# Biomelogic

> Independent systems-biology consulting reframing SIBO, MCAS, long COVID, and chronic dysbiosis as downstream consequences of colonocyte bioenergetic failure. Founded and operated by Mohammed Attallah, a self-taught systems-biology researcher based in Maryland. The site articulates the Host Capacity Model (HCM) — a unified causal framework for complex chronic gut, mast cell, post-viral, and energetic conditions.

Biomelogic is educational systems-biology consulting. It does not diagnose, treat, or replace licensed medical care. The work is delivered as written mechanistic analysis intended for the client's existing care team to review and discuss.

## Core framework

- [The Host Capacity Model — canonical exposition](https://biomelogic.net/host-capacity-model): The full framework. Argues that colonocyte bioenergetic failure — driven by Fe-S cluster insufficiency, NAD⁺ depletion via CD38 induction, SIRT3 disabling, and SLC5A8 silencing — is the candidate upstream mechanism for SIBO, MCAS, long COVID, and dysbiosis. ~7,500 words.
- [Interactive systems map](https://biomelogic.net/host-capacity-model-map): Clickable systems-biology cascade with definitions, mechanism summaries, related articles, and uncertainty per node.
- [Living simulator](https://biomelogic.net/host-capacity-model-simulator): Phase-portrait simulator of the HCM dynamical system; shows the two stable equilibria (healthy and collapsed) under varying inflammatory drive, NAD⁺ support, SLC5A8 expression, and butyrate availability.
- [Mechanism Atlas](https://biomelogic.net/mechanism-atlas): Searchable index of every mechanism, pathway, and entity referenced across the framework.
- [Decision Room](https://biomelogic.net/decision-room): Guided reasoning tool for case complexity and triage.
- [Explore relationships & contradictions](https://biomelogic.net/explore): Interactive explorer for cross-cutting mechanisms, tensions, and unresolved questions across the framework.
- [Start here](https://biomelogic.net/start-here): Onboarding path for first-time visitors to the Host Capacity Model.
- [Systems biology framework](https://biomelogic.net/systems-biology-framework): Foundational principles of the systems-biology approach applied in the practice.

## Articles (long-form mechanistic essays)

- [The Host Capacity Model: an introduction](https://biomelogic.net/articles/host-capacity-model-introduction): 14 min. Why colonocyte bioenergetic failure, not microbial overgrowth, is the upstream lesion.
- [The CD38–NAD⁺–SIRT3 cascade in chronic illness](https://biomelogic.net/articles/cd38-nad-sirt3-cascade): 11 min. How inflammation drives CD38 upregulation, NAD⁺ collapse, and SIRT3 disabling.
- [Stratifying MCAS](https://biomelogic.net/articles/mcas-stratification): 9 min. Four mechanistically distinct mast cell activation patterns (barrier-driven, vagal, chemical, clonal) and the interventions that match each.
- [The 90-day oocyte mitochondrial protocol](https://biomelogic.net/articles/oocyte-mitochondrial-protocol): 12 min. Fertility optimization framed through the folliculogenesis window.
- [H₂S Complex IV poisoning in recurrent SIBO](https://biomelogic.net/articles/h2s-complex-iv): 8 min. Why H₂S-producing dysbiosis creates a self-reinforcing bioenergetic loop.
- [Case reasoning: a long-haul presentation](https://biomelogic.net/articles/case-reasoning-long-haul): 16 min. Mechanistic re-read of a six-year case with overlapping POTS, MCAS, and gut dysfunction.
- [The mycotoxin–mitochondria trap](https://biomelogic.net/articles/mycotoxin-mitochondria-trap-detox-failure): 12 min. Why standard detox protocols fail.
- [GLP-1 agonists and gut bioenergetics](https://biomelogic.net/articles/glp1-agonists-gut-bioenergetics-host-capacity-model): 14 min. How GLP-1RAs intersect with the HCM.
- [Perimenopause and the worsening of chronic illness](https://biomelogic.net/articles/perimenopause-chronic-illness-hormonal-cascade-women-40s): 32 min. The hormonal cascade driving symptom emergence in women's 40s.
- [All articles](https://biomelogic.net/articles)

## Trust, scope, and methodology

- [Framework Audit](https://biomelogic.net/framework-audit): Every major claim, tiered by evidence level, with counterarguments and unresolved questions.
- [Counterargument Library](https://biomelogic.net/counterarguments): The strongest objections to the framework, named and answered.
- [Claim Ledger](https://biomelogic.net/claim-ledger): Source-tracked log of major framework claims.
- [Hard Questions](https://biomelogic.net/hard-questions): The skeptical FAQ.
- [Trust Console](https://biomelogic.net/trust-console): Public corrections log, methodology transparency, and integrity monitoring.
- [Observatory](https://biomelogic.net/observatory): Reality-check dashboard tracking framework exceptions, tensions, and pattern validations.
- [Where this model may not apply](https://biomelogic.net/host-capacity-model#scope): Explicit scope limits of the framework.
- [Disclaimer & Scope of Practice](https://biomelogic.net/disclaimer): Educational only. Not diagnosis or treatment. Mohammed Attallah is not a licensed clinician.

## Practice and consultation

- [How I work](https://biomelogic.net/how-i-work): The consultation process — Gate 1 triage, full case review, live session, written mechanistic summary.
- [Services](https://biomelogic.net/services): Service catalog and pricing.
- [Work with me](https://biomelogic.net/work-with-me): Consultation details. $650 per engagement (case review + session + written summary).
- [Request consultation (Gate 1)](https://biomelogic.net/request-consultation): Triage form to determine fit.
- [Sample mechanistic report](https://biomelogic.net/sample-mechanistic-report): Fictional sample of the deliverable.
- [For clinicians / practitioners](https://biomelogic.net/for-clinicians): How the analysis fits alongside conventional, functional, and integrative care.
- [Maryland & DMV consulting](https://biomelogic.net/maryland-dmv): Regional information.

## Free educational tools

- [Tools overview](https://biomelogic.net/tools): Six AI-grounded educational tools.
- [Host Capacity Score](https://biomelogic.net/host-capacity-score): 18-question self-assessment across six axes.
- [Lab Result Interpreter](https://biomelogic.net/lab-interpreter): Mechanistic reading of CBC, CMP, GI-MAP, OAT, stool reports.
- [Symptom Timeline Builder](https://biomelogic.net/symptom-timeline): Chronological mapping of infections, antibiotics, exposures, symptoms.
- [Framework Stress-Test Tool](https://biomelogic.net/protocol-simulator): Pre-mortem analysis of a proposed protocol.
- [Mechanistic Possibility Explorer](https://biomelogic.net/differential-explorer): Four to six mechanistically distinct possibilities for a presentation.
- [Drug & Microbiome Checker](https://biomelogic.net/drug-microbiome): Per-item microbiome and mucosal impact analysis.
- [Mechanistic Snapshot](https://biomelogic.net/mechanistic-snapshot): One-page diagnostic snapshot synthesizing case inputs against the framework.

## About the author

- [Mohammed Attallah](https://biomelogic.net/about): Self-taught systems-biology researcher. Based in Bowie, Maryland. Egyptian-American heritage. Developer of the Host Capacity Model. Active collaboration with Dr. Christine Houghton (Cell-Logic, Australia) toward formal manuscript publication.
- [Substack — @mohammedattallah](https://substack.com/@mohammedattallah)
- [Medium — @mattallah922](https://medium.com/@mattallah922)
- [Contact](https://biomelogic.net/contact): research@biomelogic.net

## Optional

- [Use & citation](https://biomelogic.net/use-and-citation): How to cite the framework.
- [Visual assets](https://biomelogic.net/visual-assets): Diagrams available for educational reuse.
- [External presence](https://biomelogic.net/external-presence): Where the framework appears off-site.
- [Privacy and health data handling](https://biomelogic.net/privacy-health-data)