A Selection Of Representative Labs With Commentary

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CHAPTER 1

LIFE
How varied and detailed is life on Earth?

6) Key Out 100 Plants In A Local Park [6WKS] [or a two session blitz just to collect 100 different plants and press them]

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

there is a bewildering variety

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?

And how complex is their behavior?
2) collect insects and watch their behavior in a terrarium
after much observation you can find out:
4.5) List of 270 Skills That a Honeybee Has


Can we get a handle on it from computer science? 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.


CHAPTER 6
COMPUTERS
It's not so easy to see how animals work, maybe we can at least try to make some robots that act as complex and see from scratch how it might work?

8) from logic gates to computer [1/2 hr?] show them, or make some simple circuits in digi-lab.

61.2) write simple computer programs in machine code: binary search, sort, rule 30 etc... [hr]

61.3) program John Horton Conway's game of life, Mandelbrot set, and Lorenz attractor in basic or something or maybe the lego bot language
[hr?] show them?

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.

9) show them well programmed lego bots ( (intro to another whole workshop) and listings of 1000 lined programs [1/2hr]

But we still Can't do it! Our robots are clunky and stupid in comparison with a honeybee!



CHAPTER 1
SO BACK TO CRITTERS FOR HELP

16) watch videos of animal development

This is an amazing process. And it works because animals are colonies of living cells, all talking with each other, feeling each other out and reproducing and sending their kids to the right places. We build machines from the outside in factories, but animals and plants are built from within by cells. What are cells?



CHAPTER 2
CELLULAR LIFE
Some critters are a single cell all in one, lets watch some:

22) watch single cell pond creatures [hr]
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...

So what kind of 'things' are cells?
27) molecular video "inner life of cell" [10min] more?


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.

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


25) grow oscillatoria in water and glass jar. watch it move. then at second to last session, weigh it, dry it, last session, burn it, weigh the ash
[10min sessions a few times]



PART 2
PHYSICS AND MATH

So how do cells do it? Well, no need to go to biology for the complexity of cells, the capabilities 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?

So what is the molecular world like that it gives life it's subtle creative qualities? What are we 'made of'

Well, how many molecules are there in a cell?
73.2) Brownian motion: hints at the existence of many tiny molecules, constantly in motion due to heat, and hints at how small they are, how many in a drop of water.

73.3) monomolecular lipid layer: another clue to how big molecules are. Then we sketch out how the number of molecules in a glass of water can be calculated from experiments like these
[hr]

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.

any labs we can do to show how molecules interact? orgo reactions, soap/oil/water, collisions? orientations? chirality..
72.2) show how many ways an ethanol molecule can respond to its chemical environment?

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 moving, 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!

Show diagrams/video of how simple molecular interactions cooperate to form complex structures and processes:

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


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' tendency? Well, life is not a closed system!

One process that helps is positive and negative feedback. Lets explore some machines and simple processes that can do this.

64.2) chaotic waterwheel, thermostat and heater, door buzzer [hr]


In our next labs
33) show steam engine (with governor?) can i show that it needs hot and cold?

34) Then Benard convection
[hr]

We show the basic system animated by energy flow: Benard convection: We start off with wood (or some kind of fuel, highly ordered in any case) 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 It.

The flame will heat from below a pan of shallow water. As the bigger closed system of wood and air and water run down to ashes and luke-warm carbon dioxide and water, 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 thermodynamic equilibrium systems 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.

Can life even arise spontaneously from chemistry?

42) The Beloussov Zhabotinsky reaction : a simple far from equilibrium chemical system that you can watch forming periodic spatial patterns

Put convection and chemical reaction cycles together and you get:
44) play with a flame: [hr]

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: a simple system of simple rules wherein there are patterns of many classes of behaviors, and simple patterns can develop into surprisingly complex ones. we can even make a finite pattern that results in an endlessly interesting one

53) One dimensional cellular automata rules 30 and 110 even dirt simpler set of rules that produces an endless stream of creativity
[1/2hr] [1/2 hr]

56) 3n+1: a simple number game with complex behavior we have yet to fully understand

57) e/o Fibonacci system: another one with much more complex behavior. these only involve addition and division.

58) Iterated logistic equation to Mandelbrot set: simple math rules give the most complex geometric structure we've ever imagined

60) Lorenz attractor: a simple dynamic system that results in a curious subtly behaving system with a sprinkling of unpredictability. By the way, it is very similar in behavior to the chaotic waterwheel.
[hr]



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.


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.

74) show periodic chart with samples of diff elements: gas, liquid, metal, graphite, sulfur, semiconductor..

76) phases of sulfur: even with one kind of atom, depending on temperature, we get wildly different behaviors
75) and breath on a window pane: ditto for water molecules, how do they 'calculate' the beautiful patterns of 'jack frost' on window panes?
[1/2 hr]

70) mineral exhibit a dozen elements, a dozen transition metals and 2000+ combinations all for free.[1/2 hr? depends where]



CHAPTER 8
IT ALL COMES FROM MATH
At root, why is this universe so full of patterns? MATH!

From mathematics alone, we get surprising complexity but not total chaos from the simplest 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.

87) enumeration of finite graphs: keep adding one more edge to a graph and you discover radical new behaviors. clues to things like how we get the behaviors in the periodic chart of elements?[1/2 hr]

81) classification of finite simple groups: example of simple static rules giving surprisingly diverse but only a tiny bit of chaotic pattern [1/2hr]



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.

96) Tierra a system of programs that can reproduce, evolve, and form ecosystems [hr]



CHAPTERS FOR FURTHER STUDY:

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.



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.