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Towards a Logical Data Model for Genetics 4 of 4 - Predicting the Nature of Genetics, a Deeper Dive

Exploring preliminary predictions about the nature of genetic information

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Warren Jones, Lana Rubalsky (2010) "Towards a Logical Data Model for Genetics - Predicting the Nature of Genetics, a Deeper Dive", wJones Research, August 3, 2010

Figure - Erwin Schrödinger, What is Life? 
pages 61, 67

The Gene Is Data

Erwin Schrödinger wrote of the gene is an information carrier (Schrödinger 1944). Although he was suspect of attempts to define its physical structure as a pathway toward understanding its true nature, he was, as evidenced by the calculations in the Figure, very much aware of the gene’s information carrying potential. Note that his observations were made a decade before Watson and Crick would discover the double helix or Eckert and Mauchly would invent the programable computer.

The common thread that differentiates non-existence from existence is molecular structures that contain DNA, such as chromatin. This was proven conclusively in 1952 by Hershey and Chase (Watson 1980) and strongly suggests the information carrier of the gene, must contain the information needed to create and sustain life, which is a superset of intelligent existence.

"Coding" Genes are Only a Small Part of Read-only Identity

In building a storage mechanism for intelligence, it was impossible to design an information basis without Form types more diverse than the information content of coding DNA, i.e. genes (Jones, Rubalsky 2010). Genes primarily contain protein synthesis data which, although important, would form only a small part of a “working” genetic information base, unless defining a very simple creature. Thus far requirements for a “minimal computable system” include substantial graph information we call contextual fabric, and subforms that symbolically define shape, coincidence, state domains, transformations, controllers, sensors, ancestry and media. All of this must be contained within the the purpose hypergraph of a Stored Purpose system and accordingly, in the genetic information store, chromatin.
Platonic_Forms_-_Primatives SymbolicMemory

Agent Identity would Contain Multiple Purpose Groups

Identity_vs_Self

The way we author an SP agent Identity is to start with the definition of the Goals of a single agent Purpose. Typically an agent has multiple Purposes that may be shared and thus constrained by the Patron (system owner) or evolutionary and thus unique to the agent’s role. Development of even simple Purpose necessitates a large base of symbolic definitions for primitives such as a rectangle which is used as a basis ancestor for a plank, which is in turn used as a basis ancestor for a door.

The Basis for Intelligence would be in Every Cell

Although many in the AI community believed intelligence began at birth and newborns started as a blank slate, we found that to create an entity that can grow, reproduce, see, smell, understand shapes, engage in attraction, move muscles, eat and do all the things life can do from infancy, all the needed Platonic Form data to make that possible, must exist within the genetic database. That means all the Form primitives that define the shapes, coincidence, state domains and context of everything an intelligent entity can do at birth, must exist within it’s genetic material. This must be true if the force that created life is bound by the same physical laws that govern all observed nature.
Platonic_Form_-_Convert_Shape

More Complex Life would Have a Lower Proportion of Coding DNA

Statistically, we would expect to see a significant amount of graph-like data in chromatin, what geneticists have called junk or more recently non-coding DNA (Ahnert 2008). This would be encountered particularly in complex eukaryotes where more Purpose is oriented more toward diverse application of physical structures rather than in simpler Prokaryotes, where structural synthesis represents a higher proportion of Identity (Griswold 2008).

Non-coding DNA would be Integral to Identity

If genes were like SPG, they would not only have large datasets that dwarf the known coding gene, but that large dataset would have to be carried intact, whenever a gene was moved from one animal to another. The fact that non-coding DNA is essential information could be demonstrated by identifying similar “coding” DNA sequences in diverse species and determining if near non-coding DNA were also present (Dermitzakis 2004).

Minimal Genetic Information would Include All Symbolic Form Data Needed to Understand and Sustain Self

Existential entities require a complex symbolic information store to sustain Identity. The most efficient structure for symbolic Identity we’ve discovered is the structure of a very long contextual fabric (i.e. node-edge-node, node-edge-node …. door-panel, door-hinge) with embedded Form data that is part of Stored Purpose’s Existence model architecture (Ema). Ema’s Platonic Forms include various types such as state domain graphs that define “right” ranges for symbol pairs such as hot-cold, up-down, close-open, flow-stay. These domain graphs would also include linkages to base technology pairs such as closure-separation that would enable entities to align Self with predicted and measured ranges.

For existence, each entity would require no less than the Form primitives needed for Self synthesis, i.e. an entity would need to possess the symbolic knowledge needed to define and sustain itself, including all the shapes, sequence, coincidence, and technology to continue and reproduce. This would necessarily include a tremendous amount of knowledge of earth ecosystem, including knowledge and understanding of phenomena such as light, gravity, air.

Surveys of chromatin data indicate the requisite information diversity to support the predicted requirements is present (Ahnert 2008).

Chromosomes May Represent Evolutionary Clusters of Purpose

There would not be need for multiple chromosomes unless the genome was not simply evolved, but a result of clustered improvements, i.e. different Purposes evolved in stages and from different organisms.

The presence of prerequisite Form primitives in older Purpose would mean newer Purpose could be more brief. Subsequent acquired Form Purpose might include Form primitives, if the source host did not have compatible ancestor chromosomes and thus integrated Form primitives with the newer Purpose.

The Genetics of All Life within the Ecosystem would Require Some Level of Compatibility

To create a sustainable L5 Mica ecosystem, a certain amount of Form primitives must be compatible across all agents of the system. That means that even if an entity were to evolve for billions of years, some types of standard control Forms would need to persist, unaltered (Tanabe 2002).

Chromosome Form Data would be Propagated and Aligned with Sensor and Controller Technology

Gia_-_Detail
The folded structure of chromatin would need to allow some connection with input/output technology (i.e. mRNA, cell wall proximity) that can read its data. That requires there be either some means of establishing contact with chromatin in its folded form or the Form segments in a chromosome applicable to the operational context of the cell would have to be unfolded and presented to “reading technology” within the cell nucleus when “processing,” i.e. between mitosis (Brown 2007).

Chromosomes Must be Subject to Connection

In animals (SPm) such as humans where cell roles are highly diverse and “fixed” during the lifespan, different parts of chromosome content would be exposed to processing in cells with different functions (Cremer 2001). This would differ from some plant species where each cell can play context “flexible” roles thoughout the plant’s life. Chromosome orientation in these species would conserve across cells (Berr 2007) (Fang 2005).
To be compatible with Gia, there would have to be evidence of active existence processing, i.e. Goal Pursuit. This would be identifiable as a two way expression of data with DNA or an RNA copy, i.e.. propagation of intent as well as comparison and alignment of measured states (Bartova 2010) (Williams 2005).

Mediation

Stored Purpose was designed to reduce the level of human effort needed to service and sustain computing machines. This was an interesting challenge as a single SP metacomputer will host many intelligent agents, each with its own symbolic mind. Thus the complexity is not in simply keeping each component agent and instrument device running, but in keeping the entire system "on track," i.e. fulfilling its intended Purpose on each level of existence.

We call the design that makes it possible to maintain systemic Purpose, mediation, a term that is notably used in classic Artificial Intelligence semantic reasoning to describe data normalization. Mediation in Stored Purpose systems is the external component of a series of complex, independently active controls. It complements the control processes of Valuation and Prioritization. Together, internal agent Valuation, Prioritization and external system Mediation make possible to sustain balance and control within a multi-agent intelligent "ecosystem."

Understanding Levels, Purpose and Identity is an important part of understanding the maintenance process that Mediation sustains. Each part of a system may have different and conflicting Purposes. This is because at each level of existence within a system, the Goals of Purpose at each point of context may differ. Understanding these differences is an important part of understanding the existential maintenance process.

To understand this concept, we will describe a very simplified version of skin cell Identity using (SPG). On Level 1 (cell level), its Purpose is to convert energy and persist with structural shape and construction defined by Platonic Forms in its genome. When near the end of its life as defined in another shape graph or in the context of an adjacent cell's death, its L2 (area level) Purpose will be to simply die or divide and send the dead cell to the food chain. If many cells in the region are impaired by damage such as radiation or infection, its L3 (organ level) Purpose might be to regenerate or even kill adjacent cells. Its L4 (entity-body level) Purpose might be to facilitate hair growth for warmth or perspiration for cooling. Its L5 (ecosystem level) Purpose might be to simply die without replacement (see Improvement below). Note that the Forms that define the Identity of a skin cell must be stored contextually along with the Identity of all cell types (including the slightly different skin cell to the left) within the genome.

With our new found knowledge of how to maintain existence on each level, there are a few things we can predict about intelligent entities living within a sustaining L5 ecosystem. For one, we believe the three tier (Valuation, Prioritization, Mediation) control structure described above is a minimum design framework. This means that if we were to build a complex ecosystem, we would need to design all but the most limited entities with read-only "features" that constrain their Purpose to what’s defined in their genome. We also need to "design-in" features that ensure each entity is subject to external mediation. We believe that in ecology, the role of viruses, bacteria, and other entities such as the mosquito is similar to that of the Stored Purpose mediating messenger class agent in “curtailing” independent agents of a system such that they stay in balance and stick to assigned Purpose.

In a complex ecosystem, diverse messenger agent types would be required to ensure completeness in mediation coverage and redundancy. Although most mediation Forms would be hard coded into the genetic material of all existing agents, a “backup force” of messenger agents would be essential because a failure to curtail success in any single agent, might lead to failure of the ecosystem. Each mediation agent would need to be tuned to affect some segment(s) of the total agent population and have capabilities to perform some mediation function or functions.

Types and modes of Mediation functions supported by messenger agents would minimally include:
  • Amending current generation Identity
  • Amending selection weights for evolutionary choices at reproduction
  • Curtailing active processing at a cellular level
  • Amending reproductive ability
In a natural ecosystem, these messenger agents must be capable of transmitting mediation influence across a very disparate range of life forms. A good example of a natural messenger agent is the Escherichia (E.) coli genome. This genome contains externally sourced message information in the form of extrachromosomal DNA molecules that may be circular (as expected in prokaryotic entities) or linear (as would be found in eukaryotes) (Griswold 2008). The fact that it carries both identity that defines itself and externally sourced information makes the E. coli design very much like an internet message class. An interesting example of nature’s use of this messenger feature, is its use of E. coli like bacteria in the rapid and efficient propagation of antibiotic resistance.

A prediction in need of a study is that within the genetic Identity of all members of the ecosystem, there must be receptor logic that renders each entity “open” to mediation. That means all life must have one or more standard interfaces that allow nature’s messenger agents to curtail.

Improvement

We describe in Article #2 certain requirements in a mechanical system related to "version control" of the processes of upgrade or "evolution" in existential intelligent systems. One of those requirements is periodic agent cold start, i.e. life and death, as significant changes to technology available to a life form would cause systemic instability otherwise. This means that within the genome, there must be Platonic Forms that define decay, and at various points of context within the ecosystem, those "design features" must be activated on a schedule defined within those Forms (Kerr 1972).

Although the details go beyond the scope of this article, it appears that humans are subject to curtailment by Mediation and Improvement controls evolved possibly to balance our unique gift of choice freedom, the ability to go "off the script" of Identity, written into our genome. This "read-write" capacity, enabled by the technology of our brains, gives us each tremendous capacity to expand and pursue new goals, for the limited span of a life. There also appear to be systemic features that may significantly limit that choice freedom.

<< Understanding Logic Design in Genetics, Ten (10) Predictions | References >>


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