Evolution s destiny evolving chemistry of the invironment and life

R J P Williams and R E M Rickaby Evolution’s Destiny Co-evolving Chemistry of the Environment and Life Evolution’s Destiny Co-evolving Chemistry of the Environment and Life RSC Nanoscience & Nanotechnology Series Editors: Professor Paul O’Brien, University of Manchester, UK Professor Sir Harry Kroto FRS, University of Sussex, UK Professor Ralph Nuzzo, University of Illinois at Urbana-Champaign, USA Titles in the Series: 1: Nanotubes and Nanowires 2: Fullerenes: Principles and Applications 3: Nanocharacterisation 4: Atom Resolved Surface Reactions: Nanocatalysis 5: Biomimetic Nanoceramics in Clinical Use: From Materials to Applications 6: Nanofluidics: Nanoscience and Nanotechnology 7: Bionanodesign: Following Nature’s Touch 8: Nano-Society: Pushing the Boundaries of Technology 9: Polymer-based Nanostructures: Medical Applications 10: Metallic and Molecular Interactions in Nanometer Layers, Pores and Particles: New Findings at the Yoctolitre Level 11: Nanocasting: A Versatile Strategy for Creating Nanostructured Porous Materials 12: Titanate and Titania Nanotubes: Synthesis, Properties and Applications 13: Raman Spectroscopy, Fullerenes and Nanotechnology 14: Nanotechnologies in Food 15: Unravelling Single Cell Genomics: Micro and Nanotools 16: Polymer Nanocomposites by Emulsion and Suspension 17: Phage Nanobiotechnology 18: Nanotubes and Nanowires: 2nd Edition 19: Nanostructured Catalysts: Transition Metal Oxides 20: Fullerenes: Principles and Applications, 2nd Edition 21: Biological Interactions with Surface Charge Biomaterials 22: Nanoporous Gold: From an Ancient Technology to a High-Tech Material 23: Nanoparticles in Anti-Microbial Materials: Use and Characterisation How to obtain future titles on publication: A standing order plan is available for this series A standing order will bring delivery of each new volume immediately on publication For further information please contact: Book Sales Department, Royal Society of Chemistry, Thomas Graham House, Science Park, Milton Road, Cambridge, CB4 0WF, UK Telephone: +44 (0)1223 420066, Fax: +44 (0)1223 420247, Email: books@ rsc.org Visit our website at http://www.rsc.org/Shop/Books/ Evolution’s Destiny Co-evolving Chemistry of the Environment and Life R J P Williams Inorganic Chemistry Laboratory, University of Oxford, Oxford, OX1 3QR UK Email: bob.williams@chem.ox.ac.uk R E M Rickaby Department of Earth Sciences, University of Oxford, Oxford, OX1 3AN UK Email: rosr@earth.ox.ac.uk ISBN: 978-1-84973-558-2 A catalogue record for this book is available from the British Library # R J P Williams and R E M Rickaby 2012 All rights reserved Apart from fair dealing for the purposes of research for non-commercial purposes or for private study, criticism or review, as permitted under the Copyright, Designs and Patents Act 1988 and the Copyright and Related Rights Regulations 2003, this publication may not be reproduced, stored or transmitted, in any form or by any means, without the prior permission in writing of The Royal Society of Chemistry or the copyright owner, or in the case of reproduction in accordance with the terms of licences issued by the Copyright Licensing Agency in the UK, or in accordance with the terms of the licences issued by the appropriate Reproduction Rights Organization outside the UK Enquiries concerning reproduction outside the terms stated here should be sent to The Royal Society of Chemistry at the address printed on this page The RSC is not responsible for individual opinions expressed in this work Published by The Royal Society of Chemistry, Thomas Graham House, Science Park, Milton Road, Cambridge CB4 0WF, UK Registered Charity Number 207890 For further information see our web site at www.rsc.org Printed and bound in Great Britain by CPI Group (UK) Ltd, Croydon, CR0 4YY, UK Preface This book is written as an addition both to Darwin’s work and that of molecular biologists on evolution, so as to include views from the point of view of chemistry rather than just from our knowledge of the biology and genes of organisms By concentrating on a wide range of chemical elements, not just those in traditional organic compounds, we show that there is a close relationship between the geological or environmental chemical changes from the formation of Earth and those of organisms from the time of their origin These are considerations that Darwin or other scientists could not have explored until very recent times because sufficient analytical data were not available They lead us to suggest that there is a combined geo- and biochemical evolution, that of an ecosystem, which has had a systematic chemical development In this development the arrival of new very similar species is shown to be by random Darwinian competitive selection processes such that a huge variety of species coexist with only minor differences in chemistry and advantages, which is in agreement with previous studies By way of contrast, we observe that on a large scale, groups of such species have special, different energy and chemical features and functions so that in fair part they support one another It is more difficult to understand how they evolved and therefore we examine their energy and chemical development in detail Overall we know that there is a cooperative evolution of a chemical system driven by capture of energy, mainly from the Sun, and its degradation, in which the chemistry of both the environment and organisms are facilitating intermediates We will suggest that the overall drive of the whole joint system is to optimise the rate of this energy degradation The living part of the system, the organisms, is under the influence of inevitable inorganic environmental change which moves rapidly to equilibrium conditions, though much of it was forced by the different chemicals added to it by organisms at different times We are also able to explore some ways in which the organic chemicals of Evolution’s Destiny: Co-evolving Chemistry of the Environment and Life R J P Williams and R E M Rickaby # R J P Williams and R E M Rickaby 2012 Published by the Royal Society of Chemistry, www.rsc.org v vi Preface organisms evolved Such evolution was dependent on the inevitably changing environment for all its chemicals and therefore much novel organic chemistry followed a determined path We recognise that as complexity of the chemistry of organisms increased, the organisms had to become part of a cooperative overall activity and could not remain as isolated species Prokaryotes and bacteria managed by long-distance exchange between different cells; eukaryotes evolved by incorporating some bacteria – the organelles The eukaryotes also had increasing numbers of other compartments found in both animals and plants Later division of essential activities was by direct combination of differentiated cells and by further different forms of symbiosis Only in the last chapter we attempt to make a connection between the changing chemistry of organisms with the coded molecules, DNA, of each cell which have to exist to explain reproduction This book has to encompass the full spectrum of chemistry, from the extreme of Earth Sciences to those of Biological Sciences No author can claim to cover all these disciplines to an appropriate depth The authors of this book apologise for misjudgements of any particular topics and trust that readers will inform them of any errors Acknowledgements We are indebted to the University of Oxford and to the Royal Society for support We are also grateful to Susie Compton for her help in typing the documents and David Sansom for the illustrations RR acknowledges financial support from the ERC, grant SP2-GA-2008-200915 Evolution’s Destiny: Co-evolving Chemistry of the Environment and Life R J P Williams and R E M Rickaby # R J P Williams and R E M Rickaby 2012 Published by the Royal Society of Chemistry, www.rsc.org vii 306 Chapter 20 J R Waldbauer, L S Sherman, D Y Summer and R E Summons, Precambrian Res., 2009, 169, 28 21 A D Anbar and A H Knoll, Science, 2002, 297, 1137 22 C L Dupont, S Yang, P Palenik and P E Bourne, Proc Nat Acad Sci USA, 2006, 103, 17822 (and see reference 53) 23 Y Zhang and N V Gladyshev, Chem Rev., 2009, 109, 4828 (and references therein) 24 K Hoelm and M E Nicpon, Human Anatomy and Physiology, 7th edn, Benjamin Cummings, San Francisco, 2007 25 F M Harold, The Way of the Cell, Oxford University Press, Oxford, 2001 26 E Carafoli and C Klee, Calcium as a Cell Regulator, Oxford University Press, New York, 1998 27 C Toyoshima and G Inesi, Annu Rev Biochem., 2004, 73, 269 28 D Krogh, A Brief Guide to Biochemistry and Physiology, Prentice and Hall, New York, 2007 29 Y Jiang, A Lee, J Chen, V Ruta, M Cadane, B T Chait and R Mackinnon, Nature, 2003, 423, 33 30 D Purves, G J Augustus, D Fitzpatrick, W E Hall, A S L’Amantia, J O McNamara and L E White, Neuroscience, 4th edn, Sinauer Associates, Sunderlands, , MA, 2008 31 R A Colvin, W R Holmes, C P Fontaine and W Maret, Metallomics, 2010, 2, 306 32 C Andreini, L Banci, I Bertini and A Rosato, Proteome Res., 2008, 7, 209 33 A L David and E J Alm, Nature, 2011, 469, 93 34 R Dawkins, The Selfish Gene, Oxford University Press, Oxford, 2006 35 J M Smith and R Szathmary, The Major Transitions in Evolution, W H Freeman, San Francisco, 1995 36 S A Kauffman, The Origin of Order, Oxford University Press, Oxford, 1993 37 A Lazcano and S L Miller, J Mol Evol., 1994, 39, 546 38 L E Orgel, Origins of Life: a Review of Facts and Speculations, Elsevier, Amsterdam, 1998 39 C de Duve, Life Evolving: Molecules, Mind and Meaning, Oxford University Press, New York, 2002 40 S J Gould, The Structure of Evolutionary Theory, Harvard University Press, Cambridge, , MA, 1995 41 D J Depew and B Weber, Darwinism Evolving, MIT Press, Cambridge, , MA, 1995 42 S Conway Morris, Philos Trans R Soc., B, 2006, 361 43 L Margulis, Symbiotic Universe, Basic Books, New York, 1998 44 M L Arnold and N D Forgarty, Int J Mol Sci., 2009, 10, 3836 45 A Moat, J W Foster and M P Specktor, Microbial Physiology, WileyLiss, New York, 2002 46 J Spring, J Struct Funct Genomics, 2004, 3, 19 47 J C Herron, Evolutionary Analysis, 4th edn, Freeman-Scott, New York, 2008 48 N Lane and W Martin, Nature, 2010, 467, 929 The Amalgamation of the Chemical and the Genetic Approaches to Evolution 307 49 S Ohno, Evolution by Gene Duplication, Springer Verlag, Berlin, 1970 50 M Linch and J S Conery, Science, 2000, 290, 1151 51 J S Taylor and J Raes, Annu Rev Genet., 2004, 38, 615 52 I Zhang, Trends Ecol Evol., 2003, 18, 292 53 E V Koonin, Nucleic Acids Res., 2009, 37, 1011 54 A L Hughes, Proc Natl Acad Sci USA, 2005, 102, 8791 55 J M McClintock, R Carlson, D M Mann and V E Prince, Development, 2001, 128, 2471 56 J Platigorsky and G Wistow, Science, 2008, 252, 1078 57 P Deschamps, H Moreau, A Z Worden, D Douvillee and S G Ball, Genetics, 2008, 178, 2373 58 T M Embley and W Martin, Nature, 2006, 440, 623 59 C Andreini, I Bertini, G Cavallero, G M Holliday and J M Thornton, Bioinformation, 2009, 25, 2088 60 C L Dupont, A Butcher, R E Valas, P E Bourne, G Caetano-Anolles, Proc Natl Acad Sci USA, 2010, 107, 10567 61 L Decaria, I Bertini and R J P Williams, Metallomics, 2010, 2, 706 62 L Decaria, I Bertini and R J P Williams, Metallomics, 2011, 3, 56 63 M H Serves, A R.W Kerr, T J McCormack and M Riley, Biol Direct, 2009, 4, 46 64 B Conrad and E Antonarakis, Annu Rev Genomic Hum Genet., 2007, 8, 17 65 J Mellor, The Biochemist, 2010, 32, 14 (and references therein) See also eight following articles, pages 18–33 66 A Petronis, Nature, 2010, 465, 721 67 E Jablonka and M Lamb, Evolution in Four Dimensions: Genetics, Epigenetics, Behavioural and Symbolic Variation in the History of Life, MIT Press, Cambridge, , MA, 2005 68 E J Richards, Nat Rev Genet., 2006, 7, 395 69 E Jablonka and G Roaz, Q Rev Biol., 2009, 84, 131 70 J Travers, Science, 2009, 324, 580 (and references therein) 71 R Chatwin, S N Wantakal and S Roa, Trends Genet., 2010, 26, 443 72 M E Feder, J Exp Biol., 2007, 210, 1653 73 A M Nedeleu, Proc R Soc London, Ser B, 2007, 272, 1935 74 I Karasov, P W Messer and D A Petrov, PloS Genet., 2010, 6, e1000987 75 T F MacKay, Philos Trans R Soc London, Ser B, 2010, 365, 1229 76 S W Ding, Nat Rev Immunol 2010, 10, 632 77 J Lovelock, Homage to Gaia, 2000, Oxford University Press, Oxford Subject Index Note : page numbers in italic refer to figures and tables abiotic energization 45 abiotic environment 253 pre-life conditions summarised 252–7 Acantharia 85, 88, 92, 172 acritarchs 77, 130, 133 active sites 6, 158 adenosine di-phosphate (ADP) 106–7 adenosine tri-phosphate (ATP) 106– 7, 109, 111, 159, 258 aerobic prokaryotes 76, 80, 125–30 algae 76, 79, 85, 133, 140, 175, 228–9, 241 and biomineralisation 85, 86 genetic analysis 139–41 aluminium 46 silicates 16, 47 amino acids, first formation of 112–13 ammonia, 40, 112, 113, 125, 233, 273 anaerobic conditions 110 anaerobic prokaryotes beginnings of 45, 59, 60, 76, 80, 291 early cell types 119–20 early cellular chemistry 39, 101–5, 263–4 and vesicular systems 257–61 genome and proteome 115–20 metabolism/biochemistry energy transduction and use 105–10 essence of 122–5 probable original features 103, 110–15 metalloproteins 224–7 progression to eukaryotes 133, 134, 291–2 prokaryote diversity/differences 119–20, 125 structures cell walls and membranes 121–2 internal and protein production 113, 120–1 see also aerobic prokaryotes Anammox 125 antibodies 287 apatite as biomineral see calcium phosphate early deposits 170–1 arabidopsis, 247, 283, 284 aragonite 65, 176, 194 Archaea 14, 104, 119–20 and endosymbiosis 131 and metalloproteins 229 atmosphere composition 61, 70, 303 early reducing/changes in 40, 41, 42, 43, 45 modelling changes 60–3 see also oxygen ATP see adenosine tri-phosphate 308 Subject Index ATPase pumps 137, 191 Banded Iron Formations (BIF) 41, 44, 49, 51, 52, 265 and rare earth probes 52–3 and transition elements 56–7 barium sulfate 172 binding/binding constants 7, 211–13 protein binding domains 224, 225, 226 thermodynamic equilibrium 213–21 biological organic chemistry 166, 167 distinctive features summarised 157–63 evolution of 102, 105, 258 first organic molecules 42–3 functions of the elements 268 initial in cells 101, 104–5 prerequisite vesicular systems 257–61 prokaryote metabolism 105–10, 125–31 see also cells biominerals 2–3, 4, chemistry and structure 70–1, 79, 87–9 composites/matrices 89–91, 97, 149, 193, 198–9 evolution of 176, 193–8, 240 growth patterns 91–2, 97 biological induction and control 92–4 indicative of catalytic process 24 and multicellular organisms 151–2 related to organism 79, 80, 86–7 types/modes of formation 84–7 see also fossil record bioorganic chemistry see biological organic chemistry bitumen 94 Black Sea 57, 58 black smokers 35, 42, 49, 57 see also hydrothermal activity bonds, reaction rates of 11 309 bone 81, 87, 152 bone synthesis/growth 195–6 early development 79, 81 and growth patterns 91–2 piezoelectric properties 195 skeletal structures 90 boring billion years, the 49, 51, 68, 93 brain 162, 192–3 buffering, sulfur/iron 47, 48–9, 59, 110, 160, 209 cadmium 242–3 calcite 65, 194 calcium biominerals see calcium carbonate; calcium phosphate ion pumps 88, 108, 137, 158, 183, 184 in organisms 149, 170, 173–7, 196, 199–200 rejection of ions 105, 107–8, 109, 149, 167, 177, 271, 290 see also calcium signalling calcium carbonate biominerals 79, 80, 86–7, 93, 151, 176 role of inorganic mineralisation 193–5 see also carbonate calcium oxalate 86 calcium phosphate/hydroxyphosphate biomineral 79, 86, 90, 151, 195–6 early apatite deposits 170–1 calcium proteins 182 calcium signalling 138, 139, 177, 179, 271 basics of 182 evolution in eukaryotes 180–8, 200 signal proteins 185 calmodulin 137, 183–4 Calvin cycle 111 Cambrian Explosion 45, 59, 145–6 changes in sea minerals 63–5 and fossil record 77–82, 96 310 carbon carbon cycle 41–2, 60–1 and fossil fuel 62, 81, 94–7, 300, 304 isotopes 65–6 carbon dioxide absorbed into cells 17, 108 catalytic/light aided redox 17 changing levels of 40, 41, 60, 61, 70 decreased by release of Ca/Mg 19 relative thermodynamic stability carbonates aragonite and calcite 65, 176, 194 formation 38 and solubility 14 Carboniferous Period 81, 95, 150 carrier proteins 218–19 catalysis 1–2, 5–6, 17, 62 and carbon dioxide reduction 108 danger and novelty in evolution 26–7, 221, 278 in early prokaryote cells 107 evolutionary roles clarified 20–6 initial organic chemistry 43, 44, 108 new biochemistry after dioxygen 206 and redox 18–19 role of different trace elements 206, 207 see also enzymes cell membranes see membranes cells chemical aspects of catalytic elements in 44 and complex ions 16 energy states within 22–3 phosphorus in 168–71 sulfur in 171–3 early 5–6, 7, 39 metabolism 108–10 organic chemistry of 100–4 evolution of summarised 291–3 time-lines 80, 102 and flow 11–12 waste from 17, 25 Subject Index see also aerobic prokaryotes; anaerobic prokaryotes; eukaryotes cellular gene 275 cellulose 89, 149 change, rates of 20–6 chaos 28–9 chaperones 138, 185, 217 chemical approach to evolution, summary of 251–4, 289–99 abiotic beginnings inorganic chemistry 254–7 organic chemistry 257–61 supporting evidence 261–3 environmental oxidation 264–6 and oxidative chemistry 266–70 factors driving evolution 270–3 future possibilities 299–303 genetic and biological connections see genes and reproduction major chemical steps listed 272 chemical cycling 59 carbon 41–2, 60–1 sulfur and iron 47 chemical evolution see chemical approach chemotypes 9, 120, 126, 204 chitin 89, 149, 150, 237 chlorine/chloride 167, 168, 199 chlorophyll 105–6, 113, 175, 219, 263 structure 175 chloroplasts, 85, 102, 132, 134, 142, 160, 168, 182, 230, 236, 278, 280 Choanoflagellate 143 cholesterol 102, 131, 142, 156, 196, 269, 280 circulation, extracellular fluid 152–3 cladogram 146 climate change/fluctuations 29, 63 and global warming 300, 304 coal 62, 81, 95 coalescence, gene 279–80, 282, 295 cobalt 128–9, 229 coded life 24–5, 82 Subject Index coenzymes 107, 178 coffinite 50 collagen 149, 150, 152, 234, 236 complex ions 15–17, 70–1 stability constants 7, 10–11, 16 cones, mineralised 91 conjugation 121 connective tissue, 154, 161, 172, 177, 187, 206, 234, 236, 237, 238, 246, 268, 269, 272, 293 continents, movement of 37, 38 cooling, Earth’s surface 36–7 copper 57, 246 binding 216–17 limitations on uptake 221–2 and messaging 150, 154 as oxidative catalyst 126, 127, 138– 9, 142, 158, 234 proteins and enzymes 235 sea concentrations over time 69 coral 85 crystal nucleation 24 cyanobacteria 68, 126, 222 photochemistry 109 cycles see chemical cycles cysts 98 cytoplasm 110–11, 138, 160 metal ion concentration 167, 216 cytosome-c oxidase 226 Darwinism 7–9, 146, 163, 297–8 and man’s impact 82 tree of life see also evolutionary trees denitrification 128, 129 diatoms 197 diffusion 27–8 DNA 115–19, 158–9 eukaryote nucleus 136–7 evolution of summarised 293–9 first development 113 junk DNA 282, 283 see also genes; genetic analysis dolomite 19, 176 311 drugs and drug resistance 285–6, 288, 297, 298 duplication, 184, 254, 281–288, 295, 297, 298 Earth chemical development of see geochemical evolution composition of 9–10 abundance of elements 22 pre-life conditions summarised 252–7 structure and physical evolution 33–9 surface cooling 36–7, 67, 254 Ediacaran Period 76–7 electrolytic gradients 153, 154–5 elements 29, 167 abundance on earth 22 bulk biological evolutionary roles of 4–10, 29–30, 166–8 changes in eukaryotes 265 overview 199–201 see also entries for individual elements main biochemical functions 268 oxidative chemistry summarised 266–70 Periodic Table see also trace elements endocytosis 133, 142 endoplasmic reticulum 131–2, 134, 138, 148, 183, 186, 187 endosymbiosis 131, 132 energisation, abiotic 45 energised trap 20, 21 energy barriers 7, 20, 21 energy sources and cellular activity 7, 110, 159 man’s continued exploitation of 300 Sun as 7, 21–2, 32–3 energy transduction, cellular 259, 260 anaerobic prokaryotes 105–8 312 the earliest primary metabolisms 108–10 and eukaryotes 134–5 entatic states 204 environmental oxidation 3, 32–3, 46– 7, 126, 204, 262 overview 264–70 quantitative analysis of 50–2 see also oxygen environmental stress 284–6, 286–7, 297 enzymes 104, 127, 158 carbonic anhydrases 242–3 and cell protection 138–9 cellular evolution see metalloproteins enzyme structure 117 isoenzymes 282–6 metal centres in 70–1, 126–7, 158 copper 235 iron 226 molybdenum 233 selenium 244 zinc 237, 239, 242–3 selective catalytic action 205 epigenetics 117, 136–7, 286–8 equilibrium 10–13 erosion 37–8 Eubacteria 76, 104, 120 cell membrane 122 and endosymbiosis 131 ion distribution in 181 and metalloproteins 229 eukaryotes cell basic biochemistry 131 filaments in 137 nucleus 135–7 structure 132 early fossil record 76, 79, 80 evolution of general overview 141–2, 227, 280 metalloprotein development 227–30 Subject Index progression from prokaryotes 130– 5, 134, 160–7 genetic analysis 139–41 and modes of mineralisation 85, 86 single-cell species of 133 see also multicellular organisms europium 54 evolution see chemical approach to evolution evolutionary trees 8, 266, 289 chemical collaboration between branches 145 eukaryotes from fossil/gene data 86 prokaryotes to eukaryotes 134 exocytosis 133 extinctions 62, 63, 77, 298 and fossil record 82–4 extra-terrestrial life 9–10, 79 extracellular fluids 152–3 extremophiles 120 filaments, eukaryote 137 fitness, see survival of the fittest flows 11–12, 13, 256 air and water 32 melts 32–3 fluids, extracellular 152–3 folic acid 108 Foraminiferae 85, 133 formaldehyde 43, 106, 113, 270 fossil fuels 62, 81, 94–7, 300, 304 fossil record 2–3, 73–5 biomineralisation 77–81, 96–7, 176 and coded life 82 early organisms 77 evolution of 193–5 multicellular organisms 78, 79 onset of 77, 80 single-cell eukaryotes 80, 81 fossil imprints 75–7, 75, 96, 97, 130 molecular fossils 94 plants/Carboniferous Period 81, 94–5 see also biominerals; extinctions fungi 85 Subject Index Gaia 303–5 gas, natural 62, 81 genes and reproduction 9, 115, 116, 274–6 duplication and epigenetics 286–8, 295–6 and isoenzymes 282–6, 295 gene transfer and coalescence 277– 81, 282, 295 loss of genes 156–7, 281–2 genetic analysis 273 algae and metazoans 139–41 and gene loss 157 multicellular organisms 155–6 geochemical dating 39 geochemical evolution broad overview/summary 67–70, 254–6 early/largely reducing change (before 3.0 Ga) 40–5, 68 later redox revolution (3.0 to 0.4 Ga) 45–52 trace elements and 52–7 see also physical evolution; weathering geological periods global warming 299–300 glucogenesis 111 glycobiology 149 glycolysis 114 Golgi body 132, 138, 150 Gondwanaland 37 grass 85 ground state 20, 21 growth and growth patterns multicellular organisms control and shape in 147–8 evolution of biominerals in 151–2 single-cell organisms 91–2, 97 trace element concentration effects 241–2 and zinc hydroxylases 285 growth messengers 153–4 Grypania 130, 133 313 haem 224, 226, 232, 236, 283–4 histones 117, 120, 136, 287–8, 295 homeostasis 177–8 hopanes 94 hormones 144, 153–4, 285 hot vents see hydrothermal activity Hox proteins 285 hydrogen 17, 42, 43, 109, 126 hydrogen sulfide 48, 172 and early life 110–11 early oxidation of 109–10 early sources 40 photochemistry of 43, 58 hydrogenases 231 hydrothermal activity 4, 35, 42–3, 49 and non-uniform sea 57 as source of Fe/Mg cations 40 as source of lanthanides 54 hydroxides and complex ion formation 16 and insolubility of metal cations 14, 15 hydroxyurea 285, 288, 297 immune system, human 287, 295, 297 inheritance see genes inorganic chemistry see geochemical evolution inositol triphosphate 170, 185 intimate symbiosis 292 introns 136 iodine 148, 243–4 ion pumps 108, 123, 138, 158, 183, 184 APTases 137, 191 and biomineralisation 88, 89 iron 209 cellular roles 178, 230–1 cell interactions 232 central value of 239 in early life 111, 126, 127 hydroxylases 226 message systems 150 cycling 47 314 from thermal vents 40 iron/sulfur buffering 47, 48–9, 59, 110, 160, 209 limitations on uptake 221–3 oxidation/ environmental oxygen loss 4, 43–4, 110, 209 and redox potentials 50–1 sea concentrations over time 69 see also Banded Iron Formation; haem irreversibility 28–9 Irving-Williams series 1, 56, 215 isoenzymes 283–6 isotopic studies 32, 39, 68 carbon 65–6 molybdenum 54–6 oxygen 66–7 rare earth elements 54 sulfur 48–9 jellyfish 146 junk DNA 282, 283 Jurassic Period 83 keratin 149, 150 kerogens 94 kinetics Krebs cycle 111, 112, 114, 130 lanthanides 52–4, 56 life beginnings of 68, 76, 291, 298 non-coded origins 122 early cellular chemistry 101–5, 122–5 extinctions 62, 63, 77, 82–4 extra-terrestrial 9–10, 79 pre-life vesicular systems 257–61 tree of light capture see photochemistry; photosynthesis lignin 81, 89, 149, 150, 234 lipids 12, 101, 113, 114, 270 magnesium Subject Index cellular 173–5, 178, 179, 199–200, 237, 239 from thermal vents 40 magnetozomes 148 man 82, 162 DNA 229 future and further evolution 299– 303 industrial activity 210, 242, 302 manganese 217, 233–4 and oxygen from water 126 mantle 33–4, 35 Mars, composition of 10 matrices, biomineral 89–91, 97, 149, 151–2, 193, 198–9 melts membranes/walls, cell 12, 158 eukaryote 131, 132 membrane proteins 148–9 primitive vesicular systems 257–61 prokaryote chemistry 121–2 message systems see signalling metabolism, cell aerobic 125–30, 131 anaerobic 105–8 earliest features 108–10 see also biological organic chemistry metallomes 77, 204, 206, 216, 220, 223–4 metalloproteases 237 metalloproteins 116 duplication of 282–6 evolution of 220, 223–4, 239, 279 eukaryotes 227–30, 247 prokaryotes 224–7 protein binding domains 224, 225 see also enzymes metallothioneins 229 metamorphosis 147–8 metazoans 139–41 meteorites 53, 82, 83 methotrexate 285, 288, 297 micro-aerobic conditions 110 micro-aerobic prokaryotes 125–30 Subject Index microfossils 98 mid-ocean ridges 35, 42 minerals classes of 3–4 early evolution of 1, 2, 33–4, 40–1, 49–50 in the sea 3–4, 46, 63–5, 69 solubility 40 as source of trace elements 5, 54–7 see also biominerals mitochondria 134, 148, 278 molecular fossils 94 molluscs 79 molybdenum 54–6, 233, 245 isotopes of 39 major enzymes 233 role in cells 113, 126, 127, 128 sensitivity to sulfide oxidation 19 morphogenic fields 92 morphogens 147, 185 mRNA 115 multicellular organisms 161 chemical collaboration/symbiosis 145, 147 and loss of genes 155–7 common features of 142–4, 238 differentiation/division of space 146–7 extracellular fluids 152–3 genetic analysis 155–6 growth and shape control 147–8 evolution of biomineralisation 151–2 message systems 153–5, 161, 238 see also signalling rapid biochemical development 145 muscle cells 149 mutation 276, 286–7, 295 neodymium isotopes 39, 54 nervous system 240–1, 269 brain 162, 192–3, 298 message systems 188–93, 200 315 nerve cells 154–5, 162, 188, 189, 295 nickel 57, 128, 229 limitations on uptake 223 significance to early life 14, 15 silicates 16 superoxide dismutase 237 nitrate 69, 119, 126, 233, 273 inability of higher animals to reduce 161, 172 nitrogen oxides 109, 126 denitrification 128, 129 nitric oxide reductase 226 nitrogenases 215, 231, 232, 233 non-coded life 122 notochord 90 nucleation 24 nucleus, cell 132, 135–7 Nuna 37 oceanic crust 34, 35 oil 62, 81 olivine 34, 49, 57 organelles 134–5, 138, 142, 160, 278 organic chemistry beginnings of 42–3, 253, 257, 270 vesicular systems 257–61 first amino acids 112–13 see also biological organic chemistry organic ligands 16–17 organic sediments 62 organisms see cells; life; multicellular organisms organs 146, 186 oxidases, duplication of, 283, 284, 286, 297 oxidation see environmental oxidation; redox oxidation states changes in the sea 17–18 trace elements 205 oxidative phosphorylation 106–7, 111–12, 139, 233–4 limited enzymatic duplication 286 316 oxygen 126, 227–8, 234, 262 changing atmospheric levels 39, 41, 265 during last 600 million years 60, 61 early buffering against 110 first early rise 45, 68, 109–10, 209 second rise 45, 59, 81–2, 110, 209 danger to cells 109–10 protection in single-cell eukaryotes 138–9 exploited by organisms 160 organism increase 271 isotopes 66–7 released by cells 17, 191, 204 P450 cytochromes 154, 234, 283 Pangaea 37 peat 95 Periodic Table periplasm 122, 126, 127, 128, 130, 160 Permian Period 62, 83 phosphorite minerals 76, 89 phosphorus, cellular 167, 168–71, 199 phosphorylation see oxidative phosphorylation photochemistry 48 in cells 105–10, 135 of hydrogen sulfide 43, 58 photosynthesis 79, 133–5 algae 76, 85, 140, 175, 228 evolution of metalloproteins 226 and genetic analysis 140–1 and sulfur 96 physical evolution, Earth’s 33–9 Planctomycetes 125 planets, composition of 9–10 plants 144, 153, 161, 197 and biomineralisation 85, 86, 93 buried organic matter 95–6 early evolution 81 stress and gene multiplication 284–5 vascular cells 149 plasmids 121, 277–8 plate tectonics 33, 34–5 porphyrins 214, 219, 263–4 Subject Index potassium 167–8, 199 message systems 188–93 Pre-Cambrian Period 62, 83 precipitation 24 predictability 28–9 prokaryotes see aerobic prokaryotes; anaerobic prokaryotes proteins expression 117 first formation of 112–13 membrane 148–9 and multicellular organisms 148– 51, 161 and prokaryote cells 120–1 structure of 116, 118, 119 see also binding; metalloproteins proteome 115, 115–19 pyrite formation 48, 109 weathering 60 radioactivity 21 isotopes 39 Radiolaria 79, 85 random selection 10 rare earths isotopes of 39 probes 52–4 rates of reaction of bonds 11 and catalysis 20–6 and diffusion 28 Reaction/Diffusion Theory 147 redox potentials 7, 11, 33 the redox revolution 45–52 redox titration curve 47, 68 sea oxidation states 17–18 of simple organic molecules 26 sulfur and iron redox curve 50–1 reducing environment 40, 45–6, 49, 54, 56, 69 reproduction see genes respiration 107 reticulate evolution 277 rhenium isotopes 39 Subject Index ribosomes 115, 116 ribulose-1,5-bisphosphate carboxylase/oxygenase see RubisCO RNA 115–17, 158–9 eukaryote 136, 137 first development of 113 genetic analysis 139–41, 155–6 RuBisCO 111, 141, 276–7 sea changing redox potentials 17–19, 45–8 chemical transformations in 3–4, 59 diffusion in 27–8 lack of homogeneity 33, 57–8, 209– 10 metal ion content 46, 63–5 Fe/Zn/Cu concentrations over time 69 trace transition metals in 54–7 sediments 3, 35, 262 and erosion 38 organic content 60, 62 reflecting sea conditions 46 selenium 139, 243–4 shales 94 shape see growth shells 78, 79, 85, 89, 151, 194 and growth patterns 70, 91–2, 93 siderophores 222 signalling and message systems 6–7, 16, 269, 271 basic introduction to 177–80 calcium signalling 138, 139, 179, 271 evolution in eukaryotes 180–8, 200 and multicellular organisms 153–5, 161 oxidative synthesis of small molecules 235 sodium/potassium messages 188–93 silica, biomineral 79, 151, 196–8 silicates 38, 47 317 and insolubility of metal cations 14 and solubility 14 silicon 1734, 196 single-cell eukaryotes see eukaryotes Skaărgaard Intrusion 57 skeleton 90, 152, 253 skin 93, 143, 146, 150, 152, 292 small signalling molecule messengers see signalling Snowball Earth 29, 82, 83 sodium 24, 199 message systems 188–93 rejection of ions 105, 107–8, 158, 167, 271, 290 soil 38, 95, 96 solubility and solubility products 7, 10–11, 33, 57, 218 metal cations 14, 15 organic compounds 14–15 somantic hypermutation 288 species, definition of 288–9, 294 sponges 79, 92, 146, 198 steady state 12–13 steranes 94 stress, environmental 284–5, 286–7, 297 stromatolites 84, 122, 126, 265 strontium sulfate 79, 88, 92, 172 subduction 35, 42 sulfates 47, 151, 172, 173 assisting cell energetics 110 by oxidation of sulfides 4, 19, 48, 209 sulfide and complex ion formation 16 insolubility of metal cations 14, 15 oxidation 4, 19, 48, 209 sulfur 47, 167, 199 in cells 17, 107, 171–4 cycling 47 and early loss of environmental oxygen 43 estimating oxidation to sulfate 48 isotope fractionation 48–9 sedimentary deposits 96 318 Subject Index sulfur/iron buffering 47, 48–9, 59, 160, 209 Sun and Earth’s temperature 36–7 energising ocean surface 13, 18 as energy source 7, 21–2, 32–3 super-continents 37, 38 superoxide dismutase 138–9, 229, 236–7 surface minerals, classification of 3–4 survival of the fittest 7, 9, 276, 294, 297–8 symbiogenesis 132 symbiosis 145, 147, 153, 204, 230, 269 and definition of species 288–9 and loss of genes 156–7 sea conditions and 4, 45–6, 54–7, 64 see also catalysis transcription factors 285 see also zinc fingers transduction of energy, 44, 104–109, 116, 128, 134, 168, 169, 257, 259, 263, 275, 290 transition metals see trace elements transposons 277, 287 trees 150, 197 Triassic Period 83 trilobite 87 troponin 137 tubulins 148 tungsten 55 T-cells 287, 297 tectonic plates 33, 34–5 teeth 90 thermodynamics 2, and binding constants 213–21 thorium minerals 47, 49–50 trace elements 62 availability and environmental change 208–13 concentration effects on growth 241–2 limitations on uptake of ions 221–3 binding and transfer in cells 211–13 binding constants/thermodynamic equilibrium 213–21 catalysing initial organic chemistry 43, 44 concentrations in organisms 206 cytoplasmic fluid 167, 216 evolutionary role 5, 55, 168 in biorganic chemistry 204, 204, 206, 268 evolving uses surveyed 230–41 summary and overview 244–8 oxidation states of 205 and Periodic Table 5, 207 as poisons 26–7, 221, 278 rare earth probes 52–4 uraninite 47, 49–50 uroporphyrin 214, 219 Venus, composition of 10 vertebrates 79, 85 vesicles 15, 19, 137–8, 148, 160 calcium binding sites 187–8 mineralisation in 88 pre-life vesicular systems 257–61 vitamin B12 219–20, 229, 241 vitamin D 148 volcanoes 33, 34, 35, 37, 42 Volvox 143, 146 water exchange rate 24 weathering 28–9, 32, 256–7 before 3.0 Ga 37–8, 40, 68 from 3.5 to 0.75 Ga 58–60 after 0.75 Ga 60–5 minerals from 1, 2, 19 rate of 25–6 Wood–Ljungdahl pathway 108 yeast cells 183 yttrium 54 zinc 57, 229, 246 and binding 217 Subject Index cellular role 127, 128, 138–9, 142, 152, 239–40 enzymes 237, 239 carbonic anhydrases 242–3 hydroxylases 285 319 limitations on uptake 222 sea concentrations over time 69 zinc fingers 136, 147–8, 161, 217, 229, 238, 239 and gene duplication 283, 295 ... easily seen in fossils (see Table 1.2).3 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... Organisms 7.5 Anaerobic Cellular Chemistry to 3.0 Ga 7.6 The Oxidation of the System 7.7 Summary of the Evolution of the Oxidative Chemistry of the Elements 7.8 Summary of Why the Chemistry of the. .. Evolution s Destiny Co -evolving Chemistry of the Environment and Life RSC Nanoscience & Nanotechnology Series Editors: Professor Paul O’Brien, University of Manchester, UK Professor Sir Harry