi\u27s Old Sacristy of San Lorenzo in Florence

The Old Sacristy of San Lorenzo in Florence, Italy, was constructed during the years 1419-1428 and is considered one of the most influential buildings of the early Italian Renaissance. Brunelleschi\u27s Old Sacristy, in its original design, was pristine and void of the architectural ornamentation that had come to characterize so many buildings that preceded it and which would come to be associated with the sacristy itself on account of later alterations. Indeed, the original sacristy was characterized by a purely articulated space free of additional ornamentation to the architecture. However, shortly after the termination of construction, the Old Sacristy became a battleground for new and evolving notions concerning the ornamentation of sacred spaces. A veritable who\u27s who of early Quattrocento Florence including the architect Filippo Brunelleschi, the sculptor Donatello, and the wealthy and increasingly powerful Medici family took a stand. Although, the initial lack of ornamentation has been researched, scholarship thus far neglected to fully explain the decision to profoundly alter the ornamentation of the original space. This thesis interprets and evaluates the research that has been done on the Old Sacristy and, in turn, offers an explanation for the current arrangement of architectural ornamentation in light of both aesthetic considerations and patronage

Nonlocal Models in Biology and Life Sciences: Sources, Developments, and Applications

Nonlocality is important in realistic mathematical models of physical and biological systems at small-length scales. It characterizes the properties of two individuals located in different locations. This review illustrates different nonlocal mathematical models applied to biology and life sciences. The major focus has been given to sources, developments, and applications of such models. Among other things, a systematic discussion has been provided for the conditions of pattern formations in biological systems of population dynamics. Special attention has also been given to nonlocal interactions on networks, network coupling and integration, including models for brain dynamics that provide us with an important tool to better understand neurodegenerative diseases. In addition, we have discussed nonlocal modelling approaches for cancer stem cells and tumor cells that are widely applied in the cell migration processes, growth, and avascular tumors in any organ. Furthermore, the discussed nonlocal continuum models can go sufficiently smaller scales applied to nanotechnology to build biosensors to sense biomaterial and its concentration. Piezoelectric and other smart materials are among them, and these devices are becoming increasingly important in the digital and physical world that is intrinsically interconnected with biological systems. Additionally, we have reviewed a nonlocal theory of peridynamics, which deals with continuous and discrete media and applies to model the relationship between fracture and healing in cortical bone, tissue growth and shrinkage, and other areas increasingly important in biomedical and bioengineering applications. Finally, we provided a comprehensive summary of emerging trends and highlighted future directions in this rapidly expanding field.Comment: 71 page