Part Bibliography and Relation Register
Part 1: On the Origin of Life | Bibliographic consolidation and relation-control support document | source-locked | Issue 1
Control field | Value |
|---|---|
Document ID | OOL-P1-SD04-BIBLIOGRAPHY |
Version / issue | Issue 1 |
Date | 2026-09-22 |
Status | Final controlled Part-level bibliography and relation-control support document for Part 1 Issue 1, source-locked to the finalised GOT-V1-1-1 / GOT-V1-1-2 / GOT-V1-1-3 papers, their fixed literal heading locators, and final SD-01-SD-03 controls. Secondary to canonical papers. |
Supersedes | Earlier Issue 1 source-lock states, including the FD15 / v17 / v14 and FD15 / v18 / v15 locks, plus the numbering-aligned working state. This final Issue 1 release locks the register to the final paper identities, fixed literal heading locators, and final SD-01-SD-03 controls. |
Function | Consolidates the admitted Paper 1-3 bibliographies into one deduplicated Part bibliography while preserving paper-local relation status, cross-paper differences, hold/exclusion branch-memory, adjacency residual, and handoff to the later Series Master Bibliography. |
Canonical rule | Paper bibliographies and local endnotes remain authoritative for paper-level scholarly use. Paper 1 compact relation metadata now records the completed targeted audit upgrade; Paper 2 and Paper 3 coded metadata remains historical audit provenance revalidated by the current posture/delta checks where the paper relation and locator remain unchanged. This document does not create new technical warrant or Indexed Inheritance. |
Protocol rule | GOT-SD-BIB-01 governs E/F/P/C/A/I classification, relation tags, inheritance levels, hold/exclusion discipline, residual, and upward consolidation. |
Source-lock rule | Use only the final Issue 1 primary papers GOT-V1-1-1, GOT-V1-1-2, and GOT-V1-1-3; GOT-SD-BIB-01; and the final Part 1 SD-01-SD-03 controls as the active conceptual/source lock. Primary-paper relation anchors must use the current literal heading locator map; cited locators omit the terminal display full stop. The v17/v14 Paper 2/Paper 3 audit records remain historical provenance for coded metadata; the completed Paper 1 targeted audit and current Paper 2/Paper 3 posture checks are control-state updates only and do not import downstream concepts. Superseded paper revisions and prior working drafts are excluded. |
Template rule | Part 1 SD-01-SD-03 provide final support-stack control and release discipline. Bibliographic identity and paper-local relation statements are re-verified against the final GOT-V1-1-1 / GOT-V1-1-2 / GOT-V1-1-3 Issue 1 files and their fixed literal heading locators. The final release records the Paper 1 targeted-audit outcome and the Paper 2/Paper 3 no-change delta checks without promoting or strengthening relations by aggregation. |
1. Purpose and governing rules
This document is the controlled Part 1 consolidation layer required by the bibliographic protocol. It deduplicates the bibliographic record across the three papers while keeping the scholarly relation local to the paper in which that relation was earned. It is not a substitute bibliography for any paper, and it does not move citation authority upward merely because a source appears more than once.
The governing distinction is between bibliographic identity and relational use. One publication may appear once in the Part bibliography and still carry different relations in different papers. The relation register therefore preserves paper-local comparator, evidence, dependency, adjacency, inheritance, and hold status rather than assigning a single Part-wide meaning to the source.
No relation is strengthened by aggregation. Repetition across papers is not evidence of Indexed Inheritance, priority, correctness, or framework-level dependence. Promotion remains subject to deliberate review under GOT-SD-BIB-01; local demotion or correction may be made whenever the source record requires it.
The local endnotes and bibliography of each paper remain the reader-facing scholarly apparatus. This Part document is control infrastructure: it supports deduplication, cross-paper consistency, branch-memory, later Series consolidation, and the prevention of authority transfer by accumulation.
0.1 Source-lock register
Seq. | Current consolidation input | Verification / status | Permitted use |
|---|---|---|---|
P1 | GOT-V1-1-1 - On the Origin of Life - Issue 1.docx | Final Issue 1 source-locked bibliography-integrated Paper 1 input; sha16 b46a62c660223454. The file is byte-identical to the approved FD16 source-locked copy. FD16 preserves the FD15 canonical technical body and adds the approved Lizier et al. (2007) and Kolchinsky & Wolpert (2018) scholarly apparatus. The completed targeted audit supplies coded relation and hold/exclusion branch-memory for Paper 1. Heading locators are the final fixed literal locators. | Published bibliography and local endnote relations; current Paper 1 audit-control metadata. |
P2 | GOT-V1-1-2 - The Identification of Life - Issue 1.docx | Final Issue 1 source-locked bibliography-integrated Paper 2 input; sha16 0f1f564c3786f208. The file is byte-identical to the approved v18 source-locked copy. Published bibliography and local endnote relations were re-verified; the 2026-08-12 posture/delta check found no reader-facing bibliography or technical change. Relation anchors cite the final fixed literal heading locators. | Published bibliography, local endnotes, and paper-local relation anchors. |
P3 | GOT-V1-1-3 - The Life Attribution Procedure - Issue 1.docx | Final Issue 1 source-locked bibliography-integrated Paper 3 input; sha16 6c6d2b60203198e8. The file is byte-identical to the approved v15 source-locked copy. Published bibliography and local endnote relations were re-verified; the 2026-08-12 posture/delta check found no reader-facing bibliography or technical change. Relation anchors cite the final fixed literal heading locators. | Published bibliography, local endnotes, and paper-local relation anchors. |
P2 audit | 2. The Identification of Life - Bibliographic and Adjacency Audit Record - Issue 1 - v17 Aligned.docx | Historical working non-canonical audit record aligned to canonical v17. Retained only as provenance for coded Paper 2 maturity/class/tag/inheritance metadata already embodied in this register; not a source lock for v18. | Historical classification, hold/exclusion, and residual provenance where the current v18 paper relation and locator remain unchanged. |
P3 audit | 3. The Life Attribution Procedure - Bibliographic and Adjacency Audit Record - Issue 1 - v14 Aligned.docx | Historical working non-canonical audit record aligned to canonical v14. Retained only as provenance for coded Paper 3 maturity/class/tag/inheritance metadata already embodied in this register; not a source lock for v15. | Historical classification, hold/exclusion, and residual provenance where the current v15 paper relation and locator remain unchanged. |
Protocol | GOT - Bibliographic Identification Classification and Adjacency Discovery Protocol - Issue 1.docx | GOT-SD-BIB-01 | Issue 1 | 2026-08-07. | Bibliographic classes, relation tags, inheritance levels, upward consolidation, hold/exclusion, residual, and anti-drift rules. |
P1 SD-01 | Concept Compression Map - Issue 1.docx | Final Issue 1 source-lock control; sha16 a256c5229849f993. | Part structure and source-discipline control reference. |
P1 SD-02 | Glossary - Issue 1.docx | Final Issue 1 controlled vocabulary reference; sha16 e97712ced4e2b095. | Vocabulary and canonical-home control reference. |
P1 SD-03 | Guardrail and Failure-Mode Register - Issue 1.docx | Final Issue 1 failure-control reference; sha16 794360cc1ff16519. | Failure-control and release-discipline reference. |
Excluded source class: superseded Part 1 paper revisions and bibliography-integration outputs, including FD15; historical v17/v14 Paper 2/Paper 3 audit records except as provenance for coded metadata revalidated in the current papers; unadmitted external sources except where explicitly retained as hold/exclusion branch-memory; prior generated answers; and any external publication not admitted or held by the completed paper-level audit state. This Part consolidation does not run a new discovery sweep.
2. Consolidation architecture
Layer | Function | Control rule |
|---|---|---|
Paper bibliography | Reader-facing local scholarly apparatus. | Full reference list plus local endnotes. The paper decides why a source is present. |
Part bibliography | Deduplicated bibliographic identity across Papers 1-3. | One bibliographic record per publication, with paper-occurrence markers. It does not flatten local relations. |
Relation register | Preserves the source-to-paper relation that was actually earned. | Paper-local class / tag / inheritance metadata where established by a completed audit. Current Paper 1 targeted-audit metadata and revalidated Paper 2/Paper 3 historical codes remain paper-local; no Part-level strengthening is permitted. |
Cross-paper controls | Expose material differences where the same publication is used more than once. | Prevents repeated citation from becoming authority transfer or silent conceptual inheritance. |
Hold / exclusion branch-memory | Preserves material candidates not admitted to a local paper bibliography. | Stops excluded or scoped material being rediscovered without context and prevents provenance duplication across papers. |
Part residual | Carries limits of the completed paper-level sweeps upward. | No claim of exhaustive prior-art discovery; unsearched, inaccessible, or unrecognised adjacency remains residual. |
Series handoff | Feeds the later Series Master Bibliography and dependency/provenance controls. | Deduplicate bibliographic identity again at Series level while retaining all paper- and Part-local relation records. |
Upward consolidation therefore proceeds as: individual paper bibliography -> Part bibliography -> Series Master Bibliography. At each step the bibliographic record may be deduplicated; the indexed relation may not be collapsed merely for convenience.
3. Part 1 deduplicated publication bibliography
The following forty-three entries are the union of the three current paper bibliographies after bibliographic deduplication. The paper-occurrence field is descriptive only: it identifies where the publication is locally admitted. It does not assign a Part-level class or imply that a repeated publication carries the same relation in each paper.
Part ID | Deduplicated bibliographic record | Paper(s) |
|---|---|---|
PB01 | Bartlett, S. J. (2024). Causal leverage density: A general approach to semantic information. arXiv:2407.07335. https://doi.org/10.48550/arXiv.2407.07335 | P1 |
PB02 | Bernat, J. L., Culver, C. M., & Gert, B. (1981). On the definition and criterion of death. Annals of Internal Medicine, 94(3), 389-394. https://doi.org/10.7326/0003-4819-94-3-389 | P2 |
PB03 | Chalmers, D. J. (1996). Does a rock implement every finite-state automaton? Synthese, 108(3), 309-333. https://doi.org/10.1007/BF00413692 | P1 |
PB04 | Cleland, C. E., & Chyba, C. F. (2002). Defining 'life'. Origins of Life and Evolution of the Biosphere, 32(4), 387-393. https://doi.org/10.1023/A:1020503324273 | P1 |
PB05 | Deacon, T. W., Srivastava, A., & Bacigalupi, J. A. (2014). The transition from constraint to regulation at the origin of life. Frontiers in Bioscience (Landmark Edition), 19(6), 945-957. https://doi.org/10.2741/4259 | P1 |
PB06 | Diener, T. O. (1971). Potato spindle tuber "virus": IV. A replicating, low molecular weight RNA. Virology, 45(2), 411-428. https://doi.org/10.1016/0042-6822(71)90342-4 | P3 |
PB07 | Doulcier, G., Takacs, P., & Bourrat, P. (2024). Evolutionary transitions in individuality and life cycle closure. Philosophy of Science, 91(5), 1393-1403. https://doi.org/10.1017/psa.2023.162 | P2 |
PB08 | England, J. L. (2015). Dissipative adaptation in driven self-assembly. Nature Nanotechnology, 10, 919-923. https://doi.org/10.1038/nnano.2015.250 | P1 |
PB09 | Forterre, P. (2011). Manipulation of cellular syntheses and the nature of viruses: The virocell concept. Comptes Rendus Chimie, 14(4), 392-399. https://doi.org/10.1016/j.crci.2010.06.007 | P2; P3 |
PB10 | Green, J., Hoehler, T., Neveu, M., Domagal-Goldman, S., Scalice, D., & Voytek, M. (2021). Call for a framework for reporting evidence for life beyond Earth. Nature, 598, 575-579. https://doi.org/10.1038/s41586-021-03804-9 | P3 |
PB11 | Hordijk, W., & Steel, M. (2015). Autocatalytic sets and boundaries. Journal of Systems Chemistry, 6, Article 1. https://doi.org/10.1186/s13322-014-0006-2 | P1 |
PB12 | Horsman, C., Stepney, S., Wagner, R. C., & Kendon, V. (2014). When does a physical system compute? Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, 470(2169), 20140182. https://doi.org/10.1098/rspa.2014.0182 | P1 |
PB13 | Huh, D., Matthews, B. D., Mammoto, A., Montoya-Zavala, M., Hsin, H. Y., & Ingber, D. E. (2010). Reconstituting organ-level lung functions on a chip. Science, 328(5986), 1662-1668. https://doi.org/10.1126/science.1188302 | P3 |
PB14 | Jeffries, K. M., Hinch, S. G., Donaldson, M. R., Gale, M. K., Burt, J. M., Thompson, L. A., Farrell, A. P., Patterson, D. A., & Miller, K. M. (2011). Temporal changes in blood variables during final maturation and senescence in male sockeye salmon Oncorhynchus nerka: Reduced osmoregulatory ability can predict mortality. Journal of Fish Biology, 79(2), 449-465. https://doi.org/10.1111/j.1095-8649.2011.03042.x | P3 |
PB42 | Kolchinsky, A., & Wolpert, D. H. (2018). Semantic information, autonomous agency and non-equilibrium statistical physics. Interface Focus, 8(6), 20180041. https://doi.org/10.1098/rsfs.2018.0041 | P1 |
PB15 | Krakauer, D., Bertschinger, N., Olbrich, E., Flack, J. C., & Ay, N. (2020). The information theory of individuality. Theory in Biosciences, 139(2), 209-223. https://doi.org/10.1007/s12064-020-00313-7 | P2 |
PB16 | Landauer, R. (1961). Irreversibility and heat generation in the computing process. IBM Journal of Research and Development, 5(3), 183-191. https://doi.org/10.1147/rd.53.0183 | P1 |
PB17 | Latil, M., Rocheteau, P., Chatre, L., et al. (2012). Skeletal muscle stem cells adopt a dormant cell state post mortem and retain regenerative capacity. Nature Communications, 3, 903. https://doi.org/10.1038/ncomms1890 | P3 |
PB18 | Lennon, J. T., & Jones, S. E. (2011). Microbial seed banks: The ecological and evolutionary implications of dormancy. Nature Reviews Microbiology, 9(2), 119-130. https://doi.org/10.1038/nrmicro2504 | P2; P3 |
PB43 | Lizier, J. T., Prokopenko, M., & Zomaya, A. Y. (2007). Detecting non-trivial computation in complex dynamics. In F. Almeida e Costa, L. M. Rocha, E. Costa, I. Harvey, & A. Coutinho (Eds.), Advances in artificial life: 9th European Conference, ECAL 2007 (Lecture Notes in Computer Science, Vol. 4648, pp. 895–904). Springer. https://doi.org/10.1007/978-3-540-74913-4_90 | P1 |
PB19 | Merlo, L. M. F., Pepper, J. W., Reid, B. J., & Maley, C. C. (2006). Cancer as an evolutionary and ecological process. Nature Reviews Cancer, 6(12), 924-935. https://doi.org/10.1038/nrc2013 | P3 |
PB20 | Montévil, M., & Mossio, M. (2015). Biological organisation as closure of constraints. Journal of Theoretical Biology, 372, 179-191. https://doi.org/10.1016/j.jtbi.2015.02.029 | P1; P2 |
PB21 | Moran, N. A., & Sloan, D. B. (2015). The hologenome concept: Helpful or hollow? PLOS Biology, 13(12), e1002311. https://doi.org/10.1371/journal.pbio.1002311 | P2 |
PB22 | Nasralla, D., Coussios, C. C., Mergental, H., et al. (2018). A randomized trial of normothermic preservation in liver transplantation. Nature, 557, 50-56. https://doi.org/10.1038/s41586-018-0047-9 | P3 |
PB23 | Neveu, M., Hays, L. E., Voytek, M. A., New, M. H., & Schulte, M. D. (2018). The Ladder of Life Detection. Astrobiology, 18(11), 1375-1402. https://doi.org/10.1089/ast.2017.1773 | P3 |
PB24 | Parenteau, N., Hoehler, T., Davila, A., Getty, S., Lau, G., Neveu, M., Shkolyar, S., Des Marais, D., Rios, A., Jahnke, L., Bebout, L., Quinn, R., & Pohorille, A. (2025). Life Detection Knowledge Base: Assessment Criteria for Potential Biosignatures. Astrobiology, 25(7), 474-481. https://doi.org/10.1089/ast.2024.0104 | P3 |
PB25 | Parrondo, J. M. R., Horowitz, J. M., & Sagawa, T. (2015). Thermodynamics of information. Nature Physics, 11, 131-139. https://doi.org/10.1038/nphys3230 | P1 |
PB26 | Partridge, E. A., Davey, M. G., Hornick, M. A., et al. (2017). An extra-uterine system to physiologically support the extreme premature lamb. Nature Communications, 8, 15112. https://doi.org/10.1038/ncomms15112 | P3 |
PB27 | Pradeu, T. (2016). Organisms or biological individuals? Combining physiological and evolutionary individuality. Biology & Philosophy, 31(6), 797-817. https://doi.org/10.1007/s10539-016-9551-1 | P2 |
PB28 | Prusiner, S. B. (1982). Novel proteinaceous infectious particles cause scrapie. Science, 216(4542), 136-144. https://doi.org/10.1126/science.6801762 | P3 |
PB29 | Queller, D. C., & Strassmann, J. E. (2009). Beyond society: The evolution of organismality. Philosophical Transactions of the Royal Society B: Biological Sciences, 364(1533), 3143-3155. https://doi.org/10.1098/rstb.2009.0095 | P2 |
PB30 | Rafiei, S. K. S., & Asadi Anar, M. (2026). Membrane information organization at the origin of life: From interfaces to informational bodies. BioSystems, 265, 105830. https://doi.org/10.1016/j.biosystems.2026.105830 | P2 |
PB31 | Roger, A. J., Munoz-Gomez, S. A., & Kamikawa, R. (2017). The Origin and Diversification of Mitochondria. Current Biology, 27(21), R1177-R1192. https://doi.org/10.1016/j.cub.2017.09.015 | P3 |
PB32 | Ruiz-Mirazo, K., Peretó, J., & Moreno, A. (2004). A universal definition of life: Autonomy and open-ended evolution. Origins of Life and Evolution of the Biosphere, 34(3), 323-346. https://doi.org/10.1023/B:ORIG.0000016440.53346.DC | P1 |
PB33 | Salje, J. (2021). Cells within cells: Rickettsiales and the obligate intracellular bacterial lifestyle. Nature Reviews Microbiology, 19, 375-390. https://doi.org/10.1038/s41579-020-00507-2 | P3 |
PB34 | Seifert, U. (2012). Stochastic thermodynamics, fluctuation theorems and molecular machines. Reports on Progress in Physics, 75(12), 126001. https://doi.org/10.1088/0034-4885/75/12/126001 | P1 |
PB35 | Shannon, C. E. (1948). A mathematical theory of communication. Bell System Technical Journal, 27(3), 379-423; 27(4), 623-656. https://doi.org/10.1002/j.1538-7305.1948.tb01338.x; https://doi.org/10.1002/j.1538-7305.1948.tb00917.x | P1 |
PB36 | Sharma, A., Czégel, D., Lachmann, M., Kempes, C. P., Walker, S. I., & Cronin, L. (2023). Assembly theory explains and quantifies selection and evolution. Nature, 622, 321-328. https://doi.org/10.1038/s41586-023-06600-9 | P1 |
PB37 | Shewmon, D. A. (2001). The brain and somatic integration: Insights into the standard biological rationale for equating "brain death" with death. The Journal of Medicine and Philosophy, 26(5), 457-478. https://doi.org/10.1076/jmep.26.5.457.3000 | P2 |
PB38 | Suárez, J., & Stencel, A. (2020). A part-dependent account of biological individuality: Why holobionts are individuals and ecosystems simultaneously. Biological Reviews, 95(5), 1308-1324. https://doi.org/10.1111/brv.12610 | P2 |
PB39 | Szostak, J. W., Bartel, D. P., & Luisi, P. L. (2001). Synthesizing life. Nature, 409, 387-390. https://doi.org/10.1038/35053176 | P3 |
PB40 | Varela, F. G., Maturana, H. R., & Uribe, R. (1974). Autopoiesis: The organization of living systems, its characterization and a model. BioSystems, 5(4), 187-196. https://doi.org/10.1016/0303-2647(74)90031-8 | P1 |
PB41 | Woodward, J. (2003). Making things happen: A theory of causal explanation. Oxford University Press. https://doi.org/10.1093/0195155270.001.0001 | P1 |
4. Cross-paper relation controls
Three publications occur in more than one Part 1 bibliography. Their duplicate bibliographic identity is consolidated above, but their paper-local relation remains separate. A fourth cross-paper control is recorded for Montévil and Mossio because Paper 3 explicitly holds the Paper 2 organisational-closure family out of its own bibliography to avoid duplicating provenance.
Source / control | Paper 1 relation | Paper 2 relation | Paper 3 relation | Part-level control |
|---|---|---|---|---|
PB09 Forterre (2011) | Not locally admitted in the current Paper 1 bibliography. | A3; C / REF / 0. Throughput-identity comparator at heading 5.5, note 4. The free virion / intracellular virocell distinction is close to free-phase / host-completed attribution, but Life-in-Potential is not inherited from the virocell concept. | A3; C / REF / 0. Procedural comparator at headings 5.3 and 5.4, note 4. Supports separation of inert free phase from host-completed intracellular phase; the Paper 3 attribution sequence and classifications remain independent. | One publication; two related but distinct comparator uses. No inheritance. |
PB18 Lennon & Jones (2011) | Not locally admitted in the current Paper 1 bibliography. | E / N-A / 1. heading 5.3, note 3. Empirical support for dormancy as reversible reduced activity; intrinsic resumability remains the Paper 2 attribution criterion. | E / N-A / 1. heading 5.1, note 2. Empirical support for low-activity yet resumable biological states; GOT dormant-Life classification is not inherited from the source. | Same empirical literature supports two local claims. Operational evidence use does not transfer the surrounding framework. |
PB20 Montévil & Mossio (2015) | Local endnote relation: close organisational neighbour; acknowledged without technical dependence. Closure of constraints does not establish the Paper 1 NTC/IPL burden. | A3; C / OVL / 0. heading 1.6 maintained-interface comparator, note 2. Organisational closure may help mark interacting biological boundaries, but closure alone does not establish Attribution Locus or life-status. | Not admitted. Paper 3 H03 is a scoped X6 hold on the Paper 2 biological-individuality / holobiont / organisational-closure family because Paper 3 inherits attribution architecture and should not duplicate Paper 2 provenance merely because exemplars apply it. | Deduplicate the publication record; preserve P1 and P2 local meanings and the P3 non-duplication boundary. |
Control consequence | Repeated citation has no upgrading effect. | Paper-local coded relation governs. | Paper-local coded relation or scoped hold governs. | No source is promoted to dependency or Indexed Inheritance by accumulation across Part 1. |
5. Paper-local relation index
This index preserves the local scholarly reason for each admitted reference. Paper 1 now records the compact grammar established by the completed targeted audit upgrade against FD16. Paper 2 and Paper 3 retain the compact grammar from their earlier coded audit records where the current posture/delta checks confirm that the relation and locator remain unchanged. No relation is strengthened by Part-level consolidation.
Part ID | Paper | Source | Local status / compact grammar | Local anchor | Source-locked relation |
|---|---|---|---|---|---|
PB01 | P1 | Bartlett (2024) | A3; C / OVL / 0 | Endnote 7 | Examined methodological adjacency to a possible Baseline Dynamics intervention/readout; does not establish physically supported alphabet, BD adequacy, or IPL localisation. |
PB03 | P1 | Chalmers (1996) | A3; C / OVL / 0 | Endnote 1 | Computational-implementation / triviality problem; motivates constraints beyond arbitrary physical-to-computational mapping but does not supply TC/NTC. |
PB04 | P1 | Cleland & Chyba (2002) | A3; C / SPEC / 0 | Endnote 10 | Theory-level life-definition context; does not establish that the present discriminator succeeds. |
PB05 | P1 | Deacon et al. (2014) | A3; C / OVL / 0 | Endnote 6 | Close organisational neighbour; no technical dependence. Constraint organisation alone does not establish NTC/IPL. |
PB08 | P1 | England (2015) | A3; C / SPEC / 0 | Endnote 9 | Negative comparator: driven dissipative self-assembly may be structured without meeting the IPL-mediated NTC maintenance burden. |
PB11 | P1 | Hordijk & Steel (2015) | A3; C / SPEC / 0 | Endnote 11 | Autocatalytic-set / boundary architecture as chemistry-to-life candidate scaffold; does not by itself establish the life discriminator. |
PB12 | P1 | Horsman et al. (2014) | A3; C / OVL / 0 | Endnote 1 | Computational implementation / triviality problem; does not supply the present TC/NTC discriminator. |
PB42 | P1 | Kolchinsky & Wolpert (2018) | A3; C / OVL / 0 | Endnote 8 | Information-maintenance comparator: semantic information is defined through causal necessity for maintaining physical-system viability under counterfactual scrambling. Paper 1 does not inherit semantic-information or viability formalism and retains its own IPL/NTC/BD life threshold. |
PB16 | P1 | Landauer (1961) | F / DEP / 1 | Endnote 4 | Canonical physical irreversibility result for logically irreversible information operations; grounds physical cost/constraint claim, not NMF layering. |
PB43 | P1 | Lizier et al. (2007) | A3; P / N-A / 0; secondary C / OVL / 0 | Endnote 1 | Prior technical use of “non-trivial computation” acknowledged for terminology/provenance and comparison. Their distributed information-storage/transfer/modification framework does not supply Paper 1 organisation-mediated, comparator-tested NTC. |
PB20 | P1 | Montévil & Mossio (2015) | A3; C / OVL / 0 | Endnote 6 | Close organisational neighbour; no technical dependence. Constraint organisation alone does not establish NTC/IPL. |
PB25 | P1 | Parrondo et al. (2015) | F / DEP / 1 | Endnote 4 | Modern thermodynamics-of-information framework; grounds physical cost/constraint claim, not NMF layering. |
PB32 | P1 | Ruiz-Mirazo et al. (2004) | A3; C / SPEC / 0 | Endnote 8 | Organisation-centred life comparator; present life threshold does not require autonomy plus open-ended evolution as a primitive discriminator. |
PB34 | P1 | Seifert (2012) | F / DEP / 1 | Endnote 2 | Standard nonequilibrium / stochastic-thermodynamic reference; NMF layer structure remains Paper 1 construction. |
PB35 | P1 | Shannon (1948) | F / DEP / 1 | Endnote 3 | Channel-relative mathematical framework for entropy, mutual information, alphabets, noise, and capacity used at the Shannon layer. |
PB36 | P1 | Sharma et al. (2023) | A3; C / SPEC / 0 | Endnote 12 | Assembly Theory acknowledged as lower-ladder state-space / complex-chemistry adjacency, not evidence of NTC or Life. |
PB40 | P1 | Varela et al. (1974) | A3; C / SPEC / 0 | Endnote 8 | Autopoiesis comparator; present local threshold does not require autopoietic self-production as a primitive discriminator. |
PB41 | P1 | Woodward (2003) | F / DEP / 1 | Endnote 5 | Interventionist causal background. Baseline Dynamics is the stronger paper-specific comparator discipline. |
PB15 | P2 | Krakauer et al. (2020) | A3; C / OVL / 0 | heading 1.5, note 1 | Candidate-framing / individuality comparator; no inheritance. |
PB20 | P2 | Montévil & Mossio (2015) | A3; C / OVL / 0 | heading 1.6, note 2 | Maintained-interface / closure comparator; closure alone does not establish Attribution Locus or life-status. |
PB38 | P2 | Suárez & Stencel (2020) | A3; C / OVL / 0 | heading 7.5, note 6 | Part-dependent individuality comparator for symbiosis / mutualism and topology versus unity. |
PB30 | P2 | Rafiei & Asadi Anar (2026) | A3; C / OVL / 0 | heading 1.6, note 2 | Informational membrane boundary comparator; boundary account not inherited. |
PB07 | P2 | Doulcier et al. (2024) | A3; C / OVL / 0 | heading 7.7, note 7 | Higher-order identity / life-cycle-closure comparator; not Paper 2 death / branch-closure. |
PB27 | P2 | Pradeu (2016) | A3; C / OVL / 0 | heading 1.5, note 1 | Biological-individuality comparator; does not supply Attribution Locus or life discriminator. |
PB09 | P2 | Forterre (2011) | A3; C / REF / 0 | heading 5.5, note 4 | Close comparator to free-phase / host-completed attribution; Life-in-Potential not inherited from virocell. |
PB18 | P2 | Lennon & Jones (2011) | E / N-A / 1 | heading 5.3, note 3 | Empirical dormancy support; intrinsic resumability is Paper 2 criterion. |
PB02 | P2 | Bernat et al. (1981) | A3; C / OVL / 0 | heading 5.7, note 5 | Death / organismal integration comparator; whole-brain criterion not inherited. |
PB37 | P2 | Shewmon (2001) | A3; C / OVL / 0 | heading 5.7, note 5 | Counterpressure on brain-centred somatic integration; Paper 2 branch-closure remains broader. |
PB29 | P2 | Queller & Strassmann (2009) | A3; C / OVL / 0 | heading 7.7, note 7 | Organismality comparator for higher-order locus; no dependency. |
PB21 | P2 | Moran & Sloan (2015) | A3; C / OVL / 0 | heading 7.5, note 6 | Critical pressure against automatic holobiont unity; comparator only. |
PB23 | P3 | Neveu et al. (2018) | A3; C / OVL / 0 | heading 5.0, note 1 | Staged life-detection methodological comparator; no technical dependence. |
PB10 | P3 | Green et al. (2021) | A3; C / OVL / 0 | heading 5.0, note 1 | Claim-strength / evidence-reporting comparator; does not supply attribution grammar. |
PB24 | P3 | Parenteau et al. (2025) | A3; C / OVL / 0 | heading 5.0, note 1 | False-positive / false-negative and biosignature-assessment comparator; no attribution dependence. |
PB18 | P3 | Lennon & Jones (2011) | E / N-A / 1 | heading 5.1, note 2 | Empirical dormancy support; dormant-Life classification not inherited. |
PB14 | P3 | Jeffries et al. (2011) | E / N-A / 1 | heading 5.2, note 3 | Empirical support for terminal active senescence exemplar; classification remains local. |
PB09 | P3 | Forterre (2011) | A3; C / REF / 0 | headings 5.3 and 5.4, note 4 | Virus/virocell comparator to free-phase / host-completed attribution; no ontology inheritance. |
PB33 | P3 | Salje (2021) | E / N-A / 1 | heading 5.5, note 5 | Empirical support for obligate intracellular bacterial dependence without automatic loss of biological organisation. |
PB31 | P3 | Roger et al. (2017) | E / N-A / 1 | heading 5.6, note 6 | Empirical mitochondrial integration/dependence basis; attribution remains locus/completion question. |
PB19 | P3 | Merlo et al. (2006) | E / N-A / 1 | heading 5.7, note 7 | Empirical tumour cellular/population organisation; does not establish tumour-scale Attribution Locus. |
PB22 | P3 | Nasralla et al. (2018) | E / N-A / 1 | heading 5.8, note 8 | Empirical organ preservation under external technical support; not evidence of organismal living locus. |
PB13 | P3 | Huh et al. (2010) | E / N-A / 1 | heading 5.8, note 8 | Empirical organ-level function on chip; not evidence that the device-supported system is an organismal living locus. |
PB26 | P3 | Partridge et al. (2017) | E / N-A / 1 | heading 5.9, note 9 | Empirical developmental support; developing organism remains the attributed locus. |
PB28 | P3 | Prusiner (1982) | E / N-A / 1 | heading 5.10, note 10 | Empirical prion propagation contrast; primary class remains an attribution question. |
PB06 | P3 | Diener (1971) | E / N-A / 1 | heading 5.10, note 10 | Empirical viroid RNA propagation contrast; primary class remains an attribution question. |
PB39 | P3 | Szostak et al. (2001) | A3; C / OVL / 0 | heading 5.11, note 11 | Synthetic-cell / protocell comparator for chemistry-to-life band; no life-discriminator inheritance. |
PB17 | P3 | Latil et al. (2012) | E / N-A / 1 | heading 5.12, note 12 | Empirical post-mortem dormant stem-cell survival; supports constituent reframing after organismal closure. |
6. Hold and exclusion branch-memory
The Part bibliography contains only admitted publications. Material candidates held or excluded at paper level remain control records rather than being promoted into the Part publication set. The following entries preserve the current branch-memory that is material to cross-paper consolidation.
Paper | Candidate / family | Current control state | Reason / update condition |
|---|---|---|---|
P1 | Walker & Davies (2013), The Algorithmic Origins of Life | Hold; A3; C / SPEC / 0; X6 | Strong problem-level neighbour on information gaining causal efficacy in living systems, but top-down causation is central to the external proposal and is not required by Paper 1. Revisit only if hierarchical/top-down causation becomes locally load-bearing. |
P1 | Anderson & Piccinini (2024), The Physical Signature of Computation | Hold; A3; C / OVL / 0; X3 | Major contemporary physical-computation comparator, but Chalmers, Horsman, and the now-published Lizier provenance/comparator relation already cover the local implementation/triviality burden. Revisit if Paper 1 expands its general theory of physical computation. |
P1 | Solé et al. (2024), Fundamental constraints to the logic of living systems | Hold; A2; A / ADJ / 0; X3 | Broad thermodynamic/informational/computational constraint adjacency. Current Paper 1 already decomposes this neighbourhood through more specific admitted sources; revisit if universal living-system constraint families become a distinct claim. |
P1 | Terminology residual: Counterfactual Order Advantage; Information Processing Locus; Nested Multiscale Framework; Baseline Dynamics | Residual; X5 where applicable | No material prior technical construct matching Counterfactual Order Advantage was identified in the targeted sweep. IPL, NMF, and Baseline Dynamics have generic/descriptive lexical neighbours but no verified relation sufficient for publication beyond the admitted bibliography. Preserve as terminology branch-memory; do not claim exhaustive uniqueness. |
P2 | Clegg (2001), cryptobiosis | Hold; X3 | Redundant for current text once Lennon & Jones represents dormancy. Revisit if cryptobiosis becomes load-bearing. |
P2 | DiFrisco (2018), biological process identity/persistence | Hold; A2 / A-ADJ-0 | Real adjacency but outside the minimum sufficient set. Revisit if a process-identity comparator becomes explicit. |
P2 | Moreira & López-García (2009), virus/life debate | Hold; A2 | Useful opposing literature but too binary for the present local relation. Revisit if the virus comparator is expanded. |
P2 | Kirchhoff et al. (2018), Markov blankets | Exclude; X3 / X6 | Formal/statistical boundary does not establish maintained informational boundary or Attribution Locus. Revisit only if a formal statistical-boundary apparatus is adopted. |
P2 | Gilbert, Sapp & Tauber (2012); Clarke (2010); West et al. (2015) | Hold; X3 | Redundant biological-individuality neighbourhood once the admitted comparator set is present. |
P2 | Hinrichs et al. (2026) preprint, Life as Plasmas | Hold; A2; C / SPEC / 0; X6 | Source identity and adjacency are now sufficiently verified to move beyond A0/X7. The work concerns physical admissibility/minimal-autonomy criteria and fits the life-threshold/autonomy neighbourhood more strongly than Paper 2 attribution architecture. Revisit only if those criteria become locally material to Attribution Locus or continuity. |
P3 | Catling et al., exoplanet biosignature Bayesian assessment | Hold; A2 / X3 / X6 | Relevant to probabilistic biosignature warrant but redundant locally once Neveu / Green / Parenteau represent the closer methodological neighbourhood. |
P3 | Yao, three-way decision theory | Exclude; A1 / X5 / X6 | Accept / reject / noncommitment is only a high-level resemblance. Paper 3 residual deferral is not a third class or generic decision region. |
P3 | Paper 2 biological individuality / holobiont / organisational-closure comparator family | Scoped hold; X6 | Primary bibliographic home is Paper 2. Paper 3 inherits the attribution architecture and should not duplicate Paper 2 provenance merely because its exemplars apply it. |
7. Part-level adjacency residual
This Part consolidation does not expand the discovery perimeter beyond the completed paper-level work. Paper 1 now carries a targeted audit upgrade against FD16, including the admitted Lizier et al. terminology/provenance comparator and Kolchinsky & Wolpert information-maintenance comparator, plus explicit hold/exclusion branch-memory. Paper 2 and Paper 3 carry their historical coded audits forward only where the 2026-08-12 posture/delta checks found no material change in relation, locator, or update condition.
Paper 3 retains the deliberate scope boundary that biological-individuality, holobiont, and organisational-closure comparators owned by Paper 2 are not duplicated merely because the procedure applies the inherited attribution architecture. The same ownership discipline applies upward: later-Part concepts are not imported into Part 1 to pre-install downstream architecture.
No further material adjacency is asserted by this document. Unsearched, inaccessible, held, excluded, or unrecognised adjacency remains residual. The Part bibliography should therefore be read as the current minimum-sufficient recoverable publication set, not as an exhaustive literature survey.
8. Series handoff and release control
This document is the first upward consolidation layer under GOT-SD-BIB-01. Its forty-three unique publications and forty-six paper-local admitted relations are now separable objects: bibliographic identity is deduplicated at Part level while each local relation remains controlled by the paper in which it was earned. No source is promoted to Indexed Inheritance by accumulation.
Release check | State | Control note |
|---|---|---|
Paper-local recoverability | Pass | Each paper retains its own bibliography and endnotes; this Part document does not replace them. |
Bibliographic deduplication | Pass | Forty-six raw current-paper bibliography occurrences consolidate to forty-three unique Part records. The increase from the prior lock is exactly the two approved Paper 1 additions: Kolchinsky & Wolpert (2018) and Lizier et al. (2007). |
Cross-paper relation preservation | Pass | Forterre, Lennon & Jones, and Montévil & Mossio retain distinct paper-local relations; no repeated publication is promoted by aggregation. |
Paper-level audit status | Pass | Paper 1 targeted audit metadata is now coded in this register; Paper 2 and Paper 3 historical codes were revalidated by current posture/delta checks with no reader-facing changes. No downstream concept was imported upstream. |
Hold/exclusion branch-memory | Pass | Material Paper 1, Paper 2, and Paper 3 holds/exclusions are carried forward without promotion; the Hinrichs Paper 2 candidate is updated to a verified A2 scoped hold rather than publication. |
Inheritance anti-drift | Pass | No publication is promoted by repetition. No new Indexed Inheritance is created at Part level. |
Adjacency residual | Pass | Discovery limits remain explicit; no exhaustiveness claim is made. |
Series handoff | Ready | Use this final source-locked Part bibliography, together with final SD-01-SD-03, as the Part 1 input to the later Series Master Bibliography and dependency/provenance controls. |
Release rule: if any paper bibliography changes, update that paper first, then re-run Part-level deduplication and relation preservation before updating the Series Master Bibliography. A Part-level correction must never be used to silently overwrite the paper-local scholarly relation.