Table Of ContentPreface
Traditional attitudes to biological evolution were based on the examination of mor-
phological 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 evo-
lution of living organisms is a slow incremental process of natural selection among ran-
domly 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 phys-
ical 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 sur-
roundings 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 treat-
ments and the success and appeal of the limited chemistry within genetics and molec-
ular 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 com-
ponents are not just derived from "organic" elements- carbon, hydrogen, oxygen,
viii PREFACE
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 concentra-
tions and those of the compounds they form, their energetics, the space they occupy and
their organisafion, 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,
mulficellular 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 geo-
chemicals 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 energi-
sation 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 pro-
duction 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 envi-
ronmental 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 degra-
dation 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 mate-
rial 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 re-
evaluation 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
PREFACE ix
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 devel-
oped 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 envi-
ronment 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 evo-
lution 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 deci-
sion making. Use of scientific knowledge has increased the independence of the indi-
vidual 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 self-destructive though evolution will continue. This education, which we hope
this book will provide, will need to generate a different political will in the manage-
ment of our science-based society. It will require scientists not only to teach the nature
of ecological systems, but to become political since only they have the necessary
knowledge to advise. Mankind has now the power to maintain, perhaps to advance, its
inheritance but that will require careful limitation of exploitation of the ecosystem.
We stress that in this book we follow certain earlier views on evolution while we
remove any religious undertones. For example the essence of Descartes' thinking is as
follows: If in the beginning the world had been given only the form of chaos (we
replace chaos by the Big Bang) and provided the laws of nature were then established
all material things could in the course of time come to be just as we see them. In this
approach and in our book there are no acts of creation other than the Big Bang and
there is no need for intelligent design, except for the laws of nature.
R.J.P. WILLIAMS
J.J.R. FRAI~ISTO DA SILVA
Oxford and Lisbon, June 2005
stnemegdelwonkcA
Our special thanks go to Mrs. Susie Compton who has managed the whole manuscript
and the authors.
R.J.P. Williams acknowledges the continued support of the Inorganic Chemistry
Laboratory, Oxford University and in his career of Wadham College, Oxford and of
The Royal Society.
J.J.R. Frafsto da Silva acknowledges the Foundation for Science and Technology,
Ministry for Science and Technology Portugal, for general support of research activi-
ties. Special thanks are due to Dr. Marina Fratisto da Silva and Eng. Jos6 Nascimento
for the reproduction and redrawing of most figures of the book, and to Mrs. Teresa
Maria Carreiras da Silva and Miss Cristina Sequeira da Silva for proficient secretarial
assistance and concomitant considerable patience.
CHAPTER 1
The Evolution of Earth-The Geochemical Partner of the
Global Ecosystem (5 Billion Years of History)
1.1. INTRODUCTION .......................................................... 1
1.2. THE FORMATION OF THE ATOMIC ELEMENTS: ABUNDANCES .......................... 2
1.3. EARTH'S PHYSICAL NATURE: TEMPERATURE AND PRESSURE ........................... 4
1.4. EARTH'S ATMOSPHERE AND ITS COMPOSITION .................................... 7
1.5. THE INITIAL FORMATION OF MINERALS ........................................ 8
1.6. THE REFORMING OF SOLIDS FROM MELTS: MINORITY SOLIDS ....................... 12
1.7. THE SETTLING DOWN OF EARTH'S PHYSICAL NATURE .............................. 14
1.8. THE INITIAL FORMATION OF THE SEA AND ITS CONTENTS .......................... 15
1.9. DETAILED COMPOSITION OF THE ORIGINAL SEA: AVAILABILITY ...................... 17
1.10. GEOLOGICAL PERIODS -- CHEMICAL AND FOSSIL RECORDS ........................... 21
1.11. FISSURES IN THE SURFACE AND IMPACTS OF METEORITES ............................ 26
1.12. THE GEOCHEMICAL EFFECTS OF OXYGEN ....................................... 27
1.13. CONCLUSION ........................................................... 31
FURTHER READING ........................................................... 33
1.1. Introduction
This book concerns the Earth's evolving ecology, where ecology is defined by the
study of the relationship between organisms and their physical and chemical sur-
roundings. We begin with an account of geological chemistry starting from the Big
Bang, which created the first light chemical elements, especially hydrogen and
helium, from which in order stars, e.g. the Sun, and planets, including the Earth,
were formed. At the same time, this event generated the very uneven distribution of
energy, including that of the Sun, which is the major source of the energy for bio-
logical chemistry on Earth. A main intention of the book is then to show that when
our planetary system formed, less than 5 billion years ago, the chemical element
content of the Earth and the forms in which the elements occurred, described in
Chapter 2, imposed gross restrictions on whatever chemistry, biological or other,
could develop on its surface before mankind appeared. These restrictions are mainly
due to the availability of chemicals in the atmosphere and surface waters, which
have access to the Sun's energy. The understanding of the possibilities of this chem-
istry has come with the development of studies of elements and compounds largely
in the last 200 years (Chapter 2). Given the background of geological chemistry and
our more general understanding of what are called inorganic and organic
chemistries we can proceed to consider ways in which chemical systems such as we
2 The Chemistry of Evolution
see in primitive life could have been energised. In Chapters 3 and 4 we introduce
the global ecological system for it is not just biological chemistry that must be
examined when we consider such evolution; we must remember that the geological
chemistry of Earth's surface changed when life developed waste, mainly oxygen
gas. The new energised surface chemicals then back-reacted with the biological sys-
tem and forced it to change. The whole of the geosphere, hydrosphere, atmosphere
and biosphere is seen to be one large chemical system evolving in a strictly
restrained chemical fashion (Chapters 5-9). Throughout these chapters we stress
strongly the role of the chemical elements, rather than particular types of compound,
e.g. DNA or proteins, in evolution since in this way we knit together the chemistry
of the Earth's mineral surface and life. In Chapter 10, we will consider the influence
of mankind on the ecosystem and then in Chapter 11, we shall bring all the previ-
ous developments together. In order to present this ecological system in a manage-
able way we describe separately in this chapter the initial state of Earth and then
how oxygen, no matter what was its source (we know it was due to organisms),
changed Earth's surface chemistry in the atmosphere and waters. This allows us to
describe the more striking evolution of organisms in Chapters 5-9, the principles of
the chemistry and biochemistry having been described in Chapters 2-4, with refer-
ence to its dependence upon the environment at different times, see cover picture.
1.2. The Formation of the Atomic Elements" Abundances
Whatever the nature of the ecosystem, it has to be based on the chemical ele-
ments on Earth. Our first task then is to describe what they are and where they are
to be found. We begin with an outline of their formation (see EA. Cox in Further
Reading). The chemical elements were formed in giant stars by successive thermo-
nuclear fusion followed by other secondary processes - neutron and proton cap-
ture. The amounts of the different elements that were synthesised were controlled
by the rates of reactions of the nuclei starting from hydrogen and helium, the light-
est of the elements, which originated from the Big Bang some 13.7 x 901 years ago.
These two elements were and have remained of very high abundance in the uni-
verse (a total of about 99%) showing that subsequent nuclear reactions used only
a small fraction of them and have not been completed. The reactions in giant stars,
followed by the explosion of these stars when the state of supernovae was reached,
gave rise to heavier elements up to the radioactive and unstable nuclei, which fin-
ish at the nuclear stability limit, the element uranium. Scientists have investigated
many of these nuclear reactions and have created even heavier radioactive elements
in very small amounts (see Chapter 10). The explosive reactions in the giant stars
produced a well-defined pattern of abundances of elements of intermediate size
between helium and uranium, shown in Figure 1.1. The elements lithium, beryl-
lium and boron did not accumulate in large amounts due to the kinetics of nuclear
reactions in the giant stars, so that the next most abundant elements in the universe
after hydrogen and helium are carbon, nitrogen and oxygen. Abundance then
The Evolution of Earth 3
11 c~ o odd atomic numbers
10 e---e even atomic numbers
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5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90 95
Atomic number, Z
FIG. 1.1. Relative abundances of the 'unchangeable' elements in the universe (based on log
(abundance of Si) - 6). Filled circles (-), even atomic numbers; open circles ((cid:14)9 odd atomic
numbers. ('Unchangeable' refers here to atoms of elements. Thus we ignore, for the purposes of
this book, any transmutation of elements.)
decreases somewhat irregularly until above atomic weight 50, i.e. around atomic
number 25. The appearance around this atomic weight of a few elements in high
abundance, such as iron and nickel, is due to the special stability of their nuclei.
After iron, abundance decreases to very low levels at atomic weight of uranium.
Note that elements of odd atomic number are less common, hence there is more
iron and nickel than there is cobalt, and more carbon and oxygen than nitrogen. We
believe all these facts to be important in the evolution of Earth and life. The abun-
dance of all the elements is now well understood in terms of nuclear reaction the-
ory of processes in giant stars (see EA. Cox in Further Reading).
It is believed that our small star, the Sun, was formed by gravitational attraction
of the dust of the exploded giant stars giving the distribution of elements shown in
Figure 1.1 at a very high temperature. Probably, a nearby interaction with another
passing star generated a great plume of solar nebula extending billions of miles
away from the Sun's central hot mass. Cooling of this plume led to the formation
