Table of Contents ............................................... 3
List of Tables .................................................. 5
List of Figures and Illustrations ............................... 6
CHAPTER ONE: INTRODUCTION ....................................... 9
1.1 Introduction ............................................... 9
1.2 Problem Description ........................................ 9
1.3 Life Sciences Foundation .................................. 11
1.3.1 The Double Helix and the Sequence Hypothesis ....... 11
1.3.2 The Human Genome Project ........................... 12
1.3.3 Computational Biology and System Biology ........... 13
1.4 Biological Definitions and Terminology .................... 15
1.4.1 Basic Definitions .................................. 15
1.4.2 The DNA Molecule ................................... 17
1.4.3 The Central Dogma .................................. 18
1.4.4 The Genetic Code and the Proteins .................. 22
1.5 Information Theoretical Entropy ........................... 25
1.5.1 Information Contents and Redundancy ................ 31
1.5.2 Shannon's Statistical Language Models .............. 33
1.5.3 Information Theory and Biological Sequences ........ 36
1.6 Holography ................................................ 37
1.6.1 Operational Principle .............................. 37
1.6.2 The Concept of Holographic Universe ................ 38
1.6.3 The Holographic Theory of the Brain ................ 45
CHAPTER TWO: STRUCTURAL CHARACTERIZATION OF BIOMOLECULES
AND ITS IMPLICATION ............................................ 48
2.1 Information Deficiency of DNA ............................. 48
2.1.1 Law of Requisite Variety ........................... 50
2.1.2 Biology's Enigmas .................................. 52
2.1.3 Alternative Splicing ............................... 54
2.1.4 Active Role of DNA ................................. 55
2.2 Information Theoretical Analysis of DNA Sequences ......... 57
2.2.1 Incompressibility of DNA sequences ................. 58
2.2.2 Structural Redundancies in Proteins ................ 61
2.3 Entropy Transformation along the Protein Synthesis
Path ...................................................... 62
2.4 Analysis of Epigenetic Influences on Organism
Development ............................................... 67
2.4.1 Epigenetic Mechanism ............................... 67
2.4.2 Epigenetic Inheritance and the Memory Problem ...... 70
2.4.3 Biological Complexity and Entangled Life ........... 73
CHAPTER THREE: BIOLOGICAL INFORMATION PROCESSING AS CLOUD
COMPUTING ...................................................... 75
3.1 The Emerging Cloud Computing Paradigm ..................... 75
3.2 A Cloud Computing Model for Biological Information
Processing ................................................ 77
3.3 Interactive feedbacks in the organization of the
holographic Universe ...................................... 79
3.4 Hypothesized Properties of Biomolecules and the
Operational Significance of their Structure ............... 88
3.5 Possible detecting of absolute orientation with respect
to the holographic reference beam ......................... 93
3.5.1 Testing the effects on radioactive decay rate ...... 94
3.5.2 Testing the effects on stem cell lineage
commitment ......................................... 95
3.5.3 Testing of the effects of prion folding ............ 97
3.5.3.1 Prion Disease Contradiction to the
Central Dogma ............................. 97
3.5.3.2 Prion Proteins as Entangled Molecules ..... 99
CHAPTER FOUR: CONCLUSION ...................................... 101
REFERENCES .................................................... 105
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