William Connelly reading, "A World of Becoming"

1. Summary of key points...

2. Develop an argument about compelling points:

There’s a break between the humanities and the sciences, for several reasons, but there’s this complexity theory that might be able to bridge that gap. It purports the following 3 ideas:

From any given moment and perspective in time, we’re unable to predict what will arise in the future, especially on a large scale. This is because everything that happens depends in some part on its environment. Some of the changes that happened in the past, which resulted in some sort of occurrence (or in the field of organismal biology, some trait) that hasn't been lost since then, might encounter novel aspects in the environment at just a time to make that trait or occurrence become suddenly important. These are unpredictable from our perspective, because we don’t understand all of the dynamic rules that are in flux and the underlying, “unimportant” traits or properties that will mix under such rules and fluctuations. And if we don’t understand those rules, how could we understand either the potentials for what they might become, or the direction these elements will take in the present-and-given-future?

I was trying to figure out what Poincare resonances are when I stumbled onto this interesting blog, http://quantumresonance.wordpress.com/tag/poincare/.  First let me just take a moment to say that it’s RIDICULOUS when a class transmits some understanding that then becomes the ability to read meaning and information where I previously would have gotten gibberish. Second, this blog helped me interpret the meaning of Poincare resonances through the example of a harmonic string that vibrates in response to a string nearby of the same note that vibrates first. The transmission that happens there is due to complex rules in the environment (it seems to me, btw that this examples makes it impossible to reduce the world to something we only experience in our heads) allowing the strings and the vibrations to resonate with one another. To make the string example greater, think of an orchestra. If a whole bunch of strings are vibrating together next to another, then the string from one cello is likely causing vibrations in a harmonic string from the next cello, so on and so forth, creating a vibrational effect that…may be undetectable to the normal ear?...but has a subliminal effect that may explain why we’re so drawn to live music, or huge orchestras. And probably this is a horrible example, but potentially there’s some self-organizational aspect, in that the composer works from both the individual sounds and the subliminal sounds of the vibrations, to inform his composing so that these sounds build into one another and inform each other in a way that leads to this incredible musical phenomena… And while we could say that these reactions or these huge (emergent) creations are due to chance, the very fact of this being inside of a system (or environment) means that the result is due to complex interactions that come about thru the play of the system’s rules and the actual causal point (or more appropriately, infinite points of causality, each informing the next). And here I’m going to refer again to this blog post I found, because I think he took this concept even further…

“Causality has from a philosophical viewpoint two integrated elements: The causal potential and the complex harmonic receptor effects. Together they form a complex adaptive system of resonant layers between which new phenomenons emerge where resonances support information/energy exchange.”

I think this is essentially saying what I blathered on about. Each causal point informs every other causal point when it’s effect filters around through time and space, such that each changing point in the system ripples through time, space, and the changes each mechanism or agent caused can to become potentially larger than the cause it initially started, because one small change can cause changes nearby that cause huge changes later on (i.e. the butterfly effect).

“Those layers of emergent properties are on the lowest layers seperated by boundaries of symmetry-breaking phase transitions. More on those in my next posts.”

And then…wtf? The closest I can think of this (using models!) is that one emergent property, i.e. resonating strings, is in a way delineated by another emergent property, such as matter and sound waves, so that only nearby strings of the same note or harmonic can vibrate in response to the original string. 

I think I touched on this already, as it pretty flawlessly flows from the previous 2 points Connelly made. But I’m curious about the idea of systems being open. This may somewhat contradict the previous point made by my bloggist, and his idea of “symmetry-breaking phase transitions.” Or they may inform one another, and this is actually an example of how what you know really informs how much and the caliber of what you get from information. Scary thought…We're all trapped in our own perspective.

...

 Agency AND creativity! Each thing has a mechanical ability to become something in this world. This is both dependent upon its abilities and it’s environments, and also the springboard for its agency. The becoming, as I see it now, is something like…(the strong desire for sleep, which is all that I crave now)…no, it’s like the emergent phenomena of things acting inside a system. The emergent phenomena of e.coli eating shit in our gut is the digestive system! Or a part of it. The becoming of neurons firing and synapsing electrically is our brain…and more importantly our perceived SELF.

And because of previous points, let’s keep in mind that this act of becoming through our agency is unpredictable, and certainly not progressive. Here’s how he finally defines agency, which isn’t totally how I would have thought about it (I thought anything being able to interact with anything else would have some degree of mechanical agency):

And then of course he goes on to make the distinction between agency, mechanical stuff, and proto-agency, tying in the idea of emergent properties with the idea of becoming and attaching a degree of human-centered ideation and progress on his values of agency. It feels a little out of character with everything else he says. But he does eventually mention mechanical agency and how even things like electricity can be harnessed and formed into something with degrees of becoming. He talks about a power grid, I prefer to think of a streak of lightning…

Agency is further examined and broken down into the parts of minimal agency (something reacts to rules and does stuff), proto-agency involves life, meaning, and values (and so can react with intention, such as a baterium performing chemotaxis to find glucose), and complex agency, which humans and certainly some other primates seem to possess.

And what I said earlier about the butterfly effect, I'm realizing can be stated better: change to one agent in a system sets off concatenations of reactions. Whether we're discussing mechanical, proto-, or complex agents, the interactions of these things in a system of rules can cause novel or creative changes to emerge, that were not foreseen from the behaviors and understanding of the rules before that novel change emerged. 

To hearken back to my boyfriend's argument about free will, if we were some transcendent being that new all of the parts and the rules at every scale, every emergent property would be inevitable. There would be no creativity or surprise. Our sense of emergence comes from being embedded in the system.

3. Words I learned today:
concatenations: connected or linked in a series
confluences: a gathering, flowing, or meeting together at one juncture or point
dynamical: changing, objects in motion (adj)
apodictic: demonstrably true, incontrovertible
incontrovertible: impossible to dispute, unquestionable
flouts: to show contempt for or scorn
holism: The theory that living matter or reality is made up of organic or unified wholes that are greater than the simple sum of their parts

John Holland reading, "Emergence from Chaos to Order"

Re-reading points:
generators = laws
agents = laws that interact to create emergence
building blocks = the basic parts interacting in the emergent system
(these are all 'mechanisms')


1. Summary of key points...

What draws us into the world, into questioning? Observation and wonder of complexity coming from the unlikeliest places…

Examples of emergence, of something seemingly more than the sum of its parts, is everywhere!

These systems are constantly changing, though the rules stay the same. As scientists, we think it’s because of  the “historical contingency” of the individual parts, which are moving and being moved under the rules of their systems. From this we get patterns - the interaction of rules, patterns, and agents leads to emergence and novelty.

The regular rules are what we end up seeing, because humans see patterns, and we form hypotheses or models to help us find those rules, then to better study the parts and their inherent processes.

The parts are the agents, mechanisms of change, obeying the rules of their system.

These agents can be recombined in innumerable ways in order to create something magnificent, each end product different from the rest. If we just recombine the building blocks in different ways, without a central agent (on the same scale?), they can adapt to one another and alter each other, and then we have great potential for something emerging from the basic system.

 And each level or scale of agents can be the building blocks under a different set of rules for yet another scale.

 In science, we try to find these rules and break down, or reduce how each agent is most likely to interact with others or otherwise react to the rules of its system. We try to find the generalities and apply a greater level of generalities to each greater complexity using the rules of the previous scale, when the interactions of agents has probably redesigned rules altogether at the greater level through emergent properties. So reduction is useful to a point, but emergence is another aspect of systems that reductionism may be unable to examine. Despite the effort of many scientists, emergence is about the interactions of all these pieces and their "historical contingency" of their previous behavior and rules, not just one rule affecting elements at greater scales in the same linear way.

2. Develop an argument about compelling points:

Somehow I never quite thought of using metaphors for models. I should make it my goal now to find models, translate them into metaphors, and then explain them to other people (students, friends, family, coworkers). One day I might create my own working model…

...

With discovery comes greater discovery. The more time passes, the greater the average human IQ becomes - not because we're collectively smarter, but because collectively we know so much more, and are building our lives around the emergent properties forming from years of rules interacting together...

Being able to produce models is a way in which we can study rules underlying a system. When we want to inspect something complex, like how a tree comes from a seed, then we build models to find out where we should look. 

As our investigation progresses, we keep refining and changing our models, to direct our search, and also to build upon observed, repeated phenomenon that appear to be the result of rules in the system.

But, this requires a great deal of abstraction, which pretty much becomes the same thing as reductionism. As Holland says, "When we talk of numbers, nothing is left of shape, or color, or mass, or anything else that identifies an object, except the very fact of its existence."

Indeed, the very way humans operate is to reduce their surroundings to recognizable building blocks, and then build those blocks back up into the coherent whole or complex surroundings...Which eventually leads us to ask if everything is just a process of reducible parts and rules. The key point is that after we reduce the system down to its parts and rules, we must recognize the new rules that emerge from the interactions of the previous level.
Really, using metaphors to explain models is almost a form of modeling itself. Your break the important bits down, translate them to something easier to understand, and then build those new pieces back into the overarching concept of the original model. It's like humans are meant to understand things by changing scale or by pulling information from a variety of places and ideas.

3. Words I learned...
recondite: concealed, hidden, or not easily understood, ambiguous.
invariant: doesn't vary, static
propitiate: to appease an offended power

serendipitous: lucky in making unexpected discoveries

scintillation: to sparkle or shine, be brilliant

a fortiori: for similar but more convincing reasons

perforce: by necessity

efficacious: producing or capable of producing a desired effect

Merleau-Ponty reading, parts 1 & 2

Merleau-Ponty, Eye and Mind, parts 1 and 2

1. Summarize key points:
Ponty bashes on science because science tries to reduce the world to small parts and to reconstruct it with the tools and models we have built from our perception of the world, which is inherently non-objective.

Our perception of the world is non-objective because we see the physical world around us. We also can see ourselves, and see ourselves seeing, and this makes us a) exist inside of the world, and b) exist inside of ourselves. Our vision gives us the ability to distinguish between inside and outside.

From this meeting of inside and out, we get perception, and from perception we have life. But there's a duality about this whole process. Think of a mirror seeing and reflecting the world around it, and from that we can see and reflect on a reflection...our minds produce a similar phenomenon, we interpret our vision so that the individual parts of a visual collective make a whole, like shadows and lines and lighting make a mountain on the horizon.

Painters, when they paint, are immersed in a world of vision, of taking the reception of reality down to perception, and building perception into a painting, which is then seen by others who receive the painter's reality. And it resonates within us because vision rises beyond the actual, existing world, and tugs at a part of us that makes emotional associations with visual perceptions.

And finally, we can tie this altogether into the thought that beyond (or fundamentally holding together) everything we see, is some Being, some existence that is inside of us and outside, all around, each of us embedded inside of it.

"Further, associated bodies must be brought forward along with my body - the 'others,' not merely as my congeners, as the zoologist says, but the others who haunt me and whom I haunt; the 'others' along with whom I haunt a single, present, and actual Being as no animal ever haunted those beings of his own species, locale, or habitat."

2. Develop an argument about compelling points:

Part 1
1st, he bashes on science. Not for the scientists purpose in life which is fundamentally curious, but for the embedded process by which we take apart the world, and reconstruct meaning in it using the tools we built from it. His argument against science is that it, "admits only the most 'worked-out' phenomena, more likely produced by the apparatus than recorded by it. From this state of affairs arises all sorts of vagabond endeavors." I like that he calls science a bunch of vagabond endeavors. I'm a little offended, even though he's mostly right and I've struggled with such thoughts myself... He thinks that "science's agile and improvisatory thought will learn to ground itself," that it will come to understand "the 'others,' not merely as my congeners, as the zoologist says, but the others who haunt me and whom I haunt; the others along with whom I haunt a single, present, and actual Being as no animal ever haunted those beings of his own species, locale, or habitat." This line opens up new doors, in my eyes, to view the window of the world in which everything is one, comes from one thing, and the process of perspective is as important to individuality and becoming as is its actual being or agency.

Part 2
Here are quotes about painters and painting that had a particular resonance or understanding with me...

This illuminates how paintings can often be so weird, and feel so blank to me. Almost soulless. They aren't often statements, they're a singular way of viewing the world, and from that viewing can come any interpretation. There is no right and wrong, no command buried inherently. Just visual interpretation and appreciation.

How we see things ("our motor projects") is unique and is also embedded in how we exist. We have vision, so we view the world. We are a part of the physical world, so we only see what is physically around us. We view the world with our eyeballs and interpret the image in our minds, so what we see and how we see it is a part of the actual world, but is not all of the world. And since we view the world and are a part of it, the world also views us. He does say that, "the see-er does not appropriate what he sees; he merely approaches it by looking," but I think that in our subconscious mind are enough filters that we can say this isn't true - we filter what we see before we even realize we've seen it, which is why the mind takes on its own agency in the process of our viewing.

Not so much an enigma as it explains why we think as we do. We are in the world, we see the world, and we see ourselves seeing. So we become the center of the world, we sense the world and we sense the ability to sense inside our self, so we become the center of the physical world. Because we have a continuous moment of sensing/seeing, and realizing that we sense and see, we have a past and a future, and an elusive present that's forever slipping away into past or future time. It also ties back together why Merleau-Ponty thinks science has it wrong - it isolates these things when really, there is a continuation between the sensed and the sensing, and "vision happens among, or is caught in things." It also hints at why we go about analyzing the world as we do. Everything is separate from us, because we see it, but also everything is a part of us because we are embedded in it. And so we have an unflappable curious desire to know what it is, to know what we are, but must break what we see into pieces so we can isolate one rule or phenomenon from each other, and build back up into a coherent part with a model of the world...

What is life? It's the process of seeing and being seen, when recognition of these things comes together as perspective inside our minds. We are alive because there is a meeting of the outer and the inner, of seeing and being seen. Life is being part of the whole and separate from it, all at once.

From the awareness of our own existence, we can create an abstraction of the world. First we see (and unaware of it, our mind processes what we see) and then that image is granted to our mind for analyzation, for appreciation, for intake and rumination. And from that rumination comes our image of the image, and icon of what we view. And we have associations, which cause us to have emotional responses to images, and to ideas. And that in turn becomes its own thing, has its own moment of becoming something, once it is painted, photographed, or otherwise seen (internally or externally). It is the imaginary, and this imaginary is real in its own way. It's a real map for my mind and body to use as a representation of something in the actual world, but it's also just an actual trace of lines, colors, etc, in which an exchange between the outside (the painting) and the inside (my associations which inform my reading of the painting).

The eye is like a computer, it learns from seeing and sees from what it learns. And it takes the world and puts some part of it to painting, it makes something that can be possessed only at a distance, just like vision takes the world and makes it something that can be possessed, but only thru vision.

A painting is created from vision, and from the vision of the painter passing thru the objects, holding them in his mind as some sort of icon, and interpreting that icon into texture, color, and shapes that make up the painters playground. He takes the outer world with his vision, his vision sees it in the private world, and as a painter he makes it into a shared world.

...

To tie it all together - the painter takes the elements of the visible world, such as lines, shadow and depth, and tries to pull them altogether in a way that still allows us to see the thing it makes up, such as a mountain. He doesn't know what all the elements of vision are, or how they react together to make a painting, but he's always painting in order to take that vision and translate it, with those elements present, into a whole thing.

The painter looks at the world and the world looks at him, and thus his act of painting is an act of continuous birth, because according to Ponty a birth, a new existence occurs when something is simultaneously looked at and looks back, simultaneously becomes "visible for itself and us." Though personally, this reminds me of Schroedinger's cat, which I always understood to be anthro-centric, and kinda ridiculous. I think Ponty would have been more on target if he'd stuck to life being a process of visualization that allows for a perception of internal and external, though I think he was trying to extend that to include the external also looking back at you....which seems very cool and eastern.

And as the world looks back at you, painters begin to see a big circular vision, with one vision encompassing another vision endlessly, such that you have to question if there is a "total or absolute vision, outside of which there is nothing and which closes itself over them." It goes back to his original enigma - that the body simultaneously sees and is seen. The painter sees, is seen, and creates a new seeing on his canvas, and the rest of the world can see that seeing in the canvas, and each person then sees and is seen. In a way, it makes us alive, and brings the painter back to life, because we are seeing the painter see. As the painter sees he paints, and as we see his painting we are seeing him seeing, and in a ghostly way, we see him see as well.

3. Words that I learned:
congeners: a member of the same kind, class, or group
transubstantiations: conversion of one substance into another
antinomies: a paradox, two truths or principles that seem opposing but equally necessary.
obverse: counterpart or complement, the more conspicuous of two alternatives
idios kosmos: latin for private world
koinos kosmos: latin for shared world
profane: contempt for what is sacred, or secular
oneiric: of, relating to, or suggestive of dreams

Sick dogs and sunny gardens

Held hostage in my backyard by a sick dog... on a sunny Seattle summer day.

Sure his drawn-up, puking face makes my stomach churn in pity, and I can't imagine how the weather channel calls this 66 degrees Fahrenheit, because it certainly feels like 90 (I prefer 60). 

Certainly I'm missing work, and when there's so much that needs doing, that makes my hand itch. 

I'm missing my daily 5.5.mile bike ride to campus, and as I imagine the touch of a cooling breeze and fierce sunshine on my shoulders, I long to be out riding on the peaceful (albeit bumpy) Burke-Gilman trail.

But really, I have to thank my sick, trembling puppy (who, at seven, isn't really a puppy anymore. But I indulge myself.). I've been craving a day like this. 

The house, normally noisy and boisterous with the sounds and problems of my family, is mine and deliciously silent. There's food to be eaten that tantalizes every taste bud on my tongue (earthy mushrooms, sweet onions, and soft, warm quinoa, anyone?). 

And when my puppy turns his unhappy blue eyes on me, and comes to lean against my leg for comfort after another upending of his po' tummy, my heart melts. Sometimes I forget how much he craves affection, but just like a child, it couldn't be clearer that he needs me right now.

So we bask in the 95 degree garden, sick and missing work and perfectly content. One of the birds nesting in our neighbor's vent came to visit, catching a fly before darting off. Insects come and go - honeybees sipping nectar from our flowers and hording the pollen, earwigs nesting in one of our heads of lettuce, an Ichneumon wasp prowling for insects to devour. 

Borage plant

The soles of my feet are brown with dirt, my legs are reddening from the sunshine (I can only imagine how sunburnt my face will be in a few hours), and a string of drool/vomit coming from Surge's mouth has collected chunks of beauty bark, and dangles hilariously from the left side of his muzzle.

My sick Catahoula "puppy"

In commemoration of this gorgeous day, I'm posting some photos of lovely insects, and a few of my puppy. Some from the beginning of June, when the insects seemed more abundant, or at least more diverse. Most from today, when Surge and I panted and sweated and puked...and leaned into one another, reveling in the brilliant, shining sun.

busy bee!

Calliphoridae (fly) on a sunflower

Andrenidae (mining bee) on a lily

Bee mimicking flies are cool!

A darting little hoverfly

Warm, sleepy puppy!

Aww...

A Siricidae (horntail wasp), scouting for prey...

Apis mellifera

We spent almost half an hour chasing this fly around with a jar. Now Surge is checking it out...

This.

Ratcliff et al 2012, Experimental evolution of multicellularity

Do you see this?




I DID THIS.

Okay, I didn't do exactly this experiment and publish this paper. But, following the Ratcliff et al protocol, with a few minor tweaks, I evolved multicellularity. In just 23 days. Here's a photo of my yeast.