Biosphere Origin and Evolution (eBook)

Preface 5
Contents 10
Contributors 14
Part I Problems of Biosphere Evolution and Origin of Life 20
On Important Stages of Geosphere and Biosphere Evolution 21
References 38
Microbial Biosphere 42
Introduction 43
Limits for Actualistic Principle 45
Relict Microbial Communities 46
Formation of Landscape in Prokaryotic Biosphere 49
Trophic Structure of Cyano-bacterial Community 54
References 57
Part II Prebiological Stages of Evolution and RNA World on the Earth and in the Space 60
Astrocatalysis Hypothesis for Origin of Life Problem 61
Evolution of the Surroundings and the Life Origin 61
Astrophysics and Planetology 63
Astrocatalysis, "RNA World" and Life Origin 64
Conclusions 68
References 69
Comets, Carbonaceous Meteorites and the Origin of the Biosphere 70
Introduction 71
Comets, Meteorites, and the Origin and Distribution of Life 73
Microfossils of Cyanobacteria in the Orgueil and Murchison Meteorites 75
Morphotypes of Cyanobacteria in Carbonaceous Meteorites 76
Conclusions 79
References 80
Hierarchical Scale-Free Representation of Biological Realm-Its Origin and Evolution 84
Introduction 84
Identification of Referents 86
Defining Sets of Referents 87
Referents and Hierarchy of Complexity 90
From a Linnaean Hierarchy to the Hierarchy of Complexity 90
Two Directions in the Architecture of Complexity 92
Transition Thresholds and the Irreversibility of Transition 94
Formalization of the Referent Representation 95
Space of the Referent Signs 95
Evolutionary Equation 96
Growing of the Referent Hierarchy 98
Conclusions 100
References 101
The Prebiotic Phase of the Origin of Life as Seen by a Physical Chemist 104
References 116
Prebiotic Carbohydrates and Their Derivates 117
Introduction 117
The Formose Reaction 118
Prebiotic Synthesis of Lower (C2–C3) Carbohydrates 120
Selective Prebiotic Synthesis of Carbohydrates 122
Carbohydrates Synthesis Catalyzed by Natural Minerals 123
Selective Synthesis of Carbohydrates Phosphates 123
Co-condensation of Lower Carbohydrates and Formladehyde 124
Putative Prebiotic Synthesis of Carbohydrates fromForm aldehyde 125
Important Prebiotic Organics from Carbohydrates 126
Synthesis of Heterocycles from Carbohydrates and Ammonia 126
A ‘‘Sugar Model’’ by A.L. Weber 126
Synthesis of Cytidine Ribonucleotides on Sugar Phosphate 128
Conclusions 129
References 130
Theoretical and Computer Modeling of Evolution of Autocatalytic Systems in a Flow Reactor 132
Introduction 132
The ‘‘Only’’ Statements 132
On the Main Properties of Living Beings 133
Key Problem Is Due to Attempts to Explain the Exact Origin of Earth’s Life Form 133
Presuppositions Capable of Eliminating the Problem 134
On the Nature of the Predecessor 134
Description of Computer Model and Conditions of Real Experiment 137
Results of the Computer Simulation and Discussion 139
Conclusions 140
References 141
RNA World: First Steps Towards Functional Molecules 143
First RNA Monomers: Puzzle of Isomers 143
Prebiotic Synthesis of RNA Oligomers 145
Emergence of Catalytic RNAs 147
RNA Recombination: Elongation and Diversity 148
Concluding Remarks 152
References 152
Trans Hammerhead Ribozyme: Ligation vs. Cleavage 155
Introduction 155
RNA Ligation by Trans Hammerhead Ribozymes 157
Binary Hammerhead Ribozymes 160
Conclusion 164
References 165
Paradoxical Bistate Status of a Prebiotic Microsystem: Universal Predecessor of Life 168
Introduction 168
Fundamental Properties of Biological Systems 169
Stabilized Bifurcation as a Starting Point of Life 170
Main Properties of a Chemical System Close to the Bifurcation Point 171
The Corresponding Characteristics of a Living Cell 172
Bistate System as Prototype of a Living Organism: Theoretical Substantiation 173
Conclusion 176
References 176
Part III Archaen–Proterozoic Ecosystems: Their Interaction and Contemporary Analogues 178
The Ancient Anoxic Biosphere Was Not As We Know It 179
Introduction 179
Ccarb of Early Precambrian Carbonates 181
Diagenetic Concretions in the Early Precambrian 183
Isotopic Composition of Archaean Concretions 183
Isotopic composition of Palaeoproterozoic concretions 187
Corg Recycling 192
Prior to c. 2000 Ma 192
After c. 2000 Ma 193
BIF-Associated Carbonates 193
OM Recycling and the Lomagundi-Jatuli Isotopic Event 194
References 195
Evolutionary Aspects of Geochemical Activity of Microbial Mats in Lakes and Hydrotherms of Baikal Rift Zone 199
Introduction 199
Hot Spring Phototrophic Microbial Mats 201
Non-phototrophic Biofilms 206
Microbial Mats of Saline and Soda Lakes 207
Terminal Destruction Processes in Microbial Mats 208
Conclusion 209
References 210
On the Concept for the Organization of the Modern Biosphere in the Terrestrial Subsurface 212
Introduction 212
The Zone of the Hydrocarbon-Oxidizing Bacterial Filter 213
The Zone of the CO2-H2 Bacterial Filter 214
The Zone of Naphthidiobiosis 215
Evaluation of the Subsurface Biota 216
Conclusion 216
References 217
Biomineralization and Evolution. Coevolution of the Mineral and Biological Worlds 219
Introduction 219
Definition of Coevolution 219
Biomineralization Is Coevolution of the Mineral and Biological Worlds 221
Modern Understanding and Types of Biomineralization 221
Evolution of the Composition, Structure, and Functions of Biominerals 223
References 225
Visualization of the Silicon Biomineralization in Cyanobacteria, Sponges and Diatoms 227
Introduction 227
Silicification of Cyanobacteria 228
Sponges 230
Diatoms 232
Studies of Morphogenesis of Early Stages of Diatom Valves 232
Discovery of Silicic Acid Transporters 233
References 236
Transformational Changes in Argillaceous Minerals due to Cyanobacteria 239
Introduction 239
Experimental 240
Objectives 240
Methods 241
Results and Discussion 242
Biological Activity of Cyanobacteria in the Presence of Clays 242
Changes in Argillaceous Minerals After Incubation with Cyanobacteria 244
Conclusions 248
References 248
Part IV Coevolution of Geological and Biological Events in Phanerozoe 251
Ecological Revolution Through Ordovician Biosphere (495 to 435 Ma ages): Start of the Coherent Life Evolution 252
References 260
Part V Ecosystems and Molecular Genetic Factors of Organism Evolution 262
Evolution by Gene Duplications: from the Origin of the Genetic Code to the Human Genome 263
Origin of the Genetic Code: Duplication in tRNA 263
Domains of tRNAs and the Paradox of Two Codes 263
Dual Complementarity in tRNAs Points to Ancient Duplication 266
Simultaneous Sense-Antisense Coding Might Predetermine Two Complementary Modes of tRNA Aminoacylation 267
Epigenetic Regulation of Expression, Repositioning and Evolutionary Fate of New, Redundant Gene Copies 271
Loss-or-Gain Dilemma, Effective Population Size and the Duplication-Degeneration-Complementation Model 271
The Epigenetic Complementation Model 272
Repositioning Favors Survival of Duplicate Genes 273
Repositioning Increases Mutational Asymmetry 275
Adaptive Evolution of Young Duplicates 276
EC Model and G-Value Paradox 279
References 280
Evolution of the Translation Termination System in Eukaryotes 283
The Evolutionary Origin of Termination Factors 283
The Structural Organization of Termination Factor eRF3 285
Evolution of Genes Encoding for eRF3 288
GSPT2 as a New Phylogenetic Marker 290
References 292
The Hedgehog Signaling Cascade System: Evolution and Functional Dynamics 294
Introduction 294
Modeling of the Hedgehog Signaling Cascade 296
Molecular Evolution of Hedgehog Signaling Cascade 299
Comparison of the Evolution Mode of the Hh Signaling Cascade Genes with Their Functional Load and Response Type 301
Discussion 301
Conclusions 304
References 305
Approaches to the Resolution of Contradictions Between Phylogenetic Systems Based on Paleontological and Molecular Data 307
Introduction 307
Historical Vertebrate Zoogeography and Molecular Phylogeny of Mammals 310
Global Historical Geography of Land Vertebrates as a Source of Information on Divergence Events in Mammalian Phylogeny 310
Basic Events in the History of Mammalian Faunas 312
Zoogeographical Dating Compared with the Phylogenetic Reconstruction Based on Molecular Data 314
References 316
Chromosomes and Speciation 319
Introduction 320
Sibling Species of South American Caviomorph Rodent Thrichomys 320
Chromosome Races of the House Musk Shrew 322
Chromosome Races of the Common Shrew 324
Conclusions 327
References 327
Biotic Turnover in Superorganism Systems: Several Principles of Establishment and Sustenance (Theoretical Analysis, Debatable Issues) 330
Introduction 330
The Measure of Closure of Biotic Matter Cycle for Systems Based on Matter Supply 332
Mathematical Model of Simple Homogenous Closed Ecosystem on Matter Supply 334
Base Model Description 334
Conditions for Establishment of Biotic Matter Cycle 336
Examples of Closure Coefficients Calculation 339
On Realizability of Some Mechanisms of Sustaining Highly Closed Cycle of the Matter 342
Ecological Principle of Biological Cycle Closure 342
‘‘Evolutionary’’ Type of Closure 342
Interaction of Microevolutionary Population Parameters 344
General Degree of Biocycle Closure 346
Conclusions 348
References 350
Chromosomes and Continents 352
Introduction 353
Karyotype Structure in the Genus Chironomus 353
Divergence of Banding Sequences in the Genus Chironomus on Various Continents 355
Basic Banding Sequences as Markers of Evolutionary Divergence of Species Genomes 360
Scenario of BS Divergence 362
Dispersal of Species and Banding Sequences 367
Chromosome Evolution and Speciation 369
References 370
Part VI Biosphere And Human Being 373
Genetic Landscape of the Central Asia and Volga-Ural Region 374
Introduction 374
Materials and Methods 375
mtDNA Variation 376
Y-Chromosome Variation 379
References 380
Problems of Reconstruction of Paleoenvironment and Conditions of the Habitability of the Ancient Man by the Example of Northwestern Altai 383
Introduction 383
Material 384
Results 384
Contemporaneous Animals of the Anui Valley 384
Small Mammals from the Pleistocene of Denisova Cave 385
Small Mammals from the Ust’-Karakol Paleolithic Site 387
Mammal Fauna and Activity of the Paleolithic Man 387
References 393
The Settling of the Ancient Man by the Example of North-Western Altai 395
References 404
Evolutionary History of Wheats-the Main Cereal of Mankind 407
Material and Methods 408
Plant Materials 408
Total DNA Isolation and PCR Amplification 409
DNA Sequencing and Phylogenetic Analysis 410
Results and Discussion 410
Pile-Dwelling Wheat 410
Spherical Grains 411
Compact Spike 411
Chloroplast Evidence of Wheat Evolution 411
Nuclear Loci 414
Evolutionary Scenario of Genus Triticum 417
References 418
Subject Index 420