Quantum information and the problem of mechanisms of biological evolution

Progressive evolution of plants: A critical review

A comprehensive review of the evolutionary mechanisms in plants has been performed. This review examines fundamental questions regarding plant evolution, including the development of sexes, convergent characteristics, and neutral effects in plant ecosystems. The available evidence suggests that plant evolution is not a random process, as previously hypothesized. Instead, a substantial body of evidence points to the existence of directed and predictable patterns in plant evolution, applicable not only to plants but also to other organisms. The concept of directed evolution is explored in the context of plant biology.

Quantum Health Accelerator® Ameliorates CFA-Induced Animal Model of Rheumatoid Arthritis: Investigating the Role of Immunomodulatory and Anti-Oxidative Effects

Introduction: Rheumatoid arthritis (RA) is a systemic inflammatory and autoimmune disease characterized by joint swelling, pain, damage to the cartilage, and disability. In the present study, we aimed to evaluate the anti-oxidant, anti-inflammatory, and immune-modulatory properties of Quantum Health Accelerator® as water enriched with vital bio-quantum information/energy (EW) following complete Freund's adjuvant (CFA)-induced RA in rats. Methods: Forty adult male Wistar rats (180-220 g) were divided into five groups. Arthritis was induced on day one using a single subcutaneous injection of CFA into the left hind footpad of the rat. Rats were assigned to receive methotrexate (MTX, 2 mg/kg/week, intraperitoneally), EW (orally, instead of normal water ad libitum), or their combination for 29 days. The anti-RA activities were determined by paw edema, joint diameter, arthritis score, and several nociceptive behavioral tests (thermal hyperalgesia, cold allodynia, and tactile allodynia). The levels of inflammatory (TNF-α, CRP, RF, and anti-CCP), anti-inflammatory (IL-10), and oxidative stress (NO, MDA, and GSH) markers were measured in serum. In addition, the levels of IFN-γ, IL-4, IL-17, and TGF-β were assessed in the spleen-isolated lymphocytes. Results: We found that treatment with MTX, EW, and their combination remarkably ameliorated thermal hyperalgesia, cold allodynia, and tactile allodynia results following CFA-induced RA in rats. In addition, EW also notably attenuated arthritis score, joint diameter, inflammatory cytokines, and oxidative markers while propagating anti-inflammatory and anti-oxidative mediators. Conclusions: We reveal that EW possesses anti-arthritic effects, possibly through anti-oxidative, anti-inflammatory, and immunomodulatory properties. Collectively, EW may be a promising therapeutic agent for treating RA.

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.

Aging and group selection: New arguments in favor of partially directed evolution

In this study, theories of aging and its mechanisms under various environmental conditions were analyzed. The analysis of published data suggested that aging is a controlled process. It is known that many mathematical algorithms utilize an analogy of aging. However, this is possible only when a "target set" is known in advance. Various forms of selection in relation to aging were analyzed both collectively and separately. The general conclusion is that aging is one of the mechanisms of directed evolution. A model was constructed, which shows how aging is integrated into partially directed evolution.

Mutations, sex, and genetic diversity: New arguments for partially directed evolution

A review of the theories of the existence of sexes, genetic diversity, and the distribution of mutations among organisms shows that all these concepts are not a product of random evolution and cannot be explained within the framework of Darwinism. Most mutations are the result of the genome acting on itself. This is an organized process that is implemented very differently in different species, in different places in the genome. Because of the fact that it is not random, this process must be directed and regulated, albeit with complex and not fully understood laws. This means that an additional reason must be included in order to model such mutations during evolution. The assumption of directionality must not only be explicitly included in evolutionary theory but must also occupy a central place in it. In this study an updated model of partially directed evolution is constructed, which is capable of qualitatively explaining the indicated features of evolution. Experiments are described that can confirm or disprove the proposed model.

Quantum-like Data Modeling in Applied Sciences: Review

This work presents a brief review on the modern approaches to data modeling by the methods developed in the quantum physics during the last one hundred years. Quantum computers and computations have already been widely investigated theoretically and attempted in some practical implementations, but methods of quantum data modeling are not yet sufficiently established. A vast range of concepts and methods of quantum mechanics have been tried in many fields of information and behavior sciences, including communications and artificial intelligence, cognition and decision making, sociology and psychology, biology and economics, financial and political studies. The application of quantum methods in areas other than physics is called the quantum-like paradigm, meaning that such approaches may not be related to the physical processes but rather correspond to data modeling by the methods designed for operating in conditions of uncertainty. This review aims to attract attention to the possibilities of these methods of data modeling that can enrich theoretical consideration and be useful for practical purposes in various sciences and applications.

Viruses, immunity and evolution

In this article, the evolution of viruses is analyzed in terms of their complexity. It is shown that the evolution of viruses is a partially directed process. The participation of viruses and mobile genetic elements in the evolution of other organisms by integration into the genome is also an a priori directed process. The high variability of genomes (including the genes of antibodies), which differs by orders of magnitude for various viruses and their hosts, is not a random process but is the result of the action of a molecular genetic control system. Herein, a model of partially directed evolution of viruses is proposed. Throughout the life cycle of viruses, there is an interaction of complex biologically important molecules that cannot be explained on the basis of classic laws. The interaction of a virus with a cell is essentially a quantum event, including selective long-range action. Such an interaction can be interpreted as the "remote key-lock" principle. In this article, a model of the interaction of biologically important viral molecules with cellular molecules based on nontrivial quantum interactions is proposed. Experiments to test the model are also proposed.

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.

Chirality: The Backbone of Chemistry as a Natural Science

Chemistry as a natural science occupies the length and temporal scales ranging between the formation of atoms and molecules as quasi-classical objects, and the formation of proto-life systems showing catalytic synthesis, replication, and the capacity for Darwinian evolution. The role of chiral dissymmetry in the chemical evolution toward life is manifested in how the increase of chemical complexity, from atoms and molecules to complex open systems, accompanies the emergence of biological homochirality toward life. Chemistry should express chirality not only as molecular structural dissymmetry that at the present is described in chemical curricula by quite effective pedagogical arguments, but also as a cosmological phenomenon. This relates to a necessarily better understanding of the boundaries of chemistry with physics and biology.

Outline of a unified Darwinian evolutionary theory for physical and biological systems

The scheme of a unified Darwinian evolutionary theory for physical and biological systems is described. Every physical system is methodologically endowed with a classical information processor, which turns every system into an agent being also susceptible to evolution. Biological systems retain this structure as natural extensions of physical systems from which they are built up. Optimization of information flows turns out to be the key element to study the possible emergence of quantum behavior and the unified Darwinian description of physical and biological systems. The Darwinian natural selection scheme is completed by the Lamarckian component in the form of the anticipation of states of surrounding bio-physical systems.

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.