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

Category theory for scientists (Old version)

There are many books designed to introduce category theory to either a mathematical audience or a computer science audience. In this book, our audience is the broader scientific community. We attempt to show that category theory can be applied throughout the sciences as a framework for modeling phenomena and communicating results. In order to target the scientific audience, this book is example-based rather than proof-based. For example, monoids are framed in terms of agents acting on objects, sheaves are introduced with primary examples coming from geography, and colored operads are discussed in terms of their ability to model self-similarity. A new version with solutions to exercises will be available through MIT Press.Comment: 267 pages, 5 chapters, 280 exercises, an index. This book was written as course notes for a special subjects Math class at MIT called "18-S996: Category Theory for scientists", taught in Spring 2013. The class had a diverse enrollment: At the end, the number of registered students was 18 = 7 undergrad + 11 grad = 5 math + 4 EECS + 3 physics + 3 engineering + 3 othe

Applications of Category Theory to Programming and Program Specification

Category theory is proving a useful tool in programming and program specification - not only as a descriptive language but as directly applicable to programming and specification tasks. Category theory achieves a level of generality of description at which computation is still possible. We show that theorems from category theory often have constructive proofs in the sense that they may be encoded as programs. In particular we look at the computation of colimits in categories showing that general theorems give rise to routines which considerably simplify the rather awkward computation of colimits. The general routines arising from categorical constructions can be used to build programs in the 'combinatorial' style of programming. We show this with an example - a program to implement the semantics of a specification language. More importantly, the intimate relationship between these routines and algebraic specifications allows us to develop programs from certain forms of specifications. Later we turn to algebraic specifications themselves and look at properties of "monadic theories". We establish that, under suitable conditions: 1. Signatures and presentations may be defined for monadic theories and free theories on a signature may be constructed. 2. Theory morphisms give rise to ad junctions between categories of algebras and moreover a collection of algebras of a theory give rise to a new theory with certain properties. 3. Finite colimits and certain factorisations exist in categories of monadic theories. 4. Many-sorted, order-sorted and even category-sorted theories may be handled by somewhat extending the notion of monadic theories. These results show that monadic theories are sufficiently well-behaved to be used in the semantics of algebraic specification languages. Some of the constructions can be encoded as programs by the techniques mentioned above

Components as coalgebras

In the tradition of mathematical modelling in physics and chemistry, constructive formal specification methods are based on the notion of a software model, understood as a state-based abstract machine which persists and evolves in time, according to a behavioural model capturing, for example, partiality or (different degrees of) nondeterminism. This can be identified with the more prosaic notion of a software component advocated by the software industry as ‘building block’ of large, often distributed, systems. Such a component typically encapsulates a number of services through a public interface which provides a limited access to a private state space, paying tribute to the nowadays widespread object-oriented programming principles. The tradition of communicating systems formal design, by contrast, has developed the notion of a process as an abstraction of the behavioural patterns of a computing system, deliberately ignoring the data and state aspects of software systems. Both processes and components are among the broad group of computing phenomena which are hardly definable (or simply not definable) algebraically, i.e., in terms of a complete set of constructors. Their semantics is essentially observational, in the sense that all that can be traced of their evolution is their interaction with the environment. Therefore, coalgebras, whose theory has recently witnessed remarkable developments, appear as a suitable modelling tool. The basic observation of category theory that universal constructions always come in pairs, has motivated research on the duality between algebras and coalgebras, which provides a bridge between models of static (constructive, data-oriented) and dynamical (observational, behaviour-oriented) systems. At the programming level, the intuitive symmetry between data and behaviour provides evidence of such a duality, in its canonical initial-final specialisation. This line of thought entails both definitional and proof principles, i.e., a basis for the development of program calculi directly based on (actually driven by) type specifications. Moreover, such properties can be expressed in terms of generic programming combinators which are used, not only to calculate programs, but also to program with. Framed in this context, this thesis addresses the following main themes: The investigation of a semantic model for (state-based) software components. These are regarded as concrete coalgebras for some Set endofunctors, with specified initial conditions, and organise themselves in a bicategorical setting. The model is able to capture both behavioural issues, which are usually left implicit in state-based specification methods, and interaction through structured data, which is usually a minor concern on process calculi. Two basic cases are considered entailing, respectively, a ‘functional’ and an ‘object-oriented’ shape for components. Both cases are parametrized by a model of behaviour, introduced as a strong (usually commutative) monad. The development of corresponding component calculi, also parametric on the behaviour model, which adds to the genericity of the approach. The study of processes and the ‘reconstruction’ of classical (CCS-like) process calculi on top of their representation as inhabitants of (the carriers of) final coalgebras, in an essentially pointfree, calculational style. An overall concern for genericity, in the sense that models and calculi for both components and processes are parametric on the behaviour model and the interaction discipline, respectively. The animation of both processes and components in CHARITY, a functional programming language entirely based on inductive and coinductive categorical data types. In particular this leads to the development of a process calculi interpreter parametric on the interaction discipline.PRAXIS XXI - Projecto LOGCAMP; POO11/IC-PME/II/S -Projecto KARMA; Fundação para a Ciência e Tecnologia; ALGORITMI Research Center