Evolution's Destiny

by Williams, R. J. P.; Rickaby, R. E. M.

• ISBN13: 9781849735582
• ISBN10: 1849735581
• Format: Hardcover
• Copyright: 2012-07-20
• Publisher: Royal Society of Chemistry

Summary

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

Glossary	p. xv
Abbreviations	p. xix
About the Authors	p. xxi
Outline of the Main Chemical Factors in Evolution
Introduction to the Chemistry of the Ecosystem	p. 1
The Involvement of the Elements in Evolution	p. 4
Equilibrium and Steady State Conditions	p. 10
Solubility	p. 14
Complex Ion Formation	p. 15
Standard Oxidation/Reduction Potentials	p. 17
Rate Controls and Catalysis	p. 20
The Dangers of Catalysis	p. 26
Diffusion	p. 27
Irreversibility, Chaos and Predictability	p. 28
Summary	p. 29
References	p. 31
Geological Evolution with Some Biological Intervention
Introduction	p. 32
Physical Evolution from the Earliest Times to Today	p. 33
The Value of Isotope Studies: Indicators of Chemical Changes and Geochemical Dates	p. 39
The Early Chemical Development of the Environment before 3.0 Ga	p. 40
Energy Capture and Surface Geochemical Changes: The Beginning of Organic Chemistry and Oxygen in the Atmosphere	p. 42
The Environment after 3.0 Ga: Revolution in Redox Chemistry before 0.54 Ga	p. 45
Sulfur Isotope Fractionation from 3.5 to 0.5 Ga; Dominance of Iron/Sulfur Buffering	p. 48
Evolving Mineral outputs from the Ocean: Further Evidence for Redox Chemistry before 0.54 Ga	p. 49
Banded Iron Formations and the State of Iron in Solution	p. 49
Uranium and Thorium Minerals	p. 49
Quantitative Analysis of Oxidation Conditions	p. 50
Geochemical Changes of Trace Elements	p. 52
Rare Earth Probes of the Environment	p. 52
Trace Transition Metals in the Sea	p. 54
The Non-Uniform Sea	p. 57
Summary of Weathering from 3.5 Ga to 0.75 Ga	p. 58
Weathering and Chemical Conditions from 0.75 Ga	p. 60
Changes in Major Non-Redox Mineral Elements in the Sea from 0.54 Ga	p. 63
Carbon Isotopes	p. 65
Oxygen Isotopes	p. 66
Summary of Geological 'Inorganic' Chemistry Evolution	p. 67
A Note: The Relationship between Metal Structures in Organisms, Minerals and Chemicals Models	p. 70
References	p. 71
Organism Development from the Fossil Record and the Chemistry of the Nature of Biominerals
Introduction	p. 73
The Fossil Record	p. 75
Extinctions	p. 82
Types of Biominerals	p. 84
The Chemistry of Biominerals: The Handling of Inorganic Elements	p. 87
The Chemistry of Biominerals: Organic Components, Composites	p. 89
Shape of Organisms and Biominerals and Genetics	p. 91
Induced and Controlled Biomineralisation and Genetics	p. 92
Molecular Fossils	p. 94
Carbon and Carbon/Hydrogen Deposits	p. 94
Sulfur Deposits	p. 96
Conclusions	p. 96
Note	p. 98
References	p. 98
Cells: Their Basic Organic Chemistry and their Environment
Introduction	p. 100
The Proposed Beginnings of Life: Anaerobic Prokaryotes	p. 104
Energy Transduction and use	p. 105
Major Features of the Original Anaerobic Organic Chemistry	p. 110
The Genome and the Proteome: Concentration Terms and Controls of Expression	p. 115
Differences between Anaerobic Cell Types	p. 119
Internal Structure of Prokaryotes and Production of New Proteins	p. 120
Prokaryote Cell Walls and Membranes	p. 121
The Essence of the Chemistry of Anaerobic Life	p. 122
A Note on Prokaryote Diversity	p. 125
Resources and the Coming of Oxygen: Micro-Aerobic and Aerobic Prokaryotes	p. 125
The Single-Cell Eukaryotes	p. 130
The Eukaryote Cell Nucleus	p. 135
Filaments in Single-Cell Eukaryotes	p. 137
Vesicles in Single-Cell Eukaryotes	p. 137
Protection in Single-Cell Eukaryotes	p. 138
Genetic Analysis of Unicellular Eukaryotes: Algae and Metazoans	p. 139
Summary of the Evolution of Unicellular Eukaryotes	p. 141
The Multicellular Eukaryotes	p. 142
The Evolution of the Divisions in Space in Multicellular Organisms	p. 146
Control of Growth and Shapes	p. 147
Building Larger Structures: Internal and Extracellular Tissue Proteins	p. 148
The Evolution of Biominerals and their Associated Structures	p. 151
Extracellular Fluids	p. 152
Signalling with Organic Molecules and Electrolytic Gradients in Multicellular Eukaryotes	p. 153
Genetic Analysis of Multicellular Animals	p. 155
Loss of Genes and Organism Collaboration: Internal and External Symbiosis	p. 156
Summary of the Distinctive Features of Biological Organic Chemistry	p. 157
References	p. 163
Other Major Elements in Organism Evolution
Introduction	p. 166
Phosphorus in Cells	p. 168
Sulfur in Cells	p. 171
An Introduction to Magnesium, Calcium and Silicon Chemistry in Organisms	p. 173
Magnesium in Cells	p. 174
Calcium in Organisms	p. 175
Introduction to Signalling	p. 177
Detailed Calcium Protein Signalling and its Evolution in Eukaryotes	p. 180
Weaker Binding Sites in Vesicles	p. 187
Sodium/Potassium Messages	p. 188
The Evolution of Biominerals	p. 193
Calcium and Phosphates: Apatite	p. 195
Silica	p. 196
The Nature of the Matrices Supporting Mineralisation: Summary	p. 198
Conclusions	p. 199
References	p. 201
Trace Elements in the Evolution of Organisms and the Ecosystem
Introduction	p. 203
The Chemistry of the Trace Elements
The Availability of the Trace Elements	p. 208
The Principles of Binding and Transfer of Trace Elements in Cells	p. 211
The Importance of Quantitative Binding Strengths and Exchange in Cells	p. 213
Examples of the Thermodynamic and Kinetic Limitations on Uptake of Metal Ions	p. 221
The Evolution of the Metalloproteins, the Metallosomes and their Functional Value
Introduction	p. 223
The Evolution of the Metalloproteins of Prokaryotes	p. 224
The Evolution of the Metalloproteins of Eukaryotes	p. 227
Survey of the Evolving uses of Trace Elements	p. 230
Effects of Metal Ion Limitations and Excesses on Growth	p. 241
The Value of Zinc and Cadmium: 'Carbonic Anhydrases'	p. 242
The Special Case of Two Non-Metals: Selenium and Iodine	p. 243
Conclusions	p. 244
References	p. 248
The Amalgamation of the Chemical and the Genetic Approaches to Evolution
A Summary of the Chemical Approach
Introduction	p. 251
The Reasons for the Conditions of Earth Before Life Began and its Evolution: Equilibrium, Thermodynamics and Kinetic Limitations	p. 254
The Reasons for the Evolution of Organic Chemistry before Life Began: Kinetic and Energy Controls	p. 257
The Direct and Indirect, Deduced, Evidence for Evolution of the System: Environment and Organisms	p. 261
Anaerobic Cellular Chemistry to 3.0 Ga	p. 263
The Oxidation of the System	p. 264
Summary of the Evolution of the Oxidative Chemistry of the Elements	p. 266
Summary of Why the Chemistry of the Environment/Organism System Arose and Evolved	p. 270
Added Note on a Novel Genetic Analysis Related to Chemical Development	p. 273
The Connections Between the Chemical, the Biological and the Genetic Approaches to Evolution
The Nature of Genes: Gains and Losses of Genes and Inheritance	p. 274
DNA Gene Duplication: A Possible Resolution of the Problem of Gene/Environment Interaction	p. 282
Epigenetics and the Mechanism of Duplication	p. 286
The Definition of Species and Symbiosis	p. 288
Concluding Perspectives
Final Summary of Chemical Evolution with Reproduction	p. 289
The Chemical System and Mankind Today and its Future	p. 299
A Note on Gaia	p. 303
References	p. 305
Subject Index	p. 308
Table of Contents provided by Ingram. All Rights Reserved.