Contents

ULTIMATE COMPUTING 1

Contents 2

0 Prelude 5

0.1 Acknowledgements 6

0.2 Dedication 6

1 Toward Ultimate Computing 7

1.1 Mind/Tech: Merger in the Nanoscale 7

1.2 Evolution of Technology 8

1.3 Collective Intelligence 10

1.3.1 Parallelism 12

1.3.2 Connectionism 15

1.3.3 Cooperativity and Coherence 17

1.4 Molecular Computing 20

1.5 Dynamic Pattern Representation 22

1.5.1 Reaction Diffusion Systems 22

1.5.2 Holograms 24

1.5.4 Cellular Automata 26

2 Brain/Mind/Computer 33

2.1 Metaphors of Consciousness 33

2.2 Historical Perspectives—Consciousness as 35

2.2.1 Consciousness as Particle/Wave Physics 35

2.2.2 Consciousness as a Property of Protoplasm 36

2.2.3 Consciousness as Learning 36

2.2.4 Consciousness as a Metaphysical Imposition 37

2.2.5 The Helpless Spectator Theory 37

2.2.6 Emergent Evolution 38

2.2.7 Behaviorism 38

2.2.8 Consciousness as Dynamic Activities of the Brain's Reticular Activating System 39

2.2.9 Neural Net Connectionism 41

2.2.10 Holography 42

2.2.11 Cytoskeletal Basis of Consciousness 44

3 Origin and Evolution of Life 47

3.1 Soup vs Mud, Chicken vs Egg 47

3.2 Prokaryote to Eukaryote—Symbiotic Jump 50

3.3 Centrioles—Evolution's Hijackers 53

3.4 Biotech Evolution—The Next Symbiosis 57

4 From Brain to Cytoskeleton 59

4.1 Nervous System Evolution 59

4.2 Nervous System Organization 59

4.2.1 Architecture 60

4.2.2 Neuronal Signaling 61

4.2.3 Interneuronal Synapses 61

4.3 Representation of Information 64

4.3.1 Integration—Sherrington's Reflex Centers 65

4.3.3 Connectionism and Neural Networks 67

4.3.4 Distributedness 71

4.3.5 Synaptic Mechanisms of Learning and Memory 73

4.3.6 Axoplasmic Transport 76

4.3.7 Parallelism, Collective Cooperativity, and the Grain of the Engram 77

4.4 Toward Molecular Consciousness 79

5 Cytoskeleton/Cytocomputer 80

5.1 The Nature of Cytoplasm 80

5.2 Microtubules 84

5.2.1 Microtubule Structure and Function 84

5.2.2 Microtubule Assembly and the Generation of Form 88

5.2.3 Microtubule Organizing Centers (MTOC) and Centrioles 93

5.2.4 Microtubule Associated Proteins (MAPs) 97

5.3 Intermediate Filaments 103

5.4 The Cytoplasmic Ground Substance 105

5.4.1 The Microtrabecular Lattice (MTL) 105

5.4.2 The Cytomatrix 108

5.4.3 Cytoplasmic Solid State 109

5.5 Cytoskeletal Motility 111

5.5.1 Cytoplasmic Probing 112

5.5.2 Bending Sidearms 116

5.5.3 Ciliary and Collective Movement 118

5.5.4 Geodesic Tensegrity Gels 119

5.6 The Cytoskeleton and Development 121

5.7 The Cytoskeleton and Medicine 124

5.8 Intelligence in the Cytoskeleton 126

6 Protein Conformational Dynamics 129

6.1 Protein Structure 129

6.2 Protein Conformation 131

6.3 Proteins and Energy 134

6.4 Protein Cooperativity—Historical View 135

6.5 Living Water and Hydrophobic Interactions 136

6.6 Electret, Piezo, and Pyroelectric Effects 139

6.7 Solitons/Davydov 140

6.8 Coherent Excitations /Fröhlich 143

6.9 Massless Bosons, Cytoskeletal Self-Focusing 146

7 Anesthesia: Another Side of Consciousness 148

7.1 Levels of Anesthesia/Consciousness 148

7.2 Memory 151

7.3 Mechanisms of Anesthesia 153

8 Models of Cytoskeletal Computing 157

8.1 Energy and Information in Microtubules 157

8.2 Cytoskeletal Information Processing 158

8.2.1 MT Sensory Transduction/Atema 158

8.2.2 MT Mechano-lonic Transducers/Moran and Varela 159

8.2.3 Cytomolecular Computing/Conrad and Liberman 160

8.2.4 MT Signal Processing/DeBrabander 160

8.2.5 Cytoskeletal String Processors/Barnett 163

8.2.6 Microtubule "Gradions"/Roth, Pihlaja, Shigenaka 164

8.2.7 Gyroscopic Centrioles/Bornens 166

8.2.8 Centriole-MT Signaling/Albrecht-Buehler 167

8.2.9 Dynamic Tensegrity/Heidemann and Jarosch 170

8.2.10 Dynamic MT Probing/Kirschner and Mitchison 171

8.2.11 Sphere Packing Screw Symmetry/Koruga 172

8.2.12 Cytoskeletal Self-Focusing/Del Giudice 174

8.2.13 MT Automata, Holography/Hameroff, Watt, Smith 174

8.3 The Cytoskeletal Connection 181

9 Viruses/Ambiguous Life Forms 184

9.1 What Is the Essence of Living Matter? 184

9.2 Virus (Mis)Behavior 184

9.3 Virus Structure and Collective Oscillations 186

9.4 Nature and Origin of Viruses 187

9.5 Domesticated Viruses 188

10 NanoTechnology 190

10.1 Early NanoTechnologists 190

10.2 Scanning Tunneling Microscopes (STMs) 192

10.3 STM/Feynman Machines (FMs) 203

10.4 Micro/Nano STM Contest 205

10.5 STM/FMs and Molecular Computing 205

10.6 STM/FMs and Biomedical Applications 211

10.7 Replicating Automata 215

11 The Future of Consciousness 217

12 Bibliography 219

12.1 STM References 248

12.2 Near-Field Scanning Optical Microscopes 256

12.3 Other STM-Related Instruments 256

12.4 Replicating Systems References 257

12.5 Collective Computing References 259

12.6 Quantum Computing References 261

Index 264

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