Primordial Brain Layer v0.1 · HIR-Governed Neurophysical Architecture

Section 1

Scope and Boundary Statement

This document specifies a first-pass architecture for a HIR-governed neurophysical brain mapping system. It organizes physical brain data — structure, signal, pathways, physiological state, measurable output effects, neuroplasticity, and measurement provenance — into a typed, uncertainty-aware schema governed by the HIR (Honesty, Integrity, Respect) framework.

This is a bounded architecture planning document. It is not a clinical tool, a diagnostic system, a forensic instrument, or a consciousness model. It does not infer identity, intent, morality, character, personhood, or continuity. It does not produce medical diagnoses. It does not replace clinical evaluation.

In scope	Out of scope
Gross anatomical structure	Consciousness, identity, personhood, soul
Functional zone mapping (with uncertainty)	Moral character, intent, dangerousness, capacity claims
Physical neural pathways	Psychiatric diagnosis without validated clinical context
Physiological state variables	Predictions about individual behavior from group-level data
Measurable output effects (movement, speech, etc.)	Reincarnation, past-life, metaphysical continuity
Neuroplasticity and remapping (as uncertainty)	Legal competence, fitness, culpability assessments
Measurement provenance and artifact detection	Any unsupported person-level claim

HIR Gate	Application to this layer
Honesty (H)	Label what is directly measured vs. inferred. Declare source, modality, anatomical scale, signal type, uncertainty, and evidence limits. Unknown must remain labeled unknown.
Integrity (I)	Do not collapse categories. Structure ≠ function. Activity ≠ intention. Symptom ≠ confirmed cause. Group findings ≠ individual proof. Modeled output ≠ direct evidence.
Respect (R)	Block unsupported person-level claims. Do not infer morality, character, capacity, dangerousness, identity, or diagnosis beyond validated evidence limits.

Section 2

Normalized Source Layer Model

These source layers supply the reference data for brain structure, function, connectivity, and clinical context. All sources must carry provenance metadata. Sources marked REVIEW_REQUIRED require additional verification before ingestion.

Source ID	Source Name	Type	Layer Role	Key Limits	Status
MNI152	MNI152 Standard Brain (Montreal Neurological Institute)	Structural	Coordinate reference frame; structural normalization template	Population-averaged; individual brains vary substantially; adult template	Active
Desikan-Killiany	FreeSurfer Desikan-Killiany Atlas	Structural	Cortical parcellation; 68 cortical regions	Parcellation boundaries are approximate; not cytoarchitectonically exact	Active
AAL3	Automated Anatomical Labeling v3	Structural	Whole-brain atlas including subcortical structures	Coarser resolution than FreeSurfer; MNI-space only	Active
Brodmann	Brodmann Cytoarchitectonic Areas	Structural	Cytoarchitectonic region labels (BA44, BA17, etc.)	Historical; boundaries vary across individuals; not directly MRI-measurable	Use with caution
BigBrain	BigBrain Histological Atlas	Structural	Ultra-high-resolution histological reference (20 μm)	Single donor brain; not population-representative	Active
AllenBrain	Allen Human Brain Atlas	Structural Gene expr.	Gene expression mapping across brain regions	Small donor set; gene expression ≠ function; tissue processing artifacts possible	Active
JHU-DTI	Johns Hopkins University DTI White Matter Atlas	Connectivity	White matter tract labels from diffusion tensor imaging	DTI resolves crossing fibers poorly; tract boundaries approximate	Active
HCP	Human Connectome Project (HCP)	Connectivity Functional	Tractography, resting-state fMRI, structural connectivity	Healthy young adult cohort; resting-state ≠ task activation; atlas registration required	Active
NeuroSynth	NeuroSynth Meta-Analytic Functional Database	Functional meta	Coordinate-based meta-analysis of fMRI activation literature	Reverse inference risk; association ≠ specialization; publication bias; term overlap	Use with caution
EEG-Normative	EEG Normative Databases	Electrophysiology	Normative electrophysiological reference ranges	Site-specific; age-dependent; device-dependent; sleep/wake state dependent	REVIEW_REQUIRED
iEEG-Clinical	Intracranial EEG / ECoG Clinical Datasets	Electrophysiology	Direct neural recording during surgery or monitoring	Highly site-specific; electrode placement varies; patient population is clinical; ethics constraints	REVIEW_REQUIRED
VLSM-Lesion	Voxel-Based Lesion-Symptom Mapping Databases	Lesion	Lesion-behavior mapping; causal inference from damage	Lesion location ≠ sole cause of symptom; mass effect; diaschisis; sample size often small	REVIEW_REQUIRED
Peds-Atlas	Pediatric Brain Atlases (various)	Structural	Age-appropriate reference for developing brain	Do not apply adult atlases to pediatric brains; developmental state must be documented	REVIEW_REQUIRED
Clinical-Provenance	Clinical Scan / Report Metadata	Provenance	Scanner model, field strength, protocol, sedation, medication, scan date	Often incomplete; must be tracked per-record; missing metadata downgrades confidence	REVIEW_REQUIRED per record

Section 3

First-Pass Brain Region Registry

Each region entry defines anatomical class, primary physical role, associated measurable output effects, measurement modalities, key uncertainty notes, and overclaim risks. Functional roles are described as primary associations in healthy adult populations — individual variation, age, injury, and plasticity may alter these substantially.

Region ID	Name	Class	Primary Physical Role	Output Effects	Modalities	Uncertainty Notes	Overclaim Risk
BR-01	Frontal Lobe	Cortex	Voluntary movement initiation; executive planning; working memory; speech production (inferior frontal)	Motor control, goal-directed action, speech, behavioral inhibition	MRI, fMRI, EEG, TMS, PET, lesion studies	Large heterogeneous lobe; sub-regional specialization varies; PFC function highly distributed	High — Do not infer "executive function loss" from frontal lesion alone; do not infer "personality" or "moral character" from imaging
BR-02	Parietal Lobe	Cortex	Somatosensory integration; spatial processing; sensorimotor integration; attention direction	Touch localization, proprioception, spatial awareness, tool use, numerical cognition	MRI, fMRI, EEG, TMS, lesion studies	Hemispheric asymmetry in spatial processing; posterior parietal roles highly context-dependent	Medium — Neglect/inattention symptoms vary widely; spatial claims must be bounded
BR-03	Temporal Lobe	Cortex	Auditory processing; language comprehension (superior temporal); object recognition (inferior temporal); memory (medial)	Hearing, speech comprehension, face/object recognition, memory encoding	MRI, fMRI, EEG, iEEG, PET, lesion studies	Medial vs. lateral temporal roles differ substantially; language lateralization varies	Medium — Language association must specify left/right; comprehension ≠ production
BR-04	Occipital Lobe	Cortex	Primary and higher visual processing; retinotopic organization	Visual detection, motion perception, color processing, object form analysis	MRI, fMRI, EEG (VEP), TMS, lesion studies	Hierarchical processing V1→V2→V4/MT; dorsal ("where") and ventral ("what") streams extend beyond occipital	Lower — V1 damage → contralateral visual field loss is well-established; higher visual claims need more specificity
BR-05	Motor Cortex (M1)	Cortex	Voluntary movement execution; somatotopic body representation (motor homunculus)	Contralateral voluntary movement; fine motor control	MRI, fMRI, TMS, EEG (ERP), iEEG, lesion studies	M1 organization is well-characterized but somatotopy is not rigidly fixed; proximal limb representation overlaps	Lower — Contralateral weakness from M1/corticospinal damage is well-established; use caution with bilateral or incomplete lesions
BR-06	Somatosensory Cortex (S1)	Cortex	Primary somatosensory processing; touch, pressure, pain, proprioception; somatotopic map	Contralateral sensation; localization of touch and pain	MRI, fMRI, TMS, EEG (SSEP), lesion studies	Pain processing is distributed (thalamus, insula, ACC); S1 damage does not eliminate all pain	Medium — Pain has major central and peripheral components; S1 ≠ complete pain map
BR-07	Visual Cortex (V1/Primary)	Cortex	Primary visual cortex; retinotopic representation; orientation and spatial frequency detection	Conscious visual perception; contralateral visual field	MRI, fMRI, EEG (VEP), TMS, lesion studies	Blindsight exists after V1 damage; conscious vision requires more than V1; feedback from higher areas important	Lower — Retinotopic mapping well-established; do not claim V1 activity = conscious experience
BR-08	Primary Auditory Cortex (A1)	Cortex	Primary auditory processing; tonotopic frequency mapping; basic sound feature extraction	Contralateral auditory detection; frequency discrimination	fMRI, EEG (ABR, ASSR), MEG, lesion studies	Bilateral auditory cortex representation means unilateral lesion rarely causes complete deafness	Medium — A1 damage ≠ deafness; higher auditory processing is distributed in superior temporal gyrus
BR-09	Language Regions (Broca's / Wernicke's)	Cortex	Broca's area (IFG, BA44/45): speech production, syntactic processing. Wernicke's (posterior STG, BA22): speech comprehension	Speech production, comprehension, syntactic processing, repetition	fMRI, EEG, MEG, lesion studies, Wada test, iEEG	Language is a distributed network; >95% left-lateralized in right-handers but not universal; individual variation is high; Broca's ≠ production-only	High — Always specify lateralization, task, and method; aphasia taxonomy requires clinical evaluation; "language area" is a significant oversimplification
BR-10	Cerebellum	Hindbrain	Motor coordination, balance, timing, fine-tuning of movement; error correction; some cognitive and affective roles	Gait, balance, fine motor coordination, timing of voluntary movement, postural control	MRI, fMRI, EEG, lesion studies, clinical exam	Cognitive and affective cerebellar roles are recognized but less characterized than motor roles; ipsilateral effects (vs. cortex which is contralateral)	Medium — Ipsilateral motor effects (not contralateral); cognitive claims require additional specificity and source validation
BR-11	Brainstem	Brainstem	Cranial nerve nuclei; consciousness arousal (reticular activating system); autonomic control; breathing; heart rate; swallowing; eye movement	Vital sign regulation, eye movement, facial sensation/movement, swallowing, arousal	MRI, MRA, CT, clinical exam, brainstem evoked potentials	Midbrain, pons, and medulla have distinct roles; small lesions can have outsized effects due to dense structure	High — Brainstem lesion effects depend critically on location, laterality, and extent; do not generalize; arousal claims must reference specific reticular structures
BR-12	Thalamus	Subcortical	Sensory relay to cortex (all modalities except olfaction); sleep/wake gating; consciousness modulation	Sensory gating, attention modulation, consciousness modulation, sleep spindle generation	MRI, fMRI, DTI, lesion studies	Thalamus is a relay hub with many nuclei; nuclei have distinct targets; thalamic damage effects depend on nucleus involved	Medium — Specify which thalamic nucleus; "thalamic damage" without specificity is too broad; consciousness claims are highly restricted
BR-13	Hypothalamus	Subcortical	Autonomic regulation; neuroendocrine control (pituitary); circadian rhythm; thermoregulation; hunger/satiety; thirst	Hormone release, temperature regulation, sleep-wake cycle, feeding, fluid balance	MRI (limited resolution), lesion studies, clinical endocrine evaluation	Extremely small structure (~4g); MRI resolution often insufficient for detailed nucleus-level mapping	Medium — Functional claims require clinical endocrine/autonomic evidence; imaging alone insufficient at standard resolution
BR-14	Hippocampus	Medial Temporal	Episodic memory encoding; spatial navigation; pattern separation/completion; memory consolidation	New memory formation, spatial navigation, context-based recall	MRI (volumetry), fMRI, lesion studies, depth electrodes	Memory is a distributed system; hippocampus is necessary but not sufficient; right vs. left show spatial vs. verbal asymmetry	High — Do not infer "no memory" from hippocampal atrophy alone; memory type and lateralization matter; long-term memory storage is elsewhere
BR-15	Amygdala	Medial Temporal	Emotional salience detection; threat and fear conditioning; emotional memory modulation; social signal processing	Fear conditioning, emotional memory enhancement, threat detection, social cue processing	MRI (volumetry), fMRI, depth electrodes, lesion studies	Amygdala responds to many emotional states, not only fear; activity is context-dependent; not simply a "fear center"	High — Do NOT label as "fear center"; amygdala activity ≠ fear experience; activity cannot be used to infer threat perception or dangerousness
BR-16	Basal Ganglia	Subcortical	Motor control and coordination; action selection; habit and procedural learning; reward-based learning; cortico-striatal loops	Movement initiation, motor sequencing, habit formation, reward salience	MRI, fMRI, PET (dopamine), DTI, lesion studies	Heterogeneous structure (caudate, putamen, globus pallidus, subthalamic nucleus, substantia nigra); each subregion has distinct roles	Medium — Specify which subregion; reward/motivation claims must be carefully bounded; "addiction" claims require substantial additional evidence
BR-17	Corpus Callosum	White Matter	Interhemispheric communication; transfer of sensory, motor, and cognitive information between hemispheres	Bilateral motor coordination, cross-hemispheric sensory comparison, cognitive integration	MRI, DTI, lesion studies (split-brain research)	Regionalized: genu (frontal), body (parietal/motor), splenium (occipital/temporal); partial commissurotomy has graded effects	Medium — Do not over-interpret split-brain findings as "two persons"; specify which callosal region; individual variation in compensation is high

Section 4

Physical Pathway Registry

Pathway ID	Name	Connected Structures	Signal / Output Role	Disruption Effects	Measurement Limits	Uncertainty Class
PW-01	Corticospinal Tract (CST)	M1 → internal capsule → brainstem → spinal cord → motor neurons	Descending voluntary motor command to contralateral limbs	Contralateral weakness/paralysis (hemiplegia/hemiparesis); upper motor neuron signs	DTI traces tract but cannot distinguish fiber subtypes; partial damage effects are graded	A — Individual variability in tract anatomy
PW-02	Dorsal Column–Medial Lemniscal Pathway	Peripheral receptor → spinal cord (ipsilateral dorsal column) → brainstem (decussation) → thalamus → S1	Fine touch, vibration, proprioception (contralateral after decussation in medulla)	Loss of fine touch, proprioception, and vibration sense; positive Romberg	Cannot distinguish pathway segment from imaging alone without clinical correlation	A — Decussation level varies
PW-03	Spinothalamic Tract	Peripheral nociceptor → spinal cord (decussation at entry level) → thalamus → S1 / anterior insula	Pain, temperature, crude touch (contralateral)	Contralateral loss of pain and temperature below lesion level; dissociated sensory loss	Difficult to image directly; functional assessment via clinical exam more reliable	B — Pain is subjective; clinical assessment has significant provenance requirements
PW-04	Visual Pathway (Optic Radiations)	Retina → optic nerve → optic chiasm → LGN → optic radiations → V1	Visual information from contralateral visual field to primary visual cortex	Hemianopia, quadrantanopia depending on lesion site; chiasm lesion → bitemporal hemianopia	DTI of Meyer's loop (temporal portion of optic radiation) has variable reliability; lesion localization well-established clinically	A — Meyer's loop anatomy highly variable across individuals
PW-05	Auditory Pathway	Cochlea → cochlear nuclei → superior olivary complex → inferior colliculus → MGN → A1	Auditory signal processing from both ears; bilateral representation throughout	Unilateral cortical lesion rarely causes complete deafness due to bilateral decussation	Central auditory processing disorders difficult to image; ABR/ASSR for brainstem level; fMRI for cortical	A — Bilateral representation makes lesion localization complex
PW-06	Arcuate Fasciculus / Superior Longitudinal Fasciculus	Broca's area (IFG) ↔ Wernicke's area (posterior STG) via arcuate fasciculus; multiple SLF branches connect frontal–parietal–temporal regions	Language network connectivity; phonological and syntactic processing; repetition	Arcuate fasciculus damage associated with conduction aphasia (impaired repetition); SLF damage with spatial/attention deficits	DTI resolves AF/SLF but cannot distinguish individual fiber functions; lateralization must be confirmed separately	A — High individual variability; left/right lateralization not universal
PW-07	Limbic / Autonomic Pathways (Cingulum, Uncinate)	Cingulate cortex ↔ hippocampus (cingulum); IFG ↔ temporal pole (uncinate fasciculus); hypothalamus ↔ brainstem ↔ spinal cord (autonomic)	Emotional regulation, memory-emotion integration, visceral autonomic control	Cingulum damage associated with memory/emotional dysregulation; uncinate with social-emotional processing; autonomic pathway disruption affects visceral regulation	Emotional effects of tract damage are difficult to isolate; function/emotion attribution must be treated with high caution	B — Emotional/behavioral outcomes are highly measurement-limited and provenance-dependent
PW-08	Dentato-Thalamo-Cortical Pathway (Cerebellar)	Dentate nucleus → superior cerebellar peduncle → thalamus (VL) → motor cortex	Cerebellar output to motor cortex; coordination, timing, and error correction of voluntary movement	Disruption: ipsilateral ataxia, dysmetria, tremor, coordination failure	Peduncle visible on MRI; tract detail requires DTI; cognitive cerebellar pathways less well-characterized	A — Cognitive cerebellar output pathways incompletely mapped
PW-09	Interhemispheric (Corpus Callosum)	All cortical regions ↔ homotopic contralateral cortical regions; genu (prefrontal), body (motor/sensory), splenium (occipital/temporal)	Coordination of bilateral motor activity; cross-hemisphere sensory comparison; cognitive integration	Splenium damage: alexia; genu: frontal disconnection; complete section: split-brain syndrome	Callosal structure well-imaged by MRI/DTI; function of specific callosal fibers remains incompletely mapped	A — Fiber-level function within callosum is not fully resolved

Section 5

Neurophysical Output-Effect Model

These are measurable output effects — physical, behavioral, or physiological — that can be associated with brain structure and signal states. The distinction between what can be measured and what cannot be safely inferred is the Integrity gate for this layer.

Output ID	Output	Primary Structures / Pathways	Observable Effects	What Can Be Measured	What Cannot Be Safely Inferred
OUT-01	Movement	M1, CST, cerebellum, basal ganglia, PW-01, PW-08	Voluntary limb movement, speed, strength, precision	Grip strength, gait analysis, motor evoked potentials (TMS), EMG	Intent, motivation, effort; "can't vs. won't" distinction
OUT-02	Balance	Cerebellum, vestibular nuclei, brainstem, proprioceptive input (PW-02)	Postural stability, gait steadiness, Romberg sign	Posturography, clinical balance tests, VEMPs	Central vs. peripheral vestibular origin without further investigation; subjective dizziness quality
OUT-03	Speech Production	Broca's area, motor cortex (face/larynx), PW-06, basal ganglia, cerebellum	Articulation, fluency, prosody, word-finding	Standardized aphasia batteries, fluency ratings, acoustic analysis	Thought content, language competence from production deficit alone, reading comprehension from speech output
OUT-04	Speech Comprehension	Wernicke's area, superior temporal gyrus, PW-05, PW-06	Ability to follow spoken instructions, word discrimination	Token Test, comprehension subtests of aphasia batteries, behavioral response paradigms	Intelligence, knowledge, or intention from comprehension scores; written vs. spoken dissociation inferred without testing both
OUT-05	Hearing	Cochlea, PW-05, A1	Sound detection, frequency discrimination, speech-in-noise	Audiometry, ABR, ASSR, OAE	Central auditory processing from peripheral hearing thresholds alone; subjective tinnitus origin
OUT-06	Vision	Retina, PW-04, V1, ventral/dorsal visual streams	Visual acuity, visual field, motion detection, color perception	Visual field testing, VEP, acuity charts, OCT	Visual experience, recognition performance from acuity alone; higher visual function from V1 testing only
OUT-07	Pain / Sensation	PW-03, PW-02, S1, insula, ACC, thalamus	Pain report, sensory threshold, sensitivity measures	QST (quantitative sensory testing), clinical sensory exam, evoked potentials	Subjective pain experience from physiology alone; malingering vs. functional disorder from exam alone; "pain level" is a subjective report, not a directly measured signal
OUT-08	Sleep / Wake Regulation	Brainstem (reticular formation), hypothalamus, thalamus	Sleep architecture, arousal, circadian rhythm	Polysomnography (PSG), actigraphy, EEG sleep staging	Dream content, consciousness during sleep stages; cause of insomnia from PSG alone
OUT-09	Memory Encoding / Retrieval	Hippocampus, parahippocampal gyrus, prefrontal cortex, PW-07	New learning, delayed recall, recognition	Standardized memory batteries, word-list learning, delayed recall tasks, fMRI encoding paradigms	Semantic memory from hippocampal measures alone; memory capacity from volume; future memory function from single assessment
OUT-10	Attention	Parietal cortex, frontal cortex, thalamus, noradrenergic pathways	Sustained attention, selective attention, attention shifting	Continuous performance tasks, attention batteries, ERP (P300)	Attention capacity across contexts from lab tasks; ADHD diagnosis from attention tests alone without clinical evaluation
OUT-11	Impulse Control	Prefrontal cortex (OFC, vmPFC, DLPFC), ACC, basal ganglia	Inhibitory control, decision delay, response suppression	Go/No-Go tasks, stop-signal tasks, delay discounting tasks	Moral agency, culpability, dangerousness, or legal responsibility from behavioral inhibition measures; lab findings ≠ real-world behavior
OUT-12	Emotional Regulation	Amygdala, prefrontal cortex, insula, ACC, hippocampus, PW-07	Emotional reactivity, regulation strategy use, affect intensity	Psychophysiological measures (HR, skin conductance), behavioral ratings, fMRI emotion tasks	Emotional experience from physiological response; psychiatric diagnosis from imaging; emotional state from brain activity alone; dangerousness or character
OUT-13	Autonomic Regulation	Hypothalamus, brainstem (NTS, DVAGN), insula, PW-07 (autonomic)	Heart rate variability, blood pressure regulation, sweating, pupillary response	HRV analysis, tilt table test, autonomic reflex screens	Emotional state from autonomic measures alone; lie detection; autonomic cause from a single test without full clinical workup
OUT-14	Breathing / Heart-Rate Control	Medulla (pre-Bötzinger complex, NTS), pons, brainstem	Respiratory rate, rhythm, chemoreception, cardiac rate modulation	Respiratory monitoring, ABG, cardiac telemetry	Central vs. peripheral respiratory failure without full evaluation; brainstem function from respiratory monitoring alone

Section 6

Uncertainty Taxonomy

The fundamental distinction — preserved throughout all schemas and rules — is between unknowns arising from neurophysics itself (Category A) and unknowns arising from the quality or provenance of the data (Category B). No uncertainty class may raise confidence or become hidden positive evidence.

Category A — Neurophysical Unresolvedness

The structure/signal/effect may be real and observed, but the mechanism, meaning, or consequence is not fully understood.

Effect: increases uncertainty weight · does NOT automatically invalidate observation
Rule: may NOT become positive evidence without additional validated support

Category B — Measurement / Provenance Unresolvedness

The data itself may be unreliable, artifact-heavy, incomplete, context-contaminated, or not well-documented.

Effect: increases uncertainty weight · MAY suspend or invalidate interpretation
Rule: may NOT become positive evidence · hard override if severe

Class ID	Class	Cat.	Effect on interpretation	May suspend?	May raise confidence?
UA-01	mechanism_unknown	A	Neural mechanism producing observed signal or effect is not established	No	Never
UA-02	compensatory_rewiring_possible	A	Function may have remapped after injury; current structure-function mapping unreliable	No	Never
UA-03	multi_region_dependency	A	Function depends on distributed network; single-region attribution inappropriate	No	Never
UA-04	individual_variability	A	Group-level anatomy or functional map does not apply to this individual	No	Never
UA-05	developmental_variability	A	Adult mapping does not apply; developmental stage must be specified	Conditional	Never
UA-06	plasticity_state_unknown	A	Reorganization history unknown; current mapping may not reflect original organization	No	Never
UA-07	functional_role_context_dependent	A	Region/pathway role varies by task, state, or context; static label inadequate	No	Never
UA-08	lateralization_variable	A	Assumed lateralization (e.g., left-language) not confirmed for this individual	Conditional	Never
UA-09	subcortical_surface_interaction_unclear	A	Deep nuclei interactions with cortex not fully characterized	No	Never
CATEGORY B — MEASUREMENT / PROVENANCE
UB-01	motion_artifact	B	Head motion during scan produces signal contamination; functional connectivity/activation unreliable	Yes	Never
UB-02	low_resolution	B	Spatial or temporal resolution insufficient for claimed inference; small structures unresolvable	Yes	Never
UB-03	missing_metadata	B	Scanner parameters, protocol, acquisition date, or clinical context not documented	Yes	Never
UB-04	device_limit	B	Scanner field strength, coil, or modality inherently insufficient for target feature	Yes	Never
UB-05	timing_context_unknown	B	Time since symptom onset, injury, or medication change not documented; acute vs. chronic state unknown	Yes	Never
UB-06	medication_state_unknown	B	Psychoactive medication status at time of scan unknown; alters BOLD, connectivity, neurotransmitter signal	Yes	Never
UB-07	sleep_state_unknown	B	Sleep/wake state at scan time not controlled or documented; significantly affects connectivity and EEG	Yes	Never
UB-08	injury_history_unknown	B	Prior head injury, surgical history, or neurological events not documented	Yes	Never
UB-09	clinical_context_missing	B	No referral question, clinical indication, or examination correlate provided	Yes	Never
UB-10	source_unverified	B	Scan origin, chain of custody, or dataset source cannot be confirmed	Yes — hard override	Never
UB-11	signal_contamination	B	EEG/MEG signal contaminated by muscle, cardiac, or eye-movement artifact	Yes	Never
UB-12	preprocessing_undocumented	B	Data processing pipeline, software version, or parameter choices not recorded	Yes	Never
UB-13	atlas_registration_mismatch	B	Individual brain poorly registered to template; region labels unreliable	Yes	Never

Section 7

Typed Schema Draft — Brain Mapping Feature Record

This schema defines a single brain-mapping feature record. All uncertainty fields are typed separately. No field may be implicitly unset — all flags default to declared values. The field inference_allowed defaults to false.

// Brain mapping feature record schema — Primordial Brain Layer v0.1
{
  // --- Identity ---
  "feature_id":                  "string  // globally unique ID for this record",
  "source_id":                   "string  // e.g. MNI152 | HCP | JHU-DTI | Clinical-Provenance",
  "atlas_or_reference_frame":    "string  // e.g. MNI152 | Desikan-Killiany | AAL3 | native_space",
  "created_at":                  "ISO8601 timestamp",
  "record_version":              "string  // schema version",

  // --- Anatomical Location ---
  "anatomical_region":           "string  // e.g. left_hippocampus | right_M1 | corpus_callosum_splenium",
  "region_class":               "enum    // cortex | subcortical | brainstem | cerebellum | white_matter | peripheral",
  "region_id":                  "string  // BR-01 through BR-17 or custom",
  "hemisphere":                 "enum    // left | right | bilateral | unknown",
  "mni_coordinate_xyz":         "float[3] | null  // if registered to MNI space",
  "pathway_id":                 "string | null  // PW-01 through PW-09 or null if not pathway-linked",

  // --- Measurement ---
  "modality":                   "enum    // MRI_structural | fMRI | DTI | EEG | MEG | PET | CT | iEEG | TMS | clinical_exam | lesion_study | postmortem | other",
  "signal_type":               "enum    // BOLD | hemodynamic | T1w | T2w | FA | MD | electrical | magnetic | radiotracer | structural_volume | clinical_observation | unknown",
  "measurement_context":        "string  // task, resting-state, clinical exam context, medication state, sleep state",
  "scanner_field_strength_T":   "float | null  // e.g. 1.5 | 3.0 | 7.0",
  "acquisition_protocol":       "string | null  // or MISSING_METADATA flag",

  // --- Observed and Inferred Effects ---
  "observed_effect":            "string  // what was directly measured or observed",
  "inferred_effect":            "string | null  // what is proposed as an inference — must be bounded",
  "inference_allowed":          "bool   // DEFAULT false. true only if all uncertainty fields are clean and source is validated",
  "inference_basis":           "string | null  // citation, clinical context, or mechanism supporting inference",
  "output_effect_id":          "string | null  // OUT-01 through OUT-14",

  // --- Neurophysical Uncertainty (Category A) ---
  "neurophysical_unknown_class": "enum[]  // UA-01 through UA-09 | none",
  "plasticity_remapping_possible": "bool  // true = UA-02 applies; current mapping may differ from original",
  "lateralization_confirmed":   "bool  // false = UA-08 applies; assume group average, not confirmed individual",

  // --- Measurement / Provenance Uncertainty (Category B) ---
  "measurement_unknown_class":  "enum[]  // UB-01 through UB-13 | none",
  "provenance_class":           "enum    // verified | partially_documented | metadata_incomplete | chain_broken | unverified",
  "artifact_flag":              "bool   // true = artifact detected in data; type must be specified in measurement_unknown_class",
  "medication_state":           "enum    // documented | undocumented | none_reported | unknown",
  "sleep_wake_state":           "enum    // awake | light_sedation | deep_sedation | natural_sleep | unknown",
  "injury_history":             "enum    // documented | partial | unknown",

  // --- Confidence and Status ---
  "confidence_level":           "enum    // high | medium | low | very_low | not_assessable",
  "interpretation_status":      "enum    // valid | caution | suspended | invalidated",
  "hard_override_triggered":    "bool   // true = Category B failure sufficient to invalidate interpretation",
  "person_level_claim_blocked":  "bool   // true = Respect gate blocks further inference about individual",

  // --- Notes and Links ---
  "notes":                      "string[]  // free text; unresolved items marked REVIEW_REQUIRED",
  "linked_source_records":      "string[]  // accessions, report IDs, scan UIDs"
}

Critical schema constraint: inference_allowed defaults to false. It may only be set to true when: neurophysical_unknown_class = none OR known and bounded, AND measurement_unknown_class = none, AND provenance_class = verified, AND artifact_flag = false, AND confidence_level ∈ {high, medium}. Even then, person_level_claim_blocked applies independently — inference_allowed = true does not authorize identity, character, intent, or diagnosis claims.

Section 8

HIR-Safe Rule Set — R-01 through R-12

R-01 — Unknown mechanism cannot increase confidence

If neurophysical_unknown_class includes mechanism_unknown (UA-01), confidence_level may not be set above "low" for any mechanistic claim. Unresolved mechanism preserves possibility space but does not support positive evidence.

R-02 — Artifact-heavy data cannot support interpretation

If artifact_flag = true OR measurement_unknown_class includes motion_artifact (UB-01) or signal_contamination (UB-11), interpretation_status must be set to "suspended" and inference_allowed must remain false. Artifact presence is not a soft downgrade — it is a hard block on interpretation.

R-03 — Missing metadata downgrades confidence

If measurement_unknown_class includes missing_metadata (UB-03), preprocessing_undocumented (UB-12), or acquisition_protocol = null, confidence_level must be set to "low" or "very_low". Missing metadata may not be treated as implicitly clean. Any scan without documented scanner parameters, clinical context, and medication state is provisionally degraded.

R-04 — Measurement / provenance failure may suspend or invalidate interpretation

If provenance_class ∈ {chain_broken, unverified} OR source_unverified (UB-10), hard_override_triggered must be set to true and interpretation_status must be set to "invalidated". Unverified source is not a low-confidence record — it is an invalid record until provenance is established.

R-05 — Structure–function mapping must remain bounded

A record establishing structural features of a brain region may not be used to assert functional capacity. Structure is not function. fMRI activation in a region does not establish the region's necessity for that function. Lesion evidence provides stronger causal inference than activation, but is still subject to multi_region_dependency (UA-03) and plasticity_state_unknown (UA-06).

R-06 — No diagnosis unless clinically validated source and context exist

No diagnostic label (ADHD, depression, epilepsy, TBI, etc.) may appear in an output record unless the source is a validated clinical evaluation with documented clinical context, qualified clinician review, and jurisdiction-appropriate evaluation protocol. Research or research-protocol data may not substitute for clinical diagnosis. Model outputs are not diagnoses.

R-07 — No person-level moral, identity, intent, or character inference

person_level_claim_blocked = true applies whenever any output record would be used to infer: moral character, dangerousness, criminal culpability, legal competence, intent, motivation, consciousness, identity continuity, or capacity claims. These inferences are blocked regardless of confidence_level or inference_allowed status. This rule may not be overridden by any downstream layer.

R-08 — Group-level findings cannot be treated as individual proof

Any finding derived from a population study (fMRI meta-analysis, normative atlas, lesion database, case series) may not be applied to an individual as confirmatory evidence. Population statistics inform prior probability — they do not confirm individual-level structure, function, or outcome. individual_variability (UA-04) applies to all group-level source records.

R-09 — Plasticity / remapping must be treated as uncertainty unless directly measured

If injury_history ≠ none AND plasticity_remapping_possible is not confirmed false by current validated functional mapping, plasticity_state_unknown (UA-06) and compensatory_rewiring_possible (UA-02) must be included in neurophysical_unknown_class. A brain that has experienced injury, stroke, or surgical intervention cannot be assumed to have the same structure-function relationships as a naive brain. This rule applies even when structural imaging appears "normal."

R-10 — All outputs must include evidence limits

Every record produced by this system must include a populated interpretation_status field, a non-empty notes field if any uncertainty class is set, and an explicit statement of what the record does not support. Output records with only positive claims and no uncertainty documentation are schema-invalid.

R-11 — Symptom is not a confirmed cause

A behavioral or physiological observation (symptom) may not be attributed to a specific brain structure, pathway, or mechanism without a validated causal chain. Association (fMRI correlation, lesion overlap) is not causation. Reverse inference from meta-analytic databases (e.g., NeuroSynth) must carry the reverse_inference_risk flag. The reverse inference problem — inferring mental state from brain region activation — is not resolved by high activation magnitude or statistical threshold.

R-12 — Any attempt to convert uncertainty into positive evidence is rejected

No uncertainty class — Category A or Category B — may be used to argue for, support, or raise the probability of a positive claim about structure, function, identity, or person-level inference. Uncertainty is uncertainty. An unknown mechanism is not "consistent with" a specific interpretation in the absence of independent positive evidence. This rule applies to both explicit and implicit probability reasoning within this system.

Section 9

Staged Ingest Plan

1

Gross Anatomy / Region Registry

Sources: MNI152, Desikan-Killiany, AAL3 · Status: ACTIVE (this document)

Establish region IDs BR-01 through BR-17+. Define anatomical class, hemisphere, coordinate system, known limits. Schema must be stable before any functional or pathway layer is added.

2

Functional Zones

Sources: HCP resting-state, NeuroSynth (with caution flag), task fMRI references

Add functional role descriptions with bounded uncertainty tags. All functional claims must carry source, modality, and reverse-inference risk flag where applicable. NeuroSynth-derived claims must carry UA-04 (individual variability) and R-11 (association ≠ causation) flags unconditionally.

3

Connectivity / Pathways

Sources: JHU-DTI atlas, HCP tractography, lesion-based pathway evidence

Add pathway registry PW-01 through PW-09+. DTI-derived tracts must carry device_limit (UB-04) flag for crossing-fiber regions. Lesion-based pathway evidence is stronger for causal inference but carries atlas_registration_mismatch (UB-13) risk.

4

Physiological State Data

Sources: clinical metadata, medication records, sleep staging, autonomic monitoring

Medication state, sleep/wake state, arousal level, cardiac/respiratory status as context fields. Required before any individual record can move from interpretation_status = caution to valid. Missing state data invokes UB-05 through UB-08.

5

Output-Effect Mapping

Sources: clinical neurological exam, standardized assessment batteries, validated behavioral paradigms

Link OUT-01 through OUT-14 to feature records with validated clinical or behavioral measures. No output-effect mapping may be created from imaging alone without a corresponding behavioral or clinical measurement.

6

Neuroplasticity / Remapping

Sources: longitudinal MRI, TMS mapping, task-fMRI pre/post, clinical history

Plasticity evidence requires longitudinal data or direct functional mapping (TMS/iEEG). Cross-sectional imaging alone does not establish remapping. R-09 applies to all records without direct plasticity evidence.

7

Measurement / Provenance Metadata

Sources: DICOM headers, scan reports, clinical records, acquisition protocols

Scanner field strength, protocol, date, technician, motion metrics, preprocessing pipeline documentation. Required for every individual record. Schema validation fails for records with provenance_class = unverified.

8

Clinical Interpretation Layer (Conditional)

Requires: qualified clinical context, validated evaluation protocol, jurisdiction-appropriate standards

Only added when: a specific clinical referral question exists, a qualified clinician is responsible for interpretation, and R-06 through R-07 can be verified as satisfied. This layer does not produce diagnoses — it produces bounded clinical interpretation notes that must be reviewed by a qualified clinician before any person-level claim is made. Not a default layer; requires explicit activation with documented authorization.

Section 10

OSF-Ready Packet Recommendation

Primordial_Brain_Layer_v0.1_Collin_D_Weber/ │ ├── 000_READ_ME_FIRST.md ← scope, boundary, what this is and is not, HIR invariant ├── 001_SCOPE_AND_BOUNDARY.md ← non-clinical / non-diagnostic / non-forensic / non-identity scope declaration ├── 002_SOURCE_LAYER_MODEL.json ← 14 source entries with status, limits, REVIEW_REQUIRED flags ├── 003_BRAIN_REGION_REGISTRY.json ← BR-01 through BR-17, full typed entries per schema ├── 004_PATHWAY_REGISTRY.json ← PW-01 through PW-09, full typed entries per schema ├── 005_OUTPUT_EFFECT_MODEL.json ← OUT-01 through OUT-14, can/cannot-infer boundaries ├── 006_UNCERTAINTY_TAXONOMY.json ← UA-01–09 and UB-01–13 with effect rules and hard-override flags ├── 007_FEATURE_SCHEMA_v0.1.json ← full JSON Schema with required fields, enums, and defaults ├── 008_HIR_RULE_SET_v0.1.json ← R-01 through R-12 as machine-readable rule objects ├── 009_SAMPLE_FEATURE_RECORDS.jsonl ← 15–20 example records: clean case, artifact case, plasticity unknown, overclaim-blocked case ├── 010_STAGED_INGEST_PLAN.md ← Layers 1–8 with prerequisites and source requirements ├── 011_VALIDATION_REPORT_TEMPLATE.md ← template for per-record validation: what was checked, what remains REVIEW_REQUIRED ├── 012_MANIFEST.md ← per-file inventory with classification and provenance └── 013_SHA256_CHECKSUMS.txt ← checksums for all files

009_SAMPLE_FEATURE_RECORDS.jsonl must include: at least one fully clean record (inference_allowed = true), at least one artifact-blocked record (interpretation_status = suspended), at least one plasticity-uncertainty case (UA-02 + UA-06 applied), at least one person-level-claim-blocked case (R-07 triggered), and at least one missing-provenance record (UB-10, hard_override_triggered = true). These test cases document the boundary conditions of the rule set.

Section 11

Plain-Language Explanation

What this does

It organizes what we actually know about the physical brain — its structures, pathways, signals, and measurable effects — into a structured system that keeps careful track of what we're certain about, what's uncertain, and what we simply don't know yet.

It distinguishes between two very different kinds of unknowns: when science hasn't yet figured out how a brain region works, versus when the data we have about a particular brain isn't reliable enough to use. These are not the same problem and must not be treated as the same.

What it does not do

It does not diagnose conditions. It does not tell you what a person is thinking, intending, or capable of. It does not map consciousness, identity, or personality. It does not produce legal opinions about competence or dangerousness. It does not identify who someone is from brain structure alone.

It does not claim that an unusual scan result proves anything about a person's character, morality, or future behavior. It does not treat a population average as an individual fact.

Why it matters for health AI

AI systems applied to brain data risk making overclaims — inferring too much from too little evidence, collapsing uncertainty into false confidence, or using group-level brain science to make individual-level claims about real people.

This architecture builds uncertainty management into the foundation, so that any AI system built on it is constrained from the start to stay within what the evidence actually supports. The GPS can tell you the roads exist. It cannot tell you where the person is going or who they are.

How HIR governs it

Honesty: Every data record must declare what it measured, how reliably, and what it can't conclude. Unknown must remain labeled unknown.

Integrity: Categories must stay separate. Brain structure is not the same as brain function. A correlation is not a cause. A population finding is not an individual fact. These boundaries are enforced in the schema, not just in prose.

Respect: No inference about a person's identity, character, intent, or capacity may be drawn beyond what the validated evidence explicitly supports. The architecture blocks these inferences at the data layer.