EquationsOfLife - Keithl wiki

The Equations Of Life

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

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 frogmouth walks 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

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

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 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

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

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

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

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