Physics of Biology

TGD Based View About Classical Fields in Relation to Consciousness Theory and Quantum Biology

Authors: Matti Pitkänen
Comments: 18 Pages.

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.

1. 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.
2. 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).
3. 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.

Category: Physics of Biology

Surmounting the Cartesian Cut: Klein Bottle Logophysics, the Dirac Algebra and the Genetic Code

Authors: Diego Lucio Rapoport
Comments: 22 Pages.

We reintroduce the Klein Bottle (KB) logophysics at the foundations of the unification of quantum geometry, cell biology, embryology and evolution, to extend it to the genetic code and allosteric recognition. We find that the genetic code has three possible fractal topologies: two different families of KBs embedded in HyperKBs, or still a 2-torus, depending which pair of three subalphabets for the genetic “letters” is chosen; this does not require the double helix. We complete the genetic codification of embryological differentiation introduced in an accompanying article. We discuss the Hadamard-KB representation of this codification and discuss its robustness and that of embryological development with respect to environmental noise. We discuss this KB codification of the 64 codons with its isomorphic representation in terms of the Dirac Algebra (DA) of Quantum Mechanics, in the Nilpotent Universal Computational Rewrite System (NUCRS), a self-referential syntax that generates much of mathematics and the fundamental symmetries of physics. We show that the double helix can be obtained from the duplication of the KB associated with the bistable perception of the tetrahedron representation of the four genetic letters. The DA and its double tetrahedron codification in NUCRS is found to be associated with a pair of superposed KBs, yielding the double 3D (space and momentum) space of physics, and the double helix of DNA, which thus appears related to a pair of KBs, being the case that only one is necessary to construct the genome. We show that the depth-time variable of visual perception materializes as space Thus, the DA is derivable from two KBs, and the purported dualism of physics as presented in NUCRS, is rendered to be based in the non-dualistic KBL. We discuss the relations with a theory of evolutions, and between biological periodicities and the KB of the Mendeleev table (Boeyens). We present relations between metacognition and the HyperKlein Bottle, and evolution in terms of time waves defining in toto the different structures. We present rudiments of the ontoepistemology of the Hyper KB Logic, its relations with the anthropic principles and the universal physical constants, which are found to be contextual.
Category: Physics of Biology

On the Fusion of Physics and Klein Bottle Logic in Biology, Embryogenesis and Evolution

Authors: Diego Lucio Rapoport
Comments: 20 Pages.

We introduce a new paradigm for embryological differentiation with its relations to the genome and evolution, in terms of the fusion of logic and physics: logophysics (LGP), associated to the ontology and epistemology of the Klein Bottle (KB). We introduce LGP through the subversion of the fixed dualistic categories of exterior and interior, basis for much of science, in terms of the eversion: turning inside-out of the two dimensional elastic sphere (ovum), which is the actual case. We propose bauplans unfolding from a 6d space in which time waves manifest through torsion fields in real space and in which the eversion is mediated by KBs. We present the torsion geometry, quantum and elastodynamical, of self-referential biology. We apply this to the problem of the physics of embryological differentiation in terms of quantum torsion-elastodynamics waves and the light tensegrity of the cell. We associate it with a topological transformation which extends the proposal by Maxwell and Poynting, founders of electromagnetics, for the interaction of the inanimate and animate worlds. We present a new conception of the world in terms of time waves and the KB, that appears in the natural number system, in cosmology, in vision recognition, in the topographic map of the sensorium, in the periodic table of elements, the genome, etc. We surmount the ancient problem of what life is, providing a LGP basis for both the inanimate and animate realms.
Category: Physics of Biology

A Thermodynamic Perspective on the Interaction of Radio Frequency Radiation with Living Tissue

Authors: Michael Peleg
Comments: 8 Pages.

The existence of biological effects of radio frequency (RF) radiation on living tissue is well established, including also effects which are not caused by plain warming. Still the exact mechanisms of interaction between the RF radiation and the living tissue are mostly unknown. In this work a thermodynamic perspective relevant to some aspects of those yet unknown mechanisms is presented. This perspective reveals that living tissue under RF radiation should not be assumed to be in thermal equilibrium since it is governed by two temperatures: The ambient temperature of its surroundings and a vastly higher temperature TR which is assigned by certain criteria to the RF radiation. The criteria presented here to determine the radiation temperature TR are not unique and other approaches may lead to different temperature values, however TR as presented here has an interesting physical significance. The possible relevance of this approach to the interaction mechanisms is presented.
Category: Physics of Biology

Sheldrake's Morphic Fields and TGD View About Quantum Biology

Authors: Matti Pitkänen
Comments: 11 Pages.

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.

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.

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.

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.

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.

Category: Physics of Biology

Quantum Model for Remote Replication

Authors: Matti Pitkänen, Peter Gariaev
Comments: 10 Pages.

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.

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.

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.

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.

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.

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.

Category: Physics of Biology

Oil Droplets as a Primitive Life Form?

Authors: Matti Pitkänen
Comments: 12 Pages.

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.

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.

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.

Category: Physics of Biology

Generalization of Thermodynamics Allowing Negentropic Entanglement and a Model for Conscious Information Processing

Authors: Matti Pitkänen
Comments: 11 Pages.

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.

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.

Category: Physics of Biology

DNA Waves and Water

Authors: Matti Pitkänen
Comments: 11 Pages.

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.

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.

Category: Physics of Biology

Model for the Findings About Hologram Generating Properties of DNA

Authors: Peter Gariaev, Matti Pitkänen
Comments: 27 Pages.

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> 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.

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.

Category: Physics of Biology

Heating by Cooling

Authors: Ron Bourgoin
Comments: 3 pages.

When a body is quickly cooled by thrusting it in a very cold medium, does its internal temperature go up? We examine the case of a heatstroke patient thrust in ice-water to lower his or her temperature. Recent research in photon science suggests that core temperature increases.
Category: Physics of Biology

De Broglie Matter Waves and the Evolution of Consciousness

Authors: John A. Gowan
Comments: 2 pages

In 1923 Louis de Broglie introduced the notion of matter waves, the particle-wave duality of matter which is the reciprocal extension of the notion of the particle-wave duality of light. The wave nature of matter is evidently a "memory" of its origin in light, much as the particle aspect of light suggests its capacity to create matter. Such dualities are part of the connective tissue of the Cosmos and its two principle energy forms, light and matter (free and bound electromagnetic energy). The less massive the particle, the more strongly is its wave nature expressed. The wave nature of the tiny electron is very pronounced, as is famously demonstrated by the interference phenomena of the canonical 2-slit experiment of quantum mechanics. In the extreme case of neutrinos, which apparently have almost no mass, their wave nature completely dominates their particle nature. However, as particles become heavier and more massive, their wave nature becomes rapidly overwhelmed, until for ordinary macroscopic masses to which we are sensible it is completely obscured.
Category: Physics of Biology

What I Was Doing When I Was Einstein's Age of Discovery

Authors: David Martin Degner
Comments: 37 pages

AWhen I was in my twenties I worked on the problem: What is Life? In 1980/81 I was a research associate in molecular genetics at the University of California at Berkeley working for a professor in bacteriology. I wrote for the professor a 57 legal sized page, hand written and unedited essay in the form of a sequence of 72 questions and answers that focused on Gram (+) prokaryotic cells, the hydrogen of biology. The professor failed to comment or ask a single question. Back then I was into equilibrium and non-equilibrium thermodynamics, reversible and irreversible processes, chemical interactions and kinetics, static and dynamic phase organization, mass/energy and information flow, information definition and information processing, and modeling biological cells as chemical computers, i.e. Turing machines. I've faithfully transcribed that unedited sequence of questions and answers here. It's at times quite tedious and there were some major errors but there also is some really good science. There is always chaos embedded in new work. This is a qualitative, phenomenological model of the central processing unit of the prokaryotic cell that is the first step in obtaining a fully quantitative model for biology.
Category: Physics of Biology

What is Life?

Authors: David Martin Degner
Comments: 12 pages

A static and dynamic physical model is presented for the Gram (+) prokaryotic cell, the hydrogen of biology. It is discovered that cells are chemical computers and the fundamental Turing machine architecture of biology is laid out.
Category: Physics of Biology

Teilhard de Chardin Prophet of the Information Age

Authors: John A. Gowan
Comments: 9 pages. This paper has also been published as a Google "Knol".

Teilhard de Chardin's notions of the "Noosphere" and the "Omega Point" are explored in the context of current knowledge and theory, especially J.E. Lovelock's conception of "Gaia" - planet Earth as a superorganism. Space-faring humans are seen as the "seeds" or dispersal agents of Gaia's reproductive phase, carrying Earth-life into the Galaxy. "Noah's Ark" is a vision of the future, not the past.
Category: Physics of Biology

The Fractal Organization of Nature

Authors: John A. Gowan
Comments: 13 pages. This paper has also been published as a Google "Knol".

A General Systems model of the Universe is presented, based on a fractal paradigm. A 4x3 "metric" or fractal algorithm is proposed as the organizing principle of the Microphysical, Biophysical, Astrophysical, and Metaphysical realms. The algorithm is expressed through the conservation laws and forces of physics, the families of elementary particles, the dimensions of spacetime, the quantum rules of atomic order, the structure of baryons, alpha particles, carbon atoms, carbon's molecular and crystal bonds, DNA, the genetic code, gravitation, and the nucleosynthetic pathway of stars. The human mind has discovered this order both intuitively and rationally, where it finds expression in the 4x3 (and 4x4) patterns of mythological, occult, religious, philosophical, and scientific "world systems" and cosmologies. A general model of the human "metaphysical realm", and a model of the unified field theory are presented as examples of how the fractal algorithm may be used in system modeling. In its most general form, the 4-part algorithm consists of an input of energy, followed by two complementary conservation modes, concluding with a restorative force which either returns the system to its original state, or elevates it to a "harmonic complexion" or resonant analog of the original state (the various levels of the model
Category: Physics of Biology

Section 12: Man's Role in Nature

Authors: John A. Gowan
Comments: 4 pages, This paper has also been published as a Google "Knol".

Man's role in nature seems to divide naturally in two parts: 1) the dispersal of Earth-Life into the galaxy; 2) the enhancement and development of the self-awareness and creativity of the Cosmos. Humanity is, in the first instance, the practical, scientific tool of Gaia, or Mother Earth, evolved as her reproductive agent; and in the second instance, humanity is the perceptual or intelectual tool of the Cosmos, evolved to carry the intelligence and self-awareness of the Cosmos, the agent by which the Cosmos explores, understands, and appreciates itself, including exploring new modes of creativity. Our native spiritual awareness appears to be our intuitive recognition of this cosmic connection. The first role is Earth-oriented, manifesting socially as Science; the second role is Universe-oriented, manifesting socially as Art and Religion, in all their forms. It should be obvious that the first role is in no way intrinsically at odds with the second.
Category: Physics of Biology

Section 8: General Systems, Complex Systems

Authors: John A. Gowan
Comments: 9 pages, This paper has also been published as a Google "Knol".

General Systems, as I use the term, denotes a repeating pattern of natural organization - a fractal algorithm or ordering principle in the Cosmos. While not enforced with the same stringency as a natural law (such as energy conservation), the pattern-forming impulse is nevertheless all-pervasive in nature and seems to proceed from such fundamental principles as resonance and the pathway of least energy or least resistance. It is just simpler, more efficient, and takes less energy to create a universe using self-similar repeating patterns than following any other plan. The "Tetrahedron Model" of cosmic order presents a General System based on a 4x3 universal fractal algorithm.
Category: Physics of Biology

The Human Connection

Authors: John A. Gowan
Comments: 12 pages, This paper has also been published as a Google "Knol".

I discuss some specifically human (meta-physical) connections with the Cosmos. Life is the information pathway by which the universe awakens to and explores itself; humans are (locally) the most advanced expression of this evolving cosmic self-awareness and consciousness. Human life is significant to the extent it enriches the self-awareness, knowledge, creativity, general and personalized experience of the Cosmos.
Category: Physics of Biology

The Information Pathway

Authors: John A. Gowan
Comments: 18 pages, This paper has also been published as a Google "Knol".

The Fractal Organization of Nature is seen as an information pathway whereby the Universe becomes selfaware through the spiritual awakening of humanity. The natural hierarchy is modeled as a sort of "Jacob's ladder" whereby Homo sapiens ascends to the astrophysical realm, realizing our destiny as galactic citizens, and dispersing Earth-life into the Cosmos.
Category: Physics of Biology

Electro Mechanical Contributions to Low Frequency Dielectric Responses of Biological Cells in Colloidal Suspension

Authors: Andrew Beckwith
Comments: 18 pages. Part of a different analogy to bio phyics dielectric constants explored by the author with Dr. Patrick Xie and Dr. James Claycomb at the Texas center for super conductivity, Houston, Texas, in early 2002.

We investigate electro-mechanical contributions to the low frequency dielectric response of biological cells in colloidal suspension. Prior simulations of biological cells in colloidal suspension yield maximum dielectric constant values about 10³ in magnitude as the frequency of applied electric fields drops below the kHz range. Experimentally measured relative dielectric values in yeast cells , on the other hand, have maximal values up to 10⁷ - 10⁸ . We consider both electrical and mechanical energy stored in cellular suspension and show that low frequency mechanical contributions can give rise to dielectric constant values of this magnitude.
Category: Physics of Biology

Photorefractive Protein Bacteriorhodopsin, BR , as a Material for Holographic Data-Recording

Authors: Rafael-Andrés Alemañ-Berenguer, María Gomariz
Comments: 7 pages

The search of materials of biological origin with specific estates of potential technologic applications whose structure and functions come out from a process of adaptive evolution experienced by the organisms in extreme environments, is one of the most active fields in the modern biophysics. In short, the protein bacteriorhodopsin, acts like a protonic bomb whose photocycle has demonstrated interesting implications in the technologies of optic storage of information by means of holographic methods. In the present work some results of the investigation undertaken by our group are exposed, consistent mainly in the study of the influence that working conditions (pH, state of aggregation of the environment, intensity and time of illumination, etc.) have over photophysical and photochemical states of bacteriorhodopsin as well as in the tracking of the possible presence of bacteriorhodopsin proteins and xantorhodopsin, in the salines of Santa Pola (Alicante, Spain).
Category: Physics of Biology

Genes and Memes

Authors: Matti Pitkänen
Comments: 554 pages

The first part of book discusses the new physics relevant to biology and the vision about Universe as topological quantum computer (tqc). Second part describes concrete physical models.

1. The notion of many-sheeted DNA and a model of genetic code inspired by the notion of Combinatorial Hierarchy predicting what I call memetic code are introduced. The almost exact symmetries of the code table with respect to the third letter inspire the proposal that genetic code could have evolved as fusion of two-letter code and single-letter code.
2. A model for how genome and cell membrane could act as tqc is developed. Magnetic flux tubes containing dark matter characterized by large value of Planck constant would make living matter a macroscopic quantum system. DNA nucleotides and lipids of the cell membrane would be connected by magnetic flux tubes and the flow of the 2-D liquid formed by lipids would induce dynamical braiding defining the computation.
3. The net of magnetic flux tubes could explain the properties of gel phase. Phase transitions reducing Planck constant would induce a contraction of the flux tubes explaining why biomolecules manage to find each other in a dense soup of bio-molecules. The topology of the net would be dynamical and ADP ↔ ATP transformation could affect it. The anomalies related to ionic currents, nerve pulse activity, and interaction of ELF radiation with vertebrate brain find an explanation in this framework.
4. The discoveries of Peter Gariaev about interaction of ordinary and laser light with genome combined with ideas about dark matter and water memory lead to a model for the interaction of photons with DNA. Dark ↔ ordinary transformation for photons could allow to "see" dark matter by allowing ordinary light to interact with DNA.
5. A physical model for genetic code emerged from an attempt to understand the mechanism behind water memory. Dark nuclei which sizes zoomed up to atomic size scale could represent genes. The model for dark nucleon consisting of three quarks predicts counterparts of 64 DNAs, 64 RNAs, and 20 aminoacids and allows to identify genetic code as a natural mapping of DNA type states to amino-acid type states and consistent with vertebrate genetic code.

The third part of the book discusses number theoretical models of the genetic code based on p-adic thermodynamics and maximization of entropy or negentropy. These models reproduce the genetic code but fail to make killer predictions.
Category: Physics of Biology

Quantum Hardware of Living Matter

Authors: Matti Pitkänen
Comments: 552 pages

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. 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 Kähler 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.

1. 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.
2. 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 have a natural identification as wormhole contacts emerged.
3. 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.
4. 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.

I must apologize the fact that the introduction is somewhat ahead of the chapters of the book which have developed slowly during the last decade. In particular, the implications of the dark matter revolution which has occurred during last year and still continues, have not been thoroughly considered. Same applies to the implications of zero energy ontology.
Category: Physics of Biology

Bio-Systems as Self-Organizing Quantum Systems

Authors: Matti Pitkänen
Comments: 288 pages

The quantum theory of self organization represents a rather old layer of TGD inspired theory of consciousness.

1. Self organization is a non-deterministic process and corresponds to the evolution of conscious entities - selves - to asymptotic self-organization patters via quantum jumps. This requires macroscopic quantum coherence.
2. Space-time surfaces are analogous to Bohr orbits and the failure of the classical non-determinism in the conventional sense of the word makes it possible to interpret space-time surfaces as representations of both quantum states and sequences of quantum states assignable to the sequences of quantum jumps. The huge vacuum degeneracy of Kähler action implies spin glass degeneracy in 4-dimensional sense providing maximal resources to represent information about external world by mapping its states to its own internal states. Space-time sheets would be four-dimensional statues gradually carved by a sequence of quantum jump to a shape representing asymptotic self-organization pattern.
3. Magnetic body is the intentional agent controlling the biological body. The fractal hierarchy of copies of standard model physics involving in particular a hierarchy of electro-weak bosons and gluons with increasingly longer weak/confinement length scale is an essential piece of the story. The concrete quantum model for how intentions are transformed to actions provides additional insights to quantum self-organization.
4. The new view about time and energy justifying time mirror mechanism involving sending of negative energy phase conjugate photons to geometric past is crucial for the models of long term memory, intentional action, and remote metabolism.
5. The model of self organization involves cyclotron radiation from the cyclotron transitions assignable with the Bose-Einstein condensates of charged bosons at the magnetic bodies and Josephson radiation from Josephson junctions assignable to the cell membrane and also other layer like structures (electrets).

Zero energy ontology and hierarchy of Planck constants complete this vision. Zero energy ontology justifies time mirror mechanism and explains how arrow of subjective time emerges. Dark matter hierarchy implies macroscopic quantum coherence, inspires vision about bio-catalysis and quantum computation in living matter, explains evolutionary leaps, and suggests generalization of the notion of genome and new realizations of genetic code. The topics of the book are following. The first chapters explain the vision about biological self organization in TGD framework. The last chapters of the book discuss quantum control and coordination in living matter according to TGD.
Category: Physics of Biology

Wheeler-Feynman Generalized Bohm Quantum Potential for Open Far-from-Equilibrium Biological Dissipative Structures with Non-Unitary Post-Quantum Retro-Causal Signal Nonlocality

Authors: Jack Sarfatti
Comments: 6 pages

Bohm's micro-quantum ontological interpretation for closed systems in sub-quantal thermal equilibrium is generalized to open macro-quantum coherent systems using the Wheeler-Feynman-Cramer Ansatz. A connection to the Freeman-Vitiello model of the brain is suggested.
Category: Physics of Biology

TGD Based View About Classical Fields in Relation to Consciousness Theory and Quantum Biology

Authors: Matti Pitkänen
Comments: 18 Pages.

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.

1. 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.
2. 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).
3. 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.

Category: Physics of Biology

Sheldrake's Morphic Fields and TGD View About Quantum Biology

Authors: Matti Pitkänen
Comments: 11 Pages.

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.

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.

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.

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.

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.

Category: Physics of Biology

Quantum Model for Remote Replication

Authors: Matti Pitkänen, Peter Gariaev
Comments: 10 Pages.

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.

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.

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.

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.

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.

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.

Category: Physics of Biology

Oil Droplets as a Primitive Life Form?

Authors: Matti Pitkänen
Comments: 12 Pages.

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.

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.

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.

Category: Physics of Biology

Generalization of Thermodynamics Allowing Negentropic Entanglement and a Model for Conscious Information Processing

Authors: Matti Pitkänen
Comments: 8 Pages.

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.

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.

Category: Physics of Biology

DNA Waves and Water

Authors: Matti Pitkänen
Comments: 11 Pages.

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.

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.

Category: Physics of Biology

Model for the Findings About Hologram Generating Properties of DNA

Authors: Peter Gariaev, Matti Pitkänen
Comments: 27 Pages.

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> 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.

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.

Category: Physics of Biology

Teilhard de Chardin Prophet of the Information Age

Authors: John A. Gowan
Comments: 9 pages. This paper has also been published as a Google "Knol".

Teilhard de Chardin's notions of the "Noosphere" and the "Omega Point" are explored in the context of current knowledge and theory, especially J.E. Lovelock's conception of "Gaia" - planet Earth as a superorganism. Space-faring humans are seen as the "seeds" or dispersal agents of Gaia's reproductive phase, carrying Earth-life into the Galaxy. "Noah's Ark" is a vision of the future, not the past.
Category: Physics of Biology

The Human Connection

Authors: John A. Gowan
Comments: 13 pages, This paper has also been published as a Google "Knol".

As Carl Sagan famously said, we are "star stuff" exploring the stars. Life is the information pathway by which the universe achieves self-awareness and explores itself, including evolving new modes of creativity and beauty. In terms of creativity, humans represent a fractal iteration of the creative energy of the Cosmos, as well as of its evolutionary powers. Because the entire material universe devolves from light, matter and life are a conserved form of the information content latent in light, expressed primordially through the broken symmetry of light leading to atomic matter and charge conservation. The charges of matter are the symmetry debts of light (Noether's Theorem), and through these charges the energy of light is transformed into the information content of the world. Hence it is ultimately through the connection between atoms and light, charge conservation and symmetry conservation, that humans retain their connection to the primordial creative energies and latent information content of the universe (and the multiverse). "We come trailing clouds of glory..."
Category: Physics of Biology

The Human Connection

Authors: John A. Gowan
Comments: 12 pages, This paper has also been published as a Google "Knol".

I discuss some specifically human (meta-physical) connections with the Cosmos. Life is the information pathway by which the universe awakens to and explores itself; humans are (locally) the most advanced expression of this evolving cosmic self-awareness and consciousness. Human life is significant to the extent it enriches the self-awareness, knowledge, creativity, general and personalized experience of the Cosmos.
Category: Physics of Biology

The Information Pathway

Authors: John A. Gowan
Comments: 19 pages, This paper has also been published as a Google "Knol".

The Fractal Organization of Nature is seen as an information pathway whereby the Universe becomes selfaware through the spiritual awakening of humanity. The natural hierarchy is modeled as a sort of "Jacob's ladder" whereby Homo sapiens ascends to the astrophysical realm, realizing our destiny as galactic citizens, and dispersing Earth-life into the Cosmos.
Category: Physics of Biology

The Information Pathway

Authors: John A. Gowan
Comments: 19 pages, This paper has also been published as a Google "Knol".

The Fractal Organization of Nature is seen as an information pathway whereby the Universe becomes selfaware through the spiritual awakening of humanity. The natural hierarchy is modeled as a sort of "Jacob's ladder" whereby Homo sapiens ascends to the astrophysical realm, realizing our destiny as galactic citizens, and dispersing Earth-life into the Cosmos.
Category: Physics of Biology

Genes and Memes

Authors: Matti Pitkänen
Comments: 640 pages

The first part of book discusses the new physics relevant to biology and the vision about Universe as topological quantum computer (tqc).

1. The notion of many-sheeted DNA and a model of genetic code inspired by the notion of Combinatorial Hierarchy predicting what I call memetic code are introduced. The almost exact symmetries of the code table with respect to the third letter inspire the proposal that genetic code could have evolved as fusion of two-letter code and single-letter code.
2. A model for how genome and cell membrane could act as tqc is developed. Magnetic flux tubes containing dark matter characterized by large value of Planck constant would make living matter a macroscopic quantum system. DNA nucleotides and lipids of the cell membrane would be connected by magnetic flux tubes and the flow of the 2-D liquid formed by lipids would induce dynamical braiding defining the computation.
3. The net of magnetic flux tubes could explain the properties of gel phase. Phase transitions reducing Planck constant would induce a contraction of the flux tubes explaining why bio-molecules manage to find each other in a dense soup of bio-molecules. The topology of the net would be dynamical and ADP ↔ ATP transformation could affect it. The anomalies related to ionic currents, nerve pulse activity, and interaction of ELF radiation with vertebrate brain find an explanation in this framework. The number theoretic entanglement entropy able to have negative values could be seen as the real quintenssence associated with the metabolic energy transfer, and the poorly understood high energy phosphate bond could be interpreted in terms of negentropic entanglement rather than ordinary bound state entanglement.
4. The discoveries of Peter Gariaev about interaction of ordinary and laser light with genome combined with ideas about dark matter and water memory lead to a model for the interaction of photons with DNA. Dark ↔ ordinary transformation for photons could allow to "see" dark matter by allowing ordinary light to interact with DNA.
5. A physical model for genetic code emerged from an attempt to understand the mechanism behind water memory. Dark nuclei which sizes zoomed up to atomic size scale could represent genes. The model for dark nucleon consisting of three quarks predicts counterparts of 64 DNAs, 64 RNAs, and 20 aminoacids and allows to identify genetic code as a natural mapping of DNA type states to amino-acid type states and consistent with vertebrate genetic code.

The third part of the book discusses number theoretical models of the genetic code based on p-adic thermodynamics and maximization of entropy or negentropy. These models reproduce the genetic code but fail to make killer predictions.

Category: Physics of Biology

Genes and Memes

Authors: Matti Pitkänen
Comments: 602 pages

The first part of book discusses the new physics relevant to biology and the vision about Universe as topological quantum computer (tqc). Second part describes concrete physical models.

1. The notion of many-sheeted DNA and a model of genetic code inspired by the notion of Combinatorial Hierarchy predicting what I call memetic code are introduced. The almost exact symmetries of the code table with respect to the third letter inspire the proposal that genetic code could have evolved as fusion of two-letter code and single-letter code.
2. A model for how genome and cell membrane could act as tqc is developed. Magnetic flux tubes containing dark matter characterized by large value of Planck constant would make living matter a macroscopic quantum system. DNA nucleotides and lipids of the cell membrane would be connected by magnetic flux tubes and the flow of the 2-D liquid formed by lipids would induce dynamical braiding defining the computation.
3. The net of magnetic flux tubes could explain the properties of gel phase. Phase transitions reducing Planck constant would induce a contraction of the flux tubes explaining why biomolecules manage to find each other in a dense soup of bio-molecules. The topology of the net would be dynamical and ADP ↔ ATP transformation could affect it. The anomalies related to ionic currents, nerve pulse activity, and interaction of ELF radiation with vertebrate brain find an explanation in this framework.
4. The discoveries of Peter Gariaev about interaction of ordinary and laser light with genome combined with ideas about dark matter and water memory lead to a model for the interaction of photons with DNA. Dark ↔ ordinary transformation for photons could allow to "see" dark matter by allowing ordinary light to interact with DNA.
5. A physical model for genetic code emerged from an attempt to understand the mechanism behind water memory. Dark nuclei which sizes zoomed up to atomic size scale could represent genes. The model for dark nucleon consisting of three quarks predicts counterparts of 64 DNAs, 64 RNAs, and 20 aminoacids and allows to identify genetic code as a natural mapping of DNA type states to amino-acid type states and consistent with vertebrate genetic code.

The third part of the book discusses number theoretical models of the genetic code based on p-adic thermodynamics and maximization of entropy or negentropy. These models reproduce the genetic code but fail to make killer predictions.
Category: Physics of Biology

Quantum Hardware of Living Matter

Authors: Matti Pitkänen
Comments: 602 Pages.

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>
Category: Physics of Biology

Quantum Hardware of Living Matter

Authors: Matti Pitkänen
Comments: 598 Pages.

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>
Category: Physics of Biology

Quantum Hardware of Living Matter

Authors: Matti Pitkänen
Comments: 472 pages

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.

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 Kähler 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.

1. 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.
2. 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 Kähler 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.
3. 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.
4. 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 Kähler 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.

Category: Physics of Biology

Quantum Hardware of Living Matter

Authors: Matti Pitkänen
Comments: 552 pages

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. 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 Kähler 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.

1. 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.
2. 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 have a natural identification as wormhole contacts emerged.
3. 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.
4. 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.

I must apologize the fact that the introduction is somewhat ahead of the chapters of the book which have developed slowly during the last decade. In particular, the implications of the dark matter revolution which has occurred during last year and still continues, have not been thoroughly considered. Same applies to the implications of zero energy ontology.
Category: Physics of Biology

Bio-Systems as Self-Organizing Quantum Systems

Authors: Matti Pitkänen
Comments: 397 Pages.

The quantum theory of self organization represents a rather old layer of TGD inspired theory of consciousness. <p></p> <OL><LI> Self organization is a non-deterministic process and corresponds to the evolution of conscious entities - selves - to asymptotic self-organization patterns via quantum jumps. This requires macroscopic quantum coherence. <LI> Space-time surfaces are analogous to Bohr orbits and the failure of the classical non-determinism in the conventional sense of the word makes it possible to interpret space-time surfaces as representations of both quantum states and sequences of quantum states assignable to the sequences of quantum jumps. The huge vacuum degeneracy of K&auml;hler action implies spin glass degeneracy in 4-dimensional sense providing maximal resources to represent information about external world by mapping its states to its own internal states. Space-time sheets would be four-dimensional statues gradually carved by a sequence of quantum jump to a shape representing asymptotic self-organization pattern. <LI> Magnetic body is the intentional agent controlling the biological body. The fractal hierarchy of copies of standard model physics involving in particular a hierarchy of electro-weak bosons and gluons with increasingly longer weak/confinement length scale is an essential piece of the story. The concrete quantum model for how intentions are transformed to actions provides additional insights to quantum self-organization. <LI> The new view about time and energy justifying time mirror mechanism involving sending of negative energy phase conjugate photons to geometric past is crucial for the models of long term memory, intentional action, and remote metabolism. <LI> The model of self organization involves cyclotron radiation from the cyclotron transitions assignable with the Bose-Einstein condensates of charged bosons at the magnetic bodies and Josephson radiation from Josephson junctions assignable to the cell membrane and also other layer like structures (electrets). <LI> The vision about life residing in the intersection of real and p-adic worlds is central for the approach. In particular, the existence of number theoretic entanglement entropy, which can have negative values, makes possible to identify a measure of conscious information and negentropic entanglement replaces metabolic energy feed as the basic prequisite of life. </OL> Zero energy ontology and hierarchy of Planck constants complete this vision. Zero energy ontology justifies time mirror mechanism and explains how arrow of subjective time emerges. Dark matter hierarchy implies macroscopic quantum coherence, inspires vision about bio-catalysis and quantum computation in living matter, explains evolutionary leaps, and suggests generalization of the notion of genome and new realizations of genetic code. </p><p> The topics of the book are following. The first chapters explain the vision about biological self organization in TGD framework. The last chapters of the book discuss quantum control and coordination in living matter according to TGD.
Category: Physics of Biology

Bio-Systems as Self-Organizing Quantum Systems

Authors: Matti Pitkänen
Comments: 397 Pages.

The quantum theory of self organization represents a rather old layer of TGD inspired theory of consciousness. <p></p> <OL><LI> Self organization is a non-deterministic process and corresponds to the evolution of conscious entities - selves - to asymptotic self-organization patterns via quantum jumps. This requires macroscopic quantum coherence. <LI> Space-time surfaces are analogous to Bohr orbits and the failure of the classical non-determinism in the conventional sense of the word makes it possible to interpret space-time surfaces as representations of both quantum states and sequences of quantum states assignable to the sequences of quantum jumps. The huge vacuum degeneracy of K&auml;hler action implies spin glass degeneracy in 4-dimensional sense providing maximal resources to represent information about external world by mapping its states to its own internal states. Space-time sheets would be four-dimensional statues gradually carved by a sequence of quantum jump to a shape representing asymptotic self-organization pattern. <LI> Magnetic body is the intentional agent controlling the biological body. The fractal hierarchy of copies of standard model physics involving in particular a hierarchy of electro-weak bosons and gluons with increasingly longer weak/confinement length scale is an essential piece of the story. The concrete quantum model for how intentions are transformed to actions provides additional insights to quantum self-organization. <LI> The new view about time and energy justifying time mirror mechanism involving sending of negative energy phase conjugate photons to geometric past is crucial for the models of long term memory, intentional action, and remote metabolism. <LI> The model of self organization involves cyclotron radiation from the cyclotron transitions assignable with the Bose-Einstein condensates of charged bosons at the magnetic bodies and Josephson radiation from Josephson junctions assignable to the cell membrane and also other layer like structures (electrets). <LI> The vision about life residing in the intersection of real and p-adic worlds is central for the approach. In particular, the existence of number theoretic entanglement entropy, which can have negative values, makes possible to identify a measure of conscious information and negentropic entanglement replaces metabolic energy feed as the basic prequisite of life. </OL> Zero energy ontology and hierarchy of Planck constants complete this vision. Zero energy ontology justifies time mirror mechanism and explains how arrow of subjective time emerges. Dark matter hierarchy implies macroscopic quantum coherence, inspires vision about bio-catalysis and quantum computation in living matter, explains evolutionary leaps, and suggests generalization of the notion of genome and new realizations of genetic code. </p><p> The topics of the book are following. The first chapters explain the vision about biological self organization in TGD framework. The last chapters of the book discuss quantum control and coordination in living matter according to TGD.
Category: Physics of Biology

Bio-Systems as Self-Organizing Quantum Systems

Authors: Matti Pitkänen
Comments: 315 pages

The quantum theory of self organization represents a rather old layer of TGD inspired theory of consciousness.

1. Self organization is a non-deterministic process and corresponds to the evolution of conscious entities - selves - to asymptotic self-organization patterns via quantum jumps. This requires macroscopic quantum coherence.
2. Space-time surfaces are analogous to Bohr orbits and the failure of the classical non-determinism in the conventional sense of the word makes it possible to interpret space-time surfaces as representations of both quantum states and sequences of quantum states assignable to the sequences of quantum jumps. The huge vacuum degeneracy of Kähler action implies spin glass degeneracy in 4-dimensional sense providing maximal resources to represent information about external world by mapping its states to its own internal states. Space-time sheets would be four-dimensional statues gradually carved by a sequence of quantum jump to a shape representing asymptotic self-organization pattern.
3. Magnetic body is the intentional agent controlling the biological body. The fractal hierarchy of copies of standard model physics involving in particular a hierarchy of electro-weak bosons and gluons with increasingly longer weak/confinement length scale is an essential piece of the story. The concrete quantum model for how intentions are transformed to actions provides additional insights to quantum self-organization.
4. The new view about time and energy justifying time mirror mechanism involving sending of negative energy phase conjugate photons to geometric past is crucial for the models of long term memory, intentional action, and remote metabolism.
5. The model of self organization involves cyclotron radiation from the cyclotron transitions assignable with the Bose-Einstein condensates of charged bosons at the magnetic bodies and Josephson radiation from Josephson junctions assignable to the cell membrane and also other layer like structures (electrets).
6. The vision about life residing in the intersection of real and p-adic worlds is central for the approach. In particular, the existence of number theoretic entanglement entropy, which can have negative values, makes possible to identify a measure of conscious information and negentropic entanglement replaces metabolic energy feed as the basic prequisite of life.

Zero energy ontology and hierarchy of Planck constants complete this vision. Zero energy ontology justifies time mirror mechanism and explains how arrow of subjective time emerges. Dark matter hierarchy implies macroscopic quantum coherence, inspires vision about bio-catalysis and quantum computation in living matter, explains evolutionary leaps, and suggests generalization of the notion of genome and new realizations of genetic code.

The topics of the book are following. The first chapters explain the vision about biological self organization in TGD framework. The last chapters of the book discuss quantum control and coordination in living matter according to TGD.

Category: Physics of Biology

Bio-Systems as Self-Organizing Quantum Systems

Authors: Matti Pitkänen
Comments: 288 pages

The quantum theory of self organization represents a rather old layer of TGD inspired theory of consciousness.

1. Self organization is a non-deterministic process and corresponds to the evolution of conscious entities - selves - to asymptotic self-organization patters via quantum jumps. This requires macroscopic quantum coherence.
2. Space-time surfaces are analogous to Bohr orbits and the failure of the classical non-determinism in the conventional sense of the word makes it possible to interpret space-time surfaces as representations of both quantum states and sequences of quantum states assignable to the sequences of quantum jumps. The huge vacuum degeneracy of Kähler action implies spin glass degeneracy in 4-dimensional sense providing maximal resources to represent information about external world by mapping its states to its own internal states. Space-time sheets would be four-dimensional statues gradually carved by a sequence of quantum jump to a shape representing asymptotic self-organization pattern.
3. Magnetic body is the intentional agent controlling the biological body. The fractal hierarchy of copies of standard model physics involving in particular a hierarchy of electro-weak bosons and gluons with increasingly longer weak/confinement length scale is an essential piece of the story. The concrete quantum model for how intentions are transformed to actions provides additional insights to quantum self-organization.
4. The new view about time and energy justifying time mirror mechanism involving sending of negative energy phase conjugate photons to geometric past is crucial for the models of long term memory, intentional action, and remote metabolism.
5. The model of self organization involves cyclotron radiation from the cyclotron transitions assignable with the Bose-Einstein condensates of charged bosons at the magnetic bodies and Josephson radiation from Josephson junctions assignable to the cell membrane and also other layer like structures (electrets).

Zero energy ontology and hierarchy of Planck constants complete this vision. Zero energy ontology justifies time mirror mechanism and explains how arrow of subjective time emerges. Dark matter hierarchy implies macroscopic quantum coherence, inspires vision about bio-catalysis and quantum computation in living matter, explains evolutionary leaps, and suggests generalization of the notion of genome and new realizations of genetic code. The topics of the book are following. The first chapters explain the vision about biological self organization in TGD framework. The last chapters of the book discuss quantum control and coordination in living matter according to TGD.
Category: Physics of Biology