A System's View of the Evolution of Life
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J. R. Soc. Interface (2007) 4, 1049–1070 doi:10.1098/rsif.2007.0225 Published online 17 April 2007 REVIEW A system’s view of the evolution of life Robert J. P. Williams* Inorganic Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QR, UK Previous treatments of biological evolution have concentrated upon either the general appearance or habits of organisms or the sequences of molecules, such as their proteins and DNA (RNA), within species. There is no consideration of the changing relationship of the chemistry of organisms to the elements and energy available from the environment. In essence, organisms at all times had to accumulate certain elements while rejecting others. Central to accumulation were C, N, H, P, S, K, Mg and Fe while, as ions, Na, Cl, Ca and other heavy metals were largely rejected. In order to form the vital biopolymers, C and H, from CO2 and H2O, had to be combined generating oxygen. The oxygen then slowly oxidized the environment over long periods of time. These environmental changes were relatively rapid, unconstrained and continuous, and they imposed a necessary sequential adaptation by organisms while increasing the use of energy. Then, evolution has a chemical direction in a combined organism/environment ecosystem. Joint organization of the initial reductive chemistry of cells and the later need to handle oxidative chemistry has also forced the complexity of chemistry of organism in compartments. The complexity increased to take full advantage of the environment from bacteria to humans in a logical, physical, compartmental and chemical sequence of the whole system. In one sense, rejected material can be looked upon as waste and, in the context of this article, leads to the consideration of the importance of waste from the activities of humankind. Keywords: systems: chemical; evolution: chemical; chemistry of evolution; organisms: evolution; biological chemistry; compartments of cells 1. INTRODUCTION no parallel system. The nature of these three singular events is certainly outside the scope of this article for Evolution of our whole system from the gross level of the further very good reason that I have no ability to the Universe to very local happenings has to be seen as a say anything useful about them. However, a logical consequence of either initial local inevitable and analysis has been given for the evolution over all time of generalizable events traceable in a time sequence from the first two, the material and energy of the Universe the Big Bang or local ‘accidents’, chance one-off events, and those of Earth. Physical/chemical studies have which occur at a given time and in a given place and given rise to collections of observable materials and which are not open to a logical treatment. There are observations of changes in them and then to rational three major events in the evolution of the Universe, explanation. The way forward is usually termed which have this ‘one-off’ nature. The first is the Big reductive analysis, a seeking for the basic ingredients Bang itself for which we can offer only a very of today’s material and its energies from given origins in speculative ‘explanation’. The second is the formation the Universe and on Earth. This has led to concepts of of Earth with the Sun’s other planets. Here, we can give variables, such as pressure and temperature, and a a possible physical explanation of an accident 4.5 Gyr description of them in terms of the properties of basic ago, but we do not know the chance of a very closely materials in phases. The materials have been broken similar event. Exploration may be possible here, but down into particles, atoms in the Periodic Table in any definite evidence about another Earth/Sun chemical studies (e.g. figure 1), together with the creation in the Universe has not yet been found and it description of the energy of their interactions in is not likely to be easily obtained. The third case is the compounds and their movements at all levels. Mean- origin of life, critically dependent on the Earth/Sun while, energy has been analysed in a somewhat different relationship. We have no evidence except a probable ‘particulate’ analysis of quanta with a duality of mass time, 3.5–4.0 Gyr ago, for this happening and there is and wave characteristics. By contrast, the evolution of living objects has frequently been treated as if there is *[email protected] some principle operative, which is outside the usual run Received 20 December 2006 Accepted 19 February 2007 1049 This journal is q 2007 The Royal Society 1050 Review. A system’s view of the evolution of life R. J. P. Williams 1 2 3 4 5 6 7 8 9 101112131415161718 H He Li Be BCNOFNe Na Mg Al Si P S Cl Ar K Ca Sc Ti V Cr Mn Fe Co Ni Cu Zn Ga Ge As Se Br Kr Rb Sr YZrNbMoTcRuRhPdAg Cd InSn Sb TeI Xe Cs Ba Ln Hf Ta W Re Os Ir Pt Au Hg Ti Pb Bi Po At Rn Fr Ra Ac Th Pa U bulk biological trace elements believed possibly essential elements to be essential for bacteria, trace elements for plants or animals some species Figure 1. The Periodic Table showing the elements required by all life. Note how almost the whole possible variety of chemistry is covered, in that there are representative elements from 15 of the 17 chemically active groups in cells. Homo sapiens present culture tools insects whales hominids crabs birds elephants monkeys starfish amphibians reptiles warm blood 100 million mammals flowering sea urchins walkers plants bivalves cephalopods fish echinoderms 500 million arthropods today's free oxygen molluscs vertebrates 1 billion seed ferns multicellular plants animals fungi bacteria systems some free oxygen 2 billion blue-green algae chloroplasts mitochondria eukaryotes nucleated cells 3 billion earliest cells photochemistry DNA 4 billion earth no free oxygen 5 billion the origin of the solar system (years ago) Figure 2. A standard evolutionary tree based on the characteristics of organisms or their DNA which appears to indicate an independence of different branches of life. of physics and chemistry. There is a clash with religions arisen in a set of material bodies either with shapes and and beliefs outside experimental tests, and also even the behaviours (classical biology) or with these and other scientific approaches of biologists’ analyses are not on characteristics related to molecule sequences (molecu- the same basis as those used in the study of the Universe lar biology). The observed similarities in these proper- and Earth. Organisms are said to have evolved as ties have allowed the development of evolutionary trees species by chance improvement of survival, and the of seemingly independent organisms (figure 2). The possibility of a logical description of their evolution, trees can be made extremely detailed beyond the level even in large classes based on chemistry and physics, of classes to that of individual species of organisms. The has not been examined. Species are described as having changes of the environment of organisms in the J. R. Soc. Interface (2007) Review. A system’s view of the evolution of life R. J. P. Williams 1051 branches of trees are not considered when they are the effect of the energy flow has also allowed the described. The whole is then a driven branching growth formation and loss of unstable organic chemicals in for the success of particular organisms in a struggle for synthesis/degradative cycles in cells. survival. These views put forward by Darwin have been reaffirmed recently in a book by Maynard-Smith & energy Szathma`ry (1995) and in the proceedings of a recent Royal Society Discussion (Cavalier-Smith et al. 2006). environmental organic systems, Maynard-Smith & Szathma`ry conclude, in agreement elements with many biologists, that although organisms increase in complexity, this is neither ‘universal nor inevitable’. heat Although features of neo-Darwinism have some element of environmental determination, there is no The organic systems are not just based on H, C, N, O, S physical/chemical analysis following the style of those and P, but, as we shall see, they contain a considerable of the nature of today’s Universe and Earth. Here, as number of mineral elements. The energy trapping in stated, the examination and experimentation reach such a system from high-energy chemicals or the Sun back to, in fact beyond, the level of atoms in materials can create unstable ‘organic’ chemicals either of high- and their energy. As all biological materials are made energy content, for example in the reaction from atoms in and energy from the environment, the C energy$$% C surface of Earth and the Sun, it seems appropriate here CO2 2H2O CH4 O2; to go back to the same features and their known or in the form of physical gradients of concentration of changes in time to see if we can work forward in the charge or particles, inorganic or organic, across manner of a physical/chemical examination in a search boundaries. It is important to remember that only certain for a rational physical/chemical explanation of the elements can be energized chemically for considerable evolution of living systems (Morowitz 1992, 2002; de periods of time as their chemical bonds have sufficient Duve 2002). We start from an analysis of the energy kinetic stability and so can give rise to particular organic inputs to the environment and organisms treating them compounds of long life. We shall categorize these as one system. compounds and also analyse the way in which the energized materials can be trapped physically in isolated 2.