Metalanguage

Most sufficiently complicated non-linear systems can be sufficiently described by a few handy rules of thumb. In the case of the way light interacts with groups of atoms we have color. For the change in the number of ways in which atoms can be organized given a change in the energy of any particular arrangement we have temperature. For organic chemistry there are a certain number of rules of thumb that allows an organic chemist to design and implement reactions in which they know how the chemicals will change given the pKa's, Gibbs free energy, proposed reaction mechanism, and other salient aspects of the reaction (these being a finite list).

What if the way in which our "rules of thumb" are generated could be generalized for any sufficiently complicated non-linear system. In other words, what if the constraints in the possible outcomes given any input could be formalized?

In more explicit terms, what if it was possible to generate a language which would create contraints given a particular input (or environment), which in turn would create unforseen constraints, which could then change the original constraints as well as the environment. In other words, a system which given a continual input of environmental variation produces both order (predictable or individually defined constraints) as well as unintended constraints (e.g. ensemble defined constraints, or the sum total of unexpected by-products from each individual constraint) which lead to greater environmental variation. This in turn leads to the creation of different predictable constraints which also creates more unintended constraints, which in turn continues to increase environmental variation. In nature the envirnoment is very rich and diverse (highly variable), which can be viewed as coming from the earth being an open system as well as the fact that life (the sum total of unexpected by-products of chemical reactions) arises from the laws of chemistry (predictable, individually defined constraints).

Such a language could be considered a metalanguage since it would be constantly bootstrapping its own meaning. Or in other words, if one thinks of the ensemble constraints as being a meaningful interpretation of the sum total of individual constraints between elements of the system, the system would be constantly producing meaningful and new interpretations of itself as it expanded outwards into greater and greater diversified forms. A language which writes itself.

Do You Realize?

What is life?

This question is a horribly difficult question to answer in a universal way. A friend recently brought to my knowledge the word "holon." A "holon" is a system that fails to be adequately described by either a top-down or a bottom-up perspective (for example a liver, or a heart, or a cell, or a brain, or an ecosystem). Life appears to be composed of many interacting holons composed of holons embedded within holons. This makes it seem like an impenetrable mess that cannot be understood completely from any perspective. One can describe aspects of a system (such as the DNA sequence of an organism, or the number of individuals in a population, or the behavior of an organism in a particular environment), but to get the whole framework with every level, layer, and permutation of significant information is for all practical purposes impossible. This is because the sheer volume of information appears to be prohibitively enormous...and how much of that information is actually useful is and more importantly how confident are we that we know how to define usefulness is anybody's guess. It seems ridiculous to try to describe the behavior of a human being based upon the solution to the Hamiltonian that gives the wavefunction which describes a person.

A subset of what you would need to know (obviously a very incomplete list):
Given any DNA sequence,type of organism, probability distribution of suite of molecules in any and all cells be able to predict:
Protein Structure
RNA Structure
Active sites in catalytic entities (proteins, RNA, protein-RNA complexes, others...)
Kinetics of all catalytic entities (diffusion limited, Michaelis-Menten, other approximations...)
Protein interaction sites on any proteins or protein complexes
Allosteric sites on proteins and protein complexes
Protein networks formed
Metabolome (-all metabolites in a cell)
Post-Transcriptional modifications
(alternate splicing, introns, exons, etc...)
Post-Translational modifications
(Methylation,Amination,Acetylation,etc...)
Lipid catabolism and anabolism
Protein catabolism and anabolism
Carbohydrate catabolism and anabolism
*Other molecule* catabolism and anabolism
Formation of higher order structures (e.g. organelles) and how that affects all other activities in the cell.
Physical model of the cell
Energy transduction pathways
Signal transduction pathways
Information flow within a cell represented as:
Be able to define all steady-states of the system given ANY perturbation at ANY level of information
Gene networks
Protein networks
Time resolved evolution of all components of the cell and hence:
Cell cycle
Cell apoptosis
All salient reactions in a cell given its steady-state

With previous set of information extending upwards...
Be able to define all cell types as different steady-states of the same model
All interactions between all groups of cells
Developmental interactions between cells (time-resolved evolution of groups of cells)
Higher-order pattern formation (e.g. spiral waves in heart, zebra stripes, leopard spots)
Complete physical model of groups of cells scaling all the way up to entire organisms
How this higher order information (organ level/organism level) changes the particular steady-state of any cell (e.g. going from starvation mode to energy storage mode, or a rest state to an active state)
Homeostasis
Cell differentiation
Morphology of organisms

Extending upwards...
Given a population of organsims be able to predict:
Response to any form of selection at any level of information and how it changes all levels of information
Mutation accumulation
Changes in all moments of distribution of phenotypes
Evolution of higher order structure in information structures composing organisms (e.g. how evolutionary forces affect and produce gene regulation, signal transduction pathways, higher order steady-states for more complicated functions of information arising in organisms)
Complete ecologies and ecosystems given a known physical/chemical environment

And that will get you one millionth of the way there.

The idea of steady-states and perturbations from steady-states is very important, and if one could understand the appropriate geometry of the interactions between all elements of the system, one could know exactly the paths between steady-states given a particular parameterization, intial condition, and perturbation. The question becomes if there are any universal features of the geometry of interactions between elements in the system, and more specifically how do the higher order structures created by underlying variables (e.g. organs/groups of cells performing one function created by proteins, DNA, RNA, etc...) in turn affect their own synthesis and function and the synthesis and function of other groups of cells. This is where the geometry becomes very warped and self-referential. On a simple level, DNA -> mRNA -> proteins which then can go back to DNA and can change which genes are being transcribed. But say one's liver is trying to detoxify a thousand different chemicals in varying concentrations (not an unreasonable assumption)... The presence of any one chemical, or in this case an ensemble of chemicals can have a different effect on the states of the cells. Say in the case of a 1000 chemicals of varying concentrations the liver decides to allocate the most toxic chemicals the most energy (e.g. makes an effort to divert as much precious cellular energy as possible) to degrade that chemical, and the least toxi chemicals the least energy. Or, if concentration was a more important factor, the liver could decide to degrade the most abundant chemical (e.g. ethanol after a night of binge drinking) as opposed to a more toxic chemical in lower concentration (e.g. ammonia). Each of these scenarios could lead to radically different spatiotemporal distributions of underlying molecular species in any particular cell in the liver, and potentially the entire organism (e.g. if one gets alcohol poisoning)

Stars, or why god exists(/doesn't exist)

Each progressive symbol builds on previous symbols. Each symbol builds on itself causing stars (symbols) to burst outwards in a cacophony of constellations. These constellations constantly coalesce into greater galaxies (meta-symbols). Not linearly, but broken; jagged. Hidden relationships revealed, with vast expanses of nothingness in

-

between. But what, nothingness? Hardly. No symbol can capture nothingness, just like no symbol can capture itself. HA! Fooled you, because you can capture yourself...or can you? But what are you doing right now?


Galaxies grow without bound into universes. The universe, is not singular (uni-). The multiverse falls plague to the same paradox. How can there be many everythings? Infinity plus one. But why must there be a symbol that encaptures everything, including itself?

An infinitely recursive worm ouroboros expanding outwards in every conceivable and inconcevable direction, swallowing its own tail. Hidden meta-ouroboroses cause god to trip and fall. (How heavy was that stone?) But, a god, the god, only god, un-god, is beyond the constellation, beyond the confines of the symbols. God gOd goD is hidden in the nothingness and the infinities that lie in the blind spot of the mind's eye.

But...what happens, when the galaxies themselves wake up. What happens when the universe wakes up? All symbols (stars) coalesce into a singular point, that reverberates across the cosmos, faster than the speed of light, infusing all existence with...essence

What happens when nothingness wakes up? What happens when the wall comes crumbling, exploding, disintegrated...until symbols fill existence with pure...........................