A brief outline of the complexity lab manual: 11 chapters
I was originally motivated to put together the Complexity Lab Manual in order to give people the tools they need to think about how evolutionary biology and even the origins of life from chemistry could possibly work. I feel that the standard biology and chemistry education doesn't always point out the necessary insights, especially interconnections between far flung fields of studies.
The Complexity Lab Manual is an interdisciplinary set of labs, videos, diagrams, games you play on paper, pointers into the literature etc.. that explore examples of how complex order is achieved by interactions of simple parts. It spans biology, chemistry, geology, computer science, and mathematics. The level of the labs runs from elementary school on up to open ended research.
There are many books that cover some of these ideas (with a lot of hand waving) but I feel very few show concrete enough examples in detail, and explain how to actually perform experiments so that the reader can get first hand experience in complex pattern formation and therefore come to their own conclusions. Also many books and courses on complexity don't dive into the nitty gritty of the molecular nature of life and explore what chemistry is capable of.
The experience proceeds from the every day macroscopic down to microscopic cellular life, even deeper into chemistry, and to the very mathematics of the universe itself. The chapters are:
(1) Natural history: explore the diversity of organisms and how detailed they are.
(2) Computer science: one way we know how to build complexity from simple parts. can we make a robot organism? not yet!
(3) How DO organisms build themselves? living cells keep replicating and arranging themselves into patterns.
(4) Watch single celled protozoa, what are they? Giant whorlwind dances of molecules.
(5) Explore the molecular world: trillions of sticky parts bumping into each other and responding to each other.
(8) Chemistry at rest: the dozen most common elements can form over 800 different minerals.
(6) Chemistry in motion: watch energy flow animate systems into dynamic stable patterns.
(7) Chemistry is hard to do, so work out mathematical dynamical systems that show how repeating simple rules can lead to extreme complexity.
(9) Static mathematical systems, the roots of complexity ARE math.
(10) Watch complex programs evolve in computer operating systems.
(11) Now you have enough experience and imagination to begin your studies of chemistry of the origins of life!
Each chapter has labs, like collecting and keying out plants, learning to program in machine code, watching single celled protozoa, setting up convection cells in fluids, chemisty that create patterns like the Belousov Zhabotinsky reaction, programming cellular automata like John Horton Conway's Game of Life...
MORE EXTENDED DESCRIPTION WITH EXAMPLE LABS
Chapter 1 is natural history of macroscopic life, then once we experience the diversity and complexity of it, we ask: can we make robots that can mimic what an organism can do?
[6] learn to identify 100 different plant species, [4.5] study how honeybees perform over 270 different tasks and ultimately reproduce themselves,
So Chapter 2 moves to digital electronics and computer programming. This gives concrete experience in the complexity we have so far been able to build out of many simple parts and give us an idea how hard the task is, because NO we cannot build such robots. So we ask how does life do it?
[8] learn the hierarchy from transistors to logic gates to processing units, to programmable computers, [9] write some computer programs using only a simple set of machine instructions, [61] watch a team of robot dogs play soccer
Chapter 3 explores developmental biology, in which we conclude life can do this because life is a property of its simplest components: cells. Cells build us from the inside, by growing and reproducing.
[17] observe how plants are constructed out of cells under the microscope, [16] watch videos of animal development or maybe watch snails develop on glass of an aquarium
Chapter 4 watches living protozoa and does some simple chemical analysis to ask WHAT ARE THEY? This moves us to the center of this lab.
[22] watch single celled protists in pond water, [25] watch Oscillatoria grow from just water, air and glass in a jar, [26] do some paper chromatography to get hints at how many different parts these creatures are made out of, [27] look at electron microscope pictures to see how complex inside
Chapter 5 explores what is the molecular world? Molecules come in a combinatorically bewildering variety of forms, they are in constant motion probing each other, are reactive... But how does this build dynamic complexity? Then we peek at the bewildering complexity of the molecular biology of the living cell. How can simple chemistry give rise to this? The answers are energy flow and mathematics.
[] burn that dried Oscillatoria back into air, water and ash, [72] watch Brownian motion, a first hint at the discrete nature of matter, [73] try to make a lipid mono-layer on water to try to count the number of molecules, [29] count how many bricks there are in a large metropolitan city, [30] learn what Avogadro's number is and what it's implications are: more molecules in a cell than bricks in NYC, [27] study how clathrin coated pits are cooperative systems of molecules in a cell that can achieve global goals, [31] do some organic chemistry to watch how molecules can be sensitive to the conditions around them and to each other
(i'm not so experienced with the chemistry! I'd really like to find simple labs to hint at the discrete nature of chemistry, a way to suggest Einstein's and Perrin's work to measure Avogadro's number!)
But first, in Chapter 8 (I think it's best to put it here now), we first look at the complexity that chemistry can give us even before we move to dynamic systems, the complexity already inherent in the periodic chart of elements, the bewildering set of minerals on earth, phase transitions, snowflakes..
[70] explore how the periodic chart of elements is already a curious mix of complexity but not total chaos. Why does simply adding one more proton at a time create qualitative changes?, [71] explore the world of minerals. 840 different minerals can form from just the dozen most common elements, [76] watch phase transitions in water and sulfur, [75] observe snowflakes and various forms of frost develop
Now we bring in energy flow. Chapter 6 explores dissapative systems, macroscopic and chemical examples of how energy flow through fluids and chemical systems produces dynamic, creative and stable patterns. But can the patterns achieve the complexity of life? At this point the chemistry becomes hard to do, so we move to mathematical dynamical systems, where we can watch real complexity develop before our eyes.
[64.2] build the chaotic waterwheel, [33] build a thermo-acoustic engine or sterling engine, [34] watch Benard convection in a shallow fluid, [35] make the mercury beating heart oscillator, [42] watch 5 simple chemicals create dynamic spiral patterns in a petri dish: Belousov Zhabotinsky reaction, [44] watch chemistry and convection form a flame
Chapter 7 explores mathematical dynamical systems both discrete and continuous that show surprising examples of complex pattern formation by the iterations of simple sets of rules.
[48] play with John Horton Conway's game of life on a checker board, [48.5] program it on a computer and really have fun, [48.6] program Langton's ant on a computer and watch the simplest rule evolve a structure that takes 9000 steps! [53] explore the range of behaviors in 1 dimensional cellular automata, [58] learn how the Mandelbrot set (the most complicated mathematical object) is formed from simple geometrical rules
Finally to attempt to explore the ultimate roots of complexity Chapter 9 explores pattern formation in static mathematics: we watch how a small simple set of constraints can determine an interestingly complex but not infinitely chaotic array of structures.
[79] the definition of prime numbers is easy but leads to a non repeating pattern who's properties we've yet to fully comprehend
[87] combinatorics of finite graphs: how many ways can you put together Styrofoam balls with 1 toothpick, 2, 3... [80] now make the only 5 platonic solids, [81] review the surprising complexity in the classification of the finite simple groups
The two last chapters, Chapter 10 on evolutionary biology and Chapter 11 on Origins of Life studies, will be just hints. We've laid the foundational tools, they can be another book! Chapter 10 will explore systems like Tom Ray's Tierra and Hiroki Sayama's evoloops where we watch complex structures evolve. I don't know what I want to put in chapter 11 yet.
[96] watch Tom Ray's Tierra evolve computer programs and ecosystems, [97] watch Sayama's evo loops evolve chaotically
Here is a Visual Introduction that covers some of this material
Here is more complete material and description of labs
It's still a mess. I need to combine the two and rewrite them!
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