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| <div class="gridbg"></div><div class="helix"></div><div class="stars"></div> |
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| <header class="wrap"> |
| <div class="kicker"><span class="dot"></span> Biological Uncertainty · GRCh38 Source Layer 1</div> |
| <h1>Unknown biology is not bad evidence. <span>Untrusted evidence is not biology.</span></h1> |
| <p class="sub">A public HIR/OAM map for genomic uncertainty, GRCh38 reference limits, provenance gates, measurement failure, and hard blocks against hidden positive evidence.</p> |
| <div class="actions"> |
| <a class="btn" href="#invariant">Read invariant</a> |
| <a class="btn secondary" href="#map">Explore source model</a> |
| <a class="btn secondary" href="https://huggingface.co/spaces/HirModel/primordial-code-ecosystem" target="_blank" rel="noopener">Parent hub</a> |
| </div> |
| </header> |
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| <nav> |
| <div class="wrap"> |
| <a href="#invariant">Invariant</a> |
| <a href="#map">GRCh38 layer</a> |
| <a href="#rules">HIR rules</a> |
| <a href="#roadmap">Staged ingest</a> |
| <a href="#boundary">Boundary</a> |
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| <main> |
| <section class="wrap" id="invariant"> |
| <h2>Non-negotiable invariant</h2> |
| <div class="invariant"> |
| <p><strong>Unknown biology may preserve possibility space. Untrusted data may invalidate the comparison. Neither may be converted into hidden positive evidence.</strong></p> |
| <p><strong>Biological unresolvedness ≠ measurement/provenance unresolvedness.</strong> These categories must remain separate throughout all schemas, scoring, and downstream layers.</p> |
| </div> |
| </section> |
|
|
| <section class="wrap" id="map"> |
| <h2>GRCh38 first-pass source model</h2> |
| <p class="lead">GRCh38 is treated as Source Layer 1: an initial baseline reference frame, not a complete model of human diversity and not a final biological authority.</p> |
| <div class="grid"> |
| <article class="card" style="--accent:#70e8ff"><div class="top"><div class="icon">🧬</div><span class="pill ok">Layer 1</span></div><h3>Reference frame</h3><p>GRCh38 / GRCh38.p14 anchors first-pass coordinates and feature typing while carrying explicit reference limitations.</p><div class="tags"><span class="tag">GRCh38</span><span class="tag">reference</span></div></article> |
| <article class="card" style="--accent:#ffd27a"><div class="top"><div class="icon">⚠️</div><span class="pill stop">Limits</span></div><h3>Known gaps</h3><p>Gap-adjacent, centromeric, telomeric, repeat-dense, and segmentally duplicated regions must carry reference confidence limits.</p><div class="tags"><span class="tag">gaps</span><span class="tag">confidence</span></div></article> |
| <article class="card" style="--accent:#a05cff"><div class="top"><div class="icon">🧾</div><span class="pill ok">Provenance</span></div><h3>Evidence chain</h3><p>Contamination, mixed sample, broken chain of custody, and undocumented provenance invalidate or suspend comparison authority.</p><div class="tags"><span class="tag">provenance</span><span class="tag">chain</span></div></article> |
| <article class="card" style="--accent:#7dffad"><div class="top"><div class="icon">🔬</div><span class="pill ok">Feature</span></div><h3>Typed features</h3><p>SNPs, indels, structural placeholders, gap regions, regulatory placeholders, and unknown unresolved features require explicit status.</p><div class="tags"><span class="tag">schema</span><span class="tag">feature classes</span></div></article> |
| <article class="card" style="--accent:#ff6b8a"><div class="top"><div class="icon">⛔</div><span class="pill stop">Hard stop</span></div><h3>No hidden positives</h3><p>Unknown biological or measurement/provenance classes may not be promoted into positive similarity, identity, or continuity evidence.</p><div class="tags"><span class="tag">blocked</span><span class="tag">HIR</span></div></article> |
| <article class="card" style="--accent:#70e8ff"><div class="top"><div class="icon">🧭</div><span class="pill ok">Next</span></div><h3>Staged layers</h3><p>Layer expansion should proceed through T2T-CHM13, pangenome references, and functional annotation only after schema validation.</p><div class="tags"><span class="tag">T2T</span><span class="tag">pangenome</span></div></article> |
| </div> |
| </section> |
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| <section class="wrap" id="rules"> |
| <h2>HIR rule layer</h2> |
| <div class="split"> |
| <div class="panel"> |
| <h3>Honesty</h3> |
| <p>Every feature record must carry explicit status, uncertainty class, reference confidence, and coverage confidence.</p> |
| <div class="equation">Unknown must be labeled unknown. |
| No field may be implicitly clean. |
| Not assessed cannot default to high confidence.</div> |
| </div> |
| <div class="panel"> |
| <h3>Integrity + Respect</h3> |
| <p>Biological unresolvedness and measurement/provenance unresolvedness remain separate; identity and family-relation claims are blocked beyond declared evidence limits.</p> |
| <div class="equation">Category A ≠ Category B. |
| Biological unknown ≠ sample failure. |
| Sample failure ≠ biology. |
| No identity/family/continuity inference.</div> |
| </div> |
| </div> |
| </section> |
|
|
| <section class="wrap" id="roadmap"> |
| <h2>Staged ingest discipline</h2> |
| <p class="lead">Do not ingest raw genome files or perform scoring until schema, uncertainty classes, and provenance rules are validated with sample records.</p> |
| <div class="panel"> |
| <div class="equation">1. GRCh38 / GRCh38.p14 — active Source Layer 1 |
| 2. Machine-readable HIR rule table |
| 3. Structured GRCh38 gap-region catalog |
| 4. Sample feature records in JSONL |
| 5. T2T-CHM13 source model |
| 6. Liftover / coordinate alignment spec |
| 7. Pangenome graph-coordinate extension before HPRC Layer 3</div> |
| </div> |
| </section> |
|
|
| <section class="wrap" id="boundary"> |
| <h2>Boundary</h2> |
| <div class="danger"> |
| <p><strong>This is not a genomic analysis pipeline or medical/forensic authority.</strong></p> |
| <p>This Space is a bounded architecture and public review prototype. It is not clinical advice, diagnosis, treatment guidance, identity proof, family-relation proof, forensic conclusion, ancestry result, genetic counseling, or validated genomic-comparison software.</p> |
| <p>GRCh38 is used as a reference frame only. All genomic inferences beyond declared evidence limits are explicitly blocked by the HIR rule set.</p> |
| <p><strong>Structural correspondence, not ontological equivalence.</strong></p> |
| </div> |
| </section> |
| </main> |
|
|
| <footer class="wrap"> |
| <strong>Biological Uncertainty Stack</strong><br/> |
| Created and developed by Collin D. Weber · HIR/OAM genomic uncertainty architecture.<br/> |
| Source search target: <code>Primordial_DNA_GRCh38_First_Pass_Architecture_Plan_v0.1.html</code> |
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