TNFR research program: organization, dynamics and predictive state¶

Scientific objective¶

Determine which justified states, laws and interactions allow organized structures to form, persist, change and compose, and which information predicts their response. The engine, conditional mathematics and retained experiments make these questions concrete. Universal realization, autonomous hierarchy, a uniquely selected fundamental law and physical identification remain open.

An organized object is an instrument for investigating those questions. Its support, preparation, identity and complete law make a claim decidable under explicit premises. A successful construction establishes that scoped result; it does not make its graph, coefficients or event schedule mandatory for TNFR. The ontology distinguishes graph birth, regional formation and a sufficient effective description. None substitutes for another.

This program and its linked chapters form one maintained research account. The program owns orientation and the current decision; each technical chapter owns its definitions, proofs, counterexamples, protocols or implementation contracts. Published pages are generated from those canonical Markdown files. Verified corrections govern current claims. Superseded errors, duplicate overviews and completed task logs belong in Git history; valid negative results and the evidence needed to assess a correction remain part of the research. Some protocol chapters retain evaluated prospective prefixes verbatim, including historical references to retired plans. Those references preserve evidence context; this program alone owns the current task. Historical study instructions do not activate work. The theory-to-execution map locates code and tests.

Reading the research as one program¶

Start with the conceptual core for structure, sufficient state, identity and complete dynamics. Its claim-strength table, dependency map and progressive examples explain how to read the technical proofs below. Use the glossary for concept classification and the relevant chapter for the actual definition, law or proof. The route is core -> glossary as needed -> model owner -> implementation/tests -> current task.

Part	Scientific question and technical entry
State and complete laws	Which coordinates and independent premises determine evolution? Parameter foundations, relation foundations
Organization and identity	What is acquired, how long does it persist, and what counts as its transformation? Ontology, pattern dynamics
Interaction and composition	Which constituent and boundary information survives contact? Relational composition, resonance foundations
Structural actions and grammar	Which actions and ordered words descend to an organization? Operator contracts, grammar
Scale and predictive state	When can constituents be grouped, eliminated or approximated? Scale and bridge, relational memory
Observation and discrimination	Which alternatives can an admitted reading distinguish? Diagnostic scope, minimal-state boundary
Mathematical and computational methods	Which proof, representation and numerical allowance establish the claim? The corresponding technical derivations, shared kernels and testing guide
Physical comparison and auxiliary studies	Which additional measurement or mathematical premises are supplied? Physical atlas, arithmetic and auxiliary chapters

Read each study with its complete model. Native relational dynamics, normalized-sine comparisons and supplied source-port laws have distinct pressure, phase, capacity, support and clock contracts. Their shared language supports comparison; a transfer of a theorem requires matching its premises. Arithmetic, graph-wave, Hamiltonian and gauge constructions retain their own assumptions and can contribute methods or counterexamples without becoming prerequisites for every organized-object investigation.

What the repository currently supports¶

The strongest reusable capabilities concern explicit mathematical objects, not an empirically validated universal realization. Distinguish a theorem on a domain, one retained event or numerical response, and an executable policy.

Capability	Established scope and remaining boundary
Formation and recovery	Native and sine studies provide admitted capture, prepared acquisition, recovery and obstructions. Source, identity, loss and uncertainty belong to each model; preparation is not generally autonomous.
Organized interaction	Formed classes have actual contact responses, nonlinear discrimination and causal interfaces. Contact work, source history and boundary association remain part of the claim.
Predictive information	Exact charts, retained memory, information-loss counterexamples and finite error theorems distinguish sufficient state from diagnostic summaries. A tangent closure need not close the nonlinear law.
Structural transformation	All thirteen registered actions have implementation contracts and scoped mathematical studies. Collective admission, work, successor laws and occurrence are separate obligations.
Hierarchy	Actual parent and child words have created two hierarchy levels with separately acquired histories. New coordinates and parent metadata do not establish a maintained larger organization.
Certified computation	Shared primitive admission, outward arithmetic, proof readers and retained protocols support reproducible conditional results. A passing implementation test is not a physical measurement.

The hierarchy evidence already includes a maintained-parent birth, a committed Coupling event and post-Silence retention of all 53 principal edge branches on the 21-node support through elapsed [0,1/2]. The connected child then acquired its own three samples and Dissonance history. Its completed OZ,THOL,SHA word created a level-two descendant: 22 nodes with the same 53 edges. That descendant is isolated and has no acquired temporal baseline. Repeating these mechanisms would need a new scientific discriminator.

On a different, dissipative 45-node source, the joint orbit state retains the full primary state modulo one global child exchange. Its generic dimension remains 90. Separate results prove hidden relaxation and tracking by an independently evolved symmetric core. The latter requires matched initialization, unit capacities and no events. These results distinguish exact retained information, instantaneous tolerance and accumulated prediction error. They do not supply the conservative hierarchy source with attraction or a smaller universal NFR state.

The thirteen actions as capabilities, not a prescribed itinerary¶

The mechanism audit owns detailed actions and execution paths. The following map states why each can matter scientifically and what must still be admitted when it is used.

Registered action	Available mechanism	Consumed premise or open boundary
Emission (AL)	Changes form on existing support; scoped collective AL/SHA actions	Targets, source and reset work; no node creation or derived input selection
Reception (EN)	Mixes existing incoming-neighbor forms; collective EN/IL/SHA	Actual neighbor counts and context; the unweighted mix can raise weighted storage
Coherence (IL)	Contracts stored pressure; complete paths also align phase	Nonzero neighbor resultant, branch, phase work and constitutive refresh
Dissonance (OZ)	Perturbs stored pressure with configured propagation	Refresh can erase the continuous effect; retained pressure needs its own law
Coupling (UM)	Changes phase and optional capacity; proposes actual links	Candidate access, affinity, support work, live compatibility and occurrence
Resonance (RA)	Compatible-neighbor form mixing and configured phase/capacity changes	Its full reset and retention domain; neither support creation nor automatic passivity
Silence (SHA)	Attenuates capacity and records latency	Changed future rows and means; finite positive attenuation need not freeze motion
Expansion (VAL)	Raises capacity and, under the default policy, changes form	Form origin, reset work and subsequent law; no derived new dimension or clock
Contraction (NUL)	Lowers capacity and rescales pressure/form according to policy	Valid grammar and endpoint identity do not guarantee future maintenance
Self-organization (THOL)	Pressure action or admitted nested-child construction	Own associated history, hierarchy, resource rule and disconnected successor law
Mutation (ZHIR)	Phase reset after a live signed-growth test	Separate temporal evidence, grammar, reset work and successor identity
Transition (NAV)	Contextual pressure, phase and capacity changes	Regime and latency history; an admitted action can leave the prior acute sector
Recursivity (REMESH)	Advisory, delayed same-support mixing and explicit topology APIs	These are distinct actions; association, actual mixing and support changes need their own contracts

An object can realize a useful subset. A registered catalog does not establish that every organization admits every action, that all words preserve one identity, or that the continuous law selects their occurrence. Collective words require descent at every prefix, including actual targets, history, context and successor state. Supplied selectors remain executable policies until their selection law is justified.

How the next question is selected¶

Begin with the scientific consequence, then compare candidate questions on three grounds. Impact: would the answer establish or exclude a missing organizational capability, or resolve a premise consumed by several results? Discrimination: can a proof, matched counterexample or admitted observation separate the live alternatives? Feasibility: can that separation be reached with available sources, mathematical methods and a credible total budget?

These are reasons to compare explicitly, not numerical scores. Prefer a question that advances the same capability with fewer unsupported premises or a clearer discriminator. Reject an infeasible evaluation even when its target is important; name the prerequisite instead. Ease of extending recent code, a larger repetition count or an attractive visualization is insufficient.

For the selected question:

Name the object, intended capability and observation; distinguish formation, retention, prediction, action and occurrence.
Inventory the sufficient state, complete law, source and relevant existing results. Include boundary associations and every discarded coordinate.
Try an analytical obstruction or equivalence before adding computation. Check conserved quantities, symmetry, accessibility and observational ambiguity.
Choose the smallest discriminating claim. Record the competing explanations, acceptance conditions, resource limits and what an unavailable result means.
Freeze any new evaluation prospectively, preserving inspected evidence as prior information. Run only the admitted calculation and affected controls.
Close with a proof, counterexample or named missing premise. Reconsider the global priorities before selecting another extension of the same example.

Continuation point: foundations reviewed, research not resumed¶

Status: final conceptual and documentation-layout review complete. No new research has been started. This ordered checklist is the persistent continuation record for future sessions. Its completed deliverables precede selection of the next research question; future edits must preserve their clarity and evidence boundaries. Keep its status here; agent instructions and entry points link to this record.

Order	Deliverable and acceptance condition	Status
D1	A compact conceptual core connects NFR identity, sufficient state, complete evolution and interaction, with one technical definition owner per concept.	Complete
D2	The core distinguishes working premises, supplied model laws, derived identities, conditional theorems, computational evidence, policies and open hypotheses.	Complete
D3	A dependency map connects foundational claims to their premises, downstream uses, proof owners and relevant code/tests; distinct complete laws remain distinct.	Complete
D4	Progressive worked examples explain state, change, interaction, lost information and operator/identity limits using existing admitted models.	Complete
D5	Align the glossary, README, agent mirror and generated navigation; verify links, documentation examples and the strict site build; preserve unrelated proofs and frozen evidence.	Complete

The conceptual core owns the reading deliverables D1-D4; its linked technical chapters retain definitions and proofs. All five deliverables are complete, with generated navigation, reference, example, archive-prefix and strict site checks. This is a conceptual reading review, not a new proof or a scientific revalidation of every technical chapter. Preserve full derivations and counterexamples in their owners; remove obsolete instructions and repeated summaries only where their replacement is explicit. No research producer, new trajectory, parameter search or frozen replay belongs to this documentation task.

The final review separates identity/maintenance from acquisition, and prediction with retained memory from an autonomous law on current aggregate coordinates. Deterministic prediction also requires existence, uniqueness, domain retention and specified event behavior. Supplied operator maps and algebraic diagnostics retain their actual status. These clarifications are in the linked foundation owners; no new primitive or constitutive law is selected by this review.

The maintained layout now has a small program and one canonical Markdown file per chapter, with metadata-only navigation and preserved evidence associations. The execution map has its own chapter. Generated compatibility files retain historical local links without restoring their former task instructions. The review covers the foundational reading route and its dependencies; it is not a new proof audit of every technical result or a physical validation.

On resumption, apply the global selection criteria to the clarified dependencies before activating a bounded scientific question. The retained candidate below is available for that comparison; its prior position does not automatically make it the next experiment.

Retained research candidate: collective identity after birth and contact¶

Can the existing parent-child composition support a prospectively specified relational identity and subsequent response that distinguish collective organization from admitted birth, connection and inherited branch geometry?

If selected after the documentation gate, the task is analytical admission of one such identity/response contract, or a precise obstruction or missing premise. It does not activate a new event, response producer, trajectory, parameter search or repeat of the retained hierarchy evidence. The starting object is the existing 21-node parent-child composition; the later isolated descendant is separate evidence.

Re-admit the actual source, support, conductances, positive capacities, phase lifts, clock and complete law from the retained THOL/UM records. Choose and declare the continuous segment being discussed: UM changes support and Silence changes capacities, so their continuations are different parameter states. The weighted conservative two-row law supplies no positive loss. The dissipative 45-node source and its child-relaxation theorem cannot supply missing contraction, constants or formation evidence for this object.

The contract must specify a relational observation with a domain before and after the support change. An unavailable pre-birth observation is not a measured absence. Identity must have a justified width and signal floor, an absence criterion, an entry criterion, a declared lifetime and a continued response without resetting the acquired state. The common-organization contract provides those obligations; its localized source and coefficients do not transfer.

Compare against the corresponding disconnected continuation and any equally informed alternative needed by the claim. Connectedness, nonlinear response, transient overlap or a common label alone cannot be the discriminator. Check compatibility with the actual storage, both means, phase geometry and complete rows before proposing a finite evaluation. Conservative volume and recurrence obstructions retain their domains; they neither promise permanent attraction here nor exclude every finite-lived or internally moving identity.

State separately what predicts the selected response. Test proposed collective coordinates against fine-state ambiguity; retain hidden initialization, boundary association or derived memory when necessary. A sufficient full-state description can establish an organization without a reduced autonomous law. Failure of a proposed reduction answers that information question, not the existence question.

Completion is one admitted contract with its analytical feasibility and exact remaining evidence requirements, or a scoped obstruction that explains which premise must change. No formation verdict follows merely from this admission. A future evaluation needs its own prospective freeze; existing inspected responses cannot become reserved evidence for a newly chosen identity.

The symmetric-core tracking result is closed. A hybrid extension through a word would require reset comparison, changed-capacity dynamics and a joint mean/error budget. It is a deferred technical dependency, reopened only if the selected organizational prediction consumes it.

Shared scientific admission¶

Stage	Required record
F1: state	Identity, domains, units, chart, support, constituent/boundary association, observations and discarded information
F2: law	Independently specified pressure and every consumed phase, capacity, clock, source and event law; held quantities and remaining freedom
F3: consistency	Actual-model symmetries, boundaries, conserved means, storage/loss, event work and execution path
F4: discrimination	A prediction, equivalence or obstruction with fixed source, law, observation, horizon, uncertainty and numerical budget

Constitutive uniqueness requires independent information that distinguishes retained countermodels. A matched equilibrium, tangent, storage balance or successful organization does not select the nonlinear law. Conditional formation research can proceed while that uniqueness question remains open. Support, conductance, length, capacity and clock have distinct roles; spatial distance and a laboratory time unit require their own admission.

Retain both evolution rows and their actual capacity factors. Positive held capacity arguments need not remain uniform near zero. Stored pressure, constitutive refresh, predicted derivatives and acquired temporal samples are different evidence. A child inherits no parent's measured history. Continuous loss, support-event work and an independently supplied reservoir are separate balances. Missing observations remain unavailable.

Dependencies available when a selected claim needs them¶

The following are reopening conditions, not additional active tasks. Their technical owners retain full derivations and unresolved cases.

Dependency	Required reason and retained owner
Hybrid prediction and capacity renewal	A named sustained response requiring events or replenishment; admit reset, successor law, means and resources. Source-word dynamics, tracking scope
Grammar across scales and autonomous hierarchy	A selected action or occurrence claim consuming collective context, history, resource and support laws. Collective descent
Localized common organization and prepared envelopes	Initial absence, a compatible mechanism and credible whole-pipeline bounds. Formation compatibility, retention mechanisms
Stationary contact and source-directed formation	A global mechanism or independently constrained preparation; retain asymmetric/nonacute/degenerate candidates and own-law barriers. Contact maintenance, conservative preparation
Receiver accessibility and operational saddle sources	A downstream claim consuming unresolved transfer or positive source width, with all source errors and forward horizons. Receiver comparison, transfer study
Alternative mobility, wider pulses and nonlinear rebound	A named response outside the proved regime; establish actual-law circulation, invariant density or nonlinear remainder. Mobility, resonance
Partial observation and reduced memory	A selected prediction, admitted joint uncertainty and hidden preparation; bound coupled predicted histories. Environmental memory, pair state
Chemical hidden state	A specific mapping or prediction under its supplied matrix, clock, initial bromide and illumination; re-derive its time-dependent kernel. Chemical admission
Independent storage comparison	A new foundational need and separate source/observation/numerical freeze. The eight-history observer has no frozen attempt or response.

Frozen evidence and resource constraints¶

Keep source archives, prospective declarations, responses, failures and verdicts unchanged. Corrections have separate records. Hashes associate bytes; they do not authenticate acquisition or chronology. Routine regression and editorial reorganization do not regenerate research producers. The evidence guide and archive index retain recovery responsibilities.

Two deferred numerical boundaries deserve an explicit reminder:

The relative-coupling freeze remains unevaluated: four nominal twenty-coordinate states, sixteen steps of 1/4096 per branch, order twelve and outward dyadic128 arithmetic. The single bounded attempt allows 120 wall seconds per branch, 512 MiB memory and a 32 MiB response; no retries or changed steps/order.
The canonical variational study retains its pi/4 carrier, periodic m=1/2 profile, phase time and error class. Apply gain 512 once to accumulated initial error, defects and joins. The target remains 2^-24, pre-gain allowance at most 2^-34, with analytical tails separate. Preserve signed cancellation, both rows, endpoint carry, every residual degree and independent joins; admit total cost before reopening.

Other completed studies keep their own exact budgets in their technical chapters and immutable protocols. An allowance cannot be borrowed from a different source or observation. Unavailable within budget is not a negative physical result; a failed sufficient certificate is not a nonexistence proof.

Physical comparison: a separate admission¶

Stage	Obligation
P1	Correct diagnostics and causal access; separate calibration from evaluation
P2	Independently admit measurement, preparation, input, clock and uncertainty
P3	Freeze reserved predictions and equally informed alternatives; evaluate without refitting
P4	Test partial observation and memory under the same law and information budget
P5	Test the formation, maintenance, recovery and transitions required by the claim

No dataset has passed this complete bridge. The physical atlas is a comparison library. Name a supported measurable property before selecting a comparison; EPI need not itself be a sensor reading. Use workstation-accessible terrestrial data or separately admitted ordinary laboratory protocols. Astronomical, satellite and large-facility campaigns remain outside scope. Independently calibrated geometry and clock can support a scoped comparison; deriving all spacetime is not its prerequisite.

Working with the research chapters¶

This program owns the objective, current task and scientific admission. Each linked technical chapter is a separate maintained Markdown file with one definition or proof owner. Open those files directly in the editor; ordinary Markdown preview loads one chapter at a time. The metadata-only research_catalog.json supplies chapter order and generated navigation. The compiled site is another view of the same sources.

Edit this program for priority decisions and the corresponding chapter for its definitions, proofs or examples. Preserve frozen prospective prefixes, counterexamples and evidence associations. Do not restore parallel plans or edit generated site pages. The retired plan, strategy and portfolio routes remain generated compatibility views with no active instructions.

After changing chapter metadata or concept cards, regenerate checked views:

python scripts/check_documentation.py --write-generated
python scripts/verify_internal_references.py --ci
python scripts/prepare_docs.py
python -m mkdocs build --strict

The program has a separate small-file budget; each technical chapter and maintained guide retains the 4,000-line limit. scripts/research_book.py provides chapter lookup and optional extract/replace commands, but direct editing of the canonical chapter file is the ordinary workflow.

Theory to execution¶

The theory-to-execution map connects mathematical owners with shared implementation and representative tests. It is maintained as a separate chapter so this program remains a small planning and reading entry point. Existing chapter bookmarks below are generated navigation.