Levels

End of The Gene

Exhibit A: Reductio Ad Absurdum

Exhibit B: Genetic Dark Matter

“A fruit fly study suggests the whole-genome approach may be the way to go.”

Exhibit C: The Genome vs The Gene

Exhibit D: The Proteome vs The Genome

“you need to look at the things that the genes are producing, and what’s happening after the genetics.”

Entanglement

Daniel asks, Does the Mind Influence Physical Processes?

Proof: our mind sets out to modify our environment in particular ways (i.e. set goals); then we act in ways consistent with that intention; more often than chance, our environment changes in those intended ways (i.e. goals are achieved).

This is a form of entanglement — spooky action at a distance — between our minds and the environment (which includes other minds), but we usually dismiss this as trivial, not very spooky. On the other hand, we know that quantum entanglement exists and it seems spooky to us because we have no mechanism to explain it.

We also observe that there are quantum effects in the basic architecture of the brain (nanotubules) and wonder if these are somehow the “ghost in the machine” of consciousness. But this could be just a red herring. Perhaps quantum effects matter to consciousness, perhaps they don’t. Still quantum effects are part of the human experience in some sense — and so …

Synthesis of Complexity Theory

As careful readers of this blog will note, I’ve been obsessed with Alex Ryan’s visualization of the way new levels of organization come into being (e.g. atoms –> molecules –> cells, etc).  In an attempt to complement and extend his model, here’s a visualization of how I think of the various concepts coming together:

Evolution Emergence Synthesis

First off, I know that this may not make sense to most people.  The relationships implied by proximity, color, dimension, etc are not totally accurate.  The problem is, I’ve reached the limit of my personal ability to create a good visualization.  So I’m throwing this out there half-baked hoping that the crowd (that’s you) will help bring this together in a more coherent way.

I’m especially interested in hearing from people who have great design skills.  If you don’t, then at the least you can ask probing questions to suss out the sources of confusion, which will then feed into the redesign process.

A more detailed explication of these concepts can …

Convergence

As readers of my blog posts know, I talk a lot about evolutionary systems, the formal structure of cooperation, the role of both in emergence of new levels of complexity, and I sometimes use cellular automata to make points about all these things and the reification of useful models (here’s a summary of how they all relate).  I’ve also touched on this “thing” going on with the system of life on Earth that is related to technological singularity but really is the emergence or (or convergence) of an entirely new form of intelligence/life/collective consciousness/cultural agency, above the level of human existence.

From The Chaos Point. Reproduced with permission from the author.

In a convergence of a different sort, many of these threads which all come together and interrelate in my own mind, came together in various conversations and talks within the last 15 hours.  And while it’s impossible to explain this all in details, it’s really exciting to find other people who are on …

Comments on Human Cultural Transformation

This is a followup to Ben’s post on Human Cultural Transformation Triggered by Dense Populations.  Too many links for this to be accepted into the comments directly…

In thinking about these questions, it helps me to remind myself of the difference between evolution and emergence. Evolution happens whenever you have a population of agents with heritable variation and differential reproduction rates. There are at least two types of emergence, both of which can create new types of agents. Various self-reinforcing mechanisms lead to stronger and more stable agency. We may not even recognize the emergence of nascent agents for what they are until said agency (or coherence) becomes strong enough. For instance, many people have a hard time wrapping their head around cultural agency of any form.

Obviously none of us on here have a problem with the concept of non-human agency, but as Alex and Ben collectively point out, cultural agents depend on human agents for their very existence.  Yet …

Cancer as a Complex Adaptive System

Heng, et al recently published a review paper that brings together and touches on many different aspects of cancer complexity.  I thought this an opportunity to selectively quote the paper and organize the quotes loosely around various complex systems concepts they relate to.  I’m curious whether this makes sense to readers of this blog, or whether there’s too much unexplained jargon and too many large conceptual leaps.  Please ask questions or make comments freely below.

One preface I think will help is to understand that genome, karyotype and chromosome refer roughly to the same thing.  Here are several schematics that I will present without explanation that together illustrate how genes relate to genome/karyotype/chromosome structure, and how that in turn relates to the so-called genetic network (loosely equivalent to the “proteome”).  Of course “gene” is an outdated and inaccurate concept, so don’t get too hung up looking for genes here, just understand that they are sub-structural elements of the genome.

From MSU website

Micro –> Macro –> Micro, etc.

Kevin has a few threads regarding the effect that micro behaviors have when aggregated to macro behaviors:

It occurred to me as I was reading this Huffington Post article that there is a reverse-emergent dynamic that occurs when countries (often through their leaders) send signals to other countries through word and action.…

Superfoo

Response to Superorganism as Terminology.

I was actually about to post something about terminology, so I’m glad this came up. It’s just so difficult to choose words to describe concepts that have little precedent, without going to the extreme of overloading on the one end (e.g. “organism”) or the other extreme of being totally meaningless (e.g. “foo”). I have tried to use terms that are the closest in meaning to what I’m after but there’s no avoiding the misinterpretation. I can only hope by defining and redefining to an audience that is not quick to make snap judgments but rather considers the word usage in context, we can converge to at least a common understanding of what I am claiming. From there at least we have a shot at real communication of ideas and hopefully even agreement.…

Response to "Superorganism Considered Harmful"

This is a response to Kevin’s post responding to my post.

Rafe makes an analogy to cells within a multicellular organism. How does this support the assertion that there will only be one superorganism and that we will need to subjugate our needs to its own?  Obviously, there are many multicellular organisms. Certainly, there are many single-celled organisms that exist outside of multicelluar control today.  So where is the evidence that there will be only one and that people won’t be able to opt out in a meaningful sense?

The Conflict Between Complex Systems and Reductionism

The following is a recent paper by Henry Heng published in JAMA.  I’ve linked concepts mentioned in the paper to corresponding explications from this blog.


JAMA. 2008;300(13):1580-1581.
The Conflict Between Complex Systems and Reductionism
Henry H. Q. Heng, PhD
Author Affiliations: Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, Michigan.

Descartes’ reductionist principle has had a profound influence on medicine. Similar to repairing a clock in which each broken part is fixed in order, investigators have attempted to discover causal relationships among key components of an individual and to treat those components accordingly. …

Encoding Life's Complexity

Will Wright’s demo of Spore illustrates some key concepts of complex systems, including the notion of simple rules generating complex behaviors, and also the power of recursively applied (i.e. fractal) computation at different levels.  Living systems leverage these same principles.…

Complex Systems Concept Summary

I figured it was time for a reset and so the following is a summary of much of the foundational posting that I’ve done on this blog so far.  As always, a work in progress, subject to refinement and learning……

Response to "Thoughts on Ants, Altruism and the Future of Humanity"

[ This is an edited version of a blog comment on Brandon Kein’s Wired Science post here ]

The question of whether we will “break through” to a superorganism or collapse through any number of spiraling cascades or catastrophic events is the subject of Ervin Laszlo’s book, The Chaos Point, which I highly recommend.  In it, he gives a sweeping view of the complex evolutionary dynamic (focusing on human society), and makes a solid argument that we are at an inflection point in history right now, similar to the “saltation” that begat multicellularity.…

Notes from TED

Here are some notes that I took at TED 2008.  I have a bunch more on each of the speakers individually which I may post as time permits.  Let me know if you want me to expand any of the notes below into a full post.

What is a Gene?

Not having had any serious biological training I have to go to Wikipedia and Google to learn the basics. And I’m often surprised to find that concepts everyone uses don’t have good consensus amongst scientists. When reading the Wikipedia entry for “gene”, it occurs to me that if the concept didn’t predate the discovery of DNA, it would not exist.…

Types of Emergence

Stability can be thought of as a measure of agency. That is, the more stable a system is, the better we are able to recognize it as a distinct agent, a system that actively, structurally or by happenstance persists through time, space and/or other dimensions. Burton Voorhees defines a concept of virtual stability as a “state in which a system employs self-monitoring and adaptive control to maintain itself in a configuration that would otherwise be unstable.” He clarifies that virtual stability is not the same as stability or metastability and gives formal definitions of all three.* By making a distinction between stability, metastability and virtual stability, we can gain further clarity on agency itself and the emergence of new agents and new levels of organization.…

Generalized Evolutionary Theory

Over the years evolutionary theory has itself evolved to encompass new and more disciplines: social Darwinism, genetic algorithms, co-evolution of biology and culture, evolutionary psychology, economics, psychoanalysis, and more. Attempts to formalize evolution typically have focused on several elements or preconditions for natural selection:

  1. a POPULATION of individual agents
  2. a REPRODUCTION mechanism
  3. a MUTATION mechanism that yields differential fitness of agents
  4. a SELECTION mechanism which favors highly fit agents over others for reproduction

Inter-Level Interactions

For me, the following metaphor really helps to envision the relationship between levels and their interactions. Imagine a clear rectangular container viewed from the side. Inside the container are various substances with various degrees of attraction to and repulsion from one another, such as sand, water, vegetable oil, alcohol, pebbles, ice, motor oil, etc. …

Mechanisms of Agency

The following is a non-exhaustive catalog. Note that these mechanisms are in fact emergent properties of the system under study, a fact which has some fairly profound consequences when considering the lowest known levels in physical systems. Read Ervin Laszlo’s chapter, Aspects of Information, in Evolution of Information Processing Systems (EIPS) for more theoretical background.

Stasis

The most trivial form of stability we can think of is an agent existing in the same place over time without change. This may only make sense as you read on, so don’t get caught up here.

Movement

Keeping time in the equation but allowing physical location to vary, we see that agents can move and continue to exist and be recognized as the “same”. This is obvious in the physical world we live in, but consider what is going on with gliders in the Game of Life. The analogy is more than loose since cellular automata are network topologies which mirror physical space in one or two …

Cultural Agency

Talking about culture from a complex systems standpoint requires a bit of inductive leap of faith as follows. If you buy the argument that agents emerge from agents (and interactions thereof) at lower levels, then it is clear that there is some level of agency above individual humans.* What we call this level varies according to who is telling the story and what the thrust of their thesis is: population, culture, society, memetics, economy, zeitgeist, etc. The reality is that all of these levels (and more) co-exist, and we are talking about interlocking systems at varying “partial levels” with dynamic, and only loosely constrained, information flow. Nonetheless, there are common elements and properties that we can discuss that are at the very least distinct from the realm of an isolated individual human being.

Agency

To understand the concept of agency and emergence thereof, it helps to think about very pure systems that exhibit agency emergence. One such system is Conway’s Game of Life, a kind of cellular automata system which exhibits some uncanny life-like behaviors. You should read the synopsis of Life as well as watch various simulations of it unfold so you get an understanding and an intuition about what’s happening. A remarkable aspect of Life that the rules that govern everything that happens in the system are extremely simple and only apply to a local neighborhood on a grid. What emerges as a run of Life unfolds could hardly be called simple though.…

Networks

One useful model of how information flows between elements of a level is the mathematical abstraction of a graph, more plainly known as a network. The internet is our current exemplar, but most levels of organization are amenable to network modelling of information flow: social networks, biochemical pathways, molecular latices (aka crystals), etc. The basic components of a network are nodes (i.e. the elements/agents of the level of choice in the previous post) and links from one node to another. The links in our abstract model define which nodes can pass messages to (aka share information with) which other nodes. If we wish to have a complete understanding of information flow using network modeling, there has to be a link between every pair of nodes/agents that might interact in some way.*…

Levels of Organization

One of the paradigms in complex adaptive systems thinking that has great explanatory power is the idea that there are distinct systems organized hierarchically in various levels of complexity. So, for instance, you can look at atoms as being a system at one level of organization, on top of which sits the next level of atomically bonded compounds (aka molecules), on top of which sits the next level of molecular reactions (e.g. chains of enzyme reactions), and so on. It’s well-understood that within a given level, the individual elements (i.e. atoms at the atomic level, molecules at the molecular level, etc.) interact with one another and can be thought of as passing messages or sharing information. At the atomic level the interactions (mainly) come in the form of atomic bonds: two hydrogen atoms bind to an oxygen atom in a particular configuration in a standard and repeatable way. Incidentally — from the standpoint of the atom — we come to recognize this pattern and classify …