Bound SynCom35, Deepwater and enamel graph claims to primary evidence (batch 29)

docs/communities/Defined_Multispecies_Enamel_Caries_Model.html

@@ -618,26 +618,16 @@ <h2>Ecological Interactions</h2>
                 <div class="network-tooltip" id="network-tooltip" role="status" aria-live="polite"></div>
                 <svg id="network-svg" role="img" aria-labelledby="network-svg-title network-svg-desc">
                     <title id="network-svg-title">Ecological interaction network for Defined Multispecies Enamel Caries Model</title>
-                    <desc id="network-svg-desc">Bipartite graph where circle nodes represent taxa and each ecological interaction is drawn as a distinct non-circular symbol, with colour repeating the same distinction (cross-feeding, competition, colonization facilitation).</desc>
+                    <desc id="network-svg-desc">Bipartite graph where circle nodes represent taxa and each ecological interaction is drawn as a distinct non-circular symbol, with colour repeating the same distinction.</desc>
                 </svg>
                 <div class="network-legend">
                     <div class="legend-item">
                         <span class="legend-swatch legend-circle" style="background: #7a7a7a;"></span> Taxon
                     </div>
                     <div class="legend-item">
                         <svg class="legend-symbol" width="14" height="14" viewBox="-9 -9 18 18"
-                             aria-hidden="true" data-symbol="symbolDiamond"
-                             data-color="#57c7ab"></svg> Cross-feeding
-                    </div>
-                    <div class="legend-item">
-                        <svg class="legend-symbol" width="14" height="14" viewBox="-9 -9 18 18"
-                             aria-hidden="true" data-symbol="symbolTimes"
-                             data-color="#a91919"></svg> Competition
-                    </div>
-                    <div class="legend-item">
-                        <svg class="legend-symbol" width="14" height="14" viewBox="-9 -9 18 18"
-                             aria-hidden="true" data-symbol="symbolPlus"
-                             data-color="#edab12"></svg> Colonization facilitation
+                             aria-hidden="true" data-symbol="symbolTriangle2"
+                             data-color="#929caa"></svg> Other
                     </div>
                 </div>
             </div>
@@ -646,13 +636,24 @@ <h2>Ecological Interactions</h2>
             <div class="interaction-card">
                 <div class="interaction-header">
                     <h3>Four-Species Enamel Biofilm Formation</h3>
-                    <span class="interaction-type">COLONIZATION_FACILITATION</span>
                 </div>
-                <p class="prewrap interaction-description">Lactobacillus casei, Streptococcus mutans, Streptococcus salivarius, and Streptococcus sanguinis formed a defined biofilm on salivary-pellicle-coated enamel slabs during the four-day in vitro caries assay.</p>
+                <p class="prewrap interaction-description">The four canonical taxa were inoculated onto salivary-pellicle-coated enamel for the four-day assay with daily medium changes. This records the defined starting community and biofilm platform, not demonstrated interspecies colonization facilitation or persistence of all four members in every treatment; S. sanguinis was below detection in the calcium arms.</p>
 
 
 
 
+                <p><strong>Participating Taxa:</strong>
+
+                    Lactobacillus casei,
+
+                    Streptococcus mutans,
+
+                    Streptococcus salivarius,
+
+                    Streptococcus sanguinis
+
+                </p>
+
 
 
 
@@ -670,21 +671,6 @@ <h3>Four-Species Enamel Biofilm Formation</h3>
 
 
 
-                <div class="interaction-flow">
-                    <strong>Downstream Effects:</strong>
-
-                    <div class="flow-item">
-                        <span class="flow-arrow">→</span> Sucrose-Responsive Viable Biofilm Shift
-                        <p class="prewrap causal-description">The established four-species enamel biofilm provided the viable biomass whose cell counts shifted across the sucrose, fluoride, and calcium arms.</p>
-                    </div>
-
-                    <div class="flow-item">
-                        <span class="flow-arrow">→</span> Mineral-Dependent Demineralization Restraint
-                        <p class="prewrap causal-description">Four days of multispecies biofilm growth on enamel slabs created the demineralization readout modulated by fluoride and calcium.</p>
-                    </div>
-
-                </div>
-
 
 
                 <h4>Evidence</h4>
@@ -709,13 +695,24 @@ <h4>Evidence</h4>
 
             <div class="interaction-card">
                 <div class="interaction-header">
-                    <h3>Sucrose-Responsive Viable Biofilm Shift</h3>
-                    <span class="interaction-type">CROSS_FEEDING</span>
+                    <h3>Treatment-Dependent Viable Biofilm Counts</h3>
                 </div>
-                <p class="prewrap interaction-description">Changing sucrose in the replacement medium was part of a treatment matrix that significantly altered viable-cell counts in the four-species enamel biofilms.</p>
+                <p class="prewrap interaction-description">Sucrose, fluoride and calcium treatments altered selected viable-count outcomes in the inoculated model. Higher sucrose increased total counts and L. casei; calcium did not significantly change total counts or S. mutans. Species-specific responses are not a uniform community increase or demonstrated cross-feeding. Acid selection remains a proposed explanation, not a selectively perturbed mechanism.</p>
+
 
 
 
+                <p><strong>Participating Taxa:</strong>
+
+                    Lactobacillus casei,
+
+                    Streptococcus mutans,
+
+                    Streptococcus salivarius,
+
+                    Streptococcus sanguinis
+
+                </p>
 
 
 
@@ -767,13 +764,24 @@ <h4>Evidence</h4>
             <div class="interaction-card">
                 <div class="interaction-header">
                     <h3>Mineral-Dependent Demineralization Restraint</h3>
-                    <span class="interaction-type">COMPETITION</span>
                 </div>
-                <p class="prewrap interaction-description">Higher fluoride and calcium concentrations reduced surface-microhardness change, and 0.8-1.0 ppm fluoride also lowered integrated mineral loss and lesion depth in the enamel slabs.</p>
+                <p class="prewrap interaction-description">Higher-fluoride arms had lower enamel surface-microhardness change, lesion depth and integrated mineral loss. Calcium at 2 mM reduced surface-microhardness change relative to lower calcium arms, not every mineral-loss endpoint. These are treatment-dependent material outcomes, not microbial competition or proof that altered cell counts mediate protection; proposed calcium/EPS mechanisms were not tested.</p>
 
 
 
 
+                <p><strong>Participating Taxa:</strong>
+
+                    Lactobacillus casei,
+
+                    Streptococcus mutans,
+
+                    Streptococcus salivarius,
+
+                    Streptococcus sanguinis
+
+                </p>
+
 
 
                 <p><strong>Metabolites:</strong>
@@ -790,17 +798,6 @@ <h3>Mineral-Dependent Demineralization Restraint</h3>
 
 
 
-                <p><strong>Biological Processes:</strong></p>
-                <ul>
-
-                    <li>
-                        biofilm formation
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0042710"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0042710</a>)
-                    </li>
-
-                </ul>
-
 
 
 
@@ -843,6 +840,25 @@ <h4>Evidence</h4>
 
         <!-- Associated Datasets -->
 
+        <section id="discussions">
+            <h2>Knowledge gaps &amp; discussions <span class="muted">(1)</span></h2>
+
+            <div class="discussion">
+                <h3>
+                    <span class="role-badge">KNOWLEDGE_GAP</span>
+                    <span class="role-badge">OPEN</span>
+                    Which microbial processes mediate the observed treatment-dependent counts and enamel outcomes?
+                </h3>
+                <p class="prewrap">The primary paper and Tables 1-2 support positive experimental outcomes but not cross-feeding, reciprocal competition, calcium/EPS mediation or selective pH causality. Distinguish starting roster from recoverable members. The Results prose and Table 2 superscripts differ on one L. casei calcium comparison; no disputed 1-versus-2 mM claim is used here. The two removed arrows described assay context, not mechanistic mediation. Non-graph follow-up: #1380.</p>
+
+                <p class="muted small">Attaches to: <code>ecological_interactions#Four-Species Enamel Biofilm Formation</code>, <code>ecological_interactions#Treatment-Dependent Viable Biofilm Counts</code>, <code>ecological_interactions#Mineral-Dependent Demineralization Restraint</code></p>
+
+
+
+
+            </div>
+
+        </section>
 
         <!-- Environmental Factors -->
 
@@ -1112,7 +1128,7 @@ <h4 style="color: var(--text);">Evidence</h4>
 
         (function() {
             var intId = "interaction:0";
-            var intType = "COLONIZATION_FACILITATION";
+            var intType = "UNKNOWN";
             var metabolites = [];
 
             var processes = [];
@@ -1136,11 +1152,28 @@ <h4 style="color: var(--text);">Evidence</h4>
 
 
 
+            var participantKeys = [
+
+                "Lactobacillus casei",
+
+                "Streptococcus mutans",
+
+                "Streptococcus salivarius",
+
+                "Streptococcus sanguinis"
+
+            ];
+            participantKeys.forEach(function(key) {
+                if (taxonNodeIds[key]) {
+                    links.push({ source: taxonNodeIds[key], target: intId });
+                }
+            });
+
         })();
 
         (function() {
             var intId = "interaction:1";
-            var intType = "CROSS_FEEDING";
+            var intType = "UNKNOWN";
             var metabolites = [];
 
 
@@ -1157,7 +1190,7 @@ <h4 style="color: var(--text);">Evidence</h4>
 
             nodes.push({
                 id: intId,
-                label: "Sucrose-Responsive Viable Biofilm Shift",
+                label: "Treatment-Dependent Viable Biofilm Counts",
                 type: "interaction",
                 interactionType: intType,
                 metabolites: metabolites,
@@ -1168,11 +1201,28 @@ <h4 style="color: var(--text);">Evidence</h4>
 
 
 
+            var participantKeys = [
+
+                "Lactobacillus casei",
+
+                "Streptococcus mutans",
+
+                "Streptococcus salivarius",
+
+                "Streptococcus sanguinis"
+
+            ];
+            participantKeys.forEach(function(key) {
+                if (taxonNodeIds[key]) {
+                    links.push({ source: taxonNodeIds[key], target: intId });
+                }
+            });
+
         })();
 
         (function() {
             var intId = "interaction:2";
-            var intType = "COMPETITION";
+            var intType = "UNKNOWN";
             var metabolites = [];
 
 
@@ -1183,10 +1233,6 @@ <h4 style="color: var(--text);">Evidence</h4>
 
             var processes = [];
 
-
-            processes.push("biofilm formation");
-
-
             var evidenceCount = 2;
 
             nodes.push({
@@ -1202,6 +1248,23 @@ <h4 style="color: var(--text);">Evidence</h4>
 
 
 
+            var participantKeys = [
+
+                "Lactobacillus casei",
+
+                "Streptococcus mutans",
+
+                "Streptococcus salivarius",
+
+                "Streptococcus sanguinis"
+
+            ];
+            participantKeys.forEach(function(key) {
+                if (taxonNodeIds[key]) {
+                    links.push({ source: taxonNodeIds[key], target: intId });
+                }
+            });
+
         })();
 
 

history/records/Dangl_SynComm_35/2026-10-06T052450Z-codex-4c42b0.yaml

@@ -0,0 +1,31 @@
+history_version: 1
+target:
+  kind: record
+  path: kb/communities/Dangl_SynComm_35.yaml
+  slug: Dangl_SynComm_35
+session:
+  id: 2026-10-06T052450Z-codex-4c42b0
+  timestamp: '2026-10-06T05:24:50Z'
+  actors:
+  - type: ai_agent
+    name: codex
+    model: unspecified
+    agent_tool: codex
+links:
+  issues:
+  - https://github.com/CultureBotAI/CommunityMech/issues/1375
+events:
+- type: EDIT
+  outcome: changed
+  sections:
+  - interactions
+  - discussions
+  summary: Retain positive root immune suppression at community scope; do not assign community
+    readouts exclusively to MF79.; Retain the primary-body WRKY observation without converting
+    proposed regulatory/homeostasis roles into proven causality; abstract snippet support
+    is explicitly partial.; Retain the tested MF79 secretion-system mechanism and existing
+    arrow with strain-specific scope and unresolved effector identity.; Retain experimentally
+    supported colonization facilitation, distinguish assay contexts and incomplete canonical
+    participants, and remove reciprocal-fitness attribution.
+  details: Primary-source self-adversarial repair, qualification and removal; no new nodes
+    or arrows. reports/causal_graph_review/decisions/20261006-three-records-batch29.yaml

history/records/Deepwater_Horizon_Deep_Sea_Oil_Plume_Succession/2026-10-06T052450Z-codex-df845f.yaml

@@ -0,0 +1,30 @@
+history_version: 1
+target:
+  kind: record
+  path: kb/communities/Deepwater_Horizon_Deep_Sea_Oil_Plume_Succession.yaml
+  slug: Deepwater_Horizon_Deep_Sea_Oil_Plume_Succession
+session:
+  id: 2026-10-06T052450Z-codex-df845f
+  timestamp: '2026-10-06T05:24:50Z'
+  actors:
+  - type: ai_agent
+    name: codex
+    model: unspecified
+    agent_tool: codex
+links:
+  issues:
+  - https://github.com/CultureBotAI/CommunityMech/issues/1376
+events:
+- type: EDIT
+  outcome: changed
+  sections:
+  - interactions
+  - discussions
+  summary: Retain measured cold biodegradation and qualified bioremediation potential; consolidate
+    duplicate oxygen context without asserting syntrophy or oxygen conservation.; Retain positive
+    Colwellia-dominated flocs while qualifying their proposed contribution to degradation
+    and removing unsupported facilitation.; Retain positive SIP/genome evidence and the complementary-pathway
+    hypothesis, distinguish surface/deep and laboratory/field contexts, and retain alternative
+    explanations.
+  details: Primary-source self-adversarial repair, qualification and removal; no new nodes
+    or arrows. reports/causal_graph_review/decisions/20261006-three-records-batch29.yaml

history/records/Defined_Multispecies_Enamel_Caries_Model/2026-10-06T052450Z-codex-bf5211.yaml

@@ -0,0 +1,28 @@
+history_version: 1
+target:
+  kind: record
+  path: kb/communities/Defined_Multispecies_Enamel_Caries_Model.yaml
+  slug: Defined_Multispecies_Enamel_Caries_Model
+session:
+  id: 2026-10-06T052450Z-codex-bf5211
+  timestamp: '2026-10-06T05:24:50Z'
+  actors:
+  - type: ai_agent
+    name: codex
+    model: unspecified
+    agent_tool: codex
+links:
+  issues:
+  - https://github.com/CultureBotAI/CommunityMech/issues/1377
+events:
+- type: EDIT
+  outcome: changed
+  sections:
+  - interactions
+  - discussions
+  summary: Retain the inoculated biofilm platform without interspecies facilitation or universal
+    persistence claims.; Retain treatment- and species-specific viable-count outcomes without
+    cross-feeding or a uniform calcium effect.; Retain endpoint-specific enamel mineral outcomes
+    without microbial competition or an untested mediation mechanism.
+  details: Primary-source self-adversarial repair, qualification and removal; no new nodes
+    or arrows. reports/causal_graph_review/decisions/20261006-three-records-batch29.yaml