# Science 117/Fall 2012

Boundaries and Co-existence (in Biology and Human Life)
Science 117, SF Art Institute, Fall 2012
The primary text will be Degrees of Freedom: Living in Dynamic Boundaries, Alan Rayner's remarkable book on how fungi, cells, and people confound the general ideas of fixed, clear boundaries as they negotiate cooperation, alliance, competition and coexistence while growing and changing. We will read it together with Maturana and Varela's classic The Tree of Knowledge, and bring in other texts from system theory, psychology/self-help literature, business management theory, philosophy, and biology, with possible diversions along the way into experiments, field trips, performance projects, and other explorations.
Lecture Wednesday 4:15PM - 7:00PM, Main Campus Building, Room 20B

Syllabus: (pdf, odt)

Various weeks' homework handouts are linked at the project page.

                             August              September
Su Mo Tu We Th Fr Sa  Su Mo Tu We Th Fr Sa
1  2  3  4                     1
5  6  7  8  9 10 11   2  3  4  5  6  7  8
12 13 14 15 16 17 18   9 10 11 12 13 14 15
19 20 21 22 23 24 25  16 17 18 19 20 21 22
26 27 28 29 30 31     23 24 25 26 27 28 29
30

October               November              December
Su Mo Tu We Th Fr Sa  Su Mo Tu We Th Fr Sa  Su Mo Tu We Th Fr Sa
1  2  3  4  5  6               1  2  3                     1
7  8  9 10 11 12 13   4  5  6  7  8  9 10   2  3  4  5  6  7  8
14 15 16 17 18 19 20  11 12 13 14 15 16 17   9 10 11 12 13 14 15
21 22 23 24 25 26 27  18 19 20 21 22 23 24  16 17 18 19 20 21 22
28 29 30 31           25 26 27 28 29 30     23 24 25 26 27 28 29
30 31

15 weeks.


## Investigations

• Handout about mid-semester investigations: [log]doc, pdf

Fungi:

• Get mushroom growing kit at Far West Fungi, SF Ferry Bldg.
• Mycological Society of SF does edu. outreach and has some "quick start" material about collecting mushrooms, identifying, etc.
• North American Myco. Society: A foray in Scotts Valley CA Dec. 13-16, and Mushroom Dye Workshop; Registry of Mushrooms in Works of Art
• Thu Sept 27: "Fungus Among Us" at CA Academy of Sciences Nightlife series (in GG park). 6-10pm. \$12 for adults.
• Fri Sept 21: http://events.sfgate.com/los_altos_ca/events/show/275561025-the-secret-life-of-fungi-a-talk-by-john-taylor - in Los Altos, probably too hard to get to, and might be kind of basic.
• Foot fungus
• Mold
• Lichen = fungus + algae
• Fungus killing frogs in the Sierra Nevada: http://news.sfsu.edu/blood-samples-show-deadly-frog-fungus-work-wild - "High levels of an aquatic fungus called Batrachochytrium dendrobatidis (Bd) disrupt fluid and electrolyte balance in wild frogs, the scientists say, severely depleting the frogs’ sodium and potassium levels and causing cardiac arrest and death."
• http://en.wikipedia.org/wiki/Category:Fictional_fungi
• But that category doesn't include The Wonderful Flight to the Mushroom Planet! (And it should possibly mention Terence McKenna too...)
• Paul Stamets
• Video
• Get a video about growing mushrooms on coffee grounds, phone books, toxic sites, etc. Growing stuff like that would make a good student project.
• David Attenborough, The Private Life of Plants, "Living Together" episode: fungal associates, jellyfish, etc.
• Have been talking with Nik about doing a joint thing where we put mushrooms in place of the exotic English Ivy on the campus meadow
• Students could cultivate something fungal at the Tenderloin National Forest? Some of the student housing is down by there.
• Fungi in history: Irish potato famine; ergot and LSD
• R. Schmid, 1992, Diversity of plants and fungi, full of stories

Autopoiesis and cybernetics:

Personal boundaries:

• Rayner uses this analogy. Maybe flesh it out with some reading from the business field?

## Week 1: August 29

• Go over the syllabus and how the course will work.
• Introduce the two books
• There's a lot of reading in this class - expect to work hard.
• learning to read is probably part of taking this class
• learning to skim and to look for the main points
• Use a dictionary, use the concordancer. Use google and wikipedia. Feel free to talk to people.
• resources: Academic Support Services; Academic Advising - on the mezzanine, pblackman@sfai.edu; Academic Support Center and Tutoring tutor@sfai.edu; Writing Program cboufis@sfai.edu; ESL coordinator dskolnick@sfai.edu; and me.
• writing and reading tutorials at Int'l Student Center for everyone.
• The main book is Degrees of Freedom.
• It may be hard to keep up with but it's also very interesting.
• It's about the fungal kingdom: mushrooms, truffles, mold, yeast, etc. Mycology. There may be more species of fungi than plants and more mass of fungi than of animals. We eat them, make bread, beer, wine, soy sauce, etc. Some are poisonous, some produce antibiotics, some are powerful drugs. They're not very well understood compared to plants and animals, and different in some ways.
• One way is that they sometimes don't divide so clearly into individuals. For example, some fungi spend most of their life as a mat of hyphae (a mycelium) but then produce several fruiting bodies. Rayner is very interested in what life is like when it's not clearly divided into individuals and groups of individuals
• The conflict between our desires and the needs of others. Competition and cooperation.
• creativity of exploring the possibilities of fluid boundaries
• Ways of coexisting besides hierarchical structures.
• We'll start from the beginning, and take the ride with him.
• The other book is The Tree of Knowledge.
• The language is more like English, but the ideas are probably unfamiliar.
• It's about the biology of cognition. How living creatures know about the world, and are able to do what it takes to live.
• It's a scientific way of understanding the world, but very different from the standard scientific ideas.
• For example, every creature isn't just in a world; it brings forth a world.
• Things that happen in the world don't make an organism do something - the organism responds in a certain way depending on its structure. It becomes structurally coupled to parts of its world, and they both influence each other at the same time. We become structurally coupled to each other too.
• Interesting, powerful, useful, and aesthetically beautiful.
• This one too, we'll dive into and take the ride.
• I'll try to bring in other things too.
• Mushroom kit, maybe some visitors.
• I'll be interested in exploring the ideas together in various ways, including artistically.
• Again, the reading may be challenging and require a lot of work. I'll try to be helpful.
• Also, confusion, discomfort, and even anxiety might happen.
• pre-teach the reading for week 2
• Give a mini-lecture on natural selection.
• Aka part of Darwin's theory of evolution, which changed the world
• The basic idea - population, reproduction, inheritance, variation, differential reproduction.
• People who study evolution and natural selection are very concerned with cooperation and altruism: "the conflict between our desires and the needs of others".
• Example: say we have a forest with fungi growing in the ground. They live on the leaf litter and some other nutrients. If we start to get fungi that grow and reproduce faster, they'll overconsume the resources. There won't be as much. But that's "selected for".
• This explains why "self-sacrifice . . . is an evolutionary dead-end".
• "reciprocal altruism" and "group selection" are evolutionary theories to explain why real creatures sometimes cooperate.

• Intro
• Conflict between our desires and the needs of others
• Don't draw such sharp distinctions
• reductionistic and holistic approaches
• Indeterminacy - "open-endedness"
• hyphae branch apart to collect nutrients and then reassociate to form mushrooms
• compare to a car, maybe
• vs. genes, creatures competing, being discarded by natural selection
• Predigest
• living systems are not like sophisticated machines
• Chapter 1
• 1. Uncertainty.
• Boundaries we need, we define, we use to classify
• Discrete: distinct and separate. Examples: grains of sand vs. water; counting numbers vs. real numbers ("decimals").
• Competition, coexistence, natural selection etc. require discreteness (Rayner vs. scientific mainstream)
• Taxonomy, species, genera, etc. - help students with the terms
• 2. Individuals and Collectives
• scale of observation and context - examples: human body as community; sand castle
• Association, disassociation, reassociation; Integration, enclosure, coalescence
• 3. Self, nearself and nonself.
• reciprocal altruism, group selection, evolution, self-interest (assumes self!) - meanwhile, things do collectivize whether it's via self interest or not, and "bear fruit" as in mushrooms
• symbiotic: "living together" - when two or more creatures are closely connected to each other
• 4. Holism and reductionism.
• there's a creative interplay between individualism and collectivism at all levels
• synthesis of holism and reductionism $\to$ paradigm shift: sudden emergence of a new way of thinking
• 5. Stage directions --- Opportunity and Competition.
• Natural selection is the famous mechanism
• but how can it be creative?
• it's the living things generating variation that's creative
• too much disciplining $\to$ no innovation. there has to be "evolutionary playtime". Breeders know this. It can unleash huge creativity!
• 6. Niches - Cradle of Complexity.
• He doesn't explain what a niche is - I need to.
• The ongoing problem of defining niches.
• Need to look at how the nature of an organism determines its niche as well as v. versa.
• Let's skip section 6. I don't think we need it.

### Notes on Knowledge chapter 1

• Preface
• A completely new look at the biological roots of understanding
• cognition: knowing. Meaning effective action.
• Chapter 1. Knowing how we know
• let go of certainty
• words: phenomenon: an observed occurrence; aphorism: a "saying" or proverb.
• The hands-on experiments: the world isn't just there, what it is depends on us
• the blind spot: we do not see that we do not see
• Do "decapitation" and light bulb experiment in class.
• the shadow: we see green even though we have only red and white light
• All doing is knowing and all knowing is doing
• Everything said is said by someone
• and every act of knowing brings forth a world
• seeking a scientific explanation for cognition
• starting point: Knowing (cognition) is effective action.

### Checklist for 8/29

• bring red light.
• bring the 2 books.
• get mushroom kit at Ferry Building.
• upload all the stuff to the Moodle.
• copies of the optical illusion page.
• print the lecture notes (pdf).
• print the syllabus.
• print the homework questions.
• sign-in sheet for roll. list of students enrolled, to match people's names
• assign roles to students for next time, to help facilitate discussion?
• do attendance tracking paperwork after class
• send in syllabus to administration

## Week 2: Sept. 5

• Degrees of Freedom:
• Introductory sections
• 1. Defining dynamic boundaries 1-24 (24pp)
• Tree of Knowledge:
• Foreword and preface (8pp)
• 1. Knowing How We Know (16pp)

Sept. 10: end of add/drop period.

• What was it like?
• Report from what people wrote
• People seem interested, some good ideas in the books
• Do people agree?
• What's the first chapter of Degrees about?
• What stuck with you?
• If there's interesting variation in the question answers, do peer instruction
• Read the marbles thing together (section 2)
• bring jar of marbles
• do the reading out loud, with interruptions, questions, thinking out loud.
• Note that while the books' authors use complex language, we don't need to do that unless it helps us be clear.
• My version of the first chapter of Degrees:
• Boundaries can be fluid
• Individuals aren't completely discrete
• Interplay between Association and dissociation is key.
• Somewhere in between holism/reductionism
• Ass/diss messes with ideas about natural selection, classification, competition/altruism/self-interest
• My recap of chapt 1 of Tree:
• Knowing depends on the knower
• The question: "Fine, but what color is it really?". I really know that it's green. Everything said is said by someone. "Observer-based reality".
• All knowing is doing, and all doing is knowing. We can't know anything about the world without perceiving it, and that's doing something. We are active when we perceive. This is bringing forth a world. Later we'll talk about cooperating in bringing forth a world together, just doing it alone for now.
• Why talk about knowing? Why cognition, why not digestion, reproduction, moving around? It's about effective action - why are we (creatures) able to get along okay in the world? This is knowing. This is why "all doing is knowing."
• Note: change in syllabus.
• Chapter 2 of Degrees, sections 1 - 5 only.
• Scaling Hierarchies: Individuals and Collectives from Molecules to Communities
• we're not discrete - dynamic interplay between association and dissociation - "no individual entity can have complete freedom"
• This chapter is looking at the interplay of association and dissociation at different levels of scale, from small to big
• The questions I wrote for this reading are less about testing you and more about offering a pathway along the main thread of the chapter
• molecules are made of atoms, or of smaller groups of atoms
• polymers are made of monomers: proteins and nucleic acids
• Huge amount of detail about DNA
• let's review the basics about DNA, nucleic acids, RNA, amino acids, and proteins
• nucleic acids and proteins - more of a partnership than a command relationship
• don't need to know all the detail for our purposes, though it's all worth knowing.
• Look out for: association and dissociation.
• On from there to bigger things - ribosomes and chromosomes
• How they're put together out of smaller things
• How genes appear in the DNA. Why genes are sometimes linked, and pass to offspring together.
• Note - talk about recombination to make sense of this
• They also are likely to be "switched off and on" together.
• Cell boundaries.
• Viruses illustrate what happens when you don't have a cell boundary with friendly liquid inside
• Viruses show that nucleic acids and proteins aren't enough on their own.
• This part is interesting to compare with the Knowledge reading, because it also talks about the importance of the cell membrane
• The insides of cells are necessary for themselves and for viruses.
• In there is a watery zone where energy conversions can happen.
• "Both the bounding of cytoplasm, and the energy conversions within it, involve . . . the water-excluding "lipids" and the water-incorporating "carbohydrates"".
• Prokaryotic cells have less complex boundaries, eukaryotic cells are more complex
• lots of detail about organelles here
• some organelles were probably once separate organisms that became integrated into eukaryotic cells: endosymbiosis.
• Therefore euk. cells, like DNA, are "parcels of parcels".
• cell membranes are not completely closed: they allow some information and material in and out. "They are partial boundaries which serve to maintain a balance between the opening up and sealing off of communication channels."
• membranes can break and reseal (dissociate and reassociate) to enclose or eject things
• All the parts are associated into the cell.
• Chapter 2 of Knowledge, see below
• Ideas for investigations?
• Talk about proposals next week, collect proposals the week after.

### To do for Sept. 5

• Grade and return people's Chapter 1 homework
• Or, write up my answers to the questions, anyway.
• Write questions for chapter 2 ✓
• Get a video together?
• Plan discussion
• Prepare preteaching for chapter 2

just before

• bring these plastic bags that got separated from the mushroom kits
• Print the questions for next time.
• Print copies of the marble section.
• Print some copies of the vocab list.

### Notes on Freedom chapter 2

Scaling Hierarchies: Individuals and Collectives from Molecules to Communities

• 1. Before Beginning
• we're not discrete - dynamic interplay between association and dissociation - "no individual entity can have complete freedom"
• recurs: happens more than once
• no clear boundaries $\to$ no clear origin moment of life
• clear moment of origin - a "fundamental reductionist assumption" - why is this?
• sub-atomic: smaller than atoms
• Therefore he won't start at the "beginning" or at the "bottom". We'll start at molecules and go up to the social.
• 2. Molecular assembly and disassembly
• nucleic acids and proteins - more of a partnership than a command relationship
• genetic: involved with genes
• genes: the information stored in DNA molecules, which is copied from parents to children
• compounds: kinds of molecules
• innumerable: too many to count
• treatise: a long, formal scholarly text
• euphoria: great happiness
• elucidation: explanation
• envisage: imagine
• twenty-six characters: twenty-six letters
• heredity: passing qualities faithfully from parents to children
• "primer": something that gets things ready before a process starts.
• 3. Assembling molecular assemblies - ribosomes and chromosomes
• refers to: nucleic acids; eukaryotes;
• nucleoproteins - nucleic acids and proteins combined!
• ribosome is an example
• DNA in chromosomes is coiled up several times over (rubber band analogy)
• why no mention of what ribosomes do?
• 4. Genes and supergenes
• refers to: chromosomes, DNA, genes, introns (in 1st paragraph), polypeptide
• particulate: complete and never broken apart
• defies: resists
• en bloc: all moving together
• translatable: can be translated
• Individuals have fuzzy boundaries, but maybe genes are really particulate? no.
• Genes close together on a single chromosome are linked, and pass to offspring together.
• Note - talk about recombination to make sense of this
• They also are likely to be "switched off and on" together.
• 'multimeric: ???
• 'antibodies: proteins that fight off germs and other things from the outside world
• disparate: different from each other
• complementary: different and helpful to each other
• Also, in order for genes to work, they need to be enclosed within the cell.
• arena: an enclosed space where things can happen
• 5. Becoming Insulated - Forming Cell Boundaries
• Viruses show that nucleic acids and proteins aren't enough on their own.
• proliferation: producing many copies
• polyhedral: many-sided
• subunits: parts of units
• lipoprotein: a combination of oils and proteins
• The insides of cells are necessary for themselves and for viruses.
• In there is a watery zone where energy conversions can happen.
• "Both the bounding of cytoplasm, and the energy conversions within it, involve . . . the water-excluding "lipids" and the water-incorporating "carbohydrates"".
• Prokaryotic cells have less complex boundaries, eukaryotic cells are more complex
• get definitions of these terms. "eukaryotic" implies nucleus???
• lots of detail about organelles here
• some organelles were probably once separate organisms that became integrated into eukaryotic cells: endosymbiosis.
• Therefore euk. cells, like DNA, are "parcels of parcels".
• cell membranes are not completely closed: they allow some information and material in and out. "They are partial boundaries which serve to maintain a balance between the opening up and sealing off of communication channels."
• the general membrane ("bilayer" of phospholipids) lets some things through: water, oxygen, CO2, alcohol
• there are also proteins here and there in the membrane that let particular things through. some do "active transport" in one direction.
• solutes: things that are dissolved in water
• they have a strategy involving ions' charges to get resources to flow in to the cell.
• cells use their stored energy to collect things from the environment that provide energy.
• like an engine that burns fuel to drive around and collect more fuel
• it can keep itself going, but how does it get started?
• "fuel" here is a different concentration inside than outside
• form a bubble in a salty puddle; then use the saltiness when the puddle gets less salty
• membranes can break and reseal (dissociate and reassociate) to enclose or eject things
• ingest: eat
• cell walls may need to be strong to resist the problem of osmosis.
• many fungal cell walls use chitin rather than cellulose -- like insects!
• permeability: whether things can flow through or not
• tensile strength: resistance to stretching
• matrix: surrounding substance
• composite: something made by combining several things

### Notes on Knowledge chapter 2

"The Organization of Living Things"

• (untitled opening section)
• nervous system
• A brief history of the earth
• first step: how materiality of living beings can serve as a guide to how living beings appear.
• scale of galaxy: light years
• equilibrium between cohesion due to gravity and radiation due to thermonuclear reactions in former star?? what?
• "main sequence" of stars - fill out details of this
• diversification of molecular species and molecular homogeneity
• morphologic and chemical diversity of organic molecules
• The emergence of living beings
• Living beings: networks of molecular reactions that produce the same types of molecules that they embody, while at the same time they set the boundaries of the space in which they are formed. - "produce themselves and set their own limits"
• "Fossil of a living being"
• Make an observation; then say there is some thing (globules); observe similarity to living beings today. Old living beings must look like living beings today?
• What is criterion for identifying a living being?
• Chemical makeup, or motion, or reproduction, or some combination? or its organization?
• Organization: relations that must be present in order for something to exist. "Chair": its organization is the relation between legs, back, and seat that makes sitting down possible. "good deed": is a particular relation between an action and its consequences
• living beings? "They are continually self-producing": autopoietic organization.
• "Autopoietic": "self-creating". This means that what its parts are doing is creating those very parts themselves. This is the particular kind of organization that living things have, and other things do not.
• Autopoietic unity
• molecular components related in network of ongoing interactions - cell metabolism
• It produces its own parts
• Some of those parts are the membrane: keeps the parts together and the outside out, making the metabolism possible
• metabolism and membrane make each other possible
• neither is before the other, you can break it by breaking either.
• Structure is the material parts that make up the object, and their relations; Organization is the relationships that must exist among the components of a system for it to be a member of a specific class.
• what can you do to the chair and preserve its organization, .. and not preserve its organization
• Belonging to a certain class means being a certain kind of thing (a chair, a good deed, a living thing). Belonging to "the class of chairs", etc.
• Distinctions and Unities: Talking about a good deed, a living being, etc. means making a distinction between that thing and everything else. Making a distinction creates a unity (a thing). A unity requires a distinction and vice versa
• write a sentence, what does it say negatively: "I put on a red shoe" => not green, not a boot, etc. - those are distinctions it makes - and what dist. does it not make.
• An autopoietic unity embodies a distinction. The membrane has something to do with this.
• Autonomy and autopoiesis
• One of the most obvious things about living beings is that they are autonomous: means "it can specify its own laws, what is proper to it" (which means what? that its organization, ways of living, structure, boundaries aren't imposed from somewhere else, I guess)
• M+V say that it's autopoiesis that makes them autonomous.
• plastic: flexible, bendy
• pliancy: things that are easy to move, shape, use in various ways are "pliant"; they have "pliancy".
• sizable: big
• demarcation: dividing a region of space from its surroundings
• therein: in that place
• operationally: in what it does
• Molecules from silicon layers are too rigid -- I think they mention this because silicon layers are things like clay, that were probably common in the early days of the earth
• terrestrial: on the planet Earth
• intracellular: inside the cell
• ribosomes, nucleus, mitochondria, endoplasmic reticulum: parts of an animal cell
• nuclear membrane: membrane of the nucleus
• phenomenology: study of phenomena, in other words explaining things that happen
• The history of a thing ("formation of a unity") explains a lot of its nature ("phenomenology")
• emergence: coming into being
• "Biological" things (or phenomenology) are things that involve autopoietic unities
• if a cell does something with molecule X, it's not determined by the properties of X but by how it is "seen" by the cell. What happens as a result of X is a result of the cell's structure as a unity.

## Week 3: Sept. 12

• Degrees of Freedom:
• 2. Scaling hierarchies: individuals and collectives from molecules to communities sections 1-5
• Tree of Knowledge:
• 2. The Organization of Living Things (22pp)

### To do

• Print lecture notes
• Print HW to hand out
• Print word lists (enough copies this time)
• Print Investigation handouts
• Fill in the TODO sections in the lecture notes
• Think of some good questions before class, review what people wrote

### Lecture notes

• explain how I'm scoring the questions from 11 to 5, etc.
• i.e. multiply by 5/11 and round to the nearest whole number.
• If late, divide in half and round up.
• Should I stop collecting the homework in advance?
• Cellular slime mold video? prob. not, I have Know your Mushrooms documentary.
• Questions!
• ToK: Unity; structure; organization; autopoiesis; biologic phenomenology
• distinctions

### Notes on Freedom, Chapter 2, sections 6-8

6. Gathering Cells.

• Some microbes (e.g. protists) live well on their own, Paramecium and Euglena for example.
• Euglena is good at ingestion, locomotion, and photosynthesis - like a plant/animal!
• A few words about taxonomy
• TODO: The kingdoms
• TODO: The meaning of capitalized names with/without italics.
• Also latin "um" and "a"
• All living things proliferate; if they don't disperse they associate. So it's not exactly hard work to associate.
• Simplest assoc., colonies - of things that could live apart
• continuous gradation all the way to multicellular organizations - no clear dividing line
• slime bacteria and cellular slime molds are like the best examples anywhere, I don't care of what.
• ephemeral association
• actinomycetes (?) and true fungi
• mycelium - can be a single big membrane with many genomes inside
• slime trails - mazelike tubes with cells traveling inside
• Are they colonies? But they have division of labor
• Are the multicellular organisms? They're not even multicellular!
• Even the definition of a cell can be challenged by true slime moulds' plasmodium (which is like The Blob, smaller)
• ("pulsating, multinucleate, slimy masses of protoplasm known as plasmodia that ooze around consuming bacteria or fungi before settling down to produce a fruit body")
• To be a single organism, an assemblage should generally have some overall integration and coordination. There's no clear division between associations that do and don't have those things either.
• Example: some algae in long filaments that are more or less the sum of parts, but some have some division of labour with reproductive cells and anchoring cells.
• Volvocales make spherical colonies, with more or less specialization and coordination.
• Blue-green algae can make filaments or clusters, some with specialization.
• Sponges are similar but are considered animals. Five cell types, a hollow inner cavity where water passes through.
• sea squirts get together and share internal cavities and blood-circulation systems!
• Sponges can be passed through cheesecloth and reassociate into a functional sponge within a few weeks.
• So maybe they're colonies. (So gatherings of sponges are colonies of colonies of cells.)
• "True" multicellularity: jellyfish, et al.
• they have layers of tissue, a nervous system, an inner cavity.
• "polyps" or "medusae": two variations of the same form. stationary vs. swimming by squirting water.
• Next: partitioning into different regions, even organs. Organization into multiple systems of tissues "becomes paramount if behaviour and development are to be considered."

7. Societies of Multicellular Organisms.

• It's also hard to distinguish among gatherings, colonies, and societies of complex organisms.
• Society: division of labour, communication
• Extreme cases: "superorganism"
• Organisms may proliferate and fail to disperse, or be attracted, or be surrounded by a barrier
• Simple: just pile up in place as "modules"
• but the system generates a boundary and constrains itself, developing into an entity per se...
• sea mats, "zooids" live in sort of housing developments, some have specialization, some colony defenders, some cleaners
• Some Bryozoan colonies are a bit more social, and some can sort of walk around the bottom of the sea
• hydroids and corals are more like mycelia, but some "free-floating 'siphonophores'" have something like organs
• hydroids are polyps with stolons, which are like hyphae or rhizomes. "Hydrorhiza"
• siphonophores are communities of multiple kinds of organisms. Includes Portuguese man-of-war, which can sting and kill swimming humans.
• Also Muggiaea which is either a colony of colonies or a superorganism of superorganisms. Parts of it are parcels that can detach and live on their own.
• stony corals live in large colonies of polyps with a hard base, and a shared gastrovascular cavity
• Now on from Cnidaria, with radial symmetry, to organisms with bilateral symmetry.
• Flatworms can be cut into pieces and regenerate. Each segment is fully able to reproduce. It's very similar to filamentous colonies, but commonly considered an individual.
• In other animals (including ourselves), the segments differentiate more.
• Some insects associate into complex societies that may be as coherent as ours.
• In insect societies and others, more social seems to = less self-sufficient. Individuals lose some powers.
• Many different societies, from Cnidaria to insects, seem to differentiate into reproductive, feeding, and protective functions (breeding, worker, and soldier ants).
• In many insects, the males only do the reproductive function (along with the Queen). For this reason, the whole colony is closely related.
• Similarly in troops of baboons, etc.
• Boundaries between these groupings are maintained by external constraints and by aggression.
• This is a form of non-self rejection that appears at all levels of organization where integration is a possibility (see Ch. 7).
• Human societies sometimes suppress the rejection behavior and have more mobility, allowing more diverse groupings to form. Tension arises as a result. Recorded knowledge (culture) is key to addressing this. However, communication of this knowledge requires integration (and lack of competition) though not disappearance of boundaries.

8. Partnerships and Communities.

• Unrelated, different organisms form mutualisms and communities.
• Mutualisms are very common and important.
• Most "higher plants" have mycorrhizal relationships with fungi. Mycorrhizae help plants collect resources in exchange for the products of photosynthesis. They can help plants feed their offspring and even out uptake of nutrients (and convey information?). Some plants can pirate mycorrhizal networks and "steal" nutrients.
• Some plants also partner with bacteria, blue-green bacteria, and actinomycetes that fix nitrogen.
• Where plants don't grow, lichens grow: a "sandwich" of green algae or blue-green bacteria between fungus. Lichens are very good in environmental extremes but vulnerable to pollution.
• Most animals have microorganisms and protists (?) as associates in our guts - whole communities with complementary, essential digestive functions.
• Some insects have digestive associates outside their bodies - they farm fungi for both food and enzymes to process cellulose
• reef-building corals have photosynthesizing protists in their tissues for mutual benefit - thus they can't go too deep where it's dark
• More ephemeral interactions are also important
• Predation in food webs is obviously a setback for the prey, but can also keep their population stable, help recycle their nutrients into later generations, and disperse their seeds.
• Competition leads to establishment and breaching of boundaries. When associations of sessile organisms run into one another's boundaries, for instance, see the fascinating photo of mycelial community inside a log. This illustrates "the dynamic processes underlying the evolution of contextual boundaries."

### Notes on Knowledge Chapter 3

History: Reproduction and Heredity

• we take on these subjects now for two reasons
• As living beings we are descended from a common ancestor
• As multicellular beings, all of our cells are descended from a single fertilized egg cell.
• Oddly, we and our cells have the same "ancestral age"
• Historical phenomena: whenever a system's state arises as a modification of a previous state

• A cell can originate another cell through division
• Mitosis: a cell rearranges its parts, creating a "plane of division", then divides into two complete cells.
• Reproduction: one unity, by some specific process, gives origin to another unity of the same class.
• requires two things: the unity, and the process.
• Note, class defined by organization.
• In this account, reproduction is not an essential quality of living beings, autopoiesis is. Reproduction is something that they sometimes do.
• This chapter: how the structural dynamics of an autopoietic unity becomes complicated in the process of reproducing, and the consequences of this in the history of living beings.
• This complication affects structural dynamics, not the essential characteristics of the unity, which are organizational.
• Organization and history: We can understand a system's dynamics by looking at its structure and revealing its organization. But to fully understand it we need to reveal its context, including its origin.

Modes of Generating Unities

• Replication: is when something can repeatedly generate unities of a given class. A car factory, for instance.
• Cells contain various "factories" producing proteins and such.
• The productive mechanism and the product are "operationally different".
• This is not a historical system, because each car produced is independent of the others, not a modification of the previous one.
• Copy: When we have a procedure for generating a unity from a previous one. For example, using a photocopier.
• Not historically connected if you keep copying the same original.
• But if you make copies of the copies, it is historical. A change to one is carried forward.
• Anamorphosis in art is an example.
• historical drift.
• Reproduction: when a unity fractures into two unities of the same class.
• examples: chalk or grapes.
• In order for this fracture to work, the structure of the unity has to be distributed so that it's all in both pieces.
• mirrors, sticks, communities, and roads can reproduce.
• radios, coins, persons, a declaration of human rights can not.
• "There is no separation between the reproducing system and the reproduced system."
• The products have the same organization but not the same structure - they are smaller, and may have different proportions of parts.
• They are historically connected.

Cell Reproduction.

• Most of the time (i.e. during interphase), fracturing a cell just destroys it.
• parts are segregated into particular places. DNA in particular is all bundled up in the nucleus.
• During mitosis, the cell decompartmentalizes its parts.
• Nuclear membrane dissolves, chromosomes get pulled apart to two sides of the cell. A plane of fracture is created.
• This is a part of autopoiesis, not an interruption of it.
• The dynamics of the cell leads to structural changes, ultimately cleavage.
• it is simpler in prokaryotes
• Either way, it's not caused by an outside event. It's a special kind of reproduction: self-reproduction.

Reproductive Heredity.

• In any historical series there is heredity: "structural configurations proper to a member of one series that reappear in the following member"
• Some things do not change throughout the series: "certain black-and-white relations in the letters"; the autopoietic organization
• In reproduction, there will always be some permanence of structural configurations because the old unity was distributed and fractured into new unities of the same class.
• organization is conserved and there is structural variation.
• things that stay the same are heredity and things that change are variation.
• each unity begins "with structural similarities and differences to its forebears"; its subsequent history will conserve some and lose some
• Heredity with variation is proper to reproduction; self-reproduction of living beings is a special case.
• Some parts of cells are especially conserved; DNA for instance
• some things are conserved a long time, like the basic mode of production of proteins; while some things change in just a few generations, like precisely which proteins are made.
• genetic means something similar to hereditary. There are multiple sites of heredity, not just nuclear DNA but also mitochondrial DNA, and the membrane.
• The Notion of Genetic Information. It is not true that genes contain the "information" that specifies a living being.
1. heredity is more general than replication of DNA molecules
2. The rest of the cellular machinery is also needed to construct the being.
• Does the constitution determine a country's history? No. It's very important, but other things also participate in determining the course of history.

### Glossary

Freedom sections 6-8

locomotion: moving oneself from place to place.  Generally done by animals.
photosynthesis: making energy from light.  Generally done by plants and blue-green algae.
apically: at the top or tip.
radiately branching: branching outward from a center point.
elongation: becoming longer
linear: like a straight line
heterogeneous: made up of parts that are different from one another
basal: at the base
algal: involving algae
gelatinous: sticky and squishy, like gelatin dessert
photosynthetic cells: cells that do photosynthesis
spherical: round like a sphere, or ball
chloroplast: organelle that does photosynthesis
flagellum: whip-like "tail" structure that some cells use to swim through water.  More than one flagellum is called flagella.
mucilaginous: similar to gelatinous but maybe a little sticker and less solid.
biflagellate: having two flagella
protoplasmic: involving cellular fluid
contractile: shrinking or squeezing
enfolding: folding within
paramount: most important

shoal: a large number of fish swimming together (also, a sandbar creating a shallow area of water).
module: a self-contained part of a system, often interchangeable with other modules.
frond: a large, divided leaf, like on a fern or palm tree
chitinous: made of chitin, a substance used in insects' shells and some fungal cells
calcium carbonate: mineral that makes up chalk and many sea shells.
impregnated: containing throughout
encrustation: crust
octocorralian: corals with 8-way symmetry
motile: able to move from place to place
tubular: tube-shaped
stolon: a horizontal connection between organisms
corrugated: shaped into parallel ridges
articulation: bending
colonial: making up a colony
ramify: extend oneself
mesogloea: some kind of thick liquid
functional specialization: having different roles
tackle: fishing equipment
zoids: zooids (see p. 55)
nuptial: marriage
parasitic: living on others' resources
fertilized egg: an egg cell that has combined with a sperm cell
consorts: is partner of
territorial: involving territory, the land that an individual or group controls
aggression: fighting or acting like fighting
mobility: ability to move
transcend: rise above

disparate: separate and different
symbiosis: a close association between two different organisms. symbioses: more than one symbiosis
embattled: caught up in fighting
deciduous trees: trees that shed their leaves each fall
beech: one kind of deciduous tree
deciduous woodland: a forest of deciduous trees
cross section: a cut across
longitudinal section: a cut along the length
intervening: in between
mosaic: art made by assembling different pieces side by side
peripheral: on the boundary
relic: something left from the past
rubbish: garbage
umbilical cord: the cord that delivers food to a mother's offspring within the mother's body
piratized: attacked by pirates
cellulose: the tough part of wood


Knowledge Chapter 3

forebears: ancestors. Parents, grandparents, etc.
ovule: egg cell
valid: good reasoning
mechanism: something made up of mechanical parts that work together
replicas: exact imitations of an original object
imperturbably: without being disturbed by anything
Xerox machine: copy machine
distinguish: to make a distinction (see chapter 2)
anamorphosis: see Figure 16.
fracture: breaking into pieces
compartmentalized: divided into separate areas
noncompartmentalized: not compartmentalized
incapacity: lack of capacity. being unable.
preexist: exist before
decompartmentalization: becoming noncompartmentalized.
dissolution: melting into the surrounding liquid
displacement: moving from their original places
cleavage: splitting into two parts
intricate: complex
exquisite: beautiful, excellent
compartmentalization: becoming compartmentalized.
fragmentation: breaking into many pieces
lineage: chain of ancestry, from parent to child to child's child, etc.
succession: series of replacements
invalidate: make wrong
conserves: keeps the same
transgenerational: across different generations
ontogeny: creation and development of a thing ("onto" means "thing", "gen" is create, as in "generate" or "genesis")
divest of: take away from


## Week 4: Sept. 19

• Degrees of Freedom:
• 2. Scaling hierarchies: individuals and collectives from molecules to communities sections 6-8
• Tree of Knowledge:
• 3. History: Reproduction and Heredity (18pp)
• Q: Mycelia have one big membrane with a bunch of genomes floating around inside. This challenges the idea of cells, let alone any clear distinction between colonies and organisms. Does it make trouble for the idea of an autopoietic unity?

### Lecture notes

• Investigations, what are people doing?
• We'll present them on Oct. 10.
• There is no midterm! Isn't that what it says on the syllabus?
• Present whatever I've got about biochemistry
• And autonomy
• Wikipedia says: Maturana's inspiration for his work in cognition came while he was a medical student and became seriously ill with tuberculosis. Confined in a sanatorium with very little to read, he spent time reflecting on his condition and the nature of life. What he came to realize was "that what was peculiar to living systems was that they were discrete autonomous entities such that all the processes that they lived, they lived in reference to themselves ... whether a dog bites me or doesn't bite me, it is doing something that has to do with itself." This paradigm of autonomy formed the basis of his studies and work.
• Randy Whitaker provides this: [Autonomous systems are] "...defined as a composite unity by a network of interactions of components that
• (i) through their interactions recursively regenerate the network of interactions that produced them, and
• (ii) realize the network as a unity in the space in which the components exist by constituting and specifying the unity's boundaries as a cleavage from the background..."
• So we have 3 related concepts: autopoiesis, autonomy, and organizational closure. The latter two more general than autopoiesis, and strongly overlapping.
• Both these books are written to challenge the orthodox scientific story. But if this is the only college science class you take, how do you know what the orthodoxy is?
• More about evolution, genes, and central controllers
• Neurons, brains, and computers
• Again: Go see Ignacio talk on Friday!
• Present the upcoming reading (below).

### To do before class

• Separate the HW answers from the questions
• Print the HW assignment
• Find good material on basic cell biology
• Look into the autonomy question
• TODOs:
• Boundaries and marbles
• Actinomycetes, myxomycetes
• A rundown about natural selection dogma and genes as controllers
• A better picture of a fairy ring
• Second half of Know Your Mushrooms
• print HW answers that didn't print at home

### Notes on Freedom, chapter 3

Chapter 3. Determinacy and Indeterminacy.
1. Immortality and the Question of Growth or Reproduction
• Living things lose some resources and inevitably need to gather more.
• Immortality is impossible, but renewal is possible as long as you can increase and change (proliferate).
• to Aquinas, angels were perfect because they never change and don't reproduce
• reproduction was a necessary evil for us because we don't have absolute boundaries
• but absolute boundaries would mean a static, motionless universe! no fun!
• proliferation has two faces: growth and reproduction
• but like everything else in this book, the boundary between the two can become indistinct
• proliferation within a contextual boundary: growth
• proliferation with separation of boundaries: reproduction
• reproduction is multiplication and division, paradoxically
• proliferation of cells on a surface is reproduction of cells and growth of the colony at the same time
• or within a multicellular organism
• the distinction between reproduction and growth depends on where we draw the boundary of the system
• TODO: connect this to the jar of marbles in Chapter 1. Do we consider an "object" within an arena, or a "subject" - the arena itself?
• if a living system has a boundary that can grow and stretch, we say it is indeterminate.
• It is potentially immortal.
• Can include death of parts together with production of new parts. Example: tree shedding yellow leaves in fall.
• We have a powerful attraction to indeterminacy in family, society... attachment to unconstrained economic growth.
• and yet we have a strong need to assert our individuality: the determinate boundary separating us from each other. Ideology of competition and individualism.
• "The central problem for us human beings, as self-conscious individuals, is that we epitomize determinacy".
• We have a well-bounded body. We can't be in two places at once, and we die after a fixed time.
• We can't change our body's boundaries.
• Snakes and worms can get longer, but they are more modular than indeterminate.
• Since our life span is fixed, we have to reproduce in order to persist.
• This may be related to our ability to move around and ingest food.
• On the other hand, many plants, fungi, etc. are indeterminate and can stay in one place and receive resources. They can potentially grow indefinitely, and can reproduce but don't have to.
• TODO: what exactly are actinomycetes?
• actinomycetes are now called actinobacteria, because they've been reclassified as bacteria. They form a mycelium. Wikipedia says they produce the peculiar odor of soil after a rain.
• myxomycetes are apparently part of the kingdom Amoebozoa. They are a kind of slime mould and produce aggregate sluglike forms and fruiting bodies.
• In "discrete" determinate individuals, natural selection is understood to be the only way of adapting over time. Development is thought to be predetermined by genes (this seems a bit overstated)
• TODO: teach some more about natural selection and the mainstream dogma about genes (at least Dawkins' robot vehicles)
• This makes determinate individuals defined by the genes from their parents. Their genes either drive them to success or not.
• We apply the same model to other living systems.
• Organizations should have central controllers (administrations).
• But indeterminate systems aren't like that. And all life forms are indeterminate on certain scales.
• Also, of course, there's no absolute boundary between determinate and indeterminate life forms.
• Discrete animals leave spreading tracks that can be followed on the landscape
• and have indeterminate growth of veins, nerves, etc. within our bodies
• the life of any dynamic system requires both collective and individual action
• individuals need to "buck the system" to expand it at the boundary
• but they need to integrate to distribute resources to keep the whole sustainable
• "The continuous mainstream of life flows through a context of indeterminate channels from which relatively discrete and specialized forms emerge as temporary, determinate offshoots, only to be resorbed when they die"
• So what can we add to our understanding about organization and evolution of living systems by understanding indeterminacy.
2. Indeterminacy and Fluid Dynamics
• these indeterminate living systems are like 'interactive "fields" - analogous to solidifying fluids"
• They are shaped by their surroundings
• influenced by genes but not controlled by them
• thus can be responsive to changing environment, not pre-determined
• four issues to be addressed
• 1. "fundamental organizational attributes of dynamic fields" (in this chapter)
• 2. "the various guises in which indeterminacy manifests itself in living systems" (in this chapter)
• 3. how these patterns are influenced by feedback processes (chapter 4)
• 4. how feedback processes work in individual cases (chapter 5)
3. General properties of fluid-dynamical systems
• Counteraction of expansive and resistive processes
• as the system becomes bigger it tends to expand outward.
• but the parts also tend to stick to each other, as in surface tension or cooling lava
• river system example
• distinction between sites of assimilation - taking in material - and distribution - putting it somewhere else - and a channel inbetween.
• because of irregularities in the landscape, the water "chooses" certain channels, and reinforces them.
• headward erosion at assimilative end
• formation of a delta at distributive end
• if the slope isn't steep, meanders in the rivercourse
• we'll continue with the water examples for a few more sections
3.1 Developing Polarity
• Pour water into a pile of sand.
• First, a round puddle expands outward isotropically.
• But then the forces build up - water pushing outward, sand pushing inward. The boundary gives way at a crisis point or several.
• Then expansion happens only in apically extending rivulets. The central pool may even shrink.
• It has broken it symmetry and developed a polarity.
• Define polarity for the students
3.2 Rippling and branching
• If you block a stream with a boulder, it will flow around it while deforming into waves or ripples
• If you dam it with a pile of sand, it will break through in certain places, forming branches like in a river delta.
• These will be narrow-angled.
• If there's too much supply at the head of a stream, there will be headward-eroding, wide-angled branches.
3.3 Coalescence, anastomosis and networking
• separate fluid systems may meet and combine. Two expanding puddles can become a dumbbell shape
• or it can happen among branches. anastomosis is branches joining, forming networks.
• Define fasciation for students: tube shape stretches into a ribbon shape
• When they join, they have less surface area but just as much volume. This means they're more likely to reach thresholds and branch.
• they will pool if they're equal. If one is lower, or flows more quickly, the other one will just dump into it.
• example: raindrops flowing down a window.
3.4 Scale shifts and degeneracy
• when a branching system becomes a network, flow is so much easier that it may abandon a lot of peripheral channels.
• Explain the idea of a sink
• Like the loop freeway around DC, it just soaks up flow and doesn't help it get distributed evenly.
• mention that this logic isn't really clear to me
• networks are prone to gridlock and failure to expand on the boundary
• but when there is an outlet, they can deliver a powerful amount of flow
• but even with outlets, as the system grows, it becomes less prone to flow outwards.
4. Indeterminacy in varied guises
• those things can happen in various physical systems. The examples of fluid flow shouldn't be taken too literally.
4.1 Developmental indeterminacy in organisms (and parts of organisms) that branch
• Developmental indeterminacy: indeterminacy in the expansion of the organism's body boundaries
• every organism begins as a zygote, a single totipotent cell - it can birth all the different kinds of cells that the organism will have.
• But then the descendant cells become determined, or committed. They are of one cell type, and their descendants will be the same
• the process is more indeterminate when this is delayed.
• relatively indeterminate systems tend to form polarized, branching structures: hyphae, blood systems, etc.
• branches can integrate into networks - nervous system for example
• Then they can have degenerative processes - collecting into subnetworks, abandoning the core, etc.
• Fungal examples.
• Discuss figure 3.2 in class (the grid of fungus).
• Hard to see the difference between squares. I guess it's more fanned out in some squares, more reaching across other squares. Hard to see, though.
• Discuss figure 3.3 in class (the two blocks).
• The hyphae branch out from the first block, then focus in on the second block and abandon other branches. Channel nutrients back from new site to old site, and fan out from the new site.
• This will be important if we plant mushrooms in the meadow. They grow differently depending on whether the medium is nutrient-rich.
• Figure 3.4: fairy rings. Kind of hard to see clearly. Why not a picture of a complete ring?
• Expanding into territory and adapting to local conditions is well suited to indeterminate development.
• But photosynthesizing, eating objects, reproducing are well suited to determinate forms, so many creatures combine the two.
• Fungal fruiting bodies, plants with leaves, flowers, and fruits. Nervous system with sense organs?
4.2 Social indeterminacy in nomads and settlements
• Determinate but motile organisms can form branching pathways and reuse them
• examples: ants' pheromone trails, wildebeest pathways during Serengeti migration. Patterns very similar to mycelia and river basins.
• some ants and humans oscillate between stationary and nomadic phases
• When the food runs low, the ants form a sort of avalanche that drags them all along and they uproot to a new place.
• Various kinds of undifferentiated flocks, slime mould bodies, etc.
• or differentiated units, like Portuguese man-of-war, etc.
• Selfish explanation for herd formation?
• new suggestions: they "shimmer and fenestrate" to confuse predators
• predators become good at herding, "irrigational engineering"
• We have a need to channel flows of crowds and traffic similarly, not to mention water
• animals may also flock because they lose some self-sufficiency. Self-sufficiency and solitude seem to go together; living in common with abandoning some abilities.
• Herbivores tend toward panoramic vision, to look out for predators. Carnivores tend to binocular vision, to locate prey.
• So herbivores have trouble pinpointing the predators. Being in a group may help with that.
• being part of a herd entails yielding and "going with the flow". Sense of relaxing into the group, or gazing at the sea or snowflakes - relaxation.
4.3 Phylogenetic indeterminacy and evolutionary trees
• The "tree of life" is actually more of an anastomosed network, due to symbiosis and horizontal gene transfer.
4.4 Mental indeterminacy in learning and problem solving
• Does unconscious = innate and conscious = adaptible?
• One would think not, but surely it's a mistake that gets made.
• anyway, humans do a lot of conscious learning, so we can change in response to our environment
• Our consciousness is indeterminate, a possible source of "free will" and individual responsibility.
• "streams of consciousness" and "lateral thinking".
• We take on an unfamiliar problem something like a foraging mycelium. Radiate out in various directions, then concentrate more attention on places that seem like good channels. "water logic".
• Other problems have clear, step-by-step solutions and we just apply them.
• Corresponding to two approaches to developing problem-solving skills: training (giving step-by-step skills) and education (giving problem-foraging skills).
• Also, learning something by practice, like riding a bicycle, is reinforcing mental boundaries, creating a "rut".
• re-learning - breaking down old boundaries

### Notes on Knowledge chapter 4

4 The Life of Metacellulars
• Ontogeny: history of structural change in a unity without loss of organization in that unity, i.e. history of an organism during its lifetime.
• its structure is always changing, either triggered by outside events or by internal dynamics
• it classifies and sees interactions with its environment according to its structure
• its structure continually changes because of its internal dynamics
• introduction of little loop diagram.
• what about the ontogeny of multiple neighboring unities?
• multiple-loop diagram
Structural coupling
• Either of the neighboring unities experiences the other as part of its environment
• their ontogenies are coupled when their interactions are recurrent and take on some stability, predictability
• recurrent interactions between unity, environment consist of reciprocal perturbations.
• environment does not specify or direct, but triggers structural changes in a-p unities
• likewise unities trigger changes in the environment
• as long as the unity and its surroundings do not disintegrate there will be a history of mutual congruent structural changes: known as structural coupling.
• or, structural coupling is a history of recurrent interactions leading to the structural congruence between two (or more) systems.
• example of a particularly recurrent interaction: cell constantly soaking up sodium or calcium ions via active transport. If it encountered cesium or lithium ions, it would soak them up and die.
• Why does the unity encounter recurrent interactions that participate in autopoiesis and not others?
• answer involves history of its lineage (phylogeny of the cellular strain): natural drift of the lineage with preservation of structural coupling of previous unities. that is, its ancestors are all cells that were compatible with the environment. they soaked up calcium and sodium, not other things.
• structural coupling with the medium is a condition of existence: this applies to all the cell's interactions.
• including interactions with other cells. In a multicellular body the surrounding medium generally is the other cells.
• consider myxomycetes: Physarum and Dicostelium
• Physarum: spore stage becomes either a motile cell with flagellum, or an amoeba. They divide, fuse together into a plasmodium, and then a fruiting body which disperses spores.
• close cellular aggregation leads to creation of a new unity: fruiting body. Formed by cellular fusion, not aggregation. It's a metacellular unit.
• Metacellular units that can reproduce through single cells have a different phenomenology than the cells that make them up do.
• They are second-order unities - things made up of first-order unities.
• Dicostelium: the cycle is similar, but the cells do not fuse; they aggregate and perform a division of labor. Some cells become part of the dead stalk of the fruit, and others go to the top and produce spores.
• The structural changes that each cell undergoes in its history of interactions with other cells are complementary to each other, within the constraints of their participation in the metacellular unity
• different cells, different ontogenies, depending on their role in the unity, through their interactions and neighboring relations.
Life cycles
• Aggregation into a metacellular is consistent with each cell's autopoiesis.
• for those cells that do it, it has a profound impact on their phylogenetic histories.
• The life of a multicellular is determined by its interactions and structure as a whole, not by its individual cells.
• But each one starts as a single cell. Apparently this is logically necessary.
• The metacellular's ontogeny starts unicellular and goes on as metacellular, but reproduction occurs as a unicellular unity.
• So the phylogeny is still a phylogeny of single cells. So multicellularity doesn't change anything in a sense.
• reproduction is still like in chapter 3, even when sexual: sperm and egg fuse, forming unicellular zygote; zygote fractures.
• There are also multicellulars that fracture as a whole: same story but happening to the organism rather than the cell.
• The consequences of sexual reproduction are seen in the rich structural recombination that results from it.
• genetics and heredity are enriched by this addition of variation
• which makes phylogenetic drift possible, see next chapter.
Tempo of transformations
• Comparing various things' sizes and duration of life cycles.
• myxomycete, frog, sequoia, blue whale.
• Bigger things take longer to grow and die.
• The same stages: initial cell; production of a metacellular; growth and whatever; production of a new zygote.
• The cycle is both conserved and transformed in time.
• Formation of second-order individuals takes time; so the generations will be less frequent.
• multicellulars have a lot in common, just as cells do.
• reproduction as a single cell.
• with plenty of structural variation, but variation around a single type.
• every variation in structure results in different ways of being in the world, because it is the structure of the unity that determines its interactions and the world it lives in.
• Metacellularity and the nervous system
• You can't understand how the nervous system works without understanding where the nervous system works.
The organization of metacellulars
• A definition! Metacellular: any unity in whose structure we can distinguish cell aggregates in close coupling.
• It is found in all five kingdoms.
• Metacellulars, being made up of cells, are second-order autopoietic systems.
• But what is their organization? Are they autopoietic unities in their own right?
• we don't know, because we don't know in detail the molecular processes that would make it so (?)
• We leave the question open.
• What we can say is that they have operational closure: their identity is specified by a network of dynamic processes whose effects do not leave that network.
• But we don't say what the specific form of that organization is.
• But that's okay. They are made up of autopoietic unities, and their lineages are formed by reproducing as cells.
• This ensures that whatever happens in metacellulars that don't die is consistent with autopoiesis of the cells.
• Therefore what we say will apply to both first-order and second-order a-p unities.
• Symbiosis and metacellularity
• Structural coupling between cells can go in two directions
• Symbiosis: "inclusion of the boundaries of both unities"
• Metacellularity: in which the cells remain distinct but establish a new coherence as a larger unity.
• might be of use...

## Week 5: Sept. 26

• Degrees of Freedom:
• 3. Determinacy and indeterminacy 67-92 (25pp)
• This is long. Split it up and have people report on their sections?
• Tree of Knowledge:
• 4. The Life of Metacellulars (20pp)
• Need to prepare a lecture on Natural selection, genetics, and the Modern Synthesis.
• Include fitness, adaptation, connections to capitalism
• Darwin, late 19th Century, establishes that species are evolved from previous types of organisms
• proposes that long-term change is due to natural selection, by analogy to artificial selection.
• Problem of blending.
• Mendel, a German monk, grows pea plants in 1850-60s.
• Here's the experiment: given two separate lines of peas: one with smooth, yellow peas, and one with green, wrinkly peas. Both were true-breeding ("purebred") lines: when the yellow-pea plant is self-fertilized it only gives yellow-pea offspring.
• Cross the two types, and keep careful track.
• Observe a 3:1 ratio (3 yellow:1 green).
• The explanation: instead of blending, peas remain in a space of four possibilities. Child plant gets one "particle" from each parent:  YY Yg gY gg
• Yellow is dominant, so if you have any, you are a yellow-pea plant.
• These are genes, but nobody knows what they are.
• 1950s, Watson and Crick (and Wilkins, and Franklin, who was ripped off, dissed and unfortunately poisoned), and genes are in the DNA. We saw these experiments in the podcast last time. (Watson is apparently a nasty person, by the way, rude and self-serving, and has said offensive, derogatory things about women and people of color that are made more problematic by his status as an expert on genetics.)
• DNA comes in long chains of base pairs. Either of the two strands is enough to reconstruct the whole thing, because of the base pairing.
• During normal cell functioning (interphase), the DNA is used to make proteins that do the cell's work. We saw pictures. Base pairs are "read" 3 at a time, to interpret them in the "language" of proteins. The proteins do all kinds of things, including moving our muscles, building and breaking up other chemicals, moving things in and out of the cells, and repairing, copying and using the DNA.
• When the cell splits, the DNA splits and gets copies, so each daughter cell gets just as much DNA as the parent, and the same sequence.
• A gene is a stretch of DNA that codes for a single protein, or RNA molecule, at least that's the basic idea.
• We have 2 copies of each gene in each cell, one from the father and one from the mother.
• These are the two alleles of Mendel. Could be one yellow, one green.
• so this is the Modern Synthesis of biology: DNA is the location of the genes that bridge between Mendel's observations of discrete inheritance, and Darwin's theory of evolution by means of natural selection.
• Natural selection: example of the peppered moth.
• Central dogma and the bottleneck of the germ cells.
• Genes as central controller, or blueprint.
• Scientifically simple story = power. Understand and control the genes; understand and control life itself.
• This story makes life into a justification of oligarchy and central control, via exaggerated rhetorical claims backed up by the institutions of science.
• Science can be political, or utopian (or oppressive).
• in natural selection, we get the idea that genes evolve and our bodies are side effects that are evaluated by natural selection.
• Dawkins: "We are survival machines -- robot vehicles blindly programmed to preserve the selfish molecules known as genes."
• Genes do what they have to to propagate themselves, in a "struggle of all against all"; "survival of the fittest"; "Nature red in tooth and claw"
• Which perfectly parallels the rise of the economic free market. Compete or die. And of course, Darwinism was used to justify letting poor people starve and die of disease. ... mention eugenics, etc.
• adaptationism: living things are the way they are because of natural selection. It would be the way to produce lots of offspring.
• Leads to evolutionary psychology: men killing stepchildren, etc.
• Also, the targetted research program that led to Watson and Crick's discovery was funded together with atomic research, and in the same ways for the same reasons: to gain control of the fundamental building blocks of nature.
• Genetics grant proposals still refer to the "success" of the Manhattan project, and scientists are hoping for a breakthrough on the scale of the atom bomb.
• The Human Genome project
• genome: the full set of genes that "define" an organism.
• 'Spelling out his "Vision of the Grail," Walter Gilbert wrote, "Three billion bases of sequence can be put on a single compact disc (CD), and one will be able to pull a CD out of ones pocket and say, 'Here is a human being; it's me!'" (Gilbert, 1992. Evelyn Fox Keller, The Century of the Gene, 2000, p. 6)
• Some of us want to understand how our world could be different, and one way to inquire about that is to understand how the natural world is different from our social world rather than making it look the same.
• Learn how to live cooperatively rather than assuming we have to have strong leaders (central controllers).
• The texts we're reading are about challenging the consensus about genes and natural selection. Not by saying they don't exist, but by showing that they're not all.
• Maturana and Varela are developing an alternative story about life that deals with the whole organism as a system, not as a centralized organization with genes in charge.
• The very idea of autopoiesis is an alternative to the central-controller model.
• They make a point of spelling out how the genes don't specify the organism. Like the constitution of a country.
• They retell the story of the one-cell bottleneck in a whole-system way.
• and redefine heredity to be not inheritance of genes but conservation of any aspect of the unity's structure.
• Rayner takes it on in various ways
• In a way, his whole book is about ways of living together and getting along with each other, from cells to corals and humans.
• points out how the process of reproduction, generations and variation is especially apropos of determinate individuals. Indeterminate entities that spread across the landscape without producing discrete offspring can respond to conditions by branching, rerouting etc., not only by adapting via natural selection.
• he's interested in how organisms grow and develop, and why these things happen in certain ways that aren't about what genes are selected for. He's about to criticize adaptationism and take an alternative approach to differentiation and integration.
• "evolutionary playtime" - periods when organisms can afford to try things out - compares it to basic research.
• Chapela talks about resistance: attempts to engineer genes and organisms meet resistance from the cells.
• Today's news (sept. 15): Gruber said he would not go into detail about the known production problems [trying to make "bio-isobutanol" for fuel and plastics] for competitive reasons. He described them as growing pains typical of new fermentation-based technologies.
"Mother Nature always tries to mess with us," he said.

• Organization: "The relations that define a machine as a unity, and determine the dynamics of interactions and transformations which it may undergo as such a unity, constitute the organization of the machine."- http://www.enolagaia.com/Tutorial1.html
• Structure: "In a composite unity, be this static or dynamic, the actual components plus the actual relations that take place between them while realizing it as a particular composite unity characterized by a particular organization, constitute its structure.
In other words, the structure of a particular composite unity is the manner in which it is actually made by actual static or dynamic components and relations in a particular space, and a particular composite unity conserves its class identity only as long as its structure realizes in it the organization that defines its class identity."

Chapter 4. Differentiation and Integration
1. Divided and United States of Being
The Combine Harvester Principle
• Get pictures of combine harvester?
• Complex tasks can be subdivided. Example: gathering a harvest, and then sorting, preparing and packaging it.
• Division of specialist labor might be more effective than generalist.
• Can be good for efficiency; reducing interference, and enhancing precision, but bad for continuity.
• And the stages will have to have a communication system (such as a conveyor belt??) to connect them.
• First differentiating (separating component tasks) and then integrating (interconnecting them), generalist homestead farmer develops a combine harvester.
• Problems with diff/int:
• If one fails, or the nature of the task changes unpredictably, the whole can fail.
• So you need extra stuff to handle these problems. Some of it will be more generalistic.
• Delicate balance between precision (specialism) and flexibility (generalism): in combine harvester and other human-made complex systems.
• So to with the task of staying alive.
• Requires delicate balance between differentiation and integration.
• Interplay between processes of gathering, conserving, distributing and redistributing energy.
• NOTE: by "energy" he means food and stuff.
• These processes complement each other but can also interfere, so they need to be kept out of each other's way.
• They are regulated flexibly, by feedbacks in the moment, or rigidly, by genes.
• Two questions about diff and int: Why and How.
• Why is evolutionary question: adaptational.
• "design constraints" can get in the way of adaptational optimization
• TODO: talk about that too.
• Comparison to companies trying to keep up with competition at expense of innovation.
• It takes daring to innovate rather than to refine in response to competition.
• TODO: lecture about how natural selection is like the capitalist marketplace
• Innovation can be foolhardy because you can't see ahead to what'll be needed.
• It often comes down to clarifying what the target is. Once that's done, it's refinement to get to the target.
• Competition makes adaptation conservative - refine your ability to achieve an already defined standard under "do-or-die" pressure.
• From this point of view we get the usual picture of "struggle for survival".
• This justifies "all manner of adversarial, uncommunicative behaviour".
• It's not enough to be competent but to be competitive.
• life at best a treadmill, at worst a holocaust.
• Alternative view
• complementary, more optimistic, less competition-oriented.
• Look more at what attributes enable than what they constrain.
• Living systems are inventive in themselves, without selective pressure to invent.
• When "evolutionary playtime" comes, for instance when new niches arise, new possibilities open up.
• Then evolutionary success comes from serendipity rather than triumph over opponents.
• Take heed, advocates of market competition: it gives you either a monopoly or a bewildering variety of limited choices...
• Adaptive necessity is strict governess of invention, not its mother.
• It's true of research progress as well.
• Teams of researchers with limited foresight "follow the seams of knowledge". "Targetted" or "near-market" research.
• On the "cutting edge". It's well justified in the short term, but expensive and doesn't provide innovation
• "Blue-sky" research on the other hand. More in a "marginal fog". Exploring uncertain regions. Research path is indeterminate and discoveries are unpredictable. Underfunded. But necessary to the future.
• Reviewing: adaptation follows invention. Explains why things are chosen or discarded, but not how they arise. Important to understand of course, just not complete.
• First we'll look at adaptational explanations of differentiation and integration and then "organizational impulse" producing them.
2. Why Disunite?

• One way to proliferate is isotropically, like a spreading pool
• TODO: Explain surface area/volume more thoroughly
• It becomes harder and harder to keep the interior supplied
• This is the understood reason why cells don't just keep getting bigger, they divide.
• Another reason is that dividing allows them to specialize and to disperse.
• When they don't disperse, they can differentiate into diverse parts of a complex whole, staying connected and coordinating.
• For example, in an animal - specialized organs, tissues, cells, etc.
• Developmentally indeterminate systems also differentiate, but less.
• tend to "divide externally" by producing branches rather than internally
• When they do disperse, we call it reproduction
• Allows for generations of dispersed organisms; avoid having all eggs in one basket; natural selection picking out the most successful
• Leads to differentiation at the population level
• Can lead to societies that divide labor, but only if there is a re-integration' process that opens communication between them.
• Can bring tension and instability as well as opportunity - see chapters 7, 8

2.2. Organizational Impulse: Destabilization

• When dispersing energy encounters resistance, you have a "dynamic field" that is excitable.
• As these systems gain energy and, use that energy to gain more energy, the rate of uptake overtakes their throughput capacity: they take in more than they can distribute to "existing sites of deformation or discharge"
• Expansion rate stops being exponential or linear, and becomes irregular.
• Can enter the "realm of ... 'deterministic chaos'"
• Examples of irregularities due to "driving systems beyond their throughput capacity"
• Turbulence when forcing an oar through water
• "Bunny-hopping" car when driver can't control clutch and accelerator
• "since any excitable system is prone to subdivide... there is no need to invent subdivision" by splitting, branching or enfolding
• as response to need for reproduction, differentiation and effective energy transfer
• rates and patterns may be modified adaptively, but subdivision just happens. "impulsively rather than compulsively".
• Discussion of nonlinear dynamics, spectrum of behaviors from equilibrium to chaos
• Discussion of fractal patterns, space-filling shapes
• Non-assigned reading. Notes to come.
3. Why Unite?
3.1. Complementary Attraction
• reasons for unification (=integration?) are usually said to be
• 'synergism - "bringing together complementary activities that work better" together
• co-ordination: timing things so they don't interfere with each other
• But Rayner thinks two other things are primary (more primary?)
• removal of competition: more equitable distribution of resources among neighbors, or mutual benefit of "spongers" that help with exploring for, conserving, or recycling resources.
• minimization of dissipation of resources that happens when there's a lot of exposed surface area.
• note: I wonder if this includes gazelles herding together to hide in the crowd from jackals, etc.
• Disorders like cancer - "proliferation of acquisitive components" are commonly described as loss of coordination
• More like: re-establishment of "competitive internal boundaries"
• disorders like this can be good in indeterminate systems, like when the boundary of a fairy ring starves out the center. More on this in chapter 5.
• timing of unification can make a big difference.
• If it's soon after differentiation, the parts will be less specialized or differentiated.
• If a long time after, competition can develop.
• More specialized -> more inflexible, self-insufficient
• Indeterminate systems can play with the balance, but determinate ones have to get it just right.
3.2 Connecting Attractors
Re-iteration and Breaking Moulds
• As in 2.2, exceeding throughput capacity leads to subdivision, strange attractors (?)
• Nonrepetitive quality of strange attractors depends on not intersecting itself.
• Anastomosis of trajectory components allows re-iteration of pathways, like limit cycles, preventing further proliferation.
• Can happen due to increase, as in periodic windows of logistic map
• This analogy seems shaky to me.
• Effect of fusion on throughput capacity
• resistances in series : lots of net resistance
• resistances in parallel: lots of throughput
• networked systems have more throughput
• In a network there are many pathways, and some may become disused.
• Even so, they can be overloaded, and do further division or "symmetry breaking".
• conduits enlarge themselves or become cable-like aggregates. Boundary can expand.
• Therefore integration into a network can allow great stability, but can also allow breaking out of the mould [sic] and becoming new structures which are not possible without integration.

5. The Natural Drift of Living Beings
• In the last 3 chapters we dealt with
• How living beings are "constituted as unities", defined by autopoietic organization
• How they generate a historical system of lineages by reproducing
• How they form metacellulars by descent from a single dividing cell, each one step in a generational cycle, and a variation on the theme of single-celled life
• this gives us:
• Ontogenies of living beings that can reproduce
• Phylogenies of reproductive lineages, intertwined in a big historical network.
• "This great network of historical transformations of living beings is the warp and woof of their existence as historical beings"
• Now we'll talk about these topics from earlier chapters, to understand organic evolution, necessary to understanding cognition.
• Key is association between differences and similarities in each reproductive stage, conservation of organizations, and structural change.
• Similaries allow a historical series, or lineage.
• Differences allow historical variations in the lineages.
• But how is it that some lineages appear and stay around, and others don't?
• Why are fish well suited to the water and horses well suited to the plains?
• Requires looking closely at interactions between living beings and their environment.
Structural Determination and Coupling
• Ontogeny of a living being
• Begins with an initial structure
• that "conditions the course of its interactions and restricts the structural changes that the interactions may trigger in it."
• It also has an environment where it is, which "appears to have a structural dynamics of its own"
• operationally distinct from the living being
• TODO: what do they mean by operationally?
• So we have two structures, operationally independent: living being, and environment.
• we have distinguished them, as observers, and characterized the unity's organization.
• Within this structural congruence, being encounters perturbations from without
• Perturbations do not determine what happens to the being; the being's structure determines what change occurs in it.
• The interaction triggers an effect, not "causes" it.
• "The changes that result from the interaction between the living being and its environment are brought about by the disturbing agent but determined by the structure of the disturbed system.
• It's true in both directions: environment's structure determines result of perturbations from the living being.
• TODO: is this Operational Closure?
• This is not distinct to living beings, it's true of all interactions with things. Scientists can only study unities that are structurally determined.
• Example of car: If pressing the gas pedal doesn't work, we look for a problem between the pedal and the wheels, not in our foot: that is, in the structure of the car. Car's structure determines how it responds to perturbation from foot.
• This attitude - to understand how a system works or why it doesn't work, look to its structure - works for living beings and social systems as well.
• Go to a doctor for health problems, replace a manager for a business problem.
• "We may choose not to explain many phenomena... however, if we wish to explain them scientifically, we must treat the subject phenomena as being structurally determined."
• structure of a unity specifies four domains:
• Domain of changes of state: ways it can change structure without changing organization (without dying)
• Domain of destructive changes: ways it can change structure with loss of organization (and no longer belonging to its class)
• Domain of perturbations: interactions that trigger structural change
• Domain of destructive interactions: interactions that trigger destructive change
• TODO: what is a domain?
• Example: trumpet picture
• Example: (lead) bullet triggers destructive change in a person, but not in a vampire.
• As a system undergoes structural changes, its four structural domains will also change, because it will respond to things differently.
• "This ongoing change in its structural domains is what is proper of the ontogeny of each dynamic unity", whatever that means :(
• When organization is not lost, observers see a compatibility or congruence between the structures of the unity and environment. This is structural coupling.
• example: automobiles' structures have changed to work within cities, and cities have changed in response to automobiles.
• I gave example of dolphin's shape in class last week.
• Maybe a video about jellyfish's shape and shapes in water?
Ontogeny and Selection
• Those things are true of any system. What is proper to living beings?
• TODO: as a side effect, this paragraph clarifies what they mean by "proper to".
• In living beings, structural determination and coupling are within the framework of conservation of the autopoiesis that defines them.
• Even the autopoiesis of cells in a metacellular is subordinate to its autopoiesis as a second-order a.p. system.
• "Ongoing structural change of living beings with conservation of their autopoiesis is occurring at every moment ... It is the throbbing of all life."
• "When we as observers speak of what happens to an organism ... we are in a peculiar situation"
• We can imagine how both organism and environment could have changed differently in the encounter, if interactions had been different.
• Thus changes in unity appear "selected" by the environment
• Example: boy not fed well when young, grows up disabled
• The same is true in reverse, changes in environment might be "selected" by the organisms that interact in it.
• Example: the air is full of oxygen because photosynthesizers put it there
• Structural coupling is always mutual - both structures change.
• If we focus on organisms, they appear to be adapting to the environment
• And when they lose autopoiesis, they have failed to adapt.
• "Every ontogeny as an individual history of structural change is a structural drift that occurs with conservation of organization and adaptation".
• Ontogenic structural change is always structural drift congruent with the structural drift of the environment.
• TODO: discuss structural drift.
Box
Dangerous Curve: Natural Selection
• "Selection" has dangerous connotations
• The environment is "choosing" which changes in the organism take place
• No - the organism is choosing them, structurally determined.
• We think of it "triggering" one of many possibilities
• But all the other possibilities exist in our mind
• So "selection" is in the mind of the observer
• We refer to a selection of paths of structural change, maybe
• Darwin used the term N.S. as a metaphor explicitly, "as if" there were a natural counterpart of artificial selection performed by a farmer
• It's too late to change the nomenclature, better to use it "but with the proper understanding".
Phylogeny and Evolution
• Now we can answer the questions we raised at the beginning of the chapter.
• we have looked microscopically at what happens in individual interactions
• Now we go telescopic: individual interactions + variations at each reproductive stage = millions of years of phylogeny
• "large (very large!) number of repetitions of the same phenomenon of individual ontogeny followed by reproductive change"
• figure 26: tree of life, including symbiogenesis
• definition of phylogeny: "succession of organic forms sequentially generated by reproductive relationships"
• evolutionary change.
• figure 27: phylogeny of ("depicts the drift of") trilobites, which are now extinct.
• Variations at the reproductive stage --> great diversity
• Each variant is coupled to an environment, "a variant of one central theme"
• At end of Triassic, environment changed dramatically.
• Most of these lineages' structures were not congruent with those changes; "consequently, the organisms that constituted those lineages did not conserve their adaptation, did not reproduce, and those lineages were interrupted."
• Eventually, all the trilobites perished because they did not conserve adaptation.
• We can reconstruct phylogenies like that for all animals and plants known today. (And now we use DNA sequencing to redo them)
• Each lineage is a "case of variations on a basic theme, over an uninterrupted sequence of reproductive changes with conservation of autopoiesis and adaptation"
• This reveals that there are a lot of structural variations that can work in a single environment.
• But not all prove equally capable of conserving adaptation as environment changes. Some lineages die out.
• In organic evolution, the essential thing is reproduction: as long as you can keep that up, your structural changes are okay.
• This will turn out to "condition significantly" the history of living beings' cognition.

## Week 6: Oct. 3

• Degrees of Freedom:
• 4. Differentiation and integration pp 93-109 (16pp)
• Tree of Knowledge:
• 5. The Natural Drift of Living Beings (28pp) up to p.107

### Notes on Knowledge, end of chapter 5

Natural Drift
• Here is an extended analogy.
• I am flicking one drop of water at a time onto the top of a hill of sand. Sort of like Per Bak but different. Also sort of like Rayner's spreading pool of water, but different.
• Each runs down a way and carves a bit of a channel, changing the world that later drops encounter.
• If we redo the experiment it'll be different.
• We can mark all the drops' trails at once and get a branching structure.
• "The analogy with living beings is obvious."
• location and direction of flicking = many descendants of common ancestor, with slight structural changes
• multiple flicks = different lineages arising from those
• hill = environment. It changes through history, partly influenced by the living beings.
• continuous descent of water = conservation of adaptation
• the reproductive stages are not part of the analogy. It's about "unfoldment of lineages"
• Natural drift follows the paths available to it at each instant
• variation of individuals at the reproductive stage PLUS variation in the environment leads to course of natural drift
• Sometimes stabilization, when env changes slowly, sometimes diversification and extension when env changes abruptly
• Persistence of forms depends on their qualities and the environment
• Now if we look at the sand from the top
• Branches out in all directions: more and more differentiation from original form
• Some stay close to the origin - bacteria etc.
• Some go far away - birds, mammals, etc.
• Some are interrupted and come to an end - like trilobites
• Many lines of descent have branched and many have ended
• Not only determined by changing environment, but also by "the conservation of structural coupling of the organisms in their own environment (niche), which they define and whose variations can go unnoticed by an observer."
• Are the water drops pushed by random fluctations, or by deterministic processes?
• Can the physicist give a descriptive account or a probabilistic one?
• Similarly, a biologist can explain some evolutionary history based on organisms' structural coupling to a changing environment, but not lots of the detail. You would have to know all the env. fluctuations and all the details of the organism's structural plasticity
• Most interesting is how the internal coherence of a group of living beings compensates for a perturbation
• If the climate gets colder, they must become able to live in cold to conserve adaptation
• Lots of ways to do that - grow fur, burn food faster, move south, etc.
• Each brings lots of other changes - fur for example requires new ways of recognizing each other and of moving.
• All changes not caused by the environmental change but by how the organisms' structures respond to it. Operationally independent.
• Because we can't see all the structural factors, the change can seem haphazard. But it always conserves the functioning of the whole unity.
• Evolution is natural drift: a product of conservation of autopoiesis and adaptation.
• The coupled change in organisms and environment produces diversity and complementarity between the two.
• No outside force needed to explain those things, nor to explain the directionality of variations. Nothing is being optimized.
• It makes whatever changes it is able to make. Like a whimsical sculptor collecting and assembling parts.
• "with no law other than the conservation of an identity and the capacity to reproduce, we have all emerged."
• "It is what interconnects us to all things in what is fundamental to us: to the five-petal rose, to the shrimp in the bay, or to the executive in New York City."
• "as long as a living being does not disintegrate, it is adapted to its environment"
• You could introduce a yardstick of your own, for instance how efficiently does it utilize oxygen.
• But does it mean they are better adapted? No, because as long as they are alive they are passing the test.
• efficiency is in the eye of the observer only. [like everything else isn't??]
Evolution
Natural Drift
• What we said here is sufficient to understand the basics of evolution.
• You don't need the mechanisms of DNA, etc.
• We've skipped over population genetics, and evidence from fossils.
• There are many schools challenging the theories of evolution by natural selection.
• You can't discount the process of evolution itself.
• But we can be freed from the idea of organisms adapting to the environment, optimizing their use of it, and making progress.
• we have only structural drift under ongoing selection. No optimization or progress; only conservation of ap and adaptation, with continuous structural coupling between org and env.
words

### Notes on Freedom section 4.4

words to mention might include niche and nuclear

4. Mechanisms of Differentiation and Integration
• Now we consider the mechanisms that cause these processes to happen in different contexts.
4.1. Segregating, Transferring, and Pooling Genes
• How genes can disperse and reassociate within and between individuals and populations.
• But first, how genes can "stay within bounds" (lines of descent).
4.1.1. Maintaining Genetic Identity
Clonal Proliferation and Cell Division Cycles

4pp

• Details of mitosis
• Genes can only multiply within the cell boundary.
• And the cell boundary can't be maintained without the genetic information.
• Genes are duplicated in the "Cell division cycle".
• Who is in control, the boundary or the genes?
• An interplay between.
• Indeterminate systems may have more "play" in this, and be more responsive to environment.
• When a cell splits both have identical genetic information
• especially eukaryotes, which have an elaborate cycle including mitosis
4.1.2. Changing Genetic Identity
Gene Transfer and Recombination

11pp

• Details of Meiosis (differentiation of germ cells), recombination, horizontal gene transfer, selfish DNA, immune system evolution
4.2. Opening, closing and Extending Cell Boundaries
4.2.1. Constraint Without Walls

2pp

• How animal cells and amoebae manage their shape
4.2.2. Setting and Deforming Walls

5pp

• How long tubelike cells extend and branch
• assimilative and non-assimilative hyphae
• rhizomorphs like international telephone cables. Very big mycelia
4.3. Intercellular Partitioning and Communication

2pp

• interactions among cells in multi- and metacellulars
• this one is pretty short
4.4. Defining Tissues

8pp

• how a zygote becomes an embryo
• where limbs and organs come from
• plants that can regenerate from one cell
• weird mutations in fruit flies
4.5. Interconnecting Tissues
Nervous and Vascular Infrastructures

10pp

• As cells and tissues differentiate they become self-insufficient and need to communicate
• how nerve cells work; fluid flow in roots and stems; blood flow in animals; circulation of hormones
4.6. Structuring Societies and Communities

2pp

• Human and non-human societies develop networked infrastructure for transport and communication
• Communication becomes more and more important for humans. We may be increasingly self-insufficient as individuals.
4.7. Conceptual Frameworks - Deductive and Inductive Reasoning

2pp

• The value of branching, indeterminate exploratory thinking and induction

## Week 7: Oct. 10

Midterm presentations.

## Week 8: Oct. 17

Note: Chapela visit rescheduled to next week.

• Degrees of Freedom:
• 4. Differentiation and integration pp 109-154 (45pp)
• (special experiment: group presentations on each subsection of the Degrees of Freedom reading)
• Tree of Knowledge:
• 5. The Natural Drift of Living Beings (28pp) from p.107

Outline for this class:

• Go over how I graded.
• 70% investigation; 10% engagement with the course material; 10% quote; 10% close reading
• Go over these, and how grades work
• 60- D; 74- C; 80- B; 90- A
• Everyone present from the reading!
• And give me a slip saying what you did.
• Hand out homework.

### Notes on next week's Degrees of Freedom reading

Chapter 5. Versatility and Degeneracy
1. Reshaping and Abandoning Boundaries: Getting Out of Ruts
1.1. Entrenchment
• Living creatures get stuck in their ways.
• Specialization of tissues and of whole organisms can make it hard to change course
• Tendency to proliferation of detail rather than shifting to a different way.
• Integration can have the same effect - making you good at what you do and worse at doing anything different
1.2. New Horizons
• Since the environment changes all the time, in both space and time, you need to be versatile.
1.3. Breaking Free
• In order to change to meet new situations, sometimes you need to cut loose of the establishment.
• Either physically cut loose from the older part of the structure (severance or reproduction)
• or put a wall between it and you, "partitioning one phase from another"
1.4. Redistribution
• If you cut loose, as in reproduction and dispersal, you have to go it alone.
• But if you put a one-way valve between you and the parent structure, it can still support you
• It becomes part of your environment, and you may become part of its demise
• Thus versatility and degeneracy are connected.
• Also, they seem to involve the same chemistry, involving oxygen.
• Oxygen is very powerful, can unleash lots of energy, and can be very destructive.
• It likes to gain an electron from something else
• Leaving a free radical in the environment, which go and cause chain reactions by making other things into free radicals.
• If the free radicals get too out of control, the cell can melt down and die.
• "Gas guzzling process" is one way: use oxidation to burn lots of food, which charges up ATP, use ATP to get more food
• Another way is by producing antioxidants to damp out the chain reactions.
• Or make the boundary stricter to keep oxygen out.
• If those things don't work, you get oxidative stress and degeneration.
• warning signs of oxidative stress can kick off protective mechanisms.
• Insulating the boundary to keep oxygen out may involve oxygen, ironically
• Boundary-insulating can also change the hydrodynamics of the cell
• make the difference between assimilative, explorative, conservative, or redistributive states.
• It may be less about keeping from drying out than about keeping safe from oxygen.
• Drying out may be most dangerous because it leads to exposure to (gaseous) oxygen.
• Skin, bark, waxy coverings, resins, etc. may be primarily to keep oxygen out, not as commonly thought, to keep water in.
• "a tree might well be considered to be a response to oxygen toxicity, as much as a device for connecting sites of water uptake in soil to a distant photosynthesizing canopy!"
• Lungs, trachea, etc might be to regulate oxygen access rather than to maximize it.
2. Outside-in Versatility in Determinate Systems
• Determinate systems diversify "from outside-in"
• Develop a fixed boundary and then differentiate within
• Indeterminate systems do it "from inside-out"
• Continue to expand boundary and change its form
• Determinate systems can also be versatile by reconfiguring/abandoning boundaries, but this involves creating a separate entity, not staying connected as indeterminate things can do
2.2. Metamorphosis
• Tadpole into frog, larva into butterfly
• When tadpole metamorphoses, its tail degerates and gets resorbed. Apoptosis is involved.
• caterpillar loses almost all its muscle system
• young form is soft and can expand, adult has stiff exoskeleton
• during growth, sometimes the cuticle (skin) hardens and molts, controlled by moulting hormone
• finally it hardens into a pupa. Seals in its boundary, stops growing, reorganizes.
• "degeneration of larval tissues and activation of embryonic cells in so-called 'imaginal discs' that have lain dormant during proliferation of larval tissues from the egg"
• degeneration is considered necessary for metamorphosis into next stage
• has been assumed to be "programmed"
• In other settings, death is considered to be an unfortunate consequence of accident, mistake, etc.
• Now we hear that programmed cell death is important in bodies without multiple stages as well. Perhaps to limit the risk of cancer.
• If we skip a "degenerative or boundary-fixing process", we may be neotenous or "babyish". This is an important kind of evolutionary change.
• Vertebrates apparently started as a neotenous descendant from a larval stage of sea squirts
• And humans a neotenous kind of primate, with a long childhood and not much hair.
• Pets may be "babyish" animals, accepting of human masters
2.2. Alternative phenotypes
• It's also useful to be able to switch between body types in arbitrary sequence, responsive to environment, not just in a fixed sequence as "metamorphosing systems" do.
• For instance, you can eradicate mosquitoes by killing their larvae, since mosquitoes can't live without passing through the larval stage.
• Some org's can shift among phenotypes, either triggered specifically by environmental "cues", or through undirected "error and trial"
• "error and trial" is risky - might not make the best choice - but can also "anticipate" by choosing the right form before the environment changes!
• Vertebrate immune system is an example (last chapter), though not reversible
• Full versatility in form of organism requires changes in gene expression, not in genetic content.
• Example: spores of certain fungi
• Erynia conica ("a parasite of certain insect larvae") produces 4 kinds of spores
• Figure 5.4: cornute, globose, stellate, coronate spores of E. conica
• The spores also produce each other.
• They travel differently, and end up in different places.
• Other examples
• big/small mouths of protists
• wings, antennae of parasitic wasps depending on their hosts
• colors/patterns of butterflies depending on season of emergence
• castes and morphs of social insects, body types depending on how they're fed
• The different phenotypes are exposed to natural selection separately
• They can diverge into separate species
• Keeping one form as a backup plan while exploring another allows for safe evolutionary innovation
• Possible to keep a base population, and a fringe exploring other forms
2.3. Evolutionary remodelling
• Biology is in a rut, thinking evolutionary change works only by changes in gene content.
• As if the DNA is a software program that responds to input by outputting an organism
• Mutation, recombination and selection on genes are primary
• Mutation is rare and generally harmful
• Recombination may not be able to make something good, given that it would need to be working with parts that have been selected out
• And if something good is discovered, recombination would tend to break it apart
• And changes in gene frequency can enhance or suppress things, but they can't bring something new or drive "large shifts in organizational pattern".
• but these shifts can happen
• Mimicry of other creatures, camouflage, etc
• different lineages converging on the same shapes (sharks and dolphins)
• rapid divergence of many forms of mammals, etc
• One way: "there can be distinct life cycle stages and alternative phenotypes which have identical genetic composition"
• Also, e.g. humans and chimps have mostly the same DNA, so it's possible to have different forms from many of the same genes, driven by context
• You can "cook different recipes" from the same "ingredients"
• Genes are "memory" but not "operating system"
• "operating system is based on feedback at contextual boundaries"
• Genetic and environmental inputs can interplay into "radical shifts in boundary configurations" without big changes in genes
• Organizational aspect of evolutionary remodeling is important
• especially if "particular sequences of boundary-defining events can be re-iterated"
• evidence that they can: creatures with alternative phenotypes, and developmental versatility of indeterminate bodies

### Notes on next week's Tree of Knowledge reading

Behavioral domains
• Do we want to go to a fortune teller?
• It would be nice if he could see what is determined to happen
• But we don't want to be deterministic - we "cherish our free will"
• But we want to be structurally determined when we go to the doctor
• Are we determined or not?
• How does our behavior relate to our body?
Predictability and the Nervous System
• Science demands structurally determined systems
• When we treat things this way, "the universe becomes comprehensible and living beings emerge in it spontaneously and naturally"
• Distinguish determinism and predictability.
• Predictability is not always possible, even in a str. det. system.
• "No one disputes that the clouds and the wind" follow physical rules
• But we can't predict the weather.
• Because we don't know the state and environment of the system well enough.
• Other things we couldn't even imagine being predictable, like turbulence
• (as if the weather isn't turbulent??)
• And other systems that are changed by observation, and prediction itself changes their behavior.
• If we see something as predictable, we are observers capable of making a valid prediction. If we see it as haphazard, we are observers incapable of explaining it scientifically.
• I.e. predictability is said by someone.
• This is important when we study organisms with nervous systems and rich behavioral domains.
• Without saying what a nervous system is, we can say that it has to contribute to the structural determination of its organism at all times.
• Both directly, as part of the structure, and also because its actions (such as language) is part of the environment that has selective role in the structural drift with conservation of adaptation.
• The past and future are meaningful to us as observers, but it's the present of the organism's structure that's meaningful in determining its structural determinism.
• Regardless of nervous system, all organisms are how and where they are because of their structural coupling.
• But animals like us seem unpredictable! Why and how?
On Frogs and Wolf Children
• how frogs eat: orient to prey (insect), snap it up with long, sticky tongue, retract it into mouth.
• Effective: tongue goes to the right place.
• Experiment: preserve the optic nerve, but rotate the eye 180 degrees in place when it's a tadpole.
• Cover the rotated eye, it can hit fly well.
• Cover the unrotated eye, and the tongue goes in the opposite direction.
• It's responding to the image on the retina, not to the actual fly.
• Not to actual world, up down front back, but to the perturbations entering its nervous system.
• internal correlation between visual perturbation and muscle action of tongue (and the rest of its body).
• "behavior arises because of the nervous system's internal relations of activity."
• But now we want to look at the organism's structural plasticity.
• If a newborn lamb spends first hours without mother, it will seem normal until the time when it would play and butt heads with other lambs, when it fails to play.
• we don't know how this happens, but its nervous system is different from others because of its different past experiences.
• an example of structural changes that perturbations trigger
• case of Hindu girl raised by wolves.
• walked and ate like wolves.
• eventually learned to eat and walk like people, but never talked well.
• they developed a different structure that worked well for the world of wolves.
On the Razor's Edge
• we are told the nervous system gets information from the environment and assembles a representation of the world.
• Like using a map of the world to plot a route.
• But the structure of the world can't specify the organism's changes, only trigger them.
• we can describe the org's behavior as though it came from a representation of the environment, or a goal-oriented process.
• But this doesn't describe the operation of the nervous system itself.
• it's not right to say information goes from the environment into the organism.
• If we develop in any old way we want in response to the world, how are we effective? and is anything possible?
• A dilemma:
• can't understand cognition if we say objects inform us
• if the nervous system doesn't know about the world, anything's possible?
• we have to walk on a razor's edge in between.
• "maintain a clear logical accounting": everything said is said by someone'
• We can perceive the unity in different domains, by making different distinctions.
• Consider its internal dynamics. Environment is irrelevant.
• Or consider its history of interactions with the environment. "Establish relations between certain features of the environment and the behavior of the unity." Internal dynamics are irrelevant.
• Both are necessary, observer correlates the two.
• Notices that structure of unity "determines its interactions by specifying which configurations of the environment can trigger structural changes."
• Recognized that environment does not determine unity's structural changes.
• But don't blur the two, say that correspondence with features of the environment is part of the operation of the unity.
• Submarine analogy. Guy follows a rulebook inside, never comes out. Doesn't know he is expert at piloting a submarine. What's a submarine?
• This is true of each of us unities.
Behavior box.
• Behavior: changes of a living being's position or attitude, which an observer describes as movements or actions in relation to a certain environment.
Behavior and the Nervous System
• Behavior is something said by us about an organism, within an environment that we distinguish.
• It acts according to its structure, so its changes of state seem suitable and familiar to it (why?)
• Does it seem adequate? depends on the environment. different actions are suited to different environments.
• Behavior is not specific to nervous system, all living beings do it in the environments we perceive them in.
• Nervous system expands the domain of possible behaviors, makes the organism plastic. See next chapter.

## Week 9: Oct. 24

Note: Chapela visit rescheduled to Oct. 31.

This week I wrote paper notes, so they're not visible here.

• Degrees of Freedom:
• 5. Versatility and Degeneracy 155-180 (25pp)
• Tree of Knowledge:
• 6. Behavioral Domains (20pp)

## Week 10: Oct. 31

First half of class:

• Go over the reading we did - DoF 5, ToK 6
• Collect HW
• Hand out next HW
• "nuclear"
• "alleles"

Second half of class:

• A visit from Ignacio Chapela of UC Berkeley.
• Ignacio will talk about Liberation Biology, the Central Dogma, Boundaries, Coexistence, Degrees of Freedom, and things that have developed since the publication of Rayner's book. Some students from his Biological Ideologies seminar may join us.
• Afterward we are invited to join them out on the town during the spooky holidays...

• Degrees of Freedom:
• 6. Balance and Circumstance 181-210 (29pp)
• Tree of Knowledge:
• 7. The Nervous System and Cognition pp 142-162

### Notes on next week's Degrees

Chapter 7. Merger, Takeover and Rejection
1. Encounters with Others - Threat and Promise
• we're ambivalent about both loneliness
• pros: simplicity, isolation, freedom, self-awareness
• cons: boredom, exposure, inadequacy, introspection
• and company
• pros: interest, protection, support, self-absorption
• cons: complication, exposure to threat, constraint, loss of individual control
• These feelings can obscure but also relate to risks and benefits of encountering others in all of biology:
• risks:
• restriction + wastage of resources due to competition
• harm due to disease or mismatch
• constrainment
• takeover
• benefits:
• mutual protection
• complementation between components or activities
2. Rejection - Incompatibility, Self-protection and Self-defense
• Troublesome, ambiguous words: resistance, defense, immunity, antagonism, incompatibility
• Let's define carefully:
• self-protection
• evasion
• repair
• self-defense
• recognition
• response
• incompatibility
• interference
• competition
• Defining boundaries + scale of consideration is important
• Incompatibility requires being within some larger boundary
• Incompatibility in coalescence: example of hyphal organelles in conflict
• Compatibility during enclosure: Invader $\to$ host: 5 cases
• compatibility
• proliferation of invader (lysis of virus, for instance)
• segregation
• elimination
• consumption
2.1. molecular incompatibility
• when two systems of nucleic acids are operating in the same space
• Interference or competition
• Results in elimination of one (by takeover or dilution), or persistent conflict
• bacterial plasmids can't all coexist in a cell
• viruses can either do "lytic cycle" - replicate and kill the cell - or "lysogenic cycle" - go into the chromosome - depending on whether virus produces lysis-suppressing protein.
• can depend on the host
• one slime mould's plasmodium can kill another, causing the nuclei to break down (plasmodium has nuclei floating around loose in one big sea of protoplasm). Then the "winner" eventually takes over the protoplasm from the other.
• Some septate hyphae, when anastomosing, replace "recipient"s two nuclei by copies of the "donor"s two nuclei (even when they're both ones own hyphae). We don't know why. [ADMR offers some adaptive explanations, but not organizational ones... ?]
• Or, "wholesale nuclear invasion from one mycelium to another", similar to the plasmodium case
• many mycelia are incompatible, even when closely related. So we get mosaic-structured populations of separate mycelia. Territoriality, natural selection, etc., like other populations and societies.

.. some other stuff ..

### Notes on this week's ToK

Operational Closure of the Nervous System
• The nervous system is part of the organism, so it doesn't violate the organism's operational closure, everything it does is a matter of internal relations between parts of the organism.
• Additionally, the nervous system itself has operational closure:
• "it is a network of active components in which every change of relations of activity leads to further changes of relations of activity"
• Everything it does is in response to activity in the nervous system, and leads to changes in the nervous system's state.
• Some things change due to the nervous system's activity, and some things are invariant.
• Example: I feel pressure and move my arm.
• "The contracting of this muscle will cause me to lift my arm".
• But this is falling off the razor's edge.
• "(like the case of our friend in the submarine) what occurs is only the constant maintenance of certain relations between sensory and motor elements that were temporarily perturbed"
• "in this case ... it is a balance between sensory activity and muscle tone" ... ????

## Week 11: Nov. 7

outline

• collect HW and give back graded ones
• Maya on the 21st.
• Dates for weekend walk.

• Degrees of Freedom:
• 7. Me and you, Us and them: Merger, Takeover and Rejection pp 211-234 (23pp)
• Tree of Knowledge:
• 7. The Nervous System and Cognition pp 162-180

### Notes on next week's Tree of Knowledge

8. Social Phenomena

recurrent interaction between multicellulars: third-order structural coupling

• i.e. social phenomena
• affects these organisms' structural drift, etc.
Third-order couplings
• various ways of bearing/raising young in the animal kingdom, aside from the patriarchal model
• even in humans, there are many ways of sharing/allocating the tasks of childrearing.
• This diversity is because of "the immense diversity of behavioral couplings afforded by the nervous system".
Social insects
• They are structurally coupled for life, unlike mating and childbearing animals.
• In most cases, the coupling is by way of chemical exchange
• Insects' behavioral roles are very rigid
• probably because their body plan, with chitinous exoskeleton, doesn't let them grow large enough to have complex nervous systems.
Social vertebrates
• antelopes move from peak to peak with one male staying back as lookout
• social life makes possible "relations and activities that arise only as coordination of behaviors between otherwise independent organisms"
• in these cases the structural coupling involves short-term changes in shape in attitude, not changes in body type as in the insects.
• wolves can hunt in packs things they couldn't otherwise
• visual and auditory modes of interaction that insects don't have
• baboons fight and hunt in groups, have rich group structure and constant interactions
• chimpanzee groups are different from baboons'

## Week 12: Nov. 14

• Degrees of Freedom:
• 7. Me and you, Us and them: Merger, Takeover and Rejection pp 234-258 (25pp)
• Tree of Knowledge:
• 8. Social Phenomena (26pp)

## Week 13: Nov. 21

• Degrees of Freedom:
• 7. Me and you, Us and them: Merger, Takeover and Rejection pp 259-267 (8pp)
• Tree of Knowledge:
• 9. Linguistic Domains and Human Consciousness (34pp)
• The Rayner reading part here is really short! Include something else!
• Done. Chapter 1 on James Hollis, The Eden Project, Jungian psychology on projection and the encounter with the Other, and the usual ways we experience that, as a promise of fusion, risk of engulfment or abandonment, etc.

## Week 14: Nov. 28

• Degrees of Freedom:
• 8. Compassion in Place of Strife: the Future of Human Relationships? 271-292 (21pp)
• Tree of Knowledge:
• 10. The Tree of Knowledge (21pp)
• Afterword (6pp)

## Week 15: Dec. 5

Final projects and stuff

## To do list

• Extra topics, activities to go with the readings.
• What to pre-teach each week.
• PI stuff.
• Pre-class questions.
• Identification of concepts.
• Concept tests.
• Discussion planning
• Roles for students.
• Discussion questions.

## Notes on Peer Instruction and Flipped Classrooms

• Peer Instruction
• Ask the class a multiple-choice question that tests a particular concept.
• Students answer individually, giving you (and them) a survey of the class's understanding.
• show of hands, or flash cards
• You can also get the multiple answers from the students - ask them first, collect some answers, then use them to poll the class
• If 40-80% of students have the right answer, "Turn to your neighbor" and discuss.
• Then survey them again - typically students with the right answer tend to convince others, so more of the class will have the right answer.
• Or, skip straight to discussion, or have a whole-class discussion instead of telling them what to think afterward.
• Use the survey:
• to evaluate understanding, after you "teach" them something
• to find out what they understand beforehand
• to poll them about opinions
• while working through an example, to work together at key steps
• for demonstrations and experiments, like testing social psychology hypotheses (or game theory activities)
• Q: will showing the cards (or hands) and discussing with neighbors be hard on students who are scared + embarrassed about math?
• Be sure to explicitly encourage students to be kind to each other.
• Flipped_classroom
• Basically, have them watch video lectures at home, then use class time to
• help them with whatever they didn't get
• put the concepts to use doing projects, applications, etc.

• sit in small groups, go around room saying what's your communication style
• in small group have people have roles
• disagreer -why wrong
• person to make sure everyone's heard from
• person to apply a specific question from the theory (e.g. structure vs organization) to what's happen in the group
• pair, then repair and tell your second partner what your first partner said
• Concept questions, peer instruction
• Have discussion questions
• Have students generate questions before class
• Read some of it in class, together [1]
• Express criticism
• (and praise)
• What about if I think people had a lot of trouble but don't want to admit it?
• If people did the reading successfully
• Have a somewhat structured discussion with roles assigned?