Evolution's Destiny

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  • Format: Hardcover
  • Copyright: 2012-07-20
  • Publisher: Royal Society of Chemistry

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This book is written as an addition to Darwin's work and that of molecular biologists on evolution so as to include views of it from the point of view of chemistry rather than just from our knowledge of the biology and genes of organisms. By concentrating on a wide range of chemical elements, not just those in traditional organic compounds, we show that there is a close relationship between the geological or environmental chemical changes from the formation of Earth and those of organisms from the time of their origin. These are considerations which Darwin or other scientists could not have explored until very recent times since sufficient analytical data were not available. They lead us to suggest that there is a combined geo- and bio-chemical evolution, that of an ecosystem, which has had a systematic chemical development. In this development the arrival of new very similar species is shown to be by random Darwinian competitive selection processes such that a huge variety of species coexist with only minor differences in chemistry and advantages. This is in agreement with previous studies. On the large scale of evolution of very different organisms, and over greater timescales, by way of contrast, we observe that groups of species have special, different, chemical features and function. It is more difficult to understand how they evolved and therefore we examine their chemical development in detail. Overall there is a cooperative evolution of a chemical system driven by capture of energy, mainly from the sun, and its degradation in which the chemistry of both the environment and organisms are facilitating intermediates. We shall suggest that the overall drive of the whole joint system is to optimise the rate of this energy degradation. Since the environmental changes are inorganic and relatively fast they move inevitably to equilibrium. The living part of the system, the organisms, under the influence of this inevitable environmental change are forced to follow but as they are increasingly energised and their reactions are slow, they move further away from equilibrium. We are able to explore the ways in which this chemical system evolved, recognising that as complexity of the chemistry of organisms increased, they had to be formed from more and more compartments and to become part of a chemically cooperative overall activity. They could not remain as isolated species. Only in the last chapter do we attempt to make a connection between the changing chemistry of organisms with the coded molecules of each cell which have to exist to explain reproduction.

Table of Contents

Glossaryp. xv
Abbreviationsp. xix
About the Authorsp. xxi
Outline of the Main Chemical Factors in Evolution
Introduction to the Chemistry of the Ecosystemp. 1
The Involvement of the Elements in Evolutionp. 4
Equilibrium and Steady State Conditionsp. 10
Solubilityp. 14
Complex Ion Formationp. 15
Standard Oxidation/Reduction Potentialsp. 17
Rate Controls and Catalysisp. 20
The Dangers of Catalysisp. 26
Diffusionp. 27
Irreversibility, Chaos and Predictabilityp. 28
Summaryp. 29
Referencesp. 31
Geological Evolution with Some Biological Intervention
Introductionp. 32
Physical Evolution from the Earliest Times to Todayp. 33
The Value of Isotope Studies: Indicators of Chemical Changes and Geochemical Datesp. 39
The Early Chemical Development of the Environment before 3.0 Gap. 40
Energy Capture and Surface Geochemical Changes: The Beginning of Organic Chemistry and Oxygen in the Atmospherep. 42
The Environment after 3.0 Ga: Revolution in Redox Chemistry before 0.54 Gap. 45
Sulfur Isotope Fractionation from 3.5 to 0.5 Ga; Dominance of Iron/Sulfur Bufferingp. 48
Evolving Mineral outputs from the Ocean: Further Evidence for Redox Chemistry before 0.54 Gap. 49
Banded Iron Formations and the State of Iron in Solutionp. 49
Uranium and Thorium Mineralsp. 49
Quantitative Analysis of Oxidation Conditionsp. 50
Geochemical Changes of Trace Elementsp. 52
Rare Earth Probes of the Environmentp. 52
Trace Transition Metals in the Seap. 54
The Non-Uniform Seap. 57
Summary of Weathering from 3.5 Ga to 0.75 Gap. 58
Weathering and Chemical Conditions from 0.75 Gap. 60
Changes in Major Non-Redox Mineral Elements in the Sea from 0.54 Gap. 63
Carbon Isotopesp. 65
Oxygen Isotopesp. 66
Summary of Geological 'Inorganic' Chemistry Evolutionp. 67
A Note: The Relationship between Metal Structures in Organisms, Minerals and Chemicals Modelsp. 70
Referencesp. 71
Organism Development from the Fossil Record and the Chemistry of the Nature of Biominerals
Introductionp. 73
The Fossil Recordp. 75
Extinctionsp. 82
Types of Biomineralsp. 84
The Chemistry of Biominerals: The Handling of Inorganic Elementsp. 87
The Chemistry of Biominerals: Organic Components, Compositesp. 89
Shape of Organisms and Biominerals and Geneticsp. 91
Induced and Controlled Biomineralisation and Geneticsp. 92
Molecular Fossilsp. 94
Carbon and Carbon/Hydrogen Depositsp. 94
Sulfur Depositsp. 96
Conclusionsp. 96
Notep. 98
Referencesp. 98
Cells: Their Basic Organic Chemistry and their Environment
Introductionp. 100
The Proposed Beginnings of Life: Anaerobic Prokaryotesp. 104
Energy Transduction and usep. 105
Major Features of the Original Anaerobic Organic Chemistryp. 110
The Genome and the Proteome: Concentration Terms and Controls of Expressionp. 115
Differences between Anaerobic Cell Typesp. 119
Internal Structure of Prokaryotes and Production of New Proteinsp. 120
Prokaryote Cell Walls and Membranesp. 121
The Essence of the Chemistry of Anaerobic Lifep. 122
A Note on Prokaryote Diversityp. 125
Resources and the Coming of Oxygen: Micro-Aerobic and Aerobic Prokaryotesp. 125
The Single-Cell Eukaryotesp. 130
The Eukaryote Cell Nucleusp. 135
Filaments in Single-Cell Eukaryotesp. 137
Vesicles in Single-Cell Eukaryotesp. 137
Protection in Single-Cell Eukaryotesp. 138
Genetic Analysis of Unicellular Eukaryotes: Algae and Metazoansp. 139
Summary of the Evolution of Unicellular Eukaryotesp. 141
The Multicellular Eukaryotesp. 142
The Evolution of the Divisions in Space in Multicellular Organismsp. 146
Control of Growth and Shapesp. 147
Building Larger Structures: Internal and Extracellular Tissue Proteinsp. 148
The Evolution of Biominerals and their Associated Structuresp. 151
Extracellular Fluidsp. 152
Signalling with Organic Molecules and Electrolytic Gradients in Multicellular Eukaryotesp. 153
Genetic Analysis of Multicellular Animalsp. 155
Loss of Genes and Organism Collaboration: Internal and External Symbiosisp. 156
Summary of the Distinctive Features of Biological Organic Chemistryp. 157
Referencesp. 163
Other Major Elements in Organism Evolution
Introductionp. 166
Phosphorus in Cellsp. 168
Sulfur in Cellsp. 171
An Introduction to Magnesium, Calcium and Silicon Chemistry in Organismsp. 173
Magnesium in Cellsp. 174
Calcium in Organismsp. 175
Introduction to Signallingp. 177
Detailed Calcium Protein Signalling and its Evolution in Eukaryotesp. 180
Weaker Binding Sites in Vesiclesp. 187
Sodium/Potassium Messagesp. 188
The Evolution of Biomineralsp. 193
Calcium and Phosphates: Apatitep. 195
Silicap. 196
The Nature of the Matrices Supporting Mineralisation: Summaryp. 198
Conclusionsp. 199
Referencesp. 201
Trace Elements in the Evolution of Organisms and the Ecosystem
Introductionp. 203
The Chemistry of the Trace Elements
The Availability of the Trace Elementsp. 208
The Principles of Binding and Transfer of Trace Elements in Cellsp. 211
The Importance of Quantitative Binding Strengths and Exchange in Cellsp. 213
Examples of the Thermodynamic and Kinetic Limitations on Uptake of Metal Ionsp. 221
The Evolution of the Metalloproteins, the Metallosomes and their Functional Value
Introductionp. 223
The Evolution of the Metalloproteins of Prokaryotesp. 224
The Evolution of the Metalloproteins of Eukaryotesp. 227
Survey of the Evolving uses of Trace Elementsp. 230
Effects of Metal Ion Limitations and Excesses on Growthp. 241
The Value of Zinc and Cadmium: 'Carbonic Anhydrases'p. 242
The Special Case of Two Non-Metals: Selenium and Iodinep. 243
Conclusionsp. 244
Referencesp. 248
The Amalgamation of the Chemical and the Genetic Approaches to Evolution
A Summary of the Chemical Approach
Introductionp. 251
The Reasons for the Conditions of Earth Before Life Began and its Evolution: Equilibrium, Thermodynamics and Kinetic Limitationsp. 254
The Reasons for the Evolution of Organic Chemistry before Life Began: Kinetic and Energy Controlsp. 257
The Direct and Indirect, Deduced, Evidence for Evolution of the System: Environment and Organismsp. 261
Anaerobic Cellular Chemistry to 3.0 Gap. 263
The Oxidation of the Systemp. 264
Summary of the Evolution of the Oxidative Chemistry of the Elementsp. 266
Summary of Why the Chemistry of the Environment/Organism System Arose and Evolvedp. 270
Added Note on a Novel Genetic Analysis Related to Chemical Developmentp. 273
The Connections Between the Chemical, the Biological and the Genetic Approaches to Evolution
The Nature of Genes: Gains and Losses of Genes and Inheritancep. 274
DNA Gene Duplication: A Possible Resolution of the Problem of Gene/Environment Interactionp. 282
Epigenetics and the Mechanism of Duplicationp. 286
The Definition of Species and Symbiosisp. 288
Concluding Perspectives
Final Summary of Chemical Evolution with Reproductionp. 289
The Chemical System and Mankind Today and its Futurep. 299
A Note on Gaiap. 303
Referencesp. 305
Subject Indexp. 308
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