Biocommunication and Natural Genome Editing (eBook)

Preface 5
Acknowledgements 7
Contents 8
1 Introduction: Metaphysical and Postmetaphysical Relationships of Humans with Nature and Life 13
1.1 Metaphysical vs. Mythological Construction of Nature 13
1.1.1 Monistic-Organismic World Views 15
1.1.2 Pluralistic-Mechanistic World Views 16
1.1.3 Organic-Morphological World View 18
1.2 Delimitations Against Metaphysics 19
1.2.1 Linguistic Turn 20
1.2.2 Manfred Eigen's Adaptation of the Linguistic Turn to Biology 21
1.2.3 Deficiencies of Manfred Eigen's Depiction Theory of Language 23
1.2.4 G'del's 'Incompleteness Theorem' and Real-Life Languages 25
1.3 The Roots of the Idea of an Exact Scientific Language 26
1.4 Postmetaphysical Thinking: Pragmatic Turn 28
1.4.1 The End of Linguistic Turn 28
1.4.2 The Fundamental Status of Communicative Intersubjectivity 30
1.4.3 Evolutionary History: History of Rule-Governed Sign-Mediated Interactions 32
1.4.4 Biology in the Realm of a Theory of Biocommunication 32
1.5 Recent Applications of Language and Communication in Biology 32
1.5.1 Biolinguistics and Bioinformatics 33
1.5.2 Biosemiotics and Biohermeneutics 34
1.5.3 Biocommunication 35
1.6 The Structural Format of the Following Chapters 36
References 37
2 Plant Communication 39
2.1 Introduction: Multilevel Communication Competence of Plants 39
2.2 Chemical Vocabulary of Plants 40
2.2.1 Context-Dependent Auxin as Neurotransmitter, Hormone, Morphogenic Sign 41
2.2.2 Hormones 41
2.2.3 RNAs 43
2.2.4 Multiply Re-usable Components 43
2.3 Interpretation of Mechanical Influences 43
2.4 Transorganismic (Transspecific) Communication 44
2.4.1 Coordination of Defence against Pests and Injury 44
2.4.2 Communicative Coordination of Symbioses 46
2.4.3 Vital Symbiosis of Plant Roots with Bacteria, Fungi and Animals 46
2.4.4 Viral Symbiotic Interactions 47
2.5 Interorganismic Communication 48
2.6 Intraorganismic Communication 49
2.6.1 Most Intercellular Communication via Plasmodesmata 49
2.6.2 Intracellular Communication 51
2.7 Plant Communication: Plant Neurobiology and the Emergence of Mind? 54
2.8 Conclusion 56
References 58
3 Communicative Competences of Honey-Bees 64
3.1 Introduction 64
3.2 Honey-Bees in the Colder Hemispheres 65
3.2.1 The Communication Process Behind the Founding of a New Colony 66
3.2.2 The Sign-Mediated Interaction of Foraging 68
3.3 Further Features of Honey-Bee Communication 69
3.3.1 The Types of Dances and Their Meanings 69
3.3.2 Forms of Communication Beyond Dances 70
3.3.3 Humans can Understand the Bee-Language 70
3.3.4 Dialects of the Bee-Language 70
3.4 Language and Communication in Bees: Context Determines Meaning 71
3.4.1 Foundation of a New Colony 72
3.4.2 Food Gathering 74
3.4.3 Dialects in Different Cultural Life-Worlds 75
References 75
4 Biocommunication of Corals 77
4.1 Introduction 77
4.2 Semiochemical Vocabulary of Corals 78
4.3 Interpretation of External Influences 80
4.4 Transorganismic (Trans-Species) Communication 81
4.4.1 Coordination of Defence and Regeneration 82
4.4.2 Communicative Coordination of Symbioses 83
4.5 Interorganismic (Species-Specific and Species-Related) Communication 84
4.6 Intraorganismic Communication 86
4.6.1 Intercellular Communication 87
4.6.2 Intracellular Communication 87
4.7 Conclusion 89
References 92
5 Biocommunication of Fungal Organisms 98
5.1 Introduction 98
5.2 Semiochemical Vocabulary of Fungi 100
5.3 Interpretation of Abiotic Indices 100
5.4 Transorganismic Communication 102
5.5 Biocommunication Among Fungal Species 104
5.6 Biocommunication Within Fungal Organisms 106
5.6.1 Intercellular Communication 106
5.6.2 Intracellular Communication 107
5.6.3 Unique Relationship Between Fungi and Viruses 109
5.7 Conclusion 111
References 112
6 Bacteria Communication 117
6.1 Introduction 117
6.1.1 Biocommunicative Competences of Bacteria 117
6.1.2 Biofilm Organisation: Interpretation and Coordination 119
6.2 Semiochemical Vocabulary and Communicative Goals 119
6.3 Transorganismic Communication 121
6.4 Interorganismic Communication 123
6.5 Intraorganismic Communication 125
6.5.1 Intracellular Communication 126
6.5.2 Bacterial Evolution and the Agents of Natural Genome Editing 127
6.5.3 Lytic versus Persistent Viral Life-Strategies 127
6.5.4 Bacteria as Biotic Matrix for Natural Genome Editing 129
6.6 Conclusion 130
References 132
7 Natural Genome Editing Competences of Viruses and Virus-Like Agents 137
7.1 Introduction 137
7.2 Non-Coding Regulatory Networks 138
7.3 Major Viral Life Strategies 139
7.4 Examples of Diverse Viral Life Strategies 141
7.4.1 Virus Escape 142
7.4.2 Wall Off 142
7.4.3 Addiction Module: Reciprocal Interaction 142
7.4.4 Multiplicity Reactivation 142
7.4.5 Sexual Isolation 143
7.5 Pre-Cellular Life: Early RNA- and DNA-Viruses 143
7.6 Origin of the Eukaryotic Nucleus 144
7.7 Origin of the Adaptive Immunity 147
7.7.1 The Acquisition of a Complex New Phenotype 148
7.7.2 Ancestral Origin of an Adaptive Immune System 150
7.8 Evolution of Placental Mammals 150
7.9 Conclusion 151
References 153
8 How Bacteria Escaped Selection Pressure of the Early RNA-World 156
8.1 Introduction 156
8.2 From Pre-Cellular RNA-Copying to RNA-Coding 156
8.3 Communal Evolution: From LUCA to LUCAs 158
8.4 Old but Good: Current Competences from an Ancient World 159
References 161
9 Viral Origins of Telomeres and Telomerases 163
9.1 Introduction 163
9.2 Different Molecular Syntax of Telomere Sequences 164
9.3 Telomere Replication in Most Cases by Telomerase 165
9.3.1 Reverse Transcriptases and Mobile Elements 165
9.3.2 Roles of Reverse Transcriptases in Natural Genome Editing 166
9.4 Telomeres are Characteristics of Eukarya 168
9.5 Agents of Natural Genome Editing 168
9.6 Superficial and Deep Grammar in Eukaryotic Genome Content 170
9.7 Conclusion 171
References 172
10 Real Life-World of Noncoding RNA-Species 176
10.1 Introduction 176
10.2 Genetic Text-Sequences Function Similar to any Natural Language 177
10.3 Cellular DNA Nucleotide Sequences as Viral Life Habitat 178
10.3.1 The Persistence of the Eukaryotic Nucleus 179
10.4 Viral Agents as Genetic Editors 180
10.4.1 Persistent Viral Life Strategies Change Genetic Host-Identities 181
10.4.2 Former Competing Genetic Parasites Built Addiction Modules 181
10.4.2.1 The Symbiogenetic Lifestyle of Retroviruses 182
10.4.2.2 'Highways' that Play Important Roles in Persistence 182
10.4.2.3 The Kinesin/Dynein Addiction Module 183
10.5 Competent Regulators of Gene Expression 185
10.5.1 Identification and Regulation by microRNAs and siRNAs 185
10.5.2 Non-coding RNAs act as Ribonucleoproteins 188
10.5.3 Small Nuclear and Small Nucleolar RNAs 189
10.5.4 Currently Identified Roles of Small Nucleolar RNAs 190
10.5.5 The tRNA Consortium 192
10.6 Reciprocal Interacting Agents 193
10.7 Conclusion 195
References 196
11 Outlook 202
11.1 From Mechanistic Biology to Biocommunication 202
11.2 Three Kinds of Signs in Biocommunication 204
11.3 Context Determines Meaning 205
11.4 Living Nature and Non-living Nature 205
11.5 Biocommunication Defines a Biotic Plus 206
11.6 The Advantages of Biocommunicative Biology 206
11.7 Linguistic and Communicative Competences in Non-human Nature 207
11.8 Complementary Roles of Linguistic and Communicative Competences 208
11.9 New Qualities for Future Decisions 208
Index 210