The Equations of Life

by Charles S. Cockell

  The remaining two: Actually, these two electrons are split up, one each in two suborbitals, 2px and 2py. As px and py exist at the same level and have the same energy, the electrons, which would really rather be separate, tend to occupy these different suborbitals.

  Two are placed in the next orbital up: Like carbon, the two electrons in the outermost 3p orbital are in separate 3px and 3py orbitals.

  Resulting from all this versatility: McGraw-Hill. (1997) Encyclopedia of Science and Technology. McGraw, New York.

  The silicon-silicon bond: Alcock NW. (1990) Bonding and Structure: Structural Principles in Inorganic and Organic Chemistry. Ellis Horwood Ltd., New York. This information is also available from other standard chemistry texts.

  Silane (SiH4): Emeléus HJ and Stewart K. (1936) The oxidation of the silicon hydrides. Journal of the Chemical Society 677–684.

  These rocky silicates: They include the layered sheets (the phyllosilicates), strings of compounds (the inosilicates), and individual silicate tetrahedra (the nesosilicates). A very good book on the wide number of silicates is Deer WA, Howie RA, Zussman J. (1992) An Introduction to the Rock-Forming Minerals. Prentice-Hall, New York.

  These photosynthesizing microbes: Brzezinski MA. (1985) The Si:C:N ratio of marine diatoms: Interspecific variability and the effect of some environmental variables. Journal of Phycology 21, 347–357.

  Plants also gather: See, for example, Currie HA, Perry CC. (2007) Silica in plants: Biological, biochemical and chemical studies. Annals of Botany 100, 1383–1389.

  Silica structures: Müller WE et al. (2011) The unique invention of the siliceous sponges: Their enzymatically made bio-silica skeleton. Progress in Molecular and Subcellular Biology 52, 251–281.

  The silicon and carbon compound: Shiryaev AA, Griffin WL, Stoyanov E, Kagi H. (2008) Natural silicon carbide from different geological settings: Polytypes, trace elements, inclusions. 9th International Kimberlite Conference Extended Abstract No. 9IKC-A-00075.

  The atom seems to form: Röshe L, John P, Reitmeier R. (2003) Organic Silicon Compounds. Ullmann’s Encyclopedia of Industrial Chemistry. Wiley-VCH, Weinheim.

  Perhaps a black-and-white view: Cells can be coaxed into incorporating silicon into organic bonds (Kan SBJ, Lewis RD, Chen K, Arnold FH. [2016] Directed evolution of cytochrome c for carbon–silicon bond formation: Bringing silicon to life. Science 354, 1048–1051). However, engineering these capacities into life does not necessarily imply that if the tape of evolution were rerun, it would use these pathways. Artificial pathways successfully incorporated into cells are not necessarily those that would naturally be found and eventually used by life when it is faced with the selection pressures of a real planetary environment.

  Germanium is the next element: Johnson OH. (1952) Germanium and its inorganic compounds. Chemical Reviews 51, 431–469. This is admittedly an old paper, but a more modern knowledge does little to change the basic conclusion that germanium life forms seem unlikely.

  An imaginative, if highly unfamiliar suggestion: Bains W. (2004) Many chemistries could be used to build living systems. Astrobiology 4, 137–167.

  The liquid nitrogen would offer: The silanes are chemical compounds consisting of one or several silicon atoms linked to each other or to one or several atoms of other chemical elements. They comprise a series of inorganic compounds with the general formula SinH2n+2. They are similar to alkanes in carbon chemistry.

  Nevertheless, within these clouds: Snow TP, McCall BJ. (2006) Diffuse atomic and molecular clouds. Annual Review of Astronomy and Astrophysics 44, 367–414.

  Protons, electrons, gamma rays: Ions are atoms that have gained or lost electrons and therefore have a negative or positive charge, respectively.

  Diffuse interstellar bands: Herbig GH. (1995) The diffuse interstellar bands. Annual Review of Astronomy and Astrophysics 33, 19–73.

  Carbon, produced by fusion: See, for example, Kaiser RI. (2002) Experimental investigation on the formation of carbon-bearing molecules in the interstellar medium via neutral-neutral reactions. Chemical Reviews 102, 1309–1358; Marty B, Alexander C, Raymond SN. (2013) Primordial origins of Earth’s carbon. Reviews in Mineralogy and Geochemistry 75, 149–181; and McBride EJ, Millar TJ, Kohanoff JJ. (2013) Organic synthesis in the interstellar medium by low-energy carbon irradiation. Journal of Physical Chemistry 117, 9666–9672.

  The six-atom rings of carbon: There are a variety of discussions on polycyclic aromatic hydrocarbons and other complex carbon compounds. See, for example, Tielens AGGM. (2008) Interstellar polycyclic aromatic hydrocarbon molecules. Annual Reviews in Astronomy and Astrophysics 46, 289–337; Bettens RPA, Herbst E. (1997) The formation of large hydrocarbons and carbon clusters in dense interstellar clouds. Astrophysical Journal 478, 585–593; and Bohme DK. (1992) PAH and fullerene ions and ion/molecule reactions in interstellar circumstellar chemistry. Chemical Reviews 92, 1487–1508.

  They form tubes: Iglesias-Groth S. (2004) Fullerenes and buckyonions in the interstellar medium. Astrophysical Journal 608, L37–L40.

  Astrochemists think: Herbst E, Chang Q, Cuppen HM. (2005) Chemistry on interstellar grains. Journal of Physics: Conference Series 6, 18–35.

  Just 390 to 490 light-years away: IRC+10216 (CW Leo).

  Around the photosphere of the star: Groesbeck TD, Phillips TG, Blake GA. (1994) The molecular emission-line spectrum of IRC +10216 between 330 and 358 GHz. Astrophysical Journal Supplemental Series 94, 147–162.

  This molecule can take part: Coutens A et al. (2015) Detection of glycolaldehyde toward the solar-type protostar NGC 1333 IRAS2A. Astronomy and Astrophysics 576, article A5.

  Isopropyl cyanide: Belloche A, Garrod RT, Müller HSP, Menten KM. (2014) Detection of a branched alkyl molecule in the interstellar medium: iso-propyl cyanide. Science 345, 1584–1586.

  Equally extraordinary: Pizzarello S. (2007) The chemistry that preceded life’s origins: A study guide from meteorites. Chemistry and Biodiversity 4, 680–693.

  Although the concentrations: Sephton MA. (2002) Organic compounds in carbonaceous meteorites. Natural Product Reports 19, 292–311; and Pizzarello S, Cronin JR. (2000) Non-racemic amino acids in the Murray and Murchison meteorites. Geochimica et Cosmochimica Acta 64, 329–338.

  Why the discrepancy? A discrepancy true for many other types of molecules.

  Sugars, the building blocks: Deamer D. (2011) First Life: Discovering the Connections Between Stars, Cells, and How Life Began. University of California Press, Berkeley.

  Meteorites come from asteroids: An astronomical unit is equivalent to the mean distance between the Sun and Earth.

  No mere blocks of ice: Altwegg K. (2016) Prebiotic chemicals—amino acid and phosphorus—in the coma of comet 67P/Churyumov-Gerasimenko. Science Advances 2, e1600285,

  carbon chemistry: The leap between simple carbon compounds and a self-replicating life form is immense, and we do not know if it is inevitable on any planet where there is liquid water and appropriate physical conditions. In this book, I do not address the question of how common life is in the universe. Rather, I am more concerned with whether, once it does emerge, it has universal characteristics. Whatever that spark or environmental condition was that allowed life to emerge, however likely or unlikely it was, it has no relevance to the observation that the conditions in which solar systems emerge produce a preponderance of organic compounds.

  The tendency of energetic environments: For a description of this experiment, see Miller SL. (1953) A production of amino acids under possible primitive Earth conditions. Science 117, 528–529. A more recent study examining the results is Bada JL. (2013) New insights into prebiotic chemistry from Stanley Miller’s spark discharge experiments. Chemical Society Reviews 42, 2186–2196.

  From above and below, young planets: Chyba C, Sagan C. (1992) Endogenous production, exogenous delivery and impact-shock synthesis of organic molecules: An inventory for the origin of life. Nature 355, 125–132.

  Its methane lakes: Raulin F, Owen T. (2002) Organic chem
istry and exobiology on Titan. Space Science Reviews 104, 377–394.

  Its brown atmospheric haze: Sagan C, Khare BN. (1979) Tholins: Organic chemistry of interstellar grains and gas. Nature 277, 102–107.

  Future robotic missions: Lorenz RD et al. (2008) Titan’s inventory of organic surface materials. Geophysical Research Letters 35, L02206.

  Of all the atoms available: See Goldford JE, Hartman H, Smith TF, Segrè D. (2017). Remnants of an ancient metabolism without phosphate. Cell 168, 1–9, for a compelling hypothesis about a precursor to modern biology that may have worked without phosphorus.

  Familiar to most of us: One landmark paper on this matter is Westheimer FH. (1987) Why nature chose phosphates. Science 235, 1173–1178.

  The molecule ATP: Maruyama K. (1991) The discovery of adenosine triphosphate and the establishment of its structure. Journal of the History of Biology 24, 145–154.

  Strung down the backbone of DNA: The classic paper of the elucidation of this structure is Watson JD, Crick FH. (1953) A structure for Deoxyribose Nucleic Acid. Nature 171, 737–738, but of course much of the deeper understanding of the properties of DNA, including its phosphorus-containing backbone, has been developed since then and can be found in a vast literature.

  Two sulfur-containing amino acids: Two molecules of the sulfur-containing amino acid cysteine. For the disulfide bridge, see Sevier CS and Kaiser CA. (2002) Formation and transfer of disulphide bonds in living cells. Nature Reviews Molecular Cell Biology 3, 836–847.

  The carbon-fluorine bond: Blanksby SJ, Ellison GB. (2003) Bond dissociation energies of organic molecules. Accounts of Chemical Research 36, 255–263.

  In the tropics: O’Hagan D, Harper DB. (1999) Fluorine-containing natural products. Journal of Fluorine Chemistry 100, 127–133.

  It can be found in cells: Baltz JM, Smith SS, Biggers JD, Lechene C. (1997) Intracellular ion concentrations and their maintenance by Na+/K+-ATPase in preimplantation mouse embryos. Zygote 5, 1–9.

  In an article published: Wolfe-Simon F et al. (2010) A bacterium that can grow by using arsenic instead of phosphorus. Science 332, 1163–1166.

  The microbe: Rosen BP, Ajees AA, McDermott TR. (2011) Life and death with arsenic. BioEssays 33, 350–357.

  The estimated half-life: A half-life is the time it takes for half of something, such as a chemical compound, to disintegrate.

  If you replace arsenate: Fekry MI, Tipton PA, Gates KS. (2011) Kinetic consequences of replacing the internucleotide phosphorus atoms in DNA with arsenic. ACS Chemical Biology 6, 127–130.

  Its uses are enigmatic: Edmonds JS et al. (1977) Isolation, crystal structure and synthesis of arsenobetaine, the arsenical constituent of the western rock lobster Panulirus longipes cygnus George. Tetrahedron Letters 18, 1543–1546.

  The energetic cost: Reich JH and Hondal RJ. (2016) Why nature chose selenium. ACS Chemical Biology 11, 821–841. This paper is a recapitulation of Westheimer’s paper “Why Nature Chose Phosphates.”

  It is an essential trace element: See, for example, Blevins DG, Lukaszewski KM. (1998) Functions of boron in plant nutrition. Annual Review of Plant Physiology and Plant Molecular Biology 49, 481–500; and Nielsen FH. (1997) Boron in human and animal nutrition. Plant and Soil 193, 199–208.

  Elements like vanadium: Many researchers are exploring the role of different elements in life, particularly the lesser-known elements. For vanadium and molybdenum, see, for example, Rehder D. (2015) The role of vanadium in biology. Metallomics 7, 730–742; and Mendel RR, Bittner F. (2006) Cell biology of molybdenum. Biochimica et Biophysica Acta 1763, 621–635.

  The imaginative may well raise their hands: A popular take on this is in the 1969 novel by Michael Crichton, The Andromeda Strain. In the novel, a returning space capsule has been contaminated with a crystal-based life form that threatens to overrun the laboratory in which it has been contained and escape into the terrestrial environment. Eventually, and happily for the Earth, it mutates into a less malignant form of life.

  Mineral surfaces as places: Mineral surfaces provide ordered structures for the assembly of polymers, which themselves become ordered and aligned. The possible role of minerals in the assembly of the first self-replicating genetic structures was discussed in Cairns-Smith AG, Hartman H. (1986) Clay Minerals and the Origin of Life. Cambridge University Press, Cambridge, and the area was reviewed nicely in Arrhenius GO. (2003) Crystals and life. Helvetica Chimica Acta 86, 1569–1586.

  CHAPTER 11

  Sometimes this is referred to: This problem is nicely summarized by Mariscal C. (2015) Universal biology: Assessing universality from a single example. In The Impact of Discovering Life Beyond Earth, edited by Dick SJ, 113–126; and Cleland CE. (2013) Is a general theory of life possible? Seeking the nature of life in the context of a single example. Biological Theory 7, 368–379.

  It is easy to get trapped: I even feel uncomfortable with the term physical principles, despite using it prolifically in this book. What do we actually mean by physical? We just mean principles by which the universe works. The word physical tends to segregate physicists and other types of scientists, removing its neutrality and encouraging proudly defended disciplinary boundaries. Maybe we should just speak of principles. Nevertheless, I use the term because it does conveniently emphasize that we are talking about principles that pertain to matter and not other principles, like legal or moral ones.

  Although many people think: It would be tempting to provide a proposed definitive list of things that are universal about life. However, I am reluctant because a person only has to make one false prediction, and the list becomes an example of the N = 1 problem, which is counterproductive. I find it more parsimonious to offer some broad suggestions. Defining such a list in greater detail and carrying out experiments to attempt to challenge it could produce worthwhile and interesting results and, over time, might generate a more robust list of characteristics at all scales of life—characteristics that most of us could agree were universal. See, for example, Cockell CS. (2016) The similarity of life across the Universe. Molecular Biology of the Cell 27, 1553–1555.

  The scaling laws: West GB. (2017) Scale: The Universal Laws of Life and Death in Organisms, Cities and Companies. Weidenfeld & Nicolson, London.

  Perhaps, like DNA: Benner SA, Ricardo A, Carrigan MA. (2004) Is there a common chemical model for life in the Universe? Current Opinions in Chemistry and Biology 8, 672–689.

  In our own Solar System: See, for example, Grotzinger JP et al. (2014) A habitable fluvio-lacustrine environment at Yellowknife Bay, Gale Crater, Mars. Science 343, doi:10.1126/science.1242777.

  Substantial liquid water oceans: There are many papers discussing the oceans of Europa, for example Hand KP, Carlson RW, Chyba CF. (2007) Energy, chemical disequilibrium, and geological constraints on Europa. Astrobiology 7, 1–18; Schmidt B, Blankenship D, Patterson W, Schenk P. (2011) Active formation of “chaos terrain” over shallow subsurface water on Europa. Nature 479, 502–505; Collins GC, Head JW, Pappalardo RT, Spaun NA. (2000) Evaluation of models for the formation of chaotic terrain on Europa. Journal of Geophysical Research 105, 1709–1716. For the moon Enceladus, see, for example, McKay CP et al. (2008) The possible origin and persistence of life on Enceladus and detection of biomarkers in plumes. Astrobiology 8, 909–919; Waite JW et al. (2009) Liquid water on Enceladus from observations of ammonia and 40Ar in the plume. Nature 460, 487–490; Waite JH et al. (2017) Cassini finds molecular hydrogen in the Enceladus plume: Evidence for hydrothermal processes. Science 356, 155–159. And for the moon Titan, see Raulin F, Owen T. (2002) Organic chemistry and exobiology on Titan. Space Science Reviews 104, 377–394.

  Even if they do, a confounding problem: See, for example, Horneck G et al. (2008) Microbial rock inhabitants survive hypervelocity impacts on Mars-like host planets: First phase of lithopanspermia experimentally tested. Astrobiology 8, 17–44; and Fajardo-Cavazos P, Link L, Melosh JH, Nicholson WL. (2005) Bacillus subtilis spores on artificial meteorites survive hypervelocity atmospher
ic entry: Implications for lithopanspermia. Astrobiology 5, 726–736.

  It is premature: We could detect these biospheres by looking for gases such as oxygen in the planetary atmosphere. That in itself would tell us something about the sorts of metabolisms that the alien life uses. However, without a laboratory sample of this life, we will be limited in the knowledge we can derive about its structure at the different levels of its hierarchy that we have been discussing in this book.

  That discovery of this first so-called exoplanet: The paper describing this finding is Mayor M, Queloz D. (1995) A Jupiter-mass companion to a solar-type star. Nature 378, 355–359. The planet is named Pegasi 51b. Planets are generally named sequentially using letters.

  Many planets: For one example of how these discoveries have reignited new efforts to explain how the alignments of the planets in our own Solar System came about, see Tsiganis K, Gomes R, Morbidelli A, Levison HF. (2005) Origin of the orbital architecture of the giant planets of the Solar System. Nature 435, 459–461.

  Alongside the bounty of hot Jupiters: Santos NC et al. (2004) A 14 Earth-masses exoplanet around μ Arae. Astronomy and Astrophysics 426, L19–L23.

  It has one-quarter the density: Bakos GA et al. (2007) HAT-P-1b: A large-radius, low-density exoplanet transiting one member of a stellar binary. Astrophysical Journal 656, 552–559.

  This inflated ball epitomizes: Mandushev G et al. (2007) TrES-4: A transiting Hot Jupiter of very low density. Astrophysical Journal Letters 667, L195–L198.

  Many of them are likely to be uninhabitable: The first planets in the super-Earth-size range were found in 1992 orbiting the pulsar PSR B1257+12. Because a pulsar is the collapsed neutron star remnant of a supernova explosion, they are not thought to be habitable or to have oceans. Wolszczan A, Frail D. (1992) A planetary system around the millisecond pulsar PSR1257 + 12. Nature 355, 145–147.

  Some are likely to be ocean worlds: Charbonneau D et al. (2009) A super-Earth transiting a nearby low-mass star. Nature 462, 891–894.