Independent mechanistic case synthesis for clinician review
BiomeLogic organizes complex histories, timelines, available laboratory findings, candidate biological mechanisms, competing explanations, and unresolved evidence into a written educational synthesis. The document is designed to support—not direct—discussion between a client and their licensed healthcare professionals.
- Independent educational analysis
- No diagnosis or prescribing
- Explicit evidence grading
- Alternative explanations included
- Fictional sample available
BiomeLogic produces independent educational analysis. It does not diagnose, prescribe, direct treatment, or replace evaluation by licensed healthcare professionals.
Methodology v2.1 · Report template v2.0 · Last reviewed 2026-08-04 · This methodology has not undergone formal external peer review.
What this service is, and what it is not
One statement of scope, given once and not repeated further down the page.
What is provided
- Structured timeline and presenting pattern
- Organization of available findings
- Candidate mechanistic pathways
- Evidence supporting and opposing each hypothesis
- Alternative explanations
- Important missing information
- Explicit uncertainty
- Questions for clinician discussion
- References for material scientific claims
What is not provided
- Diagnosis
- Treatment planning
- Prescribing
- Dosing or supplement protocols
- Medical triage
- Interpretation represented as clinical judgment
- Instructions to change existing care
- Claims of causation unsupported by available evidence
- Outcome guarantees
Deliverables
Three distinct outputs. What each one contains, who receives it, and what consent it requires.
Educational consultation
- Walk-through of the reconstructed timeline
- Discussion of candidate mechanisms and competing explanations
- Explicit statement of what the available information cannot establish
- Audience
- The client. Clinicians do not attend by default.
- Length
- Live discussion; no separate document is produced by the call itself.
- References
- References are supplied in the written synthesis, not verbally.
- Consent
- No clinician disclosure occurs at this stage.
- Fee
- Included in the consultation fee listed on the services page.
Written mechanistic synthesis
- Observation record separated from interpretation
- Candidate mechanisms with supporting and contradictory evidence
- Confidence and residual uncertainty stated separately
- Missing information and questions for clinician discussion
- Audience
- The client. It is written to be readable by a clinician and can be shared by the client at their discretion.
- Length
- Typically 10–25 pages depending on the volume of supplied material.
- References
- Yes — references are given for material scientific claims.
- Consent
- The client owns the document. BiomeLogic sends it to a clinician only on the client's documented authorization.
- Fee
- Included in the consultation fee listed on the services page.
Optional clinician brief
- One-paragraph case orientation
- Candidate mechanisms in ranked plausibility order, with the evidence limits stated
- Contradictory observations retained rather than removed
- Questions for the clinician to consider, framed as discussion points
- Audience
- A clinician the client designates, sent only with written authorization.
- Length
- 1–2 pages, condensed from the full synthesis.
- References
- Key references only; the full reference list stays in the main synthesis.
- Consent
- Written client authorization is required before it is prepared or sent.
- Fee
- Pricing is published on the services page.
The full written synthesis is already clinician-readable. The optional brief exists only to compress a long document into something reviewable in a short appointment; it removes length, not rigour.
How a case is analysed
A reproducible sequence. The framework is used to generate hypotheses, not to confirm itself.
- 01
Separate reported history from objective findings
Client-reported history, clinician-documented diagnoses, and objective measurements are recorded under distinct labels and never merged into a single narrative voice.
- 02
Construct a time-ordered case map
Events, exposures, interventions, and reported changes are placed on one timeline so temporal order is visible before any causal language is used.
- 03
Identify affected biological systems without assuming causal direction
Systems implicated by the available evidence are listed as implicated, not as causes. Direction of effect is treated as an open question at this stage.
- 04
Generate multiple candidate mechanistic explanations
At least one explanation outside the Host Capacity Model is required for every material question, including the possibility that the original diagnosis is incomplete.
- 05
Compare each explanation against supporting, contradictory, and missing evidence
Each candidate is assessed on what supports it, what argues against it, and what has never been measured.
- 06
Grade confidence and residual uncertainty
Confidence and uncertainty are graded on separate scales, because a claim can have meaningful supporting evidence and still retain substantial uncertainty.
- 07
Produce questions and evidence gaps for clinician discussion
Output is a set of open questions and identified evidence gaps for the licensed clinician to consider. It does not order, direct, or prioritize medical testing.
The Host Capacity Model is an explicit hypothesis-generating framework. A case is not considered to support the model merely because its symptoms are compatible with it.
Discordant evidence is retained and displayed rather than forced into a unified narrative.
Controls against confirmation bias
Multiple-hypothesis comparison
Every material question carries more than one candidate explanation.
Separation of observation from inference
What was observed and what was inferred from it are labelled distinctly throughout.
Contradiction logging
Observations that conflict with the leading hypothesis are recorded in the document, not omitted.
Alternative-explanation requirement
A hypothesis is not advanced unless the alternatives to it have been written down.
Confidence grading
Confidence and residual uncertainty are graded separately and never collapsed into one score.
Falsification criteria
Each substantive hypothesis states what observation would count against it.
No outcome-based retrospective rewriting
An earlier analysis is not silently revised to match how a case later progressed.
These are internal process controls. They have not been independently audited or validated by an external body.
How claims are graded
Observation, interpretation, confidence, and residual uncertainty are graded on four separate scales, using the same vocabulary as the public framework audit.
Observation type — what was seen
- Client-reported history
- Described by the client. Recorded as reported, not treated as verified fact.
- Clinician-documented diagnosis
- A diagnosis recorded by a licensed clinician in the supplied records.
- Objective measurement
- A laboratory, imaging, or instrument result present in the supplied documents.
- Longitudinal pattern
- A relationship across time between events, exposures, and reported changes.
- External literature
- Published research cited to describe a mechanism, not evidence about this case.
Interpretation type — what kind of claim it is
- Established biology
- Replicated, broadly accepted physiology described consistently across independent peer-reviewed work.
- Literature-supported mechanism
- A mechanism described in published research, typically with strong animal or in vitro support and less human consensus.
- Mechanistic inference
- A step that follows logically from established mechanisms but has not been measured directly in the population described.
- Clinical-pattern observation
- A pattern repeatedly observed in case material or reported in clinical literature, without controlled causal evidence.
- HCM interpretation
- A reading specific to the Host Capacity Model: how BiomeLogic organizes existing findings, not an external consensus position.
- Testable hypothesis
- A proposal stated precisely enough that a study could support or contradict it, but which is not yet supported enough to rely on.
- Speculative or emerging
- Plausibility-level reasoning at the edge of the available evidence, retained because it is useful to state openly.
Confidence — how strongly current evidence supports it
- High confidence
- High confidence: replicated findings from independent groups support the claim, and the main alternative explanations have been addressed.
- Medium confidence
- Medium confidence: multiple relevant findings support the claim, but important limitations, indirect evidence, or insufficient human replication remain.
- Low confidence
- Low confidence: the claim is consistent with available data, but the supporting evidence is sparse, indirect, or open to several readings.
- Insufficient evidence
- Insufficient evidence: the claim has not been tested adequately enough for a confidence judgement to be meaningful.
Residual uncertainty — how much remains unresolved
- Limited uncertainty
- Limited uncertainty: the open questions concern detail and magnitude rather than whether the effect exists.
- Meaningful uncertainty
- Meaningful uncertainty: direction of causation, size of effect, or relevance to humans is still genuinely unsettled.
- Substantial uncertainty
- Substantial uncertainty: competing explanations remain fully viable and the claim could be substantially revised.
- Not yet characterized
- Not yet characterized: the relevant uncertainty has not been formally described, so it should be treated as open.
Causal language, used precisely
“Upstream” is a positional description, not evidence of causal priority. These terms are kept distinct throughout every report.
- Temporally earlier
- Occurred before another finding in the recorded timeline. Order alone does not establish causation.
- Mechanistically proximal
- Close to the described effect in a known biological pathway.
- Causally necessary
- The effect would not occur without it. Rarely demonstrable from case material.
- Causally sufficient
- Enough on its own to produce the effect. Rarely demonstrable from case material.
- Amplifying
- Increases the magnitude of an effect that some other factor initiated.
- Maintaining
- Helps hold a state in place after the initiating factor has resolved.
- Downstream consequence
- Follows from another process rather than driving it.
- Correlated but directionally unresolved
- Associated in the available data, with the direction of effect unknown.
Eight questions asked of every material claim
- 1What is observed?
- 2What is inferred?
- 3What supports the inference?
- 4What contradicts it?
- 5What else could explain it?
- 6What evidence is missing?
- 7What would change the interpretation?
- 8Who has authority to act on it?
A worked example of the reasoning structure
Fictional and generic. It exists to show the shape of the reasoning, not to make a claim about any patient.
Illustrative only — not a case report
Observation
Symptoms recur after multiple antimicrobial courses.
Candidate interpretations
- Persistent or recurrent microbial overgrowth
- Impaired motility
- Structural predisposition
- Medication or dietary effects
- Altered bile-acid physiology
- Host–microbial ecological instability
- Incorrect or incomplete original diagnosis
Host Capacity Model interpretation
Host-state factors may contribute to recurrence in some cases.
What this observation cannot establish
Recurrence after antimicrobial exposure does not establish colonocyte dysfunction, mitochondrial impairment, or host-capacity failure.
Question for clinician discussion
What objective evidence would help distinguish persistent overgrowth from motility, structural, inflammatory, medication-related, or ecological contributors?
Where this is useful, and where it is not
Stated plainly so a clinician can decide in under a minute whether a case fits.
Where this is likely to be useful
- The history is long, multisystem, or temporally complex
- Existing data are fragmented across several reports
- Multiple mechanistic explanations remain plausible
- Prior interventions produced contradictory responses
- The client needs a structured document for discussion
- A clinician wants a concise map of hypotheses and uncertainties but not an external treatment plan
Where this is of limited value
- The primary need is urgent assessment
- A clear diagnosis already explains the presentation
- Structural, infectious, malignant, vascular, neurological, endocrine, or autoimmune disease requires direct clinical management
- The client primarily wants prescriptions or dosing
- Adequate clinical evaluation has not occurred
- Available information cannot support responsible mechanistic inference
- The case is being used to avoid recommended medical evaluation
These are not categorical exclusions from the framework's interest. They describe situations where clinician-led evaluation is the appropriate next step and where an educational synthesis cannot substitute for it.
Referral pathway
Five steps, no endorsement required, and no financial relationship of any kind.
- 01
Free fit screen
The client completes a short screening form. There is no charge and no obligation.
- 02
Structured submission
Appropriate cases are invited to submit a structured history and the records they choose to share.
- 03
Evidence-separated synthesis
BiomeLogic prepares the written synthesis with observation, inference, and uncertainty separated.
- 04
Consultation and written output
The client receives an educational consultation and the written document.
- 05
Optional clinician brief
With explicit client authorization, a clinician-facing brief may be shared with the designated professional.
- Clinicians do not need to endorse the referral.
- Referral does not create a treatment relationship with BiomeLogic.
- BiomeLogic may decline cases that fall outside its scope.
- Medical records should not be sent through ordinary email.
- The referring clinician remains free to agree with, revise, or reject the analysis.
- No referral commissions, reciprocal payments, or financial arrangements of any kind exist between BiomeLogic and referring clinicians.
Consent and clinician collaboration
With documented client authorization, BiomeLogic may send the designated clinician the client-approved written brief or participate in an educational discussion. BiomeLogic does not request that the clinician implement its hypotheses and does not issue clinical instructions.
- Are clinician calls included or separately billed?
- An educational discussion with a designated clinician is arranged case by case. Whether it is included or separately billed is confirmed in writing before it is scheduled.
- Must the client be present?
- The client may attend and is told in advance that the discussion is taking place. BiomeLogic does not hold undisclosed conversations about a client.
- Is written consent required?
- Yes. Documented client authorization is required before any disclosure to a clinician.
- Does the exchange become part of the client record?
- Correspondence relating to an engagement is retained with that engagement's materials and is subject to the same retention and deletion terms.
- Are follow-up questions allowed?
- Yes. Written follow-up questions from a designated clinician are welcome at no additional charge.
- Can a clinician send corrections?
- Yes, and they are encouraged. Corrections to source information are the fastest way to improve an analysis.
- Will a report be revised?
- Yes. When source information is shown to be incorrect, the document is revised and the revision is dated.
Privacy and data handling
What is shared, with whom, under what authority, and for how long.
Client information is used to provide the requested service and is not sold. Necessary technology providers may process information to operate the service, subject to their applicable contractual and security controls. Information is shared with a clinician only when the client authorizes that disclosure or when otherwise legally required.
- Service providers
- Hosting, database, email, and large-language-model providers process information in order to operate the service. They act as processors, not as recipients of a disclosure.
- Client-authorized clinician sharing
- Disclosure to a named clinician happens only on documented client authorization.
- Legal or safety obligations
- Disclosure may be required by court order or applicable law.
- Sale or advertising
- Client information is never sold, rented, or used for advertising or audience targeting.
- Retention
- Consultation materials are retained for the active engagement and then deleted within 30 days of close, or sooner on request.
- Deletion requests
- Email research@biomelogic.net with the subject line 'Delete my data'. Requests are processed within 14 business days and confirmed in writing.
- Backups
- Deleted material may persist briefly in routine infrastructure backups before those backups age out.
- Regulatory status
- BiomeLogic is not a HIPAA-covered entity and does not offer HIPAA-regulated services. No HIPAA-equivalent protection should be assumed.
Please do not send identifiable health information through unsecured email. Records should be supplied by the client through the intake submission, which is transmitted over an encrypted connection. BiomeLogic does not currently operate a separate clinician-to-clinician records portal.
Resources
Each link states its format so nothing is mistaken for a download that is not one.
Fictional sample report
A synthetic case showing exactly how observation, inference, contradiction, and uncertainty are laid out.
View sample onlineClinician one-page overview
A single-page summary formatted for printing or saving as PDF from the browser.
View printable pageFramework evidence audit
Every load-bearing claim in the Host Capacity Model, graded for evidence type, confidence, and residual uncertainty.
View auditClaim ledger
The traceable record of individual claims and the sources behind them.
View ledgerCounterargument library
Published objections to the framework, retained rather than answered away.
View counterargumentsScope and limitations
The formal statement of what this service is and is not.
View scopeHealth-data privacy
Transmission, processing, retention, deletion, and non-HIPAA status in full.
View privacy detailReferral pathway
The free screening form a client completes to begin.
View fit screen
A printable summary of scope, deliverables, privacy handling, and the referral path, suitable for a front desk.
Download the referral packet (PDF)Describing BiomeLogic to a colleague
Pre-written, scope-safe text you can copy into an email or a note.
Short description
BiomeLogic provides independent educational systems-biology case synthesis for complex histories. Its reports separate observations, literature-supported mechanisms, case-specific inferences, alternative explanations, and uncertainty. BiomeLogic does not diagnose, prescribe, direct treatment, or replace licensed clinical care.
Longer description
BiomeLogic provides independent educational systems-biology case synthesis for complex histories. Its reports separate observations, literature-supported mechanisms, case-specific inferences, alternative explanations, and uncertainty. BiomeLogic does not diagnose, prescribe, direct treatment, or replace licensed clinical care. It may be useful when a history is long or multisystem, when findings are fragmented across several reports, and when several mechanistic explanations remain plausible. The deliverable is a written educational synthesis containing candidate mechanisms, supporting and contradictory evidence, missing information, explicit uncertainty, and questions for discussion with the client's licensed clinicians. It is not a treatment plan, prescription, diagnosis, or supplement protocol. Sample report: https://biomelogic.net/sample-mechanistic-report Scope and limitations: https://biomelogic.net/disclaimer For clinicians: https://biomelogic.net/for-clinicians
Questions clinicians ask
+Is BiomeLogic a medical practice?
No. It is independent educational systems-biology consulting. It does not diagnose, prescribe, treat, triage, or establish a clinician–patient relationship.
+Who authors the reports?
Mohammed Attallah, working independently. He is not a licensed clinician and claims no medical license, board certification, or institutional affiliation.
+How are claims graded?
Each material claim carries an observation type, an interpretation type, a confidence level, and a residual-uncertainty level, graded on separate scales using the same vocabulary as the public framework audit.
+Does the report recommend treatment or testing?
No. It identifies evidence gaps and questions about possible evaluation for the licensed clinician to consider. It does not order, direct, or prioritize medical testing, and it does not recommend treatment.
+Can I disagree with or correct the report?
Yes. The analysis is offered as reasoning to be evaluated, not adopted. Where source information is shown to be incorrect, the document is revised and the revision is dated.
+How are records transferred?
Through the client's intake submission over an encrypted connection. Identifiable health information should not be sent by unsecured email, and there is currently no separate clinician-to-clinician records portal.
+Can the report be sent directly to my office?
Yes, but only after the client provides documented written authorization naming you as the recipient.
+Does referral create any financial relationship?
No. There are no referral fees, commissions, reciprocal arrangements, or revenue-sharing agreements of any kind.
+Has the Host Capacity Model been externally validated?
No. It is a hypothesis-generating framework. It has not undergone formal external peer review, and the public framework audit states which of its claims rest on established biology and which do not.
+What should I do if the client has urgent or red-flag symptoms?
Manage them clinically. Urgent assessment is outside this service entirely; clients presenting that way are directed to appropriate medical care rather than accepted for synthesis.