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Bernd Markert · Stefan Fränzle Simone Wünschmann Chemical Evolution The Biological System of the Elements Chemical Evolution ThiS is a FM Blank Page Bernd Markert Stefan Fraănzle Simone Wuănschmann Chemical Evolution The Biological System of the Elements Bernd Markert Environmental Institute of Scientific Networks (EISN) Haren Germany Stefan Fraănzle International Graduate School Zittau Zittau Germany Simone Wuănschmann Environmental Institute of Scientific Networks (EISN) Haren Germany ISBN 978-3-319-14354-5 ISBN 978-3-319-14355-2 DOI 10.1007/978-3-319-14355-2 (eBook) Library of Congress Control Number: 2015933157 Springer Cham Heidelberg New York Dordrecht London © Springer International Publishing Switzerland 2015 This work is subject to copyright All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed The use of general descriptive names, registered names, trademarks, service marks, etc in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use The publisher, the authors and the editors are safe to assume that the advice and information in this book are believed to be true and accurate at the date of publication Neither the publisher nor the authors or the editors give a warranty, express or implied, with respect to the material contained herein or for any errors or omissions that may have been made Cover: The cover of the book represents The Biological System of the Elements (BSE) developed by one of these authors, Prof Dr Bernd Markert, in 1994 Printed on acid-free paper Springer International Publishing AG Switzerland is part of Springer Science+Business Media (www.springer.com) Preface Generally speaking, we are concerned with the question: Where did organicchemistry-based life come from? This volume now in your hands was motivated by the attempt to discuss and to some extent explain chemical evolution from the point of view of physiological, essential, or at least beneficial activities of chemical elements in contemporary biology From these chemical features, there may be hints to the pathway which eventually enabled biological evolution to start, using evidence from chemical evolution experiments as well as the Biological System of Elements (BSE) concerning present functions or roles of these elements Chapter deals with considerations on the formation of chemical elements in cosmic systems and cosmochemistry providing building blocks for living beings within the Solar System, going back to astrophysical element syntheses ever since Big Bang took place some 13.8 billion years ago Catalytic aspects observed in experiments on prebiotic chemistry and the presence of organics and HCN in interstellar medium, meteorites, and other celestial bodies all argue for a setting which is favorable for making chemical building blocks of biology right during aggregation of planets or large moons Later on, requirements on the presence, properties, and interaction modes of environmental compartments such as atmosphere and liquidosphere in order to form life and be sustained somewhere will be discussed Thereafter (Chap 2), chemical evolution would take place following pathways which are still much of a puzzle, but finally making living beings from organic molecules (and possibly additional components; abiogenesis) During Hadean ages (4 bio years from now), these processes preceded the evolution of organisms which are distinguished by a generally cellular organization Ever since, biological evolution produced new living beings from already existing ones (biogenesis), chemical evolution is distinguished by the spontaneous formation of structures including chiral biases of organic molecules by chemical processes such as autocatalysis in some cases For this to happen, there must be flow systems and throughflow equilibria A possible (some say: most likely) reason and site for this v vi Preface are chemical and thermal gradients which exist around hot springs at the bottom of the oceans, better known as black smokers On a molecular level, biological processes follow physicochemical laws, but the actual outcomes may yet differ from “plain” chemistry due to adaptations of all organic living beings to an aqueous milieu To start with a simple example, membrane passage dynamics of Na and K cations is the other way round than would be expected This is unlike the hydratation of ions causing Naaq+ to have a larger diameter than Kaq+ (and even Rbaq+) and thus pass through (nerve and other biological) membranes only in certain conditions while K and Rb ions could so rather easily In order to account for physiological effects of chemical elements in living beings using some Biological System of Chemical Elements (BSE), the familiar Periodic Chemical System of Elements (PSE) according to Mendeleyev and Meyer (1869) had to be completed and modified also using the Geochemical System by Railsback (2003) which offered important hints and pieces of information The Biological System of Elements goes beyond accumulating essentiality investigations which have obvious technical and analytical limitations In correlations among abundances of elements in different samples of biological origins, there are deep-rooted biochemical factors and relationships which these authors started to study and describe in more detail already in the late 1990s (Markert 1994, 1996, 1998; Fraănzle and Markert 2000) Different features of chemical elements within the BSE produce the three edges of its graphic representation These refer to the capability to form highly aggregated structures, salinity of milieu, and “organicbiochemical relatedness” of chemical species formed around this element; parameters linked to these dimensions, edges, or features accordingly have multiple implications In Chap 3, the biological role of different chemical species (elements rather than their speciation forms) is discussed in more detail Essentiality or toxicity depends on the impact on enzyme activities, far beyond coordination properties and preferences considered in bioinorganic chemistry Beyond “simple” catalysis, biological reproduction, or it being compromised by certain elements, every protein which relies on metal ions inside or gets influenced by taking them up will influence its own reproduction in terms and manners of autocatalysis Stoichiometric Network Analysis (SNA), which was introduced by Clarke in the 1970s, explicitly deals with which principal modes of dynamics may be open to such autocatalytic systems in various circumstances (Chap 4) This allows us to consider and analyze aspects of bioinorganic chemistry of metalloproteins including essentiality versus toxicity of element (speciation forms), testifying their roles as building blocks or controlling entities within or connected to autocatalytic feedback loops The SNA theorems are used to produce a system of non-equations describing the possible or unlikely autocatalytic behavior of certain metals within the framework of biology This is meant to enable detailed statements and even predictions whether a certain element may be essential or beneficial to physiology, and, if so, whether there are certain ranges of redox potential or binding forms such as complexes or biomethylation products which might enable such behavior Preface vii Returning from chemical and biological evolution to the recent demands of humans, let us consider the possible role of chemical elements to be employed in medical research or health surveillance, including pharmaceutical applications of, e.g., Cr in type II diabetes or Li in a range of mental/psychical diseases While neither element should be considered as essential for humans by now, both are obviously able to relieve severe disease symptoms in patients stricken by the mentioned illnesses Chapter deals with the roles of water, soil, and atmosphere for chemical evolution Finally, Chap offers a glimpse on features of chemical evolution investigated by means of comparative (chemical) planetology, that is, we shall have a look at space research related to it, concerning both present and planned space probe missions It is obvious that this field of research will continue to yield most exciting and informative results An extended and detailed Appendix gives relevant information on the functionality of singular chemical elements Many thanks ought to be given to all the colleagues who helped us to prepare this volume, answering numerous questions in great detail In addition, many thanks to Springer and its staff for giving us the opportunity to publish this book and who supported us in many ways Dear readers, we hope to give you an impression of what chemical evolution might have been and worked like and look forward to your criticism of any kind Haren/Erika and Zittau Autumn 2014 Bernd Markert Stefan Fraănzle Simone Wuănschmann ThiS is a FM Blank Page List of Abbreviations AAN AAs ATP B&B BAF BCF BIF BP Bq BSE DM EDTA EUV FTT GC/MS GSE ICBM INTECOL IRC ISM IUBS IUPAC KBOs KT LMCT LUCA MER MLCT MT NA Aminoacetonitrile Amino acids Adenosine Triphosphate Bioindication and Biomonitoring Technologies Biological Accumulator Factor Biological Concentration Factor Banded Iron Formations Years before the Present Becquerel The Biological System of the Elements Dry Matter Ethylenediaminetetraacetic Extreme Ultraviolet Fischer–Tropsch-Type Gas Chromatography/Mass Spectrometry Geochemical System of the Elements originally: The Earth Scientist’s Periodic Table of the Elements and their Ions’ Intercontinental Ballistic Missile International Association for Ecology Catalogue of Astronomical Infrared Sources Interstellar Medium International Union of Biological Sciences International Union of Pure and Applied Chemistry 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Anomalocaris, 129, 130, 133, 135 Argentavis magnificens, 118 Arsenic, 81, 93, 107, 110, 150, 151, 156, 194 Asteroid, 19, 21, 41, 42, 126, 187, 218, 237, 240, 241, 248, 251, 252, 254 Astronomy, 6, 20, 239, 252 Atlantic, 119–121 Atmosphere hydro, 14, 31, 33 liquid, 12, 14, 33 Autocatalysis, 44, 48, 98–99, 114, 158–164, 166, 168, 169, 175, 179–181, 199, 237, 239, 246, 254 B Bacteria, 7, 15, 28, 29, 56, 68, 74, 88, 97, 100, 102, 103, 106, 110, 114, 123, 124, 135, 141, 142, 145, 153, 155, 156, 164, 165, 167, 179, 209, 211, 214, 216, 217, 219, 225, 226, 232, 233, 238, 250 Beneficial, 64, 88, 106–108, 150, 243 Big Bang, 2, 40, 104, 238, 243 Biocatalysis, 60, 96, 110, 149, 179, 190 Biogenesis, 3, 12, 31, 40, 41, 44, 45, 48, 61, 98, 100, 104, 124, 181, 198, 208, 237, 238, 243, 246, 251 Biogenetic law, 116, 117, 238 Biological System of the Elements (BSE), 63–104, 238 Biomass, 4, 5, 40, 69, 75, 99, 103, 110, 113, 114, 123, 125, 138, 147, 148, 150, 154, 156, 162, 163, 166, 167, 169, 170, 172, 174–176, 178, 215, 223, 224, 234 Biomethylation, 60, 110, 148–154, 156, 212, 216, 217, 226, 228, 229, 238 Biomineralization, 58, 102, 129, 133, 136, 238 Biosphere, 65, 83, 85, 103, 166, 169, 178, 186, 197 Black smoker, 59, 103, 168, 175, 183 BSE See Biological System of the Elements (BSE) Burgess Shale, 129, 131, 132, 139 C Cambrian, 126, 129–133, 135–137, 139, 140, 251 Carbon, 5, 11, 24, 28, 29, 36, 40, 41, 46, 65, 70, 81, 82, 91, 92, 94, 114, 123, 133, 137, 138, 146, 163, 164, 166, 168, 186, 188, 212, 244, 249 Cassini spacecraft, 202 Catalysis, 16, 17, 47–48, 50, 98, 125, 126, 128, 136, 139, 163, 179, 181, 183, 186, 230, 232, 239, 241, 244, 249 Catalyst, 46, 48, 57, 98, 99, 125, 142, 144–146, 158, 160, 163, 168, 181, 182, 190, 194, 223–225, 230, 234, 237, 238, 254 © Springer International Publishing Switzerland 2015 B Markert et al., Chemical Evolution, DOI 10.1007/978-3-319-14355-2 279 280 Cave, 137, 164, 165 Celestial body, 7, 8, 10, 12, 18–36, 45, 199, 240, 252 Chemofossil, 240 Chemosynthesis, 99, 123, 164, 165, 175 Comet, 7, 10, 12, 19, 197, 199, 204, 240, 254 Complexation, 16, 57, 60, 89, 114, 123, 135, 148, 176, 178, 179, 182, 183, 213, 219, 232, 255 Complex formation constants, 176–178, 182, 241, 246 Conodont, 133, 134 Cosmochemistry, 7, 13 Curiosity, 12, 22, 23, 25, 26, 58, 191, 201, 204, 243, 252 D Dinosaurs, 125, 137, 138, 246 Dust devil, 26, 27 E Earth early, 241 early super, 12, 22 Earth Scientist’s Periodic Table of the Elements and Their Ions See Geochemical System of the Elements (GSE) Ecosystem, 31, 64, 76, 77, 80, 83–85, 122, 123, 125, 129, 133, 159, 161, 163–169, 204, 242, 245, 254 Ediacaran, 129, 134, 140 Element, 1, 63–122, 160, 188, 209 Enceladus, 11, 39, 103, 197, 199, 202, 204 Enzyme, 40, 61, 81, 89, 97, 107, 125, 128, 135, 142, 144, 149, 159, 161, 162, 167, 180, 213–214, 219–221, 231 Equilibrium, 15, 16, 21, 22, 25, 99, 102, 103, 114, 123, 125, 160, 161, 168, 178, 187, 207, 209, 213, 233, 234, 239, 241, 243 Essentiality, 60, 63, 76, 81, 84, 97, 105–136, 139, 140, 147–150, 152, 153, 169, 176, 179–183, 209–234 Europa, 38, 103, 197, 202, 203, 207 Evolution biological, 58–62, 86, 123, 124, 186, 198, 242, 243 chemical, 1–62, 98, 99, 105, 122, 123, 158, 161, 175–179, 181, 182, 185–195, 197–207 mineral, 58 Exoplanet, 10–12, 14, 19, 20, 22, 32, 44, 198, 205, 207–208, 242 Extraterrestrial life, 7, 29, 162, 200 Index F Formaldehyde, 5, 6, 10, 11 Fossil, chemical fossils, 43 G Gas planet, 7, 10, 18, 20, 21, 31, 32, 36, 198, 207, 254 See also Planet Geochemical System of the Elements (GSE), 100–104 Glycine, 4, 6, 7, 12, 17, 48, 50, 54–56, 96, 100, 123, 124, 143, 182, 237, 248 Gravitation, 21, 22, 200, 245, 251 Green house effect, 13, 21, 44, 186, 212, 254 H Haikouichthys, 130, 132 Hallucigenia, 129, 132 Huygens probe, 33, 34, 206 Hydrogen, 2, 6, 17, 18, 22, 25, 32, 65, 73, 91, 92, 123, 141, 145, 161, 186–188, 212, 245, 248, 254 Hydrosphere, 18, 36, 65, 248, 249 I Identity cards, 149–156 Illumination, 6, 30, 141, 237, 251 Inorganics, 1, 13, 47, 64, 68, 76–81, 84, 96–98, 107, 126, 135, 137, 147, 150–153, 163, 165, 188, 189, 199, 204, 212, 223, 238, 255 Intelligent life, 2, 6, 253 Interstellar medium, 6–12, 123, 189, 199, 243 Invertebrates, 129, 213 Ionization, 82 Iron, 25, 42, 46, 49, 51, 57, 58, 61, 65, 66, 98, 117, 123, 141, 143, 187, 188, 191, 216, 222, 230, 237, 238, 241, 251 K Kuiper belt, 10–12, 199, 204, 206–207, 241, 245, 251 L Last universal ancestor (LUCA), 60, 61, 232, 233, 243, 246 Life, 2–7, 9, 12, 14, 15, 18, 25, 28, 29, 31, 32, 36–47, 60, 62, 69, 82, 91, 96, 97, 103, 105, 106, 114, 118, 119, 123, 124, 129, 164, 166, 175, 180, 181, 183, 186, 188– 193, 195, 198, 200, 202, 204, 207, 216, 223, 233, 237, 238, 243, 247, 251–254 Index 281 N Nectocaris, 130, 132, 135 Neptune, 20, 31, 32, 36, 39, 203, 205, 251 P Periodic Table of the Elements (PSE), 63, 67, 82, 83, 85, 93–96, 100–104, 147, 171, 248, 250 Photochemistry, 14, 21, 25, 31, 34, 36, 44–46, 103, 141, 251 Photoelectrochemistry, 31, 190 Photolysis, 13, 14, 18, 25, 46, 51, 123, 154, 186, 190, 194, 206, 207, 220 Photooxidation, 18, 39, 110, 141, 216, 251 Photosynthesis, 42, 58, 59, 97–99, 102, 103, 123, 124, 138, 141, 146, 164, 166–168, 175, 186, 212, 213, 220, 221, 239, 240, 251 Pikaia, 130, 132, 139 Planet dwarf, 31 exo, 10–12, 14, 19, 20, 22, 32, 44, 198, 205, 207–208, 242 gas, 7, 10, 18, 20, 21, 31, 32, 36, 198, 199, 207, 254 terrestrial, 18, 21, 32, 179, 189, 240, 247 Pluto, 13, 19, 20, 22, 39, 100, 204–207, 245 Polymers, 10, 18, 24, 29–31, 34, 35, 43, 47, 62, 95–97, 111, 124, 128, 168, 179, 181, 183, 186, 193, 232, 243, 245, 247, 249 Polymerization, 14, 194 Prebiotic reaction, 17, 47, 181 Pressure, 14–17, 20, 21, 31, 33, 35, 38, 45, 46, 49, 117, 140, 169, 185, 186, 191, 192, 194, 203, 207, 231, 247, 250 Protein, 5, 40, 47, 60, 61, 70, 71, 88, 90, 96, 105, 106, 109, 114, 117, 125, 128, 131, 133, 136, 139, 147, 161, 175, 178–180, 212, 222, 230, 231, 235, 246, 253 PRX See Viking, Pyrolytic Release Experiment (PRX) PSE See Periodic Table of the Elements (PSE) Pteranodon, 118 Pterosaurs, 118, 125, 138, 246 O Ontogeny, 116, 117, 122, 249 Organics, 1, 65, 110, 161, 186, 198 Oxidation, 12, 15, 18, 22, 38, 50, 54, 56, 57, 70, 91, 94, 95, 97, 98, 102, 111, 115, 119, 124, 127, 135, 136, 140, 142, 147, 149, 150, 152–156, 164–166, 193, 194, 213, 215, 222, 224, 230, 238, 247, 249 Oxygen, 18, 22, 25, 26, 61, 65, 92, 95, 102, 117, 120, 122, 137, 165, 207, 215, 241, 244, 245 R Radiation, 8, 10, 13, 17–19, 22, 25, 31, 33, 34, 37, 38, 44, 45, 47, 57, 76, 103, 114–116, 123, 139–141, 185, 186, 188–190, 198, 199, 206, 237, 239, 242, 248, 250, 251, 253 Reference plant, 64, 75–81, 85, 234, 252 Rover Curiosity, 23, 26, 191 New Horizons, 205 Opportunity, 27, 105 Spirit, 27 Viking, 12 Ligand, 59, 60, 72, 97, 125, 128, 138, 146–148, 150–152, 176–182, 230, 241, 243, 256 Ligand electrochemical parameter, 177 Liquidosphere, 13, 14, 22, 33, 45, 179, 185– 195 Loricifera, 119–123, 220 LUCA See Last universal ancestor (LUCA) M Magma, 18, 189, 195 Mars, 6–9, 12, 13, 16, 18, 20, 21, 23, 25–28, 30, 32, 34, 36–38, 40, 41, 43, 45, 46, 58, 102, 103, 123, 146, 180, 183, 185–187, 189–194, 197, 198, 200–203, 205–207, 240, 241, 244, 248, 251–254 Metabolism, 1, 28, 29, 43, 65, 70, 71, 89, 91, 92, 99, 102, 106, 108, 120, 122, 124, 126, 128, 134, 135, 137, 138, 163, 210, 211, 214, 215, 220, 222, 223, 226, 230, 231, 237, 251, 254 Metal, 2, 65, 105, 160, 186, 212 Meteorites, 6–10, 22, 29, 37, 41, 43, 46, 49, 51, 58, 187, 189, 202, 240, 248 Miller-Urey experiment, 8, 44, 45 Minerals, 3, 5, 8, 12, 14–19, 21–25, 29, 31, 37, 38, 41, 42, 44, 46, 48, 54, 55, 57, 58, 72, 86, 92, 97–99, 101–104, 111, 123, 126, 127, 129, 133, 155, 160, 162, 175, 180, 181, 185, 187, 190–192, 213, 238, 243, 245, 251 Moon, 2, 4, 7, 9, 13, 18, 32, 33, 36, 38, 40, 41, 44, 191, 198, 200, 202, 206, 207, 238, 240, 248, 252 282 S Saturn, 7, 19–21, 24, 32, 34, 36, 39, 202, 205, 251 Sediment, 13–15, 17, 22, 23, 40–42, 46, 97, 101, 119, 121, 125–127, 141, 163, 166, 180, 185, 233, 240, 252 SNA See Stoichiometric network analysis (SNA) Soil, 4, 18, 22, 24–26, 28, 30, 32, 34, 58, 71–73, 77, 83, 84, 92, 101, 102, 104, 109, 113, 122, 162, 164, 167–170, 172, 174, 175, 185–195, 205, 210, 212, 217–221, 223–226, 228, 229, 231, 233, 234, 244, 251, 254 Solar System, 2, 7, 11, 12, 20, 22, 24, 25, 35–37, 41, 42, 44, 45, 187, 199, 207, 208, 240, 251 Space probes, 6, 10, 187, 253 Spectroscopy, 6, 19, 20, 23, 31, 33, 204, 207, 241, 242, 248, 254 Spiniloricus, 119 Star, 2, 6, 8–12, 14, 19, 31, 32, 40, 41, 44, 45, 95, 123, 159, 200, 207, 237, 239, 243, 245, 248, 250, 252 Stardust, 12, 199 Stoichiometric network analysis (SNA), 84, 97, 99, 100, 152, 153, 157–183, 242, 245, 254 Stromatolith, 14, 15, 42 Sugar, 142, 143, 162, 193, 194, 211, 212, 227, 247 Sun, 2, 7, 10, 14, 18, 19, 24, 32, 38, 41, 46, 199, 239, 240 Supernova, 41, 44, 103, 123 Systems of the Elements Biological System of the Elements, 63–104, 238 Geochemical System of the Elements, 100–104 Periodic Table of the Elements, 63, 67, 82, 83, 85, 93–96, 100–104, 147, 171, 248, 250 T Telescope, 3, 19, 32, 239 Temperature, 15, 21, 24, 25, 31, 33–36, 44, 45, 76, 107, 137, 138, 146, 188, 190, 192, 198, 204, 207, 230, 233, 238, 240, 247, 248, 253 Index Terrestrial body, 2, 21, 24 planet, 18, 21, 32, 84, 87, 103, 114, 179, 189, 192, 240, 247 Thallium, 151, 155, 156, 254 Thyroxine, 107, 118, 119 Tin, 81, 82, 151, 153, 227 Titan, 6, 7, 13, 14, 18, 20–22, 24, 32–34, 36, 39, 43, 45, 100, 103, 187, 191, 197, 198, 202, 203, 205–207 Toxicity, 60, 63, 64, 69, 72, 74, 81, 107, 147–153, 179–183, 209–234, 238, 241, 247 Trace elements, 71, 83–85, 109, 168, 233 Triton, 10, 11, 13, 14, 20–22, 25, 36, 39, 100, 202–207 Troposphere, 34, 35, 136, 198, 203 U Universe, 2, 40, 103, 238, 243, 253 V Vendian, 129, 134, 140 Venus, 19–21, 32, 34, 36, 37, 46, 100, 189, 191–193, 205, 242, 251, 252, 254 Vertebrates, 4, 43, 60, 81, 107, 110, 111, 116, 118, 128–133, 136, 139, 140, 152, 210, 213, 218, 223, 224, 226, 227, 239, 247 Viking, Pyrolytic Release Experiment (PRX), 9, 28–31, 190, 251, 254 Volcano, 11, 13, 18, 24, 37, 46, 54, 59, 100, 187, 193, 194, 244, 253, 254 W Water liquid, 192 rainwater, 15–17, 138, 141 solid, 21 vapor, 22, 29, 32, 33 Window of Essentiality, 179–181 Z Zircon, 41, 103, 189 ... omissions that may have been made Cover: The cover of the book represents The Biological System of the Elements (BSE) developed by one of these authors, Prof Dr Bernd Markert, in 1994 Printed on acid-free... 93 2.5.2 The Biological System of the Elements 96 2.5.3 Geochemical System of the Elements 100 2.5.4 Link in Between the Three Systems of Chemical Elements... Existing Regularities in the Periodic System of the Elements to Explain Biological Functions of Chemical Elements 2.3.2 Criticism on the Classical Periodic System of the Elements