Summary Table Of Contents and Highlights

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CHAPTER 1
ORGANISMS

(1) What are animals and plants?

Let's do some field biology of organisms.

1) Collect Ant Colonies
2) Observe Ant Behavior
5) Key Out Ants Under Dissection Scope.
6) Key Out 100 Plants In A Local Park
7) Insect Diversity

By learning to key out and LOOK at organisms hard enough to distinguish their varieties, we learn two things:

there is a bewildering variety of living creatures out there: we've found over 2million different kinds already;

organisms are incredibly detailed. As close as we look at them as much as we magnify and look inward, we find levels and levels of complex details. How does it happen?

Can we get a handle on it from computer science?

8) From Transistors To Computers
In the past 60 years we have learned to build some complexity ourselves. Follow the levels of complexity as we build up from transistors a computer with elaborate software.

9) Can We Build Ant Robots?

10) Program Ant Simulations
Researchers in the field of Artificial Intelligence are now asking themselves, what it would take to build an animal, to build clever behaviors from the bottom up. We are trying to check our understanding of intelligence by building complex things and seeing if they can ACT intelligently.


Back to the critters for some help

12) Ant Anatomy: Dissect Insects
13) Ant Brains: Photomicrographs
We are nowhere NEAR there yet. Just TRY and dissect an insect brain neuron by neuron and count all the connections! Can we put it back together again?


18) How To Imagine 20Billion Neurons.
And finally, how complex is the substrate for our own minds? Is that substrate really complex enough to play one of us on it? 20billion interconnected neurons. How do you begin to get a FEEL for what it might be capable of?


So, can we build stuff as amazing as all this in our own factories?
14) Dissect An Automobile, Ants Are MORE Complicated!
15) How Are Automobiles Built?

No, we don't know how to build animals! So how do animals do it? How do animals grow to the amazing complexity that they are from a single eggcell? They go through developmental processes:

16) So How ARE Ants Built?
17) Watching Flower Or Mushroom Development


So, what builds and maintains animals and plants? What is the basis for life? One key is that all life is based on the level of organization called CELLS. Everything that We build, we build from the outside with our own hands or with large factories, but every living creature is built up from the INSIDE by the microscopic living cellular factories that it is made of. This is how creatures build THEMSELVES.



CHAPTER 2.
CELLS

So what are cells? Well, some critters are a single cell only all by itself, lets watch some:

22) Look At Pond Water.
23) Watch Stentor
24) Watch Euglena, Bacteria
Take some time to watch the intricate behaviors of living single celled organisms. Already at this level, there is so much capability. The capabilities that make life so rich are not concentrated at the top, the most centralized level, but are distributed throughout every size scale! Even at the cellular level, and below...

What kind of 'things' are cells?
28) Metabolic Wall Chart!
29) Which Has More Moving Parts: A Bacteria Or New York City?


cells are hierarchical structures of organelles, macromolecular assemblies, macromolecules, small molecules. The properties of cells are also due to the most common molecule in them: water.
25) What Are The Building Blocks For Cells?
26) Paper Chromatography
30) Visualize All The Detail In One E. Coli
They are whirlwinds of swirling interacting molecules. The structure and organization goes in several more levels deep, as complex as a whole giant city.

and finally the most common machinery: proteins. they can self assemble into complex structures like undulipodia, they can change shape, travel along tracks, act as a complex logic elements in processing information, respond to EM radiation




PART 2
PHYSICS AND MATH

So how do cells do it? Well, no need to go to biology for the complexity of cells, the capabilies of cells. Physics, chemistry, and mathematics already gives us this. We are slowly whittling away at the divide between chemistry and life!


Physics and math gives us:
1) Patterns at far from equilibrium: energy flow through systems creates ordered dynamism
2) But even at equilibrium, rest, pattern comes ultimately from mathematics
3) And the clay that physics and math get to sculpt into organisms?
molecules!



CHAPTER 3
WHAT IS THE MOLECULAR WORLD?

How many are there?
73) 10 Million Billion Billion Molecules In A Glass Of Water
29) Which Has More Moving Parts: A Bacteria Or New York City?

How many kinds? Again bewildering variety!
26) Paper Chromatography
74) Periodic Chart Of Elements

What are they like? Atoms, molecules are not building BLOCKS, they are little machines, not clunky, but fuzzy, sensitive to their environment and each other, reactive, each atom is a complex of electron orbitals which are solutions to wave equations... molecules are flexible, constantly wiggling, not alive, but... can't describe what they are in common every day terms.
72) Molecules Have Shape

any labs we can do to show how molecules interact? orgo reactions, soap/oil/water, collisions? orientations? chirality..


What's their environment, how do they interact? Just by changing temperature and pressure we can make molecules behave as solids, liquids and gasses (lab 75 etc..). For cells, the liquid state is most important. What is it? How can stuff be a liquid? is it just soft, or.. is it the consequence of trillions of tiny molecules zooming around each other?
31.1) Watch Brownian Motion: Hints To The Discrete Nature of Water

At the molecular level you already have a kind of trial and error mechanism for fitting together puzzles. one of the roots of our intelligence. molecules are always miving, wiggling, interacting with each other 10^10 times a second! molecules in a warm universe with energy flow are not like a jumble of cold automobile parts just sitting there, molecules can self assemble!
31.2) Distributed Brownian Motion Machinery: Clathrin Coated Pits


molecules pass energy to each other in reactions, store energy in bonds, thus networks of their reactions can be ordered by energy flowing through systems of molecules.
molecules react with EM radiation. vision comes for free at the lowest level
44) Play With A Candle Flame
47) Simplest Organic Redox Cycle



CHAPTER 4
DISSIPATIVE STRUCTURES: FLOW OF ENERGY THROUGH SYSTEMS CREATES PATTERNED DYNAMISM

If molecules aren't simple building blocks, then organisms are not 'things' at all, 'phenomena' would be a better adjective, or, to be less academic; 'dances'? What kind of phenomena are living cells? they are chemical systems animated by energy flow.

Our usual experience is that things wear out after a while and run down. You may have heard of the second law of thermodynamics which says "all closed systems (nothing coming in or out) run down and become less, not more ordered. If this is so, then how can life oppose this 'universal' tendancy? Well, life is not a closed system!

In our next labs
34) Benard Convection
36) Combine Convection With A Spinning Earth And We Get Global Weather Patterns
37) Storm Cells

We show how it's done. We start off with wood (highly ordered) and air (unusual, out of equilibrium with all its oxygen..) and light the wood into flame. It is important that the flame is much hotter than the air above the water.

The flame will heat from below our pan of shallow water. As the bigger closed system of wood and air and water run down to ashes and luke warm carbon dioxide, for a while, a wondrous thing happens. Our pan of water (not closed, open to heat flowing through it) becomes ordered into an hexagonal array of gyrating convection cells.

We call these subsystems FAR from equilibrium or Dissipative Systems (they dissipate heat).


And what makes CELLS swirl? this time it is the flow of chemical energy. High energy bonds come in (sugars) and again low energy bonds come out in the form of carbon dioxide. In the meanwhile the cells swirl with activity. here are some simpler examples.

42) Belousov-Zhabotinski Reaction
47) Simplest Organic Redox Cycle
Processes like these drive that swirling metabolic wall chart we find in cells, in all of life.

Put both kinds of processes together and you get:
44) Play With A Candle Flame
They are more complex than you think! And they contain complex networks of chemical reactions reminiscent of the metabolic chart!



CHAPTER 5
MATHEMATICAL DYNAMICAL SYSTEMS: EASY LABORATORY, ALL YOU NEED IS PENCIL, PAPER, COMPUTER

But living creatures are more complicated then these. Can chemistry really result in the complexity we found in living cells? Where do all those different patterns and structures come from? MATH! Mathematics gives us so much pattern for free. Simple rules repeated over and over again between many identical simple units can create surprising unpredictable patterns.
48) John Horton Conway's Game Of Life

56) 3n+1 game
57) An Integer Dynamical System With A Curious Array Of Orbits
58) Iterates Of The Unimodal Map: Intro To Concepts In Mathematical Dynamical Systems
59) 3 Body Problem In Newtonian Mechanics
60) Lorenz Attractor and Chaotic Waterwheel
61) Compare Various Combinations Of Discrete And Continuous In These Dynamical Systems



CHAPTER 6
MEDLEY OF CONCEPTS FROM COMPUTER SCIENCE AND CYBERNETICS

ok, chemistry and weather can be wildly complex, but how do these systems maintain stability? Negative feedback!

And then go even further, how can living cells maintain more subtle stability and behavior?. Sometimes even the mathematics is hard to solve, so we write computer programs. Can complex behaviors result from collections of simple algorithms?

62) Positive Feedback
63) Binary Search
63.5) Examples Of Trial And Error Algorithms
64) Negative Regulatory Feedback
65) Compare Trial And Error With Direct Prediction
66) Data vs. Algorithm
67) Hierarchical vs. Distributed Control
68) Iteration vs. Recursion
68) Exploratory Play Algorithms



CHAPTER 7
EVEN AT EQUILIBRIUM: PHYSICAL AND CHEMICAL PATTERN FORMATION

Even without the dynamical systems set into motion by energy flow, the laws of physics are fecund: We find pattern formation even at equilibrium.

70) Collect And Learn About Rocks And Minerals
71) Listen To The "How Rocks And Minerals Form" Exhibit At The American Museum of Natural History


And Carbon and Nitrogen can go crazy, see lab (87) in the math section.

The wonder is why isn't the universe a seamless haze of psychedelic chaos? Why isn't it just a bland grey blob of continuous matter? Why isn't the universe simply one huge neutron or quark or is THERE anything at the bottom? Somehow the physics and math give us all these phase transitions, clumpings for free.
75) Phase Transitions In Water: Breath, Oceans, And Snowflakes
76) Phase Transitions For Sulfur: Even Wilder!
77) We Couldn't Predict Buckyballs After 60 Years Of Quantum Chemistry

74) Periodic Chart Of Elements



CHAPTER 8
MATHEMATICS SHOWS THAT WE GET SURPRISING COMPLEXITY BUT NOT TOTAL CHAOS FROM THE SIMPLEST OF STATIC LOGICAL RULES

And why do we have this interesting periodic chart of elements, each with their potent particular properties? Physics and math again! Propose a simple set of rules and let them play out and you often find that you get a set of discrete entities which follow them that is interestingly diverse but not infinitely chaotic! This is the core of pattern formation in our universe. It's built in at the very basic logical structure of it.
80) 5 Platonic Solids
81) Classification Of Finite Simple Groups
87) Enumerations Of Finite Graphs
88) Zero One Laws In Random Graphs




PART 3
THE BIG QUESTIONS: EVOLUTION, ORIGINS OF LIFE, AND MIND


CHAPTER 9
PUTTING IT ALL BACK TOGETHER: EVOLUTIONARY BIOLOGY

Then we put it all back together again and tackle the most fascinating subject: what is it that brings us all those wonderful critters we found outside at the beginning of our exploration? Evolutionary biology.
90) Explore the Diversity And Disparity Of Life
92) Collect Fossils
95) Word Mutation Game
96) Tierra, An Ecosystem Of Evolving, Reproducing Computer Programs



CHAPTER 10
THE FINAL FRONTIER: CAN WE UNDERSTAND HOW GEOCHEMISTRY CAN BECOME LIFE?

The final frontier: is life SOLELY a consequence of chemistry and mathematics? If you perform labs in this topic, you are at the forefront of the scientific adventure.
98) Ecosystem Of Reproducing Candle Wicks?
99) Self Sustaining Ecosystem Of Reproducing Chemical Robots?
100) Chemical Origin Of Life



CHAPTER 11?
MIND

Bar, why do you leave off discussing mind and consciousness? because i'm not greedy? but the labs watching behavior of single cells, the computer science topics, 260 skills of honeybees, building AI programs to simulate critters is the start.



CHAPTER 12?
SUPERORGANISMS

And finally we come back to the ants! This is the most recent hierarchical level of complex behavior to evolve on earth. not only critters with minds who can explore and learn about and manipulate their world, but some organisms come together and build highly cohesive societies:
Ants, honeybees, wasps, termites, naked mole rats, wolves and... humans.