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. ]

Tuesday, April 12, 2011

On Hebrew Prayer: Organizing Principles and Surprise

barukh' ata yhvh 'eloheinu melekh ha'olam

"barukh 'ata" means blessed are you. I bless you (well hell, i don't really understand this ENGLISH word 'to bless' we don't really use it every day do we?), i am thankful for you i am in awe of you. You? yhvh (the 4 letters representing the holy name in Tanakh (bible) that traditional Judaism does not pronounce, though in the bible it certainly seems to function as a pronounceable personal name) is presence/miracles (which is what i call that state i am in when i am intensely aware of the miraculousness of existence itself. It is not a state of duality, ME being present TO miracles outside me, but a state of awareness that breaks down barriers between subject/object sensation/action) always available if i cut the tense headchatter worry about time and just be in this moment that is not yet death as long as i am present.

yhvh, presence, as close as breath not just something i feel, but feeling itself, the act, not something outside of me, no duality.

a personal particular name of a presence who came to my people? I suppose whenever one of us has this kind of experience it is experienced as intensely particular.

Now in traditional Jewish prayer we say 'barukh ata adonoi' so as to avoid pronouncing the name meaning blessed are you, our lord. (Some say barukh ata hashem, blessed is the name) Not Lord, Sir. I am not a slave to presence/miracles, presence/miracles is not a big man who has made it in the world, who is more capable than me, who has accumulated more than me.

it is not lord/slave, it is partnership. miracles cannot create without the stable beings we are who can catch energy flow, choosing some miracles and letting others go.

Certainly not a being at all, yet distinctive in some way? definitely presence, that i can remember, name if i want, but no name is the real name. presence/miracles is not outside of me, i can give presence/miracles no pronoun, i can't even talk ABOUT presence/miracles, only each time I want to mention presence/miracles I must BE in presence/miracles. Very similar to 'i will be who i will be' 'whoever i want to be, you can't predict', 'i am the spark who wakes you out of staleness.'

'Eloheinu (our god, 'elohim with the 'our' ending. 'Elohim looks like the plural of El also a word found in Tanakh to represent various middle eastern gods, but is not considered in the Jewish tradition to be plural.) However a friend suggested to me that the form of the word is similar to words like (water) and khayim (life), so we can take it as an all pervading force that you cant split up into pieces, the all pervading not-stuff of the universe, the patterns that make the universe, the physics, the mathematics. perhaps we can coin a new word like 'elohayim.

So if Elohayim is the physics the predictable, then yhvh is the unpredictable, the singularity, the quantum fluctuation that brings the potential of physics into being a universe.

Melekh (king)? what do Malakhim do? rule? push people around? coerce people? no, they are charismatic centers around which people organize THEMSELVES. Malkhut is the organizing principles themselves, the sets of interactions and feedback loops that allow independent agents to interact and self organize into larger processes. Elohayim is the set of principles that allow the multitude of discrete agents in 'olam (the world) to organize into patterns.

Does that work for me personally? For my community? It is a reminder that my mind does not create this world around me, that i myself am a dissipative process of molecules interacting, meaning that energy is flowing through me (not just into me) and this energy flow causes fluids and chemistry to form stable dynamic systems that can catch random fluctuations and create pattern). Can i rally around the patterns of physics and mathematics, do they give my life meaning? Well, what else do i walk with and breath with and how does this elohayim serve as an organizing center for community? why should a gathering of people show recognition of physics and mathematics and the principles of self organizing mathematics that energy flow through interacting particles creates stable creative dynamical systems?

well, for sure, every time a bunch of people want to get together and do something, they should realize how these principles work, that people self organize they are not controlled by a politician, nor should they let themselves be. they should learn the ways of dissipative and inculcate patterns of local interaction.

and of course they should at these intense moments of prayer get out of their petty little mind-worlds, human society world, and realize that there is a larger earth around them a larger set of patterns that gives them the very gravity they move in, the very electromagnetic force that makes atoms, molecules, biology cohere. thankful that the universe is an INTERESTING place, otherwise we wouldn't be.

And why does yhvh and elohayim have to be one and the same? This is one of the cornerstones of the Jewish tradition. One God. This doesn't work for me, I do not see evidence for it. I do not require a neat simple system that collapses all primal organizing principles in my life into one being. so i have to say: baruch ata yhvh who sparks into being, toda l'elohayim melekh who is expansion and organization of the sparks into an 'olam.

Friday, April 8, 2011

On Eating Animals

Life eats life to live. Creatures all the time are domesticating each other, it is the process of symbiosis, parasitism, that's one of life's defining features. mothers give birth to varied children in overabundance as experiments in this grand evolutionary game. delicately crafted creatures that we in no way are capable of crafting ourselves are just food in the scheme of things. our intensely strong consciousness of our very being, personality, individuality , our attachment to this strong sense of self, to the personality of others, these are also part of our mortal animal nature.

this is all very hard for us very conscious clinging to ego beings to take. it has always made it hard for us to take part in this cycling of life on earth. can we choose to take ourselves out of this pattern and not eat animals? i think for some that is a possible route if taking the life of animals causes them personal pain.

however even if 6billion humans become vegetarian, this is not a life of do no harm. we have to deny billions of other animals the right to their own vegetable food, room to live, not to mention the incredible burdens we put on ecosystems as a whole.

one day we will have to come to terms with the fact that we are life, and this is the way life is, it is not a mamby pamby fairy existence. life is gutsy and intricately intertwined with suffering and death. the only way out of this reality is to take the poison koolaid and believe your soul is going to live on some passing comet. (in fact it is this tendency to shy from the horrific reality of life and try to fly away to an idea of an eternal soul in heaven that i find one of the most dangerous aspects of many religions)

The bhagavad Gita has an interesting view on this. Arjuna is a warrior preparing to bring his army to battle. he is standing on a mountain watching both armies prepare. the sight overwhelms him, he begins to imagine all the death and suffering his soldiers will cause, and the families that will suffer when their soldier-fathers don't come back from battle, and... he freezes.

So Krishna comes and takes the whole rest of the book convincing him that there is no other way. if his army does not fight then the enemy army will also cause suffering to his people. Krisha brings him to the very pinnacle of experience of the horrific reality of life with its whirling giant maw of teeth and arms and eyes of creativity through destruction (for that is what the evolutionary process of life on this earth as been for the past 3.6billion years that has produced the myriad crafted beings we are and share this life with) and then brings him back down to his reality, he is a warrior and his role is too fight.

if i worried about every tiny ant i might step on, every animal who suffers in order for my crops to grow, if i worry about every person i may harm in my inept attempts at human interaction, if i worry about every chemical and machine and genetic defect out there that might cause me harm and shorter life, id never get out of the house and live. that is not the way. i was created part of this vast living couldron, and i choose to partake in it.

that's what eating animals is about.