Human Model · HM(t) at day 170

State-timeSynthetic demo data⟨ I, S_t, H_0:t, E_t, Θ_t, T, U_t ⟩ — belief, not fact; uncertainty shown, not hiddenSteering view

Localization — where is this individual biologically now?

Belief state b_t per dimension: value ± sd from within-person noise plus the observation model's semantic distance. Trajectory features (velocity, autocorrelation, recovery time) are state variables.

Dimension	b_t	dS/dt	autocorr	recovery	observation model
Therapy response	49 ± 8.3	+0.47/d	0.81	2 d	Imaging + tumour markers, interpolated · proxy · last read ≤ 14 d
Gastrointestinal function	70 ± 6	-0.04/d	0.64	3 d	Daily GI check-in · direct · today
Treatment toxicity	53 ± 8.3	+0.01/d	0.35	1 d	Labs, interpolated between draws · proxy · last draw ≤ 7 d
Inflammatory activity	65 ± 12.1	+0.03/d	0.53	1 d	CRP/ferritin + immune signature · inferred · weeks
Immune / metabolic	40 ± 11.3	+0.26/d	0.45	8 d	Metabolic panel + wearable · inferred · weeks
Nutritional sufficiency	28 ± 7.9	-0.19/d	0.29	1 d	Weight, albumin, food log · proxy · days
Adherence	38 ± 4.1	-0.14/d	0.35	2 d	Dose + to-do completion · direct · today
Function / quality of life	25 ± 5.8	+0.47/d	0.43	1 d	PRO items · direct · today
Glycaemic control	155 ± 8	0/d	0	—	CGM daily mean · direct · today

High autocorrelation and slow recovery are early-warning signatures of a critical transition (Scheffer et al.), independent of the level.

Provenance — how did they arrive here?

The path H_0:t: baseline constraints, divergence, perturbations, actions and responses in order.

day 0baselineBaseline S14: EC-03 phenotype; Rapid metabolizer; butyrate 31
day 25divergenceTrajectory diverged from the population model
day 25noteTrajectory diverged from prediction
day 84perturbationAlcohol on dosing days (-1.8)

Now: between basins, heading towards restoration.

Mechanism — which theories best explain the trajectory?

Versioned competing theories with supporting (E+), contradicting (E−) and missing-but-discriminative (E?) evidence. The contradiction engine lists what should NOT happen under each theory and whether it did.

T1 v1leading

confidence 39%

Mucosal barrier loss: drug-induced epithelial injury amplified by a FUT2-dependent glycan deficit; histamine and inflammatory load add on top.

E+

FUT2 non-secretor genotype (barrier glycan deficit)
DeepGene: Escherichia coli above range (LPS / zonulin)
DeepGene: host DNA fragmentation atypical
DeepGene: tissue recycling 73
Inflammatory load 65

E−

E? · would discriminate

Faecal calprotectin (would separate barrier from motility)
Serum DAO / histamine
Zonulin

Forbidden under this theory

✓ holdsGI should not improve while histamine intake stays high (GI velocity 0.25/day)

✓ holdsLow-residue meals should reduce GI within a week (not tested)

v1 baseline: genotype + phenotype

T2 v2competing

confidence 37%

Bile-acid diarrhoea on a low-butyrate ecology: reduced SCFA production leaves bile acids unconjugated after fat-rich meals; GI burden tracks fat intake with a one-day lag.

E+

Butyrate capacity 31/100
DeepGene: 7 keystone butyrate producers absent
DeepGene: butyrate production 169 CPM
Fat load → GI +4.8 next day
Diversity 2.5

E−

E? · would discriminate

Faecal bile acids
7α-hydroxy-4-cholesten-3-one (C4)
Rechallenge: 3 high-fat days under observation

Forbidden under this theory

✓ holdsGI should not rise on low-fat days (fat effect 4.8 over 35 low-fat days)

v1 baseline: microbiome → v2 dietary attribution

T4 v1competing

confidence 15%

Behavioural spiral: symptomatic days cut adherence and sleep, which raise GI and stress, which cut adherence further; the biology is a follower, not the driver.

E+

Adherence 38%
Stress 6.7/10

E−

E? · would discriminate

Dose-taking timestamps vs symptom timestamps
Sleep-window rechallenge

Forbidden under this theory

✓ holdsGI should not worsen on days with full adherence and good sleep (insufficient paired days)

v1 from tracker trends

T3 v1falsified

confidence 9%

Drug-exposure toxicity: pharmacokinetic over-exposure drives GI and systemic toxicity together; dietary and microbial factors are secondary.

E+

Toxicity 53
GI autocorrelation 0.67 (slow recovery)

E−

Rapid metabolizer

E? · would discriminate

Trough drug level
Dose-timing rechallenge (evening vs morning)

Forbidden under this theory

✗ violatedGI should not move with diet if exposure is the driver (5 dietary detractors with ≥ 80% confidence)

v1 baseline: pharmacogenomics

Forecast — which futures are likely under alternative actions?

30-day rollout of GI burden under the baseline model T and under each safe candidate action (effect ramps over onset). Dashed = prediction, never fact.

No action

GI 70 → 70

Under GI-04

GI 70 → 53

Under ME-01

GI 70 → 67

Under NP-02

GI 70 → 54

Intervention as measurement

Each past action as a measurement of this patient's transition dynamics: predicted ΔGI vs observed, prediction error ε_t, and the within-patient evidence patterns → individualized response confidence (observational, kept separate from randomized evidence).

No action started yet.

Decision — the Restore controller

Safe set computed first, then A* = argmax E[HealthGain + λ₁·InformationGain + λ₂·ConfidenceGain − λ₃·Risk − λ₄·Burden − λ₅·Cost]. λ₁ = 0.6 (theories near-equiprobable), λ₃ = 1.4 (fragile state). Execution stays with the clinician or the informed patient (EU MDR Class I).

Class	Action	Health	Info	Conf.	Risk	Burden	Cost	Utility
Treat	GI-04 GI Support Protocol 67% of 66 similar improved.	0.58	0.2	0.25	0.13	0.35	0.15	0.39
Escalate	CR-01 Clinician Review 100% of 12 similar improved.	0.37	0.2	0.25	0.02	0.25	0.15	0.38
Measure	Faecal calprotectin (would separate barrier from motility) Discriminates T1 from its competitors (E?).	0	0.75	0.2	0.02	0.25	0.2	0.32
Treat	NP-02 Dietary Support Protocol 64% of 36 similar improved.	0.46	0.2	0.25	0.13	0.25	0.15	0.32
Test	Serum DAO / histamine Discriminates T1 from its competitors (E?).	0	0.75	0.2	0.02	0.25	0.5	0.26
Treat	SC-12 Supportive Compound 83% of 23 similar improved.	0.38	0.2	0.25	0.08	0.25	0.4	0.26
Treat	HY-01 Hydration Protocol 100% of 2 similar improved.	0.3	0.2	0.25	0.08	0.25	0.15	0.23
Escalate	ME-01 Monitoring Escalation 100% of 44 similar improved.	0.22	0.2	0.25	0.08	0.1	0.15	0.22
Treat	DT-01 Dosing / Timing Recommendation 0% of 1 similar improved.	0.18	0.2	0.25	0.08	0.25	0.15	0.11
Observe	Continue passive collection, no perturbation A clean transition can be observed only without a new perturbation.	0	0.15	0.05	0	0.05	0	0.08
Maintain	Hold current regimen and content Protects nothing while the state deteriorates.	0.05	0.05	0.05	0.4	0.05	0	-0.49

Excluded from the safe set

BR-03 Behavioural-only action while toxicity ≥ 55: worst-case trajectory crosses the safety boundary; escalation required first.
AD-05 Behavioural-only action while toxicity ≥ 55: worst-case trajectory crosses the safety boundary; escalation required first.

Evidence weights · w = Authority × Relevance × Persistence

Biological identity Rapid metabolizer; FUT2, IL6, CYP2D6
Germline panel, baseline
0.86 (0.95·0.9·1)
High-authority clinical Toxicity 53, response 49
Labs / imaging, ≤ 14 d
0.77 (0.9·1·0.85)
Intervention response 0 within-patient responses recorded
ΔS after each action, accumulating
0.68 (0.75·1·0.9)
Deep biological state DeepGene retest day 90: damage 91/100, Shannon 1.34, butyrate 169 CPM, 4 opportunists above, 7 keystone absent
Synthetic DeepGene metagenomics + host DNA, sample 941580-R (compositional proxy)
0.35 (0.7·1·0.5)
Dynamic state GI 70, sleep 6.4 h, HRV 48, glucose 155
Companion + wearable, today
0.18 (0.6·1·0.3)
Exposure context Prepare a plain, low-fat pasta or rice meal and note how it feels afterwards; dosing per protocol; adherence 38%
Food log + dose log, event-level
0.1 (0.55·0.9·0.2)

LLIFE OS insight · the five questions, in prose

grounded · add an LLM key for prose

P-02537 is on day 170 of META-24 (EC-03, baseline S14): response stable, tolerance deteriorating, GI unstable. Over 14 days response moved +4 and GI -1; discontinuation risk is 96%. The state is between basins, heading towards restoration, after diverging from the model on day 25.

Biology sets the gain: FUT2 non-secretor, IL6 high-expression variant, Low butyrate capacity, Low microbial diversity, Baseline state S14, Cluster EC-03 (high response / high intolerance), Adherence < 60%; butyrate capacity 31/100, diversity 2.5. Pushing it down: Escherichia coli 38.323% (LPS load) (-49.2), Low butyrate capacity (-38.7), 7 keystone species absent (-28.9). Pulling it up: Protein (supports) (+27.7). From the daily log: protein -5.4 GI next day, fat +4.8 GI next day, ultra-processed +4.5 GI next day, simple carbs +4.1 GI next day.

No action has been tried yet.

Next: NP-02 — 57% of 284 similar trajectories improved, 55% probability here. CGM mean 155 mg/dL and stable: dietary support targets the glucose pattern first. This would be contradicted by a further GI rise within the onset window or falling adherence.