knowledge: learning kernel — model the estimator bias, not just sampling

Revisiting Layer 1 against Layer 1.5 (and Riis 2026, arXiv:2604.08554):
neutral Wright-Fisher is a null that BOTH neural architectures deviate
from, in opposite directions. Add a learning kernel to the refit step,
p_{t+1} = T_theta(counts/n), with two population-genetics knobs -- reset u
(mutation toward a prior = smoothing) and temperature tau (sharpening =
mode-competition) -- both identity by default, so the histogram bridge and
all 68 scientific-validation/correctness tests are unchanged.

Result: neutral drift fails both neural models, oppositely.
- VAE regime (n=6000, K=30): neutral drift is inert (no collapse), yet the
  real VAE collapsed to one mode. Sharpening tau=0.8 reproduces it -- the
  estimator ADDS collapse pressure.
- RNN regime (n=200, K=256): neutral drives H->0, but the real RNN only
  partially collapses. Mutation u=0.006 reproduces the H-floor -- the
  estimator REMOVES collapse pressure. Honest caveat: uniform-mutation
  overshoots the RNN's forward-KL, evidence its smoothing prior is
  truth-like, not uniform (future refinement).

This mechanistically explains the architecture-generality result and the
softened neural g*, and develops the estimator axis Riis names as future
work. New: knowledge/kernel.py, configs/layer1/kernel_{sharpen,smooth}.yaml,
figures/plot_kernel.py (overlays analytic arms vs committed neural
endpoints), READMEs, tests/test_kernel.py (+6, 105 total green). Strategic
Riis positioning recorded in CLAUDE.md: concede "collapse=drift" as prior
art; lead with recombination, the kernel axis, and the Lamarckian society.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

CLAUDE.md

@@ -76,6 +76,10 @@ E4's whole purpose is to isolate the effect of teacher **decorrelation ρ**, so
 
 **Finding (2026-07-05, real-MNIST `mnist_collapse`) — collapse and grounding-rescue reproduce on real images.** External-validity tier: a small **convolutional VAE** (the canonical generative-collapse model) is retrained each generation on its own generated digits. Modes = digit class × stroke-thickness bin (K=30, Zipf, ~18 tail modes); the oracle is a **frozen CNN + deterministic thickness** at **98.5% mode accuracy** (its 30×30 confusion matrix is recorded in the manifest as the measurement floor). Result (4 reps): the **dry (g=0) lineage collapses to a single mode** — forward-KL 0.5→18, support 30→1, tail truth-mass 1.0→0.06, H→0 — while **10% grounding holds all 30 modes** (KL≈0.6, full tail, H≈0.9). The VAE needs ~10% grounding here vs the synthetic histogram's ~5%, consistent with the `grounding` finding that trained neural models need more grounding than the exact operator. **Confirmation-only (signs, not magnitudes; blueprint §3.5)** — the exact synthetic oracle stays the quantitative anchor. `figures/mnist_montage.py` is an eyeball diagnostic (re-runs a short dry lineage; NOT a parquet figure). Build gates passed: CNN mode accuracy 98.5%; VAE gen-0 recovers full 30/30 support (over-smooths frequencies, KL≈0.5, no prior hole — unlike the *synthetic*-codeword VAE, which is why the MNIST VAE works where that one didn't). The MNIST tier is heavy (torchvision `--extra mnist`, downloads MNIST, ~5 min): `make mnist`, kept out of the `make neural` loop.
 
+**Finding (2026-07-05, learning kernel) — neutral drift is a null both real models fail, oppositely; the estimator bias is a signed operator.** Layer-1 extension (`knowledge/kernel.py`, `LearningKernelCfg`): the refit becomes `p_{t+1} = T_θ(counts/n)` with two pop-gen knobs — **reset `u`** (mutation toward a prior = smoothing) and **temperature `τ`** (sharpening = mode-competition) — both identity at their defaults, so the histogram bridge and every scientific-validation test are unchanged (68 core tests still green). Result: **neutral Wright–Fisher fails both neural architectures, in opposite directions.** VAE regime (`n=6000, K=30`): neutral drift is *inert* (no collapse), yet the real VAE collapsed to one mode — **sharpening `τ=0.8` reproduces it** (the estimator ADDS collapse). RNN regime (`n=200, K=256`): neutral drives `H→0`, but the real RNN only partially collapses — **mutation `u=0.006` reproduces the `H`-floor** (the estimator REMOVES collapse). Honest caveat: uniform-mutation matches the RNN `H`-floor but overshoots its forward-KL (~5 vs ~2), evidence the RNN's smoothing prior is *truth-like, not uniform* (future refinement). Configs `configs/layer1/kernel_{sharpen,smooth}.yaml`, figure `plot_kernel.py`. This mechanistically explains the architecture-generality result and the softened neural `g*`.
+
+**Strategic positioning vs Riis 2026 (arXiv:2604.08554, "Drift and selection in LLM text ecosystems").** Riis independently formalizes **collapse = Wright–Fisher drift** (his Thm 1) with n-gram agents: minority-mass martingale, rare-first extinction, single-token dropout ≈ αe^{−α}, de Bruijn-polytope fixed points, plus descriptive-vs-normative *selection* (Thm 2). **Concede as prior art:** "collapse is literally Wright–Fisher", the martingale, rare-first loss, the WF/effective-population formalism — cite him; do **not** frame these as our contribution. **Crucial distinction that protects us:** his "mixed environment" *retains the lineage's own old synthetic tokens* — there is **no injection of fresh real data from a fixed `p*`**, so his headline is *pessimistic* (Thm 1c: extinction is independent of α — retention only changes speed). Our **grounding is immigration from a non-drifting external truth**, giving a stationary `H_eq>0` and a critical `g*≪1` that *prevents* collapse — the mechanism his closed loop lacks. **Our defensible novelty, ranked:** (1) **recombination + "merge, don't average" conservation law** (E4) — he has no model-merging operator; flagship; (2) **the learning-kernel / estimator-bias axis** — he *explicitly names it as future work*; we now build+measure it; (3) grounding threshold (solid anchor, but immigration–drift balance is classic — not a flagship); (4) architecture-generality in real weights + MNIST; (5) **the Lamarckian society + the vertical/cumulative C3 claim — wholly ours, not yet run.** Reposition the paper from *"collapse is drift"* (now contested) to **a population-genetic *control theory* for sustaining open-ended knowledge**: drift is the diagnosed disease (cite Riis), our contribution is the engineered remedies and their integration.
+
 ## Build order (blueprint §7) — respect the gate
 
 1. Scaffold: repo layout (§5), container, pytest skeleton, config system, seeding utils. `make test` green.

Makefile

@@ -15,8 +15,8 @@ env-mnist:         ## add torchvision for the real-MNIST confirmation tier
 test:              ## correctness tests + scientific-validation tests (the spine of trust)
 	uv run pytest
 
-layer1:            ## run experiments E1-E6
+layer1:            ## run experiments E1-E6 + the learning-kernel bridge (analytic)
-	for e in E1 E2 E3 E4 E5 E6; do uv run python -m knowledge.experiment configs/layer1/$$e.yaml; done
+	for e in E1 E2 E3 E4 E5 E6 kernel_sharpen kernel_smooth; do uv run python -m knowledge.experiment configs/layer1/$$e.yaml; done
 
 neural:            ## run Layer 1.5 synthetic neural experiments (excludes the heavy MNIST tier)
 	for c in configs/neural/*.yaml; do case "$$c" in *mnist*) ;; \

configs/layer1/kernel_sharpen.yaml

@@ -0,0 +1,29 @@
+experiment: kernel_sharpen
+kind: lineage
+seed: 20260705
+n_replicates: 24
+
+# (Learning-kernel bridge, pro-collapse arm): does neutral Wright-Fisher explain the VAE's
+# collapse on MNIST? NO -- and that is the point. This matches the MNIST regime (K=30, n=6000,
+# Zipf) where drift is nearly inert: neutral (temperature=1.0) barely moves (H stays ~H*, ~all
+# modes alive), yet the real VAE collapsed to a SINGLE mode (results/mnist_collapse). Adding the
+# estimator's sharpening / mode-competition (temperature<1: p ~ p^(1/tau)) reproduces the
+# catastrophic collapse. tau=0.8 is calibrated to reproduce collapse-to-one-mode. This is the
+# axis Riis (2026) names as future work: the estimator, not the sampling, drives VAE collapse.
+
+truth: {K: 30, R: 1, tail: zipf, zipf_s: 1.5, tail_threshold: 0.01, init: truth}
+
+dynamics:
+  n: 6000                      # huge vs K=30 -> neutral drift is essentially inert
+  grounding: {m: 0, policy: proportional}
+  kernel: {reset: 0.0, temperature: 1.0, floor: 0.0}
+
+generations: 15
+
+metrics: {kl_floor: 1.0e-9, support_eps: 1.0e-9}
+
+sweep:
+  - param: dynamics.kernel.temperature
+    values: [1.0, 0.8]         # neutral (no collapse) vs sharpened (catastrophic collapse)
+
+output: {dir: results/kernel_sharpen}

configs/layer1/kernel_smooth.yaml

@@ -0,0 +1,32 @@
+experiment: kernel_smooth
+kind: lineage
+seed: 20260705
+n_replicates: 24
+
+# (Learning-kernel bridge, anti-collapse arm): neutral Wright-Fisher OVER-predicts the RNN's
+# collapse. This matches the RNN grounding regime (K=256, n=200, Zipf): neutral (reset=0) drives
+# H all the way to 0, but the real RNN only PARTIALLY collapses -- H plateaus ~0.68 of a possible
+# 0.88, forward-KL plateaus ~2 (does not diverge), ~half the tail stays alive (results/grounding).
+# The estimator's smoothing / regularisation supplies a diversity FLOOR. A mutation-toward-prior
+# knob (reset=u: p <- (1-u)p + u*uniform) reproduces the H-floor. reset=0.006 is calibrated to the
+# RNN's stationary dry H. Honest caveat carried in the write-up: uniform-mutation matches the
+# H-floor but overshoots forward-KL (analytic ~6 vs RNN ~2), evidence the RNN's smoothing target
+# is TRUTH-LIKE, not uniform -- a refinement for future work. The sign, though, is unambiguous:
+# the estimator here REMOVES collapse pressure (opposite to the VAE's sharpening).
+
+truth: {K: 256, R: 1, tail: zipf, zipf_s: 1.3, tail_threshold: 0.001, init: truth}
+
+dynamics:
+  n: 200
+  grounding: {m: 0, policy: proportional}
+  kernel: {reset: 0.0, temperature: 1.0, floor: 0.0}
+
+generations: 100              # long enough to show neutral -> 0 vs smoothed -> floor clearly
+
+metrics: {kl_floor: 1.0e-9, support_eps: 1.0e-9}
+
+sweep:
+  - param: dynamics.kernel.reset
+    values: [0.0, 0.006]       # neutral (H -> 0) vs smoothed (H floors, like the RNN)
+
+output: {dir: results/kernel_smooth}

figures/plot_kernel.py

@@ -0,0 +1,121 @@
+"""`kernel` figure — the learning kernel: neutral drift fails both neural models, oppositely.
+
+The Layer-1.5 architecture-generality result gets a mechanistic explanation. Neutral Wright-Fisher
+(the histogram / Riis baseline) is the null; a real learner adds an estimator bias that can point
+either way. Two regimes, each falsifying neutral drift in the OPPOSITE direction, each repaired by
+one knob of the learning kernel:
+
+* **VAE regime (n=6000, K=30):** drift is nearly inert — neutral holds ~all modes — yet the real
+  VAE collapsed to a single mode. Sharpening (temperature<1) reproduces it. The estimator ADDS
+  collapse pressure.
+* **RNN regime (n=200, K=256):** neutral drives H to 0, but the real RNN only partially collapses
+  (H floors, forward-KL plateaus). Mutation-toward-prior (reset>0) reproduces the floor. The
+  estimator REMOVES collapse pressure.
+
+Analytic arms are read from results/kernel_{sharpen,smooth}; the neural reference endpoints
+(dashed) are read from the committed results/mnist_collapse and results/grounding parquets — so the
+figure is a pure function of committed artifacts.
+
+Usage:  python figures/plot_kernel.py
+"""
+
+from __future__ import annotations
+
+import sys
+from pathlib import Path
+
+import matplotlib.pyplot as plt
+import numpy as np
+
+sys.path.insert(0, str(Path(__file__).parent))
+from _figlib import load_bundle, savefig  # noqa: E402
+
+sys.path.insert(0, str(Path(__file__).parents[1] / "src"))
+from knowledge.metrics import heterozygosity  # noqa: E402
+from knowledge.truth import make_true_distribution  # noqa: E402
+
+
+def _mean_traj(df, knob, val, col):
+    sub = df[df[knob] == val]
+    s = sub.groupby("generation")[col].mean()
+    return s.index.to_numpy(), s.to_numpy()
+
+
+def _neural_dry(results_dir, col, stationary_frac=0.0):
+    """Mean of ``col`` on the dry (g=0) neural arm — endpoint, or stationary tail if frac>0."""
+    df, _ = load_bundle(results_dir)
+    dry = df[df["g"] == 0.0]
+    if stationary_frac > 0:
+        dry = dry[dry["generation"] >= int(dry["generation"].max() * (1 - stationary_frac))]
+        return float(dry[col].mean())
+    return float(dry[dry["generation"] == dry["generation"].max()][col].mean())
+
+
+def main() -> None:
+    sh, sh_cfg = load_bundle("results/kernel_sharpen")
+    sm, sm_cfg = load_bundle("results/kernel_smooth")
+    Hstar_sh = heterozygosity(make_true_distribution(
+        sh_cfg["truth"]["K"], 1, "zipf", 0.5, sh_cfg["truth"]["zipf_s"], 0,
+        tail_threshold=sh_cfg["truth"]["tail_threshold"]).p_star)
+    Hstar_sm = heterozygosity(make_true_distribution(
+        sm_cfg["truth"]["K"], 1, "zipf", 0.5, sm_cfg["truth"]["zipf_s"], 0,
+        tail_threshold=sm_cfg["truth"]["tail_threshold"]).p_star)
+
+    # Neural reference endpoints (dashed) from the committed neural runs.
+    vae_H = _neural_dry("results/mnist_collapse", "heterozygosity")
+    vae_sup = _neural_dry("results/mnist_collapse", "support_size")
+    rnn_H = _neural_dry("results/grounding", "heterozygosity", stationary_frac=0.4)
+    rnn_KL = _neural_dry("results/grounding", "forward_kl", stationary_frac=0.4)
+
+    fig, axes = plt.subplots(2, 2, figsize=(13, 9))
+    NEU, KER = "#1f77b4", "#d62728"
+
+    # --- VAE regime: sharpening ---
+    ax = axes[0, 0]
+    for val, c, lab in [(1.0, NEU, "neutral (τ=1)"), (0.8, KER, "sharpened (τ=0.8)")]:
+        g, y = _mean_traj(sh, "temperature", val, "heterozygosity")
+        ax.plot(g, y, "-o", color=c, ms=3, label=lab)
+    ax.axhline(Hstar_sh, ls=":", color="gray", lw=1, label="$H^*$")
+    ax.axhline(vae_H, ls="--", color="#2ca02c", lw=1.3, label=f"real VAE (dry): {vae_H:.2f}")
+    ax.set(xlabel="generation", ylabel="heterozygosity $H$",
+           title="VAE regime ($n$=6000, $K$=30): neutral drift is inert;\nsharpening collapses (like the VAE)")
+    ax.legend(frameon=False, fontsize=8)
+
+    ax = axes[0, 1]
+    for val, c, lab in [(1.0, NEU, "neutral (τ=1)"), (0.8, KER, "sharpened (τ=0.8)")]:
+        g, y = _mean_traj(sh, "temperature", val, "support_size")
+        ax.plot(g, y, "-o", color=c, ms=3, label=lab)
+    ax.axhline(vae_sup, ls="--", color="#2ca02c", lw=1.3, label=f"real VAE (dry): {vae_sup:.0f}")
+    ax.set(xlabel="generation", ylabel="distinct modes alive",
+           title="Support: neutral holds ~all; sharpening → 1 mode")
+    ax.legend(frameon=False, fontsize=8)
+
+    # --- RNN regime: smoothing ---
+    ax = axes[1, 0]
+    for val, c, lab in [(0.0, NEU, "neutral (u=0)"), (0.006, KER, "smoothed (u=0.006)")]:
+        g, y = _mean_traj(sm, "reset", val, "heterozygosity")
+        ax.plot(g, y, "-", color=c, lw=1.8, label=lab)
+    ax.axhline(Hstar_sm, ls=":", color="gray", lw=1, label="$H^*$")
+    ax.axhline(rnn_H, ls="--", color="#2ca02c", lw=1.3, label=f"real RNN (dry): {rnn_H:.2f}")
+    ax.set(xlabel="generation", ylabel="heterozygosity $H$",
+           title="RNN regime ($n$=200, $K$=256): neutral → 0;\nsmoothing floors $H$ (like the RNN)")
+    ax.legend(frameon=False, fontsize=8)
+
+    ax = axes[1, 1]
+    for val, c, lab in [(0.0, NEU, "neutral (u=0)"), (0.006, KER, "smoothed (u=0.006)")]:
+        g, y = _mean_traj(sm, "reset", val, "forward_kl")
+        ax.plot(g, y, "-", color=c, lw=1.8, label=lab)
+    ax.axhline(rnn_KL, ls="--", color="#2ca02c", lw=1.3, label=f"real RNN (dry): {rnn_KL:.1f}")
+    ax.set(xlabel="generation", ylabel=r"forward-KL $D(p^*\Vert p)$",
+           title="Forward-KL: neutral diverges; smoothing plateaus\n(overshoots RNN → prior is truth-like, not uniform)")
+    ax.legend(frameon=False, fontsize=8)
+
+    fig.suptitle("learning kernel — neutral Wright–Fisher fails both neural models, oppositely: "
+                 "the estimator sharpens (VAE) or smooths (RNN)", y=1.0, fontsize=12)
+    fig.tight_layout()
+    for d in ("results/kernel_sharpen", "results/kernel_smooth"):
+        savefig(fig, d, "kernel")
+
+
+if __name__ == "__main__":
+    main()

results/kernel_sharpen/README.md

@@ -0,0 +1,42 @@
+# kernel — the learning kernel: why real learners deviate from neutral drift
+
+*(This legend covers both `results/kernel_sharpen/` and `results/kernel_smooth/`; the figure
+`kernel.png` is written into both.)*
+
+**Claim tested.** Neutral Wright–Fisher drift (the histogram bridge, and the baseline of Riis
+2026) is the *null* model of collapse. But Layer 1.5 showed real trained models deviate from it —
+and in **opposite directions**. Can a single extension of Layer 1 — a parameterized *learning
+kernel* on the refit step, `p_{t+1} = T_θ(counts/n)` — reproduce both deviations, and does neutral
+drift genuinely fail without it?
+
+**Setup.** The kernel (`knowledge/kernel.py`) has two population-genetics knobs, both reducing to
+neutral drift at their defaults (so the histogram and every scientific-validation test are
+unchanged): **reset `u`** — mutation toward a prior (`p ← (1−u)p + u·π`), i.e. smoothing; and
+**temperature `τ`** — sharpening (`p ∝ p^{1/τ}`, `τ<1` concentrates), i.e. mode-competition. Two
+matched-to-neural regimes, 24 replicates each.
+
+### The four panels (`kernel.png`; blue = neutral, red = kernel-on, green dashed = the real neural model)
+**Top row — VAE regime (`n=6000`, `K=30`), pro-collapse:**
+1. **Heterozygosity.** Neutral drift is **inert** — at `n=6000` it barely moves (`H` stays at
+   `H*`). Yet the real VAE (green) collapsed to `H≈0`. **Sharpening (`τ=0.8`) reproduces the
+   collapse.** Neutral drift is *falsified*; the estimator's mode-competition is required.
+2. **Support.** Neutral holds ~all 30 modes; sharpening → 1 mode, matching the VAE.
+
+**Bottom row — RNN regime (`n=200`, `K=256`), anti-collapse:**
+3. **Heterozygosity.** Neutral drift drives `H → 0`, but the real RNN (green) only *partially*
+   collapses (`H` floors at ~0.68). **Mutation `u=0.006` reproduces the floor.** The estimator here
+   *removes* collapse pressure.
+4. **Forward-KL.** Neutral diverges; smoothing plateaus. Honest caveat: uniform-mutation plateaus
+   *above* the RNN's KL (~5 vs ~2) — evidence the RNN's smoothing target is **truth-like, not
+   uniform** (a refinement for future work). The *sign* is unambiguous.
+
+### Takeaway
+Model collapse in real learners = **neutral drift ⊕ an architecture-specific estimator-bias
+operator that can point either way.** The histogram sits at the neutral null (`u=0, τ=1`); the VAE
+**sharpens** (adds collapse); the RNN/MLP **smooth** (add a diversity floor). This mechanistically
+explains the Layer-1.5 architecture-generality result and the softened neural `g*`, and develops
+the exact axis Riis (2026) names as future work ("different smoothing schemes… each induce their
+own fixed-point geometry… a natural direction for further work"). `u`/`τ` are calibrated from a
+single neural diagnostic and pinned in the configs. **Falsifier (not triggered):** if neutral drift
+had already reproduced the neural curves, the estimator axis would be superfluous — instead it fails
+in *both* regimes, oppositely.

results/kernel_sharpen/manifest.json

@@ -0,0 +1,14 @@
+{
+  "experiment": "kernel_sharpen",
+  "master_seed": 20260705,
+  "git_commit": "79bbc45f41822757e60d7f1994a82c5171a9e554",
+  "python": "3.14.5",
+  "libraries": {
+    "numpy": "2.5.0",
+    "scipy": "1.18.0",
+    "pandas": "3.0.3",
+    "pyarrow": "24.0.0"
+  },
+  "rows": 768,
+  "results_sha256": "d5651a841d58f12abed1339476b1839fb03fe02329e38d675d0602ccb5691e52"
+}

results/kernel_sharpen/resolved_config.yaml

@@ -0,0 +1,82 @@
+experiment: kernel_sharpen
+seed: 20260705
+n_replicates: 24
+source_config:
+  experiment: kernel_sharpen
+  kind: lineage
+  seed: 20260705
+  n_replicates: 24
+  truth:
+    K: 30
+    R: 1
+    tail: zipf
+    zipf_s: 1.5
+    tail_threshold: 0.01
+    init: truth
+  dynamics:
+    n: 6000
+    grounding:
+      m: 0
+      policy: proportional
+    kernel:
+      reset: 0.0
+      temperature: 1.0
+      floor: 0.0
+  generations: 15
+  metrics:
+    kl_floor: 1.0e-09
+    support_eps: 1.0e-09
+  sweep:
+  - param: dynamics.kernel.temperature
+    values:
+    - 1.0
+    - 0.8
+  output:
+    dir: results/kernel_sharpen
+grid:
+- label:
+    temperature: 1.0
+  lineage_cfg:
+    truth:
+      K: 30
+      R: 1
+      tail: zipf
+      zipf_s: 1.5
+      tail_threshold: 0.01
+      init: truth
+    dynamics:
+      n: 6000
+      grounding:
+        m: 0
+        policy: proportional
+      kernel:
+        reset: 0.0
+        temperature: 1.0
+        floor: 0.0
+    generations: 15
+    metrics:
+      kl_floor: 1.0e-09
+      support_eps: 1.0e-09
+- label:
+    temperature: 0.8
+  lineage_cfg:
+    truth:
+      K: 30
+      R: 1
+      tail: zipf
+      zipf_s: 1.5
+      tail_threshold: 0.01
+      init: truth
+    dynamics:
+      n: 6000
+      grounding:
+        m: 0
+        policy: proportional
+      kernel:
+        reset: 0.0
+        temperature: 0.8
+        floor: 0.0
+    generations: 15
+    metrics:
+      kl_floor: 1.0e-09
+      support_eps: 1.0e-09

results/kernel_smooth/README.md

@@ -0,0 +1,42 @@
+# kernel — the learning kernel: why real learners deviate from neutral drift
+
+*(This legend covers both `results/kernel_sharpen/` and `results/kernel_smooth/`; the figure
+`kernel.png` is written into both.)*
+
+**Claim tested.** Neutral Wright–Fisher drift (the histogram bridge, and the baseline of Riis
+2026) is the *null* model of collapse. But Layer 1.5 showed real trained models deviate from it —
+and in **opposite directions**. Can a single extension of Layer 1 — a parameterized *learning
+kernel* on the refit step, `p_{t+1} = T_θ(counts/n)` — reproduce both deviations, and does neutral
+drift genuinely fail without it?
+
+**Setup.** The kernel (`knowledge/kernel.py`) has two population-genetics knobs, both reducing to
+neutral drift at their defaults (so the histogram and every scientific-validation test are
+unchanged): **reset `u`** — mutation toward a prior (`p ← (1−u)p + u·π`), i.e. smoothing; and
+**temperature `τ`** — sharpening (`p ∝ p^{1/τ}`, `τ<1` concentrates), i.e. mode-competition. Two
+matched-to-neural regimes, 24 replicates each.
+
+### The four panels (`kernel.png`; blue = neutral, red = kernel-on, green dashed = the real neural model)
+**Top row — VAE regime (`n=6000`, `K=30`), pro-collapse:**
+1. **Heterozygosity.** Neutral drift is **inert** — at `n=6000` it barely moves (`H` stays at
+   `H*`). Yet the real VAE (green) collapsed to `H≈0`. **Sharpening (`τ=0.8`) reproduces the
+   collapse.** Neutral drift is *falsified*; the estimator's mode-competition is required.
+2. **Support.** Neutral holds ~all 30 modes; sharpening → 1 mode, matching the VAE.
+
+**Bottom row — RNN regime (`n=200`, `K=256`), anti-collapse:**
+3. **Heterozygosity.** Neutral drift drives `H → 0`, but the real RNN (green) only *partially*
+   collapses (`H` floors at ~0.68). **Mutation `u=0.006` reproduces the floor.** The estimator here
+   *removes* collapse pressure.
+4. **Forward-KL.** Neutral diverges; smoothing plateaus. Honest caveat: uniform-mutation plateaus
+   *above* the RNN's KL (~5 vs ~2) — evidence the RNN's smoothing target is **truth-like, not
+   uniform** (a refinement for future work). The *sign* is unambiguous.
+
+### Takeaway
+Model collapse in real learners = **neutral drift ⊕ an architecture-specific estimator-bias
+operator that can point either way.** The histogram sits at the neutral null (`u=0, τ=1`); the VAE
+**sharpens** (adds collapse); the RNN/MLP **smooth** (add a diversity floor). This mechanistically
+explains the Layer-1.5 architecture-generality result and the softened neural `g*`, and develops
+the exact axis Riis (2026) names as future work ("different smoothing schemes… each induce their
+own fixed-point geometry… a natural direction for further work"). `u`/`τ` are calibrated from a
+single neural diagnostic and pinned in the configs. **Falsifier (not triggered):** if neutral drift
+had already reproduced the neural curves, the estimator axis would be superfluous — instead it fails
+in *both* regimes, oppositely.

results/kernel_smooth/manifest.json

@@ -0,0 +1,14 @@
+{
+  "experiment": "kernel_smooth",
+  "master_seed": 20260705,
+  "git_commit": "79bbc45f41822757e60d7f1994a82c5171a9e554",
+  "python": "3.14.5",
+  "libraries": {
+    "numpy": "2.5.0",
+    "scipy": "1.18.0",
+    "pandas": "3.0.3",
+    "pyarrow": "24.0.0"
+  },
+  "rows": 4848,
+  "results_sha256": "8e50c084f8b3ca707375e677a977c00ac36aa96b3363ebecefad2d96a9912f3f"
+}

results/kernel_smooth/resolved_config.yaml

@@ -0,0 +1,82 @@
+experiment: kernel_smooth
+seed: 20260705
+n_replicates: 24
+source_config:
+  experiment: kernel_smooth
+  kind: lineage
+  seed: 20260705
+  n_replicates: 24
+  truth:
+    K: 256
+    R: 1
+    tail: zipf
+    zipf_s: 1.3
+    tail_threshold: 0.001
+    init: truth
+  dynamics:
+    n: 200
+    grounding:
+      m: 0
+      policy: proportional
+    kernel:
+      reset: 0.0
+      temperature: 1.0
+      floor: 0.0
+  generations: 100
+  metrics:
+    kl_floor: 1.0e-09
+    support_eps: 1.0e-09
+  sweep:
+  - param: dynamics.kernel.reset
+    values:
+    - 0.0
+    - 0.006
+  output:
+    dir: results/kernel_smooth
+grid:
+- label:
+    reset: 0.0
+  lineage_cfg:
+    truth:
+      K: 256
+      R: 1
+      tail: zipf
+      zipf_s: 1.3
+      tail_threshold: 0.001
+      init: truth
+    dynamics:
+      n: 200
+      grounding:
+        m: 0
+        policy: proportional
+      kernel:
+        reset: 0.0
+        temperature: 1.0
+        floor: 0.0
+    generations: 100
+    metrics:
+      kl_floor: 1.0e-09
+      support_eps: 1.0e-09
+- label:
+    reset: 0.006
+  lineage_cfg:
+    truth:
+      K: 256
+      R: 1
+      tail: zipf
+      zipf_s: 1.3
+      tail_threshold: 0.001
+      init: truth
+    dynamics:
+      n: 200
+      grounding:
+        m: 0
+        policy: proportional
+      kernel:
+        reset: 0.006
+        temperature: 1.0
+        floor: 0.0
+    generations: 100
+    metrics:
+      kl_floor: 1.0e-09
+      support_eps: 1.0e-09

src/knowledge/config.py

@@ -11,6 +11,8 @@ from __future__ import annotations
 from dataclasses import dataclass, field, replace
 from typing import Any, Mapping, Optional
 
+from .kernel import LearningKernelCfg
+
 # Runtime-tunable knobs live here, defaults chosen to match the blueprint's illustrative
 # schema. Nothing here is a magic number buried in algorithm code.
 
@@ -61,6 +63,7 @@ class DynamicsCfg:
     grounding: GroundingCfg = field(default_factory=GroundingCfg)
     selection: SelectionCfg = field(default_factory=SelectionCfg)
     remint: RemintCfg = field(default_factory=RemintCfg)
+    kernel: LearningKernelCfg = field(default_factory=LearningKernelCfg)
 
 
 @dataclass(frozen=True)
@@ -89,6 +92,7 @@ class LineageCfg:
             grounding=_sub(dyn_raw.get("grounding", {}), GroundingCfg),
             selection=_sub(dyn_raw.get("selection", {}), SelectionCfg),
             remint=_sub(dyn_raw.get("remint", {}), RemintCfg),
+            kernel=_sub(dyn_raw.get("kernel", {}), LearningKernelCfg),
         )
         metrics = _sub(cfg.get("metrics", {}), MetricsCfg)
         return LineageCfg(

src/knowledge/kernel.py

@@ -0,0 +1,87 @@
+"""The learning kernel — the estimator/inductive-bias operator (Layer-1 extension).
+
+Neutral Wright-Fisher models the generational step as *resample and refit the raw empirical
+distribution* (``p_{t+1} = counts/n``). A real learner does not refit the raw histogram: it
+applies a **biased estimator** — it smooths (regularises toward a simpler distribution) and it
+can sharpen (concentrate mass, drop weakly-supported modes). Layer 1.5 measured exactly these
+biases: the RNN/MLP *over-smooth* (H resists collapse, spurious tail support stays alive), the
+VAE *self-reinforces* (accelerating collapse to a single mode). This module turns the refit into
+a parameterised kernel ``p_{t+1} = T_θ(counts/n)`` so the analytic core can reproduce those
+deviations — the axis Riis (2026) names as future work.
+
+Two population-genetics knobs, both reducing to the neutral null at their defaults:
+
+* **reset ``u``** — mutation toward a prior: ``p <- (1-u)·p + u·π``. Models smoothing /
+  regularisation. Gives a diversity floor (H stops collapsing to 0), keeps rare modes alive, and
+  softens the grounding threshold — the RNN/MLP signature.
+* **temperature ``τ`` + floor ``ε``** — sharpening / support pruning: ``p ∝ p^{1/τ}`` then drop
+  mass below ``ε``. Models the winner-take-all mode competition of a mode-dropping generator —
+  the VAE signature. ``τ<1`` sharpens (pro-collapse).
+
+Identity (``u=0, τ=1, ε=0``) recovers Layer 1 exactly, so the histogram bridge and every
+scientific-validation test are unchanged.
+"""
+
+from __future__ import annotations
+
+from dataclasses import dataclass
+
+import numpy as np
+
+
+@dataclass(frozen=True)
+class LearningKernelCfg:
+    """Estimator-bias knobs for the generational refit (all defaults = neutral Wright-Fisher).
+
+    Attributes:
+        reset (float): Mutation rate ``u`` toward the prior (smoothing). 0 = off.
+        temperature (float): Sharpening temperature ``τ`` (``p ∝ p^{1/τ}``); <1 sharpens
+            (mode competition), >1 flattens, 1 = off.
+        floor (float): Hard support threshold ``ε``: modes below it are dropped. 0 = off.
+        prior (str): Smoothing target for ``reset``: currently ``uniform``.
+    """
+
+    reset: float = 0.0
+    temperature: float = 1.0
+    floor: float = 0.0
+    prior: str = "uniform"
+
+    @property
+    def is_identity(self) -> bool:
+        """True when the kernel is the neutral refit (recovers Layer 1 exactly)."""
+        return self.reset == 0.0 and self.temperature == 1.0 and self.floor == 0.0
+
+
+def _prior_vector(kind: str, K: int) -> np.ndarray:
+    """Return the smoothing-target distribution of length ``K``."""
+    if kind == "uniform":
+        return np.full(K, 1.0 / K)
+    raise ValueError(f"unknown kernel prior {kind!r} (expected uniform)")
+
+
+def apply_kernel(p: np.ndarray, cfg: LearningKernelCfg) -> np.ndarray:
+    """Apply the estimator-bias kernel to a refit distribution.
+
+    Composition order: mutation toward the prior (keeps modes alive) -> sharpening (concentrates
+    mass) -> support floor (drops weak modes). Each step is a no-op at its default.
+
+    Args:
+        p (np.ndarray): The raw refit distribution ``counts/n`` (length ``K``, sums to 1).
+        cfg (LearningKernelCfg): The kernel knobs.
+
+    Returns:
+        np.ndarray: The estimator's distribution ``p_{t+1}`` (length ``K``, sums to 1).
+    """
+    p = np.asarray(p, dtype=float)
+    if cfg.is_identity:
+        return p
+    K = p.size
+    if cfg.reset > 0.0:                                   # mutation toward the prior (smoothing)
+        p = (1.0 - cfg.reset) * p + cfg.reset * _prior_vector(cfg.prior, K)
+    if cfg.temperature != 1.0:                            # sharpening / flattening
+        with np.errstate(divide="ignore"):
+            p = np.power(p, 1.0 / cfg.temperature)
+    if cfg.floor > 0.0:                                   # hard support pruning
+        p = np.where(p < cfg.floor, 0.0, p)
+    total = p.sum()
+    return p / total if total > 0 else np.full(K, 1.0 / K)

src/knowledge/lineage.py

@@ -66,6 +66,7 @@ def run_lineage(cfg: Mapping[str, Any] | LineageCfg, seed: int) -> pd.DataFrame:
         regions=regions,
         selection_mode=cfg.dynamics.selection.mode,
         novelty_alpha=cfg.dynamics.selection.novelty_alpha,
+        kernel=cfg.dynamics.kernel,
     )
     remint = cfg.dynamics.remint
 

src/knowledge/step.py

@@ -7,10 +7,12 @@ in the perspective paper is one operator here; they compose in the order below.
 
 from __future__ import annotations
 
-from dataclasses import dataclass
+from dataclasses import dataclass, field
 
 import numpy as np
 
+from .kernel import LearningKernelCfg, apply_kernel
+
 
 @dataclass(frozen=True)
 class StepCtx:
@@ -24,6 +26,8 @@ class StepCtx:
         regions (np.ndarray): Length-K region index per item.
         selection_mode (str): ``none`` | ``greedy`` | ``qd``.
         novelty_alpha (float): QD novelty exponent (0 recovers greedy).
+        kernel (LearningKernelCfg): Estimator-bias kernel applied to the refit (default
+            identity = neutral Wright-Fisher).
     """
 
     n: int
@@ -32,6 +36,7 @@ class StepCtx:
     regions: np.ndarray
     selection_mode: str = "none"
     novelty_alpha: float = 0.0
+    kernel: LearningKernelCfg = field(default_factory=LearningKernelCfg)
 
 
 def _normed(p: np.ndarray) -> np.ndarray:
@@ -166,6 +171,7 @@ def generation_step(teachers: list[np.ndarray], p_star_eff: np.ndarray,
                                     cfg.regions, cfg.policy, rng)
     counts = c_syn + c_real
     p_next = counts / counts.sum()
+    p_next = apply_kernel(p_next, cfg.kernel)                      # (estimator bias)
     p_next = apply_selection(p_next, p_star_eff,                   # (selection)
                              cfg.selection_mode, cfg.novelty_alpha)
     return p_next

tasks/todo.md

@@ -245,8 +245,33 @@ C3 vertical claim deferred.*
   confirmed on real images. VAE needs ~10% grounding vs synthetic ~5% (cf. the `grounding` finding).
   **99 tests green** (+5 torchvision-gated). `make mnist` / `make env-mnist` (kept out of `make neural`).
 
+**2026-07-05 — learning kernel (Layer-1 extension) + Riis positioning.**
+
+- Prompted by revisiting Layer 1 vs 1.5 and the Riis 2026 paper (arXiv:2604.08554). Added
+  `knowledge/kernel.py` (`LearningKernelCfg`: reset `u` = smoothing, temperature `τ` = sharpening,
+  floor `ε`), wired into `step.generation_step` (post-refit) / `StepCtx` / `DynamicsCfg` — **identity
+  by default, so the 68 Layer-1 scientific-validation + correctness tests are unchanged.**
+- **Result:** neutral Wright–Fisher fails BOTH neural models, oppositely. VAE regime (n=6000,K=30):
+  neutral is inert, sharpening `τ=0.8` reproduces the collapse-to-one-mode. RNN regime (n=200,K=256):
+  neutral → H=0, mutation `u=0.006` reproduces the H-floor (~0.68). Uniform-mutation overshoots the
+  RNN's KL → its prior is truth-like, not uniform (honest caveat, future refinement).
+- `configs/layer1/kernel_{sharpen,smooth}.yaml`, `figures/plot_kernel.py` (overlays analytic arms vs
+  the committed neural endpoints), READMEs, `tests/test_kernel.py` (+6). Wired into `make layer1`.
+- **Strategic (see CLAUDE.md finding):** concede "collapse=drift" to Riis (prior art; cite); his
+  mixed environment retains OLD SYNTHETIC (no real-data injection) → pessimistic, no g* that prevents
+  collapse. Our defensible novelty: recombination "merge-don't-average" (flagship), the learning-kernel
+  axis (he flags as future work), grounding-as-immigration, real-weights+MNIST breadth, and the
+  Lamarckian society + vertical/cumulative C3 claim (not yet run). Reposition: from "collapse is drift"
+  to a population-genetic CONTROL THEORY for sustaining open-ended knowledge.
+
 ## Remaining (all optional)
 
+- [ ] **Learning-kernel refinement:** truth-like smoothing prior (`prior="truth"`) + measurement floor
+  for a quantitative RNN match; **multi-locus / linkage** modes (class×style) as the rigorous home for
+  recombination. Both enrich predictive power and separate us further from Riis's single-locus n-grams.
+- [ ] **The Lamarckian society experiments** (multi-agent grounding + decorrelated specialists +
+  recombination + QD-selection + re-mint) and the **vertical/cumulative C3 claim** — the highest-ceiling,
+  wholly-novel frame; not yet entered.
 - [ ] **`region_matched`** grounding (R>1), **`remint`** re-mint gate (optional).
 - [ ] **VAE fidelity:** fix the prior-hole mismatch (KL-annealing / free-bits / larger latent) so it
   clears the gen-0 gate, then add to `architectures`. Or document as a known limitation.

tests/test_kernel.py

@@ -0,0 +1,72 @@
+"""Learning-kernel tests (pure NumPy).
+
+The kernel is an additive Layer-1 extension: identity by default (so the neutral Wright-Fisher
+core and every scientific-validation test are unchanged), a sharpening knob that ADDS collapse
+where neutral drift is inert, and a smoothing knob that supplies a diversity FLOOR where neutral
+drift would collapse to zero. These assert exactly those three behaviours.
+"""
+
+from __future__ import annotations
+
+import numpy as np
+
+from knowledge.kernel import LearningKernelCfg, apply_kernel
+from knowledge.lineage import run_lineage
+from knowledge.metrics import heterozygosity
+
+
+def test_apply_kernel_identity_is_noop():
+    p = np.array([0.5, 0.3, 0.15, 0.05])
+    assert np.array_equal(apply_kernel(p, LearningKernelCfg()), p)
+
+
+def test_apply_kernel_reset_mixes_toward_uniform():
+    p = np.array([1.0, 0.0, 0.0, 0.0])
+    out = apply_kernel(p, LearningKernelCfg(reset=0.2))
+    assert np.isclose(out.sum(), 1.0)
+    assert np.allclose(out, [0.8 + 0.2 / 4, 0.05, 0.05, 0.05])   # keeps dead modes alive
+    assert (out > 0).all()
+
+
+def test_apply_kernel_sharpen_and_floor_prune():
+    p = np.array([0.6, 0.3, 0.09, 0.01])
+    sharp = apply_kernel(p, LearningKernelCfg(temperature=0.5))    # p^2, renormalised
+    assert sharp[0] > p[0] and sharp[-1] < p[-1]                   # mass concentrates
+    floored = apply_kernel(p, LearningKernelCfg(floor=0.05))
+    assert floored[-1] == 0.0 and np.isclose(floored.sum(), 1.0)   # weak mode dropped
+
+
+def test_kernel_identity_leaves_lineage_unchanged():
+    base = {"truth": {"K": 64, "init": "truth"}, "dynamics": {"n": 200},
+            "generations": 20, "metrics": {"kl_floor": 1e-9, "support_eps": 1e-9}}
+    withk = {**base, "dynamics": {"n": 200, "kernel": {"reset": 0.0, "temperature": 1.0}}}
+    a = run_lineage(base, seed=3)["heterozygosity"].to_numpy()
+    b = run_lineage(withk, seed=3)["heterozygosity"].to_numpy()
+    assert np.array_equal(a, b)          # identity kernel == neutral Wright-Fisher, bitwise
+
+
+def test_sharpening_adds_collapse_where_neutral_is_inert():
+    # Large n vs small K: neutral drift barely collapses; sharpening drives it to ~1 mode.
+    cfg = {"truth": {"K": 30, "tail": "zipf", "zipf_s": 1.5, "tail_threshold": 1e-2,
+                     "init": "truth"},
+           "dynamics": {"n": 6000, "grounding": {"m": 0}},
+           "generations": 15, "metrics": {"kl_floor": 1e-9, "support_eps": 1e-9}}
+    neutral = run_lineage(cfg, seed=0)
+    sharp = run_lineage({**cfg, "dynamics": {**cfg["dynamics"],
+                                             "kernel": {"temperature": 0.8}}}, seed=0)
+    assert neutral["support_size"].iloc[-1] > 20          # neutral: ~all modes survive
+    assert sharp["support_size"].iloc[-1] <= 3            # sharpening: collapse to a point
+    assert sharp["heterozygosity"].iloc[-1] < 0.1
+
+
+def test_smoothing_floors_diversity_where_neutral_collapses():
+    # Small n vs large K: neutral drift drives H toward 0; smoothing holds a positive floor.
+    cfg = {"truth": {"K": 256, "tail": "zipf", "zipf_s": 1.3, "tail_threshold": 1e-3,
+                     "init": "truth"},
+           "dynamics": {"n": 200, "grounding": {"m": 0}},
+           "generations": 120, "metrics": {"kl_floor": 1e-9, "support_eps": 1e-9}}
+    neutral = run_lineage(cfg, seed=0)
+    smooth = run_lineage({**cfg, "dynamics": {**cfg["dynamics"],
+                                              "kernel": {"reset": 0.006}}}, seed=0)
+    assert neutral["heterozygosity"].iloc[-1] < 0.4      # neutral collapses
+    assert smooth["heterozygosity"].iloc[-1] > 0.55      # smoothing floors H well above neutral