* Provides a novel analysis of evolution in chemical terms
* Stresses Systems Biology
* Examines the connection between life and the environment, starting with the 'big bang' theory
* Reorientates the chemistry of life by emphasising the need to analyse the functions of 20 chemical elements in all organisms
Conventionally, evolution has always been described in terms of species. The Chemistry of Evolution takes a novel, not to say revolutionary, approach and examines the evolution of chemicals and the use and degradation of energy, coupled to the environment, as the drive behind it. The authors address the major changes of life from bacteria to man in a systematic and unavoidable sequence, reclassifying organisms as chemotypes. Written by the authors of the bestseller The Biological Chemistry of the Elements - The Inorganic Chemistry of Life (Oxford University Press, 1991), the clarity and precision of The Chemistry of Evolution plainly demonstrate that life is totally interactive with the environment. This exciting theory makes this work an essential addition to the academic and public library.* Provides a novel analysis of evolution in chemical terms* Stresses Systems Biology * Examines the connection between life and the environment, starting with the 'big bang' theory* Reorientates the chemistry of life by emphasising the need to analyse the functions of 20 chemical elements in all organisms
Cover 1
The Chemistry of Evolution 4
Acknowledgements 6
Preface 8
Contents 12
The Evolution of Earth–The Geochemical Partner of the Global Ecosystem (5 Billion Years of History) 14
Introduction 14
The Formation of the Atomic Elements: Abundances 15
Earth’s Physical Nature: Temperature and Pressure 17
Earth’s Atmosphere and Its Composition 20
The Initial Formation of Minerals 21
The Reforming of Solids from Melts: Minority Solids 25
The Settling Down of Earth’s Physical Nature 27
The Initial Formation of the Sea and Its Contents 28
Detailed Composition of the Original Sea: Availability 30
Geological Periods – Chemical and Fossil Records 34
Fissures in the Surface and Impacts of Meteorites 39
The Geochemical Effects of Oxygen 40
Conclusion 44
Further Reading 46
Basic Chemistry of the Ecosystem 48
Introduction* 49
Atoms and The Periodic Table 50
Inorganic Chemistry 54
Nature of Inorganic Chemical Compounds: Groups 1 to 3 and 12 to 17 54
The Nature of Transition Metal Compounds: Groups 4 to 11 57
Variable Combining Ratios and Spin States 60
Important Heavy Elements 63
Availability 64
Non-Equilibrated Inorganic Systems: Barriers to Change 65
Non-Equilibrium Inorganic Systems: Energy Storage 66
Reactions and Catalysis by Inorganic Environmental Compounds, Especially Sulfides 68
Summary of Inorganic Compounds Related to the Global Ecosystem 69
Organic Chemistry 70
Introduction to Organic Compounds of Ecological Relevance 70
Stability and Reactivity of Organic Chemicals 71
Stereochemistry 73
The Importance of Temperature and Light: Rates of Organic Reactions 75
Bringing Inorganic and Organic Chemistry Together 76
Introduction 76
Complex Formation: Selectivity 78
Matching Redox Potentials of Inorganic and Organic Chemicals 82
Electron and Proton Transfer 83
The Importance of Rates of Exchange 84
Selective Action of Metal Ion Complexes in Catalysis 85
The Special Nature of Hydrogen 87
Summary of the Basic Chemistry Relevant to Our Global Ecosystem 87
Further Reading 89
Energy, Order and Disorder, and Organised Systems 90
Introduction 90
Energy 91
Order and Disorder: Equilibrium 92
Some Steady States and Organisation 96
Radiation Energy: Calculating its Disorder and Amount of Flow 106
Optimal Rates of Energy Conversion and Optimal Retention of Energy in Cyclic Steady States: Content of a System 108
Shape of Organised Systems and Energy: Maintained Form 109
Evolution of a System going away from Equilibrium 111
Form and Information: Multiple Component Systems 116
Organisation and Compartments 118
Organisation Messengers Feedback and Codes 121
Energy Sources and Controlled Distribution of Energy 124
Information Defined 125
Cell Organisation, Equilibrium and Kinetic Constraints 128
Informed Cellular Systems 130
Ways of Looking at Ecological Chemical Systems: Summary 131
A Note on Equilibrium Thermodynamics and Equilibrium Constants 134
Further Reading 136
Outline of Biological Chemical Principles: Components, Pathways and Controls 138
Introduction 138
Organisms: Their Classification as Thermodynamic Chemotypes 140
Organisms: Their Generalised Element Content 144
The Functional Value of the Elements in Organisms: Introduction to Biological Compounds 150
Non-Metal Chemistry and its Basic Biological Pathways: Coding 151
Informed Systems of Organic Molecules 162
Pathways and Efficiency 166
Structures and Maintained Flow: Containment 167
The Selection of Coded Molecules: DNA(RNA) 169
RNA and the Possible RNA World 170
Proteins: Folding, Catalysts and Transcription Factors 173
Proteins: Biological Machines in Water 177
Proteins in Membranes 178
Summary of Non-Metal Functions in Cells 181
Why were Metal Ions Required? 183
Combining Metal and Non-Metal Chemistry: Structures and Activities 189
The Biological Properties of Hydrogen 190
Cell Organisation and Constraints: Equilibria 191
Kinetic Controls and Networks and their Energetics 192
Summary 194
The Magnitudes of Equilibrium Constraints in Cell Systems 196
Equilibrium Redox Potential Controls 199
Molecular Machines – Efficiency and Effectiveness 200
References to Appendix 4c 203
Further Reading 204
First Steps in Evolution of Prokaryotes: Anaerobic Chemotypes Four to Three Billion Years Ago 206
Introduction 206
First Steps: The Evolution of Prokaryotes: General Considerations of the Origins of Anaerobes 208
The Two Classes of Recognised Early Prokaryotes 210
The Introduction of Coenzymes: Optimalising Basic H, C, N, O, P Distribution 215
Primitive Metal Reaction Centres 219
Metal/Organic Cofactors 224
The Use of Light to Full Advantage 231
Manganese in Cells/Oxygen Evolution 233
The Molybdenum Cofactor, Moco 235
Early Uses of Zinc, Calcium, Vanadium and Sodium 236
Summary of Anaerobic Prokaryote Metabolism 237
Energy Flow in Anaerobes 238
The Polymers in Primitive Cells 240
Gene Responses in Prokaryotes 241
Satellite DNA: Plasmids 242
Prokaryote Controls 243
Internal Flows and General Movement: Sensing and Searching Chemotaxis 245
Conclusion: Anaerobic Chemotypes and their Development 246
Further Reading 249
The Evolution of Protoaerobic and Aerobic Prokaryote Chemotypes (Three to Two Billion Years Ago) 252
Introduction 252
The Beginning of an Aerobic Environment: Protoaerobic Bacteria 257
Protection of the Cytoplasm of Protoaerobes 259
Reduction of Environmental Oxidised Compounds of Non-Metals 260
The Employment of Metal Ions in Protoaerobes and the Special Cases of Molybdenum and Vanadium 264
The Direct Use of Oxygen: Aerobes 266
The Handling of Metals by Aerobes 272
Cytoplasmic and Membrane Organisation of Proteins 275
The Need for Extra Compartments 276
The Periplasmic Space and Oxidative Metabolism 277
Novel Forms of Control and Organisation: New Genetic Features of Aerobes 279
Summary of Prokaryote Development 281
Further Reading 287
Unicellular Eukaryotes Chemotypes (About One and a Half Billion Years Ago?) 290
Introduction 290
Plant, Animal and Fungal Eukaryotes and Interactions between them 295
Connections between Eukaryotes, their Compartments and Prokaryotes 296
The Organelles of Eukaryotes 299
The uses of Other Compartments: Further Separate Activities 301
Reproduction, Growth and Form 304
The Threat of Dioxygen : The Chemistry of Protection 305
Additional Distributions of Elements in Unicellular Eukaryote Compartments: the Eukaryote Metallome and the Advantages of Compartmentalised Oxygen Metabolism 307
The Proteome and the Metabolome 310
The Proteins for Metal Ions in Eukaryotes 312
Messengers in Single-Cell Eukaryotes 314
The Crucial Nature of the Calcium Ion 316
Minerals in Unicellular Plants and Animals and their Deposition 319
Gene Development in Eukaryotes 319
Mutual Dependence of Eukaryotes and Prokaryotes 323
Further Reading 325
Multi-Cellular Eukaryote Chemotypes (From One Billion Year Ago) 328
Introduction 328
The Morphological Nature of Multi-Cellular Eukaryotes 330
The Evolution of Multi-Cellular Plants 330
The Evolution of Multi-Cellular Fungi 336
The Evolution of Multi-Cellular Animals 337
Diversity within the Major Chemotypes 341
Growth of Plants and Animals from Single Cells 342
The General Chemical Changes in the Ecosystem Some one Billion Years Ago 344
The Chemical Changes of the Environment 344
Chemical Changes in Whole Multi-Cellular Organisms 346
Novel Proteins Associated with Multi-Cellular Organisms 348
New Functional uses of Elements: General Outline 350
The Use of Elements in Compartments and in Signalling 355
Growth and Differentiation 355
The Production of Chemical Messengers between Cells in Organs 358
Connective Tissues 364
A Further Note on Calcium 368
Light Switches in Plants and Animals 369
The Protection Systems of Plants and Animals 370
Changes in Genetic Structure 371
Degradation Activity and Apoptosis 372
Conclusion 373
Further Reading 375
The Evolution of Chemotypes with Nerves and a Brain (0.5 Billion Years Ago to Today) 378
Introduction 378
Senses 380
The Development of Nerves 382
The Brain 387
The Physical Evolution of the Brain 388
The Chemical Element Composition of the Brain 391
The Brain Development as an Information Store: The Human Phenotype 392
A Note on Animal Genes and Morphology 394
The Biological Chemotypes of the Ecosystem: A Summary 395
The Relationship between Plants, Fungi and Bacteria: A Summary 397
The Relationship between Plants and Animals 399
Energised Inorganic Elements and their Uses by the End of Biological Evolution 400
The Direction of Biological Evolution 402
Further Reading 403
Evolution due to Mankind: A Completely Novel Chemotype (Less than One Hundred Thousand Years Ago) 406
Introduction 406
The Nature of Homo Sapiens 409
The Evolution of Human Beings from 100,000 Years Ago 411
The Coming of Science 414
Mankind and the Detailed Use of Chemical Elements 416
Mankind, Energy and External Machines 419
Transport 421
Human Message Systems 422
Organisation and Mankind 423
The Development of Self-Consciousness 424
Human Genes 424
Summary 426
Note on Creation and Intelligent Design: Mankind’s Inventions 426
A Note on General Culture 426
Further Reading 427
Conclusion: The Inevitable Factors in Evolution 428
Introduction 428
The Darwinian Approach to Evolution 436
Genes and Darwin’s Proposals 438
The General Thermodynamic View of Ecosystem Evolution in this Book 439
The Chemical Sequence of the Environment 442
Chemicals and their Changes in Organisms: Chemotypes 444
The Continuous Gain in Use of Energy and its Degradation 447
The Changing Use of Space 448
The Changes in Organisation 449
Symbiosis: A Form of Compartmental Collaboration 452
Different Environmental Possibilities 453
Summary of Thermodynamic Chemical Approach to Evolution 455
Chemotypes and Genotypes 456
Mankind’s Industrialised Society 462
Mankind’s Interference with the Ecosystem 464
Reproducibility: Human Inheritance of Information 466
The Individual as a Problem 467
Summary and the Possible Future of the Ecosystem 469
A Note on Gaia 474
Further Reading 475
Index 478
Preface
R.J.P. Williams; J.J.R. Fraústo da Silva, Oxford and Lisbon, June 2005
Traditional attitudes to biological evolution were based on the examination of morphological and behavioural features of organisms. They led to the classification of “species” by scientists such as Linnaeus and later to the analysis of the relationship between species by Wallace and especially Charles Darwin. It is therefore of interest to note some of Darwin’s remarks which anticipate more recent developments. In “The Origin of Species (by means of natural selection)” Darwin presented his view that evolution of living organisms is a slow incremental process of natural selection among randomly occurring variations in descendants. In his opinion, the diversity of organisms, living and extinct, was the product of blind chance and struggle. However, he also wrote that “…natural selection depends on there being places in the polity of nature which can be better occupied by some of the inhabitants of the country undergoing modification of some kind. The existence of such places will often depend on the physical changes, which are generally very slow, but the action of natural selection will probably still oftener depend on some of the inhabitants becoming slowly modified, the mutual interaction of many of the other inhabitants being thus disturbed”. Therefore… “the greatest amount of life can be supported by great diversification of structure”. (See the Introduction by J.W. Burrow to the Origin of Species, Penguin Books, 1968.) Note that there is no mention of chemical change in the environment nor in life with time and there is no analysis of the sources and deployment of energy. Since Darwin’s days, this reductionist, organism centred, approach has changed considerably. Once the concept of “genes” was established the emphasis of the discussions on evolution shifted to a new dominant description – natural selection among randomly mutated pools of genes. The connection of these changes with changes of physical and biological organism surroundings was observed in line with Darwinian thinking. However, the effect of the surrounds of organisms on evolution was not deemed to be causative.
In the last half of the 20th century a different perspective on organism evolution emerged from ecological studies which have led to the more general concept of the “ecosystem”, involving not just the changes in biota, but also of the environment now treated interactively in general thermodynamic terms. It is becoming evident that the study of evolution of life must be centred on such systems rather than on individual organisms or species and their habitats. Fluxes of materials and energy became the new focus and management of the whole ecosystem was seen to require synergism, positive or negative, among organisms. The new approaches are still consistent with Darwin’s principle of the “natural selection of species”, but the emphasis has changed; it is the ecosystem that has evolved. However, the absence of chemical detail in systems treatments and the success and appeal of the limited chemistry within genetics and molecular biology have kept the two separate.
The weakness of this new approach is then that it pays no attention to the chemical components of the environment or of their fluxes employed by organisms. Such components are not just derived from “organic” elements – carbon, hydrogen, oxygen, nitrogen, and some sulfur and phosphorus and their compounds – but include many essential metals and some other non-metals (and their ions) with which they interact and without which life would not exist. The need, stressed in this book, is to take into account the major features of the life’s physical chemistry involving these essential elements, some 20, used free and in combination, by organisms, and thereby providing a detailed treatment of the ecosystem approach. To stress the nature of our approach we classify organisms not by morphology or genes, but by their chemical elements, their concentrations and those of the compounds they form, their energetics, the space they occupy and their organisation, all in flowing systems, that is by thermodynamic variables. We call these different groupings of organisms, chemotypes. The sequence in evolution is then seen to be directional in detailed physical–chemical differences between organisms in the order of their appearance: prokaryotes (anaerobic then aerobic), unicellular eukaryotes, multicellular eukaryotes, animals with brains and human beings, see cover 1. They differ in use of oxidised chemicals in particular, of energy capture, of size and shape, and of complexity of organisation. There are within each major chemotype sub-groups which are not yet well analysed. We show that the sequence is a natural directed consequence of the interaction between the energised organisms, and the environment because the environment changed in an inevitable way before organisms, which just adapted to the changes. Species are still seen as arising within chemotypes by Darwinian selection.
In order to show that the whole evolution of the ecosystem is in fact directional through the required physical/chemical chemistry of living and environmental processes, we have to describe first the known systematic changing oxidation of geochemicals of the surface of Earth over the 5 billion years of its existence, Chapter 1. The background of all this chemistry is the ability of the chemical elements to form compounds either in stable equilibrium or in kinetically long-lasting states (Chapter 2). The latter are largely organic compounds unavoidably energised by the sun and they, with a complement of concentrated inorganic elements, gave rise to life. This energisation of chemicals leads to unavoidable reactions of synthesis and decay so that the chemistry is within cycles enforced by the degradation of light to heat, that is the production of thermal entropy (Chapter 3). In Chapter 4, we give a general description of the basic special components, selected by energy and survival criteria which have come together through these energised cycles of available elements to engender life. They are a consequence of optimal energy flux. It will be seen that since life had to reduce environmental chemicals (CO and CO2) to make such chemicals it therefore increased the oxidation of the environment. It is the combination of an increasing uptake and degradation of energy (with a corresponding increase in thermal entropy generation) together with an unavoidable utilisation of more oxidised environmental chemicals (produced through the activity of organisms) that caused evolution of the ecosystem in the direction we observe. These cycles strain to be element neutral recycling all material while degrading energy, producing no pollution except heat. The sequence is described in Chapters 5–10 following that of the order of chemotypes listed above.
Our discussion indicates that, in the light of this clearly directional evolution, a reevaluation of the role and functioning of the genetic machinery (not just of the coded molecules, DNA, RNA, proteins) is necessary. How does chance mutation lead to directional change when DNA is both conservative and changes of its sequence are undeniably linked only to chance mutation? There is growing evidence of occurrence of the so-called “epigenetic” effects of various kinds, which can change the present views on how not only inherited but also environmentally directed acquisitions may be transmitted to the offspring. An added factor is that complexity of later organisms also makes it necessary for an efficient total system to rely on cooperation between later and more primitive, earlier, organisms including distribution of genes. Cooperation not competition has led to overall ecological fitness.
In this ecological system of organisms and the environment one species has developed a remarkable brain of such power that all evolution now depends upon it, namely Homo sapiens or mankind. Mankind is cognitive and has become a special chemotype able to handle all elements (90 no longer 20), all forms of energy in much of space and in a highly sophisticated organisation. Owing to its activity, organisation which started from being just inside organisms, linked to genetic change, has passed into the environment to create ‘abiotic’ novel forms, and can even adjust genes themselves, using brains. Although in an extreme form, this development is in line with the general evolution of chemotypes as they became increasingly interactive with the environment, this activity is not element neutral and produces pollution. From this position of strength mankind is now dominant and can affect the whole ecosystem, which includes itself, very quickly. The situation is made more difficult however by the development of the individual in this species, which relies on an isolated brain not genes for decision making. Use of scientific knowledge has increased the independence of the individual so that there is no longer overall communal control. The resultant conditions of the present ecosystem with a strong element of human self-interest are examined in the last chapter. Sooner or later, mankind has to see that it is a part of the ecosystem and cannot afford such a selfish individual or even a selfish communal lifestyle. Mankind must be educated to be able to manage and sustain a biological- and environmental- friendly ecosystem which has been inherited, otherwise selfish human activity could prove...
| Erscheint lt. Verlag | 29.11.2005 |
|---|---|
| Sprache | englisch |
| Themenwelt | Naturwissenschaften ► Biologie ► Biochemie |
| Naturwissenschaften ► Chemie ► Anorganische Chemie | |
| Naturwissenschaften ► Chemie ► Organische Chemie | |
| Naturwissenschaften ► Chemie ► Physikalische Chemie | |
| Naturwissenschaften ► Geowissenschaften ► Geologie | |
| Naturwissenschaften ► Physik / Astronomie ► Angewandte Physik | |
| Technik ► Maschinenbau | |
| ISBN-10 | 0-08-046052-6 / 0080460526 |
| ISBN-13 | 978-0-08-046052-9 / 9780080460529 |
| Haben Sie eine Frage zum Produkt? |
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