Thursday, April 23, 2009

COMPLEXITY LAB MANUAL (under construction)

Complexity Lab Manual is a collection of experiments, projects, math doodling, things to read and pictures and videos to watch that aid in thinking about how life can emerge from the simple rules of chemistry. It explores how patterns form at different scales in the hierarchy of the complexities that is life.

What's unique about it is that the topics are discussed in detail, enough detail to work them out on your own. I've seen lots of books on these topics but none of them give the actual concrete details enough so that it's not just vague hand waving.

Can chemicals become life? Can rocks and mud and ocean water and air and exchanges of energy become life? Throughout recorded history most cultures have assumed that a pre-existing mind was necessary to design life out of these inanimate objects. And once life was so designed we then ask, can life, on its own, give birth to, ramify into the myriad different forms we find on earth today? Again conventional thought is that this too, needs a conscious designer.

And what animates life? Can matter and energy following physical laws animate life? Even in the past few centuries there has been debate among biologists between the mechanist view, that the laws of physics and chemistry are enough to explain how life lives and the vitalists who supposed that there was an indescribable 'vital force' responsible. And that the mind of man required an otherworldly 'soul'.

Furthermore, since the 1950s we have found that life at the cellular, molecular level is so complex beyond anyone's wildest dreams, that many have decided that life is in fact irreducibly complex, that is, it could not develop from simpler forms at all, but must have been created by a more complex mind.

For sure life seems to be cleverly crafted, artfully designed, as if by a human engineer or artist. And so the question becomes, does the evolution of intricately adapted life forms require an unexplainable supermind, or can even the human mind be explained by the mechanical interactions between its myriad parts?

It is the aim of this complexity lab manual to show that we can in fact bridge the supposed barriers between the inanimate and the animate. That we can in fact think of life and mind as the complex interactions between simple parts.

Begining in 17th century chemists have discovered that the chemistry of rock, mud, ocean and air is in fact immensely more complicated than is commonly assumed. Begining in the '50s we have discovered that the molecules of life build upon this complexity of chemistry, and are the components responsible for the complexity and capabilities of life. Also starting in the years after WWII we have realized that the flow of energy itself, from hot to cold, from sunlight to darkness, from fuel to flame can organize matter into dynamic patterns. That under this flow, the inanimate molecules of life can self organize into complex structures, can take part in coordinated movements.

In 1859, Charles Darwin laid out a scheme which suggests that simple agents interacting with each other can in fact produce solutions to engineering problems, can in fact produce artwork in much the way that human minds do. Following the hints of Freud and other workers in neurobiology, we have been doing experiments to explore the interacting components of human thought, to actually analyse what was thought to be an unanalyzable monolith of soul. Since the invention of computers, we have been exploring mind from the ground up, creating computer programs from simple components that can perform many of the processes performed by our own thinking.

Combining the insights into the way energy flow organizes matter with the ideas of computer science, engineers in the fields of cybernetics and artificial intelligence have built inanimate systems that can become animated, that can act in a goal directed fashion, that can solve problems, and can defend themselves against the chaos of everyday life.

Then, beginning in the 1970s mathematicians have discovered how systems operating under this energy flow, called dynamical systems and cellular automata, can, by following dirt simple rules, ramify all by themselves into complex forms that give hints that the seemingly irreducible complexity of the molecular biology of cells can in a similar way arise from the simple rules of chemistry.

In the '90s biologists and computer scientists have built systems of computer programs that can evolve into ecosystems of new forms.

And most recently, scientists and engineers in the nanoscience fields are begining to bridge the gap between molecules and these pattern producing, reproducing cybernetic machines.

There is still much work to be done in bridging this gap between the known capabilities of chemistry, the behavior of these simple cybernetic systems and the molecular complexity of life. Working on the examples in these labs will prepare you to join in this exciting adventure.


1) Learn to identify plants to species [lab 6], watch animal behavior to see first hand just how detailed life is [lab 2], and begin to ask specific questions of how life manages such complexity.  A honeybee can perform over 270 complex tasks, one of them being to build entire new honeybees from scratch out of pollen and nectar [lab 4.5].  How?  Could we possibly build a tiny robot that can do all this and reproduce itself? Let's try it!

2) Learn how we proceed from transistors to logic gates to computer chips [lab 8] to programmed robots [lab 61.2] [lab 61.3] [lab 9]. Gain hands on experience with building complex systems from simple parts. Are we there yet? A little, but nowhere near creating half inch long reproducing honeybee robots that can perform the more than 270 different skills they are capable of.

3) So how are critters built?  They build each other.  We'll observe slices of growing plants under the microscope [lab 17], watch videos of animal development [lab 16]. We will see that bodies can grow because they are made of tiny submodules that we call cells, and these cells can move around and even reproduce themselves.  In fact we'll see that there are living creatures that are single microscopic cells - amoebas paramecium... smaller than grains of sand.  The cells we are made of are in fact living creatures in their own right.  All life around us are single cells or growing societies of cells who stick together and coordinate.

4) So now that we've simplified the mystery of life to the mystery of cells... what are these micoscopic single celled creatures?  Are they too made of even smaller living cells?  No, we are now closer to fundamentals.  These living cells are swirling cities of molecules!

We will watch single celled organisms in pond water behave [lab 22], grow them, look within. Watch them grow more of themselves just from water air and the glass jars we keep them in [lab 25]. This is a chemical transformation.  And then we can grind them up and perform paper chromatography on them and learn that we can separate them into 100s of different chemicals [lab 26].  What are chemicals?  We can use powerful microscopes and see that even cells are made of many moving parts [lab 27].  What are these parts?  Just what is chemistry?

5) It is at this point where we start blowing our minds.  In the past 150 years we've learned that chemistry is actually a complex dance of trillions of discrete interacting transformer robots: atoms and molecules.  The algae we grow in our jars are transforming air, water and glass into squishy living creatures, much as plants do, much as plants convert air and water into wood.  And we can burn wood and get back the air and water.

We can calculate the properties of gasses by guessing that gasses are a swarm of floating whirling tiny molecules bouncing around things.  Water flows and is sticky because it is a fluid jumble of trillions of molecules that can stick together a little and then flow past each other.  solids have strength, structure, color because of the way molecules hold onto each other.  And life... life is dynamic, responsive, creative, because molecules can do all this and more...

This molecular world is so alien to our experience. Watch the jiggling of molecules (Brownian motion) [lab 72.3], make a layer of soap on water one molecule thick [lab 72.4]. Learn how we discovered that living cells are dynamic molecular cities of more transformer robot molecules than there are bricks in NYC (we will count).. [lab 29].  That they collide with each other and "decide" to attach or dissatach billions of times a second.  Do experiments to see that molecules have shapes, that they respond in particular ways to their environments, that they can store and process information, that they can interact in larger and larger groups much as we built up transistors into more and more complex circuits. [i don't know if i have these labs yet!]

Watch videos of self organizing protein structures that build scaffolding, injest food, and process information. See that the activities of the cell are coordinated by the cooperative interactions of many simple parts and not by a single command center [lab 27] [lab 31.2]

But it's US that design and build circuits out of transistors, can swirls of molecules really become organized into this complex machinery dance of life all by themselves?  We will find that yes in fact swirls of molecules DO become complex by themselves.  All it takes is energy flow (sunlight) and mathematics!  Energy flow first.

6) So how does energy flow animate and organize chemistry and life?  Energy flow organizes matter, creates stable discrete dynamic patterns. Experiment with a chaotic waterwheel [64.2], simple steam engine [lab 33], watch the flow of heat organize a fluid into a discrete array of stable gyrations (Benard convection) [lab 34], watch the release of chemical energy organize a petri dish of chemicals into a dozen chemical reactions that form intricate oscillating patterns (Belousov Zhabotinsky reaction) [lab 42], watch these processes come together to make a complex dynamic stable flame [lab 44].

7) But can these simple patterns of chemistry become more and more complex, into the bewildering molecular complexity we saw in living cells?  We saw that energy flow can induce repeated cycles in many systems, so next we'll explore how repeated cycles of simple rules can create very complex patterns: a mathematical robot with two simple rules can count to 9,684 steps to create its final stable growing pattern (Langton's ant) [lab 48.2], an array of squares with 3 simple rules determines a peculiar bewildering garden of static and dynamic patterns (Conway life, a two dimensional cellular automata) [lab 48]. We'll explore the entire gamut of possible rules for one dimensional cellular automata, and map out the range of simplicity to complexity to chaos [lab 53].  We'll watch the repeated application of two simple geometric rules create a pattern who's intricacies mathematicians have yet to completely explore (Mandelbrot set) [lab 58.2].

8) Even without energy flow, matter can settle into complex patterns. We'll study the world of 4000 minerals, 800 of which can be formed out of merely the dozen most common elements [lab 71]!  Explore how successively adding one more proton/electron pair to an atom creates new qualitative behaviors [lab 74], watch phase transitions in water, and sulfur [lab 76]. We can watch water molecules settle into the myriad forms of snowflakes [lab 75].

9) At root all the patterns in the universe come from mathematics. The fact that there ARE two dozen different kinds of atoms with their peculiar properties to arrange themselves into minerals and life comes from mathematics.  We will watch how simple sets of constraints determine interestingly complex but not infinitely chaotic arrays of structures: how many ways can you put together styrofoam balls and toothpicks (finite graphs) [lab 87]. How many of these graphs can you build around a sphere so that each styrofoam ball in the graph, with its toothpicks looks identical to all the others (5 platonic solids) [lab 80]? We'll review the surprising classification of finite simple groups that took 2000 pages to describe [lab 81]!

10) Finally, we put it all together, by watching Tierra, a system of reproducing computer programs that can evolve into whole ecosystems of new and different programs [lab 96].

I've never seen quite this sequence of topics put together. It is kind of a summary of my eclectic educational experiences over the years.


1) Ideally a two semester course on complexity for people majoring in math, physics, chemistry, computer science, biology, economics, theology, philosophy, etc...

2) A very fat book which includes the labs, philosophical commentary and historical background

3) Less fat book describing just the labs for high school and college age kids.

4) A couple dozen of the simpler labs and games for younger kids

5) A bunch of science exhibits or workshops.

6) video series?


1) Historical sketch
2) List of representative labs

3) Introduction to representative labs with links

4) Table of contents to the 100 labs
5) The labs
6) Ideas for complexity labs at a science center for kids

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