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Evolution's Destiny
Co-evolving Chemistry of the Environment and Life
By R. J. P. Williams, R. E. M. Rickaby The Royal Society of Chemistry
Copyright © 2012 R. J. P. Williams and R. E. M. Rickaby
All rights reserved.
ISBN: 978-1-84973-558-2
CHAPTER 1
Outline of the Main Chemical Factors in Evolution
1.1 Introduction to the Chemistry of the Ecosystem
This chapter contains a general introduction to the multidisciplinary subject that includes chemistry, geochemistry, biochemistry and biology of the evolution of and on Earth, i.e. both the environment and its organisms. The book does depend heavily on chemistry so we give an outline of the principles of chemistry in this chapter for a reader who is not familiar with it as a discipline. Chemists may wish to skip quickly over Sections 1.2 to 1.6. In the minds of most scientists the evolution of organisms is based solely on organic chemicals, which quantitatively form by far the largest part of all living systems. In the book we wish to explore an additional part of this evolution, which in the first instance seems to be of little relevance to that of organisms. We refer to the early presence and the evolution of the inorganic surface of Earth, i.e. the atmospheric gases, the minerals and their solutions, mainly in the sea which, together, have formed the later changing environment for life. Here we consider these two parts of evolution, inorganic and organic, to be interacting in a common ecosystem. We will show that a major feature of life and its evolution, in addition to developing organic chemistry, is a changing availability and adopted essential use of selected inorganic chemical elements from this environment in cells. Many of these chemicals were dissolved from their minerals into solution (Table 1.1), increasingly by weathering, and then were taken into the cells of organisms. (A cell can be looked upon as an enclosed volume of space, in part permeable to particular chemicals.) Eventually these chemicals were returned to the environment, frequently in a transformed state. These elements perform one essential role in cellular catalysis – they are required to activate the small molecules, such as H2O, H2 and O2, and those in some organic metabolic cellular chemical reactions. The need for them follows from the fact that, although all organic chemicals are thermodynamically unstable relative to stable CO2, especially in the presence of the small molecules H2O and O2, they are generally kinetically quite stable at 20 °C. (Virtually all organic chemicals are kinetically unstable at >150 °C, particularly to hydrolysis and oxidation, implying that life has a restricted temperature range, that of liquid water, say from -10° to 150 °C.) At low temperature, 20 °C, they require energy input and catalysed activation in order to bring about synthesis, as well as catalysts for degradation. Therefore both energy and catalysts were required to activate organic chemicals before there could be any coded cellular chemistry, which we call life. The major catalytic inorganic ions are frequently strongly bound and of moderate or slow exchange rate in molecules. They are absolutely required. The essential role of other inorganic elements, which are poor catalysts, lies in their much weaker binding and fast exchange. These properties and the larger available quantities of these elements in the sea make them irreplaceable both in the management of osmotic and electrical balance of cells and in fast transfer of information, i.e. in message transmission necessary for balance between the several restricted paths of organic chemical change in cells. Later their fast transfer from outside to inside cells enabled organisms to respond quickly to rapid changes in their environment. The advantage of the exchange of some trace catalytic elements extended to their use in maintaining metabolic homeostasis inside cells. They also acted as controls of genetic expression in transcription factors.
A special chemical interest will be in the controlled biominerals (Table 1.2), produced by, even in, many organisms and giving rise to fossils, as well as those made by their decomposition as deposits on the surface of Earth after death, e.g. the White Cliffs of Dover in the south of England and the grains of some deserts, called diatomaceous earth. All these features of fossil and general biochemistry provide firm evidence of the coupled evolution of life with that of the surface of the Earth. We shall be led to propose that as well as the Darwinian random search amongst species of organisms for those of greatest survival value, associated with the small advantages of certain of them under given slowly changing environmental conditions, there was and is a systematic larger-scale evolution dependent upon the opportunities which the large-scale evolving chemical element environment provided. It is, we believe, this strong and faster environmental development, in a given chemical direction, that guided the way to today's organisms in a systematic, overall much slower, chemical evolution. However, the increasing complexity ruled out the possibility that they could manage it all, especially the novel oxidation chemistry and the original reductive chemistry in one compartment. As stress increased from oxidation it became necessary to produce different types of prokaryotes, bacteria, and in succession multicompartment then also multicellular organisms and mutually dependent organisms (symbiosis). Many of their evolving changes are seen in the inorganic chemical content of different organisms.
A particular problem we wish to tackle then is the changing role of the inorganic elements both in solution and in minerals in the evolution of the ecosystem. We shall observe that it is the waste by-products of the cellular organic chemistry, particularly oxygen, which initiated relatively quickly the major changes in environmental inorganic chemistry. The timing of the changes depended on their redox potential. We shall then show that it is the back-reaction of these changes which in turn affected the evolution of organisms. The two are in an interactive feedback system. In summary we have to examine the evolution of environmental and cellular inorganic with that of cellular organic/ inorganic chemistry. In doing so it is extremely helpful to follow initially the geological (inorganic) chemical record of all the minerals, especially that of sediments and their impurities. The minerals include fossils, the most clear-cut evidence of organism evolution available (see Chapter 3). To do so we divide the surface minerals of Earth into four classes. (i) Minerals formed without any intervention of solution or biological activity, for example on the solidification of melts, magma. (ii) Mineral sediments, formed later by weathering of rocks (see Table 1.1). (iii) Minerals which have arisen from chemical transformations of elements in the sea and where it is release of chemicals from organisms, e.g. oxygen, which have caused their transformation such as oxidation of iron, giving Fe3O4 and Fe2O3 precipitates, and oxidation of sulfide to precipitated sulfur or released soluble sulfate and to release trace elements (see Table 1.1). With those chemicals from weathering, they gave the trace elements typical of the sea at a given time. (iv) Biominerals where the mineral remains attached to the cell surface or which grow internally in the organisms and are easily seen in fossils (see Table 1.2). Confusing the issue somewhat is the production of some of the same minerals by more than one of these routes. The history of all these geological deposits has been dated in geological periods (Table 1.3), i.e. when a variety of surface rocks and sediments formed (see Sections 2.5 to 2.11). We shall also use this geological table with reference to the timetable of evolution of organisms and related fossils with associated chemistry in the ecosystem. As we have already noted, making the main physical–chemical connection between these minerals and living organisms is the solubility of ions from them, especially in the sea. The limiting possible changes of the inorganic content of the sea at any time arose directly from hydrothermal interaction with basalt, from weathering, or indirectly from chemical reactions of the minerals with chemicals released by cells, and from the death of organisms. We turn to which elements are of importance in the environment and of great influence upon the nature of life and its evolution.
1.1.1 The Involvement of the Elements in Evolution
Not all the elements of the Periodic Table (Figure 1.1) are involved in evolution to any marked degree, certainly to 1900 AD. In addition to hydrogen, carbon and oxygen we shall be concerned with the major ions of sodium, potassium, calcium and magnesium, with the anions carbonate, silicate, sulfide (later sulfate) and phosphate in the sea, all of which are also in organisms in considerable amounts. Of these ions, carbonate and sulfide/ sulfate showed the greatest changes in concentration later in time. However biological activity is also generally catalysed and controlled by small amounts of ions of several other elements from the sea such as iron, manganese, cobalt, nickel, copper, zinc, molybdenum and selenium and a few others, in particular organisms, all of which have their geological sources largely in mineral oxides (silicates) and sulfides. The availability of some of these ions, found in many biological catalysts, without which there would be no life, changed with time, as seen in sediments. We know that life today depends on some 20 elements which differ, qualitatively and quantitatively, from those which were required initially, and that they all have aqueous solutions as their biological sources, which are for the most part connected to abiotic minerals. Note that very few other elements, if any, have ever been very available in the sea. But why were so many elements needed both in catalysis and in controls of cellular activity?
As we have already stressed there are two spatial parts of chemical activity of early cells which are of particularly different concern, the zone of the internal metabolism and biopolymers and that of the external surfaces, both of which have to be synthesised with the aid of different metal ions. As we shall show, from the beginning of life the use of internal specific powerful catalysts was required in order to activate in particular oxidation/reduction and hydrolytic reactions of rather inert chemicals, e.g. H2, CH4 and peptide molecules inside cells, while less powerful catalysts were needed for those reactions which occur relatively easily, e.g. hydrolysis of phosphates, inside and outside cells. The different concentrations of ions inside and outside cells then allowed different metal ions, mostly combined with proteins, to both catalyse and control differentially parts of both internal and external metabolism. The requirement for powerful catalysts of both acid/base and redox reactions inside cells is met by the use of some of the above transition metal ions (Fe, Cu, Zn), as they are of high electron affinity and several can change valence state readily (see Figure 1.6). Moreover several can interact with inert small molecules, such as O2, in a specific, idiosyncratic way, so that we observe specific uses for them. The outside surfaces of cells are of molecules which, later in time, say approaching 0.54 Ga, are often selectively changed differently from those inside, again with the aid of strongly but differently active metal ions. They and/or more weakly active metal ions also stabilised these surface molecules. The weaker catalysis often, of acid/base reactions, was more generally executed by non-transition metal ions of lower electron affinity, for example Mg2+ and Ca2+, both inside and outside cells. Lastly, bulk osmotic and electrical balance rested with bare ions of no catalytic activity (Na+, K+ and Cl-), which are in maintained gradients across boundary membranes. To preserve selective action, therefore, cells came to use a considerable variety of metal ions (see Figure 1.1), many of which changed in availability and use with time. Much of this inorganic/organic chemistry is retained in today's cells, but its beginnings are obscure.
Very little if any of the selective catalytic activity of the metal ions was or is due to the bare ions but it arose from active sites, themselves selected, in proteins, enzymes, so that the inorganic chemistry has to be considered with the synthesis of binding proteins as well as with the reactions of organic molecules in cells. One illustrative telling example of the development of external catalysed cell surface reactions, giving rise to biominerals common to later organisms, will be seen to be particularly intriguing during later evolution, because the earliest living cells did not mineralise. The earliest cells left little dependable fossil record, basically only imprints. We shall take it that biomineralisation required particular organic molecules for nucleation, growth and final form. They arose, relatively suddenly, at a particular time of cellular and environmental chemical change. Biomineralisation is then a signature of the evolution not just of organisms but of particular organic chemistry catalysed by special metal ions, with selected binding of other metal ions and of the oxidising strength at particular times. We shall ask what happened to the environment exactly when these special metal ions and biological mineralisation arose.
We shall also need to describe the historical development of message systems used to create and maintain control of organisation in space and in time, because at all stages of evolution both internal and external cellular activities were and are controlled by messengers. Some of these messengers are free inorganic ions (Fe2+, Mg2+, Ca2+, Na+ and K+), but many are organic molecules often requiring catalysis for their synthesis. Now synthesis of the mainly metalloenzyme catalysts is under instruction from genes, coded information, controlled by other messengers. We can of course use knowledge of the evolution of genetic molecules (DNA and RNA), and their expression as proteins, to help examine all selective internal changes of organic and inorganic cellular components with time. Some of the controlling free metal ion messengers interact with proteins bound to DNA, so-called transcription factors. However genetic information is poor before 0.54 Ga and it is in the period 3.5 to 0.5 Ga when the knowledge of inorganic element changes both in the environment and in cells is most reliable in providing evolutionary markers.
All cellular activity also depends on energy sources, which undoubtedly changed with time too. Both sources of materials (elements) and energy for very early living systems and their changes are probably directly or indirectly dependent upon the mineral environment and its changes from the earliest times. We shall then describe environmental evolution first from its very inorganic beginnings (Chapter 2). We shall try to keep these observed geochemical changes separate from changes in living systems as far as possible, so as to simplify understanding, but during extensive analysis of each separately we will have to bring them together to examine the whole ecosystem from very early times. To appreciate chemical evolution, therefore, we shall have to follow the analytical, chemical content of the inorganic environment with an examination of the later changing organic chemical content of organisms and its energy capture, including the genome, the proteome, the metabolome, and the metallome. Later all energy was from the Sun.
Because our concern is with the environment and organism chemistry and the chemicals which go between them, we need to describe the factors that are important for maintaining the states of both the inorganic and organic chemicals. The constraints on inorganic chemistry are frequently equilibria, thermodynamic relationships which are quantitatively well-defined by constants, solubility products, complex binding constants and redox potentials (see Sections 1.3 to 1.5). The constraints on organic chemistry are quite differently, overwhelmingly, kinetics, rates of reaction, controlled by energy barriers (Section 1.6). Hence many organic chemicals have to be constantly reproduced as they decay. They are energised molecules and react very slowly. They require catalysts and extra energy to change because they are in trapped forms behind energy barriers. We describe next the limiting factors in inorganic chemistry, which give us markers of evolution from geochemistry or studies of the environment and its evolution. These limitations then allow us to make a strong connection to the manner in which organic chemistry and hence organisms could evolve.
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Excerpted from Evolution's Destiny by R. J. P. Williams, R. E. M. Rickaby. Copyright © 2012 R. J. P. Williams and R. E. M. Rickaby. Excerpted by permission of The Royal Society of Chemistry.
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