Prigogine’s 1978 concept of dissipative structures, drawing parallels with living systems, forms the basis for exploring life’sunique traits. However, these identified similarities prove insufficient in capturing the entirety of life. To address this gap, ourproposed modeling approach emphasizes the distinctive ability of living organisms to observe other systems—an attributeintricately tied to quantum mechanics’ "measurement" processes, as highlighted by Howard Pattee. This article introduces acomprehensive mathematical model centered on quantum dynamical dissipative systems, portraying living systems as entitiesdefined by their observational capacities within this framework. The exploration extends to the core dynamics of these systemsand the intricacies of biological cells, including the impact of membrane potentials on protein states. Within this theoreticalstructure, the model is expanded to multicellular living systems, revealing how cells observe quantum dynamical systemsthrough protein state changes influenced by membrane potentials. The conclusion acknowledges the current theoreticalstatus of the model, underscoring the crucial need for experimental validation, particularly regarding the superposition state ofmembrane proteins under the influence of an electric field.

We look into the Age(in years) vs Amplitude of accommodation(in Diopters) of eye.We draw the natural logarithm of the age, normalised, starting with an amplitude of accommodation of an eye vs the natural logarithm of the the amplitude of accommodation of the eye, normalised. We conclude that the Age vs Amplitude of accommodation of eyes, can be characterised by a magnetisation curve of a Spin-Glass in thepresence of a little external magnetic field.

The Silies has been investigated as a possible al-- the DNA double helix - sometimes doubles up again. Researchers have now found this quadruple-stranded form in healthy human cells for the first time. Speculate that the quadruplex structure forms to hold the molecule open and facilitate the reading of the genetic code and thus the production of proteins. G-quadruplex DNA is a four-stranded structure made that can form a ’knot’ in the DNA of living cells. In these terms, it was analyzed through computationalcalculations, via MM(Molecular Mechanics), and byab initio Restricted Hartree-Fock (RHF) method, on a simple STO-3G (Slater-type orbitals with 3 Gaussians) basis, the possibility of a DNA macromolecule based on Silicon. From the basic structure of 1bna, however, you assume conditions without the presence of Carbon, replacing it with Silicon. It was obtained a cluster of G-quadruplex DNA, forming a cocoon, with great possibility for the pharmaceutical industry in capturingmolecules foreign to human DNA.

We study A Dictionary of Zoology, the fourth edition, by Michael Allaby from the Oxford University Press. We draw the natural logarithm of the number of head entries, normalised, starting with a letter vs the natural logarithm of the rank of the letter, normalised. We conclude that the Dictionary can be characterised by BP(4, $beta H=0.01$), i.e. the Bethe-Peierls curve in the presence of four nearest neighbours and little external magnetic field, $beta H= 0.01$. $beta$ is $frac{1}{k_{B}T}$ where, T is temperature and $k_{B}$ is the tiny Boltzmann constant.

We study Oxford Dictionary of Biology, the eighth edition, by Robert S. Hine. We draw the natural logarithm of the number of entries, head as well as all, normalised, starting with a letter vs the natural logarithm of the rank of the letter, normalised. We conclude that the Dictionary can be characterised by BP(4, $beta H=0.01$), i.e.the Bethe-Peierls curve in the presence of four nearest neighbours and little external magnetic field, $beta H= 0.01$. $beta$ is $frac{1}{k_{B}T}$ where, T is temperature and $k_{B}$ is the tiny Boltzmann constant.

We consider the nerve as the elastic string, the left end of which is fixed at the beginning of the coordinate system, the right end is fixed at point l and mass m is fixed between the ends of the string. We determine the classical and the quantum vibration of such system. The quantum motion is obtained by the so-called non-conventional oscillator quantization method by author. The proposed model can be also related in the modified form to the problem of the Moessbauer effect, being the recoilless nuclear resonance uorescence, which is the resonant and recoil-free emission and absorption of gamma radiation by atomic nuclei bound in a solid. (Mossbauer,1958). It is not excluded that our oscillator quantization of the string can be extended to generate the new way of the string theory of matter and physiology of nerves.

A structured model of the HPA axis that includes the glucocorticoid receptor (GR) is considered. The model includes nonlinear dynamics of pituitary GR synthesis. The nonlinear eect arises from the fact that GR homodimerizes after cortisol activation and induces its own synthesis in the pituitary. This homodimerization makes possible two stable steady states (low and high) and one unstable state. The model includes also delay on stress. It is shown that concurrence between trajectories of dynamical system, which are produced by the unstable manifold and the value of delay time τ produce slow oscillating asymptotic periodic oscillations of cortisol with a period, which is grater then 2τ. It is shown that such oscillations exist only in an interval τ1 < τ < τ2 , where exact formulas for τ1 and τ2 has been obtained. Such oscillation arise when an initial values of stress are lager of some threshold.

he core of the work is based on the replace- ment of carbon atoms by silicon atoms, on the basis of four standard bases of DNA: A, C, G and T (adenine, cytosine, guanine, thymine). Determining with minimum computational methods via "ab initio" Hartree-Fock methods, infrared spectrum and their peak absorbance frequencies. The option for simple replacement of carbon by silicon is due to the peculiar characteristics between both. Atomic interactions under non-carbon conditions were studied, with only the Hydrogen, Silicon, Nitrogen and Oxygen atoms, in STP (Standard Temperature and Pressure), for the four standard bases of DNA, A, C, G and T, thus obtaining by quantum chemistry four new compounds, named here as: ASi, CSi, GSi and TSi. Computational calculations admit the possibility of the formation of such molecules, their existence being possible via quantum chemistry. Calculations obtained in the "ab initio" Unrestricted and Restrict Hartree-Fock method, (UHF and RHF) in the set of basis used Effective core potential (ECP) minimal basis, UHF CEP-31G (ECP split valance) and UHF CEP-121G (ECP triple-split basis), CCpVTZ (Correlation-consistent valence-only basis sets triple-zeta) and 6-311G**(3df, 3pd) (Gaussian functions quadruple-zeta basis sets).

This article proposes a viral diffusion model (like Covid-19 pandemic) in the ordinary differential equations (ODE) and stochastic differential equations (SDE) framework. The classic models based on the logistic map are analyzed, and then a noise term is introduced that models the behavior of the so-called deniers. This model fairly faithfully reproduces the Italian situation in today’s period. We then move on to local analysis, arriving at an equation of continuity for what concerns the density of the number of infected in an assigned region. We, therefore, prove a Theorem according to which classical logistics is the most catastrophic of predictions. In a realistic scenario, it is necessary to take into account the inevitable fluctuations in the aforementioned density. This implies a fragmentation of the initial cluster (generated by “patient zero”) into an N disjoint sub clusters. For very large N, statistical analysis suggests the use of the two-point correlation function (and more generally, n-points). In principle, an estimate of this function makes it possible to determine the evolution of the pandemic. The distribution of the sub clusters could be fractal, exactly as it happens for the distribution of galaxies starting from a homogeneous and isotropic primordial universe, but with random fluctuations in matter density. This is not surprising, since due to the invariance in scale, fractals have a low “computational cost”. The idea that pandemics are cyclical processes, that is, they occur with a given periodicity, would therefore remain corroborated.

Controversial hypotheses to explain consciousness exist in many fields of science, psychology and philosophy. Recent experimental findings in quantum cognition and magnetic resonance imaging have added new controversies to the field, suggesting that the mind may be based on quantum computing. Quantum computers process information in quantum bits (qubits) using quantum gates. At a first glance, it seems unrealistic or impossible that the brain can meet the challenges to provide either of these. Nevertheless, we show here why the brain has the incredible ability to perform quantum computing and how that may be realized.

Forecast of critical transitions in a dynamical system is one of the most important research problems in recent time. In this short communication, we discuss a possible novel sign of critical transitions in nonlinear systems. We have shown that the higher order terms of the Taylor series play an important role in determining critical transitions in a system. Moreover, we explain our approach using the Logistic map.

Recently, it has been shown that in the absence of gravity, microgravity let us to explore some new fields which have direct effects on the communications between cells and their growth. We show that the origin of these fields may be some DNA-like structures interior of the earth's core. These structures have a long around $10^{9}$ times the diameter of the earth which are compacted in very smaller places like the core of the earth. This compacting is very similar to the compacting of DNAs interior of cells and leads to the emergence of high temperature and pressure. We measure temperature around DNA-like structures and show that it is in good agreement with predicted temperature of core. Also, we calculate number of microstates of DNA-like structures in microgravity. We will show that DNA-like structures of the core exchange microstates and fields with dark part of DNA in extra dimensions. This dark DNA includes missing genes that are needed for the animal's life and their chemical products can be observed in the activity of body. In microgravity, the absence of gravity lets to DNA-like structures to recover more states of dark DNAs. These extra states accelerate the production of extra cells and may lead to the cancer. To show this, we inject tumor cells into two fertilized eggs and incubate them for 58h. Then, we put one of them in a devices similar to clinostat and try to provide the conditions of incubation in microgravity. We consider the growth of tumor cells under microgravity and compare with normal conditions. We observe that fields of microgravity increase the velocity of production of tumor cells. This experiment confirms our theory that in the absence of gravity, communications between DNA-like structure of the earth and dark DNA leads to the an increase in number of microstates of cancerous cells.

Recently, Hargreaves ( New Scientist, Volume 237, Issue 3168, March 2018, Pages 29-31 ) has argued that some animal genomes seem to be missing certain genes, ones that appear in other similar species and must be present to keep the animals alive. He called these apparently missing genes by “dark DNA”. On the other hand, Sepehri and his collaborations ( Open Physics, 16(1), pp. 463-475) has discussed that some biological events like DNA teleportation and water memory may be due to existence of some extra genes in extra dimensions. Collecting these results, we can conclude that origin of some cancers may be evolutions of dark DNA in extra dimension. To show this, we propose a model for calculating number of microstates of a DNA for a chick embryo in extra dimension and compare with experimental data. We show that number of microstates in extra dimension for a normal chick embryo is liss than number of microstates for a cancerous chick embryo. In fact, extra microstates are transformed to four dimensions.

The idea that ion channel proteins physically rotate to enhance ion flow through the membrane is reviewed, in light of recent experimental results. Although there is still no definite answer to the question presented in the title, some recent work can be interpreted as supporting this notion. As a bonus, we present a general theory of anesthesia. Anesthetics, and alcohol, are dissolved in the membrane lipids, and (perhaps) do not directly bind to ion channels or pores. Instead, they change the properties of the surrounding lipids, thus compromising the rotations of the pores, and producing the anesthetic effects.

Special properties of the first ordinary (observable) matter, produced in the universe -the oscillating neutrinos - are discussed in a context of their use for healing and stimulation of the brain.

Diabetes is one of the major causes of premature illness and death worldwide. The prevalence of diabetes has reached epidemic proportions. The work is a study of the molecular electrostatic potential via molecular mechanics of the D-Pinitol found in the Bougainvillea species, a Nyctaginaceae. A computational study of the molecular geometry of the D-pinitol through Mm+ method of the hypoglycemic compounds present in Bougainvillea species is described in a computer simulation. It is a active antidiabetic agent compounds. The study the cyclitol resembles the hooks weed bur plant Asteraceae, it showed up as appearance of a bur molecule. Probably bind to sugar molecules contained in the blood, through hydrogen bonds.

The work is a study of the geometry of the molecules via molecular mechanics of the main alkaloids found in the seeds of prickly poppy. A computational study of the molecular geometry of the molecules through molecular mechanics of the main alkaloids compounds present in plant seeds is described in a computer simulation. The plant has active ingredients compounds: allocryptopine, berberine, chelerythrine, copsitine, dihydrosanguinarine, protopine and sanguinarine. The Argemone Mexicana Linn, which is considered one of the most important species of plants in traditional Mexican and Indian medicine system. The seeds have toxic properties as well as bactericide, hallucinogenic, fungicide, insecticide, in isoquinolines and sanguinarine alkaloids such as berberine. The studied alkaloids form two groups having distribution characteristics similar to each other loads, to which they have dipole moments twice higher than in the other group.

The work is a study of the geometry of the molecules via molecular mechanics of the main monoterpenoids found in the oil of Lemon Tahiti. Lemon Tahiti is the result of grafting of Persia file on Rangpur lime and has no seeds. A computational study of the molecular geometry of the molecules through molecular mechanics of the main monoterpenoids compounds present in fruit oil is described in a computer simulation. The fruit has active terpenoids compounds: alfa-pinene, beta-pinene, limonene and gama-terpenine. The studied monotepernoides form two groups of distribution characteristics of fillers and similar electrical potentials between groups. Since alfa-pinene and limonene present, major and minor moment of electric dipoles, respectively.

This short article presents a mathematical formula required for metric corrections in image extraction and processing when using different length scale factors in three-dimensional space which is normally encountered in cryomicrotome image construction techniques.

Analytical expressions correlating the volumetric flow rate to the inlet and outlet pressures are derived for the time-independent flow of Newtonian fluids in cylindrically-shaped elastic tubes using a one-dimensional Navier-Stokes flow model with two pressure-area constitutive relations. These expressions for elastic tubes are the equivalent of Poiseuille and Poiseuille-type expressions for rigid tubes which were previously derived for the flow of Newtonian and non-Newtonian fluids under various flow conditions. Formulae and procedures for identifying the pressure field and tube geometric profile are also presented. The results are validated by a finite element method implementation. Sensible trends in the analytical and numerical results are observed and documented.

A comparison is made between the Hagen-Poiseuille flow in rigid tubes and networks on one side and the time-independent one-dimensional Navier-Stokes flow in elastic tubes and networks on the other. Analytical relations, a Poiseuille network flow model and two finite element Navier-Stokes one-dimensional flow models have been developed and used in this investigation. The comparison highlights the differences between Poiseuille and one-dimensional Navier-Stokes flow models which may have been unjustifiably treated as equivalent in some studies.

The flow of power law fluids, which include shear thinning and shear thickening as well as Newtonian as a special case, in networks of interconnected elastic tubes is investigated using a residual based pore scale network modeling method with the employment of newly derived formulae. Two relations describing the mechanical interaction between the local pressure and local cross sectional area in distensible tubes of elastic nature are considered in the derivation of these formulae. The model can be used to describe shear dependent flows of mainly viscous nature. The behavior of the proposed model is vindicated by several tests in a number of special and limiting cases where the results can be verified quantitatively or qualitatively. The model, which is the first of its kind, incorporates more than one major non-linearity corresponding to the fluid rheology and conduit mechanical properties, that is non-Newtonian effects and tube distensibility. The formulation, implementation and performance indicate that the model enjoys certain advantages over the existing models such as being exact within the restricting assumptions on which the model is based, easy implementation, low computational costs, reliability and smooth convergence. The proposed model can therefore be used as an alternative to the existing Newtonian distensible models; moreover it stretches the capabilities of the existing modeling approaches to reach non-Newtonian rheologies.

In this paper, a pore-scale network modeling method, based on the flow continuity residual in conjunction with a Newton-Raphson non-linear iterative solving technique, is proposed and used to obtain the pressure and flow fields in a network of interconnected distensible ducts representing, for instance, blood vasculature or deformable porous media. A previously derived analytical expression correlating boundary pressures to volumetric flow rate in compliant tubes for a pressure-area constitutive elastic relation has been used to represent the underlying flow model. Comparison to a preceding equivalent method, the one-dimensional Navier-Stokes finite element, was made and the results were analyzed. The advantages of the new method have been highlighted and practical computational issues, related mainly to the rate and speed of convergence, have been discussed.

Blood is a complex suspension that demonstrates several non-Newtonian rheological characteristics such as deformation-rate dependency, viscoelasticity and yield stress. In this paper we outline some issues related to the non-Newtonian effects in blood circulation system and present modeling approaches based mostly on the past work in this field.

The flow of fluids at branching junctions plays important kinematic and dynamic roles in most biological and industrial flow systems. The present paper highlights some key issues related to the flow of fluids at these junctions with special emphasis on the biological flow networks particularly blood transportation vasculature.

The various eects of electromagnetic fields to DNA have been reported by Luc Montagnier and his group. It has been shown that genetic information can be transmitted to water through applications of electromagnetic fields, means that DNA has wave character. Here, non-particle view of DNA challenges standard paradigm of DNA and biology. Based on frequency, it can have implications for physics of cancer.

This technical report documents the theoretical, computational, and practical aspects of the one-dimensional Navier-Stokes finite element flow model. The document is particularly useful to those who are interested in implementing, validating and utilizing this relatively-simple and widely-used model.

In this paper we discussed the affect of anxiety emotion in view of system science. With the help of limit cycle model and non-equilibrium thermodynamics, it shows that the affect caused by anxiety emotion is different from person to person. Using synthesis and metabolism frequency as the basis to category the affects, we found that the affect will cause some kind of population over weighted while some kind of population will become thinner and thinner. This depends on whether synthesis and metabolism frequency decreases or increases. We gave some suggestion about getting rid of the affect caused by such kind of emotion according to different kind of population.

Based on the non-equilibrium thermodynamics point of view that a biological system is sustained by a local potential provided by stable entropy production, we construct a mathematical model to describe the metabolism of human body system. According to the stable and periodic property of human body system, the embryonic form of the model is constructed by dimensional analysis. Based on the mathematical model, stability analysis is used to discuss the response to perturbation which corresponds to the influence on human health. With the help of physiology and medical science, the parameters in the model are determined by empirical formulas in physiology. The correspondence of parameters and the observable variables such as body temperature, body weight, heart rate etc is found out. As an example, an interesting result obtained from our model is that overweight adults, even though healthy in the medical examination reports, faces the risk of being sick, because overweight decreases the metabolic frequency, however, it drives the human body system "farther" from equilibrium (death). This result shows that the body weight of over weighted ones will gradually increase rather than staying at a stable interval. Our method provides a new approach of predicting human health according to the observable vital signs.

This work is based on modification of the general relativity, which includes effects of production /absorption of matter by the vacuum. The theory (without fitting parameters) is in good quantitative agreement with cosmological observations. In this theory we got an interface between dark and ordinary matter, which very likely exist not only in cosmos, but everywhere, including our body and, especially, our brain. Subjective experiences are considered as a manifestation of that interface. This opens a possibility of a "communication" with dark matter. Probable applications of these ideas include health (brain stimulation), communication, computational capabilities and energy resources.

This article focuses on the approach to biology in terms of quantum mechanics. Quantum biology is a hypothesis that allows experimental verification, and pretends to be a further refinement of the known gene-centric model. The state of the species is represented as the state vector in the Hilbert space, so that the evolution of this vector is described by means of quantum mechanics. Experimental verification of this hypothesis is based on the accuracy of quantum theory and the ability to quickly gather statistics when working with populations of bacteria. The positive result of such experiment would allow to apply to the living computational methods of quantum theory, which has not yet go beyond the particular ''quantum effects''.

The works of Luc Montagnier and Peter Gariaev suggests remote replication of DNA is possible. The developments in the model of dark DNA allow to imagine a detailed mechanism for how water can represent DNA and how DNA could be transcribed to dark DNA - essentially the analog of DNA-RNA transcription would be in question. The transcription/association represents a rule and rules are represented in terms of negentropic entanglement in TGD framework with pairs of states in superposition representing the instances of the rule. Transition energy serves as a characterizer of a molecule - say DNA codon - and the entangled state is a superposition of pairs in which either molecule is excited or dark DNA codon is excited to higher cyclotron state with same energy: this requires tuning of the magnetic field and sufficiently large value of h_eff at the flux tube. Negentropic entanglement would due to the exchange of dark photons: this corresponds to wave DNA aspect. Dark cyclotron photons also generate negatively charged exclusion zones (EZs) discovered by Pollack and in this process transform part of protons to dark ones residing at the magnetic flux tubes associated with EZs and forming dark proton sequences. This allows to identify a mechanism of remote replication.

Emilio del Giudice et al have proposed that so collar coherent regions (CDs) of size about 1 micrometer in water are crucial for living systems and there is empirical evidence for them. Gerald Pollack and collaborators have discovered what they call exclusion zones with size up to about 200 micrometers. In the sequel a model for the formation of EZs assuming that CDs are their predecessors is proposed. The model involves also hydrogen bonds in an essential manner. The basic prediction is that the formation of CDs requires UV irradiation at energy around 12.06 eV. Solar radiation at this energy cannot propagate through atmosphere as ordinary photons but could arrive along magnetic flux tubes as dark protons.

According to Michael Levin, concerning morphogenesis and morphostasis the basic challenge is to understand how the shape of the organism is generated and how it is preserved. The standard local approach based on belief on genetic determinism does not allow one to answer these questions satisfactorily. </p><p> The first approach to this problem relies on a self-organization paradigm in which the local dynamics of cells leads to large scale structures as self-organization patterns. In TGD framework 3-D self-organization is replaced with 4-D self-organization (the failure of strict determinism of the classical dynamics is essential motivating zero energy ontology (ZEO)). One can speak about 4-D healing: expressing it in somewhat sloppy manner, the space-time surface serving as a classical correlate for the patient is as a whole replaced with the healed one: after the 4-D healing process the organism was never ill in geometrical sense! Note that in quantal formulation one must speak of quantum superposition of space-time surfaces. </p><p> Second approach could be seen as computational. The basic idea is that the process is guided by a template of the target state and morphogenesis and healing are computational processes. What Levin calls morphogenetic fields would define this template. It is known that organisms display a kind of coordinate grid providing positional information that allows cells to "decide" about the profile of genetic expression. In TGD framework magnetic body forming coordinate grid formed from flux tubes is a natural candidate for this structure. They would also realize topological quantum computation (TQC) with basic computational operations realized at the nodes of flux tubes to which it is natural to associate some biological sub-structures. </p><p> The assumption about final goal defining a template can be argued to be too strong: much weaker principle defining a local direction of dynamics and leading automatically to the final state as something analogous to free energy minimum in thermodynamics might be enough. Unfortunately, second law is the only principle that standard physics can offer. Negentropy Maximization Principle (NMP) provides the desired principle in TGD framework. Also the approach of WCW spinor field to the maximum of vacuum functional (or equivalently that of Kähler function) gives a goal for the dynamics after the perturbation of the organism causing "trauma". If Kähler function is classical space-time correlate for entanglement negentropy, these two views are equivalent. </p><p> TGD thus suggests an approach, which could be seen as a hybrid of approaches based on self-organization and computationalism. The magnetic body becomes the key notion and codes also for learned behaviors as TQC programs coded by the braiding of flux tubes. The replication of the magnetic body means also the replication of the programs behind behavioral patterns (often somewhat misleadingly regarded as synonymous with long term memories): both structure and function are replicated. This hypothesis survives the killer tests provided by the strange findings about planaria cut into two and developing new head or tail while retaining its learned behaviors: the findings indicate that behavioral programs are preserved although planaria develops a new brain.

The discovery of negatively charged exclusion zone formed in water bounded by gel phase has led Pollack to propose the notion of gel like fourth phase of water. In this article this notion is discussed in TGD framework. The proposal is that the fourth phase corresponds to negatively charged regions - exclusion zones - with size up to 100-200 microns generated when energy is fed into the water - say as radiation, in particular solar radiation. The stoichiometry of the exclusion zone is H_1.5O and can be understood if every fourth proton is dark proton residing at the flux tubes of the magnetic body assignable to the exclusion zone and outside it. This leads to a model for prebiotic cell as exclusion zone. Dark protons are proposed to fork dark nuclei whose states can be grouped to groups corresponding to DNA, RNA, amino-acids, and tRNA and for which vertebrate genetic code is realized in a natural manner. The voltage associated with the system defines the analog of membrane potential, and serves as a source of metabolic energy as in the case of ordinary metabolism. The energy is liberated in a reverse phase transition in which dark protons transform to ordinary ones. Dark proton strings serve as analogs of basic biopolymers and one can imagine analog of bio-catalysis with enzymes replaced with their dark analogs. The recent discovery that metabolic cycles emerge spontaneously in absence of cell support this view.

This article represents a brief sketch of TGD based model of water memory and homeopathy as it is after two steps of progress. First one was due to Pollack's findings about exclusion zones of water explained in terms of fourth phase of water. Second step or progress was inspired by an anomaly claimed by Tajmar et al and known as strong gravimagnetism. The attempt to understand the claim led to h<sub>eff</sun> = h_gr=h_em hypothesis unifying two TGD views about the notion of hierarchy of Planck constants proposed to characterize the phases of dark matter. </p><p> In this framework the attempt to understand homeopathy leads to additional insights about about water as living system and about prebiotic life as being based on the dark realization of genetic code realized in terms of dark proton strings which are nothing than dark variants of nuclei. Formation of exclusion zones would be formation of primitive lifeforms and primitive form of metabolism. Homeopathy could be seen as a manifestation of a fundamental form of immune system based on the recognition of invader molecules using reconnection mechanism for magnetic flux tubes and on mimicking the braiding of the magnetic bodies of invader molecules using dark variants of proteins (later proteins) and and eventually representing them symbolically in terms of dark DNA (later ordinary DNA) coding for the dark proteins. Genetic code might have geometric interpretation as coding for the 2-braiding of 3-D coordinate grids represented by magnetic flux tubes serving as the 4-D template coding not only for the structure of the organism but also its functions as spatio-temporal patterns. Protein folding would represent a behavior of protein and DNA would code also for it.

The latest news in quantum biology is the observation by the group led by Anirban Bandyopadhyay about detection of quantum vibration in microtubule scale - their lengths vary up to 50 μm. If this observation can be replicated, one can speak about breakthrough in quantum consciousness. </p><p> The findings reported in an earlier talk of Banduopadhyay give support for the general TGD inspired view about topological quantum computation (TQC) and allow for a rather detailed model in the case of microtubules. The idea is that flux tubes form a 2-D coordinate grid consisting of parallel flux tubes in two different directions. Crossing points would be associated with tubulins and the conformational state of tubulin could define a bit coding whether the braid strands defining coordinate lines are braided or not (swap or not). In this manner any bit pattern at microtubule defines a particular TQC program. If also conformations are quantum superposed, one would have "quantum-quantum computation". It however seems that conformation change is irreversible chemical reaction so that this option is not feasible. </p><p> The TGD inspired modification of the proposal in terms of flux tube coordinate grids making possible TQC architectures with tubulin dimers defining bits defining in turn TQC program looks rather natural. Coordinate grids can be fixed on basis of the experimental findings and there are 8 of them. The interpretation is in terms of different resolutions. The grids for A and B type lattices are related by 2π twist for the second end of the basic 13-unit for microtubule. An attractive interpretation for the resonance frequencies is in terms of phase transitions between A and B type lattices. If A type lattices can be generated only in phase transitions induced by AC stimulus at resonance frequencies, one could understand their experimental absence, which is a strong objection against Penrose-Hameroff model. </p><p> TGD suggests also a generalization of the very notion of TQC to 2-braid TQC with 2-D string world sheets becoming knotted in 4-D space-time. Now qubits (or their generalizations) could correspond to states of flux tubes defining braid strands as Penrose and Hameroff seem to suggest and the emergence of MTs could be seen as an evolutionary leap due to the emergence of a new abstraction level in cognitive processing.

The general strategy in attempts to understand metabolism is based on the assumption that a very large class of anomalous phenomena rely on same basic mechanism. This includes life as a phenomenon, water memory and homeopathy, free energy phenomena involving over-unity phenomena related to the dissociation of water, lightning and ball lightning, anomalous effects associated with rotating magnetic systems, phenomena related to UFOs (light balls), even remote mental interactions. One must have a unified explanation for all these phenomena based on a real theory. Plasmoids are TGD inspired proposal for prebiotic lifeforms and the input from anomalies related to electrolysis of water together with TGD based proposal that sequences of dark protons define dark nuclei realizing vertebrate genetic code leads to the vision that the biochemical metabolic machinery including photosynthesis has a simple analog realized in terms of "polymers" of water molecules with one dark proton with protons bound to sequence by color bonds. </p><p> The old view about the metabolic energy quanta as energies liberated as particle "drops" to a larger space-time sheet is modified. Metabolic energy quanta are liberated when the space-time sheet at which the particles reside expands in a phase transition increasing its p-adic prime and reducing the value of Planck constant correspondingly so that the net result is that the size of the space-time sheet remains the same. This condition implies a close relationship between p-adic and dark matter hierarchies. This process is automatically coherent since all particles suffer the change simultaneously. It applies also to a situation in which particles are in magnetic field: in this case the scale of cyclotron energies changes since the strength of the magnetic field is scaled down to guarantee the conservation of magnetic flux. This transition is not cyclotron transition but liberates essentially the same energy as coherent cyclotron transition so that magnetic fields (their "motor actions") become essential players also in metabolic activities.

The idea that that icosahedral structures assignable to water clusters could define a geometric representation of some kind of code is very intriguing. Genetic code is of course the code that comes first in mind. The observation that the number of faces of tetrahedron (icosahedron) is 4 (20) raises the question whether genetic code might have a geometric representation. In TGD framework also a second code emerges: I have christened it memetic code. Also memetic code could have a geometric realization. Another purely TGD-based notion is that of dark DNA allowing to assign the states of dark protons with DNA,RNA, tRNA and amino-acids and to predict correctly the numbers of DNA codons coding for a given amino-acid in vertebrate genetic code. A further element is the possibility of strong gravitation in TGD Universe meaning that space-time geometry and topology can be highly non-trivial even in condensed matter length scales. These ingredients allow to imagine geometric representations of genetic and memetic code.

TGD approach leads to a prediction that biophotons result when dark photons with large value of effective Planck constant and large wavelength transform to ordinary photons with same energy. The collaboration with Lian Sidorov stimulated a more detailed look for what biophotons are. Also the recent progress in understanding the implications of basic vision behind TGD inspired theory of consciousness erved as an additional motivation for a complementary treatment. <OL> <LI>The anatomy of quantum jump in zero energy ontology (ZEO) allows to understand basic aspects of sensory and cognitive processing in brain without ever mentioning brain. Sensory perception - motor action cycle with motor action allowing interpretation as time reversed sensory perception reflects directly the fact that state function reductions occur alternately to the two opposite boundaries of causal diamond (which itself or rather, quantum superposition of CDs, changes in the process). <LI>Also the abstraction and de-abstraction processes in various scales which are essential for the neural processing emerge already at the level of quantum jump. The formation of associations is one aspect of abstraction since it combines different manners to experience the same object. Negentropic entanglement of two or more mental images (CDs) gives rise to rules in which superposed n-particle states correspond to instances of the rule. Tensor product formation generating negentropic entanglement between new mental images and earlier ones generates longer sequences of memory mental images and gives rise to negentropy gain generating experience of understanding, recognition, something which has positive emotional coloring. Quantum superposition of perceptively equivalent zero energy states in given resolution gives rise to averaging. Increasing the abstraction level means poorer resolution so that the insignificant details are not perceived. <LI> Various memory representations should be approximately invariant under the sequence of quantum jumps. Negentropic entanglement gives rise to this kind of stabilization. The assumption that self model is a negentropically entangled system which does not change in state function reduction, leads to a problem. If the conscious information about this kind of subself corresponds to change of negentropy in quantum jump, it seems impossible to get this information. Quite generally, if moment of consciousness corresponds to quantum jump and thus change, how it is possible to carry conscious information about quantum state? Interaction free measurement however allows to circumvent the problem: non-destructive reading of memories and future plans becomes possible in arbitrary good approximation. </p><p> This memory reading mechanism can be formulated for both photons and photons and these two reading mechanisms could correspond to visual memories as imagination and auditory memories as internal speech. Therefore dark photons decaying to biophotons could be crucial element of imagination and the notion bio-phonon could also make sense and even follow as a prediction. This would also suggest a correlation of biophoton emission with EEG for which there is a considerable evidence. The observation that biophotons seem to be associated only with the right hemisphere suggests that at least some parts of right hemisphere prefer dark photons and are thus specialized to visual imagination: spatial relationships are the speciality of the right hemisphere. Some parts of left hemisphere at least might prefer dark phonons: left hemisphere is indeed the verbal hemisphere specialized to linear linguistic cognition. </OL> In the sequel I shall discuss biophotons in TGD Universe as decay products of dark photons and propose among other things an explanation for the hyperbolic decay law in terms of quantum coherence and echo like mechanism guaranteing replication of memory representations. Applications to biology, neuroscience, and consciousness are discussed and also the possible role of biophotons for remote mental interactions is considered. Also evidence for biophonons (Taos hum) is discussed.

A considerable progress has occurred in the understanding of TGD inspired theory of consciousness and quantum biology during the first half of 2013. The new picture allows also much better understanding of quantum biology. The work during the first half of 2013 has allowed to develop in detail several ideas about the role of the magnetic body. Magnetic flux tubes serve as correlates for the formation of quantum coherence and directed attention. The phase transitions changing the value of h_eff leading to a change of flux tube length and the reconnections of the flux tubes play a key role in bio-catalysis. The dark photons propagating along MEs parallel to the flux tubes make possible resonant interactions between the entities at their ends and the proposed view about sensory, memory, and cognitive representations relies on hypothesis that the braiding of flux tubes defines negentropically entangled systems representing information which is read consciously and non-destructively in good approximation by using interaction free quantum measurements. Dark photons transform to ordinary photons in energy conserving manner and biophotons are identified as outcome of this process. </p><p> With this background one return to the old question "What is the exact mechanism of homeopathic healing?". I have considered already earlier answers to this question but they have not been completely convincing. It turns out that one manages to add the missing piece to the puzzle by making the simple question "What is the molecular cause of illness and how homeopathic remedy eliminates it?". Amusingly, I could have identified this piece for years ago but for some reason did not pose the correct question. </p><p> The resulting model of homeopathic healing is amazingly simple and at the same time a universal model of bio-catalysis. The entity mimicking the invader molecules "steals" its cyclotron frequencies by varying the thickness of magnetic flux tube and thus magnetic field strength and cyclotron frequency until reconnection with the molecule's magnetic body becomes possible and fusion to single quantum coherent system occurs. In TGD inspired theory of consciousness this process corresponds to directed attention and conscious recognition of the presence of the invader molecule. After this the mimicking entity freezes the thickness of the flux tubes in question becoming thus capable of mimicking the invader molecule and attach to the receptors of the invader molecule and steal the attention of the host organism and induce healing. </p><p> The results summarized in the book <A HREF="http://www.amazon.com/Applied-Biophysics-Activated-Water-Applications/dp/9814271187">"Applied Biophysics of Activated Water"</A> of Vysotskii et al provide a test bench for the proposal and allow to formulate it in a more detailed manner. The basic message of the book is that the activation process yields water with anomalous physical properties including water memory and having highly non-trivial - in general positive - effects on living matter. The identification of activated water as ordered water appearing in cell interior is proposed. </p><p> This and the general features of the activation process inspire the question whether the analog of the activation process might have taken place during pre-biotic evolution and generated ordered water making DNA stable. Molecular mimicry making possibly immune system would have emerged at the same step and meant also the emergence of symbolic representations. Also the pairs formed by receptor molecules and molecules attaching to them would have emerged at this crucial step when dark matter enters the game. One of they key questions is whether it is dark water molecule clusters or dark DNA that performs the mimicry of various molecules. The results of the book lend support for the model based on dark DNA.

The article <A HREF="http://restframe.com/downloads/tachyon_monopoles.pdf">"Possible detection of tachyon monopoles in photographic emulsions"</A> by Keith Fredericks describes in detail very interesting observations by him and also by many other researchers about strange tracks in photographic emulsions induced by various (probably) non-biological mechanisms and also by the exposure to human hands (touching by fingertips) as in the experiments of Fredericks. That the photographic emulsion itself consists of organic matter (say gelatin) might be of significance as also the fact that practically all experimental arrangements involve di-electric breakdown (nerve pulses in the experiments of Fredericks). For particle physicist it is very difficult to accept the proposed interpretation as particle tracks and even more difficult to agree with the identification of particles as tachyonic magnetic monopoles. A more natural interpretation seems to be as "photographs" of pre-existing structures - either completely standard but not well-understood or reflecting new physics associated with the living matter. In TGD framework the identification as images of magnetic flux tubes carrying dark matter and associated with the emulsion - less probably with the source - is natural and the images would be very much analogous to those obtained by Peter Gariaev's group by illuminating DNA sample with visible light.

The dynamics of quasicrystals looks to me very interesting because it shares several features of the dynamics of K\"ahler action defining the basic variational principle of classical TGD and defining the dynamics of space-ti preferred extremals of Kähler action. Magnetic body carrying dark matter is the fundamental intentional agent in TGD inspired quantum biology and the cautious proposal is that magnetic flux sheets could define the grid of 3-planes (or more general 3-surfaces) defining quasi-periodic background fields favoring 4-D quasicrystals or more general structures in TGD Universe. Also 3-D quasicrystal like structures defined by grids of planes can be considered and 4-D quasicrystal structure could represent their time evolution. Quite recently it has been reported that grids consisting of 2-D curved orthogonal surfaces characterize the architecture of neural wiring so that this hypothesis might make sense. This structure would be analogous to 2-D quasicrystal and its time evolution to 3-D quasicrystal.

Ionic current flowing through a membrane pore with a helical architecture may impart considerable torque to the pore structure itself. If the channel protein is free to rotate, it will spin at significant speeds. Order of magnitude estimates of possible rotation rates are presented, as well as a few arguments why such motion could improve ion transport.

Robert Becker proposed on basis of his experimental work that living matter behaves as a semiconductor in a wide range of length scales ranging from brain scale to the scale of entire body. Direct currents flowing only in preferred direction would be essential for the functioning of living manner in this framework. One of the basic ideas of TGD inspired theory of living matter is that various currents, even ionic currents, are quantal currents. The first possibility is that they are Josephson currents associated with Josephson junctions but already this assumption more or less implies also quantal versions of direct currents. TGD inspired model for nerve pulse assumed that ionic currents through the cell membrane are probably Josephson currents. If this is the case, the situation is automatically stationary and dissipation is small as various anomalies suggest. One can criticize this assumption since the Compton length of ions for the ordinary value of Planck constant is so small that magnetic flux tubes carrying the current through the membrane look rather long in this length scale. Therefore either Planck constant should be rather large or one should have a non-ohmic quantum counterpart of a direct current in the case of ions and perhaps also protons in the case of neuronal membrane: electronic and perhaps also protonic currents could be still Josephson currents. This would conform with the low dissipation rate. In the following the results related to laser induced healing, acupuncture, and DC currents are discussed first. The obvious question is whether these direct currents are actually currents and whether they could be universal in living matter. A TGD inspired model for quantal direct currents is proposed and its possible implications for the model of nerve pulse are discussed.

Magnetic flux tubes play a key role in TGD inspired model of quantum biology. Could the networks of magnetic flux tubes containing dark particles with large \hbar in macroscopic quantum states and carrying beams of dark photons define analogs of electric circuits? This would be rather cheap technology since no metal would be needed for wires. Dark photon beams would propagate along the flux tubes representing the analogs of optical cables and make possible communications with maximal signal velocity. I have actually made much more radical proposal in TGD inspired quantum biology. According to this proposal, flux tube connections are dynamical and can be changed by reconnection of two magnetic flux tubes. The signal pathways A→ C and B→ D would be transformed to signal pathways to A→ D and B→ C by reconnection. Reconnection actually represents a basic stringy vertex. The contraction of magnetic flux tubes by a phase transition changing Planck constant could be fundamental in bio-catalysis since it would allow distant molecules connected by flux tubes to find each other in the molecular crowd. DNA as a topological quantum computer is the idea that I have been developing for 5 years or so. I have concentrated on the new physics realization of braids and devoted not much thought to how the quantum computer problems might run in this framework. I was surprised to realize how little I know about what happens in even ordinary computation. Instead of going immediately to Wikipedia I take the risk of publicly making myself fool and try to use my own brain.

The book is intended to be a concise summary about the applications of TGD in consciousness theory, living matter, and remote mental interactions. The book begins with a very concise summary about TGD in the hope that it might help the mathematically oriented reader to gain an overall view: the notion of many-sheeted space-time and topological field quantization are of special importance for understanding biology in TGD Universe. </p><p> Quantum jump identified as moment of consciousness, the notion of self reducing to that of quantum jump, Negentropy Maximization Principle (NMP), zero energy ontology (ZEO), and the new view about relationship between subjective and experienced time are essential pieces of the vision. The identification of p-adic physics as correlate for cognition, the view about life as something in the intersection of real and p-adic worlds -matter and cognition - , and the notion of number theoretic negentropy are central in biological applications. </p><p> Magnetic body carrying dark matter and forming an onion-like structure with layers characterized by large values of Planck constant is a key concept of TGD inspired biology. Magnetic body is identified as intentional agent using biological body as sensory receptor and motor instrument. The role of magnetic body in various biological functions, and the new view about metabolism and its relationship to the generation of negentropic entanglement are discussed. </p><p> The applications to neuroscience are touched. The general model for the sensory qualia and for generation of attention and qualia leads to a view resembling the Orch OR of Penrose and Hameroff. Models for nerve pulse generation and EEG - or rather a fractal hierarchy of XEGs generalizing it serving as a communication tool in commutations between biological body and magnetic body - are proposed. </p><p> The mechanisms making possible for the magnetic body to control and receive sensory information from biological body apply can be regarded as those for remote mental interactions. Therefore also remote mental interactions are briefly considered in the proposed conceptual framework. Also tests for the general vision are also considered.

In TGD Universe gauge fields are replaced with topological field quanta. Examples are topological light rays, magnetic/electric flux tubes and sheets, and flux quanta carrying both magnetic and electric fields. Flux quanta form a fractal hierarchy in the sense that there are flux quanta inside flux quanta. It is natural to assume quantization of Kähler magnetic flux. Braiding and reconnection are the basic topological operations for flux quanta. The basic question is how the basic notions assigned with the classical gauge and gravitational fields understood in standard sense generalize in TGD framework. <OL> <LI> Superposition and interference of the classical fields is very natural in Maxwell electrodynamics and certainly experimentally verified phenomena. Also the notion of hologram relies crucially on the notion of interference. How can one describe the effects explained in terms of superposition of fields in a situation in which the theory is extremely non-linear and all classical gauge fields are expressible in terms of CP_2 coordinates and their gradients? It is also rather clear that the preferred extremals for Kähler action decompose to space-time regions representing space-time correlates for quanta. The superposition of classical fields in Maxwellian sense is impossible. How can one cope with this situation? The answer is based on simple observation: only the {\it effects} of the classical fields superpose. There is no need for the fields to superpose. Together with the notion of many-sheeted space-time this leads to elegant description of interference effects without any need to assume that linearization is a good approximation. <LI> Topological quantization brings in also braiding and reconnection of magnetic flux tubes as basic operations for classical fields. These operations for flux tubes have also Maxwellian counterparts at the level of field lines. Braiding and reconnection are in a central role in TGD Universe and especially so in in TGD inspired theory of consciousness and quantum biology. The challenge is to build a coherent overall phenomenological view about the role of topologically quantized classical fields in biology and neuroscience. For instance, one can ask what is the precise formulation for the notion of conscious hologram and whether magnetic flux tubes could serve as correlates of entanglement (or at least negentropic entanglement suggested by the number theoretic vision and identified as a basic signature of living matter). <LI> Topological quantization and the notion of magnetic body are especially important in TGD inspired model of EEG. The attempt to understand the findings of Persinger from the study of what is known as God helmet leads to a considerable progress in the understanding the possible role of topologically quantized classical fields in biology and neuro-science. </OL>

<p> This article is inspired by the study of two books of Rupert Sheldrake. What makes the study of the books of Sheldrake so rewarding is that Sheldrake starts from problems of the existing paradigm, analyzes them thoroughly, and proposes solutions in the framework provided by his vision. There is no need to accept Sheldrake′s views, just the reading of his arguments teaches a lot about the fundamental ideas and dogmas underlying recent day biology and forces the reader to realize how little we really know - not only about biology but even about so called established areas of physics such as condensed matter physics. These books are precious gems for anyone trying to build overall view. </p><p> The idea that Nature would have habits just as we do is probably one of those aspects in Sheldrake's work, which generate most irritation in physicalists believing that Nature is governed by deterministic laws with classical determinism replaced with quantum statistical determinism. Sheldrake is one of those very few scientists able to see the reality rather than only the model of reality. Morphic resonance would make possible to establish the habits of Nature and the past would determine to high extent the present but on organic manner and in totally different sense as in the world of physicalist. </p><p> In this article I propose an interpretation for the vision of Sheldrake based on zero energy ontology and TGD based view about geometric time and experienced time forcing to accept the notions of 4-dimensional brain and society. In this framework the problem is to understand why our sensory perception is 3-dimensional whereas the standard problems related to memory disappear since memory corresponds to 4-D aspects of perception and of conscious experience and memory storage is 4-dimensional. The vision about gene expression as something to some extend analogous to a democratic decision of 4-D society looks rather natural in this framework and would explain some still poorly understood aspects of gene expression known from the days of Mendel. Therefore the term ″the prence of the past″ appearing in the title of one of Sheldrake's books has quite a concrete meaning in TGD Universe. This article is inspired by the study of two books of Rupert Sheldrake. What makes the study of the books of Sheldrake so rewarding is that Sheldrake starts from problems of the existing paradigm, analyzes them thoroughly, and proposes solutions in the framework provided by his vision. There is no need to accept Sheldrake′s views, just the reading of his arguments teaches a lot about the fundamental ideas and dogmas underlying recent day biology and forces the reader to realize how little we really know - not only about biology but even about so called established areas of physics such as condensed matter physics. These books are precious gems for anyone trying to build overall view. </p><p> The idea that Nature would have habits just as we do is probably one of those aspects in Sheldrake's work, which generate most irritation in physicalists believing that Nature is governed by deterministic laws with classical determinism replaced with quantum statistical determinism. Sheldrake is one of those very few scientists able to see the reality rather than only the model of reality. Morphic resonance would make possible to establish the habits of Nature and the past would determine to high extent the present but on organic manner and in totally different sense as in the world of physicalist. </p><p> In this article I propose an interpretation for the vision of Sheldrake based on zero energy ontology and TGD based view about geometric time and experienced time forcing to accept the notions of 4-dimensional brain and society. In this framework the problem is to understand why our sensory perception is 3-dimensional whereas the standard problems related to memory disappear since memory corresponds to 4-D aspects of perception and of conscious experience and memory storage is 4-dimensional. The vision about gene expression as something to some extend analogous to a democratic decision of 4-D society looks rather natural in this framework and would explain some still poorly understood aspects of gene expression known from the days of Mendel. Therefore the term ″the prence of the past″ appearing in the title of one of Sheldrake's books has quite a concrete meaning in TGD Universe.</p>

<p> A model for remote replication of DNA is proposed. The motivating experimental discoveries are phantom DNA, the evidence for remote gene activation by scattered laser light from similar genome, and the recent findings of Montagnier's and Gariaev's groups suggesting remote DNA replication. </p><p> Phantom DNA is identified as dark nucleon sequences predicted by quantum TGD with dark nucleons defining naturally the analogs of DNA, RNA, tRNA, and amino-acids and realization of vertebrate genetic code. The notion of magnetic body defining a hierarchy of flux quanta realize as flux tubes connecting DNA nucleotides contained inside flux tubes connecting DNA codons and a condensed at flux sheets connecting DNA strands is an essential element of the model. Dark photons with large value of Planck constant coming as integer multiple of ordinary Planck constant propagate along flux quanta connecting biomolecules: this realizes the idea about wave DNA. Biomolecules act as quantum antennas and those with common antenna frequencies interact resonantly. </p><p> Biomolecules interacting strongly - in particular DNA nucleotides- would be characterized by same frequency. An additional coding is needed to distinguish between nucleotides: in the model for DNA as topological quantum computer quarks (u,d) and their antiquarks would code for the nucleotides A,T,C, and G would take care of this. The proposed role of quarks in biophysics of course makes sense only if one accepts the new physics predicted by quantum TGD. DNA codons (nucleotide triplets) would be coded by different frequencies which correspond to different values of Planck constant for photons with same photon energy propagating along corresponding flux tubes. This allows to interpret the previously proposed TGD based realization of so called divisor code proposed by Khrennikov and Nilsson in terms of quantum antenna mechanism. </p><p> In this framework the remote replication of DNA can be understood. DNA nucleotides interact resonantly with DNA strand and attach to the ends of the flux tubes emerging from DNA strand and organized on 2-D flux sheets. In Montagnier's experiment the interaction between test tubes A and B would be mediated by dark photons between DNA and dark nucleon sequences and amplify the dark photon beam, which in turn would induce remote replication. In the experiment of Gariaev scattered laser light would help to achieve the same purpose. Dark nucleon sequences would be generated in Montagnier's experiment by the homeopathic treatment of the test tube B. </p><p> Dark nucleon sequences could characterize the magnetic body of any polar molecule in water and give it a "name" written in terms of genetic codons so that genetic code would be much more general than usually thought. The dark nucleon sequence would be most naturally assigned with the hydrogen bonds between the molecule and the surrounding ordered water being perhaps generated when this layer of ordered water melts as the molecule becomes biologically active. Water memory and the basic mechanism of homeopathy would be due to the "dropping" of the magnetic bodies of polar molecules as the water is treated homeopathically and the dark nucleon sequences could define an independent life form evolving during the sequence of repeated dilutions and mechanical agitations taking the role environmental catastrophes as driving force of evolution. The association of DNA, RNA and amino-acid sequences associated with the corresponding dark nucleon sequences would be automatic since also also they are polar molecules surrounded by ordered water layers. </p><p> The transcription of the dark nucleon sequences associated the with the polar invader molecule to ordinary DNA sequences in turn coding of proteins attaching to the invader molecules by the quantum antenna mechanism could define the basic mechanism for functioning and evolution of the immune system. </p>

<p> The origin of life is one the most fascinating problems of biology. The classic Miller-Urey experiment was carried out almost 60 years ago. In the experiment sparks were shot through primordial atmosphere consisting of methane, ammonia, hydrogen and water and the outcome was many of the aminoacids essential for life. The findings raised the optimism that the key to the understanding of the origins of life. After the death of Miller 2007 scientists re-examined sealed test tubes from the experiment using modern methods found that well over 20 aminoacids-more than the 20 occurring in life- were produced in the experiments. </p><p> The Urey-Miller experiments have yielded also another surprise: the black tar consisting mostly of hydrogen cyanide polymer produced in the experiments has turned out to be much more interesting than originally thought and suggests a direction where the candidates for precursors of living cells might be found. In earlier experiments nitrobenzene droplets doped with oleic anhydride exhibited some signatures of life. The droplets were capable to metabolism using oleic anhydride as ″fuel″ making for the droplet to move. Droplets can move along chemical gradients, sense each other′s presence and react to it and have also demonstrated rudimentary memory. Droplets can even ″solve″ a maze having ″food″ at its other end. </p><p> The basic objection against identification as primitive life form is that droplets have no genetic code and do not replicate. The model for dark nucleons however predicts that the states of nucleon are in one-one correspondence with DNA, RNA, tRNA, and aminoacid molecule and that vertebrate genetic code is naturally realized. The question is whether the realization of the genetic code in terms of dark nuclear strings might provide the system with genetic code and whether the replication could occur at the level of dark nucleon strings. In this article a model for oil droplets as a primitive life form is developed on basis of TGD inspired quantum model of biology. In particular, a proposal for how dark genes could couple to chemistry of oil droplets is developed.</p>

<p> Costa de Beauregard considers a model for information processing by a computer based on an analogy with Carnot's heat engine. As such the model Beauregard for computer does not look convincing as a model for what happens in biological information processing. </p><p> Combined with TGD based vision about living matter, the model however inspires a model for how conscious information is generated and how the second law of thermodynamics must be modified in TGD framework. The basic formulas of thermodynamics remain as such since the modification means only the replacement S→ S-N, where S is thermodynamical entropy and N the negentropy associated with negentropic entanglement. This allows to circumvent the basic objections against the application of Beauregard's model to living systems. One can also understand why living matter is so effective entropy producer as compared to inanimate matter and also the characteristic decomposition of living systems to highly negentropic and entropic parts as a consequence of generalized second law.</p>

<p> The group of HIV Nobelist L. Montagnier has published two articles challenging the standard views about genetic code and providing strong support for the notion of water memory. Already the results of the first article suggested implicitly the existence of a new kind nano-scale representation of genetic code and the the recent article makes this claim explicitly. The TGD based model for the findings was based on the notion of magnetic body representing biologi- cally relevant aspects of molecules in terms of cyclotron frequencies. The model involved also the realization of genetic code using electromagnetic field patterns and as dark nucleon strings and led to a proposal that the analogs of trancription and translation are realized for the dark variants of DNA, RNA, tRNa, and aminoacids represented in terms of dark nucleon strings. Also processes transcribing ordinary and dark variants of the biomolecules to each other were proposed. This would make possible R&D-like controlled evolution based on experimentation using dark representations of biomoleculesd defining kind of virtual world. </p><p> The recent findings of the group of Montagnier allow a more detailed formulation of the model and suggest a general mechanism for generalized transcription and translation processes based on the reconnection of magnetic flux tubes between the molecules in question. A new element is the proposed role of ordered water and hydrogen bonds in the formation of water memories. These representation would result from the dropping of the magnetic bodies of molecules as the hydrogen bonds connecting the molecule to water molecules of the ordered water layer around it-analogous to ice layer- are split during the mechanical agitation. A similar process occurs quite generally when external energy feed excites the resting state of cell and induces protein folding and its reversal and the formation of protein aggregates. Good metaphors for resting state and excited states are cellular winter and summer. The necessity of a repeated dilution and mechanical agitation could be understood if agitation provides metabolic energy for the replication of the magnetic bodies filling the diluted water volume and gives rise to a series of "environmental catastrophes" inducing evolutionary leaps increasing the typical value of Planck constant associated with the magnetic bodies until the energy E = hf of 7 Hz dark photons exceeds the thermal energy at room temperature.</p>

<p> A TGD inspired model for the strange replica structures observed when DNA sample is radiated by red, IR, and UV light using two methods by Peter Gariaev and collaborators. The first method produces what is tentatively interpreted as replica images of either DNA sample or of five red lamps used to irradiate the sample. Second method produce replica image of environment with replication in horizontal direction but only at the right hand side of the apparatus. Also a white phantom variant of the replica trajectory observed in the first experiment is observed and has in vertical direction the size scale of the apparatus. </p>p> The model is developed in order to explain the characteristic features of the replica patterns. The basic notions are magnetic body, massless extremal (topological light ray), the existence of Bose-Einstein condensates of Cooper pairs at magnetic flux tubes, and dark photons with large value of Planck constant for which macroscopic quantum coherence is possible. The hypothesis is that the first method makes part of the magnetic body of DNA sample visible whereas method II would produce replica hologram of environment using dark photons and produce also a phantom image of the magnetic tubes becoming visible by method I. Replicas would result as mirror hall effect in the sense that the dark photons would move back and forth between the part of magnetic body becoming visible by method I and serving as a mirror and the objects of environment serving also as mirrors. What is however required is that not only the outer boundaries of objects visible via ordinary reflection act as mirrors but also the parts of the outer boundary not usually visible perform mirror function so that an essentially 3-D vision providing information about the geometry of the entire object would be in question. Many-sheeted space-time allows this. </p><p> The presence of the hologram image for method II requires the self-sustainment of the reference beam only whereas the presence of phantom DNA image for method I requires the self-sustainment of both beams. Non-linear dynamics for the energy feed from DNA to the magnetic body could make possible self-sustainment for both beams simultaneously. Non-linear dynamics for beams themselves could allow for the self-sustainment of reference beam and/or reflected beam. The latter option is favored by data. </p>

This book represents a view about quantum hardware of living systems in TGD framework. Since the vision is bound to look highly speculative, it is good to emphasize that the most important predictions follow almost without any reference to the classical field equations using only quantum classical correspondence. </p><p> The new conceptual elements are the notion of many-sheeted space-time having fractal hierarchical structure, 4-D spin glass degeneracy of the preferred extremals of K&auml;hler action providing huge information storage capacity, topological field quantization, the notion of magnetic/field body serving as intentional agent using biological body as sensory receptor and motor instrument, zero energy ontology leading to a new view about energy and about the relationship between experienced and geometric time, dark matter hierarchy realized in terms of book like structure of 8-D imbedding space with pages labeled by values of Planck constant, the assumption that the phase transitions changing the value of Planck constant provide a key control tool in living matter, and p-adic length scale hypothesis allowing quantitative grasp to the situation. </p><p> <OL> <LI> Three chapters of this book are devoted to the model of high $T_c$ super-conductivity relying strongly on the notions of quantum criticality and dark matter. <LI> Two chapters discuss quantum antenna hypothesis inspired by topological light rays (M(assless) E(xtremals)) and the notion of wormhole magnetic fields. Notice that the notion of wormhole magnetic field was introduced much before the hypothesis that bosons and also interaction fermions have a natural identification as wormhole contacts emerged. The recent view about quantum TGD suggests the interpretation wormhole magnetic fields as dark scaled up versions of elementary particles identified as K&auml;hler magnetic flux tubes identified as pairs of magnetically charged wormhole contacts carrying at the second wormhole throat neutrino pair neutralizing the weak isospin of the fermion at the second wormhole throat. For ordinary value of Planck constant the length of is flux would be given by weak length scale. Therefore weak interactions in biological length scales are involved giving rise to large parity breaking effects. Also scaled up QCD is involved and implying hadron like states in biological length scales. <LI> Two chapters are devoted to the possible biological implications of the hypothesis that dark matter corresponds to macroscopic quantum phases characterized by a large value of Planck constant and is the key actor in living matter. <LI> A possible identification of quantum correlates of sensory qualia is discussed assuming that qualia are in one-one correspondence with the increments of quantum numbers in quantum jump. Also a simple model for sensory receptor is introduced. The recent view about cell membrane as almost vacuum extremal of K&auml;hler action explains large parity breaking effects in living matter and also the peak frequencies of photoreceptors in retina. Also a model for the cell membrane as a kind of sensory homunculus with lipids identified as pixels of a sensory map representing basic qualia follows naturally. Furthermore, EEG photons and biophotons can be identified as decay products of same dark photons. </OL>

The book describes basic quantum TGD in its recent form. <OL> <LI>The properties of the preferred extremals of Kähler action are crucial for the construction and the discussion of known extremals is therefore included. <LI>General coordinate invariance and generalized super-conformal symmetries - the latter present only for 4-dimensional space-time surfaces and for 4-D Minkowski space - define the basic symmetries of quantum TGD. <LI>In zero energy ontology S-matrix is replaced with M-matrix and identified as time-like entanglement coefficients between positive and negative energy parts of zero energy states assignable to the past and future boundaries of 4-surfaces inside causal diamond defined as intersection of future and past directed light-cones. M-matrix is a product of diagonal density matrix and unitary S-matrix and there are reasons to believe that S-matrix is universal. Generalized Feynman rules based on the generalization of Feynman diagrams obtained by replacing lines with light-like 3-surfaces and vertices with 2-D surfaces at which the lines meet. <LI> A category theoretical formulation of quantum TGD is considered. Finite n measurement resolution realized in terms of a fractal hierarchy of causal diamonds inside causal diamonds leads to a stringy formulation of quantum TGD involving effective replacement of the 3-D light-like surface with a collection of braid strands representing the ends of strings. A formulation in terms of category theoretic concepts is proposed and leads to a hierarchy of algebras forming what is known as operads. <LI>Twistors emerge naturally in TGD framework and could allow the formulation of low energy limit of the theory in the approximation that particles are massless. The replacement of massless plane waves with states for which amplitudes are localized are light-rays is suggestive in twistor theoretic framework. Twistors could allow also a dual representation of space-time surfaces in terms of surfaces of X×CP₂, where X is 8-D twistor space or its 6-D projective variant. These surfaces would have dimension higher than four in non-perturbative phases meaning an analogy with branes. In full theory a massive particles must be included but represent a problem in approach based on standard twistors. The interpretation of massive particles in 4-D sense as massless particles in 8-D sense would resolve the problem and requires a generalization of twistor concept involving in essential manner the triality of vector and spinor representations of SO(7,1). <LI>In TGD Universe bosons are in well-defined sense bound states of fermion and anti-fermion. This leads to the notion of bosonic emergence meaning that the fundamental action is just Dirac action coupled to gauge potentials and bosonic action emerges as part of effective action as one functionally integrates over the spinor fields. This kind of approach predicts the evolution of all coupling constants if one is able to fix the necessary UV cutoffs of mass and hyperbolic angle in loop integrations. The guess for the hyperbolic cutoff motivated by the geometric view about finite measurement resolution predicts coupling constant evolution which is consistent with that predicted by standard model. The condition that all N-vertices defined by fermiomic loops vanish for N>3 when incoming particles are massless gives hopes of fixing completely the hyperbolic cutoff from fundamental principles. </OL>