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
7 articles
- Case Reasoning· August 18, 2026· 24 min· Clinical pattern observation
Long COVID, Candida, and Klebsiella: When the Gut Loses Its Ecological Control
Post-COVID cases repeatedly show loss of ecological control rather than a single pathogen: Candida and Klebsiella expansion as a readout of failed colonization resistance. What that pattern implies for interpretation rather than eradication.
#long-covid#post-viral#candida - Frameworks· August 14, 2026· 17 min· HCM interpretation
The TUDCA Trap: When a “Protective” Bile Acid Feeds the Gut Problem It Was Supposed to Fix
Why a bile acid widely described as protective can behave differently inside a dysbiotic intestine, depending on microbial transformation and where it is absorbed. A reasoning framework for supplement decisions, not a recommendation.
#tudca#bile-acids#supplements - 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 - Frameworks· June 3, 2026· 3 min· HCM interpretation
The Gut Biomarker Almost No One Tests
One of the most consistent patterns I keep finding in complex gut cases is something that rarely gets discussed: low Secretory IgA (sIgA).
#biomarkers#stool-testing#lab-interpretation - Host Capacity Model· May 21, 2026· 23 min· Mechanistic inference
Why Probiotics Make You Sicker, Not Better: The Six Mechanisms Driving Probiotic Failure in MCAS, SIBO, Histamine Intolerance, and Long COVID, and Why The Field Has Been Asking The Wrong Question
What the research actually shows about why patients with chronic gut dysfunction react badly to the most widely recommended supplement in functional medicine, and where the actual lesion lives.
#probiotics#histamine#d-lactate - Host Capacity Model· May 14, 2026· 14 min· Mechanistic inference
Beyond Weight Loss: How GLP-1 Agonists Influence Gut Bioenergetics and the Host Capacity Model
Emerging research suggests GLP-1 receptor agonists do more than regulate glucose and appetite. They also influence colonocyte mitochondrial function, the gut oxygen gradient, the microbiome, and barrier integrity, with direct relevance to the Host Capacity Model.
#glp-1#semaglutide#colonocyte-bioenergetics - Frameworks· December 19, 2025· 5 min· HCM interpretation
The Alpha-7 Nicotinic Receptor: The Quiet Anti-Inflammatory Switch Inside the Gut Wall
The cholinergic anti-inflammatory pathway is a host-side brake on gut inflammation that bacteria-focused models leave out. What the alpha-7 nicotinic receptor does at the gut wall and why vagal tone matters mechanistically.
#alpha-7-nicotinic-receptor#cholinergic-anti-inflammatory-pathway#vagus
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