Bibliography and Relation Register

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 Superseded paper revisions and prior working drafts are excluded.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.

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.

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.

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

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.

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.

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.

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.