I am grateful for comments, criticism and suggestions. The following list gives table of contents for "Quantum TGD". If You want, say chapter "Construction of Quantum Theory", as a .pdf file, just click on "Construction of Quantum Theory" in the table of contents. To help the reader to get overview I have included also a list of links to the chapters in the table of contents as well as corresponding abstracts.



GENES AND MEMES



||Introduction||
PART I: Some Physical and Mathematical Background
||About the New Physics Behind Quantum Biology||Topological Quantum Computation in TGD Universe||
PART II: Physical models for genome and evolution of genetic code
||Genes and Memes||Many-Sheeted DNA||DNA as Topological Quantum Computer||The Notion of Wave-Genome and DNA as Topological Quantum Computer||Model for the Findings about Hologram Generating Properties of DNA || Quantum Model for Remote Replication || Evolution in Many-Sheeted Space-Time|| Expanding Earth Model and Pre-Cambrian Evolution of Continents, Climate, and Life|| A Model for Protein Folding and Bio-catalysis|| Three new physics realizations of the genetic code and the role of dark matter in bio-systems||
Part III: Mathematical models for genetic code and its evolution
||Could Genetic Code Be Understood Number Theoretically?||Unification of Four Approaches to the Genetic Code||Appendix||



Home

    Introduction

  1. Basic ideas of TGD

    1. TGD as a Poincare invariant theory of gravitation

    2. TGD as a generalization of the hadronic string model

    3. Fusion of the two approaches via a generalization of the space-time concept

  2. The five threads in the development of quantum TGD

    1. Quantum TGD as configuration space spinor geometry

    2. p-Adic TGD

    3. TGD as a generalization of physics to a theory of consciousness

    4. TGD as a generalized number theory

    5. Dynamical quantized Planck constant and dark matter hierarchy

    6. The contents of the book

      1. Part I: Some mathematical and physical background

      2. Part II: Physical models for genome and evolution of genetic code

      3. Part III: Mathematical models for genetic code and its evolution

      4. Unification of Four Approaches to the Genetic Code

      5. Pre-biotic Evolution in Many-Sheeted Space-time

      6. Topological Quantum Computation in TGD Universe

      7. DNA as Topological Quantum Computer



PART I: Some Physical and Mathematical Background



Home Abstract

    About the new physics behind quantum biology

  1. Introduction

    1. Macroscopic quantum phases in many-sheeted space-time

    2. Mind like space-time sheets as massless extremals

    3. Classical color and electro-weak fields in macroscopic length scales

    4. p-Adic-to-real transitions as transformation of intentions to actions

    5. Exotic super-canonical representations

  2. Dark matter and living matter

    1. Hierarchy of Planck constants and the generalization of the notion of imbedding space

    2. Dark atoms and dark cyclotron states

    3. Dark matter and mind: general ideas

    4. Dark matter hierarchy, sensory representations, and motor action

  3. MEs as mes

    1. Massless extremals

    2. MEs as absorbing and emitting quantum antennae

    3. Quantum holography and quantum information theory

    4. Many-sheeted ionic flow equilibrium controlled by MEs

    5. MEs and quantum control

    6. Experimental evidence for MEs

  4. Bio-systems as superconductors

    1. General mechanisms for superconductivity

    2. Superconductivity at magnetic flux quanta in astrophysical length scales

    3. Fractal hierarchy of EEGs and ZEGs

    4. TGD assigns 10 Hz biorhythm to electron as an intrinsic frequency scale

  5. Many-sheeted space-time, universal metabolic quanta, and plasmoids as primitive life forms

    1. Evidence for many-sheeted space-time

    2. Laboratory evidence for plasmoids as life forms

    3. Universal metabolic quanta

    4. Life as a symbiosis of plasmoids and biological life

  6. Exotic color and electro-weak interactions

    1. Long range classical weak and color gauge fields as correlates for dark massless weak bosons

    2. Dark color force as a space-time correlate for the strong nuclear force?

    3. How brain could deduce the position and velocity of an object of perceptive field?

    4. Boolean mind and dark neutrinos

  7. Exotic representations of super-canonical algebra

    1. Exotic p-adic representations as representations for which states are almost p-adic fractals

    2. Mersenne primes and Gaussian Mersennes are special

    3. The huge degeneracies of the exotic states make them ideal for representational purposes

    4. Could one assign life-forms to the exotic Super-Virasoro representations?



Home Abstract

    Topological Quantum Computation in TGD Universe

  1. Introduction

    1. Evolution of basic ideas of quantum computation

    2. Quantum computation and TGD

    3. TGD and the new physics associated with TQC

    4. TGD and TQC

  2. Existing view about topological quantum computation

    1. Evolution of ideas about TQC

    2. Topological quantum computation as quantum dance

    3. Braids and gates

    4. About quantum Hall effect and theories of quantum Hall effect

    5. Topological quantum computation using braids and anyons

  3. General implications of TGD for quantum computation

    1. Time need not be a problem for quantum computations in TGD Universe

    2. New view about information

    3. Number theoretic vision about quantum jump as a building block of conscious experience {31

    4. Dissipative quantum parallelism?

    5. Negative energies and quantum computation

  4. TGD based new physics related to topological quantum computation

    1. Topologically quantized generalized Beltrami fields and braiding

    2. Quantum Hall effect and fractional charges in TGD

    3. Why 2+1-dimensional conformally invariant Witten-Chern-Simons theory should work for anyons?

    5 Topological quantum computation in TGD Universe

    1. Concrete realization of quantum gates

    2. Temperley-Lieb representations

    3. Zero energy topological quantum computations

  5. Appendix: Generalization of the notion of imbedding space

    1. Both covering spaces and factor spaces are possible

    2. Do factor spaces and coverings correspond to the two kinds of Jones inclusions?

    3. Fractional Quantum Hall effect



PART II: Physical models for genome and evolution of genetic code



Home Abstract

    Genes and Memes

  1. Introduction

    1. Combinatorial Hierarchy of codes

    2. The product model for the evolution of the genetic code

    3. General ideas about codes and languages

  2. Combinatorial Hierarchy and Genetic Code

    1. Combinatorial Hierarchy as a model for abstraction process

    2. Interpretation of genetic code

    3. Genetic Code as a result of geometric symmetry breaking

    4. Symmetry breaking scenarios

    5. In what sense the physical genetic code is unique?

    6. Hierarchy of Genetic Codes?

    7. The structure of the negation map

    8. Combinatorial Hierarchy as a hierarchy of formal systems

    9. Summary

  3. Genes, memes and universal language

    1. Genes-memes, biology-culture, hardware-software?

    2. Pulse and frequency representations of the genetic and memetic code words

    3. Mapping of the genetic code to micro-tubular code

    4. Genes, memes, and language

    5. Does memetic code make possible communications between different species?

    6. Intronic portions of genome code for RNA: for what purpose?

  4. Corals and Men

    1. Why corals and vertebrates should have common genes?

    2. Did corals and vertebrates receive their common genes via horizontal transfer?

    3. What happened in Cambrian explosion?

    4. What ontogeny recapitulates phylogeny principle means at the level of DNA?

    5. Where did those 223 genes pop up?



Home Abstract

    Many-sheeted DNA

  1. Introduction

    1. Many-sheeted DNA

    2. Realization of the genetic program

    3. Are nonchemical transription factors and nonchemical gene expression possible?

    4. Model for the genetic code

    5. The relationship between genetic and memetic codes

    6. Super-genes and hyper-genes

  2. Background

    1. DNA and RNA

    2. Proteins

    3. Replication, transcription, translation

    4. Introns, pseudogenes, repetitive DNA, silent DNA

    5. Is Central Dogma and absolute truth?

    6. Is life nothing but biochemistry?

  3. Many-sheeted DNA

    1. Many-sheeted DNA as hierarchy of genetic programs

    2. Possible answers to the basic questions

    3. What is the number of the levels in program hierarchy?

    4. Band structures of chromosomes as an evidence for many-sheeted DNA?

  4. Model for the genetic program

    1. Genes as statements of a conscious formal system?

    2. Genes as modules of a genetic program

    3. How gene expression is regulated?

    4. Model for the physical distinction between exons and introns

    5. Are the properties of the introns consistent with the proposed model?

    6. The phenomenon of superimposed genes

    7. About genetic evolution

    8. Possible explanations of the silent DNA

  5. TGD inspired ideas about the regulation of morphogenesis

    1. Could vacuum quantum numbers control gene expression via Josephson currents?

    2. Early morphogenesis of Drosophila

    3. Hox genes

    4. Characteristic features of Hox genes

    5. TGD based model for Hox genes



HomeAbstract

    DNA as Topological Quantum Computer

  1. Introduction

    1. Basic ideas of tqc

    2. Identification of hardware of tqc and tqc programs

    3. How much tqc resembles ordinary computation?

    4. Basic predictions of DNA as tqc hypothesis

  2. Basic concepts and ideas

    1. What happens in quantum jump

    2. M-matrix

    3. Hyper-finite factors of type II1 and quantum measurement theory with a finite measurement resolution

    4. NMP and biology

    5. Generalization of thermodynamics allowing negentropic entanglement and a model for conscious information processing

  3. How quantum computation in TGD Universe differs from standard quantum computation?

    1. Universe as a topological quantum computer

    2. The notion of magnetic body and the generalization of the notion of genome

    3. General ideas related to topological quantum computation

    4. Fractal hierarchies

    5. Irreducible entanglement and possibility of quantum parallel quantum computation

    6. Connes tensor product defines universal entanglement

    7. Possible problems related to quantum computation

  4. DNA as topological quantum computer

    1. Conjugate DNA as performer of tqc and lipids as quantum dancers

    2. How quantum states are realized?

    3. The role of high Tc superconductivity in tqc

    4. Genetic codes and tqc

  5. How to realize the basic gates?

    1. Universality of tqc

    2. The fundamental braiding operation as a universal 2-gate

    3. What the replacement of linear braid with planar braid could mean?

    4. Single particle gates

    5. On direct testing of quantum consciousness and DNA as tqc

  6. About realization of braiding

    1. Could braid strands be split and reconnect all the time?

    2. What do braid strands look like?

    3. How to induce the basic braiding operation?

    4. Some qualitative tests

  7. A model for flux tubes

    1. Flux tubes as a correlate for directed attention

    2. Does directed attention generate memory representations and tqc like processes

    3. Realization of flux tubes

    4. Flux tubes and DNA

  8. Some predictions related to the representation of braid color

    1. Anomalous em charge of DNA as a basic prediction

    2. Chargaff's second parity rule and the vanishing of net anomalous charge

    3. Are genes and other genetic sub-structures singlets with respect to QCD color?

    4. Summary of possible symmetries of DNA

    5. Empirical rules about DNA and mRNA supporting the symmetry breaking picture

  9. Cell replication and tqc

    1. Mitosis and tqc

    2. Sexual reproduction and tqc

    3. What is the role of centrosomes and basal bodies?

  10. Indirect evidence for the DNA as topological quantum computer model

    1. The notion of magnetic body

    2. DNA as topological quantum computer

    3. Implications for genetics

    4. Implications for Mendelian anomalies

  11. Appendix: A generalization of the notion of imbedding space

    1. Both covering spaces and factor spaces are possible

    2. Do factor spaces and coverings correspond to the two kinds of Jones inclusions?

    3. Fractional Quantum Hall effect



Home Abstract

    Model for the Findings about Hologram Generating Properties of DNA

  1. Introduction

    1. The notion of wave genome

    2. Hologram like radiation patterns generated by DNA

    3. Basic TGD based notions involved with the model

  2. Observations

  3. Model for the findings

    1. Basic notions and ideas

    2. Method I

    3. Method II

  4. The realization of the hologram at the level of magnetic body

    1. How the reference beams and reflected beams are generated?

    2. A simple model for the dynamics of pumping and sustainment of dark photon beams

    3. A general model for the hologram substrate

    4. Is the lifetime of the hologram long enough?

    5. The amplitude for the elastic scattering from hologram

  5. Appendix: Details about methods I and I

  6. Figures



Home Abstract

    The Notion of Wave-Genome and DNA as Topological Quantum Computer

  1. Introduction

    1. The findings of Peter Gariaev and collaborators

    2. The relevant aspects of TGD based view about living matter

    3. The basic assumptions of model explaining findings of Gariaev

    4. Dark nuclear strings as analogs of as analogs of DNA-, RNA- and amino-acid sequences and baryonic realization of genetic code

  2. TGD counterpart for wave-genetics

    1. The notion of bio-hologram in TGD framework

    2. How to fuse the notion of bio-hologram with the model of DNA as tqc?

  3. The effects of laser light on living matter

    1. Phantom DNA effect

    2. Effects of the polarization modulated laser light on living matter

    3. PLR spectroscopy

  4. The scattering of incoherent UV-IR light on DNA

    1. Basic facts

    2. TGD based model for the replicas

  5. Water memory, phantom DNA effect, and development of tqc hardware

    1. A possible realization of water memory

    2. Could virtual DNAs allow a controlled development of the genome?



Home Abstract

    Model for the Findings about Hologram Generating Properties of DNA

  1. Introduction

    1. The notion of wave genome

    2. Hologram like radiation patterns generated by DNA

    3. Basic TGD based notions involved with the model

  2. Observations

  3. Model for the findings

    1. Basic notions and ideas

    2. Method I

    3. Method II

  4. The realization of the hologram at the level of magnetic body

    1. How the reference beams and reflected beams are generated?

    2. A simple model for the dynamics of pumping and sustainment of dark photon beams

    3. A general model for the hologram substrate

    4. Is the lifetime of the hologram long enough?

    5. The amplitude for the elastic scattering from hologram

  5. Appendix: Details about methods I and II

  6. Figures



Home Abstract

    Quantum Model for Remote Replication

  1. Introduction

  2. The findings that one should understand

  3. The model of remote replication consistent with DNA as topological quantum computer model

    1. Identification of phantom DNA

    2. Dark DNA and frequency coding by quantum antenna mechanism

    3. Common explanation for the findings of Montagnier and Gariaev

    4. Summing up the basic assumptions of the mechanism

  4. Possible implications

    1. Possible relevance for homeopathy and immune system

    2. Frequency coding for DNA sequences by the value of Planck constant as a realization of divisor code



Home Abstract

    Evolution in Many-Sheeted Space-Time

  1. Introduction

  2. What is known about pre-biotic evolution?

    1. Some believed-to-be facts about the early history of life

    2. Standard approaches are mechanistic

    3. The notion of primordial ocean

    4. Urey-Miller experiment

    5. RNA world

    6. How biochemical pathways and DNA-amino-acid code emerged?

    7. Problems with the polymerization in primordial ocean

    8. The notion of protocell

  3. TGD based scenario about pre-biotic evolution

    1. Basic prerequisites

    2. TGD based vision about pre-biotic evolution

    3. Pre-biotic chemistry and new physics

    4. Could high energy phosphate bond be negentropic bond with negative binding energy?

    5. DNA as a topological quantum computer

    6. Water memory and braids

  4. Physical model for genetic code and its evolution

    1. RNA world

    2. Programming of bio-molecular self assembly pathways from TGD point of view

    3. The archeology of tRNA molecules as a guideline

    4. Recent genetic code as a fusion of singlet and doublet codes?

    5. Could nanno-bacteria correspond to predecessors of the triplet life-forms?

  5. Did life evolve in the womb of Mother Gaia?

    1. Quantum version of Expanding Earth theory and Cambrian explosion

    2. Did pre-biotic life evolve in mantle-core boundary?

    3. What conditions can one pose on life at mantle-core boundary?

    4. What about analogs of EEG?

  6. Comparison of McFadden's views with TGD

    1. General ideas

    2. Enzyme action

    3. Quantum evolution

  7. Great vision about biological evolution and evolution of brain

    1. Dark matter hierarchy and big leaps in evolution

    2. Could insect colonies have "EEG"?

    3. Dark matter hierarchy, hierarchical structure of nervous system, and hierarchy of emotions

  8. Oil drops in water solution as a primitive life form?

    1. Intelligent oil droplets

    2. Some key ideas of TGD inspired quantum biology

    3. General ideas about oil droplets as a primitive life form

    4. What are the prerequisites for metabolism and topological quantum computation like processes?

    5. What about genetic code and counterpart of DNA?

    6. Another approach to protocell



Home Abstract

    Expanding Earth Model and Pre-Cambrian Evolution of Continents, Climate, and Life

  1. Introduction

  2. Experimental evidence for accelerated expansion is consistent with TGD based model

    1. The four pieces of evidence for accelerated expansion

    2. Comparison with TGD

  3. Quantum version of Expanding Earth theory

    1. The claims of Adams

    2. The critic of Adams of the subduction mechanism

    3. Expanding Earth theories are not new

    4. Summary of TGD based theory of Expanding Earth

    5. Did intra-terrestrial life burst to the surface of Earth during Cambrian expansion?

  4. Implications Expanding Earth model for the pre-Cambrian evolution of continents, of climate, and of life

    1. Super-continent theory

    2. Standard view about oceans

    3. Glaciations during Neoproterozoic period

    4. Snowball Earth model for the glaciation during pre-Cambrian era

    5. TGD point of view about pre-Cambrian period

    6. Paleo-magnetic data and Expanding Earth model

    7. Did life go underground during pre-Cambrian glaciations?



Home Abstract

    A Model for Protein Folding and Bio-catalysis

  1. Introduction

    1. Flux tubes as correlates of directed attention at molecular level

    2. A model for protein folding based on flux tube connections between amino-acids

    3. A model for protein folding based on flux tube connections between amino-acids and water molecules

  2. A model for flux tubes

    1. Flux tubes as a correlate for directed attention

    2. Does directed attention generate memory representations and tqc like processes

    3. Realization of flux tubes

    4. Flux tubes and DNA

  3. Model for the folding code based on flux tubes between amino-acids

    1. 4-D spin glass energy landscape and code of catalytic action

    2. Flux tubes and amino-acids

    3. Trying to identify the folding code

  4. A simple quantitative model for protein folding and catalyst action based on flux tube connections between amino-acids

    1. The model

    2. Basic mathematical consequences

    3. Model for the helical structures

    4. Model for beta sheets

    5. Secondary protein structures

    6. Model for protein-protein binding sites

  5. A model for protein folding based on flux tube connections between amino-acids and water molecules

    1. Could there be new physics behind hydrophoby and hydrophily?

    2. An improved model for protein folding

    3. A model in which the magnetic body of water is involved



Home Abstract

    Three new physics realizations of the genetic code and the role of dark matter in bio-systems

  1. Introduction

    1. The notions of dark matter and magnetic body

    2. Realizations of genetic code

    3. Questions

  2. A vision about evolution and codes

    1. Basic insights

    2. The simplest scenario

    3. How dark baryon code could be involved with transcription and translation mechanisms?

  3. DNA as topological quantum computer: realization of the genetic code in terms of quarks and anti-quarks

    1. Basic ideas of tqc

    2. Identification of hardware of tqc and tqc programs

    3. How much tqc resembles ordinary computation?

    4. Basic predictions of DNA as tqc hypothesis

  4. Realization of genetic code in terms of dark baryons

    1. Dark nuclear strings as analogs of DNA-, RNA- and amino-acid sequences and baryonic realization of genetic code?

    2. DNA as tqc hypothesis and dark baryon code

  5. Flux tube realization of the divisor code

    1. Divisor code

    2. Topological interpretation of the divisor code in TGD framework

    3. About detailed correspondence between DNA codons, dark baryon codons, and their divisor code counterparts

  6. A model for protein folding and catalytic action

    1. Earlier model for the folding code

    2. Hydrophily and hydrophoby number theoretically

    3. Could there be new physics behind hydrophily and hydrophoby

    4. An improved model for protein folding

    5. The model for which the magnetic body of water is involved

  7. Appendix: Generalization of the notion of imbedding space

    1. Generalization of the notion of imbedding space

    2. Phase transitions changing the value of Planck constant



PART III: Mathematical models for genetic code and its evolution



Home Abstract

    Could Genetic Code Be Understood Number Theoretically?

  1. Introduction

    1. Questions

    2. The chain of arguments leading to a number theoretical model for the genetic code

    3. What is the physical counterpart of the number theoretical thermodynamics?

  2. First model for the evolution of the genetic code

    1. Does amino-acid structure reflect the product structure of the code?

    2. Number theoretical model for the genetic code

  3. Basic ideas and concepts of the second model

    1. Genetic code from the maximization of number theoretic information?

    2. Genetic code from a minimization of a number theoretic Shannon entropy

    3. High temperature limit for bosonic, fermionic, and supersymmetric thermodynamics

  4. Could finite temperature number theoretic thermodynamics reproduce the genetic code?

    1. How to choose the Hamiltonian?

    2. Could supersymmetric n0> 0 polynomial thermodynamics determine the genetic code?

    3. Could small perturbations of Hamiltonian cure the situation?

    4. Could one fix Hamiltonian H(r) from negentropy maximization?

    5. Could the symmetries of the genetic code put constraints to number theoretical thermodynamics?

  5. Confrontation of the model with experimental facts

    1. Basic facts about aminoacids

    2. Could the biological characteristics of an aminoacid sequence be independent on the order of aminoacids?

    3. Are the aminoacids and DNAs representing 0 and 1 somehow different?

    4. The deviations from the standard code as tests for the number theoretic model

    5. Model for the evolution of the genetic code and the deduction of n→ p(n) map from the structure of tRNA

    6. Genetic code as a product of singlet and doublet codes?

  6. Exponential thermodynamics does not work

    1. What can one conclude about p-adic temperature associated with the genetic code in the case of exponential thermodynamics?

    2. Low temperature limit of exponential thermodynamics

    3. How to find the critical temperature in exponential thermodynamics?

  7. Appendix

    1. Computational aspects

    2. Number theoretic model for singlet and doublet codes as a toy model



HomeAbstract

    Unification of Four Approaches to the Genetic Code

  1. Introduction

  2. Unifying various approaches to the genetic code

    1. Geometric approach to the genetic code

    2. 4-adicity and 5-adicity as possible realizations of the symmetries of the genetic code

    3. Number theoretical thermodynamics and genetic code

    4. Divisor code

    5. Group theoretic interpretation of the divisor code

    6. Topological interpretation of the divisor code in TGD framework

    7. Is the fusion of geometric, thermodynamical, and divisor code approaches possible in the 5-adic case?

  3. 5-adicity or 4-adicity?

    1. The problems of the 4-adic model of the divisor code

    2. 5-adic model works for thermodynamics based on partitions

  4. 5-adic thermodynamical model for the genetic code

    1. The simplest model for the 5-adic temperature

    2. The simplest possible model for thermodynamics

    3. Number theoretic Hamilton depending on the number of partitions of integer characterizing DNA

    4. Number theoretical Hamiltonian identified as spin-spin interaction

  5. A possible physical interpretation of various codes in TGD framework

    1. Generalization of imbedding space and interpretation of discrete bundle like structures

    2. A possible interpretation for the divisor code

    3. About the geometric interpretation for the thermodynamics of partitions of n2)

    4. About the physical interpretation for the thermodynamics of partitions of n2)

    5. A possible interpretation for the p-adic prime labelling aminoacid and DNAs coding it

  6. Appendix: 4-adic realization of n→ n+32 symmetry, divisor code, and labelling of aminoacids by primes are not mutually consistent



Home

    Appendix

  1. Basic properties of CP2

    1. CP2 as a manifold

    2. Metric and Kähler structures of CP2

    3. Spinors in CP2

    4. Geodesic sub-manifolds of CP2

  2. CP2 geometry and standard model symmetries

    1. Identification of the electro-weak couplings

    2. Discrete symmetries

  3. Basic facts about induced gauge fields

    1. Induced gauge fields for space-times for which CP2 projection is a geodesic sphere

    2. Space-time surfaces with vanishing em, Z0, or Kähler fields

  4. p-Adic numbers and TGD

    1. p-Adic number fields

    2. Canonical correspondence between p-adic and real numbers



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