so Mirrizin says:
Nachum Braverman, a Jewish Rabbi, describes the process
"You rest your hands on its head and you confess the mistake you made. Then you slaughter the cow. It's butchered in front of you. The blood is poured on the altar. The fat is put on the altar to burn. How do you feel? (Don't say disgusted.) I'll tell you how you feel. You feel overwhelmed with emotion, jarred by the confrontation you've just had with death, and grateful to be alive. You've had a catharsis. The cow on the altar was a vicarious offering of yourself"
...
Christ took the guilt with him. The point of a Jewish sacrifice, I think as I've recently read (check with blackskimmer, perhaps? or davidmordichai? Prefect?) would be not to appease God by giving something away, but to project your guilt onto a living thing and then symbolically slaughter it to remind yourself of what you had done, and then to shock yourself back onto the right path.
Jesus wasn't killed because God likes killing. Jesus was killed because he was trying to get his (God's) point across. Christ took it all with him so that we could see the way to go.
and I said:
jesus was all about shock! his message: get out of the slumber of your everyday family life, political life, religious life and WAKE UP, drop everything and follow me and examine your life.
were's my thoughts on why god committed seppuku?
why jesus died for our sins < blackskimmer > 05/25 13:23:37
the formulation i came up with back when i lived some christianity was this:
life for humans in this universe inherently involves sinning. no way to avoid it, not hard thought nor technology. there are always mysteriously unavoidable dilemmas. i.e. abortion, saving lives, hell even just to die at your appointed time seems like a sin against such a splendid being.... that's how life is for organisms as complex as us. Sometimes we even blame ourselves for our own deaths. Certainly this is a biblical take on the situation, that human failing is responsible for the introduction of death in the world.
Even birth, to conceive a child, an act of love, of creativity, of hope, creates the possibility of danger, to the mother and the child.
so what do you do? recall Arjuna's dilemma in the baghavad gita. he was a warrior in charge of an army in a major battle. he was up on the hill watching the two sides and started to imagine all the suffering and destruction that would occur if he sent his side into battle. also all the suffering and destruction that would occur if he didn't fight and the other army attacked...
so he froze! it took the whole book for krishna to convince him there was no way possible for finite humans to understand which way to act brings less suffering in many cases, but we cant just crawl under a rock and NOT enter the fray.
what i take jesus dying on the cross to mean is that our life involves sinning, that's a given, not quite we 'inheritted it from an act of adam' but that's just how it is to be human, even to be interesting.
We are not perfect robots, but creative beings, and beings born into the act of creative evolution. all creation involves risk, involves invention of ideas and choosing between them. to be able to take part of this creative act of evolution requires that we be vulnerable. to congenital illnesses, to cancers. to death. we find this horrifying, but the alternative is to be perfect, eternally fixed.
but who can love a perfect robot? we love each other because we can identify with the other's frailties.
i figured there are two levels of responsibility? if you think YOU are responsible for getting yourself into one of these impossible dilemmas where either choice is a sin, if you think you are responsible for your own death, then you are in anguish and freeze. and even if you freeze something bad will happen anyway because you didn't act...
the message of jesus dying is: 'you are NOT responsible for being in that situation, it is the common human condition. I, God, put you there by creating you that way. i'm the only one who could forgive you for being human! so now go and choose one of the choices that you think is best, and act on it. and even if you think it is not the perfect choice, go ahead and bumble through it anyway (no perfect choice may be possible) TAKE RESPONSIBILITY for that choice and live with the consequences, but don't be burdened by thinking you put yourself into the position to make that choice.'
and then we are called to emulate god in his forgiveness, to forgive each other for not being perfect.
Saturday, June 18, 2011
Hitting Your Thumb While Trying To Hammer In Your Life
expect cursing
when you attempt to dive
into the tumultuous waters
of religion.
don't you curse
when trying to hammer in a nail
and you hit your thumb instead?
how much deeper the pain must be
when trying to drive in straight
a whole human life
and miss...
when you attempt to dive
into the tumultuous waters
of religion.
don't you curse
when trying to hammer in a nail
and you hit your thumb instead?
how much deeper the pain must be
when trying to drive in straight
a whole human life
and miss...
Friday, June 17, 2011
How An Animal Grows From a Single Egg Cell: It's Like a City Growing From One Colonist Stranded On a Lush Tropical Island
An animal is a society of tiny single celled organisms, that is growing by way of these living cells giving birth to more and more cells and informing each other and rearranging each other.
To what kind of human venture is it most like? The founding of a city? So pretend one person washes up on a beach a lush tropical island beach and for the hell of it, pretend people are unisex and reproduce by splitting in half. (quite odd, eh?) so this person eats all the cocounts and mangos and gets fat and splits. At first the fellow is doing everything, finding food, chasing away monkeys, building fire, foraging for supplies, building shelter... then the twins split and they split...
Now at first they are identical twins. But soon the colonists begin specializing in different tasks, and the more each twin specializes and perfects his craft he interacts differently with his other twins, and forces them to change their habits too. now, all the while they are still splitting so guilds form and specialization within guilds happens. A village starts to form, with twins building huts around themselves and some roads to make it easy to move resources and materials around. And then some guilds start specializing on building and roadmaking... Since they are all clones of each other, they form a very closeknit and well coordinated society.
As the village grows, more specialization happens, different groups start forcing each other to reorganize, rerouting roads etc.. More structure forms, more organization, more complex interactions, materials are processed in more elaborate chains of production. As storms come, seasons change, land gets used up, visitors come, possible invaders... the village begins behaving in more complex ways, forms complex governments, diplomatic missions, armies, traders, politicians...
In essence, the city is built from within by its 'cells'. That's how animals form. Now to make our city more like an animal, imagine the city structure build like a giant robot like one of those transformer toys. Instead of being built on the ground, the whole structure is being built in 3 dimensions, the whole city structure is flexible capable of walking about, or even flying. A giant honeybee robot!
To get closer to being like an organism, lets add one more layer of complexity. Most of the scaffolding and mechanisms of an animal are made of the cells themselves, (with some nonliving bone and fiber built in for strength...). Now, a honeybee is a million cells. That's how many people in a fairly big human city, say just manhattan. The reason that the organs and tissues of an animal are so much more flexible and responsive than human city structures is that the animal organs and tissues are build out of the living cells themselves. So all the structures are dynamic, responsive to each other.
So imagine the roads are lined with these ... ok, so imagine these colonists as not QUITE humans, a little dumber, a little more able to settle for performing very simple roles. As indeed some animals are, like oysters, and various simplified parasites... which start off as flexible swimming sensing larvae and then settle down to become basically, sessile, eating tubes producing eggs.
So imagine these colonists, making buildings out of themselsves, holding onto each other. Imagine the elevators are groups of people some holding each other making a basket for other people to ride in while the others do the climbing up and down. Some are the windows opening and closing because the 'people' that form them can sense the environment and respond the the people inside. The scaffolding is people holding onto each other so it can respond to changing loads , the building can shift over if it needs to. Cars and busses are simply bunches of people holding onto each other walking with their legs letting riders sit on them, some of them use their eyes to see, steer, communicate with other cars, some collect food and distribute it to the other 'people' that make up the car.
So all the structures and machines in the city are alive, are made of 'people' that can communicate with each other, allowing the structures to respond to each other and even think how to respond.
So that's what animals are. Cities made mostly out of societies of simpler single celled organisms. You and I are stupendous cities made of a trillion cells. that's like one hundred thousand new york cities full of people. One step in realizing that life is not a shear magical mystery is realizing the numbers involved, the complexity capable of those numbers.
If you wonder how a brain can think, realize that it is made of a hundred billion neurons. A society of one hundred billion simple critters capable of making simple decisions, inventing tiny snippets of ideas, memorizing a word or two at a time, all having conversations with each other. Typical neurons are connected to a thousand others at a time, and synthesizes information from all of them while then sending out signals to hundreds of others in the network. This society takes over 30 generations to form (typically a cell takes about a day to divide into two cells) Over the time of these 30 generations the cells form all kinds of social bonds and rearrangements and habits of communication...
And, if these cells that build the organism-city out of themselves, are themselves organisms too, simpler ones, what are THEY made of? If they are like animals, do THEY have organs and parts? Are THEY cities of even SIMPLER sub-cellular organisms?
Kind of...This living world is made of quite a few levels nested in deeper and deeper... Very strange universe! In the next chapter we will explore the world of those subcellular parts - molecules, what are they and What can they do?
To what kind of human venture is it most like? The founding of a city? So pretend one person washes up on a beach a lush tropical island beach and for the hell of it, pretend people are unisex and reproduce by splitting in half. (quite odd, eh?) so this person eats all the cocounts and mangos and gets fat and splits. At first the fellow is doing everything, finding food, chasing away monkeys, building fire, foraging for supplies, building shelter... then the twins split and they split...
Now at first they are identical twins. But soon the colonists begin specializing in different tasks, and the more each twin specializes and perfects his craft he interacts differently with his other twins, and forces them to change their habits too. now, all the while they are still splitting so guilds form and specialization within guilds happens. A village starts to form, with twins building huts around themselves and some roads to make it easy to move resources and materials around. And then some guilds start specializing on building and roadmaking... Since they are all clones of each other, they form a very closeknit and well coordinated society.
As the village grows, more specialization happens, different groups start forcing each other to reorganize, rerouting roads etc.. More structure forms, more organization, more complex interactions, materials are processed in more elaborate chains of production. As storms come, seasons change, land gets used up, visitors come, possible invaders... the village begins behaving in more complex ways, forms complex governments, diplomatic missions, armies, traders, politicians...
In essence, the city is built from within by its 'cells'. That's how animals form. Now to make our city more like an animal, imagine the city structure build like a giant robot like one of those transformer toys. Instead of being built on the ground, the whole structure is being built in 3 dimensions, the whole city structure is flexible capable of walking about, or even flying. A giant honeybee robot!
To get closer to being like an organism, lets add one more layer of complexity. Most of the scaffolding and mechanisms of an animal are made of the cells themselves, (with some nonliving bone and fiber built in for strength...). Now, a honeybee is a million cells. That's how many people in a fairly big human city, say just manhattan. The reason that the organs and tissues of an animal are so much more flexible and responsive than human city structures is that the animal organs and tissues are build out of the living cells themselves. So all the structures are dynamic, responsive to each other.
So imagine the roads are lined with these ... ok, so imagine these colonists as not QUITE humans, a little dumber, a little more able to settle for performing very simple roles. As indeed some animals are, like oysters, and various simplified parasites... which start off as flexible swimming sensing larvae and then settle down to become basically, sessile, eating tubes producing eggs.
So imagine these colonists, making buildings out of themselsves, holding onto each other. Imagine the elevators are groups of people some holding each other making a basket for other people to ride in while the others do the climbing up and down. Some are the windows opening and closing because the 'people' that form them can sense the environment and respond the the people inside. The scaffolding is people holding onto each other so it can respond to changing loads , the building can shift over if it needs to. Cars and busses are simply bunches of people holding onto each other walking with their legs letting riders sit on them, some of them use their eyes to see, steer, communicate with other cars, some collect food and distribute it to the other 'people' that make up the car.
So all the structures and machines in the city are alive, are made of 'people' that can communicate with each other, allowing the structures to respond to each other and even think how to respond.
So that's what animals are. Cities made mostly out of societies of simpler single celled organisms. You and I are stupendous cities made of a trillion cells. that's like one hundred thousand new york cities full of people. One step in realizing that life is not a shear magical mystery is realizing the numbers involved, the complexity capable of those numbers.
If you wonder how a brain can think, realize that it is made of a hundred billion neurons. A society of one hundred billion simple critters capable of making simple decisions, inventing tiny snippets of ideas, memorizing a word or two at a time, all having conversations with each other. Typical neurons are connected to a thousand others at a time, and synthesizes information from all of them while then sending out signals to hundreds of others in the network. This society takes over 30 generations to form (typically a cell takes about a day to divide into two cells) Over the time of these 30 generations the cells form all kinds of social bonds and rearrangements and habits of communication...
And, if these cells that build the organism-city out of themselves, are themselves organisms too, simpler ones, what are THEY made of? If they are like animals, do THEY have organs and parts? Are THEY cities of even SIMPLER sub-cellular organisms?
Kind of...This living world is made of quite a few levels nested in deeper and deeper... Very strange universe! In the next chapter we will explore the world of those subcellular parts - molecules, what are they and What can they do?
Tuesday, May 3, 2011
I Find The River Restful Again
The Hudson river is calm now,
before me.
by Green Island bridge
at the feet of Troy.
I imagine its green soup seeping from sundrenched algaes
that grow over pebbles in the Adirondack brooks.
The sandpipers stepping, plucking grubs.
A primeval place i could have made my home
to wake to the sounds of the speachless birds.
The river is resting.
after its busy weekend, when
on my way to the bus this past friday
the river surprised me.
Not aimless and ambling,
bland muddy,
but an swirling burls of green waters intent on passing me
faster than i had ever seen it,
toting jostling tree trunks and foam and random stuff
startlingly high.
I could almost reach below its cement berm
and touch it
where it's usually five feet below,
unreachable.
The tide was up .
And i remembered seeing the sliver moon
inching towards dawn a few mornings ago.
The rebirthing jesus moon
who called people to churches
emptying the streets of troy
last easter weekend.
Then to slipp behind the sun for rebirth.
Sun, the far seething furnace giant
birthing the elements
and the moon our brother, closer
ball of silent rock finished with its violent geology,
together shoulder to shoulder pulling
the seawaters with their tide ropes of tugging gravities
towards the hot summer noon
calling the river to flood banks, and hide tree roots.
Now the river washes me
from a weekend of rushing and conflicted interests
of indecisions
of filling my life with pencilled in commitments
pulled by the tides that distract,
from the rest,
the nourishment
of the silence of earth of foundling brooks
at Lake Tear of the Clouds
silent origin of the hudson
nested in trees far from the industry of men.
Now I dream in the green deeps of the ocean dreaming river
before the human tides of this city pull me apart
again.
before me.
by Green Island bridge
at the feet of Troy.
I imagine its green soup seeping from sundrenched algaes
that grow over pebbles in the Adirondack brooks.
The sandpipers stepping, plucking grubs.
A primeval place i could have made my home
to wake to the sounds of the speachless birds.
The river is resting.
after its busy weekend, when
on my way to the bus this past friday
the river surprised me.
Not aimless and ambling,
bland muddy,
but an swirling burls of green waters intent on passing me
faster than i had ever seen it,
toting jostling tree trunks and foam and random stuff
startlingly high.
I could almost reach below its cement berm
and touch it
where it's usually five feet below,
unreachable.
The tide was up .
And i remembered seeing the sliver moon
inching towards dawn a few mornings ago.
The rebirthing jesus moon
who called people to churches
emptying the streets of troy
last easter weekend.
Then to slipp behind the sun for rebirth.
Sun, the far seething furnace giant
birthing the elements
and the moon our brother, closer
ball of silent rock finished with its violent geology,
together shoulder to shoulder pulling
the seawaters with their tide ropes of tugging gravities
towards the hot summer noon
calling the river to flood banks, and hide tree roots.
Now the river washes me
from a weekend of rushing and conflicted interests
of indecisions
of filling my life with pencilled in commitments
pulled by the tides that distract,
from the rest,
the nourishment
of the silence of earth of foundling brooks
at Lake Tear of the Clouds
silent origin of the hudson
nested in trees far from the industry of men.
Now I dream in the green deeps of the ocean dreaming river
before the human tides of this city pull me apart
again.
doan wan no chickens here
just what were the arguments against chickens anyway? that they spread diseases like inner city blight? that they create a racket like gas exploding boombox pumping childflesh crushing automobiles ? that they'll get loose and get in people's ways like cop cars screaming around corners and tripping over curbs? or is it that their eggs will put stewart's pimps of saddam hussain juice and oversalted potato chips and sad lottery tickets stealing from the poor and give to the rich out of business?
Sunday, May 1, 2011
Ancestors of the Summer Meadow
(Writing exercise after Richard Eberhart's 'The Groundhog'. First attempt. Original text after mine)
One morning in July when i was a lad,
I visited that sweltering sundrenched meadow
strewn with flowers and freckled with butterflies,
I found a dead possum.
resting on a bare patch of earth
baking in the sun
his possum shape began its terrible transformations.
The full moist meadow breathed
earth's maw ready to consume him.
His stench struck my equilibrium.
My skin trembled and
my thoughts tumbled off reality.
Nevertheless i had to explore
those maggots' seething maelstrom's orgy
diving into his death's dark dreaming.
With revulsion, awe, then sadness
i touched him with a tentative stick.
My stomach curdled with sour thoughts.
The clouds like clotted cream
made sick the welcoming sun.
Life's flame in me drowned.
I stood there dumb
transfixed by this thing,
then sat by his side
nausea settling
and strained to hear the story.
I visited there again
in that autumn's clarifying call.
The possum's fat had melted into earth.
Only withered skin stretched taught on bones remained
I left my summer memories there
wanderings of childhood
packed my bags
and set off for college
One more year the blanketing snows fell
And sweet spring's nectars rained to cleanse the earth.
Returning, I found only his frightful teeth
grinning to the summer sun.
His last laugh to life.
I knelt to breath the moist tang of earth
and tried to listen to the meadow's tremulous singing
Returning home after many autumns passed
that possum's drama left no trace.
The meadow danced its timeless tunes.
I sighed my memories of forgotten friends
and called to the ancestors of that place:
Eohippus, saber tooth,
red skinned cheiftains with their feathered dress,
welcomed me to rest in that earthen bed.
1May2011 busride to nyc
The Groundhog
Richard Eberhart
In June, amid the golden fields,
I saw a groundhog lying dead.
Dead lay he; my senses shook,
And mind outshot our naked frailty.
There lowly in the vigorous summer
His form began its senseless change,
And made my senses waver dim
Seeing nature ferocious in him.
Inspecting close maggots' might
And seething cauldron of his being,
Half with loathing, half with a strange love,
I poked him with an angry stick.
The fever arose, became a flame
And Vigour circumscribed the skies,
Immense energy in the sun,
And through my frame a sunless trembling.
My stick had done nor good nor harm.
Then stood I silent in the day
Watching the object, as before;
And kept my reverence for knowledge
Trying for control, to be still,
To quell the passion of the blood;
Until I had bent down on my knees
Praying for joy in the sight of decay.
And so I left; and I returned
In Autumn strict of eye, to see
The sap gone out of the groundhog,
But the bony sodden hulk remained
But the year had lost its meaning,
And in intellectual chains
I lost both love and loathing,
Mured up in the wall of wisdom.
Another summer took the fields again
Massive and burning, full of life,
But when I chanced upon the spot
There was only a little hair left,
And bones bleaching in the sunlight
Beautiful as architecture;
I watched them like a geometer,
And cut a walking stick from a birch.
It has been three years, now.
There is no sign of the groundhog.
I stood there in the whirling summer,
My hand capped a withered heart,
And thought of China and of Greece,
Of Alexander in his tent;
Of Montaigne in his tower,
Of Saint Theresa in her wild lament.
One morning in July when i was a lad,
I visited that sweltering sundrenched meadow
strewn with flowers and freckled with butterflies,
I found a dead possum.
resting on a bare patch of earth
baking in the sun
his possum shape began its terrible transformations.
The full moist meadow breathed
earth's maw ready to consume him.
His stench struck my equilibrium.
My skin trembled and
my thoughts tumbled off reality.
Nevertheless i had to explore
those maggots' seething maelstrom's orgy
diving into his death's dark dreaming.
With revulsion, awe, then sadness
i touched him with a tentative stick.
My stomach curdled with sour thoughts.
The clouds like clotted cream
made sick the welcoming sun.
Life's flame in me drowned.
I stood there dumb
transfixed by this thing,
then sat by his side
nausea settling
and strained to hear the story.
I visited there again
in that autumn's clarifying call.
The possum's fat had melted into earth.
Only withered skin stretched taught on bones remained
I left my summer memories there
wanderings of childhood
packed my bags
and set off for college
One more year the blanketing snows fell
And sweet spring's nectars rained to cleanse the earth.
Returning, I found only his frightful teeth
grinning to the summer sun.
His last laugh to life.
I knelt to breath the moist tang of earth
and tried to listen to the meadow's tremulous singing
Returning home after many autumns passed
that possum's drama left no trace.
The meadow danced its timeless tunes.
I sighed my memories of forgotten friends
and called to the ancestors of that place:
Eohippus, saber tooth,
red skinned cheiftains with their feathered dress,
welcomed me to rest in that earthen bed.
1May2011 busride to nyc
The Groundhog
Richard Eberhart
In June, amid the golden fields,
I saw a groundhog lying dead.
Dead lay he; my senses shook,
And mind outshot our naked frailty.
There lowly in the vigorous summer
His form began its senseless change,
And made my senses waver dim
Seeing nature ferocious in him.
Inspecting close maggots' might
And seething cauldron of his being,
Half with loathing, half with a strange love,
I poked him with an angry stick.
The fever arose, became a flame
And Vigour circumscribed the skies,
Immense energy in the sun,
And through my frame a sunless trembling.
My stick had done nor good nor harm.
Then stood I silent in the day
Watching the object, as before;
And kept my reverence for knowledge
Trying for control, to be still,
To quell the passion of the blood;
Until I had bent down on my knees
Praying for joy in the sight of decay.
And so I left; and I returned
In Autumn strict of eye, to see
The sap gone out of the groundhog,
But the bony sodden hulk remained
But the year had lost its meaning,
And in intellectual chains
I lost both love and loathing,
Mured up in the wall of wisdom.
Another summer took the fields again
Massive and burning, full of life,
But when I chanced upon the spot
There was only a little hair left,
And bones bleaching in the sunlight
Beautiful as architecture;
I watched them like a geometer,
And cut a walking stick from a birch.
It has been three years, now.
There is no sign of the groundhog.
I stood there in the whirling summer,
My hand capped a withered heart,
And thought of China and of Greece,
Of Alexander in his tent;
Of Montaigne in his tower,
Of Saint Theresa in her wild lament.
Thursday, April 21, 2011
Life is a Dancing Swarm of Molecular Robot Parts
[This is the introduction to chapters III, IV and V out of 12 of the Complexity Lab Manual. It is preceded by a chapter and labs on natural history, and then a chapter on how to build robots to try to mimic life, from the transistors on up, giving us our first hint of the complexity involved. More concrete examples will be inserted in the future.]
Unlike our machinery, life builds itself from the inside out. Tiny robots that build each other and crawl around each other and can make chemical transformation from air to plant to animal flesh. That’s a lot to take in.
Just as we saw how to build robots hierarchically up from simple transistors and motors and pulleys and how to build their behavior hierarchically up from subroutines of subroutines... so does life:
First: our bodies are societies of a trillion amoebas. We start off as a colony of the society of amoebas that is our mother. A group of them settles in her ovary and one of them gives birth.. Well they give birth by splitting in half.. Anyway this colony population grows and as it does the members shape each other, move around each other, build ties, lay down bony scaffolding and fibrous scaffolding to hold themselves all in place. They set up dances with each other, hundreds dancing a heart some lungs, contracting muscles and the conversation that is the brain...
All the while the mother is shipping them food that they grow on and removing their garbage... eventually they are ready to leave as an independent being.
We can actually watch a critter like a snail or roundworm do this under a microscope and make a movie of it.
That these amoeba can do all this... well are they just like people themselves like the mirrors within mirrors? Nearly, but only one cell each. We can watch one of these moving pinpoints in a drop of pond water under a microscope and see that it is in fact a microscopic animal capable of many of the basic behavior of us big animals: swimming, crawling, searching, thinking, hunting food, growing, seeking mates, reproducing, dying. these single cells are the most basic level of organization of life.
Put a strand of algae in a jar of water and air and it grows more of itselves out of thin air! this is chemistry, and what are the parts inside? For we can see stuff streaming around in these little protozoans. How do algae grow themselves out of air water and stuff that leaks out of glass? How does life transform rock and air and water into life?
Some clues: we can grind up these simple critters and do paper chromatography on them you see that the stains soaking upwards on the paper separate into distinct blobs with craft, you can get a hundred or more blobs to separate. Are they distinct kinds of parts the critters are made of?
Chemistry is the most exciting scientific discovery for us living thinking beings. What is it?
The first discovery is that even though the world seems to be made out of an infinite blended variety of colors tastes and textures and smells, in fact we can chemically reduce all these substances into a FEW distinct types. Visit a museum and see a 1000 different mineral forms and colors and textures. From this we can isolate a toolbox of merely about 50 elemental substances that can't be chemically broken down any further. in fact 100s of different minerals, and indeed 99.99% of what's around us can be made solely from the dozen or so most common elemental substances. This is remarkable. These are:
The metallic elementals: Sodium, makes the sea salty. Potassium, used by the batteries in neurons. Calcium, makes bones seashells, limestone. Magnesium, makes chlorophyll green. Iron, the catalyst that can among other things, carry oxygen in our blood from lungs to muscles.
The semiconductors: Aluminum, together with Silicon, make the scaffolding that holds the metals together to make up 95% of all the rocks around us, in fact, all the earth.
The nonmetals: Carbon, the stuff in air that becomes the backbones of wood and flesh. Oxygen, which connects all these and dissolves them in water and burns. Hydrogen, that helps oxygen make water. Nitrogen, the stuff in air that compliments the Oxygen in our chemistry. Phosphorus, storing the energy currency that all life uses, and backbone to our genetic blueprints. Sulfur, the connector that holds iron catalysts in our enzymes to metabolize our food. And Chlorine, Sodium's partner in dissolving in seawater.
And this is the first hint at the essentially digital, discrete nature of the stuff of our world.
The next clue is that we can react simply carbon, hydrogen and oxygen together and get strikingly different compound substances, organic compounds, each with distinct properties. These different substances can be separated from each other and we can burn each sample back up to separate out the elements and see that each compound contains the same PROPORTIONS off each of these three elementals.
Something fishy is going on. through careful experiments and reasoning chemists guessed that these elemental substances came in discrete particles they called atoms and that the different compounds had different properties because the same atoms arranged themselves together in different geometries, either in straight chains or branched ones or rings or even more complicated. Many of the properties of stuff, like color, taste, hardness... come from the way discrete parts arrange themselves in different geometric relationships.
Finally at the beginning of the 20th century we discovered that stuff was in fact made of many discrete parts that we call atoms. The shock is how small they are and how many it takes to make up a blob of stuff. If we imagine one of our amoeba or paramecium with its cilia and vacuoles and all it's behaviors as a robot made of parts, how many parts can there be in there? You can hold in the palm of your hand 600,000, 000,000,000, 000,000,000 molecules of water. This is the Avogadro’s number that you learned in freshman chemistry. It is a painstaking experiment to measure this number. I think that it is one of our most radical scientific discoveries.
Nearly a million billion billion. even I don't know how to imagine that number, so we go hierarchical again: a glass of water is 100 cubes of water the size of sugar cubes, so each cube (cubic centimeter) has (divide the big number by a 100) 10,000, billion billion molecules. Now we can break each of those cubes up into 10X10X10 tiny cubes (draw all those cross hairs on the cube) and get 1000 tiny sandgrain cubes. So each of those has 100, billion billion molecules. now, how big are those tiny paramecium? We watched them in our microscope, they are about a 10th of the length of the side of a sandgrain cube, so we draw crosshairs again and 10X10X10, divide by a thousand again: 100, million billion molecules in the paramecium.
Now if we grind up paramecium and separate out their chemicals like we did with the paper chromatography we find out that some of the substances are a dozen times as heavy as water molecules. Those are sugars and amino acids, and fats. And there are substances that are 100s of times as heavy as those and these are proteins. So there can be 10million billion small molecules and 100thousand billion proteins in the paramecium. Now we are getting somewhere.
To help you visualize this stupendous number, let's do this guided visualization: imagine yourself standing in front of a large apartment building in New York City. a window is maybe 10X20 bricks (200) there are 20 X 20 stories worth of windows on the face of the building (so 400 windows times 200 bricks =80,000 bricks in one face) now just for the hell of it, making a gross overestimate in the number of bricks, imagine the building is solid bricks, so the building is 200 bricks deep, so the solid building would be made of 200X80,000 bricks or 16,000,000. Now there are 5X10 buildings on that block, so that’s 50X and we get 1000,000,000 bricks per block. Manhattan is about 10blocks wide by 200 blocks long so that's 2000 X or 2thousand billion bricks in Manhattan. For the hell of it lets think of 5 boroughs (nowhere near as densely built as midtown Manhattan..) and we have 10thousand billion bricks in nyc.
That's how many of these proteins there are in that tiny dot we watched in the pond water crawling around.
Ok, what are these proteins? Are they like bricks? Well, to cut to the chase, in the past century we’ve actually learned to SEE these proteins, with electron microscopes and x-ray diffraction, to watch them MOVE and change shape with fluorescent microscopy. So here is the story:
What ARE these molecules? After a 150 years of experimenting with them, here's what you can discover in an organic chemistry class. They can sense their surroundings, sense each other, sense essential qualities in each other like size and shape and electrical charge.. They can respond to each other in simple ways. They can attach to each other in specific shapes and replace parts of each other and come apart in specific ways and recombine. They are like parts of machines that don't need mechanics to put them together, because they are in constant motion, jostling, sensing each snapping together by their own internal rules. (kind of like the way each of us is a society of amoebas that sense each other and build with each other their arrangements. However, It is important to note though, that the molecules are MUCH simpler than amoebas, and are not alive, they don't eat and grow and can't perform trial and error chains of thinking). Molecules are springy and vibrate, and wiggle. They can absorb and emit specific amounts of energy that we sense as different colors and as heat. They are kind of fuzzy without discrete boundaries and this is why they can sense each other and attach and come apart.
Going in deeper, we've discovered that it's the dancing of electrons that shape and give dynamics to molecules. These electrons are at the same time discrete dots of charge and also vibrating waves (don't try to wrap your heads around this one, this is the central mystery of quantum mechanics, which after a 100 years since its discovery still puzzles the discoverers of this new kind of physics). This is what makes molecules fuzzy and sensitive and springy and interact with energy and light. It is what makes them utterly different than our clunky inert machine parts.
In a way, these electrons are like the transistors we started with some chapters ago, and the molecules are like the logic gates that we built up, layer upon layer to make our complicated 'thinking' computers. Except, that while our transistors and computer chips could process information, they could not move around and recombine with each other. But molecules CAN do these things. So in essence they are tiny pieces of computer/robots. And in fact the larger ones, the proteins made of smaller parts, the amino acids, DO act as small computers and small robots.
But they are very different than the computers and robots that we design. we use to much one pointed consciousness in our craft, to much thinking about one thing at a time and building one machine at a time from the outside. The protein robots think more like swarms of honeybees or ants or termites and get together in crowds and cooperatively construct machines. And the processes they perform is like a whole bunch of subroutines working on each other simultaneously instead of the way ours do it, executing one at a time.
And of course these protein robots, being so close to the basic level of molecules CAN build each other out of foodstuff, the water air and glass that our algae cells grew themselves from. Because they are made out of proteins.
So here is what life is: at the basic level a living creature is a swarm of 100thousand billion cooperatively coordinating tiny robots, of about 1000 different kinds, constantly interacting, building huge structures out of each other, taking these structures apart, putting them back together, taking each other apart and building new ones depending on the needs of the swarm... this happens incredibly fast: proteins change shape and jostle around millions of times a second.
I want you to meditate for a bit on where we have reached in our journey inward... the levels within levels of mechanisms made out of each other.
Again, imagine yourself taking a few days to wander around New York City, and imagine each of those bricks are one of the thousand different kinds of protein robots in a paramecium, each taking the place of one of these bricks, all swirling around interacting with each other building static and dynamic structures out of each other on the time scales of seconds, minutes, hours. You can watch them reproduce an ENTIRE CITY in a matter of DAYS.
[This is followed immediately by a chapter on how simple energy flow organizes fluids, chemistry into stable, creative dynamic patterns. How life is animated. And then a chapter of math and computer games that show how millions of simple interacting parts can take these dynamic patterns and elaborate them into surprising complexity.
Eventually we survey what we've discovered so far about the chemistry at the origins of life itself. ]
Unlike our machinery, life builds itself from the inside out. Tiny robots that build each other and crawl around each other and can make chemical transformation from air to plant to animal flesh. That’s a lot to take in.
Just as we saw how to build robots hierarchically up from simple transistors and motors and pulleys and how to build their behavior hierarchically up from subroutines of subroutines... so does life:
First: our bodies are societies of a trillion amoebas. We start off as a colony of the society of amoebas that is our mother. A group of them settles in her ovary and one of them gives birth.. Well they give birth by splitting in half.. Anyway this colony population grows and as it does the members shape each other, move around each other, build ties, lay down bony scaffolding and fibrous scaffolding to hold themselves all in place. They set up dances with each other, hundreds dancing a heart some lungs, contracting muscles and the conversation that is the brain...
All the while the mother is shipping them food that they grow on and removing their garbage... eventually they are ready to leave as an independent being.
We can actually watch a critter like a snail or roundworm do this under a microscope and make a movie of it.
That these amoeba can do all this... well are they just like people themselves like the mirrors within mirrors? Nearly, but only one cell each. We can watch one of these moving pinpoints in a drop of pond water under a microscope and see that it is in fact a microscopic animal capable of many of the basic behavior of us big animals: swimming, crawling, searching, thinking, hunting food, growing, seeking mates, reproducing, dying. these single cells are the most basic level of organization of life.
Put a strand of algae in a jar of water and air and it grows more of itselves out of thin air! this is chemistry, and what are the parts inside? For we can see stuff streaming around in these little protozoans. How do algae grow themselves out of air water and stuff that leaks out of glass? How does life transform rock and air and water into life?
Some clues: we can grind up these simple critters and do paper chromatography on them you see that the stains soaking upwards on the paper separate into distinct blobs with craft, you can get a hundred or more blobs to separate. Are they distinct kinds of parts the critters are made of?
Chemistry is the most exciting scientific discovery for us living thinking beings. What is it?
The first discovery is that even though the world seems to be made out of an infinite blended variety of colors tastes and textures and smells, in fact we can chemically reduce all these substances into a FEW distinct types. Visit a museum and see a 1000 different mineral forms and colors and textures. From this we can isolate a toolbox of merely about 50 elemental substances that can't be chemically broken down any further. in fact 100s of different minerals, and indeed 99.99% of what's around us can be made solely from the dozen or so most common elemental substances. This is remarkable. These are:
The metallic elementals: Sodium, makes the sea salty. Potassium, used by the batteries in neurons. Calcium, makes bones seashells, limestone. Magnesium, makes chlorophyll green. Iron, the catalyst that can among other things, carry oxygen in our blood from lungs to muscles.
The semiconductors: Aluminum, together with Silicon, make the scaffolding that holds the metals together to make up 95% of all the rocks around us, in fact, all the earth.
The nonmetals: Carbon, the stuff in air that becomes the backbones of wood and flesh. Oxygen, which connects all these and dissolves them in water and burns. Hydrogen, that helps oxygen make water. Nitrogen, the stuff in air that compliments the Oxygen in our chemistry. Phosphorus, storing the energy currency that all life uses, and backbone to our genetic blueprints. Sulfur, the connector that holds iron catalysts in our enzymes to metabolize our food. And Chlorine, Sodium's partner in dissolving in seawater.
And this is the first hint at the essentially digital, discrete nature of the stuff of our world.
The next clue is that we can react simply carbon, hydrogen and oxygen together and get strikingly different compound substances, organic compounds, each with distinct properties. These different substances can be separated from each other and we can burn each sample back up to separate out the elements and see that each compound contains the same PROPORTIONS off each of these three elementals.
Something fishy is going on. through careful experiments and reasoning chemists guessed that these elemental substances came in discrete particles they called atoms and that the different compounds had different properties because the same atoms arranged themselves together in different geometries, either in straight chains or branched ones or rings or even more complicated. Many of the properties of stuff, like color, taste, hardness... come from the way discrete parts arrange themselves in different geometric relationships.
Finally at the beginning of the 20th century we discovered that stuff was in fact made of many discrete parts that we call atoms. The shock is how small they are and how many it takes to make up a blob of stuff. If we imagine one of our amoeba or paramecium with its cilia and vacuoles and all it's behaviors as a robot made of parts, how many parts can there be in there? You can hold in the palm of your hand 600,000, 000,000,000, 000,000,000 molecules of water. This is the Avogadro’s number that you learned in freshman chemistry. It is a painstaking experiment to measure this number. I think that it is one of our most radical scientific discoveries.
Nearly a million billion billion. even I don't know how to imagine that number, so we go hierarchical again: a glass of water is 100 cubes of water the size of sugar cubes, so each cube (cubic centimeter) has (divide the big number by a 100) 10,000, billion billion molecules. Now we can break each of those cubes up into 10X10X10 tiny cubes (draw all those cross hairs on the cube) and get 1000 tiny sandgrain cubes. So each of those has 100, billion billion molecules. now, how big are those tiny paramecium? We watched them in our microscope, they are about a 10th of the length of the side of a sandgrain cube, so we draw crosshairs again and 10X10X10, divide by a thousand again: 100, million billion molecules in the paramecium.
Now if we grind up paramecium and separate out their chemicals like we did with the paper chromatography we find out that some of the substances are a dozen times as heavy as water molecules. Those are sugars and amino acids, and fats. And there are substances that are 100s of times as heavy as those and these are proteins. So there can be 10million billion small molecules and 100thousand billion proteins in the paramecium. Now we are getting somewhere.
To help you visualize this stupendous number, let's do this guided visualization: imagine yourself standing in front of a large apartment building in New York City. a window is maybe 10X20 bricks (200) there are 20 X 20 stories worth of windows on the face of the building (so 400 windows times 200 bricks =80,000 bricks in one face) now just for the hell of it, making a gross overestimate in the number of bricks, imagine the building is solid bricks, so the building is 200 bricks deep, so the solid building would be made of 200X80,000 bricks or 16,000,000. Now there are 5X10 buildings on that block, so that’s 50X and we get 1000,000,000 bricks per block. Manhattan is about 10blocks wide by 200 blocks long so that's 2000 X or 2thousand billion bricks in Manhattan. For the hell of it lets think of 5 boroughs (nowhere near as densely built as midtown Manhattan..) and we have 10thousand billion bricks in nyc.
That's how many of these proteins there are in that tiny dot we watched in the pond water crawling around.
Ok, what are these proteins? Are they like bricks? Well, to cut to the chase, in the past century we’ve actually learned to SEE these proteins, with electron microscopes and x-ray diffraction, to watch them MOVE and change shape with fluorescent microscopy. So here is the story:
What ARE these molecules? After a 150 years of experimenting with them, here's what you can discover in an organic chemistry class. They can sense their surroundings, sense each other, sense essential qualities in each other like size and shape and electrical charge.. They can respond to each other in simple ways. They can attach to each other in specific shapes and replace parts of each other and come apart in specific ways and recombine. They are like parts of machines that don't need mechanics to put them together, because they are in constant motion, jostling, sensing each snapping together by their own internal rules. (kind of like the way each of us is a society of amoebas that sense each other and build with each other their arrangements. However, It is important to note though, that the molecules are MUCH simpler than amoebas, and are not alive, they don't eat and grow and can't perform trial and error chains of thinking). Molecules are springy and vibrate, and wiggle. They can absorb and emit specific amounts of energy that we sense as different colors and as heat. They are kind of fuzzy without discrete boundaries and this is why they can sense each other and attach and come apart.
Going in deeper, we've discovered that it's the dancing of electrons that shape and give dynamics to molecules. These electrons are at the same time discrete dots of charge and also vibrating waves (don't try to wrap your heads around this one, this is the central mystery of quantum mechanics, which after a 100 years since its discovery still puzzles the discoverers of this new kind of physics). This is what makes molecules fuzzy and sensitive and springy and interact with energy and light. It is what makes them utterly different than our clunky inert machine parts.
In a way, these electrons are like the transistors we started with some chapters ago, and the molecules are like the logic gates that we built up, layer upon layer to make our complicated 'thinking' computers. Except, that while our transistors and computer chips could process information, they could not move around and recombine with each other. But molecules CAN do these things. So in essence they are tiny pieces of computer/robots. And in fact the larger ones, the proteins made of smaller parts, the amino acids, DO act as small computers and small robots.
But they are very different than the computers and robots that we design. we use to much one pointed consciousness in our craft, to much thinking about one thing at a time and building one machine at a time from the outside. The protein robots think more like swarms of honeybees or ants or termites and get together in crowds and cooperatively construct machines. And the processes they perform is like a whole bunch of subroutines working on each other simultaneously instead of the way ours do it, executing one at a time.
And of course these protein robots, being so close to the basic level of molecules CAN build each other out of foodstuff, the water air and glass that our algae cells grew themselves from. Because they are made out of proteins.
So here is what life is: at the basic level a living creature is a swarm of 100thousand billion cooperatively coordinating tiny robots, of about 1000 different kinds, constantly interacting, building huge structures out of each other, taking these structures apart, putting them back together, taking each other apart and building new ones depending on the needs of the swarm... this happens incredibly fast: proteins change shape and jostle around millions of times a second.
I want you to meditate for a bit on where we have reached in our journey inward... the levels within levels of mechanisms made out of each other.
Again, imagine yourself taking a few days to wander around New York City, and imagine each of those bricks are one of the thousand different kinds of protein robots in a paramecium, each taking the place of one of these bricks, all swirling around interacting with each other building static and dynamic structures out of each other on the time scales of seconds, minutes, hours. You can watch them reproduce an ENTIRE CITY in a matter of DAYS.
[This is followed immediately by a chapter on how simple energy flow organizes fluids, chemistry into stable, creative dynamic patterns. How life is animated. And then a chapter of math and computer games that show how millions of simple interacting parts can take these dynamic patterns and elaborate them into surprising complexity.
Eventually we survey what we've discovered so far about the chemistry at the origins of life itself. ]
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