Diff for "EquationsOfLife"

• http://wiki.keithl.com/EquationsOfLife

The Equations Of Life

How Physics Shapes Evolution

• Charles S. Cockell

• Multco Hillsdale . 576.801 C6661e . 2018
• pix Preface

• p001 Ch01 Life's Silent Commander

• p02 Compare massive star to ladybug

• p04 Trigonotarbids, 250 MYa archnids

• p019 Ch02 Organizing the Multitudes

• p024 active matter physics, Tamás Vicsek

• p026 formula for probability of ant choosing a pheromone trail marked by a prior ant or ants, not usable without examples and numbers
• p027 formulas obscured when many ants swarm towards multiple goals
• p028 self-organizing behavior, not supervised but seeming so
• p034 birds save energy by flying in formation and coordinating wing beats, minimizing downwash effects
• p035 18yo Cockell in the Canadian north, banding birds caught in nets, then released
  • different ducks behaved differently, unique individual "personalities"
• p035 Physics trumps individuality
• p036 cellular cytoskeleton proteins self-organize

• p037 kinesin (anterograde) and myosin (retrograde) motor molecules crawl along polar tubulin filaments

• p039 Ch03 The Physics of the Ladybug

• p044 500nm ladybug hindwings under hard elytra wing cases

• p045 chiten 10% steel strength, 10x keratin/hair strength

• p055 irrefragable irrefutable, indisputable

• p055 hemolymph insect body fluid comparable to vertebrate blood

• p056 mathematical olio heterogeneous hodgepodge

• p059 Ch04 All Creatures Great and Small

• p061 mole tolerance of high CO₂ Talpidae "true moles" in Europe, Asia, North America; marsupials in Australia with similar shape and burrowing physics

• p067 no propellers on fish, but flagella on microbes, 600 body lengths per second

• p068 low Reynolds numbers at small scale, viscosity dominates inertia

• p069 On Growth and Form 1917, by D'Arcy Wentworth Thompson

• p070 "first serious attempt to demonstrate the mathematical regularity of life"

• p070 some accuse Thompson of vitalism; instead, life is bounded by laws

• p072 Homeobox Hox genes control limb development

• p076 biological inherency, similar structures modified to suit laws prevailing in different environments

• p077 pink frogmouthwalks across sea floor on modified fins

• p077 transition from sea to land "required several experiments to succeed"

• p080 SSH Sonic Hedgehog protein gene signals limb formation, suppressed in snakes

• p083 Ch05 Bundles of Life

• p087 phospholipid membrane molecules hydrophobic inner carbon chains, hydrophilic outer head, bilayer array into membranes

• p088 David Deamer at UC Santa Cruz extracted lipids from meteorites, which spontaneously formed bilayer vesicles

• p089 Pyruvic acid can also make membranes

• p091 U. Edinburgh scientists tested thousands of alternate molecular pathways, routes used by life produce more compounds than all possible alternatives

• p092 pathways might flexibly mutate to other pathways, but nature evolved towards the optimum

• p092 np285 Barve 2014: Historical contingency and the gradual evolution of metabolic properties in central carbon and genome-scale metabolisms

• p095 Most microbial membranes surrounded by a peptidoglycan wall, "like a chicken wire mesh"

• p095 np287 Persat 2014: The curved shape of Caulobacter crescentus enhances surface colonization in flow

• p097 Gram-positive bacteria peptidoglycan cell wall with inner membrane but no outer membrane

• p097 Gram-negative bacteria peptidoglycan cell wall sandwiched between an inner and outer membrane

• p098 Simpler Gram-positive bacteria more susceptible to antibiotics

• p103 Slime mold cells gather into tentacles and move towards nutrients

• p105 Ch06 The Edge of Life

• p106 Cleveland Potash Ltd Boulby mine 1400 meters deep, 1000 km of underground roads

  • polyhalite mineral K₂Ca₂Mg(SO₄)₄·2H₂O . 1 million tonnes of Potash per year, now 1 million tonnes of polyhalite

• p107 microbes may multiply once every few thousand years

• p107 Boulby Underground Science Facility, tunnels 30℃, 86℉

• p109 Center of Earth: Pressure 360 GPa, Temperature 5700K . . . 10 km down, 100℃
• p109 chemical reaction rate doubles per 10℃, faster biomolecule breakdown

• p110 hyperthermophiles above 80℃ Methanopyrus kandleri can reproduce at 122℃ / 250℉

• p113 no replicating life below -20℃

• p114 psychrophile microbes grow best below 15℃

• p116 Guerrero Negro salt works Baja California, world's largest salt works, 9e9 kg per year

• p116 halophile microbes tolerate salt

• p118 water activity most microbes need 0.95, rare microbes tolerate 0.6

• p120 Iron Mountain streams pH 1 (~battery acid), acidophiles

• p121 Mono Lake pH 10 alkaliphiles

• p121 Kenyan Rift Valley Lake Magadi pH 11

• p123 Chroococcidiopsis cyanobacterium tolerates 15 kilograys, 1.5 Megarad, 15 grays lethal to humans

• p125 Ch07 The Code of Life

• p125 pork scratchings

• p128 DNA four codons distinguishable, more codons insufficiently distinguishable, more copying errors
• p133 3 letter amino acid code results from very specific selection
• p134 of a million alternatives, our DNA code more resistant to mistranslation errors

• p137 Did Evolution Select a Nonrandom "Alphabet" of Amino Acids? Philip Freeland 2011

• p139 Murchison Meteorite 50 amino acids, only the optimum 8 used by life

• p140 Expanded set of 76 candidate amino acids, not one out of a million subsets outperformed the natural set.

• p142 strange amino acid pyrrolysine in some methane-producing microbes; life can expand set if required

• p143 triosphospnate isomerase barrel, sandwich, and roll motifs

• p145 Ch08 Of Sandwiches and Sulfur

• p148 equation for proton motive force, typically 0.15-0.2 eV

• p149 powers ATP Synthase

• p150 Peter Mitchell ATP synthase

• p151 caffeate, caffeic acid

• p154 microbes can use electrons from an artificial electrode current 2015 AR Rowe

• p155 anammox bacterium

• p155 bioremediation using microbes to modify hazardous chemicals

• p156 Humans require about 25 watts of chemical energy

• p156 Great Oxidation Event 2.4 Gya to 3% O² and 0.75 Gya to 20% O²

• p157 enabled animal life and intelligence
• p157 strange astrobiology lecture about sulfate-reducing anaerobic aliens

• p167 Ch09 Water, the Liquid of Life

• p179 hypothetical life in Titan's cold methane lakes acrylonitrile membrane azotosome

• p180 Titan's low temperatures may preclude life

• p181 APM 08279+5255 quasar, 2e10 M⊙ black hole, 1.4e14 earth oceans of water mass

• p191 phytoliths, siliceous plant cell structure

• p192 silsesquioxane Not used for metabolism, but for structural supports like phytoliths and spicules

• p192 Heavier group 14 elements ( Ge, Sn, Pb ) not found in biomolecules? 60+ Organogermanium papers since 2021 Snarky molecular biologists like to embarrass astrobiologists?

• p193 silicon-based life in liquid nitrogen

• p195 Ch10 The Atoms Of Life

• p209 Science 2010 RETRACTED: A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus DNA with arsenic substituting for DNA phosphorus in alkaline Mono Lake

• p210 DNA halflife with phosphorus 30MY, with arsenic 60 milliseconds

• p210 sugars containing arsenic in some seaweeds, arsenobetaine in some fish, algae, lobsters

• p211 selenium in amino acid selenocysteine resists oxidation

• p217 Ch11 Universal Biology

• p224 puffy planets, low density ( <0.1 water) exoplanets

• p239 Ch12 The Laws of Life: Evolution and Physics Unified

• p239 vitalism mythical life force or energy beyond ordinary chemistry and physics

• p246 Per-Olov Löwdin quantum effects mutate DNA

• p253 Folded wrinkled human gut surface 250m², Ediacaran fauna flat, facilitating diffusion from surface

• p259 Acknowledgements

• p263 Notes

• p325 Index