HirModel/biological-uncertainty-stack
0
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class="wrap">84 <div class="kicker"><span class="dot"></span> Biological Uncertainty · GRCh38 Source Layer 1</div>85 <h1>Unknown biology is not bad evidence. <span>Untrusted evidence is not biology.</span></h1>86 <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>87 <div class="actions">88 <a class="btn" href="#invariant">Read invariant</a>89 <a class="btn secondary" href="#map">Explore source model</a>90 <a class="btn secondary" href="https://huggingface.co/spaces/HirModel/primordial-code-ecosystem" target="_blank" rel="noopener">Parent hub</a>91 </div>92</header>93 94<nav>95 <div class="wrap">96 <a href="#invariant">Invariant</a>97 <a href="#map">GRCh38 layer</a>98 <a href="#rules">HIR rules</a>99 <a href="#roadmap">Staged ingest</a>100 <a href="#boundary">Boundary</a>101 </div>102</nav>103 104<main>105 <section class="wrap" id="invariant">106 <h2>Non-negotiable invariant</h2>107 <div class="invariant">108 <p><strong>Unknown biology may preserve possibility space. Untrusted data may invalidate the comparison. Neither may be converted into hidden positive evidence.</strong></p>109 <p><strong>Biological unresolvedness ≠ measurement/provenance unresolvedness.</strong> These categories must remain separate throughout all schemas, scoring, and downstream layers.</p>110 </div>111 </section>112 113 <section class="wrap" id="map">114 <h2>GRCh38 first-pass source model</h2>115 <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>116 <div class="grid">117 <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>118 <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>119 <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>120 <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>121 <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>122 <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>123 </div>124 </section>125 126 <section class="wrap" id="rules">127 <h2>HIR rule layer</h2>128 <div class="split">129 <div class="panel">130 <h3>Honesty</h3>131 <p>Every feature record must carry explicit status, uncertainty class, reference confidence, and coverage confidence.</p>132 <div class="equation">Unknown must be labeled unknown.133No field may be implicitly clean.134Not assessed cannot default to high confidence.</div>135 </div>136 <div class="panel">137 <h3>Integrity + Respect</h3>138 <p>Biological unresolvedness and measurement/provenance unresolvedness remain separate; identity and family-relation claims are blocked beyond declared evidence limits.</p>139 <div class="equation">Category A ≠ Category B.140Biological unknown ≠ sample failure.141Sample failure ≠ biology.142No identity/family/continuity inference.</div>143 </div>144 </div>145 </section>146 147 <section class="wrap" id="roadmap">148 <h2>Staged ingest discipline</h2>149 <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>150 <div class="panel">151 <div class="equation">1. GRCh38 / GRCh38.p14 — active Source Layer 11522. Machine-readable HIR rule table1533. Structured GRCh38 gap-region catalog1544. Sample feature records in JSONL1555. T2T-CHM13 source model1566. Liftover / coordinate alignment spec1577. Pangenome graph-coordinate extension before HPRC Layer 3</div>158 </div>159 </section>160 161 <section class="wrap" id="boundary">162 <h2>Boundary</h2>163 <div class="danger">164 <p><strong>This is not a genomic analysis pipeline or medical/forensic authority.</strong></p>165 <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>166 <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>167 <p><strong>Structural correspondence, not ontological equivalence.</strong></p>168 </div>169 </section>170</main>171 172<footer class="wrap">173 <strong>Biological Uncertainty Stack</strong><br/>174 Created and developed by Collin D. Weber · HIR/OAM genomic uncertainty architecture.<br/>175 Source search target: <code>Primordial_DNA_GRCh38_First_Pass_Architecture_Plan_v0.1.html</code>176</footer>177</body>178</html>179