{"id":"methodology","title":"Methodology — How We Know, and How We Catch Ourselves","subtitle":"Matched-n, contamination gating, ecological-fallacy stratification — the reusable discipline.","category":"methods","tags":["methodology","matched-n","self-correction"],"source":"articles/docs/methodology.md","lang":"en","words":314,"readMinutes":1,"toc":[{"depth":2,"text":"1. Matched-n comparison","id":"1-matched-n-comparison"},{"depth":2,"text":"2. Contamination gating","id":"2-contamination-gating"},{"depth":2,"text":"3. Ecological-fallacy / stratified evaluation","id":"3-ecological-fallacy-stratified-evaluation"},{"depth":2,"text":"The stance","id":"the-stance"},{"depth":2,"text":"Lineage","id":"lineage"}],"html":"<h1 id=\"methodology-how-we-know-and-how-we-catch-ourselves\">Methodology — How We Know, and How We Catch Ourselves</h1><p>The reusable core of Lupine is not a result, it is a discipline. Three techniques do\nmost of the work, and the same techniques are what kill our own bad claims.</p>\n<h2 id=\"1-matched-n-comparison\">1. Matched-n comparison</h2><p>Elements (and potential families) differ in how many potentials exist for them.\nSample size <em>alone</em> tightens correlations. So any cross-group correlation is\n<strong>confounded by n</strong> until proven otherwise.</p>\n<p>The control: down-sample every group to a common n (bootstrap), then compare. A claim\nonly survives if the effect persists at matched n.</p>\n<ul>\n<li>Killed <a href=\"#/read/hyp-dband-correlation\">d-band</a>: full-sample ρ = −0.02; the\napparent signal was n, not d-band.</li>\n<li>Killed <a href=\"#/read/hyp-meam-intrinsic-2d\">MEAM-2D</a>: at matched n = 7, MEAM PR = 1.36\noverlaps Tersoff PR = 1.01.</li>\n</ul>\n<h2 id=\"2-contamination-gating\">2. Contamination gating</h2><p>A small fraction of corrupt records can manufacture a dramatic effect. Before\nbelieving any strong result in a noisy corpus, audit the records <em>driving</em> it.</p>\n<ul>\n<li>Killed the <a href=\"#/read/hyp-bccfcc-causal-shield\">BCC/FCC &quot;causal shield&quot;</a>: the\nr 0.90 vs 0.04 split was 19 corrupt records (~1.5 %). Post-purge: a modest residual,\nno Cauchy relation.</li>\n<li>Now enforced structurally: ingest gate + idempotent purge (see\n<a href=\"#/read/data-provenance\">Data &amp; Provenance</a>).</li>\n</ul>\n<h2 id=\"3-ecological-fallacy-stratified-evaluation\">3. Ecological-fallacy / stratified evaluation</h2><p>Correlations pooled across heterogeneous groups can invert when a confounder\n(element identity) is ignored — Simpson&#39;s paradox / Robinson&#39;s ecological fallacy.\nCorrect analysis requires stratified evaluation and random-effects meta-analysis\n(DerSimonian–Laird), not naive pooling. The formal spec went further and proved that\nthe <em>specific</em> Simpson&#39;s-paradox claim the original paper made\n<a href=\"#/read/formal-proof-ledger\">cannot arise</a> under the real causal graph.</p>\n<h2 id=\"the-stance\">The stance</h2><p>Strong results in a noisy corpus deserve <strong>suspicion before celebration</strong>. Every\nrefuted claim is published with its confounder named (the\n<a href=\"#/read/conjecture-ledger\">conjecture ledger</a> is the register). A method that catches its\nown mistakes is the asset; the surviving claims inherit its credibility.</p>\n<h2 id=\"lineage\">Lineage</h2><p>Sloppy models: Brown &amp; Sethna (2003), Transtrum &amp; Sethna (2011). Ecological fallacy:\nRobinson (1950), Bickel et al. (1975). Meta-analysis: DerSimonian &amp; Laird (1986).\nCausal inference: Pearl (2014).</p>\n"}