1GENES AND MEMESMatti PitkanenKoydenpunojankatu D 11, 10900, Hanko, FinlandContents0.1 Background . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10.2 Basic Ideas of TGD . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10.2.1 TGD as a Poincare invariant theory of gravitation . . . . . . . . . . . . . . . . 10.2.2 TGD as a generalization of the hadronic string model . . . . . . . . . . . . . . 20.2.3 Fusion of the two approaches via a generalization of the space-time concept . . 20.3 The ve threads in the development of quantum TGD . . . . . . . . . . . . . . . . . . 20.3.1 Quantum TGD as conguration space spinor geometry . . . . . . . . . . . . . . 20.3.2 p-Adic TGD . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30.3.3 TGD as a generalization of physics to a theory consciousness . . . . . . . . . . 30.3.4 TGD as a generalized number theory . . . . . . . . . . . . . . . . . . . . . . . . 60.3.5 Dynamical quantized Planck constant and dark matter hierarchy . . . . . . . . 70.4 Birds eye of view about the topics of the book . . . . . . . . . . . . . . . . . . . . . . 100.5 The contents of the book . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110.5.1 PART I: Some Physical and Mathematical Background . . . . . . . . . . . . . 110.5.2 PART II: Physics inspired models for genome and evolution of genetic code . . 120.5.3 Part III: Number theoretical models for genetic code and its evolution . . . . . 20I SOME PHYSICAL AND MATHEMATICAL BACKGROUND 271 About the New Physics Behind Qualia 291.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 291.1.1 Living matter and dark matter . . . . . . . . . . . . . . . . . . . . . . . . . . . 291.1.2 Macroscopic quantum phases in many-sheeted space-time . . . . . . . . . . . . 301.1.3 Mind like space-time sheets as massless extremals . . . . . . . . . . . . . . . . . 301.1.4 Classical color and electro-weak elds in macroscopic length scales . . . . . . . 301.1.5 p-Adic-to-real transitions as transformation of intentions to actions . . . . . . . 311.1.6 Exotic super-Virasoro representations . . . . . . . . . . . . . . . . . . . . . . . 311.2 Dark matter and living matter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 321.2.1 Quantum criticality, hierarchy of dark matters, and dynamical . . . . . . . . 321.2.2 From naive formulas to conceptualization . . . . . . . . . . . . . . . . . . . . . 381.2.3 Dark atoms and dark cyclotron states . . . . . . . . . . . . . . . . . . . . . . . 411.2.4 Dark matter and mind: general ideas . . . . . . . . . . . . . . . . . . . . . . . . 451.2.5 Dark matter hierarchy, sensory representations, and motor action . . . . . . . . 481.3 MEs and mes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 511.3.1 Massless extremals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 511.3.2 About the electro-weak and color elds associated with massless extremals . . 551.3.3 MEs as absorbing and emitting quantum antennae . . . . . . . . . . . . . . . . 551.3.4 Quantum holography and quantum information theory . . . . . . . . . . . . . . 571.3.5 MEs and quantum control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 631.3.6 Experimental evidence for MEs . . . . . . . . . . . . . . . . . . . . . . . . . . . 691.4 Bio-systems as superconductors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 701.4.1 General mechanisms for superconductivity . . . . . . . . . . . . . . . . . . . . . 701.4.2 Superconductivity at magnetic ux quanta in astrophysical length scales . . . . 711.4.3 Fractal hierarchy of EEGs and ZEGs . . . . . . . . . . . . . . . . . . . . . . . . 711.4.4 TGD assigns 10 Hz biorhythm to electron as an intrinsic frequency scale . . . . 72iiiiv CONTENTS1.5 Many-sheeted space-time, universal metabolic quanta, and plasmoids as primitive lifeforms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 741.5.1 Evidence for many-sheeted space-time . . . . . . . . . . . . . . . . . . . . . . . 741.5.2 Laboratory evidence for plasmoids as life forms . . . . . . . . . . . . . . . . . . 771.5.3 Universal metabolic quanta . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 791.5.4 Life as a symbiosis of plasmoids and biological life . . . . . . . . . . . . . . . . 881.6 Exotic color and electro-weak interactions . . . . . . . . . . . . . . . . . . . . . . . . . 901.6.1 Long range classical weak and color gauge elds as correlates for dark masslessweak bosons . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 911.6.2 Dark color force as a space-time correlate for the strong nuclear force? . . . . . 921.6.3 How brain could deduce the position and velocity of an object of perceptive eld? 941.6.4 Boolean mind and dark neutrinos . . . . . . . . . . . . . . . . . . . . . . . . . . 961.7 The relationship between p-adic and real physics . . . . . . . . . . . . . . . . . . . . . 971.7.1 p-Adic physics and the construction of solutions of eld equations . . . . . . . 981.7.2 A more detailed view about how local p-adic physics codes for p-adic fractallong range correlations of the real physics . . . . . . . . . . . . . . . . . . . . . 1011.8 Exotic representations of super-canonical algebra . . . . . . . . . . . . . . . . . . . . . 1051.8.1 Exotic p-adic representations as representations for which states are almost p-adic fractals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1061.8.2 Mersenne primes and Gaussian Mersennes are special . . . . . . . . . . . . . . 1071.8.3 The huge degeneracies of the exotic states make them ideal for representationalpurposes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1081.8.4 Could one assign life-forms to the exotic Super-Virasoro representations? . . . 1092 Topological Quantum Computation in TGD Universe 1232.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1232.1.1 Evolution of basic ideas of quantum computation . . . . . . . . . . . . . . . . . 1232.1.2 Quantum computation and TGD . . . . . . . . . . . . . . . . . . . . . . . . . . 1242.1.3 TGD and the new physics associated with TQC . . . . . . . . . . . . . . . . . 1262.1.4 TGD and TQC . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1272.2 Existing view about topological quantum computation . . . . . . . . . . . . . . . . . . 1282.2.1 Evolution of ideas about TQC . . . . . . . . . . . . . . . . . . . . . . . . . . . 1282.2.2 Topological quantum computation as quantum dance . . . . . . . . . . . . . . 1292.2.3 Braids and gates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1302.2.4 About quantum Hall eect and theories of quantum Hall eect . . . . . . . . . 1332.2.5 Topological quantum computation using braids and anyons . . . . . . . . . . . 1362.3 General implications of TGD for quantum computation . . . . . . . . . . . . . . . . . 1372.3.1 Time need not be a problem for quantum computations in TGD Universe . . . 1372.3.2 New view about information . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1372.3.3 Number theoretic vision about quantum jump as a building block of consciousexperience . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1382.3.4 Dissipative quantum parallelism? . . . . . . . . . . . . . . . . . . . . . . . . . . 1382.3.5 Negative energies and quantum computation . . . . . . . . . . . . . . . . . . . 1392.4 TGD based new physics related to topological quantum computation . . . . . . . . . . 1402.4.1 Topologically quantized generalized Beltrami elds and braiding . . . . . . . . 1412.4.2 Quantum Hall eect and fractional charges in TGD . . . . . . . . . . . . . . . 1472.4.3 Does the quantization of Planck constant transform integer quantum Hall eectto fractional quantum Hall eect? . . . . . . . . . . . . . . . . . . . . . . . . . 1532.4.4 Why 2+1-dimensional conformally invariant Witten-Chern-Simons theory shouldwork for anyons? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1532.5 Topological quantum computation in TGD Universe . . . . . . . . . . . . . . . . . . . 1542.5.1 Concrete realization of quantum gates . . . . . . . . . . . . . . . . . . . . . . . 1552.5.2 Temperley-Lieb representations . . . . . . . . . . . . . . . . . . . . . . . . . . . 1572.5.3 Zero energy topological quantum computations . . . . . . . . . . . . . . . . . . 1622.6 Appendix: A generalization of the notion of imbedding space . . . . . . . . . . . . . . 1642.6.1 Both covering spaces and factor spaces are possible . . . . . . . . . . . . . . . . 1642.6.2 Do factor spaces and coverings correspond to the two kinds of Jones inclusions? 165CONTENTS v2.6.3 A simple model of fractional quantum Hall eect . . . . . . . . . . . . . . . . . 167II PHYSICS INSPIRED MODELS FOR GENOME AND EVOLUTIONOF GENETIC CODE 1753 Genes and Memes 1773.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1773.1.1 Combinatorial Hierarchy of codes . . . . . . . . . . . . . . . . . . . . . . . . . . 1773.1.2 The product model for the evolution of genetic code . . . . . . . . . . . . . . . 1793.1.3 General ideas about codes and languages . . . . . . . . . . . . . . . . . . . . . 1803.2 Combinatorial Hierarchy and Genetic Code . . . . . . . . . . . . . . . . . . . . . . . . 1823.2.1 Combinatorial Hierarchy as a model for abstraction process . . . . . . . . . . . 1823.2.2 Interpretation of genetic code . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1843.2.3 Genetic Code as a result of geometric symmetry breaking . . . . . . . . . . . . 1853.2.4 Symmetry breaking scenarios . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1863.2.5 In what sense the physical genetic code is unique? . . . . . . . . . . . . . . . . 1913.2.6 Hierarchy of Genetic Codes? . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1923.2.7 The structure of the negation map . . . . . . . . . . . . . . . . . . . . . . . . . 1933.2.8 Combinatorial Hierarchy as a hierarchy of formal systems . . . . . . . . . . . . 1933.2.9 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1953.3 Genes, memes, and universal language . . . . . . . . . . . . . . . . . . . . . . . . . . . 1973.3.1 Genes-memes, biology-culture, hardware-software? . . . . . . . . . . . . . . . . 1973.3.2 Pulse and frequency representations of the genetic and memetic code words . . 1973.3.3 Mapping of the memetic code to microtubular code . . . . . . . . . . . . . . . 2013.3.4 Genes, memes, and language . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2063.3.5 Does memetic code make possible communications between dierent species? . 2083.3.6 Intronic portions of genome code for RNA: for what purpose? . . . . . . . . . . 2113.4 Corals and men . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2123.4.1 Why corals and vertebrates should have common genes? . . . . . . . . . . . . . 2133.4.2 Did corals and vertebrates receive their common genes via horizontal transfer? 2143.4.3 What happened in Cambrain explosion? . . . . . . . . . . . . . . . . . . . . . . 2153.4.4 What ontogeny recapitulates phylogeny principle means at the level of DNA? . 2173.4.5 Where did those 223 genes pop up? . . . . . . . . . . . . . . . . . . . . . . . . 2204 Many-Sheeted DNA 2294.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2294.1.1 Many-sheeted DNA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2304.1.2 Realization of the genetic program . . . . . . . . . . . . . . . . . . . . . . . . . 2314.1.3 Are nonchemical transcription factors and nonchemical gene expression possible?2324.1.4 Model for the genetic code . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2334.1.5 The relationship between genetic and memetic codes . . . . . . . . . . . . . . . 2334.1.6 Super-genes and hyper-genes . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2344.2 Background . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2344.2.1 DNA and RNA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2354.2.2 Proteins . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2364.2.3 Replication, transcription, translation . . . . . . . . . . . . . . . . . . . . . . . 2364.2.4 Introns, pseudogenes, repetitive DNA, silent DNA . . . . . . . . . . . . . . . . 2374.2.5 Is Central Dogma an absolute truth? . . . . . . . . . . . . . . . . . . . . . . . . 2394.2.6 Is life nothing but biochemistry? . . . . . . . . . . . . . . . . . . . . . . . . . . 2394.3 Many-sheeted DNA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2404.3.1 Many-sheeted DNA as hierarchy of genetic programs . . . . . . . . . . . . . . . 2414.3.2 Possible answers to the basic questions . . . . . . . . . . . . . . . . . . . . . . . 2424.3.3 What is the number of the levels in program ieharchy? . . . . . . . . . . . . . . 2444.3.4 Band structure of chromosomes as an evidence for many-sheeted DNA? . . . . 2464.4 Model for the genetic program . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2474.4.1 Genes as statements of conscious formal system . . . . . . . . . . . . . . . . . . 247vi CONTENTS4.4.2 Genes as modules of a genetic program . . . . . . . . . . . . . . . . . . . . . . 2494.4.3 How gene expression is regulated? . . . . . . . . . . . . . . . . . . . . . . . . . 2494.4.4 Model for the physical distinction between exons and introns . . . . . . . . . . 2514.4.5 Are the properties of the introns consistent with the proposed model? . . . . . 2554.4.6 The phenomenon of superimposed genes . . . . . . . . . . . . . . . . . . . . . . 2564.4.7 About genetic evolution . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2564.4.8 Possible explanations of the silent DNA . . . . . . . . . . . . . . . . . . . . . . 2604.5 TGD inspired ideas about the regulation of morphogenesis . . . . . . . . . . . . . . . . 2614.5.1 Biological alarm clocks and morphogenesis . . . . . . . . . . . . . . . . . . . . . 2614.5.2 Could vacuum quantum numbers control gene expression via Josephson currents 2624.5.3 Early morphogenesis of Drosophila . . . . . . . . . . . . . . . . . . . . . . . . . 2624.5.4 Hox genes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2634.5.5 Evolution of Hox genes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2634.5.6 Characteristic features of Hox genes . . . . . . . . . . . . . . . . . . . . . . . . 2644.5.7 TGD based model for Hox genes . . . . . . . . . . . . . . . . . . . . . . . . . . 2654.6 The new view about genetic code and evolution . . . . . . . . . . . . . . . . . . . . . . 2674.6.1 Basic vision about dark matter hierarchy . . . . . . . . . . . . . . . . . . . . . 2674.6.2 How to identify the personal magnetic body? . . . . . . . . . . . . . . . . . . . 2684.6.3 Generalization of the notion of genetic code . . . . . . . . . . . . . . . . . . . . 2694.6.4 The new view about genetic code . . . . . . . . . . . . . . . . . . . . . . . . . . 2694.6.5 Dark matter hierarchy and evolution . . . . . . . . . . . . . . . . . . . . . . . . 2715 DNA as Topological Quantum Computer 2795.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2795.1.1 Basic ideas of tqc . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2795.1.2 Identication of hardware of tqc and tqc programs . . . . . . . . . . . . . . . . 2805.1.3 How much tqc resembles ordinary computation? . . . . . . . . . . . . . . . . . 2815.1.4 Basic predictions of DNA as tqc hypothesis . . . . . . . . . . . . . . . . . . . . 2815.2 How quantum computation in TGD Universe diers from standard quantum computa-tion? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2825.2.1 General ideas related to topological quantum computation . . . . . . . . . . . . 2825.2.2 Fractal hierarchies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2845.2.3 Irreducible entanglement and possibility of quantum parallel quantum compu-tation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2855.2.4 Connes tensor product denes universal entanglement . . . . . . . . . . . . . . 2865.2.5 Possible problems related to quantum computation . . . . . . . . . . . . . . . . 2875.3 DNA as topological quantum computer . . . . . . . . . . . . . . . . . . . . . . . . . . 2895.3.1 Conjugate DNA as performer of tqc and lipids as quantum dancers . . . . . . . 2895.3.2 How quantum states are realized? . . . . . . . . . . . . . . . . . . . . . . . . . 2945.3.3 The role of high Tc superconductivity in tqc . . . . . . . . . . . . . . . . . . . . 2965.3.4 Codes and tqc . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2995.4 How to realize the basic gates? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3005.4.1 Universality of tqc . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3005.4.2 The fundamental braiding operation as a universal 2-gate . . . . . . . . . . . . 3005.4.3 What the replacement of linear braid with planar braid could mean? . . . . . . 3005.4.4 Single particle gates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3015.5 About realization of braiding . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3045.5.1 Could braid strands be split and reconnect all the time? . . . . . . . . . . . . . 3045.5.2 What do braid strands look like? . . . . . . . . . . . . . . . . . . . . . . . . . . 3045.5.3 How to induce the basic braiding operation? . . . . . . . . . . . . . . . . . . . 3055.5.4 Some qualitative tests . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3065.6 A model for ux tubes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3075.6.1 Flux tubes as a correlate for directed attention . . . . . . . . . . . . . . . . . . 3075.6.2 Does directed attention generate memory representations and tqc like processes? 3085.6.3 Realization of ux tubes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3095.6.4 Flux tubes and DNA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3115.7 Some predictions related to the representation of braid color . . . . . . . . . . . . . . . 312CONTENTS vii5.7.1 Anomalous em charge of DNA as a basic prediction . . . . . . . . . . . . . . . 3125.7.2 Chargas second parity rule and the vanishing of net anomalous charge . . . . 3135.7.3 Are genes and other genetic sub-structures singlets with respect to QCD color? 3135.7.4 Summary of possible symmetries of DNA . . . . . . . . . . . . . . . . . . . . . 3175.7.5 Empirical rules about DNA and mRNA supporting the symmetry breaking picture3195.7.6 Genetic codes and tqc . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3225.8 Cell replication and tqc . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3235.8.1 Mitosis and tqc . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3235.8.2 Sexual reproduction and tqc . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3245.8.3 What is the role of centrosomes and basal bodies? . . . . . . . . . . . . . . . . 3255.9 Appendix: A generalization of the notion of imbedding space . . . . . . . . . . . . . . 3265.9.1 Both covering spaces and factor spaces are possible . . . . . . . . . . . . . . . . 3265.9.2 Do factor spaces and coverings correspond to the two kinds of Jones inclusions? 3285.9.3 A simple model of fractional quantum Hall eect . . . . . . . . . . . . . . . . . 3296 The Notion of Wave-Genome and DNA as Topological Quantum Computer 3396.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3396.1.1 The ndings of Peter Gariaev and collaborators . . . . . . . . . . . . . . . . . . 3396.1.2 The relevant aspects of TGD based view about living matter . . . . . . . . . . 3406.1.3 The basic assumptions of model explaining ndings of Gariaev . . . . . . . . . 3406.2 TGD counterpart for wave-genetics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3416.2.1 The notion of bio-hologram in TGD framework . . . . . . . . . . . . . . . . . . 3416.2.2 How to fuse the notion of bio-hologram with the model of DNA as tqc? . . . . 3426.3 The eects of laser light on living matter . . . . . . . . . . . . . . . . . . . . . . . . . . 3436.3.1 Phantom DNA eect . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3436.3.2 Eects of the polarization modulated laser light on living matter . . . . . . . . 3436.3.3 PLR spectroscopy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3446.4 The scattering of incoherent UV-IR light on DNA . . . . . . . . . . . . . . . . . . . . 3456.4.1 Basic facts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3456.4.2 TGD based model for the replicas . . . . . . . . . . . . . . . . . . . . . . . . . 3466.5 Water memory, phantom DNA eect, and development of tqc hardware . . . . . . . . 3496.5.1 A possible realization of water memory . . . . . . . . . . . . . . . . . . . . . . 3506.5.2 Could virtual DNAs allow a controlled development of the genome? . . . . . . 3527 Evolution in Many-Sheeted Space-Time 3657.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3657.1.1 Questions and answers about evolution . . . . . . . . . . . . . . . . . . . . . . 3657.1.2 Topics of the chapter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3677.2 What is known about pre-biotic evolution? . . . . . . . . . . . . . . . . . . . . . . . . 3687.2.1 Some believed-to-be facts about the early history of life . . . . . . . . . . . . . 3687.2.2 Standard approaches are mechanistic . . . . . . . . . . . . . . . . . . . . . . . . 3687.2.3 The notion of primordial ocean . . . . . . . . . . . . . . . . . . . . . . . . . . . 3687.2.4 Urey-Miller experiment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3697.2.5 RNA world . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3697.2.6 How biochemical pathways and DNA-amino-acid code emerged? . . . . . . . . 3707.2.7 Problems with the polymerization in primordial ocean . . . . . . . . . . . . . . 3707.2.8 The notion of protocell . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3717.3 TGD based scenario about pre-biotic evolution . . . . . . . . . . . . . . . . . . . . . . 3727.3.1 Basic prerequisites . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3727.3.2 TGD based vision about pre-biotic evolution . . . . . . . . . . . . . . . . . . . 3737.3.3 Pre-biotic chemistry and new physics . . . . . . . . . . . . . . . . . . . . . . . . 3797.3.4 DNA as a topological quantum computer . . . . . . . . . . . . . . . . . . . . . 3857.4 Physical model for genetic code and its evolution . . . . . . . . . . . . . . . . . . . . . 3927.4.1 RNA world . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3937.4.2 Programming of bio-molecular self assembly pathways from TGD point of view 3937.4.3 The archeology of tRNA molecules as a guideline . . . . . . . . . . . . . . . . . 3957.4.4 Recent genetic code as a fusion of singlet and doublet codes? . . . . . . . . . . 399viii CONTENTS7.4.5 Is RNA era continuing inside cell nuclei? . . . . . . . . . . . . . . . . . . . . . . 4027.4.6 Could nanno-bacteria correspond to predecessors of the triplet life-forms? . . . 4037.5 Did life evolve in the womb of Mother Gaia? . . . . . . . . . . . . . . . . . . . . . . . 4057.5.1 Quantum version of Expanding Earth theory and Cambrian explosion . . . . . 4067.5.2 Did pre-biotic life evolve in mantle-core boundary? . . . . . . . . . . . . . . . . 4107.5.3 What conditions can one pose on life at mantle-core boundary? . . . . . . . . . 4127.5.4 What about analogs of EEG? . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4167.6 Comparison of McFaddens views with TGD . . . . . . . . . . . . . . . . . . . . . . . . 4197.6.1 General ideas . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4197.6.2 Enzyme action . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4217.6.3 Quantum evolution . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4217.6.4 Plasmoid like life forms in laboratory . . . . . . . . . . . . . . . . . . . . . . . . 4377.7 Quantum version of Expanding Earth theory and Cambrian explosion . . . . . . . . . 4377.7.1 The claims of Adams . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4387.7.2 The critic of Adams of the subduction mechanism . . . . . . . . . . . . . . . . 4397.7.3 Expanding Earth theories are not new . . . . . . . . . . . . . . . . . . . . . . . 4407.7.4 Summary of TGD based theory of Expanding Earth . . . . . . . . . . . . . . . 4407.7.5 Did intra-terrestrial life burst to the surface of Earth during Cambrian expansion?4428 A Model for Protein Folding and Bio-catalysis 4538.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4538.1.1 Flux tubes as correlates of directed attention at molecular level . . . . . . . . . 4538.1.2 The model of folding code based on ux tube connections between amino-acids 4548.1.3 A model for protein folding based on ux tubes between amino-acids and watermolecules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4558.2 A model for ux tubes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4568.2.1 Flux tubes as a correlate for directed attention . . . . . . . . . . . . . . . . . . 4568.2.2 Does directed attention generate memory representations and tqc like processes 4578.2.3 Realization of ux tubes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4588.2.4 Flux tubes and DNA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4598.2.5 Introns and DNA-protein attachment . . . . . . . . . . . . . . . . . . . . . . . 4608.3 Model for the folding code based on interactions mediated by ux tubes betweenaminoacids . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4618.3.1 4-D spin glass energy landscape and code of catalytic action . . . . . . . . . . . 4618.3.2 Flux tubes and amino-acids . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4618.3.3 Trying to identify the folding code . . . . . . . . . . . . . . . . . . . . . . . . . 4628.4 A simple quantitative model for protein folding and catalyst action assuming ux tubesbetween amino-acids . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4728.4.1 The model . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4728.4.2 Basic mathematical consequences . . . . . . . . . . . . . . . . . . . . . . . . . . 4748.4.3 Model for the helical structures . . . . . . . . . . . . . . . . . . . . . . . . . . . 4748.4.4 Model for sheets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4758.4.5 Secondary protein structures . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4758.4.6 Model for protein-protein binding sites . . . . . . . . . . . . . . . . . . . . . . . 4768.5 A model for protein folding based on ux tubes connections between water moleculesand amino-acids . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4778.5.1 Could there be new physics behind hydrophily and hydrophoby? . . . . . . . . 4778.5.2 An improve model for protein folding . . . . . . . . . . . . . . . . . . . . . . . 4788.5.3 A model for which the magnetic body of water is involved . . . . . . . . . . . . 4789 Three new physics realizations of the genetic code and the role of dark matter inbio-systems 4839.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4839.1.1 The notions of dark matter and magnetic body . . . . . . . . . . . . . . . . . . 4839.1.2 Realizations of genetic code . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4839.1.3 Questions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4849.2 A vision about evolution and codes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 484CONTENTS ix9.2.1 Basic insights . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4849.2.2 The simplest scenario . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4859.2.3 How dark baryon code could be involved with transcription and translationmechanisms? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4869.3 DNA as topological quantum computer: realization of the genetic code in terms ofquarks and anti-quarks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4879.3.1 Basic ideas of tqc . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4889.3.2 Identication of hardware of tqc and tqc programs . . . . . . . . . . . . . . . . 4889.3.3 How much tqc resembles ordinary computation? . . . . . . . . . . . . . . . . . 4899.3.4 Basic predictions of DNA as tqc hypothesis . . . . . . . . . . . . . . . . . . . . 4909.4 Realization of genetic code in terms of dark baryons . . . . . . . . . . . . . . . . . . . 4909.4.1 Dark nuclear strings as analogs of DNA-, RNA- and amino-acid sequences andbaryonic realization of genetic code? . . . . . . . . . . . . . . . . . . . . . . . . 4919.4.2 DNA as tqc hypothesis and dark baryon code . . . . . . . . . . . . . . . . . . . 4949.5 Flux tube realization of the divisor code . . . . . . . . . . . . . . . . . . . . . . . . . . 4959.5.1 Divisor code . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4959.5.2 Topological interpretation of the divisor code in TGD framework . . . . . . . . 4959.5.3 About detailed correspondence between DNA codons, dark baryon codons, andtheir divisor code counterparts . . . . . . . . . . . . . . . . . . . . . . . . . . . 4979.6 A model for protein folding and catalytic action . . . . . . . . . . . . . . . . . . . . . . 4989.6.1 Earlier model for the folding code . . . . . . . . . . . . . . . . . . . . . . . . . 4989.6.2 Hydrophily and hydrophoby number theoretically . . . . . . . . . . . . . . . . . 5009.6.3 Could there be new physics behind hydrophily and hydrophoby . . . . . . . . . 5009.6.4 An improved model for protein folding . . . . . . . . . . . . . . . . . . . . . . . 5019.6.5 The model for which the magnetic body of water is involved . . . . . . . . . . . 5019.7 Appendix: Generalization of the notion of imbedding space . . . . . . . . . . . . . . . 5029.7.1 Generalization of the notion of imbedding space . . . . . . . . . . . . . . . . . 5029.7.2 Phase transitions changing the value of Planck constant . . . . . . . . . . . . . 504III NUMBER THEORETICAL MODELS FOR GENETIC CODE ANDITS EVOLUTION 51110 Could Genetic Code Be Understood Number Theoretically? 51310.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51310.1.1 Questions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51310.1.2 The chain of arguments leading to a number theoretical model for the geneticcode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51410.1.3 What is the physical counterpart of the number theoretical thermodynamics? . 51510.2 The rst model for the evolution of the genetic code . . . . . . . . . . . . . . . . . . . 51510.2.1 Does amino-acid structure reect the product structure of the code? . . . . . . 51510.2.2 Number theoretical model for the genetic code . . . . . . . . . . . . . . . . . . 51510.3 Basic ideas and concepts underlying second model of genetic code . . . . . . . . . . . . 52210.3.1 Genetic code from the maximization of number theoretic information? . . . . . 52210.3.2 Genetic code from a minimization of a number theoretic Shannon entropy . . . 52210.3.3 High temperature limit for bosonic, fermionic, and supersymmetric thermody-namics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52310.4 Could nite temperature number theoretic thermodynamics reproduce the genetic code?52510.4.1 How to choose the Hamiltonian? . . . . . . . . . . . . . . . . . . . . . . . . . . 52610.4.2 Could supersymmetric n0 > 0 polynomial thermodynamics determine the ge-netic code? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52810.4.3 Could small perturbations of Hamiltonian cure the situation? . . . . . . . . . . 52910.4.4 Could one x Hamiltonian H(r) from negentropy maximization? . . . . . . . . 53010.4.5 Could the symmetries of the genetic code constrain number theoretical thermo-dynamics? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53310.5 Confrontation of the model with experimental facts . . . . . . . . . . . . . . . . . . . . 53610.5.1 Basic facts about aminoacids . . . . . . . . . . . . . . . . . . . . . . . . . . . . 536x CONTENTS10.5.2 Could the biological characteristics of an aminoacid sequence be independenton the order of aminoacids? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53710.5.3 Are the aminoacids and DNAs representing 0 and 1 somehow dierent? . . . . 53710.5.4 The deviations from the standard code as tests for the number theoretic model 53710.5.5 Model for the evolution of the genetic code and the deduction of n p(n) mapfrom the structure of tRNA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54010.5.6 Genetic code as a product of singlet and doublet codes? . . . . . . . . . . . . . 54110.6 Exponential thermodynamics does not work . . . . . . . . . . . . . . . . . . . . . . . . 54110.6.1 What can one conclude about p-adic temperature associated with the geneticcode in the case of exponential thermodynamics? . . . . . . . . . . . . . . . . . 54110.6.2 Low temperature limit of exponential thermodynamics . . . . . . . . . . . . . . 54310.6.3 How to nd the critical temperature in exponential thermodynamics? . . . . . 54410.7 Appendix . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54410.7.1 Computational aspects . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54510.7.2 Number theoretic model for singlet and doublet codes as a toy model . . . . . 54711 Unication of Four Approaches to the Genetic Code 55111.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55111.2 Unifying various approaches to the genetic code . . . . . . . . . . . . . . . . . . . . . . 55211.2.1 Geometric approach to the genetic code . . . . . . . . . . . . . . . . . . . . . . 55211.2.2 4-adicity and 5-adicity as possible realizations of the symmetries of the geneticcode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55211.2.3 Number theoretical thermodynamics and genetic code . . . . . . . . . . . . . . 55311.2.4 Group theoretic interpretation of the divisor code . . . . . . . . . . . . . . . . . 55311.2.5 Divisor code . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55311.2.6 Topological interpretation of the divisor code in TGD framework . . . . . . . . 55411.2.7 Is the fusion of geometric, thermodynamical, and divisor code approaches pos-sible in the 5-adic case? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55611.3 5-adicity or 4-adicity? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55611.3.1 The problems of the 4-adic model of the divisor code . . . . . . . . . . . . . . . 55611.3.2 5-adic model works for thermodynamics based on partitions . . . . . . . . . . . 55711.4 5-adic thermodynamical model for the genetic code . . . . . . . . . . . . . . . . . . . . 55911.4.1 The simplest model for the 5-adic temperature . . . . . . . . . . . . . . . . . . 55911.4.2 The simplest possible model for thermodynamics . . . . . . . . . . . . . . . . . 55911.4.3 Number theoretic Hamilton depending on the number of partitions of integercharacterizing DNA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56011.4.4 Number theoretical Hamiltonian identied as spin-spin interaction . . . . . . . 56311.5 A possible physical interpretation of various codes in TGD framework . . . . . . . . . 56511.5.1 Generalization of imbedding space and interpretation of discrete bundle likestructures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56511.5.2 A possible interpretation for the divisor code . . . . . . . . . . . . . . . . . . . 56611.5.3 About the geometric interpretation for the thermodynamics of partitions of n2) 56611.5.4 About the physical interpretation for the thermodynamics of partitions of n2) . 56611.5.5 A possible interpretation for the p-adic prime labeling amino-acid and DNAscoding it . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56811.6 Appendix: 4-adic realization of n n + 32 symmetry, divisor code, and labeling ofamino-acids by primes are not mutually consistent . . . . . . . . . . . . . . . . . . . . 569A Appendix 575A-1 Basic properties of CP2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 575A-1.1 CP2 as a manifold . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 575A-1.2 Metric and Kahler structures of CP2 . . . . . . . . . . . . . . . . . . . . . . . . 575A-1.3 Spinors in CP2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 577A-1.4 Geodesic submanifolds of CP2 . . . . . . . . . . . . . . . . . . . . . . . . . . . 578A-2 Identication of the electroweak couplings . . . . . . . . . . . . . . . . . . . . . . . . . 578A-2.1 Discrete symmetries . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 582A-3 Space-time surfaces with vanishing em, Z0, Kahler, or W elds . . . . . . . . . . . . . 583CONTENTS xiA-3.1 Em neutral space-times . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 583A-3.2 Space-times with vanishing Z0or Kahler elds . . . . . . . . . . . . . . . . . . 584A-3.3 Induced gauge elds for space-times for which CP2 projection is a geodesic sphere585List of Figures2.1 a) Illustration of Bratteli diagram. b) and c) give Bratteli diagrams for n = 4 andn = 5 Temperley Lieb algebras . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1593.1 The imbedding X64 Z126 reproducing Genetic Code and possessing Z3 type symme-try. The lengths of radial lines are 6 +d, where d = 1, 2, 3, 4, 6 is the number of DNA:sassociated with amino-acid. The angular distance between points on Z3 (Z7) orbits isto 20 (2.85) degrees. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1893.2 Z7 type imbedding X64 Z126 reproducing Genetic Code. Symmetry breaking ismuch larger for this imbedding although visually the imbedding looks perhaps moresymmetric than Z3 type imbedding. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1906.1 The left hand side gure is from [42] and represents the replica images of the instrumentsand the image interpreted by experimenters as a replica image of DNA sample (secondmethod). . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3466.2 The picture shows the discrete replica like structure of the band like image interpretedby experimenters as replica image of DNA sample (rst method). . . . . . . . . . . . . 3476.3 The picture reveals the 5-fold ne structure of the band like image interpreted by ex-perimenters as replica image of DNA sample. The 5-fold character probably correspondto ve red LEDs above the sample (second method). . . . . . . . . . . . . . . . . . . . 3486.4 Illustration of a possible vision about dark nucleus as a nuclear string consisting ofrotating baryonic strings. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3547.1 The structure of DNA hairpin (stem loop) . . . . . . . . . . . . . . . . . . . . . . . . . 3947.2 The structure of tRNA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3969.1 Illustration of the reconnection by magnetic ux loops. . . . . . . . . . . . . . . . . . . 4859.2 Illustration of the reconnection by ux tubes connecting pairs of molecules. . . . . . . 4859.3 Illustration of the book-like structure of the generalized imbedding space. . . . . . . . 4969.4 Illustration of the selection rules for magnetic ux tubes connecting magnetic bodies oftRNA and amino-acid. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49710.1 The chemical structure of amino-acids. The rst group (ala,. ..) corresponds to non-polar amino-acid side groups, the remaining amino-acids to polar side groups. The twolowest groups correspond to acidic (asp, glu) and basic side groups. . . . . . . . . . . . 52011.1 Illustration of the book-like structure of the generalized imbedding space. . . . . . . . 55511.2 Illustration of the selection rules for magnetic ux tubes connecting magnetic bodies oftRNA and amino-acid. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 556xiii0.1. Background 10.1 BackgroundT(opological) G(eometro)D(ynamics) is one of the many attempts to nd a unied description of basicinteractions. The development of the basic ideas of TGD to a relatively stable form took time of abouthalf decade [16]. The great challenge is to construct a mathematical theory around these physicallyvery attractive ideas and I have devoted the last twenty-three years for the realization of this dreamand this has resulted in seven online books [1, 2, 4, 5, 3, 6, 7] about TGD and eight online booksabout TGD inspired theory of consciousness and of quantum biology [10, 8, 9, 13, 11, 12, 14, 15].Quantum T(opological)D(ynamics) as a classical spinor geometry for innite-dimensional congu-ration space, p-adic numbers and quantum TGD, and TGD inspired theory of consciousness have beenfor last decade of the second millenium the basic three strongly interacting threads in the tapestry ofquantum TGD.For few yeas ago the discussions with Tony Smith generated a fourth thread which deserves thename TGD as a generalized number theory. The work with Riemann hypothesis made time ripefor realization that the notion of innite primes could provide, not only a reformulation, but a deepgeneralization of quantum TGD. This led to a thorough and extremely fruitful revision of the basicviews about what the nal form and physical content of quantum TGD might be.The fth thread came with the realization that by quantum classical correspondence TGD predictsan innite hierarchy of macroscopic quantum systems with increasing sizes, that it is not at all clearwhether standard quantum mechanics can accommodate this hierarchy, and that a dynamical quan-tized Planck constant might be necessary and certainly possible in TGD framework. The identicationof hierarchy of Planck constants whose values TGD predicts in terms of dark matter hierarchy wouldbe natural. This also led to a solution of a long standing puzzle: what is the proper interpretation ofthe predicted fractal hierarchy of long ranged classical electro-weak and color gauge elds. Quantumclassical correspondences allows only single answer: there is innite hierarchy of p-adically scaled upvariants of standard model physics and for each of them also dark hierarchy. Thus TGD Universewould be fractal in very abstract and deep sense.TGD forces the generalization of physics to a quantum theory of consciousness, and represent TGDas a generalized number theory vision leads naturally to the emergence of p-adic physics as physicsof cognitive representations. The seven online books [1, 2, 4, 5, 3, 6, 7] about TGD and eight onlinebooks about TGD inspired theory of consciousness and of quantum biology [10, 8, 9, 13, 11, 12, 14, 15]are warmly recommended to the interested reader.0.2 Basic Ideas of TGDThe basic physical picture behind TGD was formed as a fusion of two rather disparate approaches:namely TGD is as a Poincare invariant theory of gravitation and TGD as a generalization of theold-fashioned string model.0.2.1 TGD as a Poincare invariant theory of gravitationThe rst approach was born as an attempt to construct a Poincare invariant theory of gravitation.Space-time, rather than being an abstract manifold endowed with a pseudo-Riemannian structure,is regarded as a surface in the 8-dimensional space H = M4+ CP2, where M4+ denotes the interiorof the future light cone of the Minkowski space (to be referred as light cone in the sequel) andCP2 = SU(3)/U(2) is the complex projective space of two complex dimensions [2, 18, 19, 5]. Theidentication of the space-time as a submanifold [21, 22] of M4 CP2 leads to an exact Poincareinvariance and solves the conceptual diculties related to the denition of the energy-momentumin General Relativity [Misner-Thorne-Wheeler, Logunov et al]. The actual choice H = M4+ CP2implies the breaking of the Poincare invariance in the cosmological scales but only at the quantumlevel. It soon however turned out that submanifold geometry, being considerably richer in structurethan the abstract manifold geometry, leads to a geometrization of all basic interactions. First, thegeometrization of the elementary particle quantum numbers is achieved. The geometry of CP2 explainselectro-weak and color quantum numbers. The dierent H-chiralities of H-spinors correspond to theconserved baryon and lepton numbers. Secondly, the geometrization of the eld concept results. The2 LIST OF FIGURESprojections of the CP2 spinor connection, Killing vector elds of CP2 and of H-metric to four-surfacedene classical electro-weak, color gauge elds and metric in X4.0.2.2 TGD as a generalization of the hadronic string modelThe second approach was based on the generalization of the mesonic string model describing mesonsas strings with quarks attached to the ends of the string. In the 3-dimensional generalization 3-surfaces correspond to free particles and the boundaries of the 3- surface correspond to partons inthe sense that the quantum numbers of the elementary particles reside on the boundaries. Variousboundary topologies (number of handles) correspond to various fermion families so that one obtainsan explanation for the known elementary particle quantum numbers. This approach leads also to anatural topological description of the particle reactions as topology changes: for instance, two-particledecay corresponds to a decay of a 3-surface to two disjoint 3-surfaces.0.2.3 Fusion of the two approaches via a generalization of the space-timeconceptThe problem is that the two approaches seem to be mutually exclusive since the orbit of a particle like3-surface denes 4-dimensional surface, which diers drastically from the topologically trivial macro-scopic space-time of General Relativity. The unication of these approaches forces a considerablegeneralization of the conventional space-time concept. First, the topologically trivial 3-space of Gen-eral Relativity is replaced with a topological condensate containing matter as particle like 3-surfacesglued to the topologically trivial background 3-space by connected sum operation. Secondly, theassumption about connectedness of the 3-space is given up. Besides the topological condensatethere is vapor phase that is a gas of particle like 3-surfaces (counterpart of the baby universiesof GRT) and the nonconservation of energy in GRT corresponds to the transfer of energy between thetopological condensate and vapor phase.0.3 The ve threads in the development of quantum TGDThe development of TGD has involved four strongly interacting threads: physics as innite-dimensionalgeometry; p-adic physics; TGD inspired theory of consciousness and TGD as a generalized numbertheory. In the following these ve threads are briey described.0.3.1 Quantum TGD as conguration space spinor geometryA turning point in the attempts to formulate a mathematical theory was reached after seven yearsfrom the birth of TGD. The great insight was Do not quantize. The basic ingredients to the newapproach have served as the basic philosophy for the attempt to construct Quantum TGD since thenand are the following ones:a) Quantum theory for extended particles is free(!), classical(!) eld theory for a generalizedSchrodinger amplitude in the conguration space CH consisting of all possible 3-surfaces in H. Allpossible means that surfaces with arbitrary many disjoint components and with arbitrary internaltopology and also singular surfaces topologically intermediate between two dierent manifold topolo-gies are included. Particle reactions are identied as topology changes [23, 24, 25]. For instance,the decay of a 3-surface to two 3-surfaces corresponds to the decay A B + C. Classically thiscorresponds to a path of conguration space leading from 1-particle sector to 2-particle sector. Atquantum level this corresponds to the dispersion of the generalized Schrodinger amplitude localizedto 1-particle sector to two-particle sector. All coupling constants should result as predictions of thetheory since no nonlinearities are introduced.b) Conguration space is endowed with the metric and spinor structure so that one can denevarious metric related dierential operators, say Dirac operator, appearing in the eld equations ofthe theory.0.3. The ve threads in the development of quantum TGD 30.3.2 p-Adic TGDThe p-adic thread emerged for roughly ten years ago as a dim hunch that p-adic numbers might beimportant for TGD. Experimentation with p-adic numbers led to the notion of canonical identicationmapping reals to p-adics and vice versa. The breakthrough came with the successful p-adic masscalculations using p-adic thermodynamics for Super-Virasoro representations with the super-Kac-Moody algebra associated with a Lie-group containing standard model gauge group. Although thedetails of the calculations have varied from year to year, it was clear that p-adic physics reduces notonly the ratio of proton and Planck mass, the great mystery number of physics, but all elementaryparticle mass scales, to number theory if one assumes that primes near prime powers of two are in aphysically favored position. Why this is the case, became one of the key puzzless and led to a numberof arguments with a common gist: evolution is present already at the elementary particle level andthe primes allowed by the p-adic length scale hypothesis are the ttest ones.It became very soon clear that p-adic topology is not something emerging in Planck length scaleas often believed, but that there is an innite hierarchy of p-adic physics characterized by p-adiclength scales varying to even cosmological length scales. The idea about the connection of p-adicswith cognition motivated already the rst attempts to understand the role of the p-adics and inspiredUniverse as Computer vision but time was not ripe to develop this idea to anything concrete (p-adicnumbers are however in a central role in TGD inspired theory of consciousness). It became howeverobvious that the p-adic length scale hierarchy somehow corresponds to a hierarchy of intelligences andthat p-adic prime serves as a kind of intelligence quotient. Ironically, the almost obvious idea aboutp-adic regions as cognitive regions of space-time providing cognitive representations for real regionshad to wait for almost a decade for the access into my consciousness.There were many interpretational and technical questions crying for a denite answer. What is therelationship of p-adic non-determinism to the classical non-determinism of the basic eld equationsof TGD? Are the p-adic space-time region genuinely p-adic or does p-adic topology only serve as aneective topology? If p-adic physics is direct image of real physics, how the mapping relating themis constructed so that it respects various symmetries? Is the basic physics p-adic or real (also realTGD seems to be free of divergences) or both? If it is both, how should one glue the physics indierent number eld together to get The Physics? Should one perform p-adicization also at the levelof the conguration space of 3-surfaces? Certainly the p-adicization at the level of super-conformalrepresentation is necessary for the p-adic mass calculations. Perhaps the most basic and most irritatingtechnical problem was how to precisely dene p-adic denite integral which is a crucial element of anyvariational principle based formulation of the eld equations. Here the frustration was not due to thelack of solution but due to the too large number of solutions to the problem, a clear symptom for thesad fact that clever inventions rather than real discoveries might be in question.Despite these frustrating uncertainties, the number of the applications of the poorly dened p-adicphysics growed steadily and the applications turned out to be relatively stable so that it was clearthat the solution to these problems must exist. It became only gradually clear that the solution ofthe problems might require going down to a deeper level than that represented by reals and p-adics.0.3.3 TGD as a generalization of physics to a theory consciousnessGeneral coordinate invariance forces the identication of quantum jump as quantum jump betweenentire deterministic quantum histories rather than time=constant snapshots of single history. Thenew view about quantum jump forces a generalization of quantum measurement theory such thatobserver becomes part of the physical system. Thus a general theory of consciousness is unavoidableoutcome. This theory is developed in detail in the books [10, 8, 9, 13, 11, 12, 14, 15].Quantum jump as a moment of consciousnessThe identication of quantum jump between deterministic quantum histories (conguration spacespinor elds) as a moment of consciousness denes microscopic theory of consciousness. Quantumjump involves the stepsi Ui f ,4 LIST OF FIGURESwhere U is informational time development operator, which is unitary like the S-matrix charac-terizing the unitary time evolution of quantum mechanics. U is however only formally analogous toSchrodinger time evolution of innite duration although there is no real time evolution involved. It isnot however clear whether one should regard U-matrix and S-matrix as two dierent things or not: U-matrix is a completely universal object characterizing the dynamics of evolution by self-organizationwhereas S-matrix is a highly context dependent concept in wave mechanics and in quantum eldtheories where it at least formally represents unitary time translation operator at the limit of an in-nitely long interaction time. The S-matrix understood in the spirit of superstring models is howeversomething very dierent and could correspond to U-matrix.The requirement that quantum jump corresponds to a measurement in the sense of quantum eldtheories implies that each quantum jump involves localization in zero modes which parameterize alsothe possible choices of the quantization axes. Thus the selection of the quantization axes performedby the Cartesian outsider becomes now a part of quantum theory. Together these requirements implythat the nal states of quantum jump correspond to quantum superpositions of space-time surfaceswhich are macroscopically equivalent. Hence the world of conscious experience looks classical. Atleast formally quantum jump can be interpreted also as a quantum computation in which matrix Urepresents unitary quantum computation which is however not identiable as unitary translation intime direction and cannot be engineered.The notion of selfThe concept of self is absolutely essential for the understanding of the macroscopic and macro-temporalaspects of consciousness. Self corresponds to a subsystem able to remain un-entangled under thesequential informational time evolutions U. Exactly vanishing entanglement is practically impossiblein ordinary quantum mechanics and it might be that vanishing entanglement in the condition forself-property should be replaced with subcritical entanglement. On the other hand, if space-timedecomposes into p-adic and real regions, and if entanglement between regions representing physics indierent number elds vanishes, space-time indeed decomposes into selves in a natural manner.It is assumed that the experiences of the self after the last wake-up sum up to single averageexperience. This means that subjective memory is identiable as conscious, immediate short termmemory. Selves form an innite hierarchy with the entire Universe at the top. Self can be alsointerpreted as mental images: our mental images are selves having mental images and also we representmental images of a higher level self. A natural hypothesis is that self S experiences the experiencesof its subselves as kind of abstracted experience: the experiences of subselves Si are not experiencedas such but represent kind of averages 'Sij` of sub-subselves Sij. Entanglement between selves, mostnaturally realized by the formation of join along boundaries bonds between cognitive or material space-time sheets, provides a possible a mechanism for the fusion of selves to larger selves (for instance, thefusion of the mental images representing separate right and left visual elds to single visual eld) andforms wholes from parts at the level of mental images.Relationship to quantum measurement theoryThe third basic element relates TGD inspired theory of consciousness to quantum measurement theory.The assumption that localization occurs in zero modes in each quantum jump implies that the worldof conscious experience looks classical. It also implies the state function reduction of the standardquantum measurement theory as the following arguments demonstrate (it took incredibly long timeto realize this almost obvious fact!).a) The standard quantum measurement theory a la von Neumann involves the interaction of brainwith the measurement apparatus. If this interaction corresponds to entanglement between microscopicdegrees of freedom m with the macroscopic eectively classical degrees of freedom M characterizing thereading of the measurement apparatus coded to brain state, then the reduction of this entanglement inquantum jump reproduces standard quantum measurement theory provide the unitary time evolutionoperator U acts as ow in zero mode degrees of freedom and correlates completely some orthonormalbasis of conguration space spinor elds in non-zero modes with the values of the zero modes. Theow property guarantees that the localization is consistent with unitarity: it also means 1-1 mappingof quantum state basis to classical variables (say, spin direction of the electron to its orbit in theexternal magnetic eld).0.3. The ve threads in the development of quantum TGD 5b) Since zero modes represent classical information about the geometry of space-time surface(shape, size, classical Kahler eld,...), they have interpretation as eectively classical degrees of free-dom and are the TGD counterpart of the degrees of freedom M representing the reading of themeasurement apparatus. The entanglement between quantum uctuating non-zero modes and zeromodes is the TGD counterpart for the mM entanglement. Therefore the localization in zero modesis equivalent with a quantum jump leading to a nal state where the measurement apparatus gives adenite reading.This simple prediction is of utmost theoretical importance since the black box of the quantummeasurement theory is reduced to a fundamental quantum theory. This reduction is implied by thereplacement of the notion of a point like particle with particle as a 3-surface. Also the innite-dimensionality of the zero mode sector of the conguration space of 3-surfaces is absolutely essential.Therefore the reduction is a triumph for quantum TGD and favors TGD against string models.Standard quantum measurement theory involves also the notion of state preparation which reducesto the notion of self measurement. Each localization in zero modes is followed by a cascade of selfmeasurements leading to a product state. This process is obviously equivalent with the state prepa-ration process. Self measurement is governed by the so called Negentropy Maximization Principle(NMP) stating that the information content of conscious experience is maximized. In the self mea-surement the density matrix of some subsystem of a given self localized in zero modes (after ordinaryquantum measurement) is measured. The self measurement takes place for that subsystem of self forwhich the reduction of the entanglement entropy is maximal in the measurement. In p-adic contextNMP can be regarded as the variational principle dening the dynamics of cognition. In real contextself measurement could be seen as a repair mechanism allowing the system to ght against quantumthermalization by reducing the entanglement for the subsystem for which it is largest (ll the largesthole rst in a leaking boat).Selves self-organizeThe fourth basic element is quantum theory of self-organization based on the identication of quantumjump as the basic step of self-organization [I1]. Quantum entanglement gives rise to the generationof long range order and the emergence of longer p-adic length scales corresponds to the emergence oflarger and larger coherent dynamical units and generation of a slaving hierarchy. Energy (and quantumentanglement) feed implying entropy feed is a necessary prerequisite for quantum self-organization.Zero modes represent fundamental order parameters and localization in zero modes implies that thesequence of quantum jumps can be regarded as hopping in the zero modes so that Hakens classicaltheory of self organization applies almost as such. Spin glass analogy is a further important element:self-organization of self leads to some characteristic pattern selected by dissipation as some valley ofthe energy landscape.Dissipation can be regarded as the ultimate Darwinian selector of both memes and genes. Themathematically ugly irreversible dissipative dynamics obtained by adding phenomenological dissipa-tion terms to the reversible fundamental dynamical equations derivable from an action principle can beunderstood as a phenomenological description replacing in a well dened sense the series of reversiblequantum histories with its envelope.Classical non-determinism of Kahler actionThe fth basic element are the concepts of association sequence and cognitive space-time sheet. Thehuge vacuum degeneracy of the Kahler action suggests strongly that the absolute minimum space-timeis not always unique. For instance, a sequence of bifurcations can occur so that a given space-timebranch can be xed only by selecting a nite number of 3-surfaces with time like(!) separations on theorbit of 3-surface. Quantum classical correspondence suggest an alternative formulation. Space-timesurface decomposes into maximal deterministic regions and their temporal sequences have interpre-tation a space-time correlate for a sequence of quantum states dened by the initial (or nal) statesof quantum jumps. This is consistent with the fact that the variational principle selects preferredextremals of Kahler action as generalized Bohr orbits.In the case that non-determinism is located to a nite time interval and is microscopic, this sequenceof 3-surfaces has interpretation as a simulation of a classical history, a geometric correlate for contentsof consciousness. When non-determinism has long lasting and macroscopic eect one can identify it as6 LIST OF FIGURESvolitional non-determinism associated with our choices. Association sequences relate closely with thecognitive space-time sheets dened as space-time sheets having nite time duration and psychologicaltime can be identied as a temporal center of mass coordinate of the cognitive space-time sheet. Thegradual drift of the cognitive space-time sheets to the direction of future force by the geometry of thefuture light cone explains the arrow of psychological time.p-Adic physics as physics of cognition and intentionalityThe sixth basic element adds a physical theory of cognition to this vision. TGD space-time decomposesinto regions obeying real and p-adic topologies labelled by primes p = 2, 3, 5, .... p-Adic regions obeythe same eld equations as the real regions but are characterized by p-adic non-determinism sincethe functions having vanishing p-adic derivative are pseudo constants which are piecewise constantfunctions. Pseudo constants depend on a nite number of positive pinary digits of arguments just likenumerical predictions of any theory always involve decimal cuto. This means that p-adic space-timeregions are obtained by gluing together regions for which integration constants are genuine constants.The natural interpretation of the p-adic regions is as cognitive representations of real physics. Thefreedom of imagination is due to the p-adic non-determinism. p-Adic regions perform mimicry andmake possible for the Universe to form cognitive representations about itself. p-Adic physics space-time sheets serve also as correlates for intentional action.A more more precise formulation of this vision requires a generalization of the number conceptobtained by fusing reals and p-adic number elds along common rationals (in the case of algebraicextensions among common algebraic numbers). This picture is discussed in [E1]. The applicationthis notion at the level of the imbedding space implies that imbedding space has a book like structurewith various variants of the imbedding space glued together along common rationals (algebraics). Theimplication is that genuinely p-adic numbers (non-rationals) are strictly innite as real numbers sothat most points of p-adic space-time sheets are at real innity, outside the cosmos, and that theprojection to the real imbedding space is discrete set of rationals (algebraics). Hence cognition andintentionality are almost completely outside the real cosmos and touch it at a discrete set of pointsonly.This view implies also that purely local p-adic physics codes for the p-adic fractality characterizinglong range real physics and provides an explanation for p-adic length scale hypothesis stating thatthe primes p 2k, k integer are especially interesting. It also explains the long range correlationsand short term chaos characterizing intentional behavior and explains why the physical realizationsof cognition are always discrete (say in the case of numerical computations). Furthermore, a concretequantum model for how intentions are transformed to actions emerges.The discrete real projections of p-adic space-time sheets serve also space-time correlate for a logicalthought. It is very natural to assign to p-adic pinary digits a p-valued logic but as such this kindof logic does not have any reasonable identication. p-Adic length scale hypothesis suggest that thep = 2kn pinary digits represent a Boolean logic Bkwith k elementary statements (the points of thek-element set in the set theoretic realization) with n taboos which are constrained to be identicallytrue.0.3.4 TGD as a generalized number theoryQuantum T(opological)D(ynamics) as a classical spinor geometry for innite-dimensional congura-tion space, p-adic numbers and quantum TGD, and TGD inspired theory of consciousness, have beenfor last ten years the basic three strongly interacting threads in the tapestry of quantum TGD. Forfew yeas ago the discussions with Tony Smith generated a fourth thread which deserves the nameTGD as a generalized number theory. It relies on the notion of number theoretic compactictionstating that space-time surfaces can be regarded either as hyper-quaternionic, and thus maximallyassociative, 4-surfaces in M8identiable as space of hyper-octonions or as surfaces in M4CP2 [E2].The discovery of the hierarchy of innite primes and their correspondence with a hierarchy de-ned by a repeatedly second quantized arithmetic quantum eld theory gave a further boost for thespeculations about TGD as a generalized number theory. The work with Riemann hypothesis led tofurther ideas.After the realization that innite primes can be mapped to polynomials representable as surfacesgeometrically, it was clear how TGD might be formulated as a generalized number theory with innite0.3. The ve threads in the development of quantum TGD 7primes forming the bridge between classical and quantum such that real numbers, p-adic numbers, andvarious generalizations of p-adics emerge dynamically from algebraic physics as various completions ofthe algebraic extensions of rational (hyper-)quaternions and (hyper-)octonions. Complete algebraic,topological and dimensional democracy would characterize the theory.What is especially satisfying is that p-adic and real regions of the space-tim