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A quantum mechanical model of adaptive mutation

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Abstract

The principle that mutations occur randomly with respect to the direction of evolutionary change has been challenged by the phenomenon of adaptive mutations. There is currently no entirely satisfactory theory to account for how a cell can selectively mutate certain genes in response to environmental signals. However, spontaneous mutations are initiated by quantum events such as the shift of a single proton (hydrogen atom) from one site to an adjacent one. We consider here the wave function describing the quantum state of the genome as being in a coherent linear superposition of states describing both the shifted and unshifted protons. Quantum coherence will be destroyed by the process of decoherence in which the quantum state of the genome becomes correlated (entangled) with its surroundings. Using a very simple model we estimate the decoherence times for protons within DNA and demonstrate that quantum coherence may be maintained for biological time-scales. Interaction of the coherent genome wave function with environments containing utilisable substrate will induce rapid decoherence and thereby destroy the superposition of mutant and non-mutant states. We show that this accelerated rate of decoherence may significantly increase the rate of production of the mutated state.

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... Over the last 15 years, there have been theoretical developments and experimental verifications of quantum biological phenomena [2,4] such as quantum tunnelling effects for the efficient workings of enzymes at accelerating biological metabolic processes [5], and quantum superposition for efficient energy transfer in photosynthesis [6]. The area of quantum evolution [7], in which it is suggested that DNA base pairs remain in a superposition by sharing the proton of hydrogen bonds, still remains speculative and has practically stagnated since its theoretical inception 20 years ago [7,8]. However, recent theoretical developments on quantum genes (e.g. ...
... Over the last 15 years, there have been theoretical developments and experimental verifications of quantum biological phenomena [2,4] such as quantum tunnelling effects for the efficient workings of enzymes at accelerating biological metabolic processes [5], and quantum superposition for efficient energy transfer in photosynthesis [6]. The area of quantum evolution [7], in which it is suggested that DNA base pairs remain in a superposition by sharing the proton of hydrogen bonds, still remains speculative and has practically stagnated since its theoretical inception 20 years ago [7,8]. However, recent theoretical developments on quantum genes (e.g. ...
... Focusing on DNA, the genetic code is ultimately determined by hydrogen bonds of protons shared between purine and pyrimidine nucleotide bases [7]. Nucleotides have alternative forms known as tautomers, where the positions of the hydrogen protons in the nucleotide are swapped, changing nucleotide chemical properties and affinities [13,14]. ...
Article
Quantum biology seeks to explain biological phenomena via quantum mechanisms, such as enzyme reaction rates via tunnelling and photosynthesis energy efficiency via coherent superposition of states. However, less effort has been devoted to study the role of quantum mechanisms in biological evolution. In this paper, we used transcription factor networks with two and four different phenotypes, and used classical random walks (CRW) and quantum walks (QW) to compare network search behaviour and efficiency at finding novel phenotypes between CRW and QW. In the network with two phenotypes, at temporal scales comparable to decoherence time T D , QW are as efficient as CRW at finding new phenotypes. In the case of the network with four phenotypes, the QW had a higher probability of mutating to a novel phenotype than the CRW, regardless of the number of mutational steps (i.e. 1, 2 or 3) away from the new phenotype. Before quantum decoherence, the QW probabilities become higher turning the QW effectively more efficient than CRW at finding novel phenotypes under different starting conditions. Thus, our results warrant further exploration of the QW under more realistic network scenarios (i.e. larger genotype networks) in both closed and open systems (e.g. by considering Lindblad terms).
... McFadden J. and Al-Khalili J. [4] argue that spontaneous mutations are instigated by such events as a shift of single proton from one site to another of the DNA hydrogen bond through a quantum process (proton tunneling). The wave function describing the genome quantum state is presumed to be in a coherent linear superposition which is destroyed by a process of decoherence through the interaction of the genome wave function and the environment which acts as a measurement tool. ...
... It has been suggested by Home and Chattopadhyaya [109] that DNA could stay in a superposition of mutational states in a biomolecular version of Schrödinger's cat paradox (where a thought experiment by Erwin Schrödinger presupposes a cat confined in a box containing a radioactive source could be dead and alive at the same time). This implies the living cell elements may remain an ordered structure in line with maintaining quantum coherence at high temperatures above those that would otherwise destroy the quantum state of inanimate systems [4]. According to Patel [110] nucleotide bases can remain in a quantum superposition for a long period to take part in replication process. ...
... McFadden and Al-Khalili [4] have suggested that the environment can accelerate generation of mutant state out of the quantum superposition through accelerated decoherence. Rahman et al argue that when a pattern emerges that merit phenotypical expression, the wave functions collapse and the genetic material becomes fixed in one configuration only. ...
... therapeutic encounter, and to see whether they are compatible with those already considered. Two such alternative strategies present themselves: (1) one by considering quantum mechanical model of adaptive mutation (QMAM), 24 and (2) by observing the geometric patterns generated (i.e., conic sections) 25 by attaching a light source to a spinning gyroscope. ...
... For our purposes here, the most salient features of QMAM are that DNA can be represented by a wave function, It can exist in a superposition of mutational states for biologically feasible amounts of time, prior to decoherence into an adaptively mutated state by interaction with the environment. 24 In order to illustrate the therapeutic process, for ''DNA'' read the ''unwell'' patient to be ''stuck'' in a dis-eased state, represented by the wave function Id Px Y>. ...
... In this present article, two new metaphors have been introduced: one based on QMAM, 24 and the other derived from observation of the illuminated geometric patterns generated by a gyroscope with a built-in light source. Consideration of both metaphors indicates their relationship with each other and the original PPR entanglement metaphor (Fig. 4). ...
... Those thermodynamic fluctuations occur in response to a variety of energy impulses, such as heat, acoustic or electromagnetic waves, radiation with high-energy particles alpha, ultraviolet radiation, X-rays etc. It is well-known now that DNA mutations are initiated as quantum jumps [9,10]. A hydrogen bond joins base pairs in DNA. ...
... The stationary differential Markov process is specified by the probability distribution P(M(t), t) given by (10) [128]: (10) in which t stands for scalar time, k is the Fourier variable, , >0 are real, constant factors, and dM(t) stands for the fluctuations. ...
... The stationary differential Markov process is specified by the probability distribution P(M(t), t) given by (10) [128]: (10) in which t stands for scalar time, k is the Fourier variable, , >0 are real, constant factors, and dM(t) stands for the fluctuations. ...
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Tumorigenesis possesses no equivalent among known physical phenomena. It is initiated at the quantum level by thermodynamic fluctuations of macromolecules. Accumulation of non-lethal alterations in dynamic cellular network of genes and their regulatory protein elements facilitated by changes in microenvironment results in a weak emergence of non-complementary, malignant phenotype. The Weibull distribution of cancer incidence suggests that neuro-immuno-hormonal network modifies that process. Eucaryotic cells are supramolecular objects. They make use of quantum entanglement, quantum tunneling, coherence, and chirality in formation of novel molecular couplings with both multiple feedbacks, synergy, and hysteresis. Complementarity at each integration level and non-ergodicity are their distinguishing features. Quantum effects may contribute to the conjugated appearance of cancer mutations. Connectivity, that is, coupling between integration levels is associated with the emergence of at least three features: fractal geometry of space-time, in which growth occurs, conditional probability of events, which reduces sensitivity to the initial conditions, and entropy. The latter one determines both a capability of the supramolecular system for transfer of biologically relevant information and evolution of intercellular interactions. There is a limit for self-organization of cells into structures of higher order defined by the Fibonacci constant. A relationship between sigmoidal dynamics and the Feigenbaum diagram suggests that both growth and self-organization occur with parameters within the Mandelbrot set. The set of non-interacting, infiltrating cancer cells becomes topologically dense. It has the highest entropy. The global spatial fractal dimension approaches the integer value. Hence, the coefficient of cellular expansion is a novel quantitative measure of biological tumor aggressiveness. It is based on complexity of intercellular interactions. Neither biological complexity can be reduced to physical one, nor be fully mathematized. Computer simulations may help to elucidate details of tumorigenesis. The mathematical models should be expressed in the algebraic form of fractal sheaves and fractional equations.
... Emilio del Giudice together with his colleagues claim that a quantum effect of self-focusing electromagnetic waves in cellular cytoplasm is quite possible [13]. The paper [14] Biophysical Chemistry 217 (2016) 42 shows the possibility of quantum mechanics being involved in adaptive mutations mechanism, the latter caused by the environment rather than being absolutely random. The role of quantum effects in cytoskeletal protein structures, such as microtubules is constructively discussed in the papers [15][16][17][18][19]. Paul Davis advances the hypothesis that quantum mechanics allowed the advent of life to occur directly from the realm of atoms bypassing complex chemistry. ...
... The system of Eqs. (14), (15) and (28)-(30) determine the dynamics of DNA-hole interaction. The first four terms in the expressions (14), (15) determine the reversible charge dynamics, while the charge-DNA interaction -the second term in Eq. (7) -leads to the fifth irreversible term. ...
... (10), (11)) to reduce the Schroedinger equation to the forms of Eqs. (14), (15). In this instance, the ionization energies α a(b) , which were initially determined by the expression ...
Article
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.
... The wave function, which describes the genome quantum state, is presumed to be in a coherent linear superposition destroyed by decoherence by the interaction between the genome wave function and the environment, acting as a measurement tool. They have concluded that the \accelerated rate of decoherence may increase the mutated state's production rate" 38 (Fig. 2). ...
... 55 This claim implies that living cell elements may remain as an organized structure with preserving quantum coherence at higher temperatures, which would otherwise destroy the quantum state of insensate systems. 38 According to Patel, nucleotide bases can remain in a quantum superposition for an extended period to participate in the replication process. However, quantum superposition can be demolished when the DNA interacts with its environment. ...
... Demonstration of the accelerated decoherence imposed by the environment for mutant states. According to McFadden and Al-Khalili, the wave function of a cell undergoes mutation in two di®erent conditions: (a) nonadaptive mutation, e.g., no lactose presence, and (b) adaptive mutation, e.g., in lactose presence.38 ...
Article
Full-text available
There is no doubt that quantum mechanics has become one of the building blocks of our physical world today. It is one of the most rapidly growing fields of science that can potentially change every aspect of our life. Quantum biology is one of the most essential parts of this era which can be considered as a game-changer in medicine especially in the field of cancer. Despite quantum biology having gained more attention during the last decades, there are still so many unanswered questions concerning cancer biology and so many unpaved roads in this regard. This review paper is an effort to answer the question of how biological phenomena such as cancer can be described through the quantum mechanical framework. In other words, is there a correlation between cancer biology and quantum mechanics, and how? This literature review paper reports on the recently published researches based on the principles of quantum physics with focus on cancer biology and metabolism.
... A potential equation that may reconcile both is ER (Einstein-Rosen bridges also known as wormholes) =EPR (E=Einstein, P=Podolski, R=Rosen). This equation suggests the existence of wormhole (short cuts in space) that link distant entangled particles in space through short cuts and thus what seems to be traveling faster than speed of light is our inability to see the shortcuts taken by the particles [16]. ...
... Biological systems are the living counterparts of the physical universe and are also made up of molecules, atoms and subatomic structures, and strings of energy and therefore should obey the same laws/regularities of quantum physics and relativity. A couple of decades ago, it was suggested by some biologists and physicists that quantum mechanics may play a substantial role in the biological systems, and in sustaining life [16]. We believe that people that way, would be splitting hairs, as both points of views represent a continuum in the evolutionary process and it all is consistent with the current Darwinian evolution point of reference. ...
... As apparently opposed to classical Darwinian evolution, which states that mutations occur randomly and that those that provide advantage to an organism persist while the harmful ones perish with the death of the organism, quantum evolution suggests that mutations can occur in a somehow skewed fashion as to provide advantage for organism survival. Proponents of the quantum evolutionary theory suggest that at the quantum level, similarly to the wave-particle superposition concept, the DNA (made up of atoms and subatomic particles) is also held in a superposition of states, which eventually unfolds in a mutation that is "helpful" to the organism [16,17]. McFadden showed that mutations in mycobacteria were happening more than what would be attributed simply to chance. ...
Article
Evolutionary biology has fascinated scientists since Charles Darwin who cornered the concept of natural selection in the 19th century. Accordingly, organisms better adapted to their environment tend to survive and produce more offspring; in other terms, randomly occurring mutations that render the organism more fit to survival will be carried on and be transmitted to the offspring. Nearly a century later, science has seen the discovery of quantum mechanics, the branch of mechanics that deals with subatomic particles. Along with it, came the theory of quantum evolution whereby quantum effects can bias the process of mutation towards providing an advantage for organism survival. This is consistent with looking at the biological system as being a product of chemical-physical reactions, such that chemical structures arrange according to physical laws to form a replicative material referred to as the DNA. In this report, we attempt to reconcile both theories, trying to demonstrate that they complement each other, hoping to fill the gaps in our understandings of the versatility of the mutational status of the DNA as an essential mechanism of life compatibility.
... We call our model quantum-like (QL) to distinguish it from really quantum models in cell biology. Such models are based on "quantum reductionism", i.e., reduction of cell's behavior to behavior of quantum particles inside cell, e.g., (Ogryzko, 1997(Ogryzko, , 2008McFadden and Al-Khalili, 1999;McFadden, 2000). In particular, superpositions in cell's states are induced by real quantum superpositions of quantum particles inside the cell. ...
... There were proposed the plenty of interpretations. Those who interpret the quantum state as the physical state are completely sure that a macroscopic state of the Schrödinger's cat type can be in princi-6 By using the information interpretation of the quantum formalism we need not to keep to quantum physical reductionism as, e.g., (Ogryzko, 1997(Ogryzko, , 2008McFadden and Al-Khalili, 1999;McFadden, 2000). However, we neither have to exclude the real quantum physical effects as a possible (although very doubtful) source of the cellular QL information processing. ...
... Thus the Schrödinger equation cannot describe evolution of epimutations in an ensemble of cells towards some stationary distribution which will not be changed anymore (of course, if from the very beginning the initial state was not a stationary state of the epimutation Hamiltonian H). Some authors (Ogryzko, 1997(Ogryzko, , 2008McFadden and Al-Khalili, 1999;McFadden, 2000) exploring the quantum physical theory in cell biology used measurement to stop the Schrödinger fluctuating dynamics. Measurements are described by Hermitian operators and the act of measurement (in accordance with the standard interpretation of quantum mechanics) implies the collapse of the quantum state. ...
Conference Paper
Full-text available
We develop a quantum-like (QL) model of cellular evolution based on the theory of open quantum systems and entanglement between epigenetic markers in a cell. This approach is applied to modeling of epigenetic evolution of cellular populations. We point out that recently experimental genetics discovered numerous phenomena of cellular evolution adaptive to the pressure of the environment. In such phenomena epigenetic changes are fixed in one generation and, hence, the Darwinian natural selection model cannot be applied. A number of prominent genetists stress the Lamarckian character of epigenetic evolution. In quantum physics the dynamics of the state of a system (e.g. electron) contacting with an environment (bath) is described by the theory of open quantum systems. Therefore it is natural to apply this theory to model adaptive changes in the epigenome. Since evolution of the Lamarckian type is very rapid – changes in the epigenome have to be inherited in one generation – we have to find a proper mathematical description of such a speed up. In our model this is the entanglement of different epigenetic markers.
... Löwdin was the first one who used a twostep model for describing a genetic noise in which a base substitution (or codon transition) is due to (1) formation of the tautomeric state of a nucleotide in the non-coding strand of DNA caused by a proton transfer between two neighboring sites within the nucleotide, (2) insertion of an incorrect base into the coding strand of DNA due to unusual basepairing of the tautomeric form which may lead to a point mutation. Subsequent transcription and translation of the mutant pattern will appear at each level of the gene expression (Löwdin, 1965;McFadden and Al-Khalili, 1999). ...
... McFadden and Al-Khalili in 1999 suggested that the genetic code might be considered as a quantum state described by a wave function, so that superpositions of the states might occur which leads to spontaneous mutations in DNA strands. They have proposed that models based on the quantum theory could be crucial for understanding of the spontaneous mutations (McFadden and Al-Khalili, 1999). The most common model to obtain the transitional probabilities between codons is employing Löwdin's double-well model. ...
Article
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.
... Among the first theoretical papers devoted to quantum effects in biological systems are works of Penrose (1989), Beck and Eccles (1992), Ogryzko (1997), McFadden and Al-Khalili (1999), Igamberdiev (1993). ...
... A number of studies (Ogryzko, 1997;McFadden and Al-Khalili, 1999) have examined the possible role of quantum mechanics in adaptive mutations (Q-gene). These mutations occur after the cell is exposed to the environment. ...
... Our QL-model has to be distinguished from really quantum models in cellular biology. Such models are based on "quantum reductionism", i.e., reduction of cell's behavior to behavior of quantum particles inside cell, e.g., Ogryzko [151], [152], McFadden and Al-Khalili [147], McFadden [148]. In particular, in such works superpositions of cell's states are induced by real quantum superpositions of states of quantum particles inside the cell, e.g., some protons in DNA. ...
... By using the information interpretation of the quantum formalism we need not to keep to quantum physical reductionism as, e.g., Ogryzko[151],[152] McFadden and Al-Khalili[147], McFadden[148]. However, we neither have to exclude the real quantum physical effects as a possible (although very doubtful) source of the cellular QL information processing. ...
Chapter
In this chapter, we briefly discuss the main foundational problems of quantum mechanics, especially the problem of hidden variables—variables which might provide finer description of quantum phenomena than given by quantum states.
... This view, however, goes beyond the scope of the present work. For this model, the approach utilized by Khalili & Mcfadden [76] is used, where "the coupling between fundamental particles and the environment of living cells enables their macroscopic behavior to be determined by quantum rather than classical laws". ...
... If quantum mechanics do play such an influential role in a fundamental process of gene expression as presented here, this would contribute to an idea suggested by McFadden [77] in which the quantum world is not only a constituent of our reality but also the cause of it by assisting biological systems to solve evolutionary challenges (e.g.: energy efficiency in enzyme and photosynthesis reactions [18,19], adaptive mutations [76] and several others currently being investigated [78][79][80]). As a last remark, it is important to note that stochastic effects are found throughout our physical reality without requiring help from the quantum world. ...
Article
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The X chromosome inactivation is an essential mechanism in mammals' development, that despite having been investigated for 60 years, many questions about its choice process have yet to be fully answered. Therefore, a theoretical model was proposed here for the first time in an attempt to explain this puzzling phenomenon through a quantum mechanical approach. Based on previous data, this work theoretically demonstrates how a shared delocalized proton at a key base pair position could explain the random, instantaneous, and mutually exclusive nature of the choice process in X chromosome inactivation. The main purpose of this work is to contribute to a comprehensive understanding of the X inactivation mechanism with a model proposal that can complement the existent ones, along with introducing a quantum mechanical approach that could be applied to other cell differentiation mechanisms.
... coli) with hydrogen nuclei was cultured and the mutations in the produced cells were quantified. At the same time, a separate population was cultured, but these had deuterium nuclei (deuterons), a heavier isotope of hydrogen [50]. The results of these experiments showed that the protons within hydrogen nuclei were able to tunnel easily and thus led to many mutations. ...
... As a result, we are able to obtain a more fundamental understanding of how photosynthesis works. And can guide future research towards designing much more efficient solar cells than the ones we currently have [50]. However, they do outline that one of the biggest obstacles in designing complex organic solar cells, is the difficulty to control what happens after light is absorbed. ...
Article
Full-text available
Until recently, the complexities of biological processes and systems have emphasized classifications and empirical rules, that have lacked explanatory power and been limited by many exceptions. On the other hand, modern physics and quantum physics in particular, has a universal capacity to explain physical interactions down to the subatomic scale, including biological processes and systems. The scientific field of biology has succeeded over the past decades in explaining macroscopic phenomena that are based on an improved understanding of molecular structures and behaviours. Likewise, quantum physics has provided a non-classical approach to unintuitive characteristics, and has recently been directed towards systems of increasing complexity. With the rise of high performance computing, the field of quantum biology has rapidly developed in recent years to challenge us to rethink biological processes such as the magnetoreception of Earth’s magnetic field that allows birds to migrate, how enzymes are able to accelerate reactions at astonishing speeds, and why photosynthesis in plants is near to 100% efficient. Even biology’s primary conceptual basis, namely Charles Darwin’s and Alfred Wallace’s theory of evolution by natural selection, is now thought to be influenced by the esoteric but fundamental laws of quantum mechanics. This article will act as a guide to explain such phenomena, explore the growing interconnectedness between the two scientific fields and question the future possibilities of quantum biology.
... (v) The observation, under conditions of high environmental stress, of non-random directed mutations or "adaptive mutations" (AM). (vi) AM was quickly followed by the proposal of quantum effects that could produce sudden variations by switching the genome from a situation of coherence (quantum superposition of underlying alternative states) to a situation of decoherence in which only one of the states is the favored one to promote an AM (Ogryzko, 1997;McFadden and Al-Khalili, 1999;Davies, 2004). Finally, in a sort of intermediate position, (vii) the concept of partially-directed evolution (PDE) has been proposed (Melkikh, 2005(Melkikh, , 2008(Melkikh, , 2014a(Melkikh, ,b, 2015Melkikh and Khrennikov, 2015). ...
Article
The Darwinian interpretation (Di) of evolutionary process, and its subsequent development in the form of modern evolutionary synthesis (MES), plays a paradigmatic role in the mainstream biological thought. However, the main role in the improvement from Di to MES has depended on population genetics. Conventional ecosystem ecology has added relatively few specific insights to this endeavor in spite of the well-known combined selective influence from environment. This article integrates i) recent findings in genetics (i.e.: evolutionary capacitance); ii) orthodox topics as well as recent results from a large set of models in ecosystem ecology which have recently been encompassed under the term " organic biophysics of ecosystem " ; and iii) an epistemological analysis of the origin of On the Origin of Species.. . by reaching four main particular conclusions: (a) Despite the contemporary recognition that any kind of interspecific relationship has an evolutionary influence, the analytical emphasis of Di and MES on competition has been unwittingly oversized because of the paradoxical manner in which mutualism can emerge as an essential evolutionary force starting from competition, being this an unpublished topic that is analyzed in this manuscript by the first time. This link between two interspecific relationships that seem opposite to each other at the first glance is based on quantum effects that are totally unknown in conventional evolutionary theory due to its bias in favor of genetics, neglecting ecological considerations by contrast. (b) A holistic combination of ecological, genetic and evolutionary insights at the ecosystem level additionally confirms that the analytical role of evolutionary gradualism has also been oversized. (c) The main criterion of evolutionary success conventionally applied by Di and MES should be modified given that: (d) the preferential direction of evolutionary process theoretically proposed by Di and MES does not match with the direction of spontaneous development of natural ecosystems. The final section of this manuscript explains that these four critical outcomes in regard to Di and MES seem to have their root in epistemological inaccuracies involved in the origin of On the Origin of Species.. .that have been passed from generation to generation without being subjected to interdisciplinary scrutiny. This article showcases the need to review some of the foundational principles of Di and MES before building a " new floor " (i.e.: the extended evolutionary synthesis) supported on our current perspective about the evolutionary process. So, contrastingly with the genocentric nature of conventional evolutionary theory, R.A. Rodríguez et al. / Ecological Modelling 355 (2017) 70–83 71 large sections of our current evolutionary thought could change if we take into account some old results, as well as some recent ones, achieved by means of interdisciplinary approaches. In summary, this article concludes that the MES, despite its correct structure in essential points, could reach a significantly more complete epistemological condition than its current state if we add some fundamental results from ecosystem ecology that have been unwittingly neglected so far.
... (v) The observation, under conditions of high environmental stress, of non-random directed mutations or "adaptive mutations" (AM). (vi) AM was quickly followed by the proposal of quantum effects that could produce sudden variations by switching the genome from a situation of coherence (quantum superposition of underlying alternative states) to a situation of decoherence in which only one of the states is the favored one to promote an AM (Ogryzko, 1997;McFadden and Al-Khalili, 1999;Davies, 2004). Finally, in a sort of intermediate position, (vii) the concept of partially-directed evolution (PDE) has been proposed (Melkikh, 2005(Melkikh, , 2008(Melkikh, , 2014a(Melkikh, ,b, 2015Melkikh and Khrennikov, 2015). ...
Article
The Darwinian interpretation (Di) of evolutionary process, and its subsequent development in the form of modern evolutionary synthesis (MES), plays a paradigmatic role in the mainstream biological thought. However, the main role in the improvement from Di to MES has depended on population genetics. Conventional ecosystem ecology has added relatively few specific insights to this endeavor in spite of the well-known combined selective influence from environment. This article integrates i) recent findings in genetics (i.e.: evolutionary capacitance); ii) orthodox topics as well as recent results from a large set of models in ecosystem ecology which have recently been encompassed under the term " organic biophysics of ecosystem " ; and iii) an epistemological analysis of the origin of On the Origin of Species.. . by reaching four main particular conclusions: (a) Despite the contemporary recognition that any kind of interspecific relationship has an evolutionary influence, the analytical emphasis of Di and MES on competition has been unwittingly oversized because of the paradoxical manner in which mutualism can emerge as an essential evolutionary force starting from competition, being this an unpublished topic that is analyzed in this manuscript by the first time. This link between two interspecific relationships that seem opposite to each other at the first glance is based on quantum effects that are totally unknown in conventional evolutionary theory due to its bias in favor of genetics, neglecting ecological considerations by contrast. (b) A holistic combination of ecological, genetic and evolutionary insights at the ecosystem level additionally confirms that the analytical role of evolutionary gradualism has also been oversized. (c) The main criterion of evolutionary success conventionally applied by Di and MES should be modified given that: (d) the preferential direction of evolutionary process theoretically proposed by Di and MES does not match with the direction of spontaneous development of natural ecosystems. The final section of this manuscript explains that these four critical outcomes in regard to Di and MES seem to have their root in epistemological inaccuracies involved in the origin of On the Origin of Species.. .that have been passed from generation to generation without being subjected to interdisciplinary scrutiny. This article showcases the need to review some of the foundational principles of Di and MES before building a " new floor " (i.e.: the extended evolutionary synthesis) supported on our current perspective about the evolutionary process. So, contrastingly with the genocentric nature of conventional evolutionary theory, R.A. Rodríguez et al. / Ecological Modelling 355 (2017) 70–83 71 large sections of our current evolutionary thought could change if we take into account some old results, as well as some recent ones, achieved by means of interdisciplinary approaches. In summary, this article concludes that the MES, despite its correct structure in essential points, could reach a significantly more complete epistemological condition than its current state if we add some fundamental results from ecosystem ecology that have been unwittingly neglected so far.
... In these fields and beyond, there is still much more to discuss, neglected here is work in quantum computing, or quantum simulators as in Mostame et al [75], where biological mimetics may suggest promise. In fact "quantum effects" and the exploration thereof have indicated to be useful in various fields: DNA mutations [76], vision [77], and even consciousness [78], to name a few, all of which may also exhibit surprising quantum effects and provide fascinating avenues for future examination. ...
Article
Despite certain quantum concepts, such as superposition states, entanglement, 'spooky action at a distance' and tunnelling through insulating walls, being somewhat counterintuitive, they are no doubt extremely useful constructs in theoretical and experimental physics. More uncertain, however, is whether or not these concepts are fundamental to biology and living processes. Of course, at the fundamental level all things are quantum, because all things are built from the quantized states and rules that govern atoms. But when does the quantum mechanical toolkit become the best tool for the job This review looks at four areas of 'quantum effects in biology'. These are biosystems that are very diverse in detail but possess some commonality. They are all (i) effects in biology: rates of a signal (or information) that can be calculated from a form of the 'golden rule' and (ii) they are all protein-pigment (or ligand) complex systems. It is shown, beginning with the rate equation, that all these systems may contain some degree of quantum effect, and where experimental evidence is available, it is explored to determine how the quantum analysis AIDS in understanding of the process. © 2017 The Author(s) Published by the Royal Society. All rights reserved.
... Explanations on biological processes often revolve around ideas from quantum mechanics [5], [6]. For instance: explanations on the olfactory mechanism [7] dynamics of photosynthetic transport in plant [8] and theories on avian magnetoreception [9]. ...
Article
Full-text available
This work aims to propose a framework for the phase space representation of quantum coherence in matter. The central thesis of this work is that quantum coherence could result from weak time-periodic forcing in the absence of other types of interactions (or measurements) from the environment. Therefore the Floquet formalism is employed to depict the coherent quantum system. A phase space representation for coherent quantum systems is formulated and the resulting three uncertainty principles are presented. The mathematical structure for quantum coherent transport is constructed via a non-equilibrium thermodynamic approach. The framework presented in this paper is targeted towards the development of nanosystems and other elements; employed to design systems for quantum computing. Keywords - quantum coherence; phase space; Floquet formalism; uncertainty principles; quantum coherent transport; quantum computing
... Biological systems are dynamical with constant exchange of energy and matter with the environment in order to maintain the state of non-equilibrium characteristic of living systems. Several mechanisms within living cells operate under non-trivial features of quantum mechanics such as quantum tunneling, which has been proposed to be involved in DNA mutation biological process [13][14][15][16]. Quantum tunneling is when particles with wave-like properties at the quantum scale can tunnel through apparently impermeable energy barriers with certain probabilities. ...
Chapter
Vaccines are the most effective preventive intervention to reduce the impact of infectious diseases worldwide. In particular, tick-borne diseases represent a growing burden for human and animal health worldwide and vaccines are the most effective and environmentally sound approach for the control of vector infestations and pathogen transmission. However, the development of effective vaccines for the control of tick-borne diseases with combined vector-derived and pathogen-derived antigens is one of the limitations for the development of effective vaccine formulations. Quantum biology arise from findings suggesting that living cells operate under non-trivial features of quantum mechanics, which has been proposed to be involved in DNA mutation biological process. Then, the electronic structure of the molecular interactions behind peptide immunogenicity led to quantum immunology and based on the definition of the photon as a quantum of light, the immune protective epitopes were proposed as the immunological quantum. Recently, a quantum vaccinomics approach was proposed based on the characterization of the immunological quantum to further advance the design of more effective and safe vaccines. In this chapter, we describe methods of the quantum vaccinomics approach based on proteins with key functions in cell interactome and regulome of vector–host–pathogen interactions for the identification by yeast two-hybrid screen and the characterization by in vitro protein–protein interactions and musical scores of protein interacting domains, and the characterization of conserved protective epitopes in protein interacting domains. These results can then be used for the design and production of chimeric protective antigens.
... He termed these phenotypic changes which can cause mutations in the encoding genome as 'phenocopy' and this phenomenon is contrary to the linear pattern of DNA-RNA-Protein [1]. Again, the occurrence of adaptive mutations has challenged the neo-Darwinian principle that selection for advantageous mutations directs the evolutionary change where mutations occur randomly [4]. Cairns et al. [5] reported that when the mutant phenotype has clear selective advantage, the specific mutations take place at a much higher rate in bacteria. ...
Article
From the conventional Bird's eye, cancer initiation and metastasis are generally intended to be understood beneath the light of classical clonal genetic, epigenetic and cancer stem cell model. But inspite decades of investigation, molecular biology has shown hard success to give Eagle's eye in unraveling the riddle of cancer. And it seems, tiring Tom runs in vague behind naughty Jerry.
... mechanisms of spontaneous mutation and of action of helicases. The concept of quantum genetics, where behavior of the genetic material is interpreted by principles and rules of quantum mechanics [15], would certainly prevail in the coming era due to progressive increase in our knowledge of the structure and function(s) of our genome and our proteome. Quantum genetics might even be exceeded by nano genetics, a term coined to signify the study of behavior of subatomic components of nucleotides at a nanoscale level, because many significant pathogenetic mechanisms that result in pathophysiological alterations leading to pathogenesis of genetic disorders are not interpretable except by laws that govern the behavior of matter at electron-photon level. ...
Article
Radical prevention of genetic diseases and genetically-determined defects, through efficient prophylactic and effective curative approaches, represents the final goal of medical genetics. However, success in achieving this objective is totally dependent on comprehensive understanding of all structural and functional aspects of the human genome, transcriptome and proteome. A lot of perplexing phenomena and enigmatic problems in medical genetics, as well as in human genetics, are awaiting this understanding to be disclosed, e.g. genomic imprinting, spontaneous mutation, evolutionary adaptations, apoptosis, carcinogenesis, functions of pyknons, significance of transposons, roles of micro RNAs and many others. Although the human genome project is steadily progressing towards full structural characterization of the human genome, a parallel human genome function project is indispensable for finalizing our knowledge of our genetic constitution. Similarly, human proteome structure and human proteome function projects are necessary for the same purpose. The extreme complexity of the structure of the human genome and human proteome necessitates new accurate analytical methods to study and understand the behavior and capabilities of both of these structured biosystems. These methods should rely on laws of thermodynamics, principles of quantum mechanics and, even, concepts of nanosciences. It is hoped that these new research approaches will help in revealing and defining the underlying mechanisms responsible for maintaining integrity, stability and identity of the genome and proteome which represent prerequisite knowledge needed for controlling and directing the functions of both of them for attaining optimal health and welfare of human beings. The present article shortly addresses some of the aforementioned problems and tries to offer few hypotheses, interpretations and proposals that might prove helpful in this respect.
... Löwdin proposed that the proton in an H bond may break away from the donor atom and form a new covalent bond with the acceptor atom, by the mechanism of quantum tunnelling across the potential barrier between the donor and acceptor, and that this process may cause spontaneous mutation [3]. McFadden and Al-Khalili later demonstrated that quantum coherence between the tunnelling proton and its environment can be maintained for biological time-scales, which validates modelling the proton's dynamics as being entirely quantum mechanical [4]. ...
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We present a model of proton tunnelling across DNA hydrogen bonds, compute the characteristic tunnelling time (CTT) from donor to acceptor and discuss its biological implications. The model is a double oscillator characterised by three geometry parameters describing planar deformations of the H bond, and a symmetry parameter representing the energy ratio between ground states in the individual oscillators. We discover that some values of the symmetry parameter lead to CTTs which are up to 40 orders of magnitude smaller than a previous model predicted. Indeed, if the symmetry parameter is sufficiently far from its extremal values of 1 or 0, then the proton’s CTT under any physically realistic planar deformation is guaranteed to be below one picosecond, which is a biologically relevant time-scale. This supports theories of links between proton tunnelling and biological processes such as spontaneous mutation. Graphical abstract Open image in new window
... Quantum activity within biological systems and the applications of information theory therein have drawn much recent attention [1][2][3][4][5] . Examples of systems that exploit such phenomenon are: quantum coherence and entanglement in photosynthetic complexes [6][7][8][9][10][11][12][13][14][15] , quantum mutations 16,17 , information theory and thermodynamics of cancers 18,19 ,the avian magnetic compass [20][21][22][23] , tunneling behavior in the antioxidant breakdown of catechols present in green tea 24 , enzymatic action 25 , olfaction 26 , and genetic coding 27 . G Protein-Coupled Receptors (GPCR) are the target for the greatest portion of modern therapeutic small molecule medications 28 . ...
Article
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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 hypothesis 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.
... However, the biasing of the will by nature generates a specific pattern or distribution in the outcomes of repeated experiments carried out on identical systems. We get this clue from surprising experimental results in quantum biology in which it was recently reported that adaptive mutation happens in DNA of bacteria (Merali, 2014;McFadden et al., 1999). ...
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Although quantum mechanics can accurately predict the probability distribution of outcomes in an ensemble of identical systems, it cannot predict the result of an individual system. All the local and global hidden variable theories attempting to explain individual behavior have been proved invalid by experiments (violation of Bell’s inequality) and theory. As an alternative, Schrodinger and others have hypothesized existence of free will in every particle which causes randomness in individual results. However, these free will theories have failed to quantitatively explain the quantum mechanical results. In this paper, we take the clue from quantum biology to get the explanation of quantum mechanical distribution. Recently it was reported that mutations (which are quantum processes) in DNA of E. coli bacteria instead of being random were biased in a direction such that the chance of survival of the bacteria is increased. Extrapolating it, we assume that all the particles including inanimate fundamental particles have a will and that is biased to satisfy the collective goals of the ensemble. Using this postulate, we mathematically derive the correct spin probability distribution without using quantum mechanical formalism (operators and Born’s rule) and exactly reproduce the quantum mechanical spin correlation in entangled pairs. Using our concept, we also mathematically derive the form of quantum mechanical wave function of free particle which is conventionally a postulate of quantum mechanics. Thus, we prove that the origin of quantum mechanical results lies in the will (or consciousness) of the objects biased by the collective goal of ensemble or universe. This biasing by the group on individuals can be called as “coherence” which directly represents the extent of life present in the ensemble. So, we can say that life originates out of establishment of coherence in a group of inanimate particles.
... Quantum entanglement is essential not only for technological applications such as quantum computation [13], data base search algorithm [14] or quantum cryptography [15] and quantum secret sharing [16] but also for non-artificial systems. For instance for photosynthesis [17]- [18], navigational orientation of animals [19], the imbalance of matter and antimatter in the universe [20] and evolution itself [21]. ...
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We consider a pure 3-qubits system interacting through a XY-Hamiltonian with antiferromagnetic constant J. We employ the 3-tangle as an efficient measure of the entanglement between such a 3-qubit system. The time evolution of such a 3-tangle is studied. In order to do the above, the 3-tangle associated to the pure 3-qubit state | ψ t = c 0 t | 000 + c 1 t | 001 + c 2 t | 010 + c 3 t | 011 + c 4 t | 100 + c 5 t | 101 + c 6 t | 110 + c 7 t | 111 is calculated as a function of the initial coefficients c i t = 0 i = 0,1 , … , 7, the time t and the antiferromagnetic constant J. We find that the 3-tangle of the 3-qubit system is periodic with period t = 4 π / J. Furthermore, we also find that the 3-tangle as a function of the time t and J has maximal and minimum values. The maximal values of the 3-tangle can be employed in Quantum Information Protocols (QIP) that use entanglement as a basic resource. The pattern found for the 3-tangle of the system of three qubits interacting through a XY Hamiltonian as a function of J and the time t resembles to a quantized physical quantity.
... It has been pointed out that the fact that the genetic code is based on triplets of nucleotides of four molecules that code for 21 amino acids, is either a numerical coincidence or evidence that life is optimized for quantum computing at the molecular level. It has been suggested that the genetic code should be regarded as a quantum code, allowing superpositions of coding states to occur, leading to spontaneous mutations (45). ...
Article
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Emerging evidence indicates that quantum phenomena may be operational in biological systems despite unfavorable temperatures and environmental noise. It is possible that protein quaternary architecture may be conducive to sustaining quantum entanglement and coherence. Models ranging from quantum resonant recognition, proton tunneling in DNA, radiation wave therapy and the magnetic isotope effect have been proposed that validate the importance of the wave-particle duality of matter in persisting in and modulating biological processes. The ability of food ingredients and pharmaceutical excipients to manipulate bioeffector mechanisms via quantum effects is discussed. It is hoped that this new perspective will provide impetus for further research in this field.
... The biased will theory assumes the existence of will in every inanimate object and states that quantum processes proceed in a direction so as to achieve collective goals of the universe or coherent assembly of particles. This explains the recently reported adaptive mutation in the DNA of bacteria [39][40]. In response to a changing environment, mutations in E. Coli bacteria (which are quantum processes) instead of being random were found to be biased in a direction such that the chance of survival of the bacteria is increased. ...
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The basic idea of quantum mechanics is that the property of any system can be in a state of superposition of various possibilities (or eigen states). This state of superposition is also known as wave function and it evolves linearly with time in a deterministic way in accordance with the Schrodinger equation. However, when a measurement is carried out on the system to determine the value of that property (say position), the system instantaneously transforms to one of the eigen states and thus we get only a single value as an outcome of the measurement. Quantum measurement problem seeks to find the cause and exact mechanism governing this transformation. In an attempt to solve the above problem, in this paper, we will first define what the wave function represents in real-world and will identify the root cause behind the stochastic nature of events. Then, we will develop a model to explain the mechanism of collapse of the quantum mechanical wave function in response to a measurement. In the process of development of model, we will explain Schrodinger cat paradox and will show how Born’s rule for probability becomes a natural consequence of the measurement process.
... Researchers are beginning to question whether a percolation of quantum indeterminism to macrostates of a biological system is possible; an interesting review of the experimental situation and the philosophical implications can be found in (Stamos 2001). McFadden has proposed quantum effects (quantum Zeno paradox) as an explanation for some adaptive mutations in E. Coli (McFadden and Al-Khalili 1999). A discussion of evo-devo based on this key can be found in his book (McFadden 2001). ...
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This article aims to reformulate the concepts of "archetype" and "entelechy" starting from modern notions of microphysics. It proposes an experimental scheme able to verify the actual existence of such entities under an assumption of final causality, successively reinterpreted as a particular form of efficient causality. The possibility of connections with the domains of the ontogenesis and phylogenesis of living systems is discussed. Subsequently, the scheme is generalized in order to include a concept of psychosomatic connection.
... Our effort will be to show that if quantum version of CRW is used to describe the complex processes during protein-DNA interaction, the diffusional experimental results can be immediately obtained when the protein (the walker) exploits the speed-up properties of QW and peculiar entanglement-based behaviour enforced by the environmental fluctuations. Recently, there is a growing interest in the application of quantum properties, long-lived quantum coherence, superposition, tunneling and entanglement to biological systems [31][32][33], ranging from enzyme catalysis [34][35], to photosynthesis (although this is a controversial subject) [36][37][38], to the implication of quantum entanglement in avian navigation [39], to quantum tunneling in olfaction [40], genetic mutation [41], while speculative suggestions pay attention on the link between quantum coherence and consciousness [42]. ...
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Protein-DNA interactions play a fundamental role in all life systems. A critical issue of such interactions is given by the strategy of protein search for specific targets on DNA. The mechanisms by which the protein are able to find relatively small cognate sequences, typically 15-20 base pairs (bps) for repressors, and 4-6 bps for restriction enzymes among the millions of bp of non-specific chromosomal DNA have hardly engaged researcher for decades. Recent experimental studies have generated new insights on the basic processes of protein-DNA interactions evidencing the underlying complex dynamic phenomena involved, which combine three-dimensional and one-dimensional motion along the DNA chain. It has been demonstrated that protein molecules spend most of search time on the DNA chain with an extraordinary ability to find the target very quickly, in some cases, with two orders of magnitude faster than the diffusion limit. This unique property of protein-DNA search mechanism is known as facilitated diffusion . Several theoretical mechanisms have been suggested to describe the origin of facilitated diffusion. However, none of such models currently has the ability to fully describe the protein search strategy. In this paper, we suggest that the ability of proteins to identify consensus sequence on DNA is based on the entanglement of π-π electrons between DNA nucleotides and protein amino acids. The π-π entanglement is based on Quantum Walk (QW), through Coin-position entanglement (CPE). First, the protein identifies a dimer belonging to the consensus sequence, and localize a π on such dimer, hence, the other π electron scans the DNA chain until the sequence is identified. By focusing on the example of recognition of consensus sequences by EcoRV or EcoRI, we will describe the quantum features of QW on protein-DNA complexes during search strategy, such as walker quadratic spreading on a coherent superposition of different vertices and environment-supported long-time survival probability of the walker. We will employ both discrete- or continuous-time versions of QW. Biased and unbiased classical Random Walk (CRW) has been used for a long time to describe Protein-DNA search strategy. QW, the quantum version of CRW, have been widely studied for its applications in quantum information applications. In our biological application, the walker (the protein) resides at a vertex in a graph (the DNA structural topology). Differently to CRW, where the walker moves randomly, the quantum walker can hop along the edges in the graph to reach other vertices entering coherently a superposition across different vertices spreading quadratically faster than CRW analogous evidencing the typical speed up features of the QW. When applied to protein-DNA target search problem, QW gives the possibility to achieve the experimental diffusional motion of proteins over diffusion classical limits experienced along DNA chains exploiting quantum features such as CPE and long-time survival probability supported by environment. In turn, we come to the conclusion that, under quantum picture, the protein search strategy does not distinguish between one-dimensional (1D) and three-dimensional (3D) case. Significance Most biological processes are associated to specific protein molecules binding to specific target sequences of DNA. Experiments have revealed a paradoxical phenomenon that can be synthesized as follows: proteins generally diffuse on DNA very slowly, but they can find targets very fast overwhelming two orders of magnitude faster than the diffusion limit. This paradox is known as facilitated diffusion . In this paper, we demonstrate that the paradox is solved by invoking the quantum walk picture for protein search strategy. This because the protein exploits quantum properties, such as long-time survival probability due to coherence shield induced by environment and coin-position entanglement to identify consensus sequence, in searching strategy. To our knowledge, this is the first application of quantum walk to the problem of protein-DNA target search strategy.
... Our effort will be to show that if quantum version of CRW is used to describe the complex processes during protein-DNA interaction, the diffusional experimental results can be immediately obtained when the protein (the walker) exploits the speed-up properties of QW and peculiar entanglement-based behaviour enforced by the environmental fluctuations. Recently, there is a growing interest in the application of quantum properties, long-lived quantum coherence, superposition, tunneling and entanglement to biological systems (Mohseni et al., 2013;McFadden and Al-Khalili, 2018;Marais et al., 2018), ranging from enzyme catalysis (Kohen et al., 1999;Page et al., 1999), to photosynthesis (although this is a controversial subject) (Engel et al., 2007;Lee et al., 2007;Collini et al., 2010), to the implication of quantum entanglement in avian navigation (Ritz et al., 2004), to quantum tunneling in olfaction (Turin, 1996), genetic mutation (McFadden andAl-Khalili, 1999), while speculative suggestions pay attention on the link between quantum coherence and consciousness (Hameroff and Penrose, 1996). ...
Article
Full-text available
Protein-DNA interactions play a fundamental role in all life systems. A critical issue of such interactions is given by the strategy of protein search for specific targets on DNA. The mechanisms by which the protein are able to find relatively small cognate sequences, typically 15–20 base pairs (bps) for repressors, and 4–6 bps for re-striction enzymes among the millions of bp of non-specific chromosomal DNA have hardly engaged researchers for decades. Recent experimental studies have generated new insights on the basic processes of protein-DNA interactions evidencing the underlying complex dynamic phenomena involved, which combine three- dimensional and one-dimensional motion along the DNA chain. It has been demonstrated that protein mole-cules have an extraordinary ability to find the target very quickly on the DNA chain, in some cases, with two orders of magnitude faster than the diffusion limit. This unique property of protein-DNA search mechanism is known as facilitated diffusion. Several theoretical mechanisms have been suggested to describe the origin of facilitated diffusion. However, none of such models currently has the ability to fully describe the protein search strategy. In this paper, we suggest that the ability of proteins to identify consensus sequences on DNA is based on the entanglement of π-π electrons between DNA nucleotides and protein amino acids. The π-π entanglement is based on Quantum Walk (QW), through Coin-position entanglement (CPE). First, the protein identifies a dimer belonging to the consensus sequence, and localize a π on such dimer, hence, the other π electron scans the DNA chain until the sequence is identified. Focusing on the example of recognition of consensus sequences of EcoRV or EcoRI, we will describe the quantum features of QW on protein-DNA complexes during the search strategy, such as walker quadratic spreading on a coherent superposition of different vertices and environment-supported long- time survival probability of the walker. We will employ both discrete- or continuous-time versions of QW. Biased and unbiased classical Random Walk (CRW) have been used for a long time to describe the Protein-DNA search strategy. QW, the quantum version of CRW, has been widely studied for its applications in quantum information applications. In our biological application, the walker (the protein) resides at a vertex in a graph (the DNA structural topology). Differently to CRW, where the walker moves randomly, the quantum walker can hop along the edges in the graph to reach other vertices entering coherently a superposition across different vertices spreading quadratically faster than CRW analogous evidencing the typical speed up features of the QW. When applied to a protein-DNA target search problem, QW gives the possibility to achieve the experimental diffusional motion of proteins over diffusion classical limits experienced along DNA chains exploiting quantum features such as CPE and long-time survival probability supported by the environment. In turn, we come to the conclusion that, under quantum picture, the protein search strategy does not distinguish between one-dimensional (1D) and three-dimensional (3D) cases.
... Quantum entanglement of protons and other components of the genome can explain the epigenetic, and some authors involve a process of decoherence in the epigenetic evolution [133]. They argue that one of the main distinguishing features of the quantum description of composite systems is that, in general, the state of a compound system cannot be reconstructed from the rules of its subsystems, and this is the essence of quantum entanglement [134][135][136][137][138][139][140][141][142][143][144][145][146][147][148][149]. Page: 69 www.raftpubs.com ...
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The leading cause of illness in aging is a group known as Noncommunicable Diseases. There should be some meeting points that modify the cells homeostasis and impaired the cell physiology developing different diseases. Quantum physics studied the atomic and subatomic particles and revolutionized the reality perception with paradoxical and weird concepts. Heisenberg's uncertainty principle established that it is not possible to determine the two characteristic properties of particles with accuracy. Subatomic particles have a wave-particle duality. Two subatomic particles are entangled, something happening over here can have an instantaneous effect over there, no matter how far away there are. All these concepts have tried to apply to biology and life sciences, quantum biology is behind photosynthesis, mitochondrial respiration, enzyme activity, the sense of smell, animal migration, heredity's fidelity, and consciousness. We can apply all these concepts to diseases pathogeny. So, we describe quantum phenomena in oxidative stress, calcification, signal transduction, vitamin D production and cancer mutations. Aging diseases also could be explained by applying quantum physics concepts. It is a new, hard to believe, and an incredible path to be built, but we need to open the treatment options to our patients with new perspectives. Keywords: Oxidative stress; Calcification; Signal transduction; Vitamin D; Cancer mutations; Quantum phenomena
... While this subject remains controversial, a more established role for quantum mechanics is found in the tunnelling of electrons and protons in enzyme catalysis [7][8][9]. Beyond these examples of quantum biology, quantum entanglement has been implicated in avian navigation [10][11][12], while quantum tunnelling has been proposed to be involved in olfaction [13] and mutation [14,15]. More speculatively, some have suggested a link between quantum coherence and consciousness [16,17], though this view has little support within the neurobiology community. ...
Article
Quantum biology is usually considered to be a new discipline, arising from recent research that suggests that biological phenomena such as photosynthesis, enzyme catalysis, avian navigation or olfaction may not only operate within the bounds of classical physics but also make use of a number of the non-trivial features of quantum mechanics, such as coherence, tunnelling and, perhaps, entanglement. However, although the most significant findings have emerged in the past two decades, the roots of quantum biology go much deeper - to the quantum pioneers of the early twentieth century. We will argue that some of the insights provided by these pioneering physicists remain relevant to our understanding of quantum biology today. © 2018 The Author(s) Published by the Royal Society. All rights reserved.
Article
Prokaryotic (T4 phage) and eukaryotic (human) molecular genetic data demonstrating quantum information processing of coherent DNA states by transcriptase measurements (BioSystems 2009, 97, 73-89) are reviewed and possible contributions to quantum computing are suggested. Coherent states-within decoherence-free base pair sites-are introduced as consequences of interstrand hydrogen bond arrangement, keto-amino → enol-imine, where product protons are shared between two sets of indistinguishable electron lone-pairs, and thus, participate in coupled quantum oscillations at frequencies of ~ 1013 s-1. This quantum mixing of proton energy states introduces stability enhancements of ~ 0.25 to 7 Kcal/mole. Transcriptase genetic specificity is determined by hydrogen bond components contributing to the formation of complementary hydrogen bonds which, in these cases, are variable due to coupled quantum oscillations of coherent enol-imine protons. The transcriptase deciphers and executes genetic specificity instructions by implementing measurements on superposition proton states at G'-C', *G-*C and *A-*T sites in an interval Δt << 10-13 s. Transcriptase measurement on a coherent G' site can yield observable specification for 3 of the 4 quantum G' states where-just before transcriptase measurement-the ket for the two G' quantum protons is {box drawings light vertical}ψ > = α{box drawings light vertical}+ +> + β{box drawings light vertical}+-> + γ{box drawings light vertical}-+> + δ{box drawings light vertical}-->. Data demonstrating entanglement between coherent protons and transcriptase components are identified. After initiation of transcriptase measurement, model calculations indicate proton decoherence time, ηD, satisfies the relation Δt < ηD < 10-13 s. Decohered isomers participate in accurate Topal-Fresco replication to introduce base substitutions G' → T, G' → C, *C → T and *G → A, but coherent state *A-*T sites are evolutionarily deleted. Quantum uncertainty limits on amino protons drive the keto-amino → enol-imine arrangement. A 'rate constant' expression for introducing coherent states into duplex DNA is obtained. This allows an analytical expression for consequences of coherent states populating unstable (CAG)n repeats in human genomes. Measurements of 370 C lifetimes of the metastable keto-amino DNA hydrogen bond indicate a range of ~ 3000 to 60000 yrs. These results imply that natural selection at the quantum level has generated effective schemes (a) for introducing superposition proton states-at rates appropriate for DNA evolution-in decoherence-free subspaces and (b) for creating entanglement states that augment (i) transcriptase quantum processing and (ii) effective decoherence for complete (~100%) participation in Topal-Fresco replication of decohered isomers. In this scenario, the evolutionarily generated quantum information processing system has implemented coupled quantum proton oscillation in decoherence-free subspaces for 'low error' entangled qubits, which may provide insight into improved designs for room temperature quantum processing.
Article
Life emerged on Earth in an anaerobic environment, bathed in noxious gases. Among these gases, the role of hydrogen sulfide is significant since this gas, was required as a building block of life, contributed to abiogenic generation of organic compounds that gave rise to life and drove adaptations of life throughout its entire evolutionary path. During evolution, hydrogen sulfide contributed to sustaining life in face of harsh environmental conditions. Modern cells still utilize hydrogen sulfide as a signaling molecule, in pro and anti-inflammatory responses, for acquisition of tolerance against damage, in directing repair responses, as a source of energy and in modifying their genetic makeup and function to acquire a phenotype reminiscent of early life forms.
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Contents: Introduction in Quantum aspects of brain function, p 1-19 Quantum approaches to neurobiology: state of art, p 19-31 David Bohm: Wholeness and the implicate order, p 30-39 Henry Stapp: Attention, intention and quantum coherence, p 39-44 Roger Penrose: Consciousness and the geometry of universe, p 45-54 Stuart Hameroff: Objective reduction in brain tubules, p 55-68 Hiroomi Umezawa and Herbert Frohlich: Quantum brain dynamics, p 69-72 Mari Jibu & Kunio Yasue: Quantum field concepts, p 72-76 Johnjoe McFadden: Electromagnetic fields, p77-80 Gustav Bernroider: Ion channel coherence, p 80-85 Chris King: Cosmology, consciousness and chaos theory, p 85-92 Piero Scaruffi: Consciousness as a feature of matter, p 92-94 Danko Georgiev: the Quantum neuron, p 94-98 Andrei Khrennikov: Quantum like brain and other metaphoric QM models, p 98-102 Hu and Wu/ Persinger: Spin mediated consciousness, p 103- 106 Chris Clarke: Qualia and free will, p 106- 109 Herms Romijn: Photon mediated consciousness and recent models, p, 110-114 Stuart Kauffman: Consciousness & the poised state p, 114-116 Post-Bohmian concepts of an of a universal quantum field, p 117-121 Dirk Meijer: Cyclic operating mental workspace, p 121-131 Amit Goswami: The vacuum as a universal information field, p 132-146 Simon Raggett: A final attempt to a theory on consciousness p, 146-157 Note on cited sources, p 158 References, p 158-175 Internetsites, p 175
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Ticks are obligate hematophagous ectoparasites that infect domestic animals, humans, and wildlife. Ticks can transmit a wide range of pathogens (viruses, rickettsia, bacteria, parasites, etc.), and some of those are of zoonotic importance. Tick-borne diseases have a negative economic impact in several tropical and subtropical countries. With climate change, tick distribution and tick-associated pathogens have increased. Currently, tick control procedures have more environmental drawbacks and there are pitfalls in vaccination process. Since vaccinations have helped to prevent several diseases and infections, several vaccination trials are ongoing to control ticks and tick-borne pathogens. However, autoimmune reactions to vaccinations are reported as an adverse reaction since vaccines were used to protect against disease in humans and animals. The antibodies against the vaccine antigen might harm similar antigen in the host. Therefore, in this chapter, we attempt to shed light on the importance of raising awareness of possible adverse events associated with vaccinations and the methods that should be used to address this problem. In silico and lab work should be performed ahead of the vaccination process to evaluate the vaccine candidates and avoid the vaccination opposing consequences.
Chapter
This chapter is devoted to a model of the epigenetic cellular evolution based on the mathematical formalism of open quantum systems. We emphasize that, although in this book we restrict our QL-modeling to the epigenetic evolution, it is clear that the structure of the model allows it to be extended to describe evolution of biological organisms in general. We restrict the model to epigenetics, since here we can use a closer analogy with quantum mechanics and mimic behavior of a cell as behavior of a quantum particle. In general, we have to take into account cell death (annihilation in quantum terminology) and birth (creation). Mathematically, such a model is more complicated. One of the basic quantum information constructions used in this chapter is entanglement of quantum states. Our evolutionary model is based on representation of the epigenetic state of a cell as entanglement of various epigenetic markers.
Chapter
In this chapter, we will describe the quantum-mechanical models to accurately describe the process of creation of spontaneous, induced, and adaptive mutations. These models will be used to describe the processes of evolution and aging. The various theories of quantum evolution and epievolution will be studied as well. We then describe the Markovian chain-like classical and quantum-mechanical modeling of mutations and aging. In the same section, the hybrid quantum-classical biological channel model with memory is described as well. After that, various classical, semiclassical, and quantum models of cancer development are studied. The final section concludes the chapter.
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Synopsis As the title, The Entangled State of God and Humanity suggests, this lecture dispenses with the pre-Copernican, patriarchal, anthropomorphic image of God while presenting a case for a third millennium theology illuminated by insights from archetypal depth psychology, quantum physics, neuroscience and evolutionary biology. It attempts to smash the conceptual barriers between science and religion and in so doing, it may contribute to a Copernican revolution which reconciles both perspectives which have been apparently irreconcilable opposites since the sixteenth century. The published work of C.G. Jung, Wolfgang Pauli, David Bohm and Teilhard de Chardin outline a process whereby matter evolves in increasing complexity from sub-atomic particles to the human brain and the emergence of a reflective consciousness leading to a noosphere evolving towards an Omega point. The noosphere is the envelope of consciousness and meaning superimposed upon the biosphere a concept central to the evolutionary thought of visionary Jesuit palaeontologist Pierre Teilhard de Chardin (The Phenomenon of Man). His central ideas, like those of Jung with his archetypes, in particular that of the Self, provide intimations of a numinous principle implicit in cosmology and the discovery that in and through humanity, evolution becomes not only conscious of itself but also directed and purposive. Although in Jung's conception it was a " late-born offspring of the unconscious soul " , consciousness has become the mirror which the universe has evolved to reflect upon itself and in which its very existence is revealed. Without consciousness, the universe would not know itself. The implication for process theology is that God and humanity are in an entangled state so that the evolution of God cannot be separated from that of humankind.
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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.
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Prof. Jim-Al-Khalili explains the emerging field of quantum biology and discusses how this new discipline has developed from its inception in the 1920s until fruition in the late 1990s with the discovery of quantum effects in magnetoreception, olfaction, enzyme catalysis, and photosynthesis.
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Designing an efficient saccharide sensor in aqueous solution is an ongoing endeavour. Even though using hydrogen bonding groups on the sensor sounds like an efficient way for targeting the saccharides, it might lack accuracy due to the possibility of interaction with the solvent molecules. Boronic acid based sensors on the other hand, covalently and reversibly bind to saccharides with high sensitivity in aqueous medium. Many attempts are done to understand the mechanism of boronic acid’s reaction with diols. However, the binding affinity of fructose cannot be clearly identified in such attempts. This study employs a novel computational approach to increase both reactivity and selectivity of boronic acid towards diols. Using DFT, five different electronegative R-groups are simulated to calculate boronic acid’s reactivity towards diol by adding the tunnelling effect to the calculations, where higher electronegative R-groups reduce the proton donor-acceptor distance that induces proton tunnelling and increases the reaction rate.
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Introduction Vaccines are a major achievement in medical sciences, but the development of more effective vaccines against infectious diseases is essential for prevention and control of emerging pathogens worldwide. The application of omics technologies has advanced vaccinology through the characterization of host-vector-pathogen molecular interactions and the identification of candidate protective antigens. However, major challenges such as host immunity, pathogen and environmental factors and vaccine efficacy and safety need to be addressed. Vaccinomics provides a platform to address these challenges and improve vaccine efficacy and safety. Areas covered In this review we summarized current information on vaccinomics and proposed quantum vaccinomics approaches to further advance vaccine development through the identification and combination of antigen protective epitopes, the immunological quantum. The COVID-19 pandemic caused by SARS-CoV-2 is an example of emerging infectious diseases with global impact on human health. Expert opinion Vaccines are required for the effective and environmentally sustainable intervention for the control of emerging infectious diseases worldwide. Recent advances in vaccinomics provides a platform to address challenges to improve vaccine efficacy and implementation. As proposed here, quantum vaccinomics will contribute to vaccine development, efficacy and safety by facilitating antigen combinations to target pathogen infection and transmission in emerging infectious diseases.
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The aim of this essay is to analyze the role of quantum mechanics as an inherent characteristic of life. During the last ten years the problem of the origin of life has become an innovative research subject approached by many authors. The essay is divided in to three parts: the first deals with the problem of life from a philosophical and biological perspective. The second presents the conceptual and methodological basis of the essay which is founded on the Information Theory and the Quantum Theory. This basis is then used, in the third part, to discuss the different arguments and conjectures of a quantum origin of life. There are many philosophical views on the problem of life, two of which are especially important at the moment: reductive physicalism and biosystemic emergentism. From a scientific perspective, all the theories and experimental evidences put forward by Biology can be summed up in to two main research themes: the RNA world and the vesicular theory. The RNA world, from a physicalist point of view, maintains that replication is the essence of life while the vesicular theory, founded on biosystemic grounds, believes the essence of life can be found in cellular metabolism. This essay uses the Information Theory to discard the idea of a spontaneous emergency of life through replication. Understanding the nature and basis of quantum mechanics is fundamental in order to be able to comprehend the advantages of using quantum computation to be able increase the probabilities of existence of auto replicative structures. Different arguments are set forth such as the inherence of quantum mechanics to the origin of life. Finally, in order to try to resolve the question of auto replication, three scientific propositions are put forward: Q-life, the quantum combinatory library and the role of algorithms in the origin of genetic language.
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Reversion to Lys+ prototrophy in a haploid yeast strain containing a defined lys2 frameshift mutation has been examined. When cells were plated on synthetic complete medium lacking only lysine, the numbers of Lys+ revertant colonies accumulated in a time-dependent manner in the absence of any detectable increase in cell number. An examination of the distribution of the numbers of early appearing Lys+ colonies from independent cultures suggests that the mutations to prototrophy occurred randomly during nonselective growth. In contrast, an examination of the distribution of late appearing Lys+ colonies indicates that the underlying reversion events occurred after selective plating. No accumulation of Lys+ revertants occurred when cells were starved for tryptophan, leucine or both lysine and tryptophan prior to plating selectively for Lys+ revertants. These results indicate that mutations accumulate more frequently when they confer a selective advantage, and are thus consistent with the occurrence of adaptive mutations in yeast.
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Spontaneous mutants arise among nondividing populations of Escherichia coli in apparent response to selective conditions. In this report we investigate several hypotheses to account for the role of selection in the production of these "directed" or "adaptive" mutations. We found that the Lac+ phenotypes of some mutants that arise late after lactose selection are due to suppressor mutations that are unlinked to the mutant lacZ allele; thus the production of these Lac+ mutants does not require an information flow from successful proteins back to the DNA that encodes them. Transcriptional induction of the lac operon, even in the presence of another, utilizable carbon source, did not stimulate the occurrence of Lac+ mutants in the absence of lactose, indicating that the role of the selective agent is not merely to induce transcription. The absence of two DNA repair pathways-methyl-directed mismatch repair and alkylation repair-also did not result in an accumulation of Lac+ mutants in the absence of lactose, suggesting that these repair pathways are not normally responsible for correcting transient variants that might arise in the absence of selection. However, in one case the Lac+ mutation is likely to be due to a miscoding lesion occurring on the nontranscribed DNA strand, indicating that, at least in this instance, DNA replication is required before directed mutations can arise.
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A previous study has demonstrated that adaptive missense mutations occur in the trp operon of Escherichia coli. In this study it is shown that, under conditions of intense selection, a strain carrying missense mutations in both trpA and trpB reverts to Trp+ 10(8) times more frequently than would be expected if the two mutations were the result of independent events. Comparison of the single mutation rates with the double mutation rate and information obtained by sequencing DNA from double revertants show that neither our classical understanding of spontaneous mutation processes nor extant models for adaptive mutations can account for all of the observations. Despite a current lack of mechanistic understanding, it is clear that adaptive mutations can permit advantageous phenotypes that require multiple mutations to arise and that they appear enormously more frequently than would be expected.
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Recent reports have called into question the widespread belief "that mutations arise continuously and without any consideration for their utility" (in the words of J. Cairns) and have suggested that some mutations (which Cairns called "directed" mutations) may occur as specific responses to environmental challenges, i.e., they may occur more often when advantageous than when neutral. In this paper it is shown that point mutations in the trp operon reverted to trp+ more frequently under conditions of prolonged tryptophan deprivation when the reversions were advantageous, than in the presence of tryptophan when the reversions were neutral. The overall mutation rate, as determined from the rates of mutation to valine resistance and to constitutive expression of the lac operon, did not increase during tryptophan starvation. The trp reversion rate did not increase when the cells were starved for cysteine for a similar period, indicating that the increased reversion rate was specific to conditions where the reversions were advantageous. Two artifactual explanations for the observations, delayed growth of some preexisting revertants and cryptic growth by some cells at the expense of dying cells within aged colonies, were tested and rejected as unlikely. The trp+ reversions that occurred while trp- colonies aged in the absence of tryptophan were shown to be time-dependent rather than replication-dependent, and it is suggested that they occur by mechanisms different from those that have been studied in growing cells. A heuristic model for the molecular basis of such mutations is proposed and evidence consistent with that model is discussed. It is suggested that the results in this and previous studies can be explained on the basis of underlying random mechanisms that act during prolonged periods of physiological stress, and that "directed" mutations are not necessarily the basis of those observations.
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The cells in most tumors are found to carry multiple mutations; however, based upon mutation rates determined by fluctuation tests, the frequency of such multiple mutations should be so low that tumors are never detected within human populations. Fluctuation tests, which determine the cell-division-dependent mutation rate per cell generation in growing cells, may not be appropriate for estimating mutation rates in nondividing or very slowly dividing cells. Recent studies of time-dependent, "adaptive" mutations in nondividing populations of microorganisms suggest that similar measurements may be more appropriate to understanding the mutation origins of tumors. Here I use the ebgR and ebgA genes of Escherichia coli to measure adaptive mutation rates where multiple mutations are required for rapid growth. Mutations in either ebgA or ebgR allow very slow growth on lactulose (4-O-beta-D-galactosyl-D-fructose), with doubling times of 3.2 and 17.3 days, respectively. However, when both mutations are present, cells can grow rapidly with doubling times of 2.7 hr. I show that during prolonged (28-day) selection for growth on lactulose, the number of lactulose-utilizing mutants that accumulate is 40,000 times greater than can be accounted for on the basis of mutation rates measured by fluctuation tests, but is entirely consistent with the time-dependent adaptive mutation rates measured under the same conditions of prolonged selection.
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Selective incorporation of the stereospeciflcally deuterlated sugar moieties (<97 atom % 2H enhancements at H2′, H2″, H3′ and H5′/5′ sites, ∑85 atom % 2H enhancement at H4′ and ∑20 atom % 2H enhancement at H1′) in DNA and RNA by the ‘NMR-window’ approach has been shown to solve the problem of the resonance overlap [refs. 1, 2 & 3]. Such specific deuterium labelling gives much improved resolution and sensitivity of the residual sugar proton (i.e. H1′ or H4′) vicinal to the deuteriated centers (ref. 3). The T2 relaxation time of the residual protons also increases considerably in the partially-deuteriated (shown by underline) sugar residues in dlnucleotldes [d(CpG), d(GpC), d(ApT, d(TpA)], trlnucleotide r(A2′p5′A2′p5′A) and 20-mer DNA duplex 5′d(C1G2C3G4C5G6C7G8A9A10T11T12C13G14C15G16C17G18 C19G20)23′. The protons with shorter T2 can be filtered away using a number of different NMR experiments such as ROESY, MINSY or HAL. The NOE intensity of the cross-peaks in these experiments includes only straight pathway from H1′ to aromatic proton (I-I and 1-1 + 1) without any spin-diffusion. The volumes of these NOE cross-peaks could be measured with high accuracy as their intensity is 3 to 4 times larger than the corresponding peaks in the fully protonated residues in the normal NOESY spectra. The structural informations thus obtainable from the residual protons in the partially-deuteriated part of the duplex and the fully protonated part in the ‘NMR window’ can indeed complement each other.
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We have studied revertants, selected on lactose minimal agar medium, of the Escherichia coli lacZam strain that was first used by Cairns and his colleagues to demonstrate the phenomenon of "adaptive mutation." We have found, by performing appropriate reconstruction studies, that most of the late-arising Lac+ revertants of this lac amber strain (appearing as colonies in 3-5 days) are slow-growing ochre suppressor mutants that probably existed in the culture prior to plating and cannot, therefore, be classified as "adaptive." The appearance of a small number of fast-growing, late-arising Lac+ revertants may result from residual cell growth and turnover or from phenomena related to the fact that the lacZam mutation in strain SM195 is carried on an F' plasmid. Thus, the appearance of late-arising revertants in this lacZam system does not provide convincing evidence that selective conditions specifically increase the rate of occurrence of favorable mutations.
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One of the most studied examples of adaptive mutation is a strain of Escherichia coli, FC40, that cannot utilize lactose (Lac-) but that readily reverts to lactose utilization (Lac+) when lactose is its sole carbon source. Adaptive reversion to Lac+ occurs at a high rate when the Lac- allele is on an F' episome and conjugal functions are expressed. It was previously shown that nonselected mutations on the chromosome did not appear in the Lac- population while episomal Lac+ mutations accumulated, but it remained possible that nonselected mutations might occur on the episome. To investigate this possibility, a second mutational target was created on the Lac- episome by mutation of a Tn1O element, which encodes tetracycline resistance (Tetr), to tetracycline sensitivity (Tets). Reversion rates to Tetr during normal growth and during lactose selection were measured. The results show that nonselected Tetr mutations do accumulate in Lac- cells when those cells are under selection to become Lac+. Thus, reversion to Lac+ in FC40 does not appear to be adaptive in the narrow sense of the word. In addition, the results suggest that during lactose selection, both Lac+ and Tetr mutations are created or preserved by the same recombination-dependent mechanism.
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Adaptive mutations are mutations that occur in nondividing or very slowly dividing microbial cells during prolonged nonlethal selection and that are specific to the challenge of the selection in the sense that the only mutations that can be detected are those that provide a growth advantage to the cell. The phoPQ genes encode a two-component positively acting regulatory system that controls expression of at least 25 to 30 genes in Escherichia coli and Salmonella typhimurium. PhoPQ responds to a variety of environmental stress signals including Mg2+ starvation and nutritional deprivation. Here I show that disruption of phoP or phoQ by Tn10dCam significantly reduces the adaptive mutation rate to ebgR, indicating that the adaptive mutagenesis machinery is regulated, directly or indirectly, by phoPQ. The finding that it is regulated implies that adaptive mutagenesis does not simply result from a failure of various error correction mechanisms during prolonged starvation.
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It has been suggested that the primary evolutionary role of transposable elements is negative and parasitic. Alternatively, the target specificity and gene regulatory capabilities of many transposable elements raise the possibility that transposable element-induced mutations are more likely to be adaptively favorable than other types of mutations. Populations of Saccharomyces cerevisiae containing large amounts of variation for Ty1 genomic insertions were constructed, and the effects of Ty1 copy number on two components of fitness, yield and growth rate were determined. Although mean stationary phase density decreased with increased Ty1 copy number, the variance and range increased. The distributions of stationary phase densities indicate that many Ty1 insertions have negative effects on fitness, but also that some may have positive effects. To test directly for adaptively favorable Ty1 insertions, populations containing large amounts of variability for Ty1 copy number were grown in continuous culture. After 98-112 generations the frequency of clones containing zero Ty1 elements had decreased to approximately 0.0, and specific Ty1-containing clone families had predominated. Considering that most of the genetic variation in the populations was due to Ty1 transposition, and that Ty1 insertions had, on average, a negative effect on fitness, we conclude that Ty1 transposition events were directly responsible for the production of adaptive mutations in the clones that predominated in the populations.
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The environment surrounding a quantum system can, in effect, monitor some of the system's observables. As a result, the eigenstates of those observables continuously decohere and can behave like classical states.
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Scitation is the online home of leading journals and conference proceedings from AIP Publishing and AIP Member Societies
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It is argued that ultraviolet absorption by a DNA molecule (which gets biochemically attached to nearby photolyase enzyme so that the effect of uv absorption becomes macroscopically discernible) constitutes an intriguing example of quantum measurement. We point out that this does not merely illustrate the quantum measurement paradox in the hitherto unexplored arena of biological macromolecules, but is also instructive in highlighting specific difficulties inherent in various approaches to the measurement problem. {copyright} {ital 1996 The American Physical Society.}
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THE importance of deoxyribonucleic acid (DNA) within living cells is undisputed. It is found in all dividing cells, largely if not entirely in the nucleus, where it is an essential constituent of the chromosomes. Many lines of evidence indicate that it is the carrier of a part of (if not all) the genetic specificity of the chromosomes and thus of the gene itself. Until now, however, no evidence has been presented to show how it might carry out the essential operation required of a genetic material, that of exact self-duplication. We have recently proposed a structure¹ for the salt of deoxyribonucleic acid which, if correct, immediately suggests a mechanism for its self-duplication. X-ray evidence obtained by the workers at King's College, London², and presented at the same time, gives qualitative support to our structure and is incompatible with all previously proposed structures³. Though the structure will not
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The text is divided into 10 chapters, each of which covers a specific block of material and has its own references. The volume is meant to serve as a laboratory handbook and a desk reference, containing basic NMR theory, useful formulae and physical constants, and compiled data from the NMR literature. The volume attempts to cover the development of biological NMR through several decades of in vitro experiments that have laid the groundwork for and pointed to profitable areas of investigation for new in vivo techniques.
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The quantum Zeno effect is known as the inhibition of a system’s reversible dynamics by frequent measurements. Aharonov and Vardi [Phys. Rev. D 21, 2235 (1980)] proposed a scheme intimately related to the quantum Zeno effect. They showed that, by performing a dense sequence of measurements along a presumed path, the system is found to follow this—arbitrarily chosen—trajectory. The proof was based on the von Neumann projection hypothesis. In this paper we investigate whether this effect still holds if we model a realistic measurement process instead of the artificial instantaneous von Neumann collapse. We test the orientation of the Bloch vector of a two-level system using a third level and resonance fluorescence as the measuring apparatus. Therefore we are able to use a dynamical collapse governed by the three-level master equations. We show that a sequence of orientation measurements designed to monitor a particular trajectory indeed induces a dynamics exactly along this trajectory.
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In this article we give an operational meaning to an individual "Feynman path." In other words, we describe a process of dense measurements, made in temporal sequence, which check whether the particle moves along any given trajectory in space-time. We show that in this process the two assumptions of the space-time formulation of quantum mechanics, are realized: (a) The weight that the particle moves along a trajectory that has been checked by this process is the same for all trajectories, and in fact, we show that the particle follows, with probability 1, the trajectory that is being checked. (b) A phase is systematically accumulated, so that, at the end of this process, the state is multiplied by the familiar factor exp[(i/ℏ)∫Ldt]. As an immediate extension of the above formalism, we suggest a setup that measures the relative phase between any two trajectories. Finally, our approach points toward the possibility of extending the Feynman formalism in order to cover more general Hamiltonians.
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If the bits of computers are someday scaled down to the size of individual atoms, quantum mechanical effects may profoundly change the nature of computation itself. The wave function of such a quantum computer could consist of a superposition of many computations carried out simultaneously; this kind of parallelism could be exploited to make some important computational problems, like the prime factoring of large integers, tractable. However, building such a quantum computer would place undreamed of demands on the experimental realization of highly quantum-coherent systems; present-day experimental capabilities in atomic physics and other fields permit only the most rudimentary implementation of quantum computation.
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The energetic provisions for Löwdin's DNA mutational mechanism (Löwdin, P. O. Rev. Mod. Phys. 1963, 35, 724) of the formation of substitution DNA mutations were investigated for the guanine·cytosine Watson−Crick base pair. The structures studied involve the canonical base pair (GC1), rare base-pair tautomers that are formed from GC1 by the antiparallel simultaneous transfer of two protons in hydrogen bonds, and ion-pair structures that are formed by the transfer of a single proton. The geometries of these complexes were optimized by ab initio Hartree−Fock (HF) calculations using the 6-31G* basis set. At the same level, harmonic vibrational frequencies were determined. Nonplanar geometries featuring considerable propeller-twist angles and a pyramidal guanine amino group were found for base pairs involving the guanine anion and 6-hydroxyguanine. The relative stabilities and dissociation energies of the base pairs were determined at the higher MP2/6-31G**//HF/6-31G* level of theory. These methods were also used to locate transition states on the potential energy surface of the guanine·cytosine base pair. Starting from the geometries of two different transition states lying close to the ion-pair G-C+ minimum, the intrinsic reaction coordinate for the proton transfer from the canonical to the 6-hydroxyguanine·4-iminocytosine tautomer (GC2) was evaluated. We concluded that, in contrast to the adenine·thymine base pair (for which Löwdin's mutational mechanism is not supported by the present theoretical data), the GC1 → GC2 tautomeric transition is likely to occur in 1 in 106−109 guanine·cytosine base pairs. This frequency is significant from the point of view of the fidelity of DNA replication.
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SOME time ago it was proposed that the energy produced in biological activities is partly stored in various materials through excitation of coherent electrical vibrations (polarization waves). If strong enough, such excitations can be stabilized through non-linear effects leading to various types of deformations1,2. R. Ferreira (personal communication) has suggested that such considerations might be of importance for an understanding of the action of enzymes. In fact the properties of a model which I have considered recently (unpublished) seems to support this idea.
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On the basis of chemical considerations and model building, the Watson-Crick concept of complementary base pairing is extended to a wider range of DNA pairs that A-T and G-C (including A-C, G-T, A-A, G-G and G-A) by invoking imino or enol tautomers (or protonated species) and synisomers. The virtual absence of these additional base pairs from DNA is explained in terms of the low frequency with which these unfavoured forms occur and the two-step mechanism of DNA synthesis, whereby residues are first incorporated by the DNA polymerase and then checked. This base-pairing hypothesis is used to explain the origin, nature and level of spontaneous substitution mutations, their enhancement by base analogues, and the unique effects of certain mutator alleles.
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It has been suggested that the primary evolutionary role of transposable elements is negative and parasitic. Alternatively, the target specificity and gene regulatory capabilities of many transposable elements raise the possibility that transposable element-induced mutations are more likely to be adaptively favorable than other types of mutations. Populations of Saccharomyces cerevisiae containing large amounts of variation for Ty1 genomic insertions were constructed, and the effects of Ty1 copy number on two components of fitness, yield and growth rate were determined. Although mean stationary phase density decreased with increased Ty1 copy number, the variance and range increased. The distributions of stationary phase densities indicate that many Ty1 insertions have negative effects on fitness, but also that some may have positive effects. To test directly for adaptively favorable Ty1 insertions, populations containing large amounts of variability for Ty1 copy number were grown in continuous culture. After 98-112 generations the frequency of clones containing zero Ty1 elements had decreased to approximately 0.0, and specific Ty1-containing clone families had predominated. Considering that most of the genetic variation in the populations was due to Ty1 transposition, and that Ty1 insertions had, on average, a negative effect on fitness, we conclude that Ty1 transposition events were directly responsible for the production of adaptive mutations in the clones that predominated in the populations.
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Heisenberg's uncertainty principle in quantum mechanics underlies the genesis of evolutionary variability. When the uncertainty principle is coupled with the incontrovertible principle of the conservation of energy and material resources, there appears an uncertainty relationship between local fluctuations in the quantities to be conserved on a global scale and the rate of their local variation. Since the local fluctuations are accompanied by the non-vanishing rate of variation because of the uncertainty relationship, they generate subsequent fluctuations. Generativity latent in the uncertainty relationship is non-random and ubiquitous all through various evolutionary stages from abiotic synthesis of monomers and polymers up to the emergence of behavior-induced variability of organisms.
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Nucleic acids are replicated with conspicuous fidelity. Infrequently, however, they undergo changes in sequence, and this process of change (mutation) generates the variability that allows evolution. As the result of studies of bacterial variation, it is now widely believed that mutations arise continuously and without any consideration for their utility. In this paper, we briefly review the source of this idea and then describe some experiments suggesting that cells may have mechanisms for choosing which mutations will occur.
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Ubiquitous internal measurement of material origin and conservation laws, when combined together, uphold biological computation as a specific mode of quantum computation. Internal measurement supplemented by conservation laws can reproduce quantum mechanics or the uncertainty principle in particular. Furthermore, biological computation founded upon internal measurement provides an irreversible enhancement of organization and quantum coherency through non-algorithmic and non-programmable procedures of generating variations in accordance with the operation of the uncertainty principle.
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Artificial ferritin has been synthesized with control of both the magnetic state (antiferromagnetic or ferrimagnetic) and the particle size over an ofer of magnitude in the number of iron atoms. The magnetic properties of the artificial ferritin were compared with those of natural horse spleen ferritin in a range of temperatures (20 millikelvin to 300 kelvin) and fields (1 nanotesla to 27 tesla). In the classical regime, the blocking temperature was found to correlate with the average particle size. A correlation was also observed in the quantum regime between the resonance frequency of macroscopic quantum tunneling of the Neel vector and the particle size. At high magnetic fields (to 27 tesla), a spin flop transition with a strong dependence on orientation was seen in the natural ferritin, providing evidence of antiferromagnetism in this system.
Article
A physical interpretation of the Topal-Fresco [Nature 263, 285 (1976)] model for spontaneous base substitutions suggests that hydrogen-bonded DNA protons satisfy the criteria for a classical noninteracting isolated system. Accessible states for duplex G-C protons include the keto-amino state and the six complementary enol-imine isomers. Hydrogen-bonded enol and imine protons occupy symmetric double-minima created by the two sets of indistinguishable electron lone pairs and a single proton belonging to each enol-imine end group. These protons will consequently participate in coupled quantum mechanical flip-flop, tunneling back and forth between symmetric energy wells. This results in a quantum mixing of proton energy states where the lowest energy state will be a linear combination of available G-C isomers. The resulting conclusion is that metastable keto-amino G-C protons will populate accessible enol-imine stationary states at rates governed by quantum laws of statistical equilibrium, consistent with achieving the lowest energy condition for duplex G-C protons. Enol-imine G-C stationary states are bound more tightly, of the order of 3 to 12 kcal/mol, which requires a modified mode of Topal-Fresco replication that will inhibit reequilibration of enol and imine G and C template isomers and, thus, promote the formation of complementary mispairs. The model is demonstrated on time-dependent base substitutions expressed by T4 phage DNA systems where data are consistent with model explanations, including the prediction that time-dependent evolutionary transversion sites will exhibit both G-C-to-T-A and G-C-to-C-G transversions at replication, due to proton flip-flop alteration of G template genetic specificity. The observation that A-T sites are resistant to time-dependent evolutionary base substitutions, expressed exclusively at G-C sites, allows codons to be classified as either evolutionary sensitive (16 codons) or evolutionary resistant (8 codons). These criteria provide possible explanations for expansion properties of the CGG fragile X sequences. Enol-imine G-C stationary states appear to have been misdiagnosed as deamination of cytosine and oxidation of guanine to 8-hydroxy-guanine.
Article
Adaptive reversion of a +1 frameshift mutation in Escherichia coli, which requires homologous recombination functions, is shown here to occur by -1 deletions in regions of small mononucleotide repeats. This pattern makes improbable recombinational mechanisms for adaptive mutation in which blocks of sequences are transferred into the mutating gene, and it supports mechanisms that use DNA polymerase errors. The pattern appears similar to that of mutations found in yeast cells and in hereditary colon cancer cells that are deficient in mismatch repair. These results suggest a recombinational mechanism for adaptive mutation that functions through polymerase errors that persist as a result of a deficiency in post-synthesis mismatch repair.
In a previous article (Goswami, 1997), it was suggested that an application of quantum measurement theory under the auspices of a monistic idealist ontology (that consciousness is the ground of being) can solve many difficult problems of neo-Darwinism, e.g., alternating rapid creativity and homeostasis observed in evolution and the directionality, origin, and nature of life. In this article, we propose an epigenetic quantum mechanism to explain the connection of developmental processes and evolution, as has been evidenced in such controversial phenomena as directed mutation and phenocopies.
Article
The Darwinian paradigm of biological evolution is based on the independence of genetic variations from selection which occurs afterwards. However, according to the phenomenon of directed mutations, some genetic variations occur mostly when the conditions favorable for their growth are created. I propose that the explanation of this phenomenon should not rely on any special 'mechanism' for the appearance of directed mutations, but rather should be based on the principles of quantum theory. I consider a physical model of adaptation whereby a polarized photon, passing through a polarizer, changes its polarization according to the angle of the polarizer. This adaptation occurs by selection of the 'fitted' polarized state which exists as a component of superposition in the initial state of the photon. However, since the same state of the incoming photon should be decomposed differently depending on the angle of the polarizer, in this case the set of variations subjected to selection depends upon the selective conditions themselves. This reveals the crucial difference between this model of adaptation and canonical Darwinian selection. Based on this analogy, the capacity of a cell to grow in particular conditions is considered an observable of the cell; the plating experiments are interpreted as measurement of this observable. The only nontrivial suggestion of the paper states that the cell, analogously to the polarized photon, may be in a state of superposition of eigenfunctions of the operator which represents this observable, and with some probability can appear as a mutant upon the measurement. Alternative growth conditions correspond to the decomposition of the same state vector into a different superposition, consistent with measurement of a different observable and appearance of different mutants. Thus, consistent with the suggested analogy, directed mutations are explained as a result of random choice from the set of outcomes determined by the environment.
Article
The quantum Zero effect is the inhibition of transitions between quantum states by frequent measurements of the state. The inhibition arises because the measurement causes a collapse (reduction) of the wave function. If the time between measurements is short enough, the wave function usually collapses back to the initial state. We have observed this effect in an rf transition between two 9Be+ ground-state hyperfine levels. The ions were confined in a Penning trap and laser cooled. Short pulses of light, applied at the same time as the rf field, made the measurements. If an ion was in one state, it scattered a few photons; if it was in the other, it scattered no photons. In the latter case the wave-function collapse was due to a null measurement. Good agreement was found with calculations.
Article
The study of quantum zeno effect as model of quantum mechanical measurement theory is presented. The basic idea of of a quantum zeno effect in coordinate space is to measure the position of a moving particle while the quantum zeno effect in the double-well potential, using a two-level atom is to continuously monitor the coherent tunneling and study the measurement induced inhibition of the dynamics. A real measurement process is performed to investigate in particular, the position measurement, the corresponding zeno effect in a double-well potential and the measurement interactions as explained theoretically using master equation.
Article
Watson and Crick did not elaborate on their proposed mechanism of genetic replication in their original paper on the double helix of DNA, both in order to expedite publication and because Watson, in particular, harbored lingering fears, soon to be laid to rest, that the structure might prove incorrect. In this article, published five weeks after their original explication of the double helical structure of DNA, they clarified how the rule that governed the pairing of the bases (that adenine always bonds with thymine, and likewise guanine with cytosine) meant that the two chains of the DNA molecule were complementary, that the sequence of the bases on one chain determined the sequence on the other. When the two complementary chains of the DNA molecule unwound in the course of cell division, each formed a template for the synthesis of a second, complementary chain. The two new pairs were each a copy of the original pair, providing a mechanism for the exact duplication of the genetic material. Watson and Crick further posited that the genetic information was encoded in the seemingly random sequence of the bases, although they did not indicate how this sequence might control the synthesis of proteins, and so did not offer a full theory of genetic specificity, or take their argument substantially beyond that of their original Nature article.
Article
Present-day molecular biology, despite its name, is almost entirely committed to a macroscopic, classical picture of the organism; one in which quantum aspects play no role, except as a source of noise. Particularly is this true when dealing with informational aspects; especially "genetic information". The pervading metaphor here is an identification of "genetic information" with DNA sequence, and thence with program or software. We take a quite different view herein. If we presume, to the contrary, that microphysical processes play a role in primary genetic processes, then the "information" they can convey consists of observables evaluated on states. It is then natural to analogize a complex, consisting of (observed system + observer) with the biological partition between genome (observed system) and phenotype (observer). Such a picture immediately raises the deep issues surrounding "the measurement problem" in quantum mechanics. In our brief consideration of such matters, we suggest that standard quantum mechanics is too narrow to deal with the biological pictures, because it is inexorably tied to quantifications of classical, conservative systems; there is no such for an organism. Rather, we are led to consider subsystems we call "sites", for which there is in principle no Hamiltonian. We then query the extent to which such "genetic information" is already subsumed in traditional observables a physicist would measure in vitro in a laboratory. We suggest there is no reason to believe that "genetic information", manifested in bioactivities, is reducible to these. Finally, we contrast this view of "genetic information" with more traditional ideas of program and computability. We argue that computability (algorithms) are entirely classical concepts, in a physical sense, and quite inadequate for a biology (or even a physics) in which quantum measurement processes are important.
Article
Quantum mechanics works exceedingly well in all practical applications. No example of conflict between its predictions and experiment is known. Without quantum physics we could not explain the behavior of solids, the structure and function of DNA, the color of the stars, the action of lasers or the properties of superfluids. Yet well over half a century after its inception, the debate about the relation of quantum mechanics to the familiar physical world continues. How can a theory that can account ith precision for everything we can measure still be deemed lacking? The environment surrounding a quantum system can, in effect, monitor some of the system&apos;s observobles. As a result, the eigenstates of those observables continuously decohere and can behave like classical states.
Spontaneous point mutations that occur more often when advantageous than when neutral Genet-ics 126, 5–16. mechanism Adaptive mutagenesis at ebgR is regulated by PhoPQ
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The extraordinary dielectric properties of biological materials and the action of enzymes
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Adaptive mutation by deletions in small mononucleotide repeats [see comments]
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