Congenital programs of the behavior and nontrivial quantum effects in the neurons work

Unsolved morphogenesis problems and the hidden order

In this work, the morphogenesis mechanisms are considered from the complexity perspective. It is shown that both morphogenesis and the functioning of organs should be unstable in the case of short-range interaction potentials. The repeatability of forms during evolution is a strong argument for its directionality. The formation of organs during evolution can occur only in the presence of a priori information about the structure of such an organ. The focus of the discussion is not merely on constraining potential possibilities but on the concept of directed evolution itself. A morphogenesis model was constructed based on nontrivial quantum effects. These interaction effects between biologically important molecules ensure the accurate synthesis of cells, tissues, and organs.

Thinking, holograms, and the quantum brain

This article continues the development of the idea that all human behavior and thinking are innate. A model of thinking and functioning of the brain has been constructed, which is capable of explaining both the accuracy of molecular processes and the innateness of behaviors. The focus of the model is the phase of the wave function of the particle, which is an additional (free) parameter. It should also be emphasized that the phase of the wave function of a particle is inextricably linked with the quantum action S in the Feynman's formulation of quantum mechanics (path integrals). A hypothesis is proposed: the set of particles that make up neurons and the brain is controlled by changing the phases from the outside (by a higher order system). Such a control system must be outside our world because our measurement methods do not allow us to determine the phase of an elementary particle. In a sense, it can be viewed as an extension of Bohm's ideas about the holographic brain and the holographic universe. Experiments are proposed that could confirm or disprove this model.

From leaves to roots: Biophysical models of transport of substances in plants

The transport processes of substances in various plant tissues are extremely diverse. However, models aimed at elucidating the mechanisms of such processes are almost absent in the literature. A unified view of all these transport processes is necessary, considering the laws of statistical physics and thermodynamics. A model of active ion transport was constructed based on the laws of statistical physics. Using this model, we traced the entire pathway of substances and energy in a plant. The pathway included aspects of the production of energy in the process of photosynthesis, consumption of energy to obtain nutrients from the soil, transport of such substances to the main organelles of all types of plant cells, the rise of water with dissolved substances along the trunk to the leaves, and the evaporation of water, accompanied by a change in the percentage of isotopes caused by different rates of evaporation. Models of ion transport in the chloroplasts and mitochondria of plant cells have been constructed. A generalized model comprising plant cells and their vacuoles was analyzed. A model of the transport of substances in the roots of plants was also developed. Based on this model, the problem of transport of substances in tall trees has been considered. The calculated concentrations of ions in the vacuoles of cells and resting potentials agreed well with the experimental data.

The Brain and the New Foundations of Mathematics

Many concepts in mathematics are not fully defined, and their properties are implicit, which leads to paradoxes. New foundations of mathematics were formulated based on the concept of innate programs of behavior and thinking. The basic axiom of mathematics is proposed, according to which any mathematical object has a physical carrier. This carrier can store and process only a finite amount of information. As a result of the D-procedure (encoding of any mathematical objects and operations on them in the form of qubits), a mathematical object is digitized. As a consequence, the basis of mathematics is the interaction of brain qubits, which can only implement arithmetic operations on numbers. A proof in mathematics is an algorithm for finding the correct statement from a list of already-existing statements. Some mathematical paradoxes (e.g., Banach–Tarski and Russell) and Smale’s 18th problem are solved by means of the D-procedure. The axiom of choice is a consequence of the equivalence of physical states, the choice among which can be made randomly. The proposed mathematics is constructive in the sense that any mathematical object exists if it is physically realized. The consistency of mathematics is due to directed evolution, which results in effective structures. Computing with qubits is based on the nontrivial quantum effects of biologically important molecules in neurons and the brain.

Intra- and intercellular transport of substances: Models and mechanisms

Non-equilibrium-statistical models of intracellular transport are built. The most significant features of these models are microscopic reversibility and the explicit considerations of the driving forces of the process - the ATP-ADP chemical potential difference. In this paper, water transport using contractile vacuoles, the transport and assembly of microtubules and microfilaments, the protein distribution within a cell, the transport of neurotransmitters from the synaptic cleft and the transport of substances between cells using plasmodesmata are discussed. Endocytosis and phagocytosis models are considered, and transport tasks and information transfer mechanisms inside the cell are explored. Based on an analysis of chloroplast movement, it was concluded that they have a complicated method of influencing each other in the course of their movements. The role of quantum effects in sorting and control transport mechanisms is also discussed. It is likely that quantum effects play a large role in these processes, otherwise reliable molecular recognition would be impossible, which would lead to very low intracellular transport efficiency.

The quantum basis of spatiotemporality in perception and consciousness

Living systems inhabit the area of the world which is shaped by the predictable space-time of physical objects and forces that can be incorporated into their perception pattern. The process of selecting a "habitable" space-time is the internal quantum measurement in which living systems become embedded into the environment that supports their living state. This means that living organisms choose a coordinate system in which the influence of measurement is minimal. We discuss specific roles of biological macromolecules, in particular of the cytoskeleton, in shaping perception patterns formed in the internal measurement process. Operation of neuron is based on the transmission of signals via cytoskeleton where the digital output is generated that can be decoded through a reflective action of the perceiving agent. It is concluded that the principle of optimality in biology as formulated by Liberman et al. (BioSystems 22, 135-154, 1989) is related to the establishment of spatiotemporal patterns that are maximally predictable and can hold the living state for a prolonged time. This is achieved by the selection of a habitable space approximated to the conditions described by classical physics.

Markov Chain-Like Quantum Biological Modeling of Mutations, Aging, and Evolution

Recent evidence suggests that quantum mechanics is relevant in photosynthesis, magnetoreception, enzymatic catalytic reactions, olfactory reception, photoreception, genetics, electron-transfer in proteins, and evolution; to mention few. In our recent paper published in Life, we have derived the operator-sum representation of a biological channel based on codon basekets, and determined the quantum channel model suitable for study of the quantum biological channel capacity. However, this model is essentially memoryless and it is not able to properly model the propagation of mutation errors in time, the process of aging, and evolution of genetic information through generations. To solve for these problems, we propose novel quantum mechanical models to accurately describe the process of creation spontaneous, induced, and adaptive mutations and their propagation in time. Different biological channel models with memory, proposed in this paper, include: (i) Markovian classical model, (ii) Markovian-like quantum model, and (iii) hybrid quantum-classical model. We then apply these models in a study of aging and evolution of quantum biological channel capacity through generations. We also discuss key differences of these models with respect to a multilevel symmetric channel-based Markovian model and a Kimura model-based Markovian process. These models are quite general and applicable to many open problems in biology, not only biological channel capacity, which is the main focus of the paper. We will show that the famous quantum Master equation approach, commonly used to describe different biological processes, is just the first-order approximation of the proposed quantum Markov chain-like model, when the observation interval tends to zero. One of the important implications of this model is that the aging phenotype becomes determined by different underlying transition probabilities in both programmed and random (damage) Markov chain-like models of aging, which are mutually coupled.

Nontrivial quantum and quantum-like effects in biosystems: Unsolved questions and paradoxes

Non-trivial quantum effects in biological systems are analyzed. Some unresolved issues and paradoxes related to quantum effects (Levinthal's paradox, the paradox of speed, and mechanisms of evolution) are addressed. It is concluded that the existence of non-trivial quantum effects is necessary for the functioning of living systems. In particular, it is demonstrated that classical mechanics cannot explain the stable work of the cell and any over-cell structures. The need for quantum effects is generated also by combinatorial problems of evolution. Their solution requires a priori information about the states of the evolving system, but within the framework of the classical theory it is not possible to explain mechanisms of its storage consistently. We also present essentials of so called quantum-like paradigm: sufficiently complex bio-systems process information by violating the laws of classical probability and information theory. Therefore the mathematical apparatus of quantum theory may have fruitful applications to describe behavior of bio-systems: from cells to brains, ecosystems and social systems. In quantum-like information biology it is not presumed that quantum information bio-processing is resulted from quantum physical processes in living organisms. Special experiments to test the role of quantum mechanics in living systems are suggested. This requires a detailed study of living systems on the level of individual atoms and molecules. Such monitoring of living systems in vivo can allow the identification of the real potentials of interaction between biologically important molecules.

Paradoxes of early stages of evolution of life and biological complexity

Two of the most fundamental questions concerning the origin of life, how biologically important molecules (RNA, proteins) find their unique spatial configuration, and how coding sequences can evolve beyond a certain critical length, are discussed. It is shown that both of these problems have not been solved. Experiments that could clarify the mechanisms of interaction between biologically important molecules in the simplest cells are discussed.

The problems of replication in the early stages of evolution: enumeration of variants and spatial configurations of replicators

Two main problems of replication in the early stages of evolution are discussed: the problem of exponentially large number of conformational degrees of freedom and the problem of enumeration of variants.