The Miracle of the Cell

Michael Denton

11 Introduction

p11 "My main aim in the Privileged Species series is to present the evidence that nature is uniquely fit for life as it exists on Earth, not just for the generic carbon-based cell, but also for beings of our biology and thus to show that the cosmos is not just biocentric but also (no matter how unfashionable it may be in certain quarters) anthropocentric as well."

p11 "This particular book is focused on the fitness of nature for the familiar carbon-based cell, which is the basic unit of all life on Earth." " the properties of many of the atoms of the periodic table, including carbon, hydrogen, oxygen, and nitrogen, as well as phosphorus and several metals, to highlight their unique fitness to serve various biochemical ends in the cell." "..the evidence conveys the irresistible impression that the properties of the atoms have been crafted with incredible precision to perform highly specific functions upon which the life of the cell depends." "..collective fitness .. make up ..'primal blueprint' for the design of the carbon-based cell, a blueprint laid down in the order of things from the beginning of the universe."

15 1. The Amazing Cell

This chapter is a kind of soliloquy to the amazing cell.

p16 Like he did in "The Wonder of Water," he pays homage to Lawrence Henderson for his amazing 1913 book "The Fitness of the Environment".

Many examples of the amazing capabilities of cells.

p19 After a varied series of examples of the marvels of different types of cells, he comments "an even greater wonder is the stunning prior fitness in nature that enables the material actualization of the canonical carbon-based cell."

p20 "this prior fitness is manifest also in the extraordinary utility of water to serve as the matrix of the cell, and by chemical processes in the dark vastness of interstellar space that result in the a-biotic synthesis of many of the molecular monomers used by the first cells to build their macromolecular constituents. In other words, the 'demonic'[this alludes to Jacques Monod and his book "Chance and Necessity" where he found the catalytic properties of cells amazing enough to characterize it as 'demonic'.p19] fitness of the cell depends on a deeper fitness prefigured into the very fabric of reality. This deeper fitness is inscribed in the laws of nature from the beginning of time, a fitness that reveals the cosmos to be as Henderson proclaimed, a profoundly biocentric whole."

21 2. The Chosen Atom

p21-24 General discussion of the history and retreat of vitalism.

p23 Mentions William Prout, leading physician and chemist in early nineteenth century, author of the Eighth Bridgewater Treatise, who believed in a tiny special cell component exercising a "vital force"

p24 Major blow to vitalism when Friedrich Wohler synthesized urea in 1828. Discussed by Ahern in my Great Course video series on biochamistry, and considered to be the beginning of biochemistry. Discussion of the impact of this discovery. In 1845, Hermann Kolbe "put another nail in the coffin" of vitalism by synthesizing acetic acid. Denton says "the dam broke, and scientists synthesized more and more organic compounds in the lab."

p25 "...throughout the nineteenth century it became ever clearer that not only were the chemical constituents of living things perfectly natural compounds, but also that the carbon atom in conjunction with hydrogen, oxygen, and nitrogen (which make up the bulk of organic substances) possessed a special chemical fitness for the assembly of a vast inventory of complex and diverse organic compounds (acids, sugars, ethers, esters, alcohols) necessary to build complex biochemical systems. As Henderson commented, 'The compounds of organic chemistry gradually came to be recognized as different from inorganic substances only in the special characteristics of the elements carbon, hydrogen and oxygen when in chemical union with one another, just as the compounds of any other elements have their own specific characteristics.' "

p25 Rather than being attributed to vitalism "It was instead attributed to the unique and emergent and natural chemical and physical properties of the carbon atom in combination with hydrogen(H), oxygen(O), and nitrogen(N)."

p26 "By the beginning of the twentieth century,more than 100,000 organic compounds had been documented. And all the basic compounds of living organisms - the twenty common amino acids used in proteins adn the four nucleotides used in DNA, as well as many of the sugars and fats and fatty acids found in living organisms - had been synthesized in the lab."

p27-29 A spin through the mind-boggling variety of carbon compounds to get to a section "King Carbon".

p30 I'm kind of amused that he uses Peter Atkins characterizations of carbon. I taught a graduate Molecular Physics course using Atkins' textbook, and found him brilliant in chemistry, but having read so much about his incredible advocacy of 'scientism' and some of the things he said in his debate as an atheist with William Lane Craig, I find in him an incredible dualism. That aside, Atkins terms carbon "the King of the Periodic Kingdom" and and says the "property we call 'life' stems almost in its entirety" from the region of the kingdom containing carbon.

p30 Summarizes some of the key properties of carbon:

  • Carbon-Carbon Bonds
  • Tetravalency
  • Multiple bonds.
  • The Right Strength
p31-33 A major discussion of this idea of carbon bonds having the right strength to be in a "Goldilocks zone" for forming the compounds of life.

p34-35 Major discussion of "The Right Temperature Range" Quotes Stanley Miller and Leslie Orgel from "The Origins of Life on the Earth". The temperature range for organic compounds determines limits on the possibility of life. Using the half-life of the key amino acid alanine as a stability example:

  • At 0°C, 20 billion years
  • At 25°C, 3 billion years
  • At 150°C, 10 years

This is a decrease of more than a billion-fold, and alanine is not exceptional.

p35 Using a generous range of -50°C to 130°C, "the temperature range fit for biochemistry would still occupy only an infinitesimal fraction of the vast range of temperatures in the universe." This just "so happens to be almost the same as the temperature range in which water is a liquid in ambient conditions on the Earth, surely one of the most extraordinary and consequential bio-friendly coincidences in nature."

p36 Multiple Fitness for carbon

  1. It forms stable bonds with itself.
  2. It forms up to four bonds, being tetravalent.
  3. It forms multiple bonds with itself and other items.
  4. The energy levels of carbon bonds are just right for biochemical manipulation in the ambient temperature range - not too strong and not too weak - described as being "metastable".
  5. The energy levels of the covalent bonds that carbon forms with its other nonmetal partners in organic compounds are similar.
  6. The metastability of carbon compounds is in the same temperature range that water is a liquid.

p36 "..yet another element of fitness ... the unique directional nature of the bonds carbon forms with other atoms in orgaic compounds, which, we will see, plays a vital role in the assembly of complex macromolecules of defined 3-D shapes."

p37 Gross & Plaxco, "Astrobiology": "In the end there may very well be only a single element - carbon ... the basis of all life on Earth- that is able to support the complex chemistry presumably required to create a self-replicating chemical system."

p37 "Finally, what is particularly striking about the properties of the carbon atom is that they appear to be fine-tuned in several different but complementary way to generate the plenitude of compounds uniquely useful to life. Such a suite of properties , all seemingly arranged to generate a vast inventory of molecules ideal for the biochemistry of living cells, conveys a powerful impression of contrivance. More than a century ago Wallace expressed, in his 'World of Life':

'We see, therefore, that carbon is perhaps the most unique, in its physical and chemical properties, of the whole series of the elements, and so far as the evidence points, it seems to exist for the one purpose of rendering the development of organized life a possibility. It further appears that its unique chemical propertie, in combination with those of the other elements which constitute protoplasm, have enabled the various forms of life to produce that almost infinite variety of substances adapted for man's use and enjoyment, and especially to serve the purpose of his ever-advancing research into the secrets of the universe.'"

p37 "Many have believed (and many still do believe) that Darwin drove teleology out of biology forever. But more than a century and half of scientific research since Darwin has shown that the fitness of nature for life on Earth, exemplified so wonderfully in the chosen atom, points irresistibly to purpose and design."

p39 3. The Double Helix

p39-41 Discussion of the buildup to understanding DNA, using a number of quotes from Watson and Crick in their descriptive writing.

p41 Max Delbruck ..."He was hoping to discover new laws of physics which emerged when he looked at these extremely mysterious biological processes of how you get replication, which in those days seemed utterly baffling."

p42 The functions of enzymes and the storage and replication of information were understood better in the 20th century as utilizing the same laws of physics and chemistry. During 40s and 50s understanding of molecular structure was greatly increased by x-ray diffraction and electron microscopy. The highly specific 3-D formations of the macromolecules in the cell were revealed and associated with their functions.

p43 "Rosalind Franklin's X-ray diffraction work carried out at my alma mater, King's College in Londown, led to the discover that the atoms in DNA are deployed in the form of a double helix."

p44 " doctoral supervisor at King's College, Henry Arnstein, often referred to the shock he and many other biochemists felt when it became clear that all the atoms in a complex protein could be maintained in precise spatial conformations, and that this specificity of atomic arrangement was keY to enabling matter to carry out the seemingly miraculous chemical activities within the cell. A veil had been drawn aside. This was the molecular secret of life."

p44 One of several mentions or quotes of Judson's "The Eighth Day of Creation".

p45 "..enzymes catalyze life-essential processes by binding to specific substrates, increasing the rate of conversion to an end product by thousands, or even millions, of times per second. No enzyme could manage any such task unless the atoms around the active site were deployed in very exact spatial arrangements to bind the substrate."

p45-46 Strong Bonds Covalent bonds give bond strength and fixed directionality for building structures. 46 Quote of Atkins about covalent bonds. Ionic bonds by contrast are strong but not directional.

p48-49 Weak Bonds Higher order spatial deployment of building blocks depends upon weaker forces: van der Waals forces as well as weak bonds (I wonder why he doesn't use the term hydrogen bonds here.) Example: C-C covalent bond 350kJ/mol and weak bond 4-40 kJ/mol. "Because of their role in determining the 3D shape of macromolecules, the weak bonds are, as Watson describes them in "The Molecular Biology of the Gene", 'indispensable to cellular existence.'" Crick honored Pauling by crediting him with understanding the key importance of these weak bonds. "It is the weak bonds that fit together two different parts of an individual large macromolecule" "Watson nicely captured the nature and biological function of the weak bonds when he described them as conferring 'selective stickiness' to bio-matter, a stickiness that determines the way complex molecular structures fit together."

p49 "the spatial positioning of the atoms in the double helix is determined by these two very different types of bonds working together."

p50 Reversibility "major and vital characteristic of the weak bonds - they can be broken relatively easily and are easily reversible." "This characteristic enables the cell to pull apart the two strands of the helix during DNA replication and transcription, and enables them to easily reattach afterwards."

p51 "In short, for reversibly sticking molecules together in the cell in highly specific stereospecific complexes-the vital basis of virtually all biochemical functions- the average energy of the weak bonds has to be very close to what it is."

p52 Materialism Undermined Notes the critical nature of carbon with its partners O,H, & N as discussed previously, and also the critical nature of the fitness provided by the "two types of chemical bonds which uniquely enable the precise deployment of atoms into extraordinarily complex highly specific 3-D conformations."

p53 Denton pushes back against the materialism of Watson, Daniel Dennett, etc. by counseling them to note that in each celebration of materialism's defeat of vitalism "they overlook a crucial point: each retreat revealed some additional element of intelligent fine tuning in nature - fine tuning for life."

p53 "...highlighted a greater wonder in the fitness of nature for the assembly of complex macromolecules. .. These were not wonders beyond scientific analysis, but they were wonders nontheless,and they pointed a far greater wonder-worker who finely tuned the very fabric of nature for life on Earth."

55 4. Carbon's Collaborators

p55 In the upper right of the periodic table carbon is joined by oxygen, nitrogen, and with hydrogen in the upper left, they form a collaborative group of atoms that can form strong covalent bonds.

p55-56 George Wald (who introduced the republishing of Henderson's "Fitness" classic, and was awarded a Nobel prize for molecular photodetection) wrote "hydrogen, oxygen, nitrogen, and carbon are the four smallest elements in the periodic table that achieve stable electronic configurations by gaining, respectively, 1,2,3 and 4 electrons. ..make the tightest bonds and so the most stable molecules ...the only elements that regularly form double and triple bonds."

p56 But carbon's collaborators are "markedly different from carbon. This diversity is crucial because it allows these elements to introduce into the organic realm carboxyl (COOH), amino (NH2), methyl (CH3), and others with novel chemical properties.

p58 "In fact, it turns out that - consistent with the special fitness of nature for life on Earth- the properties of carbon's collaborators are precisely what are needed for the chemistry of the cell."

p58 Electronegativity The higher an atom's electronegativity, the greater its attraction for electrons. Of all the differences and similarities among the chemistry of hydrogen, carbon, nitrogen, and oxygen, one of the most consequential involves their electronegativities.

p58 Carbon and hydrogen have similar electronegativities, so covalent C-H bonds are essentially non-polar. One of the effects of this is to make hydrocarbon chains insoluble in water and hydrophobic - a characteristic that plays a vital role in the life of the cell.

  • ΔEN Pauling units
  • C-H 0.35
  • N-H 0.7
  • O-H 1.3
    Because of the large differences in electronegativity and unequal attraction of the electrons, the oxygen and nitrogen atoms in the O-H and N-H bonds are negatively charged while the hydrogens are positively charged.

    p59 Of crucial importance to life is the polar water molecule H-O-H, which he calls the "matrix of life". "The polar nature of water molecules is responsible for its great power as a solvent in dissolving charged ions or polar compounds." "The negatively charged oxygen atoms are attracted to positively charged ions such as Na+ or regions of electrostatic positivity in a polar compound, while the positively charged hydrogen atoms are attracted to negatively charged ions such as Cl- or regions of electronegativity in polar compounds. We call such ions and polar molecules hydrophilic."

    p59 Good perspective paragraph: "As there are nearly always many water molecules relative to solute molecules, these interactions lead to a sphere of water molecules around the solute. These hydration shells allow particles to be dispersed evenly in water and keep the charged solutes apart and unable to combine and precipitate out of the solution, and, therefore, soluble. As the majority of organic molecules - sugars, alcohols, fatty acids, amino acids, nucleotide bases - contain charged groups and are readily soluble in water. And as water is the matrix of the cell, the solubility of so many compounds is of great utility."

    p59 Non-polar, long-chain hydrocarbons are hydrophobic and are "forced into insoluble, water-avoiding clusters".

    p60 "But rather than being a defect in the order of things, the insolubility and hydrophobic character of hydrocarbons is a vital element of nature's fitness for life. The insoluble hydrocarbons form the core of the lipid bilayer membrane that surrounds the cell and many of the cell's internal organelles - one of the most important supramolecular structures in the cell, indeed in the entire biological world. It also allows newly synthesized proteins to fold into their secondary structures, one of the most important of all the biochemical processes in the cell.

    p60 Cites John Philip Trinkaus in "Cells into Organs": "Because water is itself a strongly polar molecule, the polar phosphate of the membrane lipids will inevitably be attracted to the surfaces of the membrane, both external and cytoplasmic. And just as inevitably their non-polar fatty acid parts will tend to be squeezed into a non-polar phase in the interior of the membrane." Denton "It is this dual character of the phospholipids that enable them to form membranes, without which cells would not exist."

    p61 A new idea to me: "In an additional teleological twist, these water-avoiding aggregates that are clustered together in the center of the folded protein provide the cell with tiny, non-aqueous micro-environments vital to the life of the cell. Many of the synthetic and enzymatic processes on which the cell depends can only occur in a chemical micro-environment free of water."

    p62 Very nice page on the "Finely Tuned Quartet" of C,H,O,N working together to make possible the cell membrane and the folding of proteins. "At the heart of cellular life is an extraordinary reciprocal fitness between the non-polar carbon-hydrogen (C-H) bonds and the polar oxygen-hydrogen (O-H) bonds. This reciprocity gifts life with the cell membrane and the folding of proteins. If the electronegativity of hydrogen, carbon, oxygen, and nitrogen had been the same, unquestionably there would be no carbon-based life on Earth. The cosmos has only come to life because of the different electronegativities of the four collaborators."

    p62 "in another teleological twist, it is hydrogen's electronegativity that is the cause of water's polar nature (via the electrical asymmetry of the O-H bond) and of the non-polar nature of the long hydrocarbon chains (because of the electrical symmetry of the C-H bond)."

    p63 Reflection on variations that would make life as we know it impossible. "Only when the whole suite of fitness is complete can the miracle of the cell be actualized."

    p63 "And as for water's inability to solubilize oils and fats and other hydrocarbons, this might seem a defect in the so-called universal solvent. But as we have seen, the hydrophobicity of hydrocarbons, and their insolubility in water, is one of the prime elements of natures's fitness for carbon-based life. An apparent shortcoming of water turns out to provide a previously unsuspected but vital element of nature's fitness for carbon-based life."

    p64 The Fitness of the Cell Membrane: A Checklist

    • Semipermeability
    • Self-Organizing
    • p66 Membrane Diversity
    • p67 The Right Width
      • Lipid bilayer about 5nm.
      • If cell size of pumpkin, membrane thickness of a sheet of paper
      • Thickness comparable to size of proteins in membrane
      • p68 16 to 18 carbons in lipid chains
    • Membrane potential
      • p69 Uses 30% of resting metabolic energy to maintain, up to 70% in nerve cells.
      • p70 Depends on mobility of small ions

    p71 "In short, these four atoms are mutually fit, in a myriad of improbable ways, to set in motion a succession of unique emergent phenomena, along a pathway stretching from the relative electronegativities of carbon, hydrogen, oxygen, and nitrogen to the nervous system of higher organisms. The way these elements work together to generate this unique path is stunning, conveying an irresistible impression of contrivance."

    73 5. Energy for Cells

    p76 Energy- Spelled ATP (Data from Nick Lane, "The Vital Question: Why Is Life the Way It Is?", WW Norton, 2015, p64)

    • Energy use rate about 130watts for 65kg person
    • Single cell ~ 10 million molecules of ATP per second
    • For 40 trillion cells, total turnover of ATP around 60-100kg per day, roughly our body weight.
    • We contain about 60gm of ATP, so every molecule of ATP is recharged once or twice a minute.
    • 100 kg of ATP is about 1029 molecules.
    • Worker honeybee hovering with 250 wingbeats per second turns over (i.e., hydrolyzes and resynthesizes) 1.39x1015 molecules of ATP per wingbeat cycle. (R.K. Suarez, "Oxygen and the Upper Limits to Animal Design and Performance",The Journal of Experimental Biology 201, no. 8(1998):1065-1072)

    p78 The Fitness of Phosphates

    p78-79 General discussion of why phosphates like ATP and GTP are the best in fitness for the energy transfers of life processes. In 4billion years of life, no replacement for ATP has been found.

    p80 Needham: "It is no exaggeration to say 'without phosphorus: no life.'"

    p80 Glycolysis and Respiration

    • In cytoplasm: Sugar-> 2 Pyruvic acid + 2 ATP
    • In mitochondria: Cellular respiration Pyruvate + O2 -> CO2 + H2O + 28 ATP
    • p81 Cites George Wald in Scientific American article.

    p82 Proton Pumping

    • Describes electron transport chain, ATP Synthase and oxidative phosphorylation (Nobel - Peter Mitchell)
    • p84 Electron Transport Chains
    • Proticity - ATP Synthase pumps protons back across inner mitochondrial membrane producing an ATP for each three protons pumped.
    • Cites Lane's "The Vital Question" for discussion of quantum processes employing iron-sulfur clusters.
    • p86 More detailed passage from Lane, eloquent description of the electron pumping

    p86-87 Transition Metals Remarkable discussion of the use of transition metals in electron transport chain. It looks like a typical setting is with metal centers spaced about 15 angstroms apart, with electrons transferring between them. "I'm not saying I fully understand it, but will think about it more. Iron and copper are important in the electron transport chain.

    p88-89 "In short, this chapter has provided further evidence of the striking fitness of nature for life as it exists on Earth, conveying the powerful impression that a blueprint for the production and utilization of energy by carbon-based cells was written into the laws of nature from the moment of creation."

    91 6. No Biology Without Metals

    p91-92 Discussion of the role of iron, in general, as the most abundant element on the Earth, as oxygen carrier, as 4th most abundant element in Earth's crust, as crucial to forming the geodynamo and the Earth's magnetic field, and crucial to biology. Iron and copper in the electron transport chain. Na and K critical in maintaining the membrane potential.

    p93 Cites Robert Williams, "The Symbiosis of Metals and Protein Function" as saying "biology without metal ions does not exist any more than biology exists without DNA or proteins." "The machinery of life rests with these two components, metal ions and proteins ... The all-pervadingg influence of metal ions in biological systems is such that I now declare that in my mind there is no biology without metal ions."

    p93 "close to one-third of all enzymes involve a metal ion as an essential participant ... Fe and Cu in ETC ...Na and K in membrane potential.

    p93 Dudev & Lim "Metal ions are required for growth of all life forms. Currently, about half of all proteins contain metal ions ..respiration ...hemoglobin and myoglobin (iron) .." p94 "In many cases, metal ions, e.g., Zn(II),Mg(II),Ca(II) stabilize the structure of folded proteins, while in other cases they help to fix a particular physiologically active conformation of the protein. Metal ions are an integral part of many enzymes and are indispensable in several catalytic reactions ... In particular, transition metals, such as Fe, Cu, and Mn are involved in many redox processes requiring electron transfer. Alkali and alkaline earth ions, especially Na(I),K(I), and Ca(II), play a vital role in triggering cellular responses."

    p94 "One of the fatal "defects" of a "biology without metals" is, as Williams points out, that the properties of different amino acids do not vary greatly when incorporated into proteins while the metal ion brings to proteins a great diversity of chemical properties and molecular geometries that greatly enrich their physio-chemical properties and consequent catalytic abilities."

    p94 "Crichton cites the need to transport electrons in ETCs. Transitional redox metals such as iron and copper are .. far better at doing this than organic compounds such as flavins.. Without ETCs and the metal conductors they use, the ability of cells to generate bio-energy would be greatly constrained and only the simplest types of unicellular life would be possible" " four billion years, no organism has managed to replace the electron-conducting functions of iron and copper with any organic nonmetal compounds."

    p95 Crichton: "And perhaps most important of all, he adds, metals are needed as cofactors to 'enable the proteins which we call enzymes to catalyse reactions, many of which would quite simply be impossible if we relied solely on organic molecules."

    p95 Cites Williams's 1985 paper. "We know now that at least 10 different metal atoms - sodium,potassium,magnesium, calcium, cobalt, copper, iron, manganese, molybdenum, and zinc - play essential roles in the cell.

    p96 Sodium and Potassium
    "Because Na and K bind only weakly to organic compounds, they are highly mobile and ideally suited to move electric charge at great speed, create electronic gradients across cell membranes, and ensure the maintenance of charge balance on both sides of the cell membrane."

    • Remarkable speed - up to 100 million K+ ions per second through one ion channel in cell membrane, 105 times faster than any known carrier protein.
    • Not hindered by binding to organic compounds
    • Essential for nerve conduction and a central nervous system

    p97 Calcium

    • Calcium ion release from synaptic vesicles triggers muscle contraction.
    • Can bind with specificity to another molecule like a protein.
    • Can transmit chemical information to trigger cellular function: nerve impulses, hormone release, changes following fertilization


    • Present in every cell type for catalytic action of more than 300 enzymes.
    • Binds more weakly than calcium, but uniquely fit for certain functions.
    • Associates with ATP to enable cell to use ATP energy
    • Vital role in association with Chlorophyll to enable energy capture from sunlight
      • Can be replaced by manganese, iron, cobalt, nickel, copper and zinc in various metal porphyrins
      • Light absorbing power of Mg several thousand times that of iron porphyrin
      • Mg approaches the theoretical limit for conversion of light to electrical energy.

    p100-106 The Fitness of the Transition Metals

    • Manganese, iron, cobalt,copper, zinc, molybdenum have sets of indispensable properties.
    • Iron and copper as electron carriers in ETCs.
    • Iron in hemoglobin in humans and large animals
    • Copper in the hemocyanin in the blue blood of an octopus
    • Use Cytochrome C Oxidase along with iron and copper in the ETC to finally reach oxygen to water step.
    • Also in conjunction with Cytochrome C Oxidase, zinc and magnesium may be involved in structure and release of the water molecules.
    • This "atomic machine, central to life, exploits the unique chemical and physical properties of nine of the ninety two naturally occurring elements."

    p106 Manganese

    • "Works its magic in the oxygen-evolving complex in the chloroplast where water is oxidized, releasing oxygen into the atmosphere and producing electrons and protons for the synthesis of organic molecules from CO2.
    • From beginning of life, no other mechanism for oxidizing water and releasing oxygen has appeared.
    • Essentially identical in all oxygenic photosynthetic organisms.
    • uses four manganese and one calcium atom in the OEC.

    p107 Zinc

    • About three grams of zinc in an adult human
    • Zinc essential for all of life, playing a role in more than 300 enzymes in each of the main fundamental classes.
    • Zinc in active site in enzyme carbonic anhydrase which converts CO2 to bicarbonate H2CO3 and the reverse process in the lungs to produce CO2 for exhalation.

    p109 Review summary paragraph

    p109 Molybdenum

    • Occurs in four important enzymes in our bodies.
    • Involved in nitrogen fixation in the enzyme nitrogenase, involved in virtually all the nitrogen used by living things.

    p111 "Metals Most Precious" accomplish special purposes in life: "activating ATP, forming electron-conducting wires in chloroplasts, mitochondria, and bacterial cell membranes, carrying charge across cell membranes at great speed, and acting as vital cofactors in multiple different enzymes."

    p111-112 "The empirical evidence speaks for itself. Particular metal atoms have performed the same cellular functions over billions of years. Given the astonishingly diverse environments exploited, for example by various extremophiles - temperatures of 120°C, acidic environments less than pH 1, alkaline environments at pH 10.5, hypertonic saline solutions ten times as salty as sea water - the fact that the roles of the metals are the same in all these organisms speak volumes for the special fitness of these atoms for highly specific cellular functions. Without the metals there might be some very primitive type of carbon-based life, but anything remotely as rich and complex as now exists would be impossible.

    p112 "All life forms on Earth use transition metals in electron transport chains (ETCs) that, by all appearances, are indispensable to life. In four billion years of evolutionary experimentation, since the first blue-green algae began its fateful manufacture in a vast number of diverse lineages, the same choice of transition metals have been made again and again to build ETCs. The best explanation is that no other elements, nor any types of organic compounds, can replace the transition metals for this task."

    Special fitness for us advanced aerobic organisms:

    • Magnesium for light-capture in photosynthesis
    • Iron and copper for the transport and activation of oxygen
    • Zinc for the function of carbonic anhydrase (and consequently the excretion of CO2
    • Sodium and potassium for generating membrane potentials, which enable nerve impulse transmission.


    113 7. The Matrix

    p113-115 An eloquent journey with the myriad developing cells of a human embryo which must move and develop in precise ways to create the human baby. Starting with his leucocyte chasing a bacteria, he contrasts that with millions of cells moving toward specific targets. Eloquent and condensed - just have to read it over and over.

    p115 Transitions to more of the remarkable properties of water. Albert Szent-Gyorgyi "Water is in any case the central substance ofliving nature. It is the cradle of life, the mother of life and its medium. It is our mater and matrix." From this Denton gets the chapter title. He proceeds to three more key properties of water.

    • p116 Viscosity
      • Water's viscosity determines the diffusion rate of solutes like oxygen and nutrients in aqueous solution.
        • Diffusion rate D=k/m where k is a constant and m is the viscosity of the medium.
      • Water's viscosity determines the viscous drag on objects moving through the liquid.
        • Viscous drag force directly proportional to the viscosity m.
      • Viscosity of water must be very close to what it is or there would be no embryos, no multicellular organisms, no cell movement by crawling, morphing, etc.
    • Diffusion
      • The maximum possible diameter of cells is constrained by the rate of diffusion of molecules in water.
      • Diffusion time increases with the square of the diffusion distance.
      • Diffusion rate D->D/10 would reduce maximum cell size (volume decreases by cube of radius) by a factor of a thousand.
      • If diffusion rate in water were significantly lower, the cells could not be large enough to crawl and morph and contain all the molecular machinery in the cell walls.
    • p118 Viscous Drag
      • Maximizing cell size constrains the size of capillaries that bring oxygen-enriched blood to diffuse across the cells.
        • Mammalian tissue about 1000 capillaries per square micron.
        • Most capillaries about 40 microns apartt
        • Most tissue cells about one to three cell widths from a capillary.
      • Pressure required to pump blood (about viscosity of water) through capillary bed rises with viscosity.
      • Pressure at arterial end of capillary bed about 35mmHg, about a third of pressure at aorta.
      • Higher viscosity would require more pressure, but walls of capillaries must be very thin to allow diffusion across them, and would be subject to rupture.
      • Much lower viscosity would increase diffusion rate and decrease viscous drag, but would increase Brownian motion and impacts since all particles would move faster, and could destablize the delicate architecture of macromolecules.
    • Combined considerations suggest that viscosity for circulatory system must be within a range of 0.5 to 3mP-s compared to water's 1.0 mP-s. Air to honey range 0.017 to 10,000mP-s.(Pascal is MKS unit of pressure.)

    p121 The Universal Solvent. One of the ways to make the case that water is without peer as a solvent is in the fact that it is very difficult to make very pure water - it always dissolves something in its environment. Cites Felix Franks and Lawrence Henderson. The great majority of organic molecules have polar regions, particularly proteins and other large molecules, and therefore dissolve readily in water.

    p121 The Hydrophobic Force. The one exception to the above section is the collection of molecules with long hydrocarbon chains that are non-polar because the H and C atoms have similar electronegativity. This exception is crucially important because hydrophobic regions are necessary for the formation of cell membranes and the proper folding of proteins.

    p123 The Active Matrix "life is water dancing to the tune of solids" Albert Szent-Gyorgyi. Cites Philip Ball : "water is not simply 'life's solvent' but is ...a substance that actively engages and interacts with biomolecules in complex, subtle, and essential ways." A good page of detail. Crucial example: DNA undergoes conformational changes and even loses its double helix in some apolar solvents.

    p124-125 Proton Wires "One intriguing element of fitness for bioenergetics and proton pumping arises directly out of water's hydrogen-bonded network, which provides so-called 'proton wires' consisting of long chains of linked water molecules for moving protons (H ions) around in the cell and across the inner mitochondrial membrane." This is something that I have not encountered before, and is a fascinating, apparently quantum process in water.

    Alok Jha: "protons can pass their energy along a hydrogen-bonded water wire without moving themselves at all, thanks to the so called Grotthuss mechanism." a proton attaches to one end of the wire, he explains, and in a split second, "each of the hydrogen bonds further along the length of the wire spin around in sequence so that a proton drops off the water molecule at the other end of the wire. The initial proton has not moved any further than the starting end of the wire but its charge and energy have been 'conducted' along the wire's length."

    p125 Cites Harold Morowitz, Nick Lane, and Szent-Gyorgye as being convinced that this was important in the origin of life.

    p125-128 The Prime Coincidence "The temperature range in which living things thrive on Earth, and which is fit for the chemistry of life, is almost exactly the same temperatue range in which water is a liquid." Has a couple of pages about extremophiles. A page about the molecular effects of cooking. Page of contrasts to the vast range of temperatures in the universe.

    p128 "Within this tiny temperature band, the energy levels of the covalent bonds of the organic domain can be manipulated by living systems; the weak bonds can be used for stabilizing the 3-D forms of complex molecules; and water, the only compound known to possess the many other properties essential to serve as the matrix of life exists in the liquid state."

    128 "This is little short of a miracle. If this coincidence did not hold, water would not be fit to form the matrix of the cell. All the myriad other elements of fitness of this unique fluid would be to no avail. Almost certainly there would be no carbon-based life in the cosmos. Or to put that matter more positively, it is surely an awesome coincidence, indicative of the profound fitness of water and, by extension, of nature for carbon-based life, that the optimum temperature range for the complex atomic and molecular manipulations essential for life is precisely the temperature range in which water, the ideal matrix in so many other ways, exists as a liquid at ambient conditions on Earth."

    p128-129 Unrivaled Reviews the properties of the previous few pages and ends with the sentence "In short, in the properties of water, nature appears to have had not only life in mind, but creatures like ourselves."

    131 8. The Primal Blueprint

    p131 Starts with the famous quote from Francis Crick.

    p131-133 Description of the Murchison Meteorite[Sept 28,1969]. It contained amino acids and nucleobases. Spectroscopic studies reveal many abiotically produced compounds that are also found in life. Include polycyclic aromatic compounds without nitrogen (PAHs) and with nitrogen (PNAHs). Miller Urey experiment reported three of life's amino acids, but later studies of the residue bumped it up to ten of the twenty amino acids used in life.

    p133 A kind of summary statement that reflects Denton's worldview: "Thus we see that the message brought to Earth that fateful September night, written in the chemistry of a falling star, is highly significant. As well as supporting the claim that life's emergence might have been the result of entirely natural mechanisms, it also supports the thesis central to this book and the whole Privileged Species series: Carbon-based life as it exists on Earth is no contingent afterthought of nature, no artiffactual accident, but an inherent part of the natural order. It is an inherent part of nature's grand design from the moment of creation."

    p133-135 Cosmic Abundance CHON early and abundant in universe along with He. Does not make a big deal out of the Hoyle resonance which indicates that carbon, the "king" of them all for life chemistry, was hanging by a thread and required this extraordinary fine-tuning to proceed with an abundance of carbon. CHON are core atoms that combine to compose 96% of the human body. Water is 60% of mass of body. "Other prominent constituents of life are also among the most abundant elements: Mg, Na, Ca,Fe,P,K,S. "..powerful impression that stellar nuclear synthesis ... was set up from the beginning to serve the end (the purpose) of life on Earth."

    p135 "It is important to stress that the selection of the atoms which enable the biochemistry of life is not because of their cosmic abundance, but because they possess the right chemical and physical properties to serve a vast number of highly specific physiological and biochemical functions in the cell." "So here is a genuine coinicidence indicative of a deep biocentricity in the cosmic order: the great majority of the most abundant atoms are the most fit for life."

    p135 The Elusive Path "..just how or where the transition from soup to cell occurred is an abiding mystery, among the greatest unsolved problems in science." "stromatolite formations ..mats of bacterial cells .. blue-green algae ... fossil record 3.5 billion years ago." "But we know virtually nothing about how it originated."

    p136 Comments on vast increase in our understanding of the biochemistry of life. "Yet despite our extensive knowledge of the molecular biology of the cell, we remain at a complete loss as to what may have been the basic steps which led from the Murchison monomers to the cell system in terms of the known laws of chemistry and physics."

    For statements of the dilemma, points to:

    p138 Overcoming the Impasse "So how did the transition from soup to cell occur? One obvious explanation is the idea that an intelligent agency assembled the first cell. This is an explanation popular among some supporters of intelligent design. Although it is rejected by most academic biologists, as the evidence stands it is perhaps as convincing an explanation as any available. However, an alternative possibility (my own preferred position) is that there are new laws, or novel properties of matter yet to be discovered, which enabled the path from chemistry to the cell."

    The above paragraph is really remarkable to me. It certainly appears to be candid and honest, but all his talk about fitness and his eloquent prose about the remarkable coordination of the conditions that brought about life led me to believe that he was inclined to accept some transcendent intelligence in producing those condtions. I have been surprised that he has given so much space and commentary to Peter Atkins, whom I consider to be one of the most doctrinaire advocates of scientism and the direct rejection of any transcendent intelligence, but I grudgingly admit that some of the things that Atkins did in his "The Periodic Kingdom" are quite creative - I may have to get the book! The above paragraph puts Denton in a position similar to Davies who writes all kinds of eloquent things apparently defending something transcendent in the fine tuning of the universe, but then denies any commitment to that kind of picture of the forming of the universe.

    p140 Interesting citation of Davies since I am seeing Davies and Denton as being on somewhat parallel paths, describing brilliantly the marvel of nature and life, yet pulling back from ascribing it to a Creator. I have read this in Davies before, I believe:
    "Although biological determinists strongly deny that there is any actual design, or preordained goal, involved in their proposals, the idea that the laws of nature may be slanted toward life, if not contradicting the letter of Darwinism, certainly offends its spirit. It slips an element of teleology back into nature, a century and a half after Darwin banished it."

    p140 Tommaso Bellini and colleagues term Darwininian scenarios "fantastic luck theories" which the contrast with "fine-tuning (fitness) theories"

    p141 A Primal Blueprint "..the creation of the first carbon-based cell ... was only possible because of the ensemble of fitness in nature described in this monograph - what I have termed the primal blueprint."

    1. The fitness of the carbon atom to form stable covalent bonds with itself and hydrogen, oxygen, and nitrogen, generating the vast inventory of organic compounds (Ch2)
    2. The fitness of the directional property of covalent bonds that enable the assembly of large macromolecules with defined 3-D shapes capable of specific biological functions - enzymatic, structural, and genetic (Ch3)
    3. The fitness of weak bonds to form complementary electrostatic surfaces that can reversibly stick together different parts of macromolecules (such as the two strands of DNA), enzymes to their substrates, and molecular motors to actin fibers.(Ch3)
    4. The fitness of the differences in the electronegativities of carbon, hydrogen, and nitrogen, which leads to the non-polar hydrophobic hydrocarbons and confers on water its polar hydrophilic character. The particular differences in electronegativity among these atoms give us insoluble long-chain hydrocarbons, which form the basis of the cell membrane and enable stable folded proteins.(Ch4)
    5. The fitness of the emergent properties of the cell membrane, including semi-permeability, self-organizing ability, and insulating capacity, properties fit to serve many indispensable biological ends. These include selective adhesion and crawling, and electrical properties that enable the nervous systems of higher organisms. (Ch 4)
    6. The unique abilities of phosphates to store and use energy in the aqueous medium of the cell. (Ch 5)
    7. The fitness of various metal atoms, including iron and copper, for channeling electrons down electron transport chains and for oxygen handling in hemoglobin and cytochrome c oxidase.(Ch 5 & 6)
    8. The fitness of the sodium (Na+) and potassium (K+) ions for rapid charge transport across the membrane and the maintenance of the membrane potential (Ch 6)
    9. The fitness of water to serve as the fluid matrix of the cell, including its low viscosity to serve as the medium of circulation, its unsurpassed fitness as a solvent, its hydrophobic force, and its fitness for proton conduction. (Ch 7)

    p143-144 As extensions of the "primal blueprint" appropriate to higher animals, he points to:

    • The unique reactivity of oxygen in aerobic cells provides high energy levels, using the properties of metals like iron and copper to handle the oxygen. This includes the oxygen transport to the cells by iron in hemoglobin and CO2 transport back to the lungs based on the properties of the zinc atom to provide the enzyme carbonic anhydrase to convert it to bicarbonate ions for the journey.
    • Water's low viscosity and high diffusion rates enable the infusion of oxygen into the tissues and make possible large enough cells to have the mobility necessary for embryonic development involving movement of specialized cells to their intended locations.
    • High diffusion rates of Na+, Cl-, K+ to create and maintain membrane potentials and for transmitting nerve impulses.
    • Reflects on Henderson's writing about the mutual fitness of water and carbon dioxide and their collective contribution to life processes.

    p144 Parsimony seems to be one of Denton's favorite words, and he uses it here to describe the fact that the four elements hydrogen, carbon, oxygen and nitrogen play so many roles in life, individually and in the combinations H2O, CO2 and NH3. Then oxygen in combination with hydrogen and carbon are the premiere substances for providing metabolic energy.

    His final line in this section: "Only someone committed to rejecting out of hand all evidence of teleology in nature could fail to see in these ensembles of fitness and in this elegant parsimony evidence of design." Ok, I agree with him and it takes me right back to Paley and the watchmaker, and to the continued conviction that design implies a designer, an Agent, a Creator!

    p145-147 Alien Life General description of the input of astrobiologists and the search for extraterrestrial life.

    p146 Returns to citing Lawrence Henderson for his amazing 1913 book "The Fitness of the Environment". "One century after Henderson, no fact has come to light to seriously threaten his conclusion that the laws of nature are finely tuned for life as it it exists on Earth. On the contrary, many discoveries and advances unimagined in 1913 have further confirmed it. These include the importance of the hydrophobic force, the utility of strong covalent snd weak bonds for the assembly of complex macromolecules, proton conduction, and the fitness of ten or so metal atoms for very specific cellular functions. Further confirming Henderson's conclusion are advances outside the biological sciences, such as the elucidation of cosmic abundances of the atoms, the carbon-12 resonance that enables stars to generate carbon, and the fine-tuning of the constants for life."

    147 Darwinism Diminished "Another implication of the primal blueprint is the obvious challenge it poses to the Darwinian world view. The existence of the blueprint specifying the design of the cell long before life emerged on Earth implies ...its actualization was only possible because the blueprint was already in place."

    p147 In Sum "..the miracle of the cell is only possible because of a vast prior ensemble of mutual fitness in the unique properties of a set of about one-fifth of the atoms in the periodic table. There is, I believe, no other corpus of evidence anywhere in science which provides more convincing evidence of design in nature and purpose in the universe than the fine tuning of these atoms for the carbon-based cell. On any consideration, the evidence presented in this monograph conveys the irresistible impression that the properties of the atoms have been contrived directly and purposefully to enable the existence of life in the universe."

    "As far as the actualization of the blueprint is concerned, which remains the deepest of mysteries ..."

    p 148 "Irrespective of any design inference, what science has revealed already confirms the deep intuition of the medieval Christian scholars who believed that 'in the cognition of nature in all her depths, man finds himself.'"

    p 149 Endnotes

    Windows of Creation
    Evidence from nature Is the universe designed?
    Reasonable faith
      Reasonable Faith Go Back