Bound inferred electron transfer in Geobacter-Clostridium (batch45)

history/records/Geobacter_Clostridium_Interspecies_Electron_Transfer_Coculture/2026-10-06T123147Z-codex-030fb7.yaml

@@ -0,0 +1,26 @@
+history_version: 1
+target:
+  kind: record
+  path: kb/communities/Geobacter_Clostridium_Interspecies_Electron_Transfer_Coculture.yaml
+  slug: Geobacter_Clostridium_Interspecies_Electron_Transfer_Coculture
+session:
+  id: 2026-10-06T123147Z-codex-030fb7
+  timestamp: '2026-10-06T12:31:47Z'
+  actors:
+  - type: ai_agent
+    name: codex
+    model: unspecified
+    agent_tool: codex
+links:
+  issues:
+  - https://github.com/CultureBotAI/CommunityMech/issues/1478
+events:
+- type: EDIT
+  outcome: changed
+  sections:
+  - interactions
+  - discussions
+  summary: Qualify growth-inferred electron transfer and its one retained arrow; restrict
+    product yields to responding cultures; remove duplicate outcome and unsupported mutualism;
+    correct controversy and exact anchors.
+  details: Source-based self-adversarial existing-graph repair. reports/causal_graph_review/decisions/20261006-clostridium-batch45.yaml

reports/causal_graph_review/README.md

@@ -5,6 +5,16 @@ source-based self-adversarial review. These records are not independent approval
 or proof that every graph is complete. The current inventory and summary distinguish
 `reviewed`, `pending` and `needs_research`.
 
+## Batch45: Geobacter-Clostridium
+
+[Decisions](decisions/20261006-clostridium-batch45.yaml),
+[validation](validation-20261006-batch45.json) and
+[self-adversarial review](adversarial-review-20261006-batch45.yaml) separate
+conditional measured fermentation yields from an inferred electron balance.
+The upstream arrow remains explicitly hypothetical; the duplicate outcome node
+and its restatement arrow are removed. The 2022 follow-up was reviewed at
+abstract scope only. Non-graph text is preserved, not certified.
+
 ## Batch44: UFMP, GOM and Garlic
 
 [Decisions](decisions/20261006-three-records-batch44.yaml),

reports/causal_graph_review/adversarial-review-20261006-batch45.yaml

@@ -0,0 +1,119 @@
+reviewer: codex
+review_mode: source_based_self_adversarial_review
+independent_approval: false
+base_commit: 7bdc93828cb9585f0711253d58d7382037207010
+scope:
+- kb/communities/Geobacter_Clostridium_Interspecies_Electron_Transfer_Coculture.yaml
+decision_ledger: reports/causal_graph_review/decisions/20261006-clostridium-batch45.yaml
+validation_report: reports/causal_graph_review/validation-20261006-batch45.json
+findings:
+- issue: 1478
+  severity: P2
+  status: addressed_in_this_change
+  finding: Qualify growth-inferred electron transfer and its one retained arrow; restrict product yields
+    to responding cultures; remove duplicate outcome and unsupported mutualism; correct controversy and
+    exact anchors.
+  disposition: Close only after protected main merge.
+adversarial_checks:
+- Whole 653-line record and all three original nodes/two arrows read. 2017 primary main body, Methods,
+  Table 1 and captions read; 2022 complete abstract only. No figure images, separate supplements, raw
+  data or analysis code audited.
+- Geobacter qPCR-derived growth and an acetate/biomass allocation model are not direct electron uptake
+  or current. The <0.6% value depends on the acetate-only donor, 10% biomass and 90% transfer assumptions.
+  Both the transfer node and its retained direction remain HYPOTHESIZED/PARTIAL.
+- Preserve positive 72-h product measurements while exposing 2/4 initial responders and 8/12 follow-up
+  responders. Regressions use responders; product percentages are not all-culture means or universal responses.
+  Lower Clostridium biomass and useful chemical yields do not establish mutualism.
+- Merge the duplicate product outcome into the measured response, preserve its evidence and remove the
+  tautological second arrow. Remove unsupported electron-chain annotation, SYNTROPHY and MUTUALISM classifications
+  from these nodes. Exact two canonical participants are explicit; no taxon IDs invented.
+- Correct exact discussion anchors and stale DIET filename note. Nanowire heterogeneity remains an author
+  hypothesis. The 2022 abstract supports a putative cobamide model only; no 0.22-um spent-medium assay
+  is claimed verified, and no mediator is silently promoted to established fact.
+- Graph diff inspected. Guarded writer, one append-only history and one regenerated page. All 459 other
+  records, 920 caches, canonical taxonomy and non-graph raw blocks preserved; stronger non-graph uptake/connection/product
+  claims remain outside this correction and are not certified.
+- Both-root pre-paper baseline, schema/strict/terms/references/snippets/history/rank gates retained with
+  actual outputs and hashes. All 34 existing network findings unchanged, zero structural errors. Repeated
+  renders deterministic and descriptions parser-checked across 456 published pages, without a browser
+  screenshot claim.
+- Four new focused tests plus historical and shared regressions passed, including positive/negative reference-validator
+  canaries. Participant registry 193 to 194; one new community-level-only two-member record. Census bounds
+  and production matching logic unchanged.
+- 'Dedup covered 793 all-state issue titles/bodies and ignored/hidden local files; #256/#295/#289/#306
+  bodies read. Prior contact-route and generic-snippet fixes preserved, remaining broader uptake-causation
+  and responder-scope claims addressed. Not all issue comments or PR reviews inspected.'
+- Methanosaeta/Methanosarcina source work is deferred, not counted as reviewed in this one-record PR.
+  A separate one-community Methanosaeta Edison dry run made no API calls and awaits specific spend authorization;
+  no paid job is implied by this Clostridium repair.
+- Self-adversarial review is not independent approval. Exact-head GitHub COMMENT and actual post-commit
+  docs-current are separate publication gates. Protected main queue and dependent-parent merges remain
+  required; full-corpus completion is not claimed.
+verification:
+  combined_regressions: 455 passed in 168.19s (0:02:48)
+  new_regression_tests: 4
+  schema_strict_terms_history: Passed with actual outputs and digests
+  references: 'CLI Total checks counts reported issues, not executed checks. Exit 0 means no reported
+    issues; textual matching does not establish scientific support or independent provenance. SupportingReference
+    coverage remains incomplete under #476.'
+  snippet_counts_by_record:
+    kb/communities/Geobacter_Clostridium_Interspecies_Electron_Transfer_Coculture.yaml:
+      MATCH: 22
+      RENDERING: 0
+      ASSEMBLED: 0
+      WEAK: 0
+      MISMATCH: 0
+      NOCONTENT: 0
+  network:
+    existing_findings_preserved: 34
+    added_findings: {}
+    removed_findings: {}
+  black_ruff_diff: passed
+  tested_file_sha256:
+    reports/causal_graph_review/decisions/20261006-clostridium-batch45.yaml: 91f2b38628bc946d11bf40ae7d52501867dda13969429bac62a95514be38473c
+    tests/test_causal_review_batch45.py: 73160070d62babe533dbd60e0da6582aaa2c93eeb71cf7ca497a70ab15a00203
+    tests/test_participating_taxa.py: 9420e75cb8c477620597c3edf066ceaa5e431b4d5053398e8f635d81069207a1
+    kb/communities/Geobacter_Clostridium_Interspecies_Electron_Transfer_Coculture.yaml: 2bfa8ffd6b7d147f3c471eb88aa26482f93b0cc8d7b23dc39838402715463329
+    reports/causal_graph_review/README.md: ce166b800cc8ede66788b97c0d919f82887118e68ba88002419d77a70b76ba73
+  post_commit_docs_current: Separate publication gate, not asserted before commit.
+participant_census:
+  measurements:
+    baseline:
+      records: 460
+      with_community_level: 387
+      mixed: 125
+      community_level_only: 262
+      taxa: 1494
+      credited_solely_by_the_rule: 1221
+    current:
+      records: 460
+      with_community_level: 388
+      mixed: 125
+      community_level_only: 263
+      taxa: 1496
+      credited_solely_by_the_rule: 1223
+  interpretation: One two-member graph becomes explicitly community-level for the proposed interaction
+    and conditional coculture outcome. Mixed count remains 125; registry 193 to 194. No census bounds
+    or production matching logic changed.
+corpus:
+  records: 460
+  nodes: 1465
+  edges: 681
+  review_status_counts:
+    needs_research: 12
+    pending: 280
+    reviewed: 168
+limitations:
+- Whole 653-line record, all three original nodes and both arrows read. Complete 2017 primary main body,
+  Methods, Table 1 and embedded captions read; 2022 complete abstract only, publisher confirms subscription
+  preview. No figure images, separate supplements, raw data or analysis code audited.
+- 'Repair only: three to two nodes and two to one explicitly HYPOTHESIZED arrow; no new causal structure
+  or provider spend for this record.'
+- All canonical taxonomy, non-graph raw blocks, prior history and 920 source caches preserved, not certified.
+  Non-graph uptake, nanowire and product-causation claims remain outside this graph-scoped correction.
+- 'Reference CLI Total checks counts reported issues, not executed checks; SupportingReference coverage
+  remains incomplete under #476. Textual matches do not independently establish source provenance (#1362)
+  or scientific support.'
+- Source-based self-adversarial review is not independent approval. Methanosaeta and Methanosarcina remain
+  outside this one-record edit and are not counted as reviewed. Full-corpus completion and protected-main
+  merge are not claimed.

reports/causal_graph_review/decisions/20261006-clostridium-batch45.yaml

@@ -0,0 +1,118 @@
+reviewer: codex
+review_mode: source_based_self_adversarial_review
+independent_approval: false
+base_commit: 7bdc93828cb9585f0711253d58d7382037207010
+baseline_commit: 7bdc93828cb9585f0711253d58d7382037207010
+base_tree: ae873b509fa12c69970cbafa96265ab9d55b8eb5
+issues:
+- 1478
+issue_deduplication:
+  all_state_issue_titles_and_bodies: 793
+  ignored_hidden_local_search: true
+  relevant_bodies_read:
+  - 256
+  - 295
+  - 289
+  - 306
+  local_matching_lines: 63
+  limitations: Search includes two deferred methanogen candidates and historical render/audit logs. Not all comments
+    or PR reviews inspected.
+reference_cache_original_hashes:
+  references_cache/PMID_28287150.txt: fdddff4829504900d4fcc745c214415a4cd3db3f57b1afe864237a4ec0c8c333
+  references_cache/PMID_34939136.txt: 8e7d9b0ab75beb3caf39c10356a7f7b9cf97547b1c6388ba92154c00c7e9e4ba
+limitations:
+- Whole 653-line record, all three original nodes and both arrows read. Complete 2017 primary main body, Methods,
+  Table 1 and embedded captions read; 2022 complete abstract only, publisher confirms subscription preview. No figure
+  images, separate supplements, raw data or analysis code audited.
+- 'Repair only: three to two nodes and two to one explicitly HYPOTHESIZED arrow; no new causal structure or provider
+  spend for this record.'
+- All canonical taxonomy, non-graph raw blocks, prior history and 920 source caches preserved, not certified. Non-graph
+  uptake, nanowire and product-causation claims remain outside this graph-scoped correction.
+- 'Reference CLI Total checks counts reported issues, not executed checks; SupportingReference coverage remains
+  incomplete under #476. Textual matches do not independently establish source provenance (#1362) or scientific
+  support.'
+- Source-based self-adversarial review is not independent approval. Methanosaeta and Methanosarcina remain outside
+  this one-record edit and are not counted as reviewed. Full-corpus completion and protected-main merge are not
+  claimed.
+records:
+- path: kb/communities/Geobacter_Clostridium_Interspecies_Electron_Transfer_Coculture.yaml
+  id: CommunityMech:000031
+  original_sha256: d3a7d0c3298583e167a50201c8da4cd94d0ac51c1516a8587a41259e85f4718e
+  record_sha256: 2bfa8ffd6b7d147f3c471eb88aa26482f93b0cc8d7b23dc39838402715463329
+  status: reviewed
+  outcome: changed
+  review_file: reports/causal_graph_review/decisions/20261006-clostridium-batch45.yaml
+  scope: Whole record and every original node/arrow reviewed; measurements distinguished from inferred mediator.
+  summary: Qualify growth-inferred electron transfer and its one retained arrow; restrict product yields to responding
+    cultures; remove duplicate outcome and unsupported mutualism; correct controversy and exact anchors.
+  renamed_nodes:
+    Acetate Oxidation and Interspecies Electron Transfer: Proposed Acetate Oxidation and Interspecies Electron Transfer
+    Glycerol Fermentation with Electron-Transfer-Induced Metabolic Shift: Coculture-Associated Glycerol Fermentation
+      Product Shift
+  node_decisions:
+  - node: Proposed Acetate Oxidation and Interspecies Electron Transfer
+    rationale: Retain only the HYPOTHESIZED growth-based acetate/IET model with both canonical participants; not
+      measured uptake or demonstrated syntrophy.
+  - node: Coculture-Associated Glycerol Fermentation Product Shift
+    rationale: Retain conditional measured product yields, remove mutualism and unproven electron-chain annotation;
+      incorporate duplicate outcome evidence.
+  removed_node_decisions:
+  - node: Increased 1,3-Propanediol and Butyrate Production
+    rationale: Same product shift as the fermentation-response node, not a distinct downstream causal event; preserve
+      its evidence in the surviving response.
+  edges_before:
+  - source: Acetate Oxidation and Interspecies Electron Transfer
+    target: Glycerol Fermentation with Electron-Transfer-Induced Metabolic Shift
+    description: Electrons taken up from G. sulfurreducens induce the metabolic shift in C. pasteurianum toward
+      1,3-propanediol and butyrate. The transfer route is unresolved, so this edge asserts electron uptake causing
+      the shift, not a contact-dependent mechanism.
+  - source: Glycerol Fermentation with Electron-Transfer-Induced Metabolic Shift
+    target: Increased 1,3-Propanediol and Butyrate Production
+    description: The electron-transfer-induced metabolic shift redirects glycerol fermentation products toward higher
+      1,3-propanediol and butyrate yields.
+  edges_after:
+  - source: Proposed Acetate Oxidation and Interspecies Electron Transfer
+    target: Coculture-Associated Glycerol Fermentation Product Shift
+    description: 'HYPOTHESIZED: Acetate-derived electron transfer could alter Clostridium redox regulation and thereby
+      its glycerol-fermentation product profile. Growth/product associations and an assumed electron balance motivate
+      this direction, but do not selectively establish electron uptake as the mediator. The follow-up proposes cobamides
+      and possible electron entry as alternatives or contributors, not verified replacements.'
+  retained_edge_decisions:
+  - source: Proposed Acetate Oxidation and Interspecies Electron Transfer
+    target: Coculture-Associated Glycerol Fermentation Product Shift
+    description: 'HYPOTHESIZED: Acetate-derived electron transfer could alter Clostridium redox regulation and thereby
+      its glycerol-fermentation product profile. Growth/product associations and an assumed electron balance motivate
+      this direction, but do not selectively establish electron uptake as the mediator. The follow-up proposes cobamides
+      and possible electron entry as alternatives or contributors, not verified replacements.'
+    rationale: Explicit hypothesis of redox-mediated product regulation; association and assumed balance do not
+      selectively prove the mediator.
+  removed_edge_decisions:
+  - source: Glycerol Fermentation with Electron-Transfer-Induced Metabolic Shift
+    target: Increased 1,3-Propanediol and Butyrate Production
+    description: The electron-transfer-induced metabolic shift redirects glycerol fermentation products toward higher
+      1,3-propanediol and butyrate yields.
+    rationale: A product-profile shift causing the same product-profile shift is a restatement, not a separate causal
+      link.
+  references:
+  - PMID:28287150
+  - PMID:34939136
+  issues:
+  - 1478
+  allowed_changed_fields:
+  - curation_history
+  - discussions
+  - ecological_interactions
+  curation_events_added: 1
+  history_files:
+  - history/records/Geobacter_Clostridium_Interspecies_Electron_Transfer_Coculture/2026-10-06T123147Z-codex-030fb7.yaml
+  source_review:
+    PMID:28287150:
+      cache: references_cache/PMID_28287150.txt
+      sha256: fdddff4829504900d4fcc745c214415a4cd3db3f57b1afe864237a4ec0c8c333
+      url: https://doi.org/10.1038/srep44334
+      scope: Complete appended primary main body/Methods/Table 1/captions, not figure images or separate supplements.
+    PMID:34939136:
+      cache: references_cache/PMID_34939136.txt
+      sha256: 8e7d9b0ab75beb3caf39c10356a7f7b9cf97547b1c6388ba92154c00c7e9e4ba
+      url: https://link.springer.com/article/10.1007/s00253-021-11736-7
+      scope: Complete abstract only; subscription preview. Cell-free assay not verified.

reports/causal_graph_review/inventory.tsv

@@ -180,7 +180,7 @@ kb/communities/GLBRC_Populus_Variovorax_SynCom28.yaml	CommunityMech:000028	c251f
 kb/communities/GLBRC_UFMP_Fermentation_Community.yaml	CommunityMech:000029	0cd65716c7bf522b2c8326bdc476339c3196f551d9a2ee92c405d15dc9ea9c92	3	2	87.8	reports/causal_graph_review/decisions/20261006-three-records-batch44.yaml	reviewed
 kb/communities/GOM_Oil_Degrading_Consortium.yaml	CommunityMech:000030	90d4d45224abfc9829feb8fd1cabde320c410a7a843ea3410c89dda4852cc299	3	0	65.0	reports/causal_graph_review/decisions/20261006-three-records-batch44.yaml	reviewed
 kb/communities/Garlic_Pseudomonas_SynCom6.yaml	CommunityMech:000095	0052209591a0d6d3e106ad27feaca9dde69645f9725f01ba63e41ebeb5c5c59c	1	0	65.0	reports/causal_graph_review/decisions/20261006-three-records-batch44.yaml	reviewed
-kb/communities/Geobacter_Clostridium_Interspecies_Electron_Transfer_Coculture.yaml	CommunityMech:000031	d3a7d0c3298583e167a50201c8da4cd94d0ac51c1516a8587a41259e85f4718e	3	2	100.0		pending
+kb/communities/Geobacter_Clostridium_Interspecies_Electron_Transfer_Coculture.yaml	CommunityMech:000031	2bfa8ffd6b7d147f3c471eb88aa26482f93b0cc8d7b23dc39838402715463329	2	1	75.0	reports/causal_graph_review/decisions/20261006-clostridium-batch45.yaml	reviewed
 kb/communities/Geobacter_Methanosaeta_DIET.yaml	CommunityMech:000032	3fc22ecba6b448dd63c54896e119773338b3e331d88be489b54bb1c58277fc6a	3	2	100.0		pending
 kb/communities/Geobacter_Methanosarcina_DIET.yaml	CommunityMech:000033	3c1a692277d402834b3acc3d529d8abe87a2afe7a0ae03027aae66eff187a543	3	2	100.0		pending
 kb/communities/Geobacter_Pseudomonas_Formate_Fumarate_Electroactive_Coculture.yaml	CommunityMech:000201	dbef08d1731c382db77222a55e9b0ea021f739c52993a737a73b35007e328fb4	4	2	100.0		pending

reports/causal_graph_review/summary.json

@@ -2,14 +2,14 @@
   "scope": "Every YAML under kb/communities and data/isolates; filesystem discovery includes hidden/ignored files.",
   "semantic_review_rule": "Structural checks and readiness scores do not establish causal support. Completed reviews must match the current record SHA-256, cover every node once with a rationale, and reproduce the current edge list.",
   "records": 460,
-  "nodes": 1466,
-  "edges": 682,
+  "nodes": 1465,
+  "edges": 681,
   "records_without_nodes": 8,
   "records_without_edges": 148,
   "review_status_counts": {
     "needs_research": 12,
-    "pending": 281,
-    "reviewed": 167
+    "pending": 280,
+    "reviewed": 168
   },
   "structural_defects": [],
   "network_audit": [