Quantum-like model of partially directed evolution

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.

Semantic parsing of the life process by quantum biology

A fact that an ever-increasingly number of research attention has focused on quantum biology demonstrates that it is, by no means, new to works in physic and mathematics, but to molecular biologists, geneticists, and biochemists. This is owing to that quantum biology serves as a distinctive discipline, by using quantum theory to study life sciences in combination with physics, mechanics, mathematics, statistics, and modern biology. Notably, quantum mechanics and its fundamental principles have been employed to clarify complex biological processes and molecular homeostasis within the organic life. Consequently, using the principles of quantum mechanics to study dynamic changes and energy transfer of molecules at the quantum level in biology has been accepted as an unusually distinguishable way to a better explanation of many phenomena in life. It is plausible that a clear conceptual quantum theoretical event is also considered to generally occur for short-term picoseconds or femtoseconds on microscopic nano- and subnanometer scales in biology and biosciences. For instance, photosynthesis, enzyme -catalyzed reactions, magnetic perception, the capture of smell and vision, DNA fragmentation, cellular breathing, mitochondrial processing, as well as brain thinking and consciousness, are all manifested within quantum superposition, quantum coherence, quantum entanglement, quantum tunneling, and other effects. In this mini-review, we describe the recent progress in quantum biology, with a promising direction for further insights into this field.

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.

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.