Texture of Tales Told From Generation to Generation

     This furzy old lion
     deeply wrinkled face
     texture of tales told from generation to generation
     still amazes this chemist
     who's forced to see a whirlwind of silly atoms
     coming together for a party.
     In and out they go
     some leaving some arriving
     the very house itself made of themselves coming and going
     a dynamic structure strong enough to withstand the wolf's
huffing and puffing
     ever constant stream through the door of breath.
     All getting drunk on sunlight cought in grasses cought in
sleek running muscles of gazelles
     then vomitting it up as body warmth to the cold dark hungry
reaches of outer space.
     This void of outer space forever pulling sunlight through us
all
     playing us,
     pulling his bowstring of sunflow accross the laws of physics
to set atoms dancing
     And how, how, how does it whip up this jumble of atoms rushing
through
     into the textures , the vast intricate orders we see on this
tired relaxed face?

     What story brings these atoms momentarily together
     in a lion more deeply textured than a Shakespere play?

     That God or Michaelangelo can make faces is a commonplace
     But that molecules and four forces and seven differential
equations can come together to make faces brings awe.

     There's an amazement of concentration to hear in a Beethoven
symphony  notes make up phrases, phrases make up songs , sections
of orchestra mesh with sections of orchestra, long patterns of
develpment.  All to make one symphony.  This whirlwind of sound
dance resembles merely one single cell creature out of this lion's
living flesh.  But lion is a bustling confederacy of cells.
     
     Flesh does not rot.
     form goes on to children.
     Atom goes on to mushroom and bacteria.


Humans good at inventing distinct cultures, but also good at mixing them. Nina Simone Sings Israeli Song. Wild

 In fact I think human language evolved specifically for this purpose.  It's crazy that we can learn language, but CRAZIER to me that we can learn MULTIPLE languages and keep them separate in our heads!

Anyway please enjoy this cross cultural wonder of Nina Simone singing Israeli song  “Eretz Zavat Chalav U’dvash" in African beats and on European bastardized equal tempered tuning.

https://www.youtube.com/watch?v=YBAAkJyEhlA

 

Bringing Back New Moon Rocks Might Help Us Nail Down Timing For Origins Of Life On Earth

Chang'e -5 just landed on the moon!  half the operation accomplished!  now just to collect samples, blast off, and return the samples to earth!

http://www.xinhuanet.com/english/2020-12/01/c_139556499.htm

China's Change'e-5 rocket has now reached moon orbit!  yay!  It's goal is to bring back more moon rocks!  We haven't collected samples since the Russians brought back samples in 1976.

http://www.xinhuanet.com/english/2020-11/28/c_139549921.htm

https://en.wikipedia.org/wiki/Chang%27e_5

This excites me because more samples might help us date meteoric impact events that affect the origins of life on earth.  It used to be thought that life had billions of years of Earth randomly trying different chemical reactions that eventually lead to life.  

but we've found fossils that go all the way back at least to 3,600 million years ago.  This is surprising because analyzing moon rocks suggest the surface of the earth was being completely vaporized as recently as 3,800 million years ago.  This leaves a smaller and smaller gap of time for life to form, only 200million years or less.

The difficulty of fossils from that far back or further surviving, means that life might have started even EARLIER giving it even LESS time to start.  Maybe life is EASY to start, not random!

recent re-analysis of moon rocks brought back to earth in the Apollo days however suggests that this date of 3,800 million years ago is incorrect and life again could have started as far back as 4,100million years...  at that far back, it would be dissapointingly difficult to find records in fossils...

We need more samples!  And China is starting the way.  The samples that Chang'e -5 brings back might not help us with this exact task, but surely this will open the way to more missions bringing back more diverse samples

Correct Protein Function Depends On Sequence and RATE Of Folding. Genes Code For BOTH!

 

Some fascinating technical biology. 

 

When we figured out how genes, which are like blueprints in a library, specify how to make proteins which are nanomolecular robots that make the chemical transformations that is life, that act as mini computers to process information that come together to make the mobile scaffolding that builds us... we thought we knew how the sequence of letters in each gene specified the correct sequence of the 20 different amino acids we snap together one after the other, like different tools, to make each robot. This beaded string of amino acid tools then folds into a stiff or flexy chemically active robot.

 

The code allows for specifying up to 64 different amino acids, but biology, world wide from bacteria to oak tree to human only uses 20. So there is some redundancy in the code. This has been a mystery.

 

It has also slowly become apparent that we don't understand how the strings of amino acids fold into the right shape. And indeed, under some conditions they don't!

 

A recent paper describes a clever way this redundancy allows for a gene to not only specify the correct sequence of amino acid tools to build the right protein but also to specify the speed at which the protein is built, which is essential for it folding into the correct functional shape.

 

 

 

New work hints at a reason why the genetic code is redundant! Needs to code not only for sequence of aminos but also the RATE at which the sequence gets translated to get the right shape and right function. Clever! Explainer:

 

Reading genes with 4 possible bases 3 at a time can lead to 4x4x4 possible words, translated to 64 possible amino acids to build proteins. Yet biology uses only 20! Presently most aminos are represented by 2 to 6 possible base combos. Redundant! or is it?

 

Protein function is dependent on shape. We knew shape is dependent on amino acid sequence specified in genes. But it's not like computer code, it's also physics, so shape is also dependent on RATE of building a protein. Cells need to regulate THAT. wait for it...

The redundancy in the genetic code allows for this. For each amino, different codons that code for it can have a different tRNA molecule translate the code to amino. Different versions of tRNA for each amino are made in varying amounts.

 

Needing a tRNA of low abundance will slow down the protein building process. By coding for a rare tRNA or abundant one the genes can also code for the RATE of translation (=building) of the protein and therefore its correct finally folded shape. 4/4

 

"A code within the genetic code: codon usage regulates co-translational protein folding"

 

Outline For a Biology Text (Or Narrative)

INTRO YOU IN YOUR RICH ECOSYSTEM OF EARTH
paint wild story of 100 critters processes, narrative?  like sexvines?  start out your window then get wider and wider, like prolegomenon.. mention dynamism, energy flow, and creativity
<e. coli, rhizobium, nostoc, bacillus, moss, hemlock, fern, cuscuta, milkweed, dandelion, solidago, clocer, oaks, wolffia, poa, wheat, corn, rosa multiflora, strawberry, crategus, potato, chickweed, ragweed, spyrogyra, stentor, gregarines, saprolegnia, euglena, parabasilid in termites, in cows, amoeba, physarum, dictyostelium, chytrid, pilobolus, entomophthora, rhizopus, saccaromyces, microsphaera mildew, peziza, candelaria, physcia, lecidia, lecanora, agaricus, bolete ectos, ganoderma, puccinia, sugar eater, cellulose eater, lignin eater.. cat, cow, humans, squirel, coyote, mice, raccoon, crow, ring beaked gull, passer, mocking bird, red tail hawk, woodpecker, garter snake, painted turtle, sunfish, (i don't know fish) crayfish, sowbug, millipede, centipede, ostracods, cyclops, gall mite, soil mites, argiope, funnel webber, opiliones, crab spider, dragonfly, staph beetle, japanese scarab, aphid, ambrosia beetle, firefly, periplaneta, grasshoper, cicada, spittlebug, flea, collembolans, termite, monarch, aquatic caddisfly, fruitfly, housefly, asilid hunter, mosquito, ground beetles, tent catipilar, cabbage butterfly, gall wasps, hyperparasitoid ichneumon, polistes, yellowjacket, carpenter ants, formica, bombus, honeybee, halictid, hydra, planaria, trematode parasite, tapeworm, rotifers, aquatic nematodes, plant parasite nematodes, predatory soil nematodes, trichonosis, earthworm, leech, small landsnails, common water snail, slug, waterbear>

WHEN TO BRING IN MIRACLES/WOMBS?
time, predictability, equilibrium, quantum unpredictablitiy, chaotic dynamical systems, disspative..

WHEN TO BRING IN EXAMPLES OF DISSPATIVE SYSTEMS?
mantle convection
weather and ocean convection and circulation cells
chemical cycles?

these three examples are spread across 3 diff chaps: geology, weather/oceanography, geochem to life.

EARTH AS A PLANET
orbit, rotation,


CALCULATIONS AND PHYSICS
size, scientific notation
area, volume, conversions
velocity, acceleration, force
how we measure
maybe even measuring the size of earth, cavendish, density of earth?
microscope, magnification, electron microscope
conservation of energy, friction,
electromagnetic spectrum from sun, how it makes photochemistry
photochemistry, cosmic rays build organic compounds in comets and meteors

glaciers,
wind, running water, rain, floods, rivers, deltas, [ i got lots of duplication here]

MINERALS
minerals, mineral diversity ,rocks, compounds, elements
oxygen, silicon, aluminum, iron, calcium, potassium, magnesium, sodium,
carbon, sulfur

feldspar, mica, quartz        50

TECTONICS MOUNTAIN BUILDING
gravity, iron catastrophe, differntiation
plaate tectonics, continental drift,  crust,
mantle, outer core, inner core
radioactive heating??, mantle convection (what's the source of this heat?),
continental crust, ocean crust
sea floor spreading
sea vents
subduction zone, mountain building, volcanoes

rock cycle and life's part in it
mineral cycling

globe, size, mass, volume, %life        24

OCEANOGRAPHY                                        
sea level, changes in sea level,  tides,
ocean, ice, , water vapor, estuaries,
ocean currents, surface currents, convection currents,

continental shelf,


ATMOSPHERE                              
weather,  temperature, humidity, cloudiness, wind, precipitation

latitude, altitude, topography of landforms
land and water distribution, ocean currents,
 axis tilt, uneven insolation, uneven heating, seasons, climates
climate change, ice ages,

sun, energy, outerspace spread out and cold
energy flow
radiation, conduction, convection ,advection (wind),
circular cells,
ice caps,
atmosphere circ system
hurricane
weather is chaotic, climate change is chaotic, whole techtonic ocean current, climatic system is chaotic



EROSION
weathering, mechanical, freezing water, temperature change, biotic movement
chemical, water, carbonic acid, clays,

ATMOSPHERIC COMPOSITION
ozone layer, ultraviolet radiation

nitrogen, oxygen, water vapour,  carbon dioxide

WATER CYCLE
evaporation, convection, humidity,  condensation
dew, frost, fog, clouds, rain, snow

FRESHWATER BODIES
ponds, lakes, rivers, swamps,  ground water
anomolous expansion of water


coriolis, taylor cells, tilt, seasons       111



GEOCHEMISTRY
THE ORIGINAL EARTH METABOLISM
CHEMISTRY                                   
matter, solid, liquid, gas

elements, atoms,  chemical symbol, compounds, molecules
chemical formula, structural formula,
metal, alkali and alkaline earths gr 1, 2, nonmetal, metalloids
density, boiling point, solubility

hydrogen
carbon nitrogen oxygen phosphorus sulfer chlorine
iron silicon aluminum
nickel copper zinc
vanadium chromium manganese cobolt molybdenum,
sodium magnesium potassium calcium

gasses, law of definite proportions,
Mendeleyev, periodic law, periodic chart of elements,
atomic number, electron shells, valence, electron, atomic weight, isotopes, C14 etc..

CHEMICAL REACTIONS
chemical change, physical change, reactants, products
chemical equilibrium, static equilibrium, dynamic equilibrium
non equilibrium cycles ie atmos gases under sunlight
enzymes, precipitate
reaction rate affected by temp, increased by catalysts, catalysts

MIXTURES, COMPOUNDS
mixtures, solution, solute, solvent, polar solvent, water,
non-polar solvent, detergents=cell membrane lipids,
concentration,

BONDING
electrons, ionic bond, electromagnetic attraction, charge, valence shell
covalent bond,  metalic bond, hydrogen bonding,
van der Waal's forces

small covalent molecules , covalent networks, ionic compounds, cations=metals, anions=nonmetals, metals


chemical energy, heat, light, potential energy,
exothermic reaction, combustion,
Calories

temperature, specific heat capacity, heat energy,  change of state/phase transitions

thermometer, fahrenheit, celsius, freezing point, boiling point,
conduction, convection, radiative heat txfer

KINETIC THEORY pg 178-181
fluid is gas or liquid,  evaporation, condesnsation,
brownian motion, diffusion,
atomic theory, avogadro's number,
mass, density,
pressure


CHEMICAL CALCULATIONS
gram, atomic mass,  mole


coal, graphite, diamond,
carbon dioxide,  carbonic acid, carbonate,  methane ...
carbohydrates, organic molecules, hydrocarbons,  lipids,
ammonia, amino acids,
oxygen gas, water, ozone, phosphate phosphoric acid, sulfate
ATP, nucleic acids,
hydrogen sulfide, metal ores, protein iron oxides rust,
 silicon dioxide (quartz)  (Fe, Na, Mg, K, Ca)aluminosilicate minerals
transition metal ions for enzymes, magnesium in chloroplast, etc
table salt, metal ions in biol solution, calcium carbonate, calcium sulfate
 calcium phosphate,


ACIDS BASES SALTS
ion,  acid carbonic acid
base,  salt,
pH,

oxidation, reduction,
oil  coal                162


TIMELINE OF EVOLUTION OF ECOLOGY OF LIFE

stratigraphy, paleontology, relative age, radiometric dating, age of earliest rocks, fossils, mass extinctions

GLOBAL BIOGEOCHEM CYCLES
water cycle, vegetation protects soil,
carbon cycle, redox, carbonates
oxygen, sulfates, carbonates
nitrogen cycle, bacteria        18

[so scattered we need to delineate environments to life]
serpentinization
sea vents
alkali vents
fresh/salt water
littoral
diurnal cycles
uv input
lightning
waves
tides
rain erosion
CO2 interaction with rock
precipitation

Hadean?
energy flow, entropy, maintenance of pattern, incorporation of food, growth
cells, individuals, evolution, death

earliest prokaryotic fossils
biology, organisms
autolithotrophs
synthesis, lipids cell membranes, carbon fixation
seavents
photosyntetic lithotrophs H2S back to S8
sulfides ores,
organisms interact with light
bacts that oxidize S sequester CaSo4 back to sediments viruses

microscope,  size of cells, num of cells
nutrients, 100 basic small molecules,
minerals Na, Ca, Mg, K, transition metals
vitamins, coenzymes
diffusion brownian motion, molecule,  active transport
osmosis, , exchange of food waste

CELLULAR RESPIRATION
sugars, glucose, anerobic respiration, fermentation, aerobic respiration

carbohydrates, glucose etc, polymer, macromolecule
polysaccharides starch glycogen cellulose

NITROGEN FIXATION
dinitrogen, nitrogen fixing bacteria
nitrogen cycle, legumes
22 amino acids
1000+ proteins enzymes structural proteins
nucleic acids ATP RNA DNA
<azotobacter>

asexual reproduction            63
@@@@<<< i still don't got the bacterial metabolisms down!>>>>@@@
<halophile arche
hotspring and seavent arche
e. coli
v. fisheri
i want an anaerobic chemolithoautotroph dammit
one that goes ammonia to nitrates Nitrobacter winogradskyi? Nitrosomonas?
one that goes nitrates to N2
lets see, want H2S to Sulfate: Thiobacillus
Thiobacillus ferrooxidans oxidizes ferrous compounds
H2S to S
Desulfovibrio reduces SO4 to H2S or S, to oxidize organics
produce H2 to protect from O2, released H2S reacts with iron to produce pyrite
how many phototrophs do i need? ok Chromatium is a purple sulfur that turns H2S to S in anaerobic env
Rhizobium
Azotobacter
Bdellovibrio
Aquaspirillium magnetotacticum has magnets
Pillotina, Diplocalyx are the spirochaetes that live on parabasilids in termites
prochlorococcus most common marine in world
prochloron is chloroplast
Entophysalis coccoid builds stromatilites
oscillatoria
nostoc gobs
nostoc with bryophytes
nostoc forms lichens
anabaena azollae with Azolla
Chloroflexus auranticum green nonsulfur autotroph in microbial mats with cyanos in hotsprings reduces water or
Chlorobium anoxygenic green sulfur bact rTCA H2S->S in muds
Micoplasmas smallest cells
Bacillus
Lactobacillus mild fermenter
Heliobacterium chlorum may be phaeo chloroplast
Arthrobacer can creates oxide varnishes on rocks
Streptomyces complex filaments and helical chains of actinospores, antibiotics
thermotoga deep sea vents anaerobic fermenters>
<@@ some of these are AFTER oxygen@@>


THE OXYGEN BEGINS
photosynthetic cyanos fix C, fix N
chloroplasts, chlorophyll, oxygen, hydrogen,
banded iron, oxide ores
stromatolites
mud
biofilms
anoxic mud
deep rock
plankton
bact invent flagella: motion! swimming!
methanogen release C
bacts that oxidize N
which bact turns NO3 back to N2
<cyanobacters>

MULTICELLED BACTS
cyanos make strands
<prochlorococcus, Entophysalis, Oscilatoria, nostoc, anabaena>
bdellovibrios
ecosystems            21


EUKS
Precambrian
<thermoplasma acidophilum hot springs  anc of host euks?, Rhodopseudomonas anc of mitochondria,
Paracoccus denitrificans anc of mitochondria,
Prochloron anc of chlorophyte chloroplasts,
heliobacterium anc to pahaeo chloroplasts>

bacts engulf each other and become euks
photosynthitic single cells pick some photos
the evolution of seeing begins

nucleus, endoplasmic reticulum, ribosomes, golgi ap,
chromosome,  gene, replication, nucleotide, genetic code, mRNA, tRNA, ribosomes, proteins,
vacoule, chloroplast, mitochondria, cell wall

REPRODUCTION, mitosis, chromosomes,
SEX
sexual reproduction, diploid, haploid,  heredity, genetics
gene, dominant, recessive ,homozygous, heterozygous, sickle celled anemia, genetic diseases, hybrid

fertilization, gamete production, gametes, sperm, egg ovum, crossing over,
recombination, meiosis,  law of independant assortment,

mutations, clones

diatoms sequester SiO4
cells engulph photos, herbivors  pick some examples
cells engulph herbivores food chains
detrivors bacts and any euks?
food webs
primary producers, herbivores,  predator, prey
carnivore,  omnivore, decomposers, symbiosis, parasite, host,                 67
<Chlamydomonas, stentor, euplotes, didinium, vorticella, colpoda, dinos, coccolithophores, diatoms, forams, radiolarians, phacus, amoeba, pelomyxa, codosigidae, Trebouxia, desmids, Bodo, >


BEGIN CLIMB TO LAND
littoral zone

invade fresh water
<are there freshwater only single cell euks?  which epitomise the colonization of fresh water?  theres an estruarian continuum...>
cyanos can live on land?  who can live on rocks?
coccolithophores fix CaCO3
fungi like critters invade cells
fungi like critters invade multicells
chytrids invade fungi like critters who invade multicells..
filter feeders            8

MULTICELL EUKS
euks begin multicell: algae,
alternation of life cycles: benthic algae, planktonic dispersal
algae begin fixing CaCO3 to stromatolite reefs
 , carbonates seashells limetone
ciliates eat algae filiments
forams live in benthos collecting debris, critters
animals
filter feeders sponges
tentacles hydra
corals engulf dinos start reef building in earnest
grazers of multicell algae,
who eats corals?            15

s.a to vol ratio, protists, animals, growth, tissues
organism, embryo, development, cell specialization,
organ systems:
nervous system, circ sys, resp sys, dig sys, excr sys, endocr sys, imm sys, repro sys, musc skell sys


gas exchange,
DIGESTV SYS
degestion, mechanical digestion,  extracellular digestion
enzymes, stomach, liver
absorbtion, small intestine
feces, water balance
muscles
gonads, testes,  ovaries, conception, zygote, embryo,

EXCRETORY SYSTEM
excretion, urinary system, kidney, water balance, urine

neurons, nerve impulse, synapse,
homeostasis water and heat regulation

HOMEOSTASIS
information between systems   hormones, nervous system, endocrine glands

negative feedback
metabolic rate
thermoregulation
readyness for action adrenal gland
osmoregulation kedneys,
glucose level pancreas insulin  liver glycogen   57
<lithothamnion, polysiphonia, ulva, pandora, volvox, acetabularia, chara, spyrogyra, filamentous colony diatom, fucus, kelps, vaucharia, saprolegnia (late?), labyrinthulos, rhizidiomyces on saprolegnia, colonial Spumellarian radiolarian, pelomyxa, (marine myxomyces?), chytrids, triskelion, quilted vendians>



CAMBRIAN EXPLOSION
Paleozoic
food chains get longer
shells and claws
metamorphosis: between plankton for spreading and benthos/ littoral for living
seeweeds climb up the littoral zone
<lobster, barnacles, sacculina, ostracods, cyclops, daphnia, parasitic copepods, isopod, crabs, horseshoe crab, placazoa, sponge, jelly, physonect siphonophores, hunting cubo, cora, lobelia, comb jellys, mesozoa, myxozoa, hydra, sea anemone, planaria, trematode, rotifers, nematodes, polychates, filter feeder fanworms, derworm, leech, chiton, dart snails, nudibranchs, plant slug, pulmonate freshwater snails, drilling gastropod, burrowing bivalcves, scallops, tridacna, waterbear, bryzoan, cycliophora, starfish, seacucumber, basket star, sea urchin, crinoid, chaetognath, seavent pogonophores, tunicates, pyrosoma, doliolum, oikopleura, trichoplax, loricifera, cephalochordata, unradial echinos, trilobites, opabinia, anomalocharis, sea scorpions, (include some more!)>
<Pfeisteria piscidida, malaria, gregarines, saprolegnia, Coelomomyces like critters, trypanosome, (parabasilids only symbiotes of land critters?) giardia?, myxobolus pfeifferi, Entamoeba>

Devonian period
fast large swimmers fish
Skeletal sys: bones 206, calcium phosphate, marrow, cartilage, joints, ligaments tie bones together,  vertibrae, teeth,
<flying fish, mola, manta ray, sharks, eel, seahorses, anglers, cleaner fish, lampreys, flounder, fastest, biggest, smallest, puffer, moray, sturgeon, ceolocanth ( i don't have good sense of fish ecology and evol, what are the basic fish types?), amonites, nautilus, giant squid, hawaiin bobtail squid, octopus>
@@<<< in general, which critters evolved LATER even though they fill the early niches i'm describing.  tricky>>>>@@@

transport, arteries, veins, capillaries, gills
to lungs, liver, stomach/intestines, kidneys, other tissues carbon dioxide, oxygen,
heart, blood cels, white blood cells, lymph system, water balance

SKIN
protection sensory water temperature regulation

NERVOUS SYSTEM
sensory visual auditory taste olfactory touch  others
animal senses lateral line, palps, antennae, whiskers,
motor, connecting,  voluntary fcts, cerebrum, cerebellum
involuntary fcts, medula oblongata,

amonites
fish schools
sociality
many animals invent large egg gambit, care for young
live in mud filter feed
symbiotes inside multicell animals
parasites of all kinds of cells
single cells and algae and animals invade freshwater: homeostasis
fungal detrivors            69

fossils, evolution, homologous structures, vestigial structures
island biogeography, thry of ev by natural selection, charles darwin
overpopulation, variation mutation,
differential survival (survival of the fittest)
inheritance, adaption, speciation, extinction, genetics
[do i want to put it right at the beginning of life, as a basic property of life, or down here after some examples?]                15


COLONIZATION OF LAND
do lichens evolve with single celled algae BEFORE Ulvophytes invade land?
nitrogen fixing lichens
arthropods invade land to fly to new ponds
trachea
arthropods invent flying
fishapods invade land to find new ponds and oxygen
lungs, breathing
fishapods eat arthropods
arthropod predators
arthropod herbivors
spiders invent aireal filter feeding    13
<cyanos, rhodos, ulvos, chara?, coleochytae, fucus, vaucharia, botrydium, dictyostelium? physarum? (or do they come after wood?)  (i don't know how to separate this, which critters came to land for oxygen before plants evolved.  do i put lichens here, or after plants?), lungfish, fishapods, mudskippers, crayfish, barnacles, hermit crabs, fiddler crabs, centipede? sand fleas>

ULVOS AND FUNGI INVENT HYPERSEA, SOIL
Ulvophytes and fungi invade land mycorrhyza, create hypersea

chloroplasts, vacuole 2dim fluid creature with turgor skeleton, meristem
apical tissue buds, bud
leaf,  stomate, transpiration
stem, underground rhizome stolon
root, root hairs, absorbs water and minerals, active transport, osmosis
vegetative reproduction, clone
stomates, heliotropism,, geotropism gravity, thigmotropism
plants explore their environment

single cell parasites that live in plant hypersea

biotic production of soil
soil, regolith results of weathering, plants, burrowing, worms, ants, humus
soil, climate, nitrates, phosphorus, potassium, calcium, magnesium,sulfates
northern forests humus, laterites tropics less humus
agriculture, soil waste, soil conservation

herbaceous plants, woody plants, trees, shrubs
nitrogen fixing plant symbioses
lichen that lives in antarctic rocks
insect herbivores            56
<moss, nostoc in bryos, psylium, lycopods, what's that other group the resurrection plants, hepatophytes, azolla, anabaena in azolla,  oomycotes on plants, Plasmodiophorans, definitely dictyostelium, physarum, plant parasitic chytrids, mucors, cochlonema explicatum on amoeba, thermomucor on compost, mucors attacking mucors, dactylaria candida lassoes nematodes, zygos in general, physcia, cladonia, reindeer moss, lecanora, lecidia, lepraria, verrucaria serpuloides (marine) collema inside nostoc, cryptoendolithics, saccaromyces, microshaeras on plants, cordyceps invade insects, termitomyces, peziza, morells, truffles ectomycos, claviceps on insects, rhytisma, epichloe, laboulaeniomycetes (some of these come after prairies?  i don't know... ), Amylostereum woodwasp fungus, Lepiota rozites leafcutter gardens, 1000yr old armillaria patch, tiny mycenas on leaf, agaricus, Pleurotus ostreatus rots wood, or invades nematodes, bolete ectomycorrs and monotropoid mycorrs, coprinus, laetiporus, Ganoderma, trametes, earth stars, mutinus, network phallale, birdsnests, septobasidium like system?, glomero vesicular arbuscular mycorrs, geosiphon pyriforme and nostoc punctiforme, microsporidium parasite of apicomplexan, nosema, frog, toad, eft, caecillians, axolotle, (include fossil guys), terrestrial hermit crabs, millipede, sowbugts, plant gall mites, swimming mites, soil mites, argiope, bolas, diving spiders, funnel webbers, cobwebbers, opiliones, pseudoscorpion, fisher spider, tarantula, ticks,
dragonfly, biggest rhinoceros beetle, scarab, aphid, scale insect (with septo), ambrosia beetle, diving beetle, firefly, periplaneta, katydid, tiger beetle, swarming locust, antlion, 17year cicada, spittlebug, waterboatman, reduvid bloodsucker, flea, walking stick, collembolans, mayfly, lice, Halobates, Utacapnia spends entire life cycle bottom of lake tahoe, Strepsiptera,  aquatic caddis fly, bot fly, asilid hunter, gnat, mosquito, sawfly, siricid wasp, cynipid wasps, galls, ichneumanoid wasp parasitoid, hyperparasitoids etc.., land planaria, soil nematodes, plant parasite nematodes, trichonosis, earthworm, landleech, landsnails, slugs, onychophoran, pentostomid>


FORESTS
Carboniferous period
produce wood
cambium, phloem, xylem, circulation system
fungi degest wood
fungi live in plants
fungi invade plants
fungi invade insects
termites invent gut flora chew wood digest it
forests
tree climbers
tree grazers
fishapods become herbivors

(fit Permian extinction, Mesozoic in here somewhere)
(traissic, jurassic, cretaceous)
cyanos, lichens live on tree bark
detrivors churn soil
many phyla invade land: planaria, nematodes, mollusks, earthworms, tardigrads, onychophorans,
nematodes invade plants
fungi invade nematodes
decide how to divide up the different types of symbiotes
single celled parasites that live in animal hypersea
multicelled parasites that live in animal hypersea
multihost parasites
meadows?
galling
leaf mining
narrow diet
omnivores
burrowing animals
tree nesting
dinos fly
dinos go back to the sea        45
<ferns, tree ferns, lycopod trees, horsetails, seeds, seed boring insects, mites..., redwood, welwitchia, hemlock, gingko, bristlecone pine, pine, boletes with pines, alligator, anaconda, rattlesnake, lesbian lizards, seasnakes, gegko, komodo dragon, chamelion, basilisk, legless lizards, galapagos iguana, sea turtle, galapagos tortise, mata mata, snapping turtle, (more fossil guys), herbivore dinos, trex, bronto, swimming dynos, pteradactyls, feather dinos>
<(when to put later freshwater fish? cichlids, guppies, sunfish, archer fish..>


SEEDS AND POLLEN
K/T boundary extinction somewhere here, Teirtiary
seed dispersers
pollen?
pollenators?
larvae develop in developing seeds
flowers/pollinators/seed dispersers

flowers, sepal petal, stamen anther pollen, pistil stigma ovary fruit, ovule seed, seed dispersal, germination, pollination, wind pollination, insect pollination, nectar, seeds

hymeno parasitoids invade plants, insects each other  30
<chocolate, kalanchoe with babies on leaves, boojum, rafflesia, staepelia, cocconut palm, mistletoe, cuscuta, bannana, maple, skunk cabbage, milkweed, sunflower, dandelion, baobab, solidago, Impatiens capensis, beet, bromeliad, spanish moss, prickly pear, saguaro, jade plant, cyperus, horsetail, indian pipe, clover, oaks, wolffia, creosote clone, aloe vera, century plant, onion, yucca, fig, strangler fig, Oenothera polyploids, lady slipper, wasp orchid, 9"spur orchid, bristlecone pine, Poa, bamboo, wheat/barley/rye, rice, prairie grass invent fires, elymus and epichloe and phorid, corn, phragmites, Rosa multiflora, Strawberry, Crataegus, potato, Tilia helicopters, eel grass, tumbleweed, plant with seeds survive in ground, plant travels around world on birds, plants raft to islands, any plants like moss? can colonize rock?, Hymenoscyphus ericae ericoid mycorrs, epichloe on grass, crazy anastomizing hanging one, Lobaria oregana chloro and cyano algaes supply forests with nitrogen, monotropoid mycorrs, Puccinia graminis, Gymnosporangium juniperus-virginaeae, Septobasidium, Rhizoctonia orchid mycorrs,
cat, cow, beavers, bats, dolphins, marmoset chimeras,  Devil allograft facial tumor, naked mole rats, kangaroo, platypus, fruitbats, panda, anteater, star nose mole, vampire bat, prairi dog, flying squirel, narwhal, cheeta, hyena, baboon, manatee, seal, dwarf mongoose, sea otter, elephant, giraffe, goats, raven, crow, brown thrasher, alex the grey parrot, emperor penguin, burrowing owl, bee hummingbirds, arctic tern, frigate bird, cowbird, passer domesticus, mocking bird, scrub jays, weaver nest birds in afrcia, species ring of gulls, condor, biggest harpy eagle, bowerboird, peacock, ostrich, boll weevil, many seed insects, dermestids in cumin, yucca moth, papillio dardanus batesian mimic polymorphy, monarch, heliconians, beemimic flies, well, insects explode here...figwasp, xylocopa, halictids, leafcutter bee, beewolves>


SOCIAL INSECTS TAKE OVER LAND
social insects! ants and termites take over land
now meadows!
grass invent fire cleared prairies
perennial, annual
dinosaurs invent flying: birds
warm blooded verts invade the night: mammals
mammals invent placentas live young
womb, fur, ectotherm, milk, care of young, inner ear, teeth differentiation

animals invent large egg gambit take care of young
sociality in land animals
culture
grass grazing
mammals learn to fly: bats
mammals go back to the sea: cetaceans
big brains carnivores,  cetaceans
apes become visual
Quaternary
ice ages
Holocene                33
<termites, termite fungus, termite basilids etc..., paper wasps, polistes, carpenter ants, formica rufa, slave making formica, microgyne formica, a totally parasitic ant, klepto ants, leaf cutters, army ants, fire ants, auropunctata, african weaver ants, honeypots, biggest supercolony ants, bombus, psytherus, halictids, meliponins, honeybee, wolves, cetaceans, cichlids really, beavers? prairi dog, babboon, dwarf mongoose, elephant, are there any very social birds?  scrub jay, weaver nesters, parrots..>

humans and grasses invent agriculture spread over the earth
humans extend the grasslands and fire, ultimately agriculture DOESN'T work, deserts
ecosystem in the brain
language explodes
narrative
culture explodes
art explodes
religion explodes
civilizations with specilization
conquer all biomes
world wide network of communication
humans begin mature love affair with Earth: science
human industry begins to tax the Earth
humans begin to understand how earth gives rise to life, complexity, molecules...
humans can cause a mass extinction or reproduce earth to other planets
history
archeology                25

 

 (damm bar! you got 950 words, concepts, topics.. and you aint even introduced the organisms yet.

there is some redundancy, maybe 50 to 75 terms are repeated? say at this rate i add 300 organisms

1200 details/ 10 details per page? 120 pages textbook.
not right.  some of these concepts can be defined in a sentence or a picture, others need a page or more...  don't know what the average is.

range is from 60 to 1200 pages.

this is very big.

now can you get it down to average of 6/page X30 =180 details?

don't forget the original outlines for biobook304 and prolegomenon.  you don't need all these damm terms...)

Evolution Of Life By Niche

 
BY PROFESSION:
ok, bar what are the basic niches:
ok, i got over a 100 niches 113.  now pick an interesting critter for each.  and we've got our organisms for biobook.

you know once i get to specific organisms the niches will multiply!  same variety of niches for each clade.  arggh.

you know, if you make this the narrative, you can include all the biology concepts into it.  hmm

autolithotrophs
seavents
photosyntetic lithotrophs H2S back to S8
bacts that oxidize S sequester CaSo4 back to sediments
photosynthetic cyanos fix C, fix N
stromatolites
mud
anoxic mud
deep rock
plankton
methanogen release C
bacts that oxidize N
which bact turns NO3 back to N2
cyanos make strands
bdellovibrios
bacts engulf each other and become euks
photosynthitic single cells pick some photos
diatoms sequester SiO4
cells engulph photos, herbivors  pick some examples
cells engulph herbivores food chains
detrivors bacts and any euks?
littoral zone
invade fresh water
cyanos can live on land?  who can live on rocks?
coccolithophores fix CaCO3
fungi like critters invade cells
fungi like critters invade multicells
chytrids invade fungi like critters who invade multicells..
filter feeders
euks begin multicell: algae,
alternation of life cycles: benthic algae, planktonic dispersal
algae begin fixing CaCO3 to stromatolite reefs
ciliates eat algae filiments
forams live in benthos collecting debris, critters
animals
filter feeders sponges
tentacles hydra
corals engulf dinos start reef building in earnest
grazers of multicell algae,
who eats corals?
food chains get longer
shells and claws
metamorphosis: between plankton for spreading and benthos/ littoral for living
seeweeds climb up the littoral zone
fast large swimmers fish amonites
fish schools
sociality
many animals invent large egg gambit, care for young
live in mud filter feed
symbiotes inside multicell animals
parasites of all kinds of cells
single cells and algae and animals invade freshwater: homeostasis
fungal detrivors
do lichens evolve with single celled algae BEFORE Ulvophytes invade land?
nitrogen fixing lichens
arthropods invade land to fly to new ponds
arthropods invent flying
fishapods invade land to find new ponds and oxygen
fishapods eat arthropods
arthropod predators
arthropod herbivors
spiders invent aireal filter feeding
Ulvophytes and fungi invade land mycorrhyza, create hypersea
single cell parasites that live in plant hypersea
building up of soil
nitrogen fixing plant symbioses
produce wood
fungi degest wood
fungi live in plants
fungi invade plants
fungi invade insects
termites invent gut flora chew wood digest it
lichen that lives in antarctic rocks
forests
tree climbers
tree grazers
fishapods become herbivors
cyanos, lichens live on tree bark
detrivors churn soil
many phyla invade land: planaria, nematodes, mollusks, earthworms, tardigrads, onychophorans,
nematodes invade plants
fungi invade nematodes
decide how to divide up the different types of symbiotes
single celled parasites that live in animal hypersea
multicelled parasites that live in animal hypersea
multihost parasites
meadows?
galling
leaf mining
narrow diet
omnivores
burrowing animals
tree nesting
dinos fly
dinos go back to the sea
seed dispersers
pollen?
pollenators?
larvae develop in developing seeds
flowers/pollinators/seed dispersers
hymeno parasitoids invade plants, insects each other
social insects! ants and termites take over land
pollen eating bees become social
now meadows!
grass invent fire cleared prairies
dinosaurs invent flying: birds
warm blooded verts invade the night: mammals
mammals invent placentas live young
animals invent large egg gambit take care of young
sociality in land animals
grass grazing
mammals learn to fly: bats
mammals go back to the sea: cetaceans
big brains carnivores, apes, cetaceans
humans and grasses invent agriculture spread over the earth

Important science books to go along with a 'humanities' list of "must read" books

In no particular order.  Have fun.

*Gregory Bateson, "Mind and Nature"
What processes does a mechanical system need to have to act like a mind? to evolve? are they the same?  concrete vocabulary to ask and answer.


*Alberts et. el. "Molecular Biology of the Cell"
You are a confederation of a TRILLION living amoeba, each amoeba is a dance of more nanotransformer robots than there are bricks in all of NYC


*Charles A. Sorrel and George F. Sandstrom, "Minerals of the World"
How does the chemistry of merely 2 dozen elements create the 1000s of wildly different minerals?  this is one book i learned chemistry from


*John Janovy, "Yellowlegs"
One biologist's journey to follow and enter the life of of a single migrating bird, or maybe it's a journey into his own mind as a biologist



*David Rindos, "Symbiosis and instability in Agriculture"
We were nomadic hunter gatherers for 100,000s of years and then in a flash, agriculture took us by surprise and spread like wildfire, how?

How did agriculture take over the human world so quickly? because it is unstable, always collapses, we disperse, and start it again

(this was a paper in a journal, or made into a book.  Never saw the book)


*Charles Darwin, "The Origin Of Species", 1st edition.
Darwin spent a life of exploring every nook and cranny of the living world and asked penetrating questions we are still trying to answer today


*Vernon Amadjian and Surindar Paracer?, "Symbiosis: An Introduction to Biological Associations"

Detailed examples of intimate connections between critters from deadly parasitic to mutually beneficial symbioses. do organisms have boundaries?

all the different stories of creatures living inside each other

worms that travel between snail and raccoon, fungi that


*Lynn Margulis and Karlene Schwartz, "Five Kingdoms: An Illustrated Guide to the Phyla of Life on Earth"

The 100 groups of critters on Earth that are more different from each other than plants are from animals, by lifecycle and molecular mechanics


*E. C. Pielou, "After the Ice Age: the return of life to glaciated north america"
Lush details of how our landscape and ecosystem grew back together as the Glaciers retreated over 10,000 years. Stability is not the norm



*Walter Tschinkel: "The Fire Ants"
30 years of experiments and measurements to tease apart and put back together the life stories of fire ant colonies. Step into the life of an alien species! We are no match for them!  


*Borror and White, "Peterson's Field Guide to Insects",
There may be a dozen kinds of mammals lurking 'round your back yard, but you can find at least 500 kinds of insects living there.


*Jack Harlan, "Crops and Man"
The complex ecology and evolution of weeds, humans and crops. how it all got started in multiple places in multiple ways.



*Holling Clancy Holling, "Pagoo"
Follow the story of a young hermit crab growing up in the sea. jam packed with lush illustrations of all kinds of sea critters and biology


*John C. Kricher and Gordon Morrison, "Field Guide to Eastern Forests",
Go out and see how your landscape is knit together by the myriad creatures, get to know some of them.  great details of ecological processes


*"Golden Guide to Pond Life",
Stick it in your back pocket and get to know what's happening at a pond near you.  from microscopic anamalcules to turtles and raccoons



*Donald Kroodsma, "The Singing Life of Birds"
Only 50 years ago we start LISTENING to birds.  they are singing elaborate creative patterns with rules.  we don't yet know what they are saying


*L. David Mech and Luigi Boitani, "Wolves: Behavior, Ecology, and Conservation"
Wolves are the most geographically and ecologically widespread mammals besides us.  they are also more civilized. we've hated them throughout history



*William Morton Wheeler, "The Fungus Growing Ants of North America"
How one ant sized mother eventually raises up a city of a million children the size of your living room. in south america, they are in charge.



*Paul Colinvaux, "Why Big Fierce Animals Are Rare",
2 dozen tales of how our world is knit together at the biological and chemical scale



*Lewis Thomas, "The Lives of a Cell",
These little biology essays got me started in highschool on lifelong expeditions of the biological world. They introduced me to the works of Harold J. Morowitz and Lynn Margulis.


Steven M. Stanley, "Earth System History"
The whole earth is similar to a self regulating organism with feedback loops between rock atmosphere and life.  It has an eventful history.  Learn how many processes and events have taken place.


*Frank Shu, "The Physical Universe: an Introduction to Astronomy"

Read about, do the physics of the grand drama between gravity and the 2nd law of thermodynamics which creates all the structures of our universe

Calculate how much energy the pulsar looses to glow of the crab nebula, then how far back in time it began in an explosion. yes one was recorded there 1000 years ago!


or a simpler text like:
Michael A. Seeds, "Horizons: Exploring the Universe"

or

James Binney "Astrophysics: a very short introduction"


*John Janovy, "On Becoming a Biologist"
Biology is a unique science half way between chemistry and geology, @ the human scale, ready to teach us if we listen to the critters.


*Gerald Holton and Stephen Brush, "Introduction to the Concepts and Theories in Phyiscs"

Why trust science?  each theory takes a 100 years of exacting observation, brutally honest constructive criticism, back and forth before being woven into a stable edifice

Learn how hard, how long, with what back and forth confusion to wrest basic facts of science: heat is the motion of atoms that make up matter


Jim Baggott, "Perfect Symmetry: The Accidental Discovery of Buckmisterfullerene"

Chemists dreamed about soccer ball shaped carbon compounds but Astronomers making actual observations found them.  How laboratory practices and personal interactions work in science.


*Philip Davis and Reuben Hersh, "The Mathematical Experience"
History and exercizes of the mathematician's art. details. what IS mathematics? whimsical creation of the human mind or bedrock of reality?


*Guy Alexander, "Silica and Me"
Thin. easy read. how does a scientist make sense of puzzling experiments? beautiful details. learn some chemistry. geology is silica.



*Duncan C. Blanchard, "From Raindrops to Volcanoes"
A delightful romp through observation and experiment.  how to collect microscopic water drops in sea spray? have a baby spider build you a net...

one scientists experimental journey to understand rain. how to collect microscopic water drops in sea spray? have a baby spider build you a net...


*Richard Feynman, "The Meaning of it All",
*Richard Feynman, "The Pleasure of Finding Things Out",

Science as a way of life of exploration, being able to live without certainty, striving for brutal honesty, is it valuble for human society?


*Richard feynman: six easy pieces
Master physicist introduces you to his craft.  what is matter, energy? gravity?  one experiment that describes the alien quantum world.




*Wilson: 4 colors suffice: how the map problem was solved
Math is weird: 5 color theorem takes only 9 pages to go over 5 cases, you can learn it! but 4 color theorem takes a computer to go over 1400 cases!



*rebecca stott: darwin and the barnacle
Get inside the very human world of Charles Darwin as he spends 20 years to hone his craft as a naturalist before daring to explain his world shattering theory of Evolution.



*Almost Any Freshman Biology Textbook,

*Garrett Hardin, "Biology: Its Principles and Implications" 2nd edition


I can't remember if any of Ilya Prigogne's books are well written or accessible enough to be on this list or whether I pieced together an understanding of his ideas from him and Morowitz.

I can't remember in which book I learned of Morowitz's characterization of life as a cyclic phenomenon running on energy flow.  Or his cycling theorem that states that energy flowing through a finite system induces chemical cycles.