nx_microbiome.nx source

1// nx_microbiome.nx -- loose colony of cells with collective function. 2// 3// Per [[feedback-unified-immune-architecture-three-tier]] table row: 4// "soil microbial community / gut+skin+oral microbiome." THE third- 5// tier ecosystem primitive that bridges digital substrate, land 6// stewardship, and human-health domains under a single biology-honest 7// abstraction. 8// 9// DIFFERENT from nx_organism: organism is a single multi-pathway 10// entity with tight coordination. Microbiome is a LOOSE COLLECTION 11// of independent organisms (or cells) that work together statistically 12// without central coordination -- like the gut microbiome's hundreds 13// of bacterial species, or the soil microbiome's thousands. 14// 15// THE DIVERSITY INSIGHT: a healthy microbiome has many distinct cell 16// kinds; a stressed/diseased one is dominated by one or two opportu- 17// nists. Substrate measures kind-diversity as a health metric -- 18// >=4 distinct cell kinds = HEALTHY; 1-3 = STRESSED; 0 distinct = 19// COLLAPSED (sterile). 20// 21// Composes: 22// nx_cell -- microbiome holds many cell pointers 23// nx_organism -- distinct sibling primitive at a different scale 24// nx_immune -- colony-level immune monitors microbiome health 25// nx_aerobic -- stagnant microbiome = anaerobic decomposition 26// trigger 27// nx_attention_class -- diverse attention classes in microbiome = 28// healthy "ecology" of work 29// 30// V1 ships: 31// - struct NxMicrobiome with cells ring (cell pointers + kind tags) 32// - add_cell / remove_cell / find_cell 33// - kind_diversity (count of distinct attention classes present) 34// - health verdict (sealed: HEALTHY / STRESSED / COLLAPSED) 35// 36// Gap list (V1 honest perf verdict): 37// - kind = attention_class in V1; V2 may add per-cell taxonomic tag 38// - no per-cell weight (Shannon entropy ignored; just count distinct) 39// - no temporal-trend tracking (V2 adds rolling-window health) 40 41import "nx_syscalls.nx" 42import "nx_tier.nx" 43import "nx_attention_class.nx" 44import "nx_cell.nx" 45 46// ===== Sealed enum: NxMicrobiomeHealth ============================ 47 48const NX_MB_HEALTHY: nx_int = 0 // >=4 distinct kinds 49const NX_MB_STRESSED: nx_int = 1 // 1-3 distinct kinds 50const NX_MB_COLLAPSED: nx_int = 2 // 0 cells (sterile) 51const NX_MB_N_HEALTHS: nx_int = 3 52 53// ===== Sealed enum: NxMicrobiomeVerdict =========================== 54 55const NX_MB_OK: nx_int = 0 56const NX_MB_ERR_FULL: nx_int = 1 57const NX_MB_ERR_NOT_FOUND: nx_int = 2 58const NX_MB_ERR_DUPLICATE: nx_int = 3 59 60// ===== Struct: NxMicrobiomeMember ================================= 61 62struct NxMicrobiomeMember { 63 cell_id: nx_int, 64 cell_ptr: *NxCell, 65 kind_tag: nx_int, // == cell.attention_class in V1 66 joined_us: nx_size, 67} 68 69// ===== Struct: NxMicrobiome ======================================= 70 71struct NxMicrobiome { 72 members: *NxMicrobiomeMember, 73 capacity: nx_size, 74 count: nx_size, 75} 76 77const NX_MB_MEMBER_BYTES: nx_size = 32 78 79const NX_MB_HEALTHY_DIVERSITY_THRESHOLD: nx_int = 4 80 81func nx_mb_health_is_valid(h: nx_int) -> nx_int { 82 if h < 0 { return 0 } 83 if h >= NX_MB_N_HEALTHS { return 0 } 84 return 1 85} 86 87func nx_microbiome_new(capacity: nx_size) -> *NxMicrobiome { 88 let m: *NxMicrobiome = (sys_mmap(24)) as *NxMicrobiome 89 let bytes: nx_size = capacity * NX_MB_MEMBER_BYTES 90 m.members = (sys_mmap(bytes)) as *NxMicrobiomeMember 91 m.capacity = capacity 92 m.count = 0 93 return m 94} 95 96func _mb_at(m: *NxMicrobiome, idx: nx_size) -> *NxMicrobiomeMember { 97 return (m.members as i64 + (idx as i64) * NX_MB_MEMBER_BYTES) as *NxMicrobiomeMember 98} 99 100func _mb_find(m: *NxMicrobiome, cell_id: nx_int) -> nx_int { 101 var i: nx_size = 0 102 while i < m.count { 103 let r: *NxMicrobiomeMember = _mb_at(m, i) 104 if r.cell_id == cell_id { return i as i64 } 105 i = i + 1 106 } 107 return -1 108} 109 110func nx_microbiome_add(m: *NxMicrobiome, 111 cell: *NxCell, 112 now_us: nx_size) -> nx_int { 113 if (cell as i64) == 0 { return NX_MB_ERR_NOT_FOUND } 114 if _mb_find(m, cell.cell_id) >= 0 { return NX_MB_ERR_DUPLICATE } 115 if m.count >= m.capacity { return NX_MB_ERR_FULL } 116 let r: *NxMicrobiomeMember = _mb_at(m, m.count) 117 r.cell_id = cell.cell_id 118 r.cell_ptr = cell 119 r.kind_tag = cell.attention_class 120 r.joined_us = now_us 121 m.count = m.count + 1 122 return NX_MB_OK 123} 124 125func nx_microbiome_remove(m: *NxMicrobiome, cell_id: nx_int) -> nx_int { 126 let idx: nx_int = _mb_find(m, cell_id) 127 if idx < 0 { return NX_MB_ERR_NOT_FOUND } 128 // Compact: shift remaining down 129 var i: nx_size = idx as nx_size 130 while i < m.count - 1 { 131 let dst: *NxMicrobiomeMember = _mb_at(m, i) 132 let src: *NxMicrobiomeMember = _mb_at(m, i + 1) 133 dst.cell_id = src.cell_id 134 dst.cell_ptr = src.cell_ptr 135 dst.kind_tag = src.kind_tag 136 dst.joined_us = src.joined_us 137 i = i + 1 138 } 139 m.count = m.count - 1 140 return NX_MB_OK 141} 142 143func nx_microbiome_contains(m: *NxMicrobiome, cell_id: nx_int) -> nx_int { 144 if _mb_find(m, cell_id) >= 0 { return 1 } 145 return 0 146} 147 148// ===== nx_microbiome_kind_diversity =============================== 149// 150// How many DISTINCT kind_tag values appear in the colony? Used by 151// health verdict. 152 153func nx_microbiome_kind_diversity(m: *NxMicrobiome) -> nx_int { 154 if m.count == 0 { return 0 } 155 var distinct: nx_int = 0 156 var i: nx_size = 0 157 while i < m.count { 158 let r_i: *NxMicrobiomeMember = _mb_at(m, i) 159 var seen_before: nx_int = 0 160 var j: nx_size = 0 161 while j < i { 162 let r_j: *NxMicrobiomeMember = _mb_at(m, j) 163 if r_j.kind_tag == r_i.kind_tag { seen_before = 1; break } 164 j = j + 1 165 } 166 if seen_before == 0 { distinct = distinct + 1 } 167 i = i + 1 168 } 169 return distinct 170} 171 172// ===== nx_microbiome_health ======================================= 173 174func nx_microbiome_health(m: *NxMicrobiome) -> nx_int { 175 if m.count == 0 { return NX_MB_COLLAPSED } 176 let div: nx_int = nx_microbiome_kind_diversity(m) 177 if div >= NX_MB_HEALTHY_DIVERSITY_THRESHOLD { return NX_MB_HEALTHY } 178 return NX_MB_STRESSED 179} 180 181func nx_microbiome_count(m: *NxMicrobiome) -> nx_size { 182 return m.count 183} 184 185func nx_microbiome_count_by_kind(m: *NxMicrobiome, kind: nx_int) -> nx_int { 186 var hits: nx_int = 0 187 var i: nx_size = 0 188 while i < m.count { 189 let r: *NxMicrobiomeMember = _mb_at(m, i) 190 if r.kind_tag == kind { hits = hits + 1 } 191 i = i + 1 192 } 193 return hits 194}