Tuesday, April 23, 2013

Wednesday, February 27, 2013

The Complexity Lab Manual View Of What is Life and How Can It Develop Spontaneously From Chemistry


CHAPTER 1
Diversity and Complexity of Life

1.1) you can go outside in almost any noncity street and collect 100 different kinds of plants.  Along the way you will get some experience with diversity (almost continuous variation on a theme), disparity (discontinuity between forms), and the incredible morphological details that allow us to notice these differences

1.2) not only morphological details, but behavioral.  You can watch a beehive and eventually learn that a 2cm long honeybee can execute over 270 different skills, one of which is to reproduce new elaborate honeybees out of the food they search for and collect.  How do they do this?  Can we build robots to do this?


CHAPTER 2
Computer Science

To get a handle on the levels of complexity involved in life we can get hands on experience building complexity from the ground up.

2.1) from transistors to logic gates, from logic gates to flip flops and multiplexers, from these elements to memories and arithmetic processing units, from these structures to computers with instruction sets of on the order of dozens of instructions.

2.2) once we have computers we can create wild complexity by combining these instructions again hierarchically into subroutines of subroutines ... building up programs a billion instructions long.

2.3) we can even use these programmed computers to hook up to sensors and actuators of robots.

So, can we build 2cm autonomous self feeding reproducing Honeybee robots?  No! not yet. and the reproducing part we still haven't a clue about!  But we've learned alot along the way.


CHAPTER 3
Animal and Plant Development

So, how do animals build their children out of food?

We can watch an animal develop from its egg.  we learn that an animal is actually a growing colony of self reproducing single celled organisms.  a Honey bee starts off it's life as a single celled egg/amoeba that splits in half to 2 then 4 then 8 then...to 500million swarming self organizing amoebas that remain connected and make a honeybee happen. (actually teh first 10 divisions to 1024 cells are slightly different than this)

3.1) Pretty much everything that most organisms can do, this basic unit of life: the cell, can do.  dozens of behaviors, food seeking, reproducing itself out of food.  We can watch single celled Paramecium, Stentor, Euglena go about their ways in a drop of pond water under the microscope.  With months of observation and experiments we can catch them at many of these behaviors.


CHAPTER 4
So What Is This Basic Unit Of Life, The Cell?

4.1) a 150 years of at first confusing but slowly clarifying chemistry experiments has shown us that we can grind up cells and separate them out to 100s of distinct kinds of small components and 1000s of distinct kinds of large components built of these small components.  eventually we learn that the simplest of cells, an E. coli bacteria, are swirling underwater cities of  3000 protein building machines building 2million protein worker robots swimming around and being taken apart and rebuilt out of a soup of a billion parts in a sea of 10s of billions of water molecules.

4.2) I compare this to a city because i can approximate how many bricks there are in New York City:

bricks:
100bricks per window *100windows per wall
or 100^3 bricks per building * 5x10 buildings per city block,  *10*200 city blocks in Manhattan *5 boroughs in all of new york city
=10^6x10x10x100x5
=10^10x5=50billion, yeah more atoms in an E. coli bacteria than there are bricks in new york city.


4.3) remember in our computer chapter we learned what kind of advanced behaviors we could program out of a billion parts!  but there is a profound difference between molecular biology of the cell and programmable computers:  a computer program might consist of a million subroutines and state variables, but the computer processing unit processes these ONE AT A TIME or at most with some parallelism a dozen at a time.  In a living cell, those 2million proteins equivelent to simple subroutines are ALL OPERATING IN PARALLEL, It's like having a million different computer chips interacting at once.  and they dont have to execute the billion instructions of the program, because the billion parts are also bouncing around and interacting in parallel on their own.

so a single cell is a whole qualitatively different level of complexity than a single computer running a program.


4.4) Notice I haven't discussed DNA.  at this level of discussion it doesn't add much important difference.  The 10,000 genes in a cell are simply another 10,000 subroutines running in parallel with and interacting with the 1000s of different kinds of protein robot/subroutines. [if you are into object oriented programming, you can think of them as the classes and the proteins as the objects generated by them, which of course can use the classes to generate even more objects]


CHAPTER 5
What On Earth Are These Molecular Parts?

5.05) they are constructed out of a finite set of only 2dozen distinct kinds of atoms.  The major players: Carbon, Hydrogen, Nitrogen, Oxygen, Phosphorus, Sulfur, Sodium, Potassium, Magnesium, Calcium, Chlorine.  The trace elements (but essential nonetheless) Iron, Chromium, Manganese, Cobalt, Nickel, Copper, Zinc, Molybdenum, Iodine.  (a few other elements are used by various organisms that aren't people)


5.1) these parts are always in 3 dimensional motion (swimming around in a sea if you will) the smaller peices vibrating and bumping into each other a trillion times a second and the larger ones a billion times a second.  this motion we get for free simply because the universe is a warm place.  this is what heat is, the motion of atoms and molecules.  this is also why the higher temperature we raise a system, the faster (usually) chemical reactions will take place.

we can see hints of this motion in the microscope, this is called brownian motion.  Einstein and Perrin showed us how to use these observations to calculate that there are those 100billion molecules in a cell.

5.2) they are sensitive to each other and their environment (pH, hydrophobic/hydrophilic phase etc..) so that each molecule has functional parts that can react to each other with 100s of specific rules.  One learns this in an organic chemistry class.

5.3) they spontaneously join with each other and split apart in different ways depending on these rules.  This is mediated by energy flow which is the topic of chapter 6.  No outside mechanic is required.

5.4) even without energy flow, at thermodynamic equilibrium due to their incessant motion, these parts can self assemble into larger complex structures because of the way they attract each other (like magnets) and simple mathematics.

5.5) one example of this is the formation of clathrin coated pits which cells use to engulf molecular packets around them and bring them inside the cell.

5.6) You can see things like this happen by watching various feathery patterns of ice form in winter.

5.7) or by looking at an exhibit of 100s of different mineral formations.

5.8) so we have these billions of parts randomly exploring each other and then reacting with specific rules.


CHAPTER 6
Energy Flow

living cells are systems of molecules which have energy flowing through them.

Ultimately from the 5000 degree photosphere of the sun spewing out to the 2degrees coldness of outer space.  In between plants create high energy bonds in food molecules and these release energy to the next high energy bonds etc.. till the final fermentation processes of decay release heat to the cold night sky.  This flow of energy in a system of interacting parts can:

6.1) Energy flow causes cyclic iterations in systems of interacting parts. We can build a simple steam engine that cycles off of the flow of energy of burning fuel to CO2 and heat.

It will be important to notice that it is not JUST the heat that makes a steam engine work.  if we put the whole engine INSIDE a hot oven, it will stop.  The heat source and the Cold sink are both required.  Energy must flow from high potential to low.

6.2) Energy flow creates stable dynamic patterns in systems of many many interacting parts (fluids).  We can see this in simple heat flow creating stable patterns of convection cells in fluids and the flow of chemical energy creating stable patterns of spiral waves from a homogeneous mixture of just 5 simple chemicals in the Belusov Zhabotinsky reaction.  We can combine heat and energy flow and play with a candle flame.

6.3) the patterns are stable and can damp out certain classes of perturbation

6.4) but can also preferentially amplify other classes of random fluctuations.  for instance the spiral waves in the BZ reaction are just such amplifications of random fluctuations in the otherwise homogeneous solution.

6.5) interesting unpredictable dynamics can even be created.  We can see this by building a simple chaotic water wheel.  The BZ reaction also can run in a chaotic oscillating mode.

6.6) It is important to note that the ability of life to grow in complexity does not contradict the second law of thermodynamics.  This is true both at the level of a single organism growing from an egg/seed or at the level of whole ecosystems on earth evolving more elaborate different species and interactions between species.

[Explanation coming soon]


CHAPTER 7
Emergent Complexity In Mathematical Systems

7) systems of billions of simple connected agents with simple rules of interaction, under iteration can create VERY ELABORATE patterns that keep growing.

We are just beginning to explore the world at the atomic scale of pattern with scanning tunneling atomic force microscopes.  but we can go back to our computers and play some mathematical games to see what happens when we let 1000s or millions of interacting simple components iterate their simple rules of interaction over and over again.

This is the newest area of study in this exploration!  Only 40 years old!

7.1) the first hint of this kind of behavior was John Horton Conway's game of life, which he introduced in the early 1970s.   Begin with a grid of squares each of which can either be on or off.  each square only interacts with the 8 squares around itself.  every iteration we update all the squares in parallel with these two simple rules:

1) if an on square has less than 2 or more than 3 on neighbors it turns off, else it stays on

2) if an off square has exactly 3 on neighbors, it turns on, else it stays off.

O is off, X is on

you can work out for yourself what these four patterns do:

X
XX,

XXX,

OX
OOX
XXX,

OX
XXX
OOX

be prepared to be amazed.

we can write a computer program to mechanize this (and can imagine one day being able to use nanotechnology to build a grid of molecules to execute these patterns!)

and with that power learn that we can find patterns that continue to grow forever, and we can even make a pattern that forever spits out a sequence of prime numbers so that it grows for.ever and gets more and more different.

But Conway life is not a very satisfying example.  mess around with it and you see that if you change ONE little square in an elaborate pattern the whole dynamic pattern can crash, it is not very robust, the way chemistry is.

7.2) an even simpler rule generates more stable complexity.  Langton's ant: again start with an empty square grid.  Langton's ant is a simple machine (again we can imagine building a simple nanomolecular machine to do this in the not too distant future)  (The more exciting prospect is that perhaps with advanced tools of observation we can discover conditions under which an already existing molecule can do something like this) with a simple rule: the machine sits on a square and faces one of the 4 cardinal directions (N,E,S,W).  The rule is: if the machine is on an off square, turn it on, and rotate 90degrees clockwise, or if it is on an on square, turn it off and rotate 90degrees counterclockwise.  then move forward one square and repeat.

Operating with this simple rule, Langton's ant generates an increasingly complex weird shape that slowly grows to about 100x100 squares over a period of about 10,300 steps and then switches to a periodic behavior whereby it travels back and forth diagonally with one move forward each time in a period of about 100 steps each back and forth and builds an infinite repeated patterned highway shooting off in one direction.  It is very stable, no matter how much you mess up its pattern, it will eventually build its highway.

There are many variations of Langton's ant to explore.  even multiple ants interacting.  What might happen if we had 10billion Langton's ants of a dozen different varieties interacting?  hmmm???


CONCLUSION
go over these laboratory exercises carefully and take time to mull them over.  While none of these chemical or mathematical games comes even REMOTELY close to the molecular complexity of the simplest living cell, they give at least me, a hunch that we are on our way  inventing such games or even finding them under natural chemical conditions, and thus elucidating how chemistry might be able to elaborate all on its own into life.


Thursday, January 10, 2013

what happens when i try to write "The 100 Most Weirdest Differentist Critters On Earth"

life does not come in just individual animals and humans and plants, there are a MANY more possibilites for how life can live on this earth.  Ask any person not educated in biology for the kinds of life forms on earth and they might name: people, dogs, cats, birds, horses, mice, fish, snakes, lizards, bugs, spiders, worms, snails, frogs, fish, snails, trees, plants, mushrooms, they might even have heard of amoebas, and bacteria and yeast.

but there are even MORE possibilities:

chapters:

Cat: what makes a mammal? takes care of young, placentas, milk, communicates, mates, hair, warmblooded, good hearing, young learn, flexible jaws, eats meat

Cow: or a mammal can eat plants.  now we can eat plants too, but we like fleshy plants, and tubers and fruit and nuts and grains.  but cows can eat grass.  and they can get the maximum amount of food from the grass becasue they are ruminants:  they have two stomachs in in their special stomach they ferment the grass.  they can actually digest the cellulose in the grass (cellulose also makes wood, see Termites, pg xxx).  Actually they can't digest cellulose on their own, they have special kinds of flagelated amoebas living in their stomachs and the amoebas digest the cellulaose and turn it into sugar for the cows to eat (see Mastigotes pg xxx)

Wolves: most mammals make their way on their own or sometimes live in herds, mammals are very social animals like that. But some mammals, like wolves, have a high degree of sociality.  A mother and father wolf will live together for many years and they raise a few kids each year and spend a lot of time and effort teaching them all the ways of being a wolf.  the next year the kids become teenagers and have learned much wolfing, and some of them stick around to help theirr parents hunt and raise their brothers and sisters.  As this goes on a wolf pack forms.  and wolves are master hunters of everything from bugs to mice to moose that are way larger than they are.  They do this becasue they teach their kids all the hunting skills and also work together in groups of up to a dozen (?) to bring down large and difficult prey.

two interesting things about wolves: their societies don't grow without bound like human ones do, they keep their packs to a maximum size of about 40.  very sane.  the other thing about wolves is that except for humans they are the most widespread of all mammals.  they live on all continents except australia and antarctica, they live in the arctic, tundra, prairies, forests, deserts... they live around the world and in some places as far south as north africa and mexico and india.

Beavers: also raise families like wolves, they don't hunt though, they eat the living layer of tissue inside the bark of trees, and other plants.  the interesting thing about beavers is that they are master builders and they build themselves beaver ponds out of steams by building dams.  then they build a den in the middle of the pond, this makes a nice place for them to raise their families in and protects them from predators.

Bats: some mammals can FLY.  what an invention!  not only can bats fly, but they can fly at night and even catch insects in the air in the dark because they have sonar.  One fourth of all the kinds of mammals in the world are bats.  there are 4000 different kinds of mammals, and 1000 different kinds of bats.  most of them live in the tropics.  there are bats that eat bugs, fish, frogs, fruit, nectar, even blood!

Dolphins: not only can some mammals fly, but some have learned to swim.  in fact some even spend their entire lives in the ocean and even raise their young there.  Dolphins are shaped like fish but are not fish.  they are warm blooded, must come up for air to breath, and give birth to live young and suckle them with milk.  however, they are like bats in that they also use sonar.  they can spot fish with their sonar and even communicate with each other over long distances through the ocean because their sonar penetrates to long distances.  (humpback whales can talk to each other even if they are hundreds of miles apart).  dolphins have a variety of sounds they communicate with and humpback whales sing songs that last for hours.  Dolphins can also use their sonar to 'see' inside each other and they can recognize each other that way and also tell if another dolphin is pregnant or even if they are sick.

Dolphins are very intelligent and playful and have fun playing games with people and learning new tricks.  their are dozens of kinds of dolphins and whales.  many dolphins and whales also live in packs like wolves and hunt together.  In some villages, the river dolphins and the people in the village have developed ancient customs together in that they help each other catch fish!

Dolphins are also tool users.  and they build their tools out of... bubbles!  Dolphins will often blow sheets of bubbles around schools of fish to trap them so they can catch them.  Dolphins also play with bubbles.  they can blow out bubbles and push them around and sculpt them.  some dolphins have even been seen to blow bubble  rings (like smoke rings) and then blow little bubbles throgh them!

Humans: the superflexible hypersocial imaginatory rhytmic mammal!  weird that we walk upright, dont have much hair.  we can walk, run, climb, swim, dig...  childbirth is very painful.  children take over a decade to raise up to maturity, so need lots of help.  so most mothers mate for a long time with fathers to help raise kids.  grandparents and sisters and brothers also help.

humans are hypersocial and have NO LIMIT to the number of humans that will band together (unlike our sane cousins the wolves) today, human societies are larger than the largest ant colony!  China is one coordiinated country with over a billion people.  we use verbal and written communication to keep societies together.  with laws and government.

we can live in any environment: seacoast, island hopping by boat, mountains, desert, arctic, prairies, jungles..  

we can imaginie anything and can invent any kind of tool or way of life.  we tell long stories with verse after verse after verse.  we excell at rhythm, some performing rituals of ecstatic drumming and dancing for days at a time.

we are runners par excellence (like wolves) and some people can run for a whole day, hundred miles!  we've migrated to every corner of the earth.  more than even wolves.  

we are omnivores, hunt, eat roots berries, grains... we even got caughtr up in agricultre adn alter are environments around us, cutting down trees, damming rivers, creating deserts... more than any other animal (almost more)

along with plants we've entered into symbiotic relationships with wheat barley beans squash potatoes... cows, sheep goats chickens rats pigeons honeybees...

we excell at pssing down culture from generation to generateion

we may even be the one creatures who will one day transport earth life to other planets!

Marmoset chimeras

Hela

Devil allograft facial tumor

Naked mole rats:

Rock Hyraxes: two species take care of each other's kids



Ravens: another type of animal that learned how to fly are birds.  almost all birds can fly. birds also are warm blooded have good hairing, raise their young and are very intelligent.  what's different about birds is that they lay eggs!  and they don't just breath in and out, but can swirl the air inside them continuously, that helps them get enogh exygen for the strenous activity of flying.  birds also have very light and hollow bones.  and they also have.. feathers.

feathers are amziing inventions, their construction is very fractal and the barbs are hollow.  birds can grow new feathers as the old ones wear out.  feathers are very light but very strong.  they repell water and keep birds warm.  feathers are also good for flying.  feathers also act as an external skeleton, strengthening birds wings for flying.  some birds use their hind feathers as a strong tail (like woodpeckers) birds can move many of their feathers independantly like we can move fingers!

Ravens interact with wolves, flying around and helping them spot dead animal carcasses, the wolves tear the carcasses apart and then the ravens can get in and eat some meat too.

Brown Thrasher: many birds are good at singing songs and some are VERY good.  A brown thrasher can sing up to 2000 different songs!  some songs they learn from the thrashers around them.  some songs they mimic from other birds, but mostly they make up their songs as they sing, inventing dozens of songs every minute!

other birds are good mimics and Alex the grey parrot even learned to talk with humans and learned rudimentary skills of recognizing letters and colors and counting...

Penguins: but some birds learned to swim!  all penguins live in the southern hameisphere and eat fish and other seafood.  many live very far south where the water is very cold and full of minerals and oxygen to suport abundant schools of fish.  penquins are excellent swimmers and can stay under water a long time, dive deep and chase down fish.  penguins have to come to land to lay theirr eggs and roost in large groups for protection.

the (emperor) penguins have a very peculiar way of life and march way inland to hide from predators to roost their eggs.  while they do this they have to live off their fat reserves for months without ever eating!  they huddle in the months long continuous antarctic night under the aurora borealis and keep each other and their eggs and chikcs warm in 60 degrees below winds and snows.  once the mother penguin lays her egg, she's exhausted and very hungry and leaves the egg to the father, while she makes the long march back to the sea to get more fish and build up her fat reserves again.  then she makes the long march back to the roost in time to releave the father when the eggs hatch. the fathers make th emarch back to the sea to eat, and the mothers feed thieir chicks with regurgitated food.  when the chicks are old enough they all march back to the sea for the summer feeding.

Burrowing Owl: some birds live in the ground

bee Humming Bird: these birds are the smallest birds in the world.  they are almost as small and light as bumblebees!  and like bumblebees they eat the most concentrated food source: nectar from flowers.  hummingbirds are some of the most amazing flyers, their wings beat the fastest.. and they can hover, fly up or down and even backwards.  they migrate for the winter.

-------: migration is an amzzing thing and some birds migrate for distances of up to 10,000 miles.  some migrate over the sea for days and days without ever landing!

-------: (frigate bird) this bird lays their eggs on small islands in the middle of the pacific ocean. and then they do an amazing thing.  they fly off over the ocean to catch fish.  but they can't take off from the water like cormorants and ducks so they swoop down and catch fish in midair. in order to catch enough fish for their chicks (like penguins) they often stay out at sea for days at a time, never landing.  they are the most efficient flyers of all birds and sail slowly acrss the water with the minimum of burning up their food reserces.  In order to fly for days at a time withot landing, they can't fall asleep.  so they do an amazing thing: every few hours one half of their brain goes to sleep  (mammal brains seem to need to rest and dream to stay healthy) and then a frew hours later that half wakes up and the other half falls asleep!


alligator: the most like dinosaours.  warm blooded and lay their eggs in nests like birds.  like birds they care for their young also and feed them.  they can hear their young peeping int he nest before they hatch.

Anaconda: some lizards don't have leggs!  snakes can move around by slithering.  they have the most vertebrae of all animals, some have 300 vertibrae and ribs.

rattlesnake


-----: these lizards are unusual in that there are only females.  no males of theirr kind.  the female lizard can lay eggs and have children without a father!  in essence the children are clones (which form of mixis do they perform?)  Still, they can't become pregnant unless they carry out their mating ritual with another female lizard!

seasnakes: just like dolphins and whales, these kinds of snakes have left land and spend theirr entire lives in the sea (true?  do they come to land to lay eggs and hatch ther young or are they live bearers?) they can swim and catch fish.


poison arrow frog: frogs are like lizards that they lay eggs but must lay their eggs in water like fish!  So these frogs which live in south american jungles find pools of water in bromeliads sometimes up on high tree branches and lay their eggs.  frogs are strange in that they go thogh metamorphosis!  at first they eggs hatch into tadpoles that can breath in water like fish and eat algae and plants!  then whhen the tadpole grows up, it starts sprouting legs!  and also grows lungs and absorbs its tail.  soon the new frog leaves the water and eats bugs instead of plants.

frogs also sing.  poison arrow frogs are cool in that they secrete a poison on their skin.  hunters keep these frogs as pets and use the poison secretions to dip their arrow heads in so that they can use it to kill the animals they hunt

Surinam Toad.  the mother lays eggs on the father's back!  then the eggs sink into his skin totally covered up so that they are protected.  the father can swim about so theat the eggs have fresh well oxygenated water, and can protect them against being eaten by predators.  (he also feeds them through his skin?  the eggs don't hatch into tadpoles thogh, they grow all the way into miniature frogs and hatch out of his back as minieature frogs.  very weird!

red eft: starts out as water breathing green newts.  then metamorphosize into bright orange tinay efts with red spots and spends years wandering around in the woods to find a new pond to settle in.  when they get into the pond they turn back into green newts breathing water and breed.  they are very tiny but still have legs and toes and many tiny tiny bones.

Caecillans: some salamnders are like snakes!  the caecillian looks almost like an earthworm some are bright blue!  most burrow iin the ground like earthworms.  some live in the water.

[31 LAND VERTS]

fish: but life started in the water, fish breath with gills.  they listen to the pressure waves in the water with their lateral lines (these evolved into the cochlea in our ears!)  there are 40,000 different kinds of fish.  they have bones and heart etc.. just like mammals.  like frogs and salamnanders, they lay eggs.

Guppy: live in ponds, puddles and streams in south america.  they are unusual fish in that they give birth to live yong, not eggs.  they are also unusual in that if there ar not enough males in a pond, some of the females will turn into males and can mate with the other females.  (they have penises!)

flying fish: and some fish have learned to fly!

Mola Mola: very weird.  some are 10 feet wide and flat and thin.  such a big fish is very unusual in that it's spine is only an inch long.  the fish is all head and tail!  Molas sometimes turn sideways and float flat on the surface of the sea to let birds land on them and pick off fish lice and other parasites!!  they eat jellyfish and grow very fast.  they have tiny mouths.  they are altogether very weird

Mudskippers: some fish climb around on the land!  out of the water.  they keep their skin moist and breath throgh it.  they build burrows on land to mate and lay theirr eggs in the water in the burrows.  the males climb on top of the burrows and make hooting noises in the air to attract mates!  some mudskippers even climb up the roots of mangrove trees!!!

Lungfish: can also breath out of water.  they have lungs and can leave theirr pond if it starts to dry up and crawl around on the ground using its fins to find a new pond.  if it can't find a pond in time it will burrow under the ground, and make a hard nest around itself and dry out!  it will stay like that for many months untill the spring rains moisten the soil and the lungfish comes out of its coccoon and crawls off to find a new pond.

Manta ray: these are cartiliginous fish like sharks.  they dont have hard bones!  but cartilage instead.  some grow 10 feet wide adn are very flat and fly through the water.  (can they leap out of the water?)

Eel: these live in streams in north america and europe.  but to lay their eggs they swim ALL THE WAY down their streams into the rivers and finally out to sea.  then they make their way all the way 1000s of miles to the sargasso sea and lay their eggs.  when the eggs hatch they hatch into tiny larvae called elvers, that don't look like eels at all and are transparent.  (then there is another stage?) eventually when these elvers grow up they make the long journey back 1000s of miles back to the continent to the rivers and streams.  some even make it back to the very same rivers that their parents came from!

this odd way of life might have resulted from the fact that once upon a time the two continents where one!  then they started to split apart!  at first there were long narrow lakes in the middle liek lake beikel (?) in russia. maybe the eels started their lives off in streams and layed their eggs in this lake.  as the millions of years past by, the halves of the continent pangea split further apart making the lake bigger, but the eels kept swimming back to the lake.  eventually the contients grew 100s of miles apart, then thousands, but thourgh all that time the eels kept their custom of swimming toe the middle of that lake, that now has become th eatlantic ocean

Sea Horses: the mother lays the eggs but puts them in the father's pouch!  the fatehr takes care of them adn eventually they hatch.  sea horses are shaped very strange for fish and pick off minute invertebrates from kelps with their narrow snout.  they have bony plates surrounding them.  they mate for life (?)

Cichlids: 2000 different kinds evolved in a short time in the lakes of central africa.  they lay eggs and take care of them and even take care of the babies till they hatch.  the father and mother stay together to take care of the babies.

----cichhlid lays its eggs attached to a large fallen leaf in the pond.  it then carries the leaf around in its' mouth to take it away from predators and when the old place is dangerous...etc...

-----cichlid lays its eggs and then when they hatch shoves off the kids into the brood of another cichlid or a catfish so that that fish takes care of them!

discus cichlids excrete a milky substance from theirr skin to feed their babies just like mammals do!

---cichhlid keeps it's babies safe in it's mouth!  they take turns doing this while the other parent feeds!

just like people, cichlids go through elaborate mating dances to see if they make a good couple because they will ahve to spend a long time together witht he difficult task of raising their young

Angler fish:  feet and fishhing lure and camouflage

Deep sea angler: all mouth and luminescent fishing lure with luminescent bacteria inside.  way deep under the ocean the fish are rare and far between, because there isn't much food.  so it is hard to find mates.  when male anglerr fish are very young they search for older females.  wehn they find one, they bite onto her and hold on.  eventually the wound closes and the two fish become one.  the male never grows up, the female absorbs most of the male's body and their circulartory systems merge, so the male is totally fed by the female.  in essence the only organs that are left in the male are the gonads, so that whhen the female is ready to mate, the male gonad appendge is ready right there to produce sperm.


but there are many kinds of animals!

in the sea are also crustaceans

Lobster: they have exoskeletons!  and jointed parts. they have many different kinds of 'legs' some it walks with, some it uses for swimming, some it uses as claws, and some it uses to guide food to its mouth, some are even antenae.  lobsters are filter feeders and filter the water throught heir mouths  and filter out minute particles of food.  they lay eggs

Whale Barnacles: these are like shrimp.  like most crustaceans, they hatch from their eggs as larvae called nauplius, with long antenae and arms that help them float arond in the plankton, eating single celled protozoae, as they grow instead of metamophosizeing into adult shrimp, they land on the whales head first and cement themselves to the whale skin witht heir antenae!  then they build a calcerous shell around themselves with doors at the top! then they live their lives like that  upsidown kicking their legss into the water to do their filter feeding like other crustaceans.  because whales are alwasys shedding their skin, the barnacles have to continuously burrow down deeper and deeper into the fresh layers of skin as the older outer layesrs shed off.  (to mate, barnacles have LOOONG penises that they can stick out of their shells to find a neighboring barnacle to mate with) some barnacles keep their eggs in their shells and grow them till they hatch out.

some barnacles keep the male larvae inside their shells so that when it comes ttime to mate their will be a mate available.

goosseneck barnacles

Sacculina: now the weirdness in biology REALLY STARTS!  sacculina is a barnacle that lives like a fungus!  it starts off like every other barnacle as a nauplius larvae swimming aroung.  eventually it settles on a crab.  but instead of turning upsidown and building a shell around itself and startging to feed, it injects some weird glob of cells of itslef (not even an organ!) into the crab.  these cells are not anything like any organ of usual barnacles.  these cells stick together (? separate and anastomise?) and  proceed to crawl around inside the crab and keep growing out thin tentacles like fungal mycelia (see Fungi pg xxx) and their form of jnutrition is to suck up the juices of the crabs hemolymph.  This is the whole Sacculina!  eventually it becomes a netwok of fibers throughout the crab simply absorbing the crabs nutrients like a giant flimsy stomach!

but the weirdness doesn't end there!  wehn the Sacculina is ready to breed, first it sends ot hormones to make the crab NOT breed.  then it grows a tentacle out a crack in the crabs shell where she wo9uld normally keep her eggs and tend to them, and this grows into a large blobby chamber.  the chamber grows eggs.  then a male Sacculina nauplius comes swimming by and enters the chamber.  it's not old enough to make sperm to fertilize the eggs and anyway it doesn't bother growing up to do this like normal barnacles!  (but remember the barnacles with the male larva that live inside them!)  so this male nauplisu, just like the original female one, injects a blob of its cells into the female Sacculina's blobby egg chamber organ.  these cells then grow like a sacculina parasite in the female sacculina feeding off of it, and eventually produces sperm.  these fertilize the eggs and they hatch into nauplia safe inside the chamber.  the sacculina prevented the crab from wasting food to make her own eggs, but she does care fort he sacculina eggsack just as she would her own clutch of eggs.

Hermit crabs: use snail shells as their homes.  some put sea anemonies on them.  some yong ones live in empty barnacle shells on top of snail shells with older hermit crabs in them (true?)  some live on land in burrows but have to go back to sea to lay their eggs

Coconut crab: this is a giant hermit crab a foot long and heavy with big stron gclaws.  it's too big to carry around a shell with it so goes shellless.  it climbs coconut palm trees! to find coconuts and splits them open with its' stong claws to eath them!  but it too must come back to sea to lay its eggs

caribbean Terrestrial hermit crab: spends all its adult life on land!  it collects dewdrops and rain from puddles and keeps the water inside it's shell to keep its gills moist and breathing!  but it too must go back to the sea to lay its eggs so the larvae can develop and metamorphosise into a hermit crab and crawl out of the sea to live on land.

----crabs there are crabs that spend their entire lives away from the sea in tropical rainforests.  they live in the water in tree boles, adn bromeliads and come out and crawl around the woods hunting their prey: snails and such.  then they lay eggs which hatch into baby crabs not nauplius and these live in the water pools and can also start crawling arond the forest to eventually find new water pools (get the facts right, there's lots of combinations)

---one can imagine that a hermit crab or other kind of crab can evolve eventually to totally be independent of water either brooding it's eggs inside the water in its shell or even 'brooding the eggs' inside it's body to give birth to live young.

isopods: sowbugs: one kind of arthropod that came on land

Millipedes: another arthropod that came onto land

and Centipedes: carnivores with poison fangs, the males deposit stalked spermatipores and the females pick these up and have weird mating rituals and then the male fertilizes the eggs.  do some care for the eggs?

foot long centipede

arachnids

Parasitic Galliing Mites: make galls in plants.  galls is weirdness in biology, a new plant organ that is the composite achievement of plant and mite. ash parasite

Swimming mites:

Argiope:  spinning webs is a really cool invention.  kind of like filter feeding int he air.  booklungs, lots of eyes.  lays eggs in sac cares for tehm

Bolas spider: swings sticky lasso to catch iinsects

Diving Spider with water bubble

spiders balloon!


Scorpion: stings with tail! huh!  carries babies on its back

Opilliones: eats snails, then lays eggs inside snails.  uses one pair of legs for feelers.  can loose legs.  poisonous to eat

[22 ARTHROPODS]

Dragonfly: freshwater aquatic larvae hunts invertebreates, but then to find new sreams and ponds to mate in, it metamorphosizes into adult winged dragonfly.  master flyers.  insects: spiracles, trachea, hemolymph, waxy exoskeleton, wings, 6 legs antennae..

Boll Weevil: beetle.  there are over 600,000 different kinds of beetles, the most variety of ANY kind of living thing. one third of all the kinds of living beings on teh earth are beetles!  one pair of wings is hard shell.  drills holes in seeds with snout and lays eggs in there!  there are 60,000 different kinds of weevils.

Lewis Thomases tropical Weevil: grows a whole miniature forest of lichens and algae and moss and mites and nematodes on its back for camouflage

Staph beetles that live in ant colonies.

biggest rhinocerous beetle:

Scarab Beetle: shiny flying gem, that digs up large mammal manour and rolls it into a ball and digs a burrow, the male and female cooperate to do this and digs the ball into the burrow and lays an egg in the ball and it hatches into a gross pale snaky grub and then that grub makes a chrysalis and tehn it hatches out a shiny flying gem.  model for ancient egyptian mythology.

Aphid: suck plant juices, weird alternation of generations life cycle sexual asexual

Scale insect, Septobasidium, trees.

Ambrosia Beetles: social, symbiotic with fungus that digests wood in the burrows the beetle makes in trees.  dutch elm spread by them.

diving beetle with water bubble



hymenoptera evolve a 7th appendage the movable stinger

Sawfly: saw slits in trees and lay eggs hatch as larvae which feed on leaves.

Siricid wasps: bore holes in trees with ovipositor and seed them with a fungus she carries, then lays eggs the fungus digests the wood and the larvae feed on the fungus

Agaonidae: fig wasp

Cynapid wasps: make galls or lay eggs in other galls

Ichneumenoid wasp: parasitizes catipilars, keps them alive while it feeds inside.

Trigonalyd wasp: bores slits in leaves and lays eggs.  the eggs are consmed witht eh leavs by catapillars and hatch inside but wait.  then an ichneumon wasp or tachnid fly lays it's eggs inside the catapillar and when that egg hatches inside to be a larvae feeding on the insides of the catapillar, the trigonalyd larvae invade THEM.


This can go on a few more levels: Hyperparasitoid wasp infecting a hyperparisitoid infecting a hyperparasitoid iinfecting a parasitoid of a catipillar:

R. W. Pemberton, J. H. Lee, et al. '93, "natural enemies of the Asian gypsy-moth (Lepidoptera, Lymantridae) in South Korea" Annals of teh entomological soc of america, 86: pg 423-440

P. Weinstein and A. D. Austin, 91, "The host relationships of  Trigonalyd wasps (Hymenoptera, Trigonalidae) with a review of their biology and a catalogue to world speices", Journal of Natural history, 25:399-433

Copidosoma: lays an egg inside a Trichoplusia moth catipillar.  the embryo hatches and divides into a thousand larvae!  a few of these undergo precocious development and cruise around in the catipilar killing other parasites that compete with their siblings.  they die but the other siblings metamorphisze and hatch out

Smallest insect: parasitoid wasp


Formica rufa: that tend aphids and makes huge mounds and controls forests

Slave making Formica:

a totally parasitic ant:

Leaf Cutter Ants: huge room size nests with symbiotic fungi and nitrobacters and colonies of a million

Army Ants:

Fire Ants: weird colony founding and polygyne and hybrids.

Auropunctata: weird cloning lines

African Weaver ants:

seedcollecting ant

honeypot ant

biggest supercolony ant

pharao ants in walls of hospitals

acacia fire ants


Collembolans: some spend entire life floating on water, others hatch out on the surface of fresh fallen snow! (i don't know what they do there)

Mayfly: aquatic larvae many varieties have diff feeding habits, they metamorphize into wingeed adults, some anly live a day without eating and mate and lay eggs.

Macrotermite: collect dead vegetation, grow fungus on it and eat the fungus, build huge 10foot high nests

other termites: digest wood with microbes that live inside

lice: suck blood and eat skin, spend entire life cycle on animal host

water strider Halobates: only ocean going insect

Dermestids generations live indefinitely on dry seeds grains cumin...  don't need water

Utacapnia as stonefly spends entire lifecycle at the bottom of lake tahoe!

Strepsiptera: wiinged males mate with larval females which remain in the host insect, the eggs develop inside her feeding off her.  they hatch and leave the host and hop around looking for a new one to enter.  they develkop ini there and the females remain and the males metamophosize wingsand leave in search of other females.


Papillio dardanus: batesian mimicry polymorphism

caddis flys: build nets in the water to catch food, also build shelters out of twigs and sand grains

bot fly inside flesh

sponges: weird way they feed their larvae


physonect siphonophores, and physalia: weird composite critters/colonies/organs

a trematode parasite, lookup the weirdest one, commonest one

rotifer, clonal: variety of amictic eggs to females, mictic eggs ferilized, unfertilized mictic eggs to males

some budding polychate, in many spp many segments prodce gametes, 

Syllis: asexual worms but off sexual epitokes which have the gametes in each segment.  very weird pg 276

nudibranchs: maintan stinging cells of their prey

entochonchidae are internal parasites of sea cucmbers no shell

slipper shells change sexes, there is much varitey in the gastropods...

scallops, swim and have eyes

tridacna, giant clam

shipworm bores in wood

the clam that has a fishing lure to attract a fish and then spits out glochidia larvae to parasitize the gills!


ticks that suck blood and transmit diseases

burrowing crayfish missouri

barnacles that live on floating wood

spray zone barnacles can last a long time without water (even frozen?)

trypetesa lives inside snail shells only with hermit crabs p547

tiny shell boring barnacles

limnoria: wood burrowing isopod

weird isopods living in gill chambers of crabs  p566

Arcturus baffini is weirdly shaped and holds young on really long antennae

Phronima sedentaria an amphipod lives in teh tunic or urochordates

krill

japanese spider crab largest arthropod

pea crabs live in animal tubes, cloaca of seacucumbers etc...

coral gall crab becomes encased in a chamber of coral!


pyrosoma giant colorful colonial thaliacian tunicate up to 2m long, swims!

Doliolum:

oikopleura!


the craziest rhodophyte lifecycle

rhodo that parasitizes another rhodo! maybe a nonphotosynthetic one

Porphyridium a red algae lives inside benthic forams



a chloro that makes lichens:

chlorella: where does that live?


kalanchoe: baby plants on the leaves:

boojum:


dandelion: no sex, seeds fly away

matricaria matricarioides: survives living on driveways underfoot etc..

impatiens capensis exploding seed pods

those tiny caryophyllaceae that live between the bricks at colombia u.

jade plant: and weird carbon metabolism


indian pipe!

vallisneria americana bottom dweller weird flowreing

wolffia smallest flowering plant

longest lved clone out west the bushes.. damm what are they called?


oenothera polyploids or a plant we've seen go polyploid new species

slipper orchid with orchid mychorriza

orchid what impersonates a special wasp

orchid with 9" spur for 9" tongued moth

bristlecone pine oldest tree

bamboo with 150 year synchronized cycle

wheat/barley/rice what symbiotic with humans create huge civs

prairie grass what invented prairies fires etc..

elymus and epichloe and phorid? fly

phragmites australis world wide distr?


euplotidium with bacterial stingers

dinophytes have at least 3 kinds of protists as chloroplasts: ulvo, rhodo, hapto which have rhodo (find which dino does this!)

parvillardii has movable eye

Pfeisteria piscidida creates fish toxins  is this the one that kills fish to eat them?  it has weird polymorphic life cycle

Gymnodinium microadriaticum is the most common coral symbiote?

what's the most weirdest apicomplexan life cycle?

blooms of phaeocystis poucheti produce dimethyl sulfide that seeds rain?

fucus can live out of water and even freeze

botrydium huge multicell ballons on drying mud and rhizoids with cysts

saprolegnia lives on fish fins

plasmopora viticola fully terestrial on land

opalines in frog cloaca

labyrinthula cool slime nets on zostera sea grass

forams with symbiont algae that crawl up plant leaves out of water to photosynthesise

forams have dinos, chrysos, diatoms

weirdest foram that lives on benthos and covers it eating everythign

foram that grinds up food

foram that selects precise sandgrains to make shell

spumullarian radiolarian with huge colonies

Actinosphaerium crawling freshwater heliozoan

phacus really cool euglenophyte ulvo chloros  can absorb food or photosynthesize

joenia annectans parabasilid who lives in termites with epibiotic spirochates and bacts between and internal bacts.  who digetss the cellulose?

hypermastigote with 100,000 undulis?

naegleria amoebic meningitis has flagelated alternate form

dictyostelium

physarum polycephalum, or Stemonitis or dogvomit slime mold


myxostoma cerebralis twist disease in salmon really weird lifecycle

Tuesday, January 8, 2013

Tuesday, November 13, 2012

Some More Notes About Why Science Is Remarkable

As to what qualities make science remarkable in human history and different from other human traditions... chief among them is that it is a methodology that helps us help each other get our of our heads

most human traditions and activity is steeped in thinking that human interactions and events and stories are the most interesting and important things around.  and in fact we are still steeped in 1000s of years old traditions that have imagined that the entire universe was created and is governed by  something like a human mind.  and that mindishness is something kind of like vapor, not to be ANALYZED, taken apart.  and that our own experience is due to a vapor like soul that is trapped in corrupt physical bodies that are just dungeons of pain, corruption and death.

so to me science is so remarkable because it breaks out of this pattern in a few ways.

(1) Most people are more interested in human stories rather than stories about rocks and worms.  and if they are at all interested in rocks and worms it's maybe because they could use the rocks to build a house or use a worm to help cure their grandmother's cancer.  what makes science special (akin more to poetry perhaps) is to simply see rocks as COOL or wonder what the world is like from a worm's perspective, and to value bodies and stuff as much as human life-experience.

(2) science succeeds because it is a tradition of realizing that we can easily fool ourselves in our experiments because we are sloppy or subconsciously swayed by how WE WANT the experiment to turn out, and then it is a tradition of CIVIL DISCOURSE, that we build a network of publishing our experiments in detail and critique each other's experiments when we find instances of each other subconsciously fooling ourselves (worldwide network spanning languages and cultures).  It is a tradition where doubt is cultivated and admired. while many scientists are subject to human foibles just like everyone else, it is remarkable that this is a stated goal of science: to doubt and find where we fool ourselves even if it leads to discomfort.

(3) a predominant approach of science is to analyze seemingly monolithic experiences in terms of interactions between discrete parts (akin to its general interest in stuff), and even if the project is to analyze less mechanical phenomena like fields, waves, fluids, science is certainly steeped in paying attention to the interactions between discrete parts in the experimental apparatus used to study them.  and it is the interest in stuff, playing with a prism, wondering why the positions of the moons of Jupiter lag behind the published tables.. that lead to more abstract theories about less stuff-like electromagnetic fields.

It is this interest in stuff and explanation of phenomena in terms of interactions between parts that can lead to a world view that human soul/experience might be interaction between earthen parts as opposed to some alien vapor temporarily trapped by earthen shells (good riddance too them and the Earth in the world to come).  this is a valuable perspective.

Friday, September 7, 2012

why is the universe so many stupendous numbers?

Why can we build a telescope and heave it off our planet with giant rockets to orbit above our sky and with it look out at the night and see a universe full of a...

100 billion galaxies all further and further away from each other and we can count in each galaxy a..

100 billion suns, and our sun is a

100 million miles away up in the sky and is a

million miles wide, while earth is only

8,000 miles wide which would take

24 hours to travel around at

1000 miles an hour so it's made of

256 billion cubic miles of gyrating rock but still it would take a

million earths to fill the sun and also it means that the surface of our earth is

800 million square miles, each mile being..

20x20 city blocks, and spread across the land of this earth we've become ...

7 billion squabbling singing dancing birthing dying eating shitting wondering wandering humans sharing this earth with...

1000s or millions of billions of other critters and in fact each of us ourselves is actually a colony of a

10 thousand billion living amoebas all tightly knit together into a community but each an independent living creature that is born eats dies makes decisions communicates with its neighbors and ... because our colony of amoebas launched from the shores of each of our mothers' wombs (we were one of HER amoebas...we are a continously living journey of protoplasm more than 3 and a half billion generations long.. and all these living amoebas can eat explore turn food into itself communicate tell time build an entire replica of itself because each one is in fact an entire New York City full of

1000 billion nanorobots as many as there are bricks in all of New York City with its 100x100x100 bricks per building times 100 buildings per block times 200x 10 city blocks that takes a day to traverse

swimming in a soup of a

million billion molecular parts and a way to visualize a

billion is to slice a block of tofu into 10 slices and then turn it 90 degrees and slice that 10 times so you got a 100 slivers and then turn that over and slice that 10 times so you got a

1000 tiny cubes and now go find the corner of a large 3 story building and line those 1000 tiny tofu blocks one by one along the side of that building starting from the corner on the sidewalk till it's 30 feet along and then go back and slice up another

1000 tiny tofu blocklets and line them up along the other side of the building from the corner and now you gotta concentrate hard and use your imagination and visualize the floor of the building made up of a grid of a 1000x1000 tiny tofu blocks making up a

million of them and then go slice up another 1000 tofu blocklets and pile them up along the corner of the building like 1000 Lilliputian floors up 30 feet and now REALLY concentrate hard and visualize a 1000 of those million block grids all making up that building and by the way our brains what we think and feel and imagine with is made up of as many amoebas as

100 of these buildings of a billion amoebas all the while each of these amoebas is sending out arms of protoplasm to branch 10 times to point fingertips to a 1000 other amoebas across the city of brain to have these billions of simultaneous conversations.  but what are these  100,000 billion nanorobots that make our amoebas dance anyway? they are proteins and enzymes and each is a sproingy network of

10,000 atoms of 6 different kinds linked in squaredances of electron orbitals and these nanorobot proteins can snap together and change shape and crawl across each other and make simple logic decisions (forming dense information processing networks...) interacting with dozens of each others and can even come together by the 100s to take each other apart and rebuild each other from scratch out of these atoms. go visit new york city and imagine each of those bricks you see is a flying crawling nanorobot and they all start moving around and swarming like clouds of billions of bees all rebuilding each other and reproducing an entire city in two weeks. and what the hell ARE these atoms anyway?

dozens of interacting electron orbitals each singing a different frequency and repelling each other but attracting each other in duets of dance to join with other atoms,  to make atoms springy fuzzy sensitive boundaryless slightly unpredictable sparkles and are electrons and protons and neutrons the rock bottom core of stuff the universe is made of? well every time we look inside with our cathedrals of particle accelerator experiments like the Large Hadron Collider made of

over a billion precision crafted parts taking 10 years to build in a cavern that can swallow (a cathedral?) build like a ship in a bottle down a 150 foot deep shaft into the largest vaulted cavern on earth by 3000 scientists and engineers and students from over 40 different countries and cultures and languages and religions all learning to civilly criticise each other and come to agreements about the rock bottom nature of reality..

we keep finding another level of parts more messy than the previous level and that the universe isn't made out of stuff at all but maybe it's an infinitely complex mathematical game like a...

 Mandelbrot set?