The limits are published alongside the reasoning.
- Evidence tiers
Every article carries an explicit evidence tier, so established biology is never presented as if it were clinical proof.
Read the claim ledger - What this does not prove
Mechanistic pieces are required to state their own limits and the competing explanations that would fit the same data.
See the counterarguments - Published corrections
Where the reasoning has been revised, the revision is recorded rather than quietly edited away.
Review the standards
Pick the sentence that sounds like your situation.
- Why does my SIBO keep coming back?
- Are SIBO breath tests actually reliable?
- Why don't antihistamines settle my symptoms?
- Can I have mast cell activation with normal tryptase?
- Why won't my Long COVID symptoms resolve?
- Why did COVID trigger this in me and not others?
- Why are my labs normal when I feel terrible?
- Why doesn't my stool test match my symptoms?
- Why does every protocol stop working after two weeks?
- Why did butyrate or probiotics make me worse?
- What do bile acids have to do with my gut symptoms?
- Can gut health affect my hormones and egg quality?
Educational mechanistic writing. It does not diagnose, and it does not replace the clinician treating you.
Seven mechanistic threads run through this library.
Recurrent SIBO & breath-test interpretation
14 articles · recurrent SIBO
Mast-cell activation, tryptase & histamine
19 articles · mast cell activation
Long COVID, post-viral gut–immune & POTS
13 articles · Long COVID gut symptoms
Colonocyte bioenergetics, butyrate & oxygen
19 articles · colonocyte bioenergetics
Bile acids, TUDCA & C. difficile ecology
5 articles · bile acid dysfunction
Gut–hormone axis, fertility & estrobolome
3 articles · gut microbiome and fertility
Lab-pattern interpretation
6 articles · lab pattern interpretation
30 articles · showing 12
- MCAS & Mast Cells· August 27, 2026· 18 min· Mechanistic inference
The Antihistamine–Stomach Acid Connection: Why Low Acid Is Often a Signaling Problem, Not Just a Digestion Problem
Long-term acid suppression and H2 antihistamines act on the same histamine signal that parietal cells use to secrete acid. A mechanistic look at why persistent reflux, early fullness, poor protein tolerance, iron and B12 abnormalities and recurrent dysbiosis can follow — and why low stomach acid is often a signalling problem rather than a digestion problem.
#histamine#h2-receptor#stomach-acid - Case Reasoning· August 26, 2026· 18 min· Clinical pattern observation
Long COVID, MCAS, Mold, Heavy Metals, SIBO and Mitochondrial Collapse: A Case That Shows What Happens When We Treat the Target but Forget the Host
A complex case combining Long COVID, ME/CFS physiology, hyperadrenergic POTS, MCAS-type hyperreactivity, recurrent SIBO and methanogen overgrowth, mycotoxin findings, elevated toxic metals and profound mitochondrial respiratory-chain impairment — read as a single host-capacity failure rather than a list of separate targets.
#long-covid#me-cfs#hyperadrenergic-pots - MCAS & Mast Cells· August 11, 2026· 13 min· Mechanistic inference
Why a Normal Tryptase Can Miss Mast Cell Activation: A More Precise Testing Framework
A normal baseline tryptase answers a narrower question than most people assume. A more precise framework for what mast-cell mediator testing can and cannot rule out, including timing, handling and mediator selection.
#tryptase#mcas#mast-cell-activation - MCAS & Mast Cells· August 6, 2026· 4 min· Mechanistic inference
Your Mast Cells May Be Reacting to a Gut That Never Stopped Signaling Danger
Mast cells rarely become reactive without an input. A short reading of the gut-derived signalling that keeps them primed, and why that reframes mast-cell symptoms as downstream rather than primary.
#mast-cells#mcas#dysbiosis - Case Reasoning· August 3, 2026· 12 min· Clinical pattern observation
The Microbial Metabolites That May Be Rewiring the Brain: The Hidden Link Between SIBO, IBS, MCAS, Autism, ADHD, Glutamate, and Catecholamine Dysfunction
HPHPA, hydrogen sulfide, D-lactate and ammonia are microbial metabolites that may pressure catecholamine regulation through dopamine β-hydroxylase, COMT and mitochondrial ATP. A case-anchored look at the hidden link between SIBO, IBS, MCAS, POTS, ADHD-like symptoms and autism-spectrum features — a metabolite-driven mechanism rather than a purely compositional dysbiosis.
#hphpa#clostridia#dopamine-beta-hydroxylase - Frameworks· July 30, 2026· 11 min· HCM interpretation
SIBO, MCAS, POTS and Food Intolerance May Be One Self-Sustaining System
For years, SIBO, MCAS, POTS, dysautonomia, food intolerance, chronic fatigue, neurological symptoms, and mitochondrial dysfunction have been treated as separate diagnoses.
#sibo#mcas#pots - MCAS & Mast Cells· July 17, 2026· 28 min· Mechanistic inference
Rethinking Chronic Dysbiosis, Mast Cell Activation, and the Failure of Intestinal Ecological Control
Why the microbiome may remain unstable until the intestinal epithelium regains the capacity to metabolize microbial products, consume oxygen, regulate inflammation, and rebuild itself
#dysbiosis#mast-cells#mcas - Host Capacity Model· June 11, 2026· 28 min· Mechanistic inference
Why Dysbiosis, SIBO, Hydrogen Sulfide Intolerance, MCAS, and Long COVID May All Be Downstream of a Single Event
Dysbiosis, SIBO, hydrogen sulfide intolerance, MCAS, and long COVID may all be downstream of one event: the colonocyte losing control of oxygen, butyrate, and its own mitochondria. The Host Capacity Model in full.
#host-capacity-model#colonocyte#butyrate - MCAS & Mast Cells· June 9, 2026· 13 min· Mechanistic inference
Why Mast Cell Activation May Be the Last Domino, Not the First — A Systems-Biology Reframe of MCAS
For decades, the mast cell has carried a reputation it may not fully deserve. We learned it as the cell of allergy: the histamine grenade, the hive, the wheeze, the anaphylactic emergency. In that framing, Mast Cell Activation Syndrome (MCAS) becomes a straightforward story —…
#mcas#mast-cells#systems-biology - Frameworks· June 1, 2026· 22 min· HCM interpretation
What May Be Driving Fibromyalgia? The Mitochondrial, Mast Cell, and Small Fiber Neuropathy Mechanisms Standard Treatment Misses
Fibromyalgia has four upstream drivers: mitochondrial dysfunction, mast cell activation, small fiber neuropathy, and gut-brain axis dysfunction. Lyrica and Cymbalta act on central amplification, not on the peripheral lesions producing the input — which is why response is so often partial.
#fibromyalgia#chronic-pain#mitochondrial-dysfunction - Frameworks· May 31, 2026· 22 min· HCM interpretation
What May Be Driving Chronic Migraine? A Mechanistic Reading of Treatment-Resistant Migraine
Chronic migraine has four upstream drivers: mitochondrial bioenergetic failure, dural mast cell activation, gut-brain axis dysfunction, and hormonal-vasomotor instability. Most treatment-resistant cases (including CGRP antibody non-responders) need the dominant driver addressed at its upstream point.
#chronic-migraine#migraine#cgrp - Fertility· May 30, 2026· 21 min· Mechanistic inference
Why Does Endometriosis Come Back After Surgery? The Gut, Estrobolome, and Bioenergetic Mechanism
Endometriosis recurs because excision removes lesions but not the substrate that selected for them. A mechanistic reading of the gut estrobolome, beta-glucuronidase-driven estrogen recirculation, LPS-driven inflammation, pelvic mast cell infiltration, mitochondrial dysfunction, and iron-driven oxidative damage — and why surgery and hormonal suppression contain the disease but rarely resolve it.
#endometriosis#endometriosis-recurrence#estrobolome
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