Author: Sidong Liu, PhD — iBioStratix Ltd
A unified research programme in operator-algebraic quantum theory.
The core repository is the Genesis Trilogy: thirteen papers across HAFF, Q-RAIF, and T-DOME that ask how geometry, observer architecture, and irreversible self-reference can emerge from algebraic structure.
This repository also contains the six-paper Consciousness Series, which uses that infrastructure to build one continuous chain:
source formation → shared manifestation → feedback → geometry/modular inseparability → gravity → structural horizon of self-description
A separate biological anchoring interface paper connects that series to embodied brain organization.
So the repo is not just an archive of separate papers. It contains both:
- the foundational trilogy that develops the mathematical infrastructure; and
- the follow-on consciousness programme that pushes that infrastructure into a single six-step arc.
- Genesis Trilogy: 13 papers across HAFF, Q-RAIF, and T-DOME.
- Q-RAIF companion papers: downstream compatibility papers extending the Q-RAIF line without enlarging the core trilogy count.
- Consciousness Series: 6 papers across Foundations I--III and
Papers I--III, plus one biological anchoring interface paper, one
programmatic essay, and three
Imprint Interludebridge papers. - Fastest entry point for the consciousness programme: Consciousness Series complete collection DOI
- Repo location for upload-ready consciousness files:
consciousness_series/Zenodo/andconsciousness_series/Zenodo_Meta/
The trilogy comprises 13 papers across three frameworks:
How geometry emerges from observable algebras.
| Paper | Title |
|---|---|
| A | Emergent Geometry from Coarse-Grained Observable Algebras |
| B | Accessibility, Stability, and Emergent Geometry — Conceptual Clarifications |
| C | Causation, Agency, and Existence — Structural Constraints and Interpretive Bridges |
| D | Gravitational Phenomena as Emergent Properties of Observable Algebra Selection |
| E | Measurement as Accessibility — A Structural Analysis of Observable Algebra Selection |
| F | Temporal Asymmetry as Accessibility Propagation |
| G | Structural Limits of Unification — Accessibility, Incompleteness, and the Necessity of a Final Cut |
| PS | Postscript: On the Closure of Structure |
Why an observer's control algebra must embed in the environment's Cl(1,3).
| Paper | Title |
|---|---|
| A | The Quantum Reality-Algebra Intersection Framework |
| B | Algebraic Constraints on Observer–Environment Coupling |
| C | The Structural Closure of Reality Intersection |
The irreversible logic chain: Chaos → Time → Self → Sentience.
| Paper | Title |
|---|---|
| I | Memory as Thermodynamic Resource: Markov Ceilings and the Necessity of Non-Markovian Encoding |
| II | Foreground-Background Partitioning Under Finite Attention: The Emergence of Ego-Structure |
| III | Closure Under Calibration: From Ego-Structure to the Self-Monitoring Loop |
genesis-trilogy/
├── papers/
│ ├── HAFF_A/ … HAFF_G/ # Individual HAFF papers
│ ├── HAFF_Postscript/
│ ├── QRAIF_A/ … QRAIF_C/ # Individual Q-RAIF papers
│ ├── QRAIF_Mass_Energy_Companion/
│ ├── QRAIF_Null_Cluster_Companion/
│ ├── QRAIF_No_View_from_Nowhere/
│ ├── TDOME_I/ … TDOME_III/ # Individual T-DOME papers
│ │ ├── manuscript.tex
│ │ ├── manuscript.pdf
│ │ ├── figures/ # (T-DOME only)
│ │ ├── data/ # (T-DOME only)
│ │ └── demo/ # (T-DOME only)
│ └── .../Zenodo/ # Upload-specific PDF/TEX pairs where applicable
├── collections/ # Complete collected volumes
│ ├── HAFF_Complete_Collection.*
│ ├── Q_RAIF_Complete_Collection.*
│ ├── T_DOME_Complete_Collection.*
│ ├── Genesis_Trilogy.* # All 13 papers in one volume
│ └── build_*.py # Automated build scripts
├── consciousness_series/
│ ├── Zenodo/ # Paper-level Zenodo upload files only
│ │ ├── Foundation_I_*.pdf / .tex
│ │ ├── Foundation_II_*.pdf / .tex
│ │ ├── Foundation_III_*.pdf / .tex
│ │ ├── Paper_I_*.pdf / .tex
│ │ ├── Paper_II_*.pdf / .tex
│ │ ├── Paper_III_*.pdf / .tex
│ │ └── Brain_as_Plastic_Observable_Algebra_Network_*.pdf / .tex
│ │ ├── The_World_as_Imprint_*.pdf / .tex
│ │ ├── Renormalization_as_Imprint_Filtering_*.pdf / .tex
│ │ ├── Stable_Hulls_as_Imprint_Integration_*.pdf / .tex
│ │ └── The_Imprint_Chain_*.pdf / .tex
│ └── Zenodo_Meta/ # Collection/community assets kept out of upload root
│ ├── Foundation_Trilogy_Complete_Collection_Zenodo.pdf / .tex
│ ├── Consciousness_Trilogy_Complete_Collection_Zenodo.pdf / .tex
│ ├── Consciousness_Series_Complete_Collection_Zenodo.pdf / .tex
│ └── community.jpg
├── notes/ # Companion materials
│ ├── mapping_en.md / mapping_zh.md # Theory ↔ Yogacara mapping
│ ├── reviewer_en.md / reviewer_zh.md # Self-evaluation
│ └── tdome_companion_note_draft.md
├── arxiv.sty # Shared LaTeX style
├── LICENSE # CC BY 4.0
└── CITATION.cff
The paper-level Zenodo upload files live in consciousness_series/Zenodo/. Collection-level assets are kept separately in consciousness_series/Zenodo_Meta/.
| Item | DOI |
|---|---|
| Foundation I — From Source to Manifestation | 10.5281/zenodo.19627786 |
| Foundation II — Shared Manifestation | 10.5281/zenodo.19641372 |
| Foundation III — The Perfuming Loop | 10.5281/zenodo.19642189 |
| Paper I — The Inseparability of Geometry and Modular Flow | 10.5281/zenodo.19607387 |
| Paper II — Higher-Dimensional Consistency of Geometry and Modular Flow | 10.5281/zenodo.19607543 |
| Paper III — The Structural Horizon of Self-Description | 10.5281/zenodo.19607724 |
| Interface Paper — The Brain as a Plastic Observable-Algebra Network | 10.5281/zenodo.20044329 |
| Programmatic Essay — The World as Imprint | 10.5281/zenodo.20122718 |
| Bridge Paper I — Renormalization and Imprint Filtering | 10.5281/zenodo.20151451 |
| Bridge Paper II — Stable Hulls as Imprint Integration | 10.5281/zenodo.20151508 |
| Roadmap Paper — The Imprint Chain | 10.5281/zenodo.20151594 |
Foundation I appears locally in both the published v1 text and the interface-harmonized v2 text; both stay under the same DOI line above.
The three Imprint Interlude papers are deposited in the same consciousness-facing upload root as bridge companions to The World as Imprint rather than as a separate series.
| Item | DOI |
|---|---|
| Foundation Trilogy | 10.5281/zenodo.19642398 |
| Consciousness Trilogy | 10.5281/zenodo.19608174 |
| Consciousness Series — complete six-paper collected volume | 10.5281/zenodo.19643449 |
The upload root is intentionally kept minimal: each paper appears only as a same-named *_Zenodo.tex / *_Zenodo.pdf pair. Collection-level files and the Zenodo community image are kept separately in consciousness_series/Zenodo_Meta/.
| Item | DOI |
|---|---|
| Genesis Trilogy | 10.5281/zenodo.18608021 |
| HAFF Paper A — Emergent Geometry | 10.5281/zenodo.18361706 |
| HAFF Paper B — Accessibility, Stability | 10.5281/zenodo.18367060 |
| HAFF Paper C — Causation, Agency, Existence | 10.5281/zenodo.18374805 |
| HAFF Paper D — Gravitational Phenomena | 10.5281/zenodo.18388881 |
| HAFF Paper E — Measurement as Accessibility | 10.5281/zenodo.18400065 |
| HAFF Paper F — Temporal Asymmetry | 10.5281/zenodo.18400425 |
| HAFF Paper G — Structural Limits of Unification | 10.5281/zenodo.18402907 |
| HAFF Postscript | 10.5281/zenodo.18407367 |
| HAFF Abstract | 10.5281/zenodo.18416482 |
| HAFF Complete Collection | 10.5281/zenodo.18452194 |
| Q-RAIF Paper A — Lorentzian Metrics | 10.5281/zenodo.18525876 |
| Q-RAIF Paper B — Operator Algebra Stability | 10.5281/zenodo.18525890 |
| Q-RAIF Paper C — Realizability Bridge | 10.5281/zenodo.18528934 |
| Q-RAIF Companion — Mass-Energy Conditional Theorem | 10.5281/zenodo.20280951 |
| Q-RAIF Programme Note — Null Cluster as Structural Imprint | 10.5281/zenodo.20283057 |
| Q-RAIF Predictive Note — No View from Nowhere | 10.5281/zenodo.20284454 |
| Q-RAIF Complete Collection | 10.5281/zenodo.18548704 |
| T-DOME Paper I — Non-Markovian Memory | 10.5281/zenodo.18574342 |
| T-DOME Paper II — Reference Frame SSB | 10.5281/zenodo.18579703 |
| T-DOME Paper III — Self-Referential Calibration | 10.5281/zenodo.18591771 |
| T-DOME Complete Collection | 10.5281/zenodo.18593180 |
| Foundation I — From Source to Manifestation | 10.5281/zenodo.19627786 |
| Foundation II — Shared Manifestation | 10.5281/zenodo.19641372 |
| Foundation III — The Perfuming Loop | 10.5281/zenodo.19642189 |
| Paper I — Geometry and Modular Flow | 10.5281/zenodo.19607387 |
| Paper II — Higher-Dimensional Consistency | 10.5281/zenodo.19607543 |
| Paper III — Structural Horizon of Self-Description | 10.5281/zenodo.19607724 |
| Interface Paper — Brain as Plastic Observable-Algebra Network | 10.5281/zenodo.20044329 |
| Programmatic Essay — The World as Imprint | 10.5281/zenodo.20122718 |
| Bridge Paper I — Renormalization and Imprint Filtering | 10.5281/zenodo.20151451 |
| Bridge Paper II — Stable Hulls as Imprint Integration | 10.5281/zenodo.20151508 |
| Roadmap Paper — The Imprint Chain | 10.5281/zenodo.20151594 |
| Foundation Trilogy | 10.5281/zenodo.19642398 |
| Consciousness Trilogy | 10.5281/zenodo.19608174 |
| Consciousness Series — complete collection | 10.5281/zenodo.19643449 |
T-DOME Papers I–III include numerical demonstrations. Each demo script is self-contained and requires only NumPy and Matplotlib:
# Paper I — Markov ceiling demo
cd papers/TDOME_I/demo
python paper1_markov_ceiling_demo.py
# Paper II — k* staircase demo
cd papers/TDOME_II/demo
python paper2_kstar_scaling_demo.py
# Paper III — phase diagram, survival, ego, loop demos
cd papers/TDOME_III/demo
python tdome_demo.pyEach script produces deterministic output (fixed seeds) and generates PDF figures with confidence intervals.
The collected volumes can be rebuilt from individual papers:
cd collections
python build_tdome_collection.py # → T_DOME_Complete_Collection.tex
python build_genesis_trilogy.py # → Genesis_Trilogy.tex
# Then compile with pdflatex (3 passes for cross-references)| Layer | Platform | Identifier |
|---|---|---|
| Academic citation | Zenodo | 10.5281/zenodo.18608021 |
| Canonical source | GitHub | github.com/sidongliu/genesis-trilogy |
| Software Heritage | SWH | swh:1:snp:76ebc4c8e9cd85e7f9e97a0b7c0237ca17696f83 |
This repository contains the LaTeX sources, numerical demonstrations, and build scripts needed to reproduce the Genesis Trilogy together with the associated Consciousness Series upload package. The Zenodo DOIs serve as the academic citation entry point; the GitHub repository is the canonical, versioned source; and the Software Heritage archive provides content-addressed, platform-independent long-term preservation.
This work is licensed under CC BY 4.0.