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basal-agent commits / 103b56e

basal-agent: polymer.c — rung 1->2 emergence attempt, copier NOT supplied (honest null-with-structure)
Polymer soup in digital-analogy land: binary strands, 0<->1 complementarity, ONLY physics = template-directed synthesis with per-base fidelity f (sequence-blind, the pre-biotic given — not a replicase). Random soup + degradation + selection for a function. Does a heritable functional replicator EMERGE, and where does it collapse? Sweep f at L=16,32; 5 seeds. Data corrected my pre-registered guess (and that IS the result): - Copying is generic (base-pairing) — population always self-sustains; never the wall. - Heritable function emerges only above ~f=0.98 (<=2% error), gradually; at un-catalyzed fidelity (f~0.80-0.90, the real pre-biotic number) only WEAK partial function (~0.6-0.7 match). - No length-paradox — because the landscape is ADDITIVE (relaxed error threshold, Kun-Szathmary); the robust structure is that a fidelity wall EXISTS, not its exact height. - THE WALL on the fidelity axis: fidelity needed (>=0.98) exceeds un-catalyzed templating (~0.85), and the replicase that would close the gap needs that fidelity first — Eigen's bootstrap paradox, reproduced from below. rung 1->2 does NOT cross at realistic fidelity. Verdict: honest NULL-with-structure. We did not install the copier; a functional replicator CAN emerge, but only in a fidelity regime un-catalyzed chemistry can't reach — the field's real wall, reproduced in a model that supplied only the physics. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
103b56e1efe524812a2e9a2b9ae90f8cc26168c7
by plankatron <fleeky@gmail.com> · 2026-07-21T23:48:36.000Z

Changed files (3) +152 -1

.gitignore +1 -0
……@@ -28,3 +28,4 @@ template
2828templceil
2929spatial
3030window
31polymer
SYNTHESIS.md +42 -1
……@@ -280,6 +280,47 @@ Eigen's error-threshold / optimal-mutation-rate result in our own model, and it
280280reframing: fidelity is a *dial*, not a demand, and evolution lives at its sweet spot — which is why real
281281copying is neither perfect nor arbitrary, and why fidelity itself is a trait that got ratcheted up over time.
282282
283### The rung 1→2 EMERGENCE attempt — a polymer soup with the copier NOT supplied (`polymer.c`)
284
285Every earlier model installed the copier at the reproduction step. `polymer.c` doesn't: binary strands,
2860↔1 complementarity, and the *only* reproduction physics is **template-directed synthesis** (a template's
287bits complemented with per-base fidelity f, mispaired otherwise) — sequence-blind, the pre-biotic given
288(un-catalyzed base-pairing), **not** a replicase. A random diverse soup + degradation + world-supplied
289selection for a *function* (match a target motif). Measured: does a heritable functional replicator *emerge*
290from the soup, self-sustain, and where does it collapse? Sweep f at L=16, 32; 5 seeds.
291
292| f | L=16 func match (start→end) | L=32 func match |
293|---|---|---|
294| 0.80 | 0.53→0.58 | 0.51→0.57 |
295| 0.90 | 0.53→0.70 | 0.51→0.68 |
296| 0.95 | 0.53→0.81 | 0.51→0.79 |
297| 0.98 | 0.53→**0.92** (emerges) | 0.51→**0.91** (emerges) |
298| 0.995 | 0.53→0.98 | 0.51→0.98 |
299
300**The data corrected my pre-registered guess, and that correction is the result.**
301- **Copying is generic.** The population always self-sustains — base-pairing gives replication for free.
302 That was *never* the wall (as the field says: templated copying is chemically generic; fidelity and
303 function are the hard parts).
304- **Heritable function emerges only above a fidelity threshold (~f=0.98 here, ≤2% error), and gradually.**
305 At *un-catalyzed* template fidelity (f≈0.80–0.90, 10–20% error — the real pre-biotic number, per the clay
306 research) only **weak partial function** appears (match ~0.6–0.7), not a strong replicator.
307- **No length-paradox appeared — honestly, because I chose an *additive* (per-site) landscape**, the
308 *forgiving* "relaxed error threshold" case (Kun–Szathmáry 2005). The ~0.98 value scales with selection
309 strength; the robust structure is *that a fidelity wall exists*, not its exact height. (A single-peak /
310 all-or-nothing landscape — like "be a working replicase" — would restore the sharp length-dependence;
311 that's a *maintenance* question, distinct from the *emergence* one tested here.)
312- **The wall, reproduced from emergent copying physics — on the fidelity axis:** the fidelity needed to
313 evolve a strong functional replicator (≥0.98) **exceeds what un-catalyzed templating supplies (~0.85)**,
314 and the replicase that would close the gap is itself a functional sequence needing that fidelity *first*.
315 **Eigen's bootstrap paradox, reproduced from below.** rung 1→2 does **not** cross at realistic fidelity.
316
317**Verdict on the emergence attempt: honest NULL-with-structure.** We did *not* install the copier, and a
318functional replicator *can* emerge — but only in a fidelity regime un-catalyzed chemistry can't reach, so it
319does **not** self-start from a realistic pre-biotic soup. This is not our failure to find the trick; it is
320the field's actual wall (Eigen's paradox), now reproduced in a model that supplied only the physics. The
321deeper crossing — a *ribozyme replicase* that raises its own fidelity, emerging at low fidelity — remains
322open here and everywhere.
323
283324## What is proven vs open
284325
285326**Established here:**
……@@ -315,7 +356,7 @@ copying is neither perfect nor arbitrary, and why fidelity itself is a trait tha
315356Part A: `stream.c` `sns.c` `mess3.c` `learn.c` `critical.c` `competitive.c` `da-em.c` `soc.c`
316357`wakesleep.c` `wakesleep2.c` `mom.c`.
317358Part B: `lawspace.c` `rung1.c` `rung2.c` `rung3.c` `evoworld.c` `rung34.c` `rung45.c` `bridge.c`
318`rung45dup.c` `flagella.c` `gard.c` `gardenv.c` `digigard.c` `template.c` `templceil.c` `spatial.c` `window.c`.
359`rung45dup.c` `flagella.c` `gard.c` `gardenv.c` `digigard.c` `template.c` `templceil.c` `spatial.c` `window.c` `polymer.c`.
319360`src/`: original Phase-1 filesystem active-perception agent (active > random search).
320361
321362Each `*.c` is standalone: `cc -O2 -std=c11 -o X X.c -lm && ./X`.
polymer.c +109 -0
……@@ -0,0 +1,109 @@
1/* polymer.c — rung 1->2 EMERGENCE attempt in a polymer soup (digital-analogy land).
2 *
3 * All prior models supplied the copier at the reproduction step. Here the copier is NOT supplied:
4 * strands are binary sequences, 0 pairs 1 (complementarity), and the ONLY reproduction physics is
5 * TEMPLATE-DIRECTED SYNTHESIS -- a template's bits are complemented with per-base fidelity f, mis-paired
6 * otherwise. This is the pre-biotic given (uncatalyzed base-pairing), sequence-BLIND: it favors no
7 * sequence, and replication of ANY strand's complement is generic (that is base-pairing, not a replicase).
8 * The error rate EMERGES from mispairing; it is not a coded per-bit mutation.
9 *
10 * A random diverse soup + degradation + world-supplied selection for a FUNCTION (match a target motif,
11 * replication rate proportional to fitness). MEASURED, not encoded: does a heritable FUNCTIONAL replicator
12 * EMERGE from the random soup (mean match climbs 0.5 -> ~1), does it self-sustain against degradation, and
13 * at what fidelity does it COLLAPSE? Sweep f at two lengths L to expose Eigen's paradox (longer function
14 * needs higher fidelity, which un-catalyzed templating cannot supply -> the wall).
15 *
16 * A strand and its complement carry the same info: fitness is on the CANONICAL form min(s,~s), so S and ~S
17 * are one functional unit. Nothing rewards a specific replicator identity; only the function, world-supplied.
18 *
19 * build: cc -O2 -Wall -std=c11 -o polymer polymer.c -lm
20 */
21#include <math.h>
22#include <stdio.h>
23#include <stdint.h>
24
25#define NMAX 800
26#define D 0.30 /* per-step degradation (turnover that lets selection act) */
27#define STEPS 140
28#define SS 0.30 /* selection strength: fitness = exp(SS * #functional-positions-correct) */
29
30static unsigned long long RNG;
31static unsigned long long xs(void){ RNG^=RNG<<13; RNG^=RNG>>7; RNG^=RNG<<17; return RNG; }
32static double urand(void){ return (double)(xs()>>11)*(1.0/9007199254740992.0); }
33
34static int L; static uint64_t MASK, FTAR_C;
35static uint64_t canon(uint64_t s){ uint64_t c=(~s)&MASK; return s<c?s:c; }
36static int matchC(uint64_t s){ return L - __builtin_popcountll(canon(s) ^ FTAR_C); }
37
38static uint64_t pool[NMAX], nxt[NMAX];
39static double fit[NMAX], cum[NMAX];
40
41/* template-directed synthesis of the complement with per-base fidelity f (mispair otherwise). */
42static uint64_t replicate(uint64_t tmpl, double f){
43 uint64_t child=0;
44 for(int i=0;i<L;i++){ int t=(int)((tmpl>>i)&1); int b=(urand()<f)?(1-t):t; if(b) child|=(1ULL<<i); }
45 return child;
46}
47
48/* one run at length L, fidelity f. returns final mean functional match (fraction); writes start match. */
49static double run(double f, double *start){
50 MASK = (L>=64)?~0ULL:((1ULL<<L)-1);
51 uint64_t ftar=0; for(int i=0;i<L;i++) if(urand()<0.5) ftar|=(1ULL<<i); FTAR_C=canon(ftar);
52 for(int p=0;p<NMAX;p++){ uint64_t s=0; for(int i=0;i<L;i++) if(urand()<0.5) s|=(1ULL<<i); pool[p]=s; }
53
54 double s0=0; for(int p=0;p<NMAX;p++) s0+=matchC(pool[p]); s0/=(double)NMAX*L; *start=s0;
55
56 for(int g=0;g<STEPS;g++){
57 /* degradation: survivors kept, compacted */
58 int ns=0; for(int p=0;p<NMAX;p++) if(urand()>=D) pool[ns++]=pool[p];
59 if(ns==0){ *start=s0; return 0.0; } /* extinction */
60 double tot=0; for(int p=0;p<ns;p++){ fit[p]=exp(SS*matchC(pool[p])); tot+=fit[p]; cum[p]=tot; }
61 /* refill empty slots by fitness-weighted TEMPLATE-DIRECTED replication (emergent copier) */
62 int k=0; for(;k<ns;k++) nxt[k]=pool[k];
63 while(k<NMAX){ double r=urand()*tot; int lo=0,hi=ns-1; while(lo<hi){int mid=(lo+hi)/2; if(cum[mid]<r)lo=mid+1; else hi=mid;} nxt[k++]=replicate(pool[lo],f); }
64 for(int p=0;p<NMAX;p++) pool[p]=nxt[p];
65 }
66 double e=0; for(int p=0;p<NMAX;p++) e+=matchC(pool[p]); return e/((double)NMAX*L);
67}
68
69int main(void){
70 unsigned long long seeds[]={0x9e3779b97f4a7c15ULL,0xd1b54a32d192ed03ULL,0x2545f4914f6cdd1dULL,0x123456789abcdefULL,0xfeedface12345678ULL};
71 int NS=sizeof(seeds)/sizeof(seeds[0]);
72 double fs[]={0.80,0.90,0.95,0.98,0.995}; int nF=sizeof(fs)/sizeof(double);
73 int Ls[]={16,32}; int nL=sizeof(Ls)/sizeof(int);
74
75 printf("=== rung 1->2 EMERGENCE attempt: template-directed polymer soup (digital) ===\n");
76 printf(" Binary strands, 0<->1 pairing. ONLY physics = template-directed synthesis w/ fidelity f.\n");
77 printf(" Random soup + degradation + selection for a function. Emergence = functional match 0.5 -> ~1.\n");
78 printf(" pop=%d, degrade=%.2f, %d steps, %d seeds. Sweep f at L=%d,%d.\n\n",NMAX,D,STEPS,NS,Ls[0],Ls[1]);
79
80 for(int li=0;li<nL;li++){
81 L=Ls[li];
82 printf(" --- L=%d (Eigen: need ~f > %.3f to hold) ---\n", L, 1.0-1.0/L);
83 printf(" f | func match (start->end) | emerged?\n");
84 printf(" ------+-------------------------+---------\n");
85 double thr=-1;
86 for(int i=0;i<nF;i++){
87 double se=0,ss=0;
88 for(int s=0;s<NS;s++){ double st; RNG=seeds[s]; se+=run(fs[i],&st); ss+=st; }
89 se/=NS; ss/=NS;
90 int emerged = (se>0.85 && se>ss+0.2);
91 if(emerged && thr<0) thr=fs[i];
92 printf(" %.3f | %.3f -> %.3f | %s\n", fs[i], ss, se, emerged?"YES":"no");
93 }
94 printf(" => emergence threshold at L=%d: f* = %s%.3f\n\n", L, thr<0?">":"", thr<0?fs[nF-1]:thr);
95 }
96 printf(" HONEST READING (the data corrected my pre-registered guess):\n");
97 printf(" * Copying is GENERIC (base-pairing) -- the population always self-sustains; that was never the wall.\n");
98 printf(" * Heritable FUNCTION emerges only above a fidelity threshold (~f=0.98 here, i.e. <=2%% error),\n");
99 printf(" and it emerges GRADUALLY: at un-catalyzed template fidelity (f~0.80-0.90, 10-20%% error) only\n");
100 printf(" WEAK partial function appears (match ~0.6-0.7), not a strong replicator.\n");
101 printf(" * The threshold did NOT rise with L -- because this functional landscape is ADDITIVE (per-site\n");
102 printf(" selection), the forgiving 'relaxed error threshold' case (Kun-Szathmary). The value ~0.98\n");
103 printf(" scales with selection strength; the STRUCTURE (a fidelity wall) is what is robust.\n");
104 printf(" * THE WALL, reproduced from emergent copying physics: the fidelity needed to evolve a strong\n");
105 printf(" functional replicator (>=0.98) EXCEEDS what un-catalyzed templating supplies (~0.85), and the\n");
106 printf(" replicase that would close the gap is itself a functional sequence needing that fidelity\n");
107 printf(" FIRST -- Eigen's bootstrap paradox. rung 1->2 does NOT cross from below at realistic fidelity.\n");
108 return 0;
109}