Possibility of high performance quantum computation by superluminal evanescent photons in living systems

Penrose and Hameroff have suggested that microtubules in living systems function as quantum computers by utilizing evanescent photons. On the basis of the theorem that the evanescent photon is a superluminal particle, the possibility of high performance computation in living systems has been studied. From the theoretical analysis, it is shown that the biological brain can achieve large quantum bits computation compared with the conventional processors at room temperature.     

Properties of biophotons and their theoretical implications

The word "biophotons" is used to denote a permanent spontaneous photon emission from all living systems. It displays a few up to some hundred photons/(s x cm2) within the spectral range from at least 260 to 800 nm. It is closely linked to delayed luminescence (DL) of biological tissues which describes the long term and ultra weak reemission of photons after exposure to light illumination. During relaxation DL turns continuously into the steady state biophoton emission, where both, DL and biophoton emission exhibit mode coupling over the entire spectrum and a Poissonian photo count distribution. DL is representing excited states of the biophoton field. The physical properties indicate that biophotons originate from fully coherent and sometimes even squeezed states. The physical analysis provides thermodynamic and quantum optical interpretation, in order to understand the biological impacts of biophotons. Biological phenomena like intracellular and intercellular communication, cell growth and differentiation, interactions among biological systems (like "Gestaltbildung" or swarming), and microbial infections can be understood in terms of biophotons. "Biophotonics", the corresponding field of applications, provide a new powerful tool for assessing the quality of food (like freshness and shelf life), microbial infections, environmental influences and for substantiating medical diagnosis and therapy.     

"Either-or" two-slit interference: stable coherent propagation of individual photons through separate slits

In quantum theory, nothing that is observable, be it physical, chemical, or biological, is separable from the observer. Furthermore, ". all possible knowledge concerning that object is given by its wave function" (Wigner, E. 1967. Symmetries and Reflections. Indiana University Press, Bloomington, IN), which can only describe probabilities of future events. In physical systems, quantum mechanical probabilistic events that are microscopic must, in turn, account for macroscopic events that are associated with a greater degree of certainty. In biological systems, probabilistic statistical mechanical events, such as secretion of microscopic synaptic vesicles, must account for macroscopic postsynaptic potentials; probabilistic single-channel events sum to produce a macroscopic ionic current across a cell membrane; and bleaching of rhodopsin molecules (responsible for quantal potential "bumps") produces a photoreceptor generator potential. Among physical systems, a paradigmatic example of how quantum theory applies to the observation of events concerns the interactions of particles (e.g., photons, electrons) with the two-slit apparatus to generate an interference pattern from a single common light source. For two-slit systems that use two independent laser sources with brief (<1 ms) intervals of mutual coherence (Paul, H. 1986. Rev. Modern Phys. 58:209-231), each photon has been considered to arise from both beams and has a probability amplitude to pass through each of the two slits. Here, a single laser source two-slit interference system was constructed so that each photon has a probability amplitude to pass through only one or the other, but not both slits. Furthermore, all photons passing through one slit could be distinguished from all photons passing through the other slit before their passage. This "either-or" system produced a stable interference pattern indistinguishable from the interference produced when both slits were accessible to each photon. Because this system excludes the interaction of one photon with both slits, phase correlation of photon movements derives from the "entanglement" of all photon wave functions due to their dependence on a common laser source. Because a laser source (as well as Young's original point source) will have stable time-averaged spatial coherence even at low intensities, the "either-or" two-slit interference can result from distinct individual photons passing one at a time through one or the other slit-rather than wave-like behavior of individual photons. In this manner, single, successive photons passing through separate slits will assemble over time in phase-correlated wave distributions that converge in regions of low and high probability.     

Quantum nature of photon signal emitted by Xanthoria parietina and its implications to biology

The properties of living systems are usually described in the semi-classical framework that makes phenomenological division of properties into four classes--matter, psyche, soft consciousness and hard consciousness. Quantum framework provides a scientific basis of this classification of properties. The scientific basis requires the existence of macroscopic quantum entity entangled with quantum photon field of a living system. Every living system emits a photon signal with features indicating its quantum nature. Quantum nature of the signal emitted by a sample of X. parietina is confirmed by analysing photo count distributions obtained in 20000 measurements of photon number in contiguous bins of sizes of 50, 100, 200, 300 and 500 ms. The measurements use a broadband detector sensitive in 300-800 nm range (Photo count distributions of background noise and observed signal are measured similarly. These measurements background noise corrected squeezed state parameters of the signal. The parameters are signal strength expressed in counts per bin, r = 0.06, theta = 2.76 and phi = 0.64. The parameters correctly reproduce photo count distribution of any bin size in 50 ms-6 s range. The reproduction of photo count distributions is a credible evidence of spontaneous emission of photon signal in a quantum squeezed state for macroscopic time by the sample. The evidence is extrapolated to other living systems emitting similar photon signals. It is suggested that every living system is associated with a photon field in squeezed state. The suggestion has far reaching implications to biology and provides two ways of observing and manipulating a living system--either through matter or field or a combination of the two. Some implications and possible scenarios are elaborated.     

Biological probability: cognitive processes of generating probabilities of events in biological systems.

This paper analyses relationships between probabilities of events happening in biological systems (or probabilistic disposition of systems) and cognitive properties of biological entities comprising such systems. Two kinds of cognitive properties are identified as relevant to the current problem: the ability to respond differently against different configurations of the environment (discriminability of cognition), and the ability to make an appropriate response to maintain a particular relation with the environment (selectivity of cognition). A basic framework bridging the two features of living systems, probabilistic disposition and the cognitive properties, is presented towards a general theory explaining the process generating probabilities of biological events. In this framework, a deterministic model of a system of entities is developed, in which objects are described as subjects that cognize events (i.e. entities as cognizers). Cognition is used in a wider sense, including not only biotic but also abiotic, and cognizers are conceptually distinguished from the meta-observer who describes the system externally. Based on this perspective, this paper seeks to explicate how events can occur in an uncertain, probabilistic manner, if observed from a cognizer viewpoint, even under a deterministic system. Each cognizer is identified with both the set of states that are actually taken, and its motion function which maps its state uniquely to a successor state depending on the current states of itself and of the rest of cognizers constituting the system. The model analysis reveals that the cognitive properties, discriminability and selectivity, of a cognizer can contribute to determining the probability of an event encountered by the cognizer itself-in particular, discrimination reducing the uncertainty in events occurrence for the cognizer. Biological implication of this result is discussed focusing on the concept of the probability of survival and reproduction.     

Basic biological research with the striated muscle by using cryotechniques and electron microscopy.

Several basic mechanisms underlying living phenomena are not really understood. Unequivocal interpretations of data concerning the following phenomena--to name but a few--are missing: cellular accumulation of potassium; cellular exclusion of sodium, cell volume regulation, shape change of cells (e.g. of muscle cells during contraction), electrical potential differences between inside and outside of living cells. The theoretical treatment of these phenomena as found in all current textbooks is based on the membrane-pump theory (MPT) with the following essential features. The bulk of the main cellular cation K+ is freely dissolved in free cellular water and membrane-situated pumps are responsible for the high level of K+ and the low level of Na+ found in virtually all living cells. On the other hand, the above mentioned phenomena are explained by the association-induction hypothesis (AIH) without the proposal of membrane-situated pumps and with the postulations of selective K+ adsorption to cellular proteins and of a specific cell water structure which has a low solvency for Na+ and other solutes. Experimental findings are reviewed which contradict the MPT and support the AIH. In addition, electron microscopic experiments with cryoprocessed striated muscle are reviewed which establish cellular K+ binding (adsorption) and a cellular water structure which is different from that of normal free water. Cryoexperiments with the striated muscle and model systems are proposed which may help to obtain further information on the specific interactions between proteins, ions, and water in living cells.     

A bistable model of cell polarity

Ultrasensitivity, as described by Goldbeter and Koshland, has been considered for a long time as a way to realize bistable switches in biological systems. It is not as well recognized that when ultrasensitivity and reinforcing feedback loops are present in a spatially distributed system such as the cell plasmamembrane, they may induce bistability and spatial separation of the system into distinct signaling phases. Here we suggest that bistability of ultrasensitive signaling pathways in a diffusive environment provides a basic mechanism to realize cell membrane polarity. Cell membrane polarization is a fundamental process implicated in several basic biological phenomena, such as differentiation, proliferation, migration and morphogenesis of unicellular and multicellular organisms. We describe a simple, solvable model of cell membrane polarization based on the coupling of membrane diffusion with bistable enzymatic dynamics. The model can reproduce a broad range of symmetry-breaking events, such as those observed in eukaryotic directional sensing, the apico-basal polarization of epithelium cells, the polarization of budding and mating yeast, and the formation of Ras nanoclusters in several cell types.     

Bio-soliton model that predicts non-thermal electromagnetic frequency bands,that either stabilize or destabilize living cells

Solitons, as self-reinforcing solitary waves, interact with complex biological phenomena such as cellular self-organization. A soliton model is able to describe a spectrum of electromagnetism modalities that can be applied to understand the physical principles of biological effects in living cells, as caused by endogenous and exogenous electromagnetic fields and is compatible with quantum coherence. A bio-soliton model is proposed, that enables to predict which eigen-frequencies of non-thermal electromagnetic waves are life-sustaining and which are, in contrast, detrimental for living cells. The particular effects are exerted by a range of electromagnetic wave eigen-frequencies of one-tenth of a Hertz till Peta Hertz that show a pattern of 12 bands, and can be positioned on an acoustic reference frequency scale. The model was substantiated by a meta-analysis of 240 published articles of biological electromagnetic experiments, in which a spectrum of non-thermal electromagnetic waves were exposed to living cells and intact organisms. These data support the concept of coherent quantized electromagnetic states in living organisms and the theories of Fröhlich, Davydov and Pang. It is envisioned that a rational control of shape by soliton-waves and related to a morphogenetic field and parametric resonance provides positional information and cues to regulate organism-wide systems properties like anatomy, control of reproduction and repair.     

Multi-scale lung modeling

Multi-scale modeling of biological systems has recently become fashionable due to the growing power of digital computers as well as to the growing realization that integrative systems behavior is as important to life as is the genome. While it is true that the behavior of a living organism must ultimately be traceable to all its components and their myriad interactions, attempting to codify this in its entirety in a model misses the insights gained from understanding how collections of system components at one level of scale conspire to produce qualitatively different behavior at higher levels. The essence of multi-scale modeling thus lies not in the inclusion of every conceivable biological detail, but rather in the judicious selection of emergent phenomena appropriate to the level of scale being modeled. These principles are exemplified in recent computational models of the lung. Airways responsiveness, for example, is an organ-level manifestation of events that begin at the molecular level within airway smooth muscle cells, yet it is not necessary to invoke all these molecular events to accurately describe the contraction dynamics of a cell, nor is it necessary to invoke all phenomena observable at the level of the cell to account for the changes in overall lung function that occur following methacholine challenge. Similarly, the regulation of pulmonary vascular tone has complex origins within the individual smooth muscle cells that line the blood vessels but, again, many of the fine details of cell behavior average out at the level of the organ to produce an effect on pulmonary vascular pressure that can be described in much simpler terms. The art of multi-scale lung modeling thus reduces not to being limitlessly inclusive, but rather to knowing what biological details to leave out.     

Physics,biology, and sociology: A reappraisal

To the extent that all biological phenomena are perceivable only through their physical manifestations, it may be justified to assume that all biological phenomena will be eventually represented in terms of physics; perhaps not of present day physics, but of some “extended” form of it. However, even if this should be correct, it must be kept in mind that representing individual biological phenomena in terms of physics is not the same as deducing from known physical laws the necessity of biological phenomena. Drawing an analogy from pure mathematics, it is possible that while every biological phenomenon may be represented in terms of physics, yet biological statements represent a class of “undecidable” statements within the framework of physics. Such a conjecture is reinforced by the history of physics itself and illustrated on several examples. The 19th century physicists tried in vain todeduce electromagnetic phenomena from mechanical ones. A similar situation may exist in regard to biological and social sciences. Quite generally, the possibility of representing a class B phenomena in terms of class A phenomena does not imply that the phenomena of class B can be deduced from those of class A. The consequences of the above on the relation between physics, biology, and sociology are studied. A tentative postulational formulation of basic biological principles are given and some consequences are discussed. It is pointed out that not only can the study of biological phenomena throw light on some physical phenomena, but that the study of social phenomena may be of value for the understanding of the structures and functions of living organisms. The possibility of a sort of “socionics” is indicated.     

An abstract cell model that describes the self-organization of cell function in living systems

The principal aim of systems biology is to search for general principles that govern living systems. We develop an abstract dynamic model of a cell, rooted in Mesarovi? and Takahara's general systems theory. In this conceptual framework the function of the cell is delineated by the dynamic processes it can realize. We abstract basic cellular processes, i.e., metabolism, signalling, gene expression, into a mapping and consider cell functions, i.e., cell differentiation, proliferation, etc. as processes that determine the basic cellular processes that realize a particular cell function. We then postulate the existence of a 'coordination principle' that determines cell function. These ideas are condensed into a theorem: If basic cellular processes for the control and regulation of cell functions are present, then the coordination of cell functions is realized autonomously from within the system. Inspired by Robert Rosen's notion of closure to efficient causation, introduced as a necessary condition for a natural system to be an organism, we show that for a mathematical model of a self-organizing cell the associated category must be cartesian closed. Although the semantics of our cell model differ from Rosen's (M,R)-systems, the proof of our theorem supports (in parts) Rosen's argument that living cells have non-simulable properties. Whereas models that form cartesian closed categories can capture self-organization (which is a, if not the, fundamental property of living systems), conventional computer simulations of these models (such as virtual cells) cannot. Simulations can mimic living systems, but they are not like living systems.     

Discovering functions and revealing mechanisms at molecular level from biological networks

With the increasingly accumulated data from high-throughput technologies, study on biomolecular networks has become one of key focuses in systems biology and bioinformatics. In particular, various types of molecular networks (e.g., protein-protein interaction (PPI) network; gene regulatory network (GRN); metabolic network (MN); gene coexpression network (GCEN)) have been extensively investigated, and those studies demonstrate great potentials to discover basic functions and to reveal essential mechanisms for various biological phenomena, by understanding biological systems not at individual component level but at a system-wide level. Recent studies on networks have created very prolific researches on many aspects of living organisms. In this paper, we aim to review the recent developments on topics related to molecular networks in a comprehensive manner, with the special emphasis on the computational aspect. The contents of the survey cover global topological properties and local structural characteristics, network motifs, network comparison and query, detection of functional modules and network motifs, function prediction from network analysis, inferring molecular networks from biological data as well as representative databases and software tools.     

Coherent phenomena in photosynthetic light harvesting: part two—observations in biological systems

Considerable debate surrounds the question of whether or not quantum mechanics plays a significant, non-trivial role in photosynthetic light harvesting. Many have proposed that quantum superpositions and/or quantum transport phenomena may be responsible for the efficiency and robustness of energy transport present in biological systems. The critical experimental observations comprise the observation of coherent oscillations or “quantum beats” via femtosecond laser spectroscopy, which have been observed in many different light harvesting systems. Part Two of this review aims to provide an overview of experimental observations of energy transfer in the most studied light harvesting systems. Length scales, derived from crystallographic studies, are combined with energy and time scales of the beats observed via spectroscopy. A consensus is emerging that most long-lived (hundreds of femtoseconds) coherent phenomena are of vibrational or vibronic origin, where the latter may result in coherent excitation transport within a protein complex. In contrast, energy transport between proteins is likely to be incoherent in nature. The question of whether evolution has selected for these non-trivial quantum phenomena may be an unanswerable question, as dense packings of chromophores will lead to strong coupling and hence non-trivial quantum phenomena. As such, one cannot discern whether evolution has optimised light harvesting systems for high chromophore density or for the ensuing quantum effects as these are inextricably linked and cannot be switched off.     

A new xanthene‐based two‐photon fluorescent probe for the imaging of 1,4‐dithiothreitol (DTT) in living cells

1,4‐Dithiothreitol (DTT) has wide applications in cell biology and biochemistry. Development of effective methods for monitoring DTT in biological systems is important for the safe handling and study of toxicity to humans. Herein, we describe a two‐photon fluorescence probe (Rh‐DTT) to detect DTT in living systems for the first time. Rh‐DTT showed high selectivity and sensitivity to DTT. Rh‐DTT can be successfully used for the two‐photon imaging of DTT in living cells, and also can detect DTT in living tissues and mice.     

Randomness and multilevel interactions in biology

The dynamic instability of living systems and the “superposition” of different forms of randomness are viewed, in this paper, as components of the contingently changing, or even increasing, organization of life through ontogenesis or evolution. To this purpose, we first survey how classical and quantum physics define randomness differently. We then discuss why this requires, in our view, an enriched understanding of the effects of their concurrent presence in biological systems’ dynamics. Biological randomness is then presented not only as an essential component of the heterogeneous determination and intrinsic unpredictability proper to life phenomena, due to the nesting of, and interaction between many levels of organization, but also as a key component of its structural stability. We will note as well that increasing organization, while increasing “order”, induces growing disorder, not only by energy dispersal effects, but also by increasing variability and differentiation. Finally, we discuss the cooperation between diverse components in biological networks; this cooperation implies the presence of constraints due to the particular nature of bio-entanglement and bio-resonance, two notions to be reviewed and defined in the paper.     

Do we live in a quantum world? Advances in multidimensional coherent spectroscopies refine our understanding of quantum coherences and structural dynamics of biological systems

The issue of quantum effects in biological functions reduces to determining the relevant length and/or time scales over which phase relationships (coherence) in the wave properties of matter are conserved and lead to observable interference effects. Recent advances in femtosecond laser-based two-dimensional spectroscopy and coherent control have made it possible to directly determine the relevant timescales of quantum coherence in biological systems and even manipulate such effects, respectively, and also provide direct information on the interactions between the different degrees of freedom (electronic and nuclear) with sufficient time resolution to catch the very chemical processes driving biological functions in action. The picture that is emerging is that there are primary events in biological processes that occur on timescales commensurate with quantum coherence effects.     

Differential dynamic properties of scleroderma fibroblasts in response to perturbation of environmental stimuli

Diseases are believed to arise from dysregulation of biological systems (pathways) perturbed by environmental triggers. Biological systems as a whole are not just the sum of their components, rather ever-changing, complex and dynamic systems over time in response to internal and external perturbation. In the past, biologists have mainly focused on studying either functions of isolated genes or steady-states of small biological pathways. However, it is systems dynamics that play an essential role in giving rise to cellular function/dysfunction which cause diseases, such as growth, differentiation, division and apoptosis. Biological phenomena of the entire organism are not only determined by steady-state characteristics of the biological systems, but also by intrinsic dynamic properties of biological systems, including stability, transient-response, and controllability, which determine how the systems maintain their functions and performance under a broad range of random internal and external perturbations. As a proof of principle, we examine signal transduction pathways and genetic regulatory pathways as biological systems. We employ widely used state-space equations in systems science to model biological systems, and use expectation-maximization (EM) algorithms and Kalman filter to estimate the parameters in the models. We apply the developed state-space models to human fibroblasts obtained from the autoimmune fibrosing disease, scleroderma, and then perform dynamic analysis of partial TGF-beta pathway in both normal and scleroderma fibroblasts stimulated by silica. We find that TGF-beta pathway under perturbation of silica shows significant differences in dynamic properties between normal and scleroderma fibroblasts. Our findings may open a new avenue in exploring the functions of cells and mechanism operative in disease development.     

Deformability, dynamics, and remodeling of cytoskeleton of the adherent living cell

A trail of evidence has led to an unexpected intersection of topical issues in condensed matter physics and cytoskeletal biology. On the one hand, the glass transition and the jammed state are two outstanding unsolved problems; such systems are out-of-equilibrium, disordered, and their transitions between solid-like and liquid-like states are not understood. On the other hand, cellular systems are increasingly being considered as interconnected maps of protein interactions that are highly specific and tightly regulated but, even when such comprehensive maps become available, they may be insufficient to define biological function at the integrative level because they do not encompass principles that govern dynamics at intermediate (meso) scales of organization. It is interesting, therefore, that the cytoskeleton of the living cell shows physical properties and remodeling dynamics with all the same signatures as soft inert condensed systems, although with important differences as well. Data reviewed here suggest that trapping, intermittency, and approach to kinetic arrest represent mesoscale features of collective protein-protein interactions linking underlying molecular events to integrative cellular functions such as crawling, contraction and remodeling. Because these are crucial cell functions, this synthesis may offer new perspectives on a variety of disorders including infectious disease, cardiovascular disease, asthma and cancer.