Does quantum mechanics play a non-trivial role in life?

Phase coherent quasi-particle formation in biological systems

The problem of the origin of canonical and aberrant DNA mutations and the contribution of protons to genetic stability is an essential topic in molecular biology. Based on the empirical results, we reconsidered canonical and tautomeric mutations under the two-fluid model of quantum physics. We assumed that the pressure exerted by protons (H+) in the DNA environment, through changes in pH, could alter the concentration ratio of canonical and tautomeric base pairs, which were found to be different at and beyond the criticality level, respectively. We anticipate that the deviation of the cellular system from a specific (critical) temperature at which dynamic entropy reaches a minimum and a critical pH occurs could result in tautomerization and point mutations.

Ribonucleic acid genome mutations induced by the Casimir effect

In this paper, we investigate the Casimir effect within a virus RNA, particularizing the study to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Then, we discuss the possibility of occurring damage or mutation in its genome due to the presence of quantum vacuum fluctuations inside and around the RNA ribbon. For this, we consider the geometry and the nontrivial topology of the viral RNA as having a simple helical structure. We initially compute the non-thermal Casimir energy associated to that geometry, considering boundary conditions that constrain the zero point oscillations of a massless scalar field to the cylindrical cavity containing a helix pitch of RNA ribbon. Then we extend the obtained result to the electromagnetic field and, following, we calculate the probability of occurring damage or mutation in RNA by using the normalized inverse exponential distribution, which suppresses very low energies, and consider cutoff (threshold) energies corresponding to UV-A and UV-C rays, surely responsible by mutations. Then, by taking into account UV-A, we arrive at a mutation rate per base per infection cycle, which in the case of the SARS-CoV-2 is non-negligible. We find a maximum value of this mutation rate for an RNA ribbon radius, applying it for SARS-CoV-2, in particular. We also calculate a characteristic longitudinal oscillation frequency for the helix pitch value corresponding to the local minimum of the Casimir energy. Finally, we consider thermal fluctuations of classical and quantum nature and show that the corresponding probability of mutation is completely negligible for that virus. Therefore, we conclude that only the nontrivial topology and the geometric attributes of the RNA molecule contribute to the possible mutations caused by quantum vacuum fluctuations in the viral genome.

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.

A free energy principle for generic quantum systems

The Free Energy Principle (FEP) states that under suitable conditions of weak coupling, random dynamical systems with sufficient degrees of freedom will behave so as to minimize an upper bound, formalized as a variational free energy, on surprisal (a.k.a., self-information). This upper bound can be read as a Bayesian prediction error. Equivalently, its negative is a lower bound on Bayesian model evidence (a.k.a., marginal likelihood). In short, certain random dynamical systems evince a kind of self-evidencing. Here, we reformulate the FEP in the formal setting of spacetime-background free, scale-free quantum information theory. We show how generic quantum systems can be regarded as observers, which with the standard freedom of choice assumption become agents capable of assigning semantics to observational outcomes. We show how such agents minimize Bayesian prediction error in environments characterized by uncertainty, insufficient learning, and quantum contextuality. We show that in its quantum-theoretic formulation, the FEP is asymptotically equivalent to the Principle of Unitarity. Based on these results, we suggest that biological systems employ quantum coherence as a computational resource and - implicitly - as a communication resource. We summarize a number of problems for future research, particularly involving the resources required for classical communication and for detecting and responding to quantum context switches.

Finding or Creating a Living Organism? Past and Future Thought Experiments in Astrobiology Applied to Artificial Intelligence

This is a digest of how various researchers in biology and astrobiology have explored questions of what defines living organisms-definitions based on functions or structures observed in organisms, or on systems terms, or on mathematical conceptions like closure, chirality, quantum mechanics and thermodynamics, or on biosemiotics, or on Darwinian evolution-to clarify the field and make it easier for endeavors in artificial intelligence to make progress. Current ideas are described to promote work between astrobiologists and computer scientists, each concerned with living organisms. A four-parameter framework is presented as a scaffold that is later developed into what machines lack to be considered alive: systems, evolution, energy and consciousness, and includes Jagers operators and the idea of dual closure. A novel definition of consciousness is developed which describes mental objects both with and without communicable properties, and this helps to clarify how consciousness in machines may be studied as an emergent process related to choice functions in systems. A perspective on how quantization, acting on nucleic acids, sets up natural limits to system behavior is offered as a partial address to the problem of biogenesis.

An integrated perspective on transmutation of acute inflammation into chronic and the role of the microbiome

The Continuum theory and the Levels of Health theory were separately proposed to explain the myriad responses to treatment and understand the process of health and disease in an individual. In light of accumulating evidence on the intricate relationship between the human immune system and microbiome, an attempt is made in this article to connect these two theories to explain the transmutation of the efficiently responding immune system (through the acute inflammatory response and high fever) to one involved in a low-grade chronic inflammatory process (resulting in chronic disease). There is already enough evidence to demonstrate the role of the microbiome in all chronic inflammatory diseases. In this article, we discuss the mechanism by which subjecting a healthy person to continuous drug treatment for acute inflammatory conditions (at a certain time) leads to transmutation to chronic disease. Although this hypothesis requires further experimental evidence, it calls for a reconsideration of the manner in which we treat acute infectious diseases in the population.

Quantum decision corrections for the neuroeconomics of irrational movement control and goal attainment

Quantum decision theory corrects categorical and propositional logic pathologies common to classic statistical goal-oriented reasoning, such as rational neuroeconomics-based optimal foraging. Within this ecosalient framework, motivation, perception, learning, deliberation, brain computation, and conjunctive risk-order errors may be understood for subjective utility judgments underlying either rational or irrational canonical decisions-actions used to choose, procure, and consume rewarding nutrition with variable fitness.

Reaction coupling in ADH1A alcohol dehydrogenase enzyme by exciplex formation with adenosine diphosphate moderated by low-energy electronic excited states

Two commonly accepted theories about enzymes were revisited. The first states that adenosine triphosphate (ATP)-stored energy is only released when the substrate is in place, because the substrate changes the enzyme structure when it is bound to the enzyme. In fact, as demonstrated and discussed presently, no structural changes are required, and ATP-stored energy is released when it can be used. The second states that ATP-released energy moves along the enzyme molecule in the form of molecular vibrations (Davydov's vibrational solitons). In fact, as reported presently, energy released upon ATP hydrolysis moves in the form of excited-state electrons (excitons), with no molecular vibrations involved. The relevant experimental evidence was obtained for the human ADH1A alcohol dehydrogenase enzyme. Spontaneous ATP hydrolysis in the absence of substrate was apparently prevented by electronically excited enzyme + adenosine diphosphate (ADP) + inorganic phosphate (P) complex (exciplex) formed upon ATP hydrolysis. This exciplex kept ADP + P bound and in place for the inverse reaction, until the excess energy was dissipated in the enzyme-catalyzed reaction or by energy transfer to a suitable acceptor. Additionally, and contrary to textbooks, ADH1A has required ATP, working orders of magnitude faster in its presence.

Simulating the Same Physics with Two Distinct Hamiltonians

We develop a framework and give an example for situations where two distinct Hamiltonians living in the same Hilbert space can be used to simulate the same physics. As an example of an analog simulation, we first discuss how one can simulate an infinite-range-interaction one-axis twisting Hamiltonian using a short-range nearest-neighbor-interaction Heisenberg XXX model with a staggered field. Based on this, we show how one can build an alternative version of a digital quantum simulator. As a by-product, we present a method for creating many-body maximally entangled states using only short-range nearest-neighbor interactions.

A review of applications of principles of quantum physics in oncology: do quantum physics principles have any role in oncology research and applications?

Background:

Research in the applications of the principles of quantum physics in oncology has progressed significantly over the past decades; and several research groups with professionals from diverse scientific background, including electrical engineers, mathematicians, biologists, atomic physicists, computer programmers, and biochemists, are working collaboratively in an unprecedented and pioneering economic, organisational and human effort searching for a wider and more effective, potentially definitive, understanding of the cancers. It is hypothesised that the principles of quantum physics could open new and broader understanding of the cancers and the development of new effective, targeted, accurate, personalised and possibly definitive cancer treatment.

Materials and methods:

This paper reports on a review of recent studies in the field of the applications of the principles of quantum physics in biology, chemistry, biochemistry and quantum physics in cancer research, including quantum physics principles and cancer, quantum modelling techniques, quantum dots and its applications in oncology, quantum cascade laser histopathology and quantum computing applications.

Conclusions:

The applications of the principles of quantum physics in oncology, chemistry and biology are providing new perspectives and greater insights into a long-studied disease, which could result in a greater understanding of the cancers and the potential for personalised and definitive treatment methods.

A quantum mechanical approach towards the calculation of transition probabilities between DNA codons

The role of quantum tunneling in altering the structure of nucleotides to each other and causing a mutational event in DNA has been a topic of debate for years. Here, we introduce a new quantum mechanical approach for analyzing a typical point-mutation in DNA strands. Assuming each codon as a base state, a superposition of codon states could provide a physical description for a set of codons encoding the same amino acid and there are transition amplitudes between them. We choose the amino acids Phe and Ile as our understudy bio-systems which are encoded by two and three codons, respectively. We treat them as large quantum systems and use double- and triple-well potential models to study the fundamental behaviors of them in interaction with a harmonic environment. We use the perturbation theory to calculate the transition probabilities between the codons which encoding the same amino acid and determine the transition rates of some point mutations. Moreover, we evaluate the quantum biological channel capacity for these transitions to show that the channel capacity depends on the system-environment interaction via the dissipation factor Γ. The obtained results demonstrate that the tunneling rate is under the control of capacity of the corresponding biological channel. In other words, the reduction in quantum channel capacity prevents the quantum tunneling rate to be increased.

Philosophy in Reality: Scientific Discovery and Logical Recovery

Three disciplines address the codified forms and rules of human thought and reasoning: logic, available since antiquity; dialectics as a process of logical reasoning; and semiotics which focuses on the epistemological properties of the extant domain. However, both the paradigmatic-historical model of knowledge and the logical-semiotic model of thought tend to incorrectly emphasize the separation and differences between the respective domains vs. their overlap and interactions. We propose a sublation of linguistic logics of objects and static forms by a dynamic logic of real physical-mental processes designated as the Logic in Reality (LIR). In our generalized logical theory, dialectics and semiotics are recovered from reductionist interpretations and reunited in a new synthetic paradigm centered on meaning and its communication. Our theory constitutes a meta-thesis composed of elements from science, logic and philosophy. We apply the theory to gain new insights into the structure and role of semiosis, information and communication and propose the concept of ‘ontolon’ to define the element of reasoning as a real dynamic process. It is part of a project within natural philosophy, which will address broader aspects of the dynamics of the growth of civilizations and their potential implications for the information society.

Revisiting the Quantum Brain Hypothesis: Toward Quantum (Neuro)biology?

The nervous system is a non-linear dynamical complex system with many feedback loops. A conventional wisdom is that in the brain the quantum fluctuations are self-averaging and thus functionally negligible. However, this intuition might be misleading in the case of non-linear complex systems. Because of an extreme sensitivity to initial conditions, in complex systems the microscopic fluctuations may be amplified and thereby affect the system's behavior. In this way quantum dynamics might influence neuronal computations. Accumulating evidence in non-neuronal systems indicates that biological evolution is able to exploit quantum stochasticity. The recent rise of quantum biology as an emerging field at the border between quantum physics and the life sciences suggests that quantum events could play a non-trivial role also in neuronal cells. Direct experimental evidence for this is still missing but future research should address the possibility that quantum events contribute to an extremely high complexity, variability and computational power of neuronal dynamics.

A biophysical approach to cancer dynamics: Quantum chaos and energy turbulence

Cancer is a term used to define a collective set of rapidly evolving cells with immortalized replication, altered epimetabolomes and patterns of longevity. Identifying a common signaling cascade to target all cancers has been a major obstacle in medicine. A quantum dynamic framework has been established to explain mutation theory, biological energy landscapes, cell communication patterns and the cancer interactome under the influence of quantum chaos. Quantum tunneling in mutagenesis, vacuum energy field dynamics, and cytoskeletal networks in tumor morphogenesis have revealed the applicability for description of cancer dynamics, which is discussed with a brief account of endogenous hallucinogens, bioelectromagnetism and water fluctuations. A holistic model of mathematical oncology has been provided to identify key signaling pathways required for the phenotypic reprogramming of cancer through an epigenetic landscape. The paper will also serve as a mathematical guide to understand the cancer interactome by interlinking theoretical and experimental oncology. A multi-dimensional model of quantum evolution by adaptive selection has been established for cancer biology.

Dissipationless Transfer of Visual Information From Retina to the Primary Visual Cortex in the Human Brain

Recently, the experiments on photosynthetic systems via “femto-second laser spectroscopy” methods have indicated that a “quantum-coherence” in the system causes a highly efficient transfer of energy to the “reaction center” (efficiency is approximately equal to 100%). A recent experiment on a single neuron has indicated that it can conduct light. Also, a re-emission of light from both photosynthetic systems and single neurons has been observed, which is called “delayed luminescence”. This can be supposed as a possibility for dissipationless transfer of visual information to the human brain. In addition, a long-range Fröhlich coherence in microtubules can be a candidate for efficient transfer of light through “noisy” and complex structures of the human brain. From an informational point of view it is a legitimate question to ask how human brain can receive subtle external quantum information of photons intact when photons are in a quantum superposition and pass through very noisy and complex pathways from the eye to the brain? Here, we propose a coherent model in which quantum states of photons can be rebuilt in the human brain.

Quantum dynamics of a hole migration through DNA: A single strand DNA model

A model predicting the behavior of a hole acting on the DNA strand was investigated. The hole-DNA interaction on the basis of a quantum-classical, non-linear DNA single strand model was described. The fact that a DNA molecule is formed by a furanose ring as its sugar, phosphate group and bases was taken into consideration. Based on the model, results were obtained for the probability of a hole location on the DNA base sequences, such as GTTGGG, GATGTGGG, GTTGTTGGG as well as on the sugar-phosphate groups mated with them.

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.

Neuroreceptor activation by vibration-assisted tunneling

G protein-coupled receptors (GPCRs) constitute a large family of receptor proteins that sense molecular signals on the exterior of a cell and activate signal transduction pathways within the cell. Modeling how an agonist activates such a receptor is fundamental for an understanding of a wide variety of physiological processes and it is of tremendous value for pharmacology and drug design. Inelastic electron tunneling spectroscopy (IETS) has been proposed as a model for the mechanism by which olfactory GPCRs are activated by a bound agonist. We apply this hyothesis to GPCRs within the mammalian nervous system using quantum chemical modeling. We found that non-endogenous agonists of the serotonin receptor share a particular IET spectral aspect both amongst each other and with the serotonin molecule: a peak whose intensity scales with the known agonist potencies. We propose an experiential validation of this model by utilizing lysergic acid dimethylamide (DAM-57), an ergot derivative, and its deuterated isotopologues; we also provide theoretical predictions for comparison to experiment. If validated our theory may provide new avenues for guided drug design and elevate methods of in silico potency/activity prediction.

Quantum effects in the understanding of consciousness

This paper presents a historical perspective on the development and application of quantum physics methodology beyond physics, especially in biology and in the area of consciousness studies. Quantum physics provides a conceptual framework for the structural aspects of biological systems and processes via quantum chemistry. In recent years individual biological phenomena such as photosynthesis and bird navigation have been experimentally and theoretically analyzed using quantum methods building conceptual foundations for quantum biology. Since consciousness is attributed to human (and possibly animal) mind, quantum underpinnings of cognitive processes are a logical extension. Several proposals, especially the Orch OR hypothesis, have been put forth in an effort to introduce a scientific basis to the theory of consciousness. At the center of these approaches are microtubules as the substrate on which conscious processes in terms of quantum coherence and entanglement can be built. Additionally, Quantum Metabolism, quantum processes in ion channels and quantum effects in sensory stimulation are discussed in this connection. We discuss the challenges and merits related to quantum consciousness approaches as well as their potential extensions.

Can We Advance Macroscopic Quantum Systems Outside the Framework of Complex Decoherence Theory?

Macroscopic quantum systems (MQS) are macroscopic systems driven by quantum rather than classical mechanics, a long studied area with minimal success till recently. Harnessing the benefits of quantum mechanics on a macroscopic level would revolutionize fields ranging from telecommunication to biology, the latter focused on here for reasons discussed. Contrary to misconceptions, there are no known physical laws that prevent the development of MQS. Instead, they are generally believed universally lost in complex systems from environmental entanglements (decoherence). But we argue success is achievable MQS with decoherence compensation developed, naturally or artificially, from top-down rather current reductionist approaches. This paper advances the MQS field by a complex systems approach to decoherence. First, why complex system decoherence approaches (top-down) are needed is discussed. Specifically, complex adaptive systems (CAS) are not amenable to reductionist models (and their master equations) because of emergent behaviour, approximation failures, not accounting for quantum compensatory mechanisms, ignoring path integrals, and the subentity problem. In addition, since MQS must exist within the context of the classical world, where rapid decoherence and prolonged coherence are both needed. Nature has already demonstrated this for quantum subsystems such as photosynthesis and magnetoreception. Second, we perform a preliminary study that illustrates a top-down approach to potential MQS. In summary, reductionist arguments against MQS are not justifiable. It is more likely they are not easily detectable in large intact classical systems or have been destroyed by reductionist experimental set-ups. This complex systems decoherence approach, using top down investigations, is critical to paradigm shifts in MQS research both in biological and non-biological systems.

Basis for a neuronal version of Grover's quantum algorithm

Grover's quantum (search) algorithm exploits principles of quantum information theory and computation to surpass the strong Church–Turing limit governing classical computers. The algorithm initializes a search field into superposed N (eigen)states to later execute nonclassical “subroutines” involving unitary phase shifts of measured states and to produce root-rate or quadratic gain in the algorithmic time (O(N^1/2)) needed to find some “target” solution m. Akin to this fast technological search algorithm, single eukaryotic cells, such as differentiated neurons, perform natural quadratic speed-up in the search for appropriate store-operated Ca²⁺ response regulation of, among other processes, protein and lipid biosynthesis, cell energetics, stress responses, cell fate and death, synaptic plasticity, and immunoprotection. Such speed-up in cellular decision making results from spatiotemporal dynamics of networked intracellular Ca²⁺-induced Ca²⁺ release and the search (or signaling) velocity of Ca²⁺ wave propagation. As chemical processes, such as the duration of Ca²⁺ mobilization, become rate-limiting over interstore distances, Ca²⁺ waves quadratically decrease interstore-travel time from slow saltatory to fast continuous gradients proportional to the square-root of the classical Ca²⁺ diffusion coefficient, D^1/2, matching the computing efficiency of Grover's quantum algorithm. In this Hypothesis and Theory article, I elaborate on these traits using a fire-diffuse-fire model of store-operated cytosolic Ca²⁺ signaling valid for glutamatergic neurons. Salient model features corresponding to Grover's quantum algorithm are parameterized to meet requirements for the Oracle Hadamard transform and Grover's iteration. A neuronal version of Grover's quantum algorithm figures to benefit signal coincidence detection and integration, bidirectional synaptic plasticity, and other vital cell functions by rapidly selecting, ordering, and/or counting optional response regulation choices.

Nonlinear effects of nanoparticles: biological variability from hormetic doses, small particle sizes, and dynamic adaptive interactions

Researchers are increasingly focused on the nanoscale level of organization where biological processes take place in living systems. Nanoparticles (NPs, e.g., 1-100 nm diameter) are small forms of natural or manufactured source material whose properties differ markedly from those of the respective bulk forms of the "same" material. Certain NPs have diagnostic and therapeutic uses; some NPs exhibit low-dose toxicity; other NPs show ability to stimulate low-dose adaptive responses (hormesis). Beyond dose, size, shape, and surface charge variations of NPs evoke nonlinear responses in complex adaptive systems. NPs acquire unique size-dependent biological, chemical, thermal, optical, electromagnetic, and atom-like quantum properties. Nanoparticles exhibit high surface adsorptive capacity for other substances, enhanced bioavailability, and ability to cross otherwise impermeable cell membranes including the blood-brain barrier. With super-potent effects, nano-forms can evoke cellular stress responses or therapeutic effects not only at lower doses than their bulk forms, but also for longer periods of time. Interactions of initial effects and compensatory systemic responses can alter the impact of NPs over time. Taken together, the data suggest the need to downshift the dose-response curve of NPs from that for bulk forms in order to identify the necessarily decreased no-observed-adverse-effect-level and hormetic dose range for nanoparticles.

Integration of thermodynamic, quantum and hierarchical theories of information in the context of Peircean semiosis--a review

I claim that Peirce's notion of information and sign iteration as an intermediation between potentialities that are actualized and actualities that are potentiated provides a suitable framework for interpretation of Zurek' Information gathering and using systems (IGUS). Moreover, this model can be extended to address the problem of quantum measurement (QM) since it allows exploring an alternative view based on IGUS understood as agents of internal measurement, beyond Copenhagen interpretation (CI) that invokes a classical observer that performs measurements and the "many worlds interpretation" (MWI) that rejects all sort of observers and measurements. This integrative view allows figuring out a hierarchy of IGUS-like systems of interpretation that explore new possibilities in the upper level analog boundary and consolidate actualized information in the lower level digital boundary.

Electroencephalographic field influence on calcium momentum waves

Macroscopic electroencephalographic (EEG) fields can be an explicit top-down neocortical mechanism that directly drives bottom-up processes that describe memory, attention, and other neuronal processes. The top-down mechanism considered is macrocolumnar EEG firings in neocortex, as described by a statistical mechanics of neocortical interactions (SMNI), developed as a magnetic vector potential A. The bottom-up process considered is Ca(2+) waves prominent in synaptic and extracellular processes that are considered to greatly influence neuronal firings. Here, the complimentary effects are considered, i.e., the influence of A on Ca(2+) momentum, p. The canonical momentum of a charged particle in an electromagnetic field, Π=p+qA (SI units), is calculated, where the charge of Ca(2+) is q=-2e, e is the magnitude of the charge of an electron. Calculations demonstrate that macroscopic EEG A can be quite influential on the momentum p of Ca(2+) ions, in both classical and quantum mechanics. Molecular scales of Ca(2+) wave dynamics are coupled with A fields developed at macroscopic regional scales measured by coherent neuronal firing activity measured by scalp EEG. The project has three main aspects: fitting A models to EEG data as reported here, building tripartite models to develop A models, and studying long coherence times of Ca(2+) waves in the presence of A due to coherent neuronal firings measured by scalp EEG. The SMNI model supports a mechanism wherein the p+qA interaction at tripartite synapses, via a dynamic centering mechanism (DCM) to control background synaptic activity, acts to maintain short-term memory (STM) during states of selective attention.

Quantum information and the problem of mechanisms of biological evolution

One of the most important conditions for replication in early evolution is the de facto elimination of the conformational degrees of freedom of the replicators, the mechanisms of which remain unclear. In addition, realistic evolutionary timescales can be established based only on partially directed evolution, further complicating this issue. A division of the various evolutionary theories into two classes has been proposed based on the presence or absence of a priori information about the evolving system. A priori information plays a key role in solving problems in evolution. Here, a model of partially directed evolution, based on the learning automata theory, which includes a priori information about the fitness space, is proposed. A potential repository of such prior information is the states of biologically important molecules. Thus, the need for extended evolutionary synthesis is discussed. Experiments to test the hypothesis of partially directed evolution are proposed.

Quantum biology at the cellular level--elements of the research program

Quantum biology is emerging as a new field at the intersection between fundamental physics and biology, promising novel insights into the nature and origin of biological order. We discuss several elements of QBCL (quantum biology at cellular level) - a research program designed to extend the reach of quantum concepts to higher than molecular levels of biological organization. We propose a new general way to address the issue of environmentally induced decoherence and macroscopic superpositions in biological systems, emphasizing the 'basis-dependent' nature of these concepts. We introduce the notion of 'formal superposition' and distinguish it from that of Schroedinger's cat (i.e., a superposition of macroscopically distinct states). Whereas the latter notion presents a genuine foundational problem, the former one contradicts neither common sense nor observation, and may be used to describe cellular 'decision-making' and adaptation. We stress that the interpretation of the notion of 'formal superposition' should involve non-classical correlations between molecular events in a cell. Further, we describe how better understanding of the physics of Life can shed new light on the mechanism driving evolutionary adaptation (viz., 'Basis-Dependent Selection', BDS). Experimental tests of BDS and the potential role of synthetic biology in closing the 'evolvability mechanism' loophole are also discussed.

The algorithmic origins of life

Although it has been notoriously difficult to pin down precisely what is it that makes life so distinctive and remarkable, there is general agreement that its informational aspect is one key property, perhaps the key property. The unique informational narrative of living systems suggests that life may be characterized by context-dependent causal influences, and, in particular, that top-down (or downward) causation-where higher levels influence and constrain the dynamics of lower levels in organizational hierarchies-may be a major contributor to the hierarchal structure of living systems. Here, we propose that the emergence of life may correspond to a physical transition associated with a shift in the causal structure, where information gains direct and context-dependent causal efficacy over the matter in which it is instantiated. Such a transition may be akin to more traditional physical transitions (e.g. thermodynamic phase transitions), with the crucial distinction that determining which phase (non-life or life) a given system is in requires dynamical information and therefore can only be inferred by identifying causal architecture. We discuss some novel research directions based on this hypothesis, including potential measures of such a transition that may be amenable to laboratory study, and how the proposed mechanism corresponds to the onset of the unique mode of (algorithmic) information processing characteristic of living systems.

Quantum biological channel modeling and capacity calculation

Quantum mechanics has an important role in photosynthesis, magnetoreception, and evolution. There were many attempts in an effort to explain the structure of genetic code and transfer of information from DNA to protein by using the concepts of quantum mechanics. The existing biological quantum channel models are not sufficiently general to incorporate all relevant contributions responsible for imperfect protein synthesis. Moreover, the problem of determination of quantum biological channel capacity is still an open problem. To solve these problems, we construct the operator-sum representation of biological channel based on codon basekets (basis vectors), and determine the quantum channel model suitable for study of the quantum biological channel capacity and beyond. The transcription process, DNA point mutations, insertions, deletions, and translation are interpreted as the quantum noise processes. The various types of quantum errors are classified into several broad categories: (i) storage errors that occur in DNA itself as it represents an imperfect storage of genetic information, (ii) replication errors introduced during DNA replication process, (iii) transcription errors introduced during DNA to mRNA transcription, and (iv) translation errors introduced during the translation process. By using this model, we determine the biological quantum channel capacity and compare it against corresponding classical biological channel capacity. We demonstrate that the quantum biological channel capacity is higher than the classical one, for a coherent quantum channel model, suggesting that quantum effects have an important role in biological systems. The proposed model is of crucial importance towards future study of quantum DNA error correction, developing quantum mechanical model of aging, developing the quantum mechanical models for tumors/cancer, and study of intracellular dynamics in general.

A model for homeopathic remedy effects: low dose nanoparticles, allostatic cross-adaptation, and time-dependent sensitization in a complex adaptive system

Background

This paper proposes a novel model for homeopathic remedy action on living systems. Research indicates that homeopathic remedies (a) contain measurable source and silica nanoparticles heterogeneously dispersed in colloidal solution; (b) act by modulating biological function of the allostatic stress response network (c) evoke biphasic actions on living systems via organism-dependent adaptive and endogenously amplified effects; (d) improve systemic resilience.

Discussion

The proposed active components of homeopathic remedies are nanoparticles of source substance in water-based colloidal solution, not bulk-form drugs. Nanoparticles have unique biological and physico-chemical properties, including increased catalytic reactivity, protein and DNA adsorption, bioavailability, dose-sparing, electromagnetic, and quantum effects different from bulk-form materials. Trituration and/or liquid succussions during classical remedy preparation create “top-down” nanostructures. Plants can biosynthesize remedy-templated silica nanostructures. Nanoparticles stimulate hormesis, a beneficial low-dose adaptive response. Homeopathic remedies prescribed in low doses spaced intermittently over time act as biological signals that stimulate the organism’s allostatic biological stress response network, evoking nonlinear modulatory, self-organizing change. Potential mechanisms include time-dependent sensitization (TDS), a type of adaptive plasticity/metaplasticity involving progressive amplification of host responses, which reverse direction and oscillate at physiological limits. To mobilize hormesis and TDS, the remedy must be appraised as a salient, but low level, novel threat, stressor, or homeostatic disruption for the whole organism. Silica nanoparticles adsorb remedy source and amplify effects. Properly-timed remedy dosing elicits disease-primed compensatory reversal in direction of maladaptive dynamics of the allostatic network, thus promoting resilience and recovery from disease.

Summary

Homeopathic remedies are proposed as source nanoparticles that mobilize hormesis and time-dependent sensitization via non-pharmacological effects on specific biological adaptive and amplification mechanisms. The nanoparticle nature of remedies would distinguish them from conventional bulk drugs in structure, morphology, and functional properties. Outcomes would depend upon the ability of the organism to respond to the remedy as a novel stressor or heterotypic biological threat, initiating reversals of cumulative, cross-adapted biological maladaptations underlying disease in the allostatic stress response network. Systemic resilience would improve. This model provides a foundation for theory-driven research on the role of nanomaterials in living systems, mechanisms of homeopathic remedy actions and translational uses in nanomedicine.

Prospects for the study of biological systems with high power sources of terahertz radiation

The emergence of intense sources of terahertz radiation based on lasers and electron accelerators has considerable potential for research on biological systems. This perspective gives a brief survey of theoretical work and the results of experiments on biological molecules and more complex biological systems. Evidence is accumulating that terahertz radiation influences biological systems and this needs to be clarified in order to establish safe levels of human exposure to this radiation. The use of strong sources of terahertz radiation may contribute to the resolution of controversies over the mechanism of biological organization. However the potential of these sources will only be realized if they are accompanied by the development of sophisticated pump-probe and multidimensional experimental techniques and by the study of biological systems in the controlled environments necessary for their maintenance and viability.

On genetic information uncertainty and the mutator phenotype in cancer

Recent evidence supports the existence of a mutator phenotype in cancer cells, although the mechanistic basis remains unknown. In this paper, it is shown that this enhanced genetic instability is generated by an amplified measurement uncertainty on genetic information during DNA replication. At baseline, an inherent measurement uncertainty implies an imprecision of the recognition, replication and transfer genetic information, and forms the basis for an intrinsic genetic instability in all biological cells. Genetic information is contained in the sequence of DNA bases, each existing due to proton tunnelling, as a coherent superposition of quantum states composed of both the canonical and rare tautomeric forms until decoherence by interaction with DNA polymerase. The result of such a quantum measurement process may be interpreted classically as akin to a Bernoulli trial, whose outcome X is random and can be either of two possibilities, depending on whether the proton is tunnelled (X=1) or not (X=0). This inherent quantum uncertainty is represented by a binary entropy function and quantified in terms of Shannon information entropy H(X)=-P(X=1)log(2)P(X=1)-P(X=0)log(2)P(X=0). Enhanced genetic instability may either be directly derived from amplified uncertainty induced by increases in quantum and thermodynamic fluctuation, or indirectly arise from the loss of natural uncertainty reduction mechanisms.

The quantum Zeno effect immunizes the avian compass against the deleterious effects of exchange and dipolar interactions

Magnetic-sensitive radical-ion-pair reactions are understood to underlie the biochemical magnetic compass used by avian species for navigation. Recent experiments have provided growing evidence for the radical-ion-pair magnetoreception mechanism, while recent theoretical advances have unravelled the quantum nature of radical-ion-pair reactions, which were shown to manifest a host of quantum-information-science concepts and effects, like quantum measurement, quantum jumps and the quantum Zeno effect. We here show that the quantum Zeno effect provides for the robustness of the avian compass mechanism, and immunizes its magnetic and angular sensitivity against the deleterious and molecule-specific exchange and dipolar interactions.

Unified framework for quasispecies evolution and stochastic quantization

In this paper we provide a unified framework for quasispecies evolution and stochastic quantization. We map the biological evolution described by the quasispecies equation to the stochastic dynamics of an ensemble of particles undergoing a creation-annihilation process. We show that this mapping identifies a natural decomposition of the probability that an individual has a certain genotype into eigenfunctions of the evolutionary operator. This alternative approach to study the quasispecies equation allows for a generalization of the Fisher theorem equivalent to the Price equation. According to this relation the average fitness of an asexual population increases with time proportional to the variance of the eigenvalues of the evolutionary operator. Moreover, from the present alternative formulation of stochastic quantization a novel scenario emerges to be compared with existing approaches. The evolution of an ensemble of particles undergoing diffusion and a creation-annihilation process is parametrized by a variable β that we call the inverse temperature of the stochastic dynamics. We find that the evolution equation at high temperatures is simply related to the Schrödinger equation, but at low temperature it strongly deviates from it. In the presence of additional noise in scattering processes between the particles, the evolution reaches a steady state described by the Bose-Einstein statistics.

Speculation on quantum mechanics and the operation of life giving catalysts

The origin of life necessitated the formation of catalytic functionalities in order to realize a number of those capable of supporting reactions that led to the proliferation of biologically accessible molecules and the formation of a proto-metabolic network. Here, the discussion of the significance of quantum behavior on biological systems is extended from recent hypotheses exploring brain function and DNA mutation to include origins of life considerations in light of the concept of quantum decoherence and the transition from the quantum to the classical. Current understandings of quantum systems indicate that in the context of catalysis, substrate-catalyst interaction may be considered as a quantum measurement problem. Exploration of catalytic functionality necessary for life's emergence may have been accommodated by quantum searches within metal sulfide compartments, where catalyst and substrate wave function interaction may allow for quantum based searches of catalytic phase space. Considering the degree of entanglement experienced by catalytic and non catalytic outcomes of superimposed states, quantum contributions are postulated to have played an important role in the operation of efficient catalysts that would provide for the kinetic basis for the emergence of life.

A complex vector space model of single neuronal coding and experience

A model of consciousness is proposed, in which the experience attributable to a single sensory neuron is related to its instantaneous firing rate. In that this can only be quantified within statistical limits from the incidence of spikes across multiple presentations of a stimulus, consciousness remains inaccessible to direct measurement on a single trial. In this way, the model disambiguates subjective experience from objective neural properties. The model adopts a quantum mechanical formalism, in which the state of the neuron is represented as a vector in a complex vector space.