Hugging Face's logo

Spaces:
HirModel
/
primordial-code-ecosystem
Running

App Files Community
1
primordial-code-ecosystem
File size: 89,954 Bytes
27ba41e
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
1001
1002
1003
1004
1005
1006
1007
1008
1009
1010
1011
1012
1013
1014
1015
1016
1017
1018
1019
1020
1021
1022
1023
1024
1025
1026
1027
1028
1029
1030
1031
1032
1033
1034
1035
1036
1037
1038
1039
1040
1041
1042
1043
1044
1045
1046
1047
1048
1049
1050
1051
1052
1053
1054
1055
1056
1057
1058
1059
1060
1061
1062
1063
1064
1065
1066
1067
1068
1069
1070
1071
1072
1073
1074
1075
1076
1077
1078
1079
1080
1081
1082
1083
1084
1085
1086
1087
1088
1089
1090
1091
1092
1093
1094
1095
1096
1097
1098
1099
1100
1101
1102
1103
1104
1105
1106
1107
1108
1109
1110
1111
1112
1113
1114
1115
1116
1117
1118
1119
1120
1121
1122
1123
1124
1125
1126
1127
1128
1129
1130
1131
1132
1133
<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="UTF-8">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Primordial Brain Layer v0.1 Β· HIR-Governed Neurophysical Architecture</title>
<style>
@import url('https://fonts.googleapis.com/css2?family=Instrument+Serif:ital@0;1&family=JetBrains+Mono:wght@300;400;600&family=Syne:wght@400;600;700&display=swap');

*{box-sizing:border-box;margin:0;padding:0}
:root{
  --bg:#f8f6f1;--bg2:#f1ede4;--bg3:#e8e3d8;
  --ink:#181614;--ink2:#36302a;--ink3:#66584a;
  --rule:#d0c8bc;
  --neu:#1a5c6a;--neu-bg:rgba(26,92,106,.07);--neu-border:rgba(26,92,106,.25);
  --path:#4a6a1a;--path-bg:rgba(74,106,26,.07);--path-border:rgba(74,106,26,.25);
  --func:#7a4e0a;--func-bg:rgba(122,78,10,.07);--func-border:rgba(122,78,10,.25);
  --unc-a:#1a3a7a;--unc-a-bg:rgba(26,58,122,.07);--unc-a-border:rgba(26,58,122,.25);
  --unc-b:#7a1a1a;--unc-b-bg:rgba(122,26,26,.07);--unc-b-border:rgba(122,26,26,.25);
  --caution:#7a6a0a;--caution-bg:rgba(122,106,10,.07);--caution-border:rgba(122,106,10,.25);
  --block:#6a1a1a;--block-bg:rgba(106,26,26,.07);--block-border:rgba(106,26,26,.25);
  --allow:#1a5c3a;--allow-bg:rgba(26,92,58,.07);--allow-border:rgba(26,92,58,.25);
  --mono:'JetBrains Mono',monospace;--serif:'Instrument Serif',serif;--sans:'Syne',sans-serif;
}
html{background:var(--bg)}
body{background:var(--bg);color:var(--ink);font-family:var(--sans);font-size:14px;line-height:1.6;
     padding:40px 24px 80px;max-width:1120px;margin:0 auto}

/* HEADER */
.hdr{border-bottom:2px solid var(--ink);padding-bottom:20px;margin-bottom:28px}
.hdr-kicker{font-family:var(--mono);font-size:9px;letter-spacing:3px;color:var(--ink3);text-transform:uppercase;margin-bottom:8px}
.hdr-title{font-family:var(--serif);font-size:36px;line-height:1.1;color:var(--ink)}
.hdr-title em{font-style:italic;color:var(--neu)}
.hdr-sub{font-family:var(--mono);font-size:10px;color:var(--ink3);margin-top:6px;letter-spacing:1px;line-height:1.7}
.hdr-meta{display:flex;gap:10px;flex-wrap:wrap;margin-top:10px}
.hdr-chip{font-family:var(--mono);font-size:8px;padding:3px 10px;border:1px solid var(--rule);border-radius:2px;color:var(--ink3);letter-spacing:1.5px;text-transform:uppercase}

/* INVARIANT */
.invariant{border-left:3px solid var(--unc-b);background:var(--unc-b-bg);padding:10px 14px;margin-bottom:24px;font-family:var(--mono);font-size:9px;color:var(--unc-b);line-height:1.8}
.invariant strong{color:var(--ink);font-size:9.5px}

/* GPS ANALOGY BOX */
.analogy{border:1px solid var(--neu-border);border-radius:3px;background:var(--neu-bg);padding:12px 16px;margin-bottom:24px}
.analogy-title{font-family:var(--mono);font-size:9px;letter-spacing:2px;color:var(--neu);text-transform:uppercase;margin-bottom:7px}
.analogy-grid{display:grid;grid-template-columns:repeat(3,1fr);gap:8px}
.ag-item{font-family:var(--mono);font-size:9.5px;line-height:1.6;color:var(--ink2)}
.ag-item .ag-key{color:var(--neu);font-weight:600;display:block;margin-bottom:2px}

/* SECTIONS */
.section{margin-bottom:40px}
.section-num{font-family:var(--mono);font-size:9px;letter-spacing:2px;color:var(--ink3);text-transform:uppercase;margin-bottom:4px}
.section-title{font-family:var(--serif);font-size:24px;color:var(--ink);border-bottom:1px solid var(--rule);padding-bottom:8px;margin-bottom:14px}
.section-title em{font-style:italic}
.section-body{font-family:var(--sans);font-size:13.5px;color:var(--ink2);line-height:1.7;margin-bottom:12px}
.section-body p{margin-bottom:10px}

/* DIVIDER */
.div-rule{border:none;border-top:1px solid var(--rule);margin:34px 0}

/* TABLES */
table{width:100%;border-collapse:collapse;font-family:var(--mono);font-size:10.5px;margin:10px 0}
thead th{background:var(--bg3);border:1px solid var(--rule);padding:5px 9px;text-align:left;letter-spacing:1px;text-transform:uppercase;font-size:8.5px;color:var(--ink3);font-weight:600}
tbody td{border:1px solid var(--rule);padding:5px 9px;vertical-align:top;line-height:1.5}
tbody tr:hover td{background:var(--bg2)}
.td-key{color:var(--ink);font-weight:600}
.td-sm{font-size:9.5px}

/* CHIPS */
.chip{display:inline-block;font-family:var(--mono);font-size:8px;padding:1px 5px;border-radius:2px;margin:1px;letter-spacing:.5px;white-space:nowrap}
.ch-neu{background:var(--neu-bg);color:var(--neu);border:1px solid var(--neu-border)}
.ch-path{background:var(--path-bg);color:var(--path);border:1px solid var(--path-border)}
.ch-func{background:var(--func-bg);color:var(--func);border:1px solid var(--func-border)}
.ch-a{background:var(--unc-a-bg);color:var(--unc-a);border:1px solid var(--unc-a-border)}
.ch-b{background:var(--unc-b-bg);color:var(--unc-b);border:1px solid var(--unc-b-border)}
.ch-warn{background:var(--caution-bg);color:var(--caution);border:1px solid var(--caution-border)}
.ch-block{background:var(--block-bg);color:var(--block);border:1px solid var(--block-border)}
.ch-ok{background:var(--allow-bg);color:var(--allow);border:1px solid var(--allow-border)}

/* CODE BLOCKS */
pre{background:var(--bg3);border:1px solid var(--rule);border-radius:3px;padding:14px 16px;
    font-family:var(--mono);font-size:10.5px;line-height:1.7;overflow-x:auto;margin:10px 0;color:var(--ink2)}
pre .k{color:var(--unc-a);font-weight:600}
pre .v{color:var(--allow)}
pre .s{color:var(--func)}
pre .c{color:var(--ink3);font-style:italic}
pre .e{color:var(--unc-b)}

/* RULE BLOCKS */
.rule-block{border:1px solid;border-radius:3px;padding:10px 14px;margin:7px 0;font-family:var(--mono);font-size:10.5px;line-height:1.7}
.rb-allow{border-color:var(--allow-border);background:var(--allow-bg);color:var(--allow)}
.rb-caution{border-color:var(--caution-border);background:var(--caution-bg);color:var(--caution)}
.rb-block{border-color:var(--block-border);background:var(--block-bg);color:var(--block)}
.rb-label{font-size:8.5px;letter-spacing:2px;text-transform:uppercase;margin-bottom:4px;opacity:.85}
.rb-content{color:var(--ink2)}

/* UNCERTAINTY CARDS */
.unc-grid{display:grid;grid-template-columns:1fr 1fr;gap:10px;margin:10px 0}
.unc-card{border:1px solid var(--rule);border-radius:3px;padding:10px 12px;background:var(--bg2)}
.unc-card-title{font-family:var(--mono);font-size:9.5px;font-weight:600;letter-spacing:1px;text-transform:uppercase;margin-bottom:5px}
.unc-card-body{font-family:var(--mono);font-size:9.5px;color:var(--ink3);line-height:1.6}
.uc-a{border-left:3px solid var(--unc-a)}
.uc-b{border-left:3px solid var(--unc-b)}

/* FILE TREE */
.tree{background:var(--bg3);border:1px solid var(--rule);border-radius:3px;padding:14px 16px;
      font-family:var(--mono);font-size:10.5px;line-height:1.9;color:var(--ink2)}
.tree .dir{color:var(--ink);font-weight:600}
.tree .ann{color:var(--ink3);font-size:9.5px;font-style:italic}

/* STAGE ROWS */
.stage-row{display:grid;grid-template-columns:70px 1fr;gap:0;border:1px solid var(--rule);margin-bottom:7px;border-radius:3px;overflow:hidden}
.stage-num{background:var(--bg3);display:flex;align-items:center;justify-content:center;font-family:var(--serif);font-size:24px;font-style:italic;color:var(--ink3);border-right:1px solid var(--rule);flex-shrink:0}
.stage-body{padding:9px 13px}
.stage-title{font-family:var(--sans);font-size:13px;font-weight:600;margin-bottom:2px;color:var(--ink)}
.stage-source{font-family:var(--mono);font-size:8.5px;color:var(--ink3);letter-spacing:1px;margin-bottom:4px}
.stage-body p{font-family:var(--mono);font-size:9.5px;color:var(--ink3);line-height:1.5}

/* PLAIN LANGUAGE */
.plain-grid{display:grid;grid-template-columns:1fr 1fr;gap:12px;margin:10px 0}
.plain-card{border:1px solid var(--rule);border-radius:3px;padding:12px 14px;background:var(--bg2)}
.plain-card-title{font-family:var(--sans);font-size:14px;font-weight:600;margin-bottom:7px;color:var(--ink)}
.plain-card-body{font-family:var(--sans);font-size:13px;color:var(--ink2);line-height:1.6}

/* CALLOUT */
.callout{border:1px solid var(--caution-border);border-radius:3px;background:var(--caution-bg);padding:9px 13px;margin:10px 0;font-family:var(--mono);font-size:9.5px;color:var(--ink2);line-height:1.7}
.callout strong{color:var(--caution)}

/* REVIEW TAG */
.rv{font-family:var(--mono);font-size:8px;padding:1px 6px;border-radius:2px;background:var(--caution-bg);color:var(--caution);border:1px solid var(--caution-border);white-space:nowrap}

/* FOOTER */
.footer{border-top:1px solid var(--rule);padding-top:16px;margin-top:40px;font-family:var(--mono);font-size:8.5px;color:var(--ink3);line-height:1.8}

@media(max-width:720px){
  .analogy-grid,.unc-grid,.plain-grid{grid-template-columns:1fr}
  .stage-row{grid-template-columns:50px 1fr}
}
</style>
</head>
<body>

<!-- ══ HEADER ══ -->
<div class="hdr">
  <div class="hdr-kicker">Primordial Architecture Series Β· Neurophysical Layer Β· v0.1</div>
  <div class="hdr-title">Primordial Brain Layer v0.1<br><em>HIR-Governed Neurophysical Mapping</em></div>
  <div class="hdr-sub">
    Brain Structure Β· Signal Β· Pathway Β· Physiological State Β· Measurable Output Effects Β· Neuroplasticity Β· Measurement Provenance<br>
    <strong>NOT clinical Β· NOT diagnostic Β· NOT forensic Β· NOT identity Β· NOT consciousness Β· NOT a medical opinion</strong>
  </div>
  <div class="hdr-meta">
    <span class="hdr-chip">Created and Developed by Collin D. Weber</span>
    <span class="hdr-chip">April 30, 2026</span>
    <span class="hdr-chip">Architecture Plan Β· Not Validated Clinical Tool</span>
    <span class="hdr-chip">HIR-Governed</span>
  </div>
</div>

<!-- INVARIANT -->
<div class="invariant">
  <strong>Core Invariant:</strong> Unknown neural mechanism may preserve possibility space. Noisy, incomplete, artifact-heavy, or provenance-weak brain data may invalidate interpretation.<br>
  Neither may be converted into unsupported claims about a person.<br>
  <strong>Category A (neurophysical unresolvedness) β‰  Category B (measurement/provenance unresolvedness).</strong>
  Brain structure is not brain function. Brain activity is not intention. A symptom is not a confirmed cause.
  Group-level findings are not individual diagnosis.
</div>

<!-- GPS ANALOGY -->
<div class="analogy">
  <div class="analogy-title">Core Framing β€” The GPS Analogy</div>
  <div class="analogy-grid">
    <div class="ag-item"><span class="ag-key">Neighborhoods</span>Brain regions with characteristic functions</div>
    <div class="ag-item"><span class="ag-key">Roads</span>Neural pathways β€” white matter tracts, axon bundles</div>
    <div class="ag-item"><span class="ag-key">Traffic</span>Live signaling: electrical activity, blood flow, neurotransmission</div>
    <div class="ag-item"><span class="ag-key">Construction zones</span>Neuroplasticity and functional remapping</div>
    <div class="ag-item"><span class="ag-key">Road damage</span>Injury, stroke, inflammation, degeneration, seizure, hypoxia</div>
    <div class="ag-item"><span class="ag-key">City records</span>Measurement provenance, scan quality, metadata, device limits, clinical context</div>
  </div>
  <div style="font-family:var(--mono);font-size:9px;color:var(--ink3);margin-top:8px">
    The GPS tells you road structure. It does not tell you why someone is driving, where they are going, or what they intend. Neither does a brain map.
  </div>
</div>

<!-- ════════════════════════════════════════════════════ -->
<!-- SECTION 1: SCOPE -->
<!-- ════════════════════════════════════════════════════ -->
<div class="section">
  <div class="section-num">Section 1</div>
  <div class="section-title">Scope and <em>Boundary Statement</em></div>
  <div class="section-body">
    <p>This document specifies a first-pass architecture for a HIR-governed neurophysical brain mapping system. It organizes physical brain data β€” structure, signal, pathways, physiological state, measurable output effects, neuroplasticity, and measurement provenance β€” into a typed, uncertainty-aware schema governed by the HIR (Honesty, Integrity, Respect) framework.</p>
    <p>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.</p>
  </div>

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

  <table style="margin-top:10px">
    <thead><tr><th>HIR Gate</th><th>Application to this layer</th></tr></thead>
    <tbody>
      <tr><td class="td-key">Honesty (H)</td><td>Label what is directly measured vs. inferred. Declare source, modality, anatomical scale, signal type, uncertainty, and evidence limits. Unknown must remain labeled unknown.</td></tr>
      <tr><td class="td-key">Integrity (I)</td><td>Do not collapse categories. Structure β‰  function. Activity β‰  intention. Symptom β‰  confirmed cause. Group findings β‰  individual proof. Modeled output β‰  direct evidence.</td></tr>
      <tr><td class="td-key">Respect (R)</td><td>Block unsupported person-level claims. Do not infer morality, character, capacity, dangerousness, identity, or diagnosis beyond validated evidence limits.</td></tr>
    </tbody>
  </table>
</div>

<hr class="div-rule">

<!-- ════════════════════════════════════════════════════ -->
<!-- SECTION 2: SOURCE LAYER MODEL -->
<!-- ════════════════════════════════════════════════════ -->
<div class="section">
  <div class="section-num">Section 2</div>
  <div class="section-title">Normalized <em>Source Layer Model</em></div>
  <div class="section-body">
    <p>These source layers supply the reference data for brain structure, function, connectivity, and clinical context. All sources must carry provenance metadata. Sources marked <span class="rv">REVIEW_REQUIRED</span> require additional verification before ingestion.</p>
  </div>

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

<hr class="div-rule">

<!-- ════════════════════════════════════════════════════ -->
<!-- SECTION 3: BRAIN REGION REGISTRY -->
<!-- ════════════════════════════════════════════════════ -->
<div class="section">
  <div class="section-num">Section 3</div>
  <div class="section-title">First-Pass <em>Brain Region Registry</em></div>
  <div class="section-body">
    <p>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 β€” individual variation, age, injury, and plasticity may alter these substantially.</p>
  </div>

  <table>
    <thead>
      <tr>
        <th>Region ID</th><th>Name</th><th>Class</th><th>Primary Physical Role</th><th>Output Effects</th><th>Modalities</th><th>Uncertainty Notes</th><th>Overclaim Risk</th>
      </tr>
    </thead>
    <tbody>
      <tr>
        <td class="td-key">BR-01</td>
        <td class="td-sm"><strong>Frontal Lobe</strong></td>
        <td><span class="chip ch-neu">Cortex</span></td>
        <td class="td-sm">Voluntary movement initiation; executive planning; working memory; speech production (inferior frontal)</td>
        <td class="td-sm">Motor control, goal-directed action, speech, behavioral inhibition</td>
        <td class="td-sm">MRI, fMRI, EEG, TMS, PET, lesion studies</td>
        <td class="td-sm">Large heterogeneous lobe; sub-regional specialization varies; PFC function highly distributed</td>
        <td><span class="chip ch-block">High</span> β€” Do not infer "executive function loss" from frontal lesion alone; do not infer "personality" or "moral character" from imaging</td>
      </tr>
      <tr>
        <td class="td-key">BR-02</td>
        <td class="td-sm"><strong>Parietal Lobe</strong></td>
        <td><span class="chip ch-neu">Cortex</span></td>
        <td class="td-sm">Somatosensory integration; spatial processing; sensorimotor integration; attention direction</td>
        <td class="td-sm">Touch localization, proprioception, spatial awareness, tool use, numerical cognition</td>
        <td class="td-sm">MRI, fMRI, EEG, TMS, lesion studies</td>
        <td class="td-sm">Hemispheric asymmetry in spatial processing; posterior parietal roles highly context-dependent</td>
        <td><span class="chip ch-warn">Medium</span> β€” Neglect/inattention symptoms vary widely; spatial claims must be bounded</td>
      </tr>
      <tr>
        <td class="td-key">BR-03</td>
        <td class="td-sm"><strong>Temporal Lobe</strong></td>
        <td><span class="chip ch-neu">Cortex</span></td>
        <td class="td-sm">Auditory processing; language comprehension (superior temporal); object recognition (inferior temporal); memory (medial)</td>
        <td class="td-sm">Hearing, speech comprehension, face/object recognition, memory encoding</td>
        <td class="td-sm">MRI, fMRI, EEG, iEEG, PET, lesion studies</td>
        <td class="td-sm">Medial vs. lateral temporal roles differ substantially; language lateralization varies</td>
        <td><span class="chip ch-warn">Medium</span> β€” Language association must specify left/right; comprehension β‰  production</td>
      </tr>
      <tr>
        <td class="td-key">BR-04</td>
        <td class="td-sm"><strong>Occipital Lobe</strong></td>
        <td><span class="chip ch-neu">Cortex</span></td>
        <td class="td-sm">Primary and higher visual processing; retinotopic organization</td>
        <td class="td-sm">Visual detection, motion perception, color processing, object form analysis</td>
        <td class="td-sm">MRI, fMRI, EEG (VEP), TMS, lesion studies</td>
        <td class="td-sm">Hierarchical processing V1β†’V2β†’V4/MT; dorsal ("where") and ventral ("what") streams extend beyond occipital</td>
        <td><span class="chip ch-ok">Lower</span> β€” V1 damage β†’ contralateral visual field loss is well-established; higher visual claims need more specificity</td>
      </tr>
      <tr>
        <td class="td-key">BR-05</td>
        <td class="td-sm"><strong>Motor Cortex (M1)</strong></td>
        <td><span class="chip ch-neu">Cortex</span></td>
        <td class="td-sm">Voluntary movement execution; somatotopic body representation (motor homunculus)</td>
        <td class="td-sm">Contralateral voluntary movement; fine motor control</td>
        <td class="td-sm">MRI, fMRI, TMS, EEG (ERP), iEEG, lesion studies</td>
        <td class="td-sm">M1 organization is well-characterized but somatotopy is not rigidly fixed; proximal limb representation overlaps</td>
        <td><span class="chip ch-ok">Lower</span> β€” Contralateral weakness from M1/corticospinal damage is well-established; use caution with bilateral or incomplete lesions</td>
      </tr>
      <tr>
        <td class="td-key">BR-06</td>
        <td class="td-sm"><strong>Somatosensory Cortex (S1)</strong></td>
        <td><span class="chip ch-neu">Cortex</span></td>
        <td class="td-sm">Primary somatosensory processing; touch, pressure, pain, proprioception; somatotopic map</td>
        <td class="td-sm">Contralateral sensation; localization of touch and pain</td>
        <td class="td-sm">MRI, fMRI, TMS, EEG (SSEP), lesion studies</td>
        <td class="td-sm">Pain processing is distributed (thalamus, insula, ACC); S1 damage does not eliminate all pain</td>
        <td><span class="chip ch-warn">Medium</span> β€” Pain has major central and peripheral components; S1 β‰  complete pain map</td>
      </tr>
      <tr>
        <td class="td-key">BR-07</td>
        <td class="td-sm"><strong>Visual Cortex (V1/Primary)</strong></td>
        <td><span class="chip ch-neu">Cortex</span></td>
        <td class="td-sm">Primary visual cortex; retinotopic representation; orientation and spatial frequency detection</td>
        <td class="td-sm">Conscious visual perception; contralateral visual field</td>
        <td class="td-sm">MRI, fMRI, EEG (VEP), TMS, lesion studies</td>
        <td class="td-sm">Blindsight exists after V1 damage; conscious vision requires more than V1; feedback from higher areas important</td>
        <td><span class="chip ch-ok">Lower</span> β€” Retinotopic mapping well-established; do not claim V1 activity = conscious experience</td>
      </tr>
      <tr>
        <td class="td-key">BR-08</td>
        <td class="td-sm"><strong>Primary Auditory Cortex (A1)</strong></td>
        <td><span class="chip ch-neu">Cortex</span></td>
        <td class="td-sm">Primary auditory processing; tonotopic frequency mapping; basic sound feature extraction</td>
        <td class="td-sm">Contralateral auditory detection; frequency discrimination</td>
        <td class="td-sm">fMRI, EEG (ABR, ASSR), MEG, lesion studies</td>
        <td class="td-sm">Bilateral auditory cortex representation means unilateral lesion rarely causes complete deafness</td>
        <td><span class="chip ch-warn">Medium</span> β€” A1 damage β‰  deafness; higher auditory processing is distributed in superior temporal gyrus</td>
      </tr>
      <tr>
        <td class="td-key">BR-09</td>
        <td class="td-sm"><strong>Language Regions (Broca's / Wernicke's)</strong></td>
        <td><span class="chip ch-neu">Cortex</span></td>
        <td class="td-sm">Broca's area (IFG, BA44/45): speech production, syntactic processing. Wernicke's (posterior STG, BA22): speech comprehension</td>
        <td class="td-sm">Speech production, comprehension, syntactic processing, repetition</td>
        <td class="td-sm">fMRI, EEG, MEG, lesion studies, Wada test, iEEG</td>
        <td class="td-sm">Language is a distributed network; >95% left-lateralized in right-handers but not universal; individual variation is high; Broca's β‰  production-only</td>
        <td><span class="chip ch-block">High</span> β€” Always specify lateralization, task, and method; aphasia taxonomy requires clinical evaluation; "language area" is a significant oversimplification</td>
      </tr>
      <tr>
        <td class="td-key">BR-10</td>
        <td class="td-sm"><strong>Cerebellum</strong></td>
        <td><span class="chip ch-neu">Hindbrain</span></td>
        <td class="td-sm">Motor coordination, balance, timing, fine-tuning of movement; error correction; some cognitive and affective roles</td>
        <td class="td-sm">Gait, balance, fine motor coordination, timing of voluntary movement, postural control</td>
        <td class="td-sm">MRI, fMRI, EEG, lesion studies, clinical exam</td>
        <td class="td-sm">Cognitive and affective cerebellar roles are recognized but less characterized than motor roles; ipsilateral effects (vs. cortex which is contralateral)</td>
        <td><span class="chip ch-warn">Medium</span> β€” Ipsilateral motor effects (not contralateral); cognitive claims require additional specificity and source validation</td>
      </tr>
      <tr>
        <td class="td-key">BR-11</td>
        <td class="td-sm"><strong>Brainstem</strong></td>
        <td><span class="chip ch-neu">Brainstem</span></td>
        <td class="td-sm">Cranial nerve nuclei; consciousness arousal (reticular activating system); autonomic control; breathing; heart rate; swallowing; eye movement</td>
        <td class="td-sm">Vital sign regulation, eye movement, facial sensation/movement, swallowing, arousal</td>
        <td class="td-sm">MRI, MRA, CT, clinical exam, brainstem evoked potentials</td>
        <td class="td-sm">Midbrain, pons, and medulla have distinct roles; small lesions can have outsized effects due to dense structure</td>
        <td><span class="chip ch-block">High</span> β€” Brainstem lesion effects depend critically on location, laterality, and extent; do not generalize; arousal claims must reference specific reticular structures</td>
      </tr>
      <tr>
        <td class="td-key">BR-12</td>
        <td class="td-sm"><strong>Thalamus</strong></td>
        <td><span class="chip ch-neu">Subcortical</span></td>
        <td class="td-sm">Sensory relay to cortex (all modalities except olfaction); sleep/wake gating; consciousness modulation</td>
        <td class="td-sm">Sensory gating, attention modulation, consciousness modulation, sleep spindle generation</td>
        <td class="td-sm">MRI, fMRI, DTI, lesion studies</td>
        <td class="td-sm">Thalamus is a relay hub with many nuclei; nuclei have distinct targets; thalamic damage effects depend on nucleus involved</td>
        <td><span class="chip ch-warn">Medium</span> β€” Specify which thalamic nucleus; "thalamic damage" without specificity is too broad; consciousness claims are highly restricted</td>
      </tr>
      <tr>
        <td class="td-key">BR-13</td>
        <td class="td-sm"><strong>Hypothalamus</strong></td>
        <td><span class="chip ch-neu">Subcortical</span></td>
        <td class="td-sm">Autonomic regulation; neuroendocrine control (pituitary); circadian rhythm; thermoregulation; hunger/satiety; thirst</td>
        <td class="td-sm">Hormone release, temperature regulation, sleep-wake cycle, feeding, fluid balance</td>
        <td class="td-sm">MRI (limited resolution), lesion studies, clinical endocrine evaluation</td>
        <td class="td-sm">Extremely small structure (~4g); MRI resolution often insufficient for detailed nucleus-level mapping</td>
        <td><span class="chip ch-warn">Medium</span> β€” Functional claims require clinical endocrine/autonomic evidence; imaging alone insufficient at standard resolution</td>
      </tr>
      <tr>
        <td class="td-key">BR-14</td>
        <td class="td-sm"><strong>Hippocampus</strong></td>
        <td><span class="chip ch-neu">Medial Temporal</span></td>
        <td class="td-sm">Episodic memory encoding; spatial navigation; pattern separation/completion; memory consolidation</td>
        <td class="td-sm">New memory formation, spatial navigation, context-based recall</td>
        <td class="td-sm">MRI (volumetry), fMRI, lesion studies, depth electrodes</td>
        <td class="td-sm">Memory is a distributed system; hippocampus is necessary but not sufficient; right vs. left show spatial vs. verbal asymmetry</td>
        <td><span class="chip ch-block">High</span> β€” Do not infer "no memory" from hippocampal atrophy alone; memory type and lateralization matter; long-term memory storage is elsewhere</td>
      </tr>
      <tr>
        <td class="td-key">BR-15</td>
        <td class="td-sm"><strong>Amygdala</strong></td>
        <td><span class="chip ch-neu">Medial Temporal</span></td>
        <td class="td-sm">Emotional salience detection; threat and fear conditioning; emotional memory modulation; social signal processing</td>
        <td class="td-sm">Fear conditioning, emotional memory enhancement, threat detection, social cue processing</td>
        <td class="td-sm">MRI (volumetry), fMRI, depth electrodes, lesion studies</td>
        <td class="td-sm">Amygdala responds to many emotional states, not only fear; activity is context-dependent; not simply a "fear center"</td>
        <td><span class="chip ch-block">High</span> β€” Do NOT label as "fear center"; amygdala activity β‰  fear experience; activity cannot be used to infer threat perception or dangerousness</td>
      </tr>
      <tr>
        <td class="td-key">BR-16</td>
        <td class="td-sm"><strong>Basal Ganglia</strong></td>
        <td><span class="chip ch-neu">Subcortical</span></td>
        <td class="td-sm">Motor control and coordination; action selection; habit and procedural learning; reward-based learning; cortico-striatal loops</td>
        <td class="td-sm">Movement initiation, motor sequencing, habit formation, reward salience</td>
        <td class="td-sm">MRI, fMRI, PET (dopamine), DTI, lesion studies</td>
        <td class="td-sm">Heterogeneous structure (caudate, putamen, globus pallidus, subthalamic nucleus, substantia nigra); each subregion has distinct roles</td>
        <td><span class="chip ch-warn">Medium</span> β€” Specify which subregion; reward/motivation claims must be carefully bounded; "addiction" claims require substantial additional evidence</td>
      </tr>
      <tr>
        <td class="td-key">BR-17</td>
        <td class="td-sm"><strong>Corpus Callosum</strong></td>
        <td><span class="chip ch-path">White Matter</span></td>
        <td class="td-sm">Interhemispheric communication; transfer of sensory, motor, and cognitive information between hemispheres</td>
        <td class="td-sm">Bilateral motor coordination, cross-hemispheric sensory comparison, cognitive integration</td>
        <td class="td-sm">MRI, DTI, lesion studies (split-brain research)</td>
        <td class="td-sm">Regionalized: genu (frontal), body (parietal/motor), splenium (occipital/temporal); partial commissurotomy has graded effects</td>
        <td><span class="chip ch-warn">Medium</span> β€” Do not over-interpret split-brain findings as "two persons"; specify which callosal region; individual variation in compensation is high</td>
      </tr>
    </tbody>
  </table>
</div>

<hr class="div-rule">

<!-- ════════════════════════════════════════════════════ -->
<!-- SECTION 4: PATHWAY REGISTRY -->
<!-- ════════════════════════════════════════════════════ -->
<div class="section">
  <div class="section-num">Section 4</div>
  <div class="section-title">Physical <em>Pathway Registry</em></div>

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

<hr class="div-rule">

<!-- ════════════════════════════════════════════════════ -->
<!-- SECTION 5: OUTPUT EFFECT MODEL -->
<!-- ════════════════════════════════════════════════════ -->
<div class="section">
  <div class="section-num">Section 5</div>
  <div class="section-title">Neurophysical <em>Output-Effect Model</em></div>
  <div class="section-body">
    <p>These are measurable output effects β€” physical, behavioral, or physiological β€” 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.</p>
  </div>

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

<hr class="div-rule">

<!-- ════════════════════════════════════════════════════ -->
<!-- SECTION 6: UNCERTAINTY TAXONOMY -->
<!-- ════════════════════════════════════════════════════ -->
<div class="section">
  <div class="section-num">Section 6</div>
  <div class="section-title"><em>Uncertainty Taxonomy</em></div>
  <div class="section-body">
    <p>The fundamental distinction β€” preserved throughout all schemas and rules β€” 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.</p>
  </div>

  <div class="unc-grid">
    <div class="unc-card uc-a">
      <div class="unc-card-title" style="color:var(--unc-a)">Category A β€” Neurophysical Unresolvedness</div>
      <div class="unc-card-body">
        The structure/signal/effect may be real and observed, but the mechanism, meaning, or consequence is not fully understood.<br><br>
        Effect: increases uncertainty weight Β· does NOT automatically invalidate observation<br>
        Rule: may NOT become positive evidence without additional validated support
      </div>
    </div>
    <div class="unc-card uc-b">
      <div class="unc-card-title" style="color:var(--unc-b)">Category B β€” Measurement / Provenance Unresolvedness</div>
      <div class="unc-card-body">
        The data itself may be unreliable, artifact-heavy, incomplete, context-contaminated, or not well-documented.<br><br>
        Effect: increases uncertainty weight Β· MAY suspend or invalidate interpretation<br>
        Rule: may NOT become positive evidence Β· hard override if severe
      </div>
    </div>
  </div>

  <table>
    <thead><tr><th>Class ID</th><th>Class</th><th>Cat.</th><th>Effect on interpretation</th><th>May suspend?</th><th>May raise confidence?</th></tr></thead>
    <tbody>
      <tr><td class="td-key">UA-01</td><td class="td-sm">mechanism_unknown</td><td><span class="chip ch-a">A</span></td><td class="td-sm">Neural mechanism producing observed signal or effect is not established</td><td>No</td><td style="color:var(--unc-b);font-weight:600">Never</td></tr>
      <tr><td class="td-key">UA-02</td><td class="td-sm">compensatory_rewiring_possible</td><td><span class="chip ch-a">A</span></td><td class="td-sm">Function may have remapped after injury; current structure-function mapping unreliable</td><td>No</td><td style="color:var(--unc-b);font-weight:600">Never</td></tr>
      <tr><td class="td-key">UA-03</td><td class="td-sm">multi_region_dependency</td><td><span class="chip ch-a">A</span></td><td class="td-sm">Function depends on distributed network; single-region attribution inappropriate</td><td>No</td><td style="color:var(--unc-b);font-weight:600">Never</td></tr>
      <tr><td class="td-key">UA-04</td><td class="td-sm">individual_variability</td><td><span class="chip ch-a">A</span></td><td class="td-sm">Group-level anatomy or functional map does not apply to this individual</td><td>No</td><td style="color:var(--unc-b);font-weight:600">Never</td></tr>
      <tr><td class="td-key">UA-05</td><td class="td-sm">developmental_variability</td><td><span class="chip ch-a">A</span></td><td class="td-sm">Adult mapping does not apply; developmental stage must be specified</td><td>Conditional</td><td style="color:var(--unc-b);font-weight:600">Never</td></tr>
      <tr><td class="td-key">UA-06</td><td class="td-sm">plasticity_state_unknown</td><td><span class="chip ch-a">A</span></td><td class="td-sm">Reorganization history unknown; current mapping may not reflect original organization</td><td>No</td><td style="color:var(--unc-b);font-weight:600">Never</td></tr>
      <tr><td class="td-key">UA-07</td><td class="td-sm">functional_role_context_dependent</td><td><span class="chip ch-a">A</span></td><td class="td-sm">Region/pathway role varies by task, state, or context; static label inadequate</td><td>No</td><td style="color:var(--unc-b);font-weight:600">Never</td></tr>
      <tr><td class="td-key">UA-08</td><td class="td-sm">lateralization_variable</td><td><span class="chip ch-a">A</span></td><td class="td-sm">Assumed lateralization (e.g., left-language) not confirmed for this individual</td><td>Conditional</td><td style="color:var(--unc-b);font-weight:600">Never</td></tr>
      <tr><td class="td-key">UA-09</td><td class="td-sm">subcortical_surface_interaction_unclear</td><td><span class="chip ch-a">A</span></td><td class="td-sm">Deep nuclei interactions with cortex not fully characterized</td><td>No</td><td style="color:var(--unc-b);font-weight:600">Never</td></tr>
      <tr style="background:var(--bg2)"><td colspan="6" style="font-family:var(--mono);font-size:8.5px;color:var(--unc-b);padding:4px 9px;letter-spacing:1px">CATEGORY B β€” MEASUREMENT / PROVENANCE</td></tr>
      <tr><td class="td-key">UB-01</td><td class="td-sm">motion_artifact</td><td><span class="chip ch-b">B</span></td><td class="td-sm">Head motion during scan produces signal contamination; functional connectivity/activation unreliable</td><td>Yes</td><td style="color:var(--unc-b);font-weight:600">Never</td></tr>
      <tr><td class="td-key">UB-02</td><td class="td-sm">low_resolution</td><td><span class="chip ch-b">B</span></td><td class="td-sm">Spatial or temporal resolution insufficient for claimed inference; small structures unresolvable</td><td>Yes</td><td style="color:var(--unc-b);font-weight:600">Never</td></tr>
      <tr><td class="td-key">UB-03</td><td class="td-sm">missing_metadata</td><td><span class="chip ch-b">B</span></td><td class="td-sm">Scanner parameters, protocol, acquisition date, or clinical context not documented</td><td>Yes</td><td style="color:var(--unc-b);font-weight:600">Never</td></tr>
      <tr><td class="td-key">UB-04</td><td class="td-sm">device_limit</td><td><span class="chip ch-b">B</span></td><td class="td-sm">Scanner field strength, coil, or modality inherently insufficient for target feature</td><td>Yes</td><td style="color:var(--unc-b);font-weight:600">Never</td></tr>
      <tr><td class="td-key">UB-05</td><td class="td-sm">timing_context_unknown</td><td><span class="chip ch-b">B</span></td><td class="td-sm">Time since symptom onset, injury, or medication change not documented; acute vs. chronic state unknown</td><td>Yes</td><td style="color:var(--unc-b);font-weight:600">Never</td></tr>
      <tr><td class="td-key">UB-06</td><td class="td-sm">medication_state_unknown</td><td><span class="chip ch-b">B</span></td><td class="td-sm">Psychoactive medication status at time of scan unknown; alters BOLD, connectivity, neurotransmitter signal</td><td>Yes</td><td style="color:var(--unc-b);font-weight:600">Never</td></tr>
      <tr><td class="td-key">UB-07</td><td class="td-sm">sleep_state_unknown</td><td><span class="chip ch-b">B</span></td><td class="td-sm">Sleep/wake state at scan time not controlled or documented; significantly affects connectivity and EEG</td><td>Yes</td><td style="color:var(--unc-b);font-weight:600">Never</td></tr>
      <tr><td class="td-key">UB-08</td><td class="td-sm">injury_history_unknown</td><td><span class="chip ch-b">B</span></td><td class="td-sm">Prior head injury, surgical history, or neurological events not documented</td><td>Yes</td><td style="color:var(--unc-b);font-weight:600">Never</td></tr>
      <tr><td class="td-key">UB-09</td><td class="td-sm">clinical_context_missing</td><td><span class="chip ch-b">B</span></td><td class="td-sm">No referral question, clinical indication, or examination correlate provided</td><td>Yes</td><td style="color:var(--unc-b);font-weight:600">Never</td></tr>
      <tr><td class="td-key">UB-10</td><td class="td-sm">source_unverified</td><td><span class="chip ch-b">B</span></td><td class="td-sm">Scan origin, chain of custody, or dataset source cannot be confirmed</td><td><strong>Yes β€” hard override</strong></td><td style="color:var(--unc-b);font-weight:600">Never</td></tr>
      <tr><td class="td-key">UB-11</td><td class="td-sm">signal_contamination</td><td><span class="chip ch-b">B</span></td><td class="td-sm">EEG/MEG signal contaminated by muscle, cardiac, or eye-movement artifact</td><td>Yes</td><td style="color:var(--unc-b);font-weight:600">Never</td></tr>
      <tr><td class="td-key">UB-12</td><td class="td-sm">preprocessing_undocumented</td><td><span class="chip ch-b">B</span></td><td class="td-sm">Data processing pipeline, software version, or parameter choices not recorded</td><td>Yes</td><td style="color:var(--unc-b);font-weight:600">Never</td></tr>
      <tr><td class="td-key">UB-13</td><td class="td-sm">atlas_registration_mismatch</td><td><span class="chip ch-b">B</span></td><td class="td-sm">Individual brain poorly registered to template; region labels unreliable</td><td>Yes</td><td style="color:var(--unc-b);font-weight:600">Never</td></tr>
    </tbody>
  </table>
</div>

<hr class="div-rule">

<!-- ════════════════════════════════════════════════════ -->
<!-- SECTION 7: TYPED SCHEMA -->
<!-- ════════════════════════════════════════════════════ -->
<div class="section">
  <div class="section-num">Section 7</div>
  <div class="section-title">Typed Schema Draft β€” <em>Brain Mapping Feature Record</em></div>
  <div class="section-body">
    <p>This schema defines a single brain-mapping feature record. All uncertainty fields are typed separately. No field may be implicitly unset β€” all flags default to declared values. The field <code>inference_allowed</code> defaults to false.</p>
  </div>

  <pre><span class="c">// Brain mapping feature record schema β€” Primordial Brain Layer v0.1</span>
{
  <span class="c">// --- Identity ---</span>
  <span class="k">"feature_id"</span>:                  <span class="s">"string  // globally unique ID for this record"</span>,
  <span class="k">"source_id"</span>:                   <span class="s">"string  // e.g. MNI152 | HCP | JHU-DTI | Clinical-Provenance"</span>,
  <span class="k">"atlas_or_reference_frame"</span>:    <span class="s">"string  // e.g. MNI152 | Desikan-Killiany | AAL3 | native_space"</span>,
  <span class="k">"created_at"</span>:                  <span class="s">"ISO8601 timestamp"</span>,
  <span class="k">"record_version"</span>:              <span class="s">"string  // schema version"</span>,

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

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

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

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

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

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

  <span class="c">// --- Notes and Links ---</span>
  <span class="k">"notes"</span>:                      <span class="s">"string[]  // free text; unresolved items marked REVIEW_REQUIRED"</span>,
  <span class="k">"linked_source_records"</span>:      <span class="s">"string[]  // accessions, report IDs, scan UIDs"</span>
}</pre>

  <div class="callout">
    <strong>Critical schema constraint:</strong> <code>inference_allowed</code> defaults to <code>false</code>. It may only be set to <code>true</code> when: <code>neurophysical_unknown_class = none</code> OR known and bounded, AND <code>measurement_unknown_class = none</code>, AND <code>provenance_class = verified</code>, AND <code>artifact_flag = false</code>, AND <code>confidence_level ∈ {high, medium}</code>. Even then, <code>person_level_claim_blocked</code> applies independently β€” inference_allowed = true does not authorize identity, character, intent, or diagnosis claims.
  </div>
</div>

<hr class="div-rule">

<!-- ════════════════════════════════════════════════════ -->
<!-- SECTION 8: HIR RULE SET -->
<!-- ════════════════════════════════════════════════════ -->
<div class="section">
  <div class="section-num">Section 8</div>
  <div class="section-title">HIR-Safe <em>Rule Set</em> β€” R-01 through R-12</div>

  <div class="rule-block rb-block">
    <div class="rb-label">R-01 β€” Unknown mechanism cannot increase confidence</div>
    <div class="rb-content">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.</div>
  </div>

  <div class="rule-block rb-block">
    <div class="rb-label">R-02 β€” Artifact-heavy data cannot support interpretation</div>
    <div class="rb-content">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 β€” it is a hard block on interpretation.</div>
  </div>

  <div class="rule-block rb-caution">
    <div class="rb-label">R-03 β€” Missing metadata downgrades confidence</div>
    <div class="rb-content">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.</div>
  </div>

  <div class="rule-block rb-block">
    <div class="rb-label">R-04 β€” Measurement / provenance failure may suspend or invalidate interpretation</div>
    <div class="rb-content">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 β€” it is an invalid record until provenance is established.</div>
  </div>

  <div class="rule-block rb-caution">
    <div class="rb-label">R-05 β€” Structure–function mapping must remain bounded</div>
    <div class="rb-content">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).</div>
  </div>

  <div class="rule-block rb-block">
    <div class="rb-label">R-06 β€” No diagnosis unless clinically validated source and context exist</div>
    <div class="rb-content">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.</div>
  </div>

  <div class="rule-block rb-block">
    <div class="rb-label">R-07 β€” No person-level moral, identity, intent, or character inference</div>
    <div class="rb-content">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.</div>
  </div>

  <div class="rule-block rb-block">
    <div class="rb-label">R-08 β€” Group-level findings cannot be treated as individual proof</div>
    <div class="rb-content">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 β€” they do not confirm individual-level structure, function, or outcome. individual_variability (UA-04) applies to all group-level source records.</div>
  </div>

  <div class="rule-block rb-caution">
    <div class="rb-label">R-09 β€” Plasticity / remapping must be treated as uncertainty unless directly measured</div>
    <div class="rb-content">If injury_history β‰  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."</div>
  </div>

  <div class="rule-block rb-caution">
    <div class="rb-label">R-10 β€” All outputs must include evidence limits</div>
    <div class="rb-content">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.</div>
  </div>

  <div class="rule-block rb-block">
    <div class="rb-label">R-11 β€” Symptom is not a confirmed cause</div>
    <div class="rb-content">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 β€” inferring mental state from brain region activation β€” is not resolved by high activation magnitude or statistical threshold.</div>
  </div>

  <div class="rule-block rb-block">
    <div class="rb-label">R-12 β€” Any attempt to convert uncertainty into positive evidence is rejected</div>
    <div class="rb-content">No uncertainty class β€” Category A or Category B β€” 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.</div>
  </div>
</div>

<hr class="div-rule">

<!-- ════════════════════════════════════════════════════ -->
<!-- SECTION 9: STAGED INGEST PLAN -->
<!-- ════════════════════════════════════════════════════ -->
<div class="section">
  <div class="section-num">Section 9</div>
  <div class="section-title">Staged <em>Ingest Plan</em></div>

  <div class="stage-row">
    <div class="stage-num">1</div>
    <div class="stage-body">
      <div class="stage-title">Gross Anatomy / Region Registry</div>
      <div class="stage-source">Sources: MNI152, Desikan-Killiany, AAL3 Β· Status: ACTIVE (this document)</div>
      <p>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.</p>
    </div>
  </div>
  <div class="stage-row">
    <div class="stage-num">2</div>
    <div class="stage-body">
      <div class="stage-title">Functional Zones</div>
      <div class="stage-source">Sources: HCP resting-state, NeuroSynth (with caution flag), task fMRI references</div>
      <p>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 β‰  causation) flags unconditionally.</p>
    </div>
  </div>
  <div class="stage-row">
    <div class="stage-num">3</div>
    <div class="stage-body">
      <div class="stage-title">Connectivity / Pathways</div>
      <div class="stage-source">Sources: JHU-DTI atlas, HCP tractography, lesion-based pathway evidence</div>
      <p>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.</p>
    </div>
  </div>
  <div class="stage-row">
    <div class="stage-num">4</div>
    <div class="stage-body">
      <div class="stage-title">Physiological State Data</div>
      <div class="stage-source">Sources: clinical metadata, medication records, sleep staging, autonomic monitoring</div>
      <p>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.</p>
    </div>
  </div>
  <div class="stage-row">
    <div class="stage-num">5</div>
    <div class="stage-body">
      <div class="stage-title">Output-Effect Mapping</div>
      <div class="stage-source">Sources: clinical neurological exam, standardized assessment batteries, validated behavioral paradigms</div>
      <p>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.</p>
    </div>
  </div>
  <div class="stage-row">
    <div class="stage-num">6</div>
    <div class="stage-body">
      <div class="stage-title">Neuroplasticity / Remapping</div>
      <div class="stage-source">Sources: longitudinal MRI, TMS mapping, task-fMRI pre/post, clinical history</div>
      <p>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.</p>
    </div>
  </div>
  <div class="stage-row">
    <div class="stage-num">7</div>
    <div class="stage-body">
      <div class="stage-title">Measurement / Provenance Metadata</div>
      <div class="stage-source">Sources: DICOM headers, scan reports, clinical records, acquisition protocols</div>
      <p>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.</p>
    </div>
  </div>
  <div class="stage-row">
    <div class="stage-num">8</div>
    <div class="stage-body">
      <div class="stage-title">Clinical Interpretation Layer (Conditional)</div>
      <div class="stage-source">Requires: qualified clinical context, validated evaluation protocol, jurisdiction-appropriate standards</div>
      <p>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 β€” 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.</p>
    </div>
  </div>
</div>

<hr class="div-rule">

<!-- ════════════════════════════════════════════════════ -->
<!-- SECTION 10: OSF PACKET RECOMMENDATION -->
<!-- ════════════════════════════════════════════════════ -->
<div class="section">
  <div class="section-num">Section 10</div>
  <div class="section-title">OSF-Ready <em>Packet Recommendation</em></div>

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

  <div class="callout">
    <strong>009_SAMPLE_FEATURE_RECORDS.jsonl must include:</strong> 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.
  </div>
</div>

<hr class="div-rule">

<!-- ════════════════════════════════════════════════════ -->
<!-- SECTION 11: PLAIN-LANGUAGE EXPLANATION -->
<!-- ════════════════════════════════════════════════════ -->
<div class="section">
  <div class="section-num">Section 11</div>
  <div class="section-title">Plain-Language <em>Explanation</em></div>

  <div class="plain-grid">
    <div class="plain-card" style="border-left:3px solid var(--allow)">
      <div class="plain-card-title">What this does</div>
      <div class="plain-card-body">
        It organizes what we actually know about the physical brain β€” its structures, pathways, signals, and measurable effects β€” 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.<br><br>
        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.
      </div>
    </div>
    <div class="plain-card" style="border-left:3px solid var(--unc-b)">
      <div class="plain-card-title">What it does not do</div>
      <div class="plain-card-body">
        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.<br><br>
        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.
      </div>
    </div>
    <div class="plain-card" style="border-left:3px solid var(--neu)">
      <div class="plain-card-title">Why it matters for health AI</div>
      <div class="plain-card-body">
        AI systems applied to brain data risk making overclaims β€” 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.<br><br>
        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.
      </div>
    </div>
    <div class="plain-card" style="border-left:3px solid var(--func)">
      <div class="plain-card-title">How HIR governs it</div>
      <div class="plain-card-body">
        <strong>Honesty:</strong> Every data record must declare what it measured, how reliably, and what it can't conclude. Unknown must remain labeled unknown.<br><br>
        <strong>Integrity:</strong> 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.<br><br>
        <strong>Respect:</strong> 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.
      </div>
    </div>
  </div>
</div>

<!-- ══ FOOTER ══ -->
<div class="footer">
  <strong>Created and Developed by Collin D. Weber</strong> Β· Primordial Brain Layer v0.1 Β· HIR-Governed Neurophysical Architecture Plan Β· April 30, 2026<br><br>
  This document is a bounded architecture planning study. It is not a clinical tool, a diagnostic instrument, a forensic system, or a medical opinion. It does not establish clinical validity for any purpose. All brain structure–function associations are documented from published scientific literature and are subject to the uncertainty taxonomy defined in Section 6. Unresolved items are marked REVIEW_REQUIRED.<br><br>
  This module distinguishes unknown neurophysiology from unreliable data, ensuring that unresolved brain-science questions are not confused with degraded, artifact-heavy, or provenance-weak measurements, and ensuring that neither form of uncertainty can be converted into unsupported claims about a person.
</div>

</body>
</html>