Bringing Chemistry to Life From Matter to Man

by Williams, R. J. P.; Fraústo da Silva, J. J. R.

• ISBN13: 9780198505464
• ISBN10: 0198505469
• Edition: 1st
• Format: Hardcover
• Copyright: 2000-02-24
• Publisher: OXFORD UNIVERSITY PRESS

Summary

In this book the authors describe the long journey from formless inanimate matter to man, while explaining the nature and the logic of the physical-chemical processes involved, and stressing the limitations of reductionist analyses of these processes as complexity increases and novelproperties emerge. In particular the authors develop the idea that it was chemical change of the environment that allowed evolution of life to occur and that this evolution required successive addition of new message systems and information codes connected, compatible, and cooperative with previousextant systems. To do this the authors analyse the relationship between chemical element content and speciation both in inanimate and living systems in terms of fundamental units and variables, or composite (derived) units and variables. Through such analyses the authors conclude that chemicalspeciation is very much a matter of chemical cooperativity (order versus disorder) while biological speciation requires cooperative flow of chemicals and energy (organisation versus disorder). They argue that chance mutations of DNA are far too simple to provide a basis for evolution and biologicaldiversity, though it is a representation of such diversity. It is the survival strength of systems of molecular machinery which separate and generate living species. In the final chapter they analyse the effect of man's activities on the present global and local ecosystems and speculate on thepossible nature of the emergent properties to be expected from an ever-increasing complexity of information-based modern societies.

Author Biography

J. J. R. Frausto Da Silva is Professor of Analytical Chemistry, Instituto Superior Tecnico, Universidade Tecnica de Lisboa.

Table of Contents

Units of energy and work and the values of some physical constants	xxi
The development of man's ideas concerning nature	1	(22)
The early views	1	(5)
The development of modern views	6	(5)
The periodic table	11	(8)
The abundance of elements in the universe	19	(2)
Summary	21	(2)
Forces and related energies	23	(35)
Introduction	23	(2)
Gravitational and electrical forces and fields	25	(4)
The capacity to do work: energy	29	(6)
Repulsion at very short (contact) distances: sizes of objects	31	(1)
The directional kinetic energy of masses	32	(3)
Chemical potential energy: components	35	(3)
Components as variables of composition	36	(2)
Additional energy forms and their interconversion	38	(12)
Conversion of chemical and mechanical potential energy and directed motion to random motion (thermal energy)	39	(4)
Heat and heat transfer by convection or conduction	43	(1)
Temperature, pressure and volume: pV energy	44	(2)
The kinetic theory of gases	46	(1)
The derived variables of systems	47	(1)
Chemical energy transfer into thermal energy (heat) and mechanical energy	47	(3)
Fire and radiant energy transfer	50	(5)
The variety of radiation	51	(1)
Temperature and radiation	52	(2)
Gravitational force, nuclear fusion and radiant energy	54	(1)
Summary	55	(3)
Electrons in atoms and their energetics	58	(29)
Introduction	58	(1)
The basis of the structure of the periodic table	59	(9)
The breaking of the atom	59	(1)
Classical models of the structure of atoms	60	(2)
Quantum models of the structure of atoms	62	(6)
The wave-mechanical model	68	(4)
Properties of atoms	72	(11)
Sizes of atoms	72	(3)
The exclusion principle: a new repulsion	75	(1)
Ionisation energies	76	(1)
Electron affinity energies, electronegativity, atomic combinations and components	77	(2)
Bonds	79	(1)
Atoms and ions in fields (polarisability and shapes of molecules)	79	(2)
Oxidation states	81	(2)
The energy states of atoms and atomic systems	83	(1)
Summary	84	(3)
Ordering and stability of atom and component associations	87	(29)
Introduction	87	(2)
Element combinations: qualitative analysis of binding energies and structures	89	(7)
Packing of atoms, ions and molecules	96	(3)
An aside: the value of hydrogen bonding	99	(1)
Quantitative strengths of binding	100	(2)
Stoichiometric and non-stoichiometric composition	102	(2)
Examples of phases of continuously variable composition	104	(3)
Mixed bond types in larger molecular assemblies	107	(2)
Structural isomerism	109	(1)
Order and information: properties of linear assemblies	110	(1)
Chemical speciation	110	(1)
Co-operativity and potential energy in crystal lattices: a question of mathematical linearity	111	(2)
Summary	113	(3)
The balance between order and disorder	116	(47)
Introduction	116	(4)
Systems, change and variables (functions) of state	120	(4)
Thermodynamic variables of state of bulk multi-particle systems: introduction to work	121	(1)
Thermodynamic systems: definitions	121	(3)
The physical states of bulk matter: a qualitative statistical approach to volume (pressure) and temperature	124	(3)
Order-disorder balance (equilibria)	127	(6)
Quantitative considerations of disorder	128	(3)
Irreversibility of changes: the `hidden' (dispersed) energy	131	(2)
The complete list of thermodynamic variables (functions) of states of bulk systems	133	(2)
Available (free) energy	135	(4)
Expansion and cooling in an isolated system	139	(1)
Physical States in balance	139	(9)
Latent heats and physical states of substances	139	(5)
Real systems: van der Waals equation, changes of state and complexity	144	(2)
Mixing of substances in one phase	146	(1)
Limitations on variables (phase rules)	147	(1)
Thermodynamics of polymeric molecules	147	(1)
Chemical systems in balance (equilibria)	148	(4)
The relationship between non-stoichiometric substances and temperature	151	(1)
Mixing and stoichiometry: chemical speciation and free energy considerations	152	(3)
Free energies and stationary states (components)	155	(3)
The nature of organic chemicals	155	(2)
Components and equilibria	157	(1)
Predictability of properties: chaotic systems and the interdependence of variables	158	(2)
Summary	160	(3)
Dilute solutions and order-disorder balance	163	(31)
Introduction	163	(1)
Ideal solutions	164	(1)
Water as a solvent	165	(2)
General considerations of solubility in other solvents	167	(2)
Quantitative treatment of solubility: precipitation and solubility products	169	(3)
Combination of species in solution: complex speciation and stability constants	172	(2)
Competitive affinity between metal ions and non-mental compounds in solution	174	(2)
Competition at equilibrium in solution	176	(1)
The binding together of organic molecules: self-assembly in solution	177	(1)
Partition of species between immiscible solvents	178	(1)
Species, equilibria and variables	179	(1)
Shapes of molecular species in solution	180	(2)
Oxidation-reduction equilibria in solution and electrochemistry	182	(6)
Redox potentials of complex species	184	(1)
Oxidation state diagrams	185	(3)
The conditions controlling redox potentials in solution	188	(2)
The speciation of elements in sea	190	(1)
Restrictions on availability	190	(2)
Conclusions	192	(2)
Systems with boundaries: compartments	194	(20)
Introduction	194	(2)
Shaped objects	196	(1)
Size and shape	197	(1)
The environment of a system and its shape	198	(1)
The shapes of crystals of particular substances	199	(1)
The shapes of folded polymers	199	(5)
The curious nature of biological structures	204	(1)
Composites and their shapes	204	(1)
Fatty acids and lipids: shapes of liquid crystals and their co-acervates	205	(1)
Local balance and physical fields	206	(1)
Osmotic pressure and electric potential differences between compartments	207	(4)
The nature of physical traps	211	(1)
Summary of variables of compartments and fields	211	(3)
Change and its control	214	(45)
Introduction to time and flow	215	(3)
Barriers to change	218	(2)
Variables affecting rates physical and chemical material change	220	(3)
Rate control by physical barriers	223	(7)
Selective pathways through physical barriers	223	(1)
Ion or molecule selective pathways through physical barriers	224	(1)
Electron pathways: conduction in a matrix	225	(1)
Pahtways for photons (light) in a matrix	226	(1)
Feedback control of physical pathways	226	(2)
Uphill physical transfer	228	(1)
Conclusion to physical flow in a chemical system	229	(1)
Nuclear barriers	229	(1)
Chemical bond barriers: equilibrium, stationary states and flow	230	(6)
Selection of chemical pathways by reactivity controls: catalysts	231	(1)
Solvent constraints on reactions: reactivity in water	232	(1)
Barriers to hydrolytic reactions	233	(2)
Oxidation and reduction	235	(1)
Barriers to oxidation and reduction	235	(1)
Organic reactions and energy requirements	236	(7)
The removal of water in synthesis: condensation	238	(1)
Chemical speciation in aqueous reactions	238	(1)
Control of organic reactions: a summary of single pathways	239	(1)
Steady states of chemical change: feedback control in single pathways	240	(1)
Rates of chemical reactions in physical flow systems	241	(1)
Effects of temperature on feedback	242	(1)
Energy and its distribution	243	(2)
Feedback control over energy in chemical pathways	243	(1)
Radiation flow (fire) and overall free energy flow of life	244	(1)
Conclusion to physical, chemical and energy flows	245	(1)
Functional significance	245	(3)
Feedback in concerted chemical reaction pathways	247	(1)
Biological chemical pathways and coupling to bulk spatial constraints	248	(1)
Cooperative kinetics: patterns and dissipative systems	248	(2)
Chemicals and self-assembly of equipment	250	(1)
Dynamic shape	251	(1)
Connected shapes and functional value for change: machines	252	(2)
Control over machines: information and instructions	254	(1)
Developing systems	254	(1)
Summary: the units and variables of flow systems and their restrictions	255	(4)
The evolution of Earth	259	(29)
Introduction	259	(4)
The Primitive atmosphere	263	(2)
The nature of the early sea	265	(2)
The surface of the early Earth	267	(2)
Some early non-equilibrated inorganic Compartments of interest: an aside	269	(3)
The atmosphere today	272	(1)
The nature of the sea today	273	(4)
The nature of fresh water today	275	(2)
The nature of the crust today	277	(1)
The nature of soils and soil water	278	(1)
The evolution of Earth's land: summary	279	(1)
The rate of change of element distribution	279	(3)
Dioxygen	281	(1)
Sulphur and selenium	281	(1)
The oxides of nitrogen	281	(1)
Abiotic and biotic organic compounds	282	(1)
Mineral elements	282	(1)
Clays and sulphides: origins of early life?	282	(2)
Units and variables in the evolution of Earth's chemistry	284	(1)
The resulting steady state today: Gaia?	285	(3)
The principles of the chemistry of living systems	288	(45)
Introduction	289	(3)
The atomic elements of life	292	(1)
The link to availability of elements	293	(1)
The chemicals in organisms	293	(6)
Water and organic compounds	293	(3)
Mineral elements in organisms	296	(3)
Observed limitations on cellular `component' composition	299	(3)
Required cellular control	302	(2)
Free energy sources: the capability of cells to do work	304	(1)
The capture of energy by cells	305	(6)
Molecular machines for energy transduction	307	(2)
The anaerobic conversion of sugar to give energy	309	(2)
Communication systems	311	(3)
Networks using the electron: model's in man's equipment	311	(1)
Feedback pathway control in organisms	312	(1)
Networks using messengers other than organic molecules	313	(1)
Conversion of messages to actions	314	(1)
The functional capability of elements	314	(1)
Complex molecular structures within cells	315	(2)
The need for a control code (DNA/RNA): inherited information	317	(1)
The disposition in space of ions and molecules: compartmental control	318	(1)
External shapes of organisms	319	(2)
Internal shapes of cells	320	(1)
Growth, reproduction, development and evolution	321	(1)
Cycles of reactions and cells cycles	321	(1)
Growth and the cell cycle	321	(1)
Development	322	(1)
Speciation amongst living systems: evolution	323	(1)
Units and variables in biological steady-state organisation	324	(1)
Are there `components' in living organisms?	325	(3)
Linear and non-linear systems	328	(1)
Conclusions	329	(4)
Early life: anaerobic prokaryotes	333	(30)
Introduction	333	(2)
The earliest cells	335	(3)
The earliest available elements and their uptake	338	(1)
Functions of elements in primitive life	338	(4)
Primitive energy sources	342	(3)
The use of thio-acids and thiols: redox buffering	345	(2)
Sulphate-using bacteria	346	(1)
Early electronic devices for energy capture: the use of iron/sulphur compounds	347	(1)
Remarkable early enzymes: catalysts in anaerobes	348	(2)
Structural organisation in primitive cells	350	(1)
Dynamic chemical organisation in early cells	350	(4)
Protein production: transcription and translation	350	(2)
The early chemical messengers and protein activity controls	352	(2)
The prokaryote cell cycle	354	(1)
Differentiation of prokaryotes	355	(1)
Sporulation	356	(1)
Mutation and evolution	357	(1)
Prokaryote speciation: variability	357	(1)
The beginnings of life and reproduction: a speculative approach	358	(2)
Units and variables in primitive cellular organisation	360	(3)
The development of anaerobic organisation: from prokaryotes to eukaryotes	363	(22)
Introduction	363	(1)
Compartmental changes	364	(5)
The value of extra compartments	369	(2)
The development of internal filaments and shape	371	(1)
Changes in organisation and communication	371	(2)
The major new messenger: calcium ions	373	(1)
Calcium ions and signalling	374	(2)
Other activities in vesicles and organelles	376	(1)
The structure of the new vesicular compartments	377	(1)
Difficulties of many compartments	377	(1)
Folding and positioning of proteins	378	(1)
The extracellular matrices of eukaryotes	378	(1)
Mineralisation of eukaryotes	379	(1)
Lifetimes of eukaryotes	380	(1)
Environmental change	380	(1)
The variables of eukaryotes	381	(1)
Speciation	382	(1)
Summary	383	(2)
The coming of dioxygen: unicellular organisms	385	(27)
Introduction	385	(2)
Changes in redox chemistry	387	(2)
The photochemistry of water	389	(1)
The possible new aerobic biological chemistry in prokaryotes	389	(7)
The first direct uses of dioxygen in prokaryotes	393	(3)
Catalysts of aerobic prokaryotes	396	(1)
The outer (periplasmic) space of bacteria	397	(2)
The eukaryote cell and dioxygen	399	(2)
Changes in plasma membranes	401	(1)
New signalling in eukaryotes	401	(2)
The value of zinc in aerobic metabolism	403	(1)
The value of copper in eukaryotes	404	(1)
Changes in non-metals	405	(4)
Mineralisation and rejection of elements	409	(1)
Summary	409	(3)
The coming of multicellular organisms	412	(40)
Introduction	412	(4)
Element distribution in Extracellular fluids	416	(1)
Outline structure of plants and their elements distributions in organs	417	(2)
Outline structure of animals and their element distributions in organs	419	(2)
The extracellular matrices of plants and animals	421	(4)
Cell-cell messenger systems	425	(4)
Dioxygen, multicellular organisms and new metabolic products: summary	429	(2)
New receptor systems: zinc-finger proteins	431	(2)
Interdependence of new and old pathways	433	(2)
Intracellular vesicular transfer	435	(1)
Elements falling into disfavour	436	(1)
Internal risks for multicellular organisms	436	(4)
Risks of, and protection from, dioxygen reactions	438	(1)
Risk of invasion by lower organisms: sensing self and protection	439	(1)
Growth and development patterns	440	(2)
Shapes and multicellular life	441	(1)
Cell death: apoptosis	442	(1)
Summary of multicellular organisation	442	(1)
The variety of multicellular life	443	(1)
Variables of multicellular organisms: increased complexity	444	(2)
Survival and environmental fluctuations	446	(1)
Analogies between static and dynamic changes of state	447	(2)
Summary	449	(3)
The evolution of man and his chemistry	452	(30)
Introduction	452	(2)
The evolution of the brain	454	(5)
The brain, DNA and information	459	(3)
Special chemical features of the brain	462	(2)
Nerves and brain functions	464	(2)
Classical experience and modern science	466	(1)
Man's purposeful chemistry and physics	466	(2)
The use of energy in inorganic or mineral chemistry	468	(2)
Machinery and energy	470	(1)
Organic chemistry and medicine: the development of protection	470	(2)
Elements and chemicals in the diet and in medicine	472	(1)
Genetic engineering	473	(1)
Industrial Organisation	474	(2)
The essence of industry	476	(2)
Summary of the nature of man and his activities	478	(4)
Survey and conclusions	482	(41)
Introduction	482	(2)
From Fundamental to derived and operational variables of unchanging systems	484	(7)
The capacity for change	491	(3)
Linear and non-linear systems: the mathematical consequences of descriptions in terms of bulk derived rather than fundamental particle variables	494	(1)
Variables applicable to single polymeric molecules	495	(1)
Rate of change	495	(3)
Living systems: patterns of activity and pathways	498	(3)
Selection of materials in living systems	501	(3)
Creation of lipids and polymers	501	(1)
Selection of elements	502	(2)
Feedback control	504	(2)
Self-organisation and DNA	506	(1)
Information in living systems: DNA	506	(5)
Landscape diagrams of survival strength	511	(1)
Survival strategies and evolution of complexity	512	(2)
Environmental changes and DNA response	512	(2)
Further evolution of complexity	514	(1)
The brain: a second code	514	(2)
Mankind's activities	516	(2)
The computer: a new external code	517	(1)
Survival strength of mankind: species and individuals	518	(1)
Subjectivity and objectivity	518	(3)
The evolution of society: a new organisation	520	(1)
Conclusion	521	(2)
Further reading	523	(14)
Index	537