Human Model · HM(t) at day 141

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	52 ± 9	-0.24/d	0.46	9 d	Imaging + tumour markers, interpolated · proxy · last read ≤ 14 d
Gastrointestinal function	10 ± 7.7	+0.11/d	0.73	—	Daily GI check-in · direct · today
Treatment toxicity	15 ± 7.6	+0.34/d	0.64	9 d	Labs, interpolated between draws · proxy · last draw ≤ 7 d
Inflammatory activity	20 ± 11.8	+0.16/d	0.45	10 d	CRP/ferritin + immune signature · inferred · weeks
Immune / metabolic	57 ± 11.4	-0.14/d	0.35	5 d	Metabolic panel + wearable · inferred · weeks
Nutritional sufficiency	69 ± 9.3	-0.13/d	0.38	2 d	Weight, albumin, food log · proxy · days
Adherence	91 ± 4.4	-0.05/d	0.54	2 d	Dose + to-do completion · direct · today
Function / quality of life	68 ± 6.6	-0.28/d	0.55	3 d	PRO items · direct · today
Glycaemic control	121 ± 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 S06: ET phenotype; Normal metabolizer; butyrate 23
day 12divergenceTrajectory diverged from the population model
day 12noteTrajectory diverged from prediction
day 17perturbationPoor-sleep week (-3)
day 22recommendedGI-04 recommended
day 23acceptedPatient accepted
day 31responseGI symptom burden −26% vs expected
day 37state changeTolerance state changed
day 42perturbationDaily walks resumed (3.3)
day 68perturbationLow-HRV stretch (-2.7)
day 108perturbationDietary drift (-2.6)

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 v2leading

confidence 47%

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 56
GI-04 (barrier-support protocol) improved GI

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 0.07/day)

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

v1 baseline: genotype + phenotype → v2 day 23: GI-04 response added to E+

T2 v2competing

confidence 45%

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 23/100
DeepGene: 5 keystone butyrate producers absent
DeepGene: H2S above band
Fat load → GI +5.7 next day
Diversity 2.0

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 5.7 over 42 low-fat days)

v1 baseline: microbiome → v2 dietary attribution

T4 v1competing

confidence 6%

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+

Sleep quality worsening

E−

Adherence intact

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 1%

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

E+

GI autocorrelation 0.77 (slow recovery)

E−

Normal metabolizer
Toxicity within range

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 (3 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 10 → 19

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).

Action	pred ΔGI	obs ΔGI	ε	temporality	magnitude	dechallenge	rechallenge	cross-modal	confidence
GI-04 day 23	-23	-18	+5	✓	✓	no	n/a	✓	53%

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 (stable enough). Execution stays with the clinician or the informed patient (EU MDR Class I).

Class	Action	Health	Info	Conf.	Risk	Burden	Cost	Utility
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
Test	Serum DAO / histamine Discriminates T1 from its competitors (E?).	0	0.75	0.2	0.02	0.25	0.5	0.27
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	0.05	0.05	0	0.02

Excluded from the safe set

DT-01 Not indicated for the current state.
HY-01 Not indicated for the current state.
GI-04 Not indicated for the current state.
BR-03 Not indicated for the current state.
SC-12 Not indicated for the current state.
ME-01 Not indicated for the current state.
AD-05 Not indicated for the current state.
NP-02 Not indicated for the current state.
CR-01 Not indicated for the current state.

Evidence weights · w = Authority × Relevance × Persistence

Biological identity Normal metabolizer; FUT2, CYP2D6, GLP1R
Germline panel, baseline
0.86 (0.95·0.9·1)
High-authority clinical Toxicity 15, response 52
Labs / imaging, ≤ 14 d
0.77 (0.9·1·0.85)
Intervention response 1 within-patient responses recorded
ΔS after each action, accumulating
0.68 (0.75·1·0.9)
Deep biological state DeepGene retest day 90: damage 84/100, Shannon 2.27, butyrate 414 CPM, 3 opportunists above, 5 keystone absent
Synthetic DeepGene metagenomics + host DNA, sample 936800-R (compositional proxy)
0.45 (0.7·1·0.645)
Dynamic state GI 10, sleep 6.4 h, HRV 47, glucose 121
Companion + wearable, today
0.18 (0.6·1·0.3)
Exposure context Keep meals regular; three to four moderate portions spaced through the day; dosing per protocol; adherence 91%
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-02041 is on day 141 of META-24 (ET, baseline S06): response stable, tolerance favorable, GI improving. Over 14 days response moved +4 and GI -7; discontinuation risk is 8%. The state is between basins, heading towards restoration, after diverging from the model on day 12.

Biology sets the gain: FUT2 non-secretor, Low butyrate capacity, Low microbial diversity; butyrate capacity 23/100, diversity 2.0. Pushing it down: Escherichia coli 25.768% (LPS load) (-42.1), Low butyrate capacity (-33.1), 5 keystone species absent (-24.8). Pulling it up: GI Support Protocol GI-04 (+56.3), Protein (supports) (+27.3). From the daily log: protein -6.6 GI next day, fat +5.7 GI next day, simple carbs +4.9 GI next day, ultra-processed +3.3 GI next day.

Past actions: GI-04 on day 23 → improved (26%).

No action is indicated now; the trajectory is stable relative to similar patients.