Introduction

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Why are we animals so remarkable compared to dumb clunky noisy human machines? From the earliest writings of mankind, we can see that they too wondered about this. They opened animals up and looked inside. All they saw was a mass of guts. Most early observers concluded that the intricate behaviors and structures of animals did NOT come from flesh, but from something like mind infused into animal flesh somehow. This was reasonable since their experience of their own minds was intricate and complex, powerful compared to what they saw of dead flesh.

We've learned a bit about flesh since then. In the last 150 years especially. In the last 50 years what we've learned would blow the minds of these early observers and philosophers! We've learned to look within.


WHAT ARE ANIMALS
we animals are so remarkable because rather than being built from the outside by human factories we are built up from the inside by a community of cells. Our details are exquisite and our capacities are subtle because there are MANY of these cells. And they interact with each other as people do in a society. As things go in this universe we are rather large and are built up by VERY large communities of these cells - 100 billion of them. that's more than all the people in the human race by a factor of 15!


WHAT ARE LIVING CELLS
And how do cells do it? what are they? The cells are actually living animals themselves. you can watch one of yours under a microscope. Put an epithelial cell on a petri dish and feed it and it will run mazes, react to it's neighbors, REPRODUCE and grow a coordinated society of interacting cells. They will come together and build tissues of the right shape and thickness, repair holes...Each kind of our cells knows how to build a different kind of tissue, each tissue interacts and builds the interacting organs.

But how do they do it? you can watch a single celled creature in a drop of pond water, stentor, euglena, euplotes, amoeba will do. they really do have an impressive repertoire of behaviors. They can sense multiple aspects of their environment, various nutrients, water currents, temperature, pH, light, harmful chemicals, magnetic fields, gravity... They can make decisions, follow gradients, recognize each other, move in the direction they want, build homes around themselves, find mates, have sex, repair damage, form memories... monitor their internal environments... ah.. their internal environments.


LIVING CELLS ARE SENSITIVE MOLECULES DANCING IN ENERGY FLOW
So how do cells work? What makes 'em alive? Well, they are chemistry, semi-fluid, and BIG. Yes, even though they are small compared to US, 100 of them can fit in a line across the thickness of our fingernails, far smaller than any decent machine WE can build, they are still HUMONGOUS compared to the atoms and molecules that make this universe interesting.

I must describe the STRUCTURE of these cell critters and the PROCESSES that make 'em behave. I'll go back and forth.


WHY ARE CELLS FLUID: ENORMOUS NUMBER OF SLIPPERY MOLECULES
How can something be FLUID, what is a fluid? Why can the internal 'organs' inside a cell move around? Because it's not all one gunky solid mass. Matter happens to be made up of DISCRETE parts that can slide past each other and interact. Why so fluid then? more fluid than a sandpile? Well, there are more molecules in a cell than there are grains of sand in a sandpile! Let's face it, at some point in describing the remarkable abilities of living beings we are going to have to break down and talk mathematics, because the intricacies that mathematics (the study of pattern) is capable of is one of the reasons we animals are so remarkable. You will do lots of math in the complexity labs.

After doing some of the complexity labs you find out that there are 1000s of times more molecules in a living cell than there are grains of sand in a large sandpile! Not only that but at the levels of cells molecules are always in MOTION. you can see it for yourself by watching ink diffuse in still water. no matter how much you try to still the water (you can even freeze it and the ink will still diffuse, might take years! even over millions of years different kinds of rocks can diffuse into each other!), the ink still diffuses. The molecules are moving at 1000s of miles per hour and bumping into each other billions of times a second. and what happens when they come close? most of the time they act like the same poles of a magnet and repell each other, slip past each other.

All this comes together to make a LARGE mob of water molecules like a living cell, FLUID.

In another lab we see that the number of molecules in a single cell is more than all the bricks in a large city like New York. And there are MANY kinds of molecules. In fact the reason why living cells are so capable and flexible and creative is because of molecules. Let's talk about molecules!


WHAT CAN MOLECULES DO
To bring their shocking capabilities into focus, let's mention in passing an argument that's been going around for awhile about "how could life possibly happen by chance out of the chemistry of rock and mud and water and air and lightning? Out of the random motions of molecules?" An astronomer Fred Hoyle once made a pissing remark that this was about as likely as it was to find a pile of Boeing 747 parts spontaneously assemble into a working airplane in a passing tornado.

Let's use this example to point out the differences between molecules and Boeing parts. Are you picturing that tangled heap of a million boing parts? sheets of aluminum, wires, gears, 1000s of nuts and bolts...

1) there are WAY more molecules in a cell than there are parts in an airplane. 10 thousand billion vs a mere million. a cell has more parts than 10 million airplanes! they are cities, not machines!

2) the molecules are in constant motion, bumping into each other a billion times a second. boeing parts just sit there, unless WE move 'em about. This motion does not happen because the molecules are like little animals or rocket ships but it's merely the way the universe is. all the parts have energy and this is expressed in motion. It just happens. The energy is never lost, only transfered from one form to another, from one molecule to another.

3) molecules are fascinating little machines, not machines, but how to describe it? i can either do it with physics and mathematics or a metaphore, they are like little critters themselves, not nearly as complex, yet, molecules can sense each other, they can tell each other apart! when they come together at their dizzying 1000 miles per hour in that short billionth of a second they can sense their respective orientations to each other and decide whether to change shape as they pass or even join together.

Actually, a molecule of water, one of the simpler molecules in a cell is a dance of 18 electrons arranged in a few different energy levels of dancing and embodying a complex 3 dimensional geometry of possibilities... when two of them approach each other, these electron dances in each molecule sense each other and do a complex mathematical calculation to come up with which way to react if they react at all. many things can happen! And these things DO happen. it's called chemistry.

3.5) not only are molecules in motion due to their kinetic energy, but all molecules, being made up of more than one atom, bonded to each other by waveforms of electrons dancing, jiggle, vibrate, bend, twist... I don't want to say they are alive, but to what in our size realm can i compare them to? NOTHING! This is all new experience for humanity, what the universe is built out of...

4) So molecules are in constant random motion searching the space of molecules around them sensing the molecules around them and can join with each other and come apart spontaneously. boing parts do not do this. (you are beginning to see that the creativity of the universe is spread apart on finer and finer levels at simpler and simpler levels into submodules and sub submodules..)


THE VARIETY AND STRUCTURE OF BIOLOGICAL MOLECULES
5) how many different kinds are there? Well, life is made up of 22 basic atoms. I hesitate to call them building blocks because as described above they are NOTHING like bricks, they are more like mindless bees buzzing around each other and interacting... The atoms: Carbon, Hydrogen, Oxygen, Nitrogen, Surfer, Phosphorus. The backbone ingredients. Sodium, Magnesium, Potassium, Calcium, Chlorine, Iron. The minor ingredients. Strontium, Vanadium, Chromium, Molybdenum, Manganese, cobalt, Nickel, Copper, Zinc, Iodine. The trace spices.

The 99.9% of life is the backbone CHNOPS. The Sodium, Magnesium, Potassium, Calcium, Chlorine in minute quantities subtly modulate the electrical properties of water for life. The rest of those trace metals act as catalysts, helping to join the backbone atoms together into specific combinations.


SOME MATHEMATICS HELPS: COMBINATORICS AND GEOMETRY
The combinations. In one of the complexity labs I ask you to get some clay and toothpicks and explore all the ways you can join two toothpicks together, 3, then 4, then 5, 6... by 6 toothpicks, 10 toothpicks, the number of different curious structures that you can form is surprising. rings, pyramids, linked rings, stars, cubes... and of course we are only using all the same kind of toothpick and toothpicks are not responsive, reactive as atoms are.

A more interesting lab would be to join balls with swivels and springs. Then not only would you explore the surprising array of shapes that geometry invents, but also dynamical properties: which shapes can vibrate this way, which can swivel, you can begin to explore the different kinds of machines that spontaneously arise from geometry itself.

You can see from our labs on mathematics that mathematics by itself can give us a richly complex yet not chaotic array of patterns from merely the simple differential equations governing identical electrons and protons.

The number of different molecules we can make out of a dozen carbons, hydrogens, nitrogens and oxygens, say C, C, C, C, C, C, H, H, H, H, H, O, O, O, N, N, is almost astronomical. In the cell there are over a 100 different basic small molecules that are constantly being transformed into each other in a complicated tangled network of chemical reactions. These molecules; water, 22 different amino acids, dozens of sugars, dozens of different kinds of fatty molecules, 5 different kinds of nucleotides can interact with each other in 1000s of combinations. and in fact the sugars and aminos an nucleotides join with EACH OTHER in millions of different combinations giving us proteins, enzymes, strands of RNA and DNA...

All the time we have to think, structure, process, structure process... One role of all these shapes is to build up the complex structures of the cell, but the other role of all these shapes is that they are nodes in the network of chemical reactions of the cell. It's the subtly modulating network of chemical reactions that gives the cell its' behavior. This then modulates the structures, the structures modulate the processes... round and round... you can build up quite complex behavior this way.

the amino acids are molecules that means they jiggle, they are sensitive to each other, sensitive to temperature, water, pH, other molecules. When you join up a 100 of them in a long string, they don't just sit there! they are immersed in all that jiggling of water molecules and the string of them is bending tangling, each amino feeling out the other and they fold into complicated knots. These knots however now are flexible and have many 'sensory organs' many 'hands' sticking outside of themselves. in conjunction with other small molecules called co-enzymes and with the trace metals each of which helps with a different energy level, geometry of electron transfer, these proteins can act as sophisticated machines.

They can act as catalysts that transform one of the 100 small molecules into another. In fact it is the array 1 thousand specific enzymes that acts to coordinate all those reactions that make the behavior of a cell. Or they can string up small molecules into more kinds of chains... in fact 50 different kinds of proteins and 3 kinds of strands of RNA can come together into an elaborate factory that can read blueprints and manufacture MORE proteins, all the 1000 kinds that each cell has. Then, a dozen different proteins can come together and go copy more blueprints off the DNA library, dozens more can make copies of the DNA library itself.


EXPERIENCE WITH COMPLEXITY FROM COMPUTER SCIENCE, ENGINEERING AND PHYSICS
A little computer science is in order here. you now begin to see some of the complexity happening inside a living cell. when you get experience writing computer programs out of dozens of interacting modules like this. you begin to get a feel for what kind of interesting robots you can create out of these programs. bear in mind that none of us have succeeded in writing programs this complex! we've only been at it for 60 years. millions of years of design cycles have gone into honing down the clever interactions found in cells.

Realize that these protein machines, and small molecules, subtle, sensitive, jiggly more-than-building-blocks are constantly bumping into each other testing each other out randomly trying out new possibilities millions of times a second. A simple bacteria has more bustling activity in it more moving parts than all of New York City. more molecules than bricks, more enzymes then people, more ribosome factories than buildings... more KINDS of enzymes than human professions. And fast. It takes maybe 20 to 100 years for a city to form a colony and reproduce itself. A bacteria can do it in 20 minutes!

More needs to be mentioned about process. So I've painted a picture of Millions of mindless simple parts jiggling around each other randomly making a cell. Is all that random motion of mindless simple parts enough to create the coordinated intelligent behavior of a living cell you can watch wend its way under a microscope? We need to discuss some discoveries from physics, engineering and computer science.


PHYSICS OF ORDER FROM ENERGY FLOW THROUGH FLUIDS
One thing we add to the chaotic swirling Brownian motion of molecules in cells, is energy flow. Even without biology, energy flowing through simple systems of molecules whether in swirling fluids or chemical reactions, can ORGANIZE that fluid and creates discrete structures in it. (And by energy we are talking about a ONE dimensional number. How fast a molecule is moving, or how far apart an electron is from a proton. In no way has this conception of energy anything to do with the complex frenzy of human attention or desire. None of that new age crap. It took physicists 150 years to whittle energy down to the streamlined usefully measurable concept that it is today. The complexity does not lie in the 'energy' it lies in the different interactions among the parts that the energy simply sets into motion.)

Energy flow. place a flat tray of water 5mm deep on top of something that will heat the bottom evenly. Now that layer of water is warmer below and cooler above. When you have two different temperatures heat is what happens, energy flows from below to above. the higher temperature below of course is a random jiggling of gazillions of molecules of water. and this is what we observe. everywhere in the water, random jiggling under the microscope. crank up the heat on the bottom slowly. the water molecules below jiggle more and more. they start traveling slowly throughout the layer of water. random currents of molecules, like tangled threads of fungal mycelium may form, connecting, breaking... (it is actually difficult to observe and even more difficult to describe, simulate) crank up the heat some more..

At a distinct temperature difference which is dependent on the viscocity of the water, the overall temperature and the thickness of the layer, something surprising happens. All that random motions arrange themselves into a stable pattern of stable discrete hexagonal convection cells.

Water at the bottom in the center of each cell getting warmer, expanding, becoming less dense, so rising to the surface, giving off heat to the cooler air, being pushed to the sides of the convection cell by water rising behind it, cooling some more there and becoming more dense, so sinking at the edges of the convection cell where it will pick up heat again and start the cycle over again.

Or at the molecular level: Molecules in the center of each cell picking up heat from the bottom, moving faster (more kinetic energy is what higher temperature is) traveling upwards till they get to the surface giving off their energy to the surface molecules and then to the cooler air, interact subtly with the surface tension and disperse sideways till they meet the sideways molecules of the neighboring cell and then, again interacting subtly with the surface tension, head down the sides of the cells to start again.

WATCHING TERMITE COLONIES CAN HELP GIVE INSIGHT
But the convection cells are SO MUCH larger than the tiny random motions of the molecules were before they formed. How does it happen? Ever watch a million half inch long termites build a complicated 10 foot tall termite mound full of chambers and passageways? In such colonies is a convenient parallel processing computer that we can watch that simulates something like this. The termites cannot see the whole mound. They probably don't even have a mental image of the structure of the whole mound. no one termite or even committee of them is keeping track of everything.

What happens amongst termites and social insects of all sorts is that each termite knows a small set of interactions it performs with its neighbors. each termite only senses whats in its local vicinity and what the termites it meets are doing. mostly termites are pretty sloppy and random too! they put things together, take them apart, other termites come and put the thing back together... eventually when a 'critical mass' of things starts happening the termites are organized into these remarkable structures. 'critical mass' 'organized', The invisible hand of economics? God? spirit? No, just mathematics, which we can explore.

Somewhere in there a phase transition occurs when the more and more complicated motions of tangled threads of moving molecules organizes themselves into this coherent motion.

ENERGY FLOW THROUGH CHEMICAL REACTIONS CAN DO THIS TOO
Chemical reactions can do this too. The Belousov Zabotinsky reaction. Malonic acid, Bromate, Cerium ions, in water. Different configurations form randomly, some reactions go slowly, others go quickly, reaction products diffuse.. put it all in a petri dish and watch. at some point when the concentration of one of the reactants reaches a critical point the thing begins to organize itself into spiral waves of reaction cycles pulsing like the beating heart.


MORE MATHEMATICS
How? How can these collections of randomly scattered molecules homogeneously spread out in space spontaneously break up into complex patterns of DISCRETE structures? What one must explore is the series of mathematical games i set forth in the complexity lab. Many systems of dirt simple rules played out over and over again among many simple parts can spontaneously develop order and pattern. Look at Conway life, look at the iterates of the unimodal map, look at the three body problem. look at the zero one laws in random graphs. look at the stable cyclic patterns that can spontaneously form in the random boolean networks.

Then we need to add in the concepts from cybernetics and computer science. positive feedback, negative feedback, trial and error algorithms.

Energy flow, mathematics, a few physical constants. built up module after module of complexity.