CONTENTS 1 Evolution in Many-Sheeted Space-Time M. Pitk¨anen, June 19, 2019 Email: [email protected]. http://tgdtheory.com/public_html/. Recent postal address: Rinnekatu 2-4 A 8, 03620, Karkkila, Finland. Contents 1 Introduction 5 1.1 Questions And Answers About Evolution . .6 1.2 Topics Of The Chapter . .9 2 What Is Known About Pre-Biotic Evolution? 11 2.1 Some Believed-To-Be Facts About The Early History Of Life . 11 2.2 Standard Approaches Are Mechanistic . 11 2.3 The Notion Of Primordial Ocean . 12 2.4 Urey-Miller Experiment . 12 2.5 RNA World . 13 2.6 How Biochemical Pathways And DNA-Amino-Acid Code Emerged? . 13 2.7 Problems With The Polymerization In Primordial Ocean . 14 2.8 The Notion Of Protocell . 15 3 TGD Based Scenario About Pre-Biotic Evolution 15 3.1 Basic Prerequisites . 16 3.2 TGD Based Vision About Pre-Biotic Evolution . 16 3.2.1 Is life really a result of accident? . 17 3.2.2 The notions of magnetic body and plasmoid . 18 3.2.3 Does the Earth's magnetic field have a dark counterpart? . 18 3.2.4 Emergence of symbols at molecular level and new view about hydrogen bond, water, and bio-catalysts . 19 3.2.5 Universal metabolic currencies . 20 3.2.6 Time mirror mechanism, intentional action, memory, and remote metabolism 20 3.2.7 Emergence of membrane bounded structures . 20 3.2.8 Did life evolve in Mother Gaia's womb? . 21 3.2.9 Model for the genetic code . 22 CONTENTS 2 3.2.10 What makes possible the coherence of bio-chemical activities? . 22 3.3 Pre-Biotic Chemistry And New Physics . 22 3.3.1 Overall view . 23 3.3.2 Dark matter and the emergence of symbolic representations at molecular level 23 3.3.3 Evolution of pre-biotic chemistry as a sequence of bifurcations . 23 3.3.4 What selected the bio-molecules? . 25 3.3.5 Polymerization, dehydration, phosphorylation, and new physics . 25 3.3.6 Why DNA is stable inside cell nucleus? . 29 3.4 Could High Energy Phosphate Bond Be Negentropic Bond With Negative Binding Energy? . 29 3.4.1 Basic ideas . 30 3.4.2 General formulation of the model . 30 3.4.3 Quantitative estimates . 32 3.5 Water Memory And Braids . 33 3.5.1 Water memory: general considerations . 33 3.5.2 Water memory in terms of molecular braidings . 35 3.5.3 Why experimenter had to know which bottle contained the treated water? . 35 3.6 How Bio-Polymers Were Associated With Their Dark Counterparts? . 36 3.7 Two steps towards understanding of the origins of life . 38 3.7.1 The first step: binding of dark protons to formamido-pyrimidine . 38 3.7.2 Second step: Could shock waves due to extraterrestrial impacts have pro- duced RNA bases? . 40 3.8 Could the replication of mirror DNA teach something about chiral selection? . 41 3.8.1 Dark matter and chirality selection . 42 3.8.2 Model for the replication of DNA . 43 3.8.3 Differences between standard model and TGD based description . 46 4 Model For The Hierarchy Of Josephson Junctions 46 4.1 The Most Recent Model For The Generation Of Nerve Pulse . 47 4.2 Quantum Model For Sensory Receptor . 48 4.3 The Role Of Josephson Currents . 49 4.4 What Is The Role Of The Magnetic Body? . 50 4.4.1 Is magnetic body really needed? . 50 4.4.2 Is motor action time reversal of sensory perception in zero energy ontology? 51 4.4.3 What magnetic body looks like? . 51 4.4.4 What are the roles of Josephson and cyclotron photons? . 53 4.5 Dark Matter Hierarchies Of Josephson Junctions . 54 4.5.1 Maximization of Planck constant in quantum control and communication in living matter . 54 4.5.2 Dark hierarchy of Josephson junctions with a constant thickness . 55 4.5.3 An objection against a fractal hierarchy of Josephson junctions with thickness scaling as ~ .................................... 55 4.6 P-Adic Fractal Hierarchy Of Josephson Junctions . 56 4.6.1 The possibility of a p-adic hierarchy of membrane like structures accompa- nied by Josephson junctions . 56 4.6.2 Fractal hierarchy of magnetic bodies assignable to cell . 56 5 Physical Model For Genetic Code And Its Evolution 57 5.1 RNA World . 58 5.2 Programming Of Bio-Molecular Self Assembly Pathways From TGD Point Of View 58 5.2.1 Key ideas . 59 5.2.2 TGD view about the situation . 59 5.3 The Archeology Of TRNA Molecules As A Guideline . 60 5.3.1 The structure of the tRNA molecule . 60 5.3.2 Wobble base pairing . 61 5.3.3 Anomalous em charge and color singletness hypothesis for tRNA . 62 CONTENTS 3 5.3.4 The fossilized components of tRNA as record about the evolution of the recent form of the genetic code . 63 5.3.5 The components of tRNA as ribozymes which have acted originally as RNA polymerases . 64 5.3.6 From RNA world to RNA-tRNA world to RNA-DNA-tRNA world to DNA- RNA-protein world: how it went? . 65 5.4 Recent Genetic Code As A Fusion Of Singlet And Doublet Codes? . 68 5.4.1 RNA era and the transition to RNA-amino-acid era . 69 5.4.2 Symbiosis with membrane bounded structures . 70 5.4.3 Reverse transcription of RNA to DNA . 70 5.4.4 What were the first self replicators? . 71 5.5 Is RNA Era Continuing Inside Cell Nuclei? . 71 5.6 Could Nanno-Bacteria Correspond To Predecessors Of TheTriplet Life-Forms? . 72 5.6.1 Basic facts about nanno-bacteria . 72 5.6.2 Nanno-bacteria as RNA life? . 73 5.6.3 Was the encounter of nanno-bacteria and plasmoids the moment of Gaian fertilization? . 74 6 Did Life Evolve In The Womb Of Mother Gaia? 74 6.1 Quantum Version Of Expanding Earth Theory And Cambrian Explosion . 75 6.1.1 The claims of Adams . 76 6.1.2 The critic of Adams of the subduction mechanism . 76 6.1.3 Expanding Earth theories are not new . 77 6.1.4 Summary of TGD based theory of Expanding Earth . 77 6.1.5 Did intra-terrestrial life burst to the surface of Earth during Cambrian ex- pansion? . 79 6.2 Did Pre-Biotic Life Evolve In Mantle-Core Boundary? . 80 6.2.1 Some arguments supporting IT life . 80 6.2.2 Structure of the Earth's interior and IT life . 81 6.3 What Conditions Can One Pose On Life At Mantle-Core Boundary? . 82 6.3.1 Plasmoid life as minimum option . 82 6.3.2 Could topological quantum computation like activities be considered? . 83 6.3.3 Do metabolism and photosynthesis possess signatures telling about intra- terrestrial evolution? . 84 6.4 What About Analogs Of EEG? . 85 6.4.1 Conditions from the thermal stability of the analog of EEG . 86 6.4.2 What could the analog of EEG for IT look like? . 87 7 Comparison Of Mcfadden's Views With TGD 89 7.1 General Ideas . 89 7.1.1 McFadden's view about biochemistry . 90 7.1.2 Important problems of quantum biology . 91 7.2 Enzyme Action . 91 7.3 Quantum Evolution . 92 7.3.1 How evolution can create complexity? . 92 7.3.2 Criticism of RNA world . 92 7.3.3 Evolution of metabolism . 93 7.3.4 Quantum mechanism of mutations . 95 8 Great Vision About Biological Evolution And Evolution Of Brain 97 8.1 Basic Assumptions . 97 8.1.1 How to identify the preferred values of Planck constant? . 98 8.1.2 Tables about predicted time and length scales . 99 8.1.3 Electron and u quark are different . 99 8.2 Dark Matter Hierarchy And Big Leaps In Evolution . 100 8.2.1 A sketch about basic steps in evolution . 104 8.2.2 Division of the evolution to that of biological body and magnetic body . 106 CONTENTS 4 8.2.3 Biological evolution . 107 8.2.4 The evolution of magnetic body . 108 9 Oil Droplets In Water Solution As A Primitive Life Form? 110 9.1 Intelligent Oil Droplets . 111 9.2 Some Key Ideas Of TGD Inspired Quantum Biology . 112 9.3 General Ideas About Oil Droplets As A Primitive Life Form . ..