Quantum Genetics and Quantum Automata Models of Quantum-Molecular Evolution Involved in the Evolution of Organisms and Species

Previous theoretical or general approaches to the problems of Quantum Genetics and Molecular Evolution are considered in this article from the point of view of Quantum Automata Theory first published by the author in 1971 and further developed in several recent articles. The representation of genomes and Interactome networks in categories of many-valued logic LMn –algebras that are naturally transformed during biological evolution, or evolve through interactions with the environment provide a new insight into the mechanisms of molecular evolution, as well as organismal evolution, in terms of sequences of quantum automata. Phenotypic changes are expressed only when certain environmentally-induced quantum-molecular changes are coupled with an internal re-structuring of major submodules of the genome and Interactome networks related to cell cycling and cell growth. Contrary to the commonly held view of `standard’ Darwinist models of evolution, the evolution of organisms and species occurs through coupled multi-molecular transformations induced not only by the environment but actually realized through internal re-organizations of genome and interactome networks. The biological, evolutionary processes involve certain epigenetic transformations that are responsible for phenotypic expression of the genome and Interactome transformations initiated at the quantum-molecular level. It can thus be said that only quantum genetics can provide correct explanations of evolutionary processes that are initiated at the quantum--multi-molecular levels and propagate to the higher levels of organismal and species evolution.

Biological evolution should be therefore regarded as a multi-scale process which is initiated by underlying quantum (coupled) multi-molecular transformations of the genomic and interactomic networks, followed by specific phenotypic transformations at the level of organism and the variable biogroupoids associated with the evolution of species which are essential to the survival of the species. The theoretical framework introduced in this article also paves the way to a Quantitative Biology approach to biological evolution at the quantum-molecular, as well as at the organismal and species levels. This is quite a substantial modification of the 'established’ modern Darwinist, and also of several so-called `molecular evolution’ theories

Quantum Genetics, Quantum Automata and Quantum Computation

The concepts of quantum automata and quantum computation are studied in the context of quantum genetics and genetic networks with nonlinear dynamics. In a previous publication (Baianu,1971a) the formal concept of quantum automaton was introduced and its possible implications for genetic and metabolic activities in living cells and organisms were considered. This was followed by a report on quantum and abstract, symbolic computation based on the theory of categories, functors and natural transformations (Baianu,1971b). The notions of topological semigroup, quantum automaton,or quantum computer, were then suggested with a view to their potential applications to the analogous simulation of biological systems, and especially genetic activities and nonlinear dynamics in genetic networks. Further, detailed studies of nonlinear dynamics in genetic networks were carried out in categories of n-valued, Lukasiewicz Logic Algebras that showed significant dissimilarities (Baianu, 1977) from Bolean models of human neural networks (McCullough and Pitts,1945). Molecular models in terms of categories, functors and natural transformations were then formulated for uni-molecular chemical transformations, multi-molecular chemical and biochemical transformations (Baianu, 1983,2004a). Previous applications of computer modeling, classical automata theory, and relational biology to molecular biology, oncogenesis and medicine were extensively reviewed and several important conclusions were reached regarding both the potential and limitations of the computation-assisted modeling of biological systems, and especially complex organisms such as Homo sapiens sapiens(Baianu,1987). Novel approaches to solving the realization problems of Relational Biology models in Complex System Biology are introduced in terms of natural transformations between functors of such molecular categories. Several applications of such natural transformations of functors were then presented to protein biosynthesis, embryogenesis and nuclear transplant experiments. Other possible realizations in Molecular Biology and Relational Biology of Organisms are here suggested in terms of quantum automata models of Quantum Genetics and Interactomics. Future developments of this novel approach are likely to also include: Fuzzy Relations in Biology and Epigenomics, Relational Biology modeling of Complex Immunological and Hormonal regulatory systems, n-categories and Topoi of Lukasiewicz Logic Algebras and Intuitionistic Logic (Heyting) Algebras for modeling nonlinear dynamics and cognitive processes in complex neural networks that are present in the human brain, as well as stochastic modeling of genetic networks in Lukasiewicz Logic Algebras

Łukasiewicz-Moisil Many-Valued Logic Algebra of Highly-Complex Systems

A novel approach to self-organizing, highly-complex systems (HCS), such as living organisms and artificial intelligent systems (AIs), is presented which is relevant to Cognition, Medical Bioinformatics and Computational Neuroscience. Quantum Automata (QAs) were defined in our previous work as generalized, probabilistic automata with quantum state spaces (Baianu, 1971). Their next-state functions operate through transitions between quantum states defined by the quantum equations of motion in the Schroedinger representation, with both initial and boundary conditions in space-time. Such quantum automata operate with a quantum logic, or Q-logic, significantly different from either Boolean or Łukasiewicz many-valued logic. A new theorem is proposed which states that the category of quantum automata and automata--homomorphisms has both limits and colimits. Therefore, both categories of quantum automata and classical automata (sequential machines) are bicomplete. A second new theorem establishes that the standard automata category is a subcategory of the quantum automata category. The quantum automata category has a faithful representation in the category of Generalized (M,R)--Systems which are open, dynamic biosystem networks with defined biological relations that represent physiological functions of primordial organisms, single cells and higher organisms

Degree of Sequentiality of Weighted Automata

Weighted automata (WA) are an important formalism to describe quantitative properties. Obtaining equivalent deterministic machines is a longstanding research problem. In this paper we consider WA with a set semantics, meaning that the semantics is given by the set of weights of accepting runs. We focus on multi-sequential WA that are defined as finite unions of sequential WA. The problem we address is to minimize the size of this union. We call this minimum the degree of sequentiality of (the relation realized by) the WA. For a given positive integer k, we provide multiple characterizations of relations realized by a union of k sequential WA over an infinitary finitely generated group: a Lipschitz-like machine independent property, a pattern on the automaton (a new twinning property) and a subclass of cost register automata. When possible, we effectively translate a WA into an equivalent union of k sequential WA. We also provide a decision procedure for our twinning property for commutative computable groups thus allowing to compute the degree of sequentiality. Last, we show that these results also hold for word transducers and that the associated decision problem is PSPACE -complete

Applications of Automata and Graphs: Labeling-Operators in Hilbert Space I

We show that certain representations of graphs by operators on Hilbert space have uses in signal processing and in symbolic dynamics. Our main result is that graphs built on automata have fractal characteristics. We make this precise with the use of Representation Theory and of Spectral Theory of a certain family of Hecke operators. Let G be a directed graph. We begin by building the graph groupoid G induced by G, and representations of G. Our main application is to the groupoids defined from automata. By assigning weights to the edges of a fixed graph G, we give conditions for G to acquire fractal-like properties, and hence we can have fractaloids or G-fractals. Our standing assumption on G is that it is locally finite and connected, and our labeling of G is determined by the "out-degrees of vertices". From our labeling, we arrive at a family of Hecke-type operators whose spectrum is computed. As applications, we are able to build representations by operators on Hilbert spaces (including the Hecke operators); and we further show that automata built on a finite alphabet generate fractaloids. Our Hecke-type operators, or labeling operators, come from an amalgamated free probability construction, and we compute the corresponding amalgamated free moments. We show that the free moments are completely determined by certain scalar-valued functions.Comment: 69 page