{
  "slug": "2026-09-09-molecular-proofreading",
  "published_activity_data": {
    "measurements": 317,
    "unique_groups": 213,
    "excluded_footer_rows": [
      319,
      320,
      321,
      322,
      323,
      324,
      325,
      326,
      327,
      328,
      329,
      330
    ],
    "original_text_values_checked": 317,
    "source_interval_flags": [
      3,
      4,
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    ],
    "original2018_cells_matching_reformatted": 2219,
    "descriptive_spearman_mu_inverse_copy": 0.47360190791728546,
    "limits": "Original2018 table compared to2026 reformatted table, not new experiments or raw colony counts. Each variant receives one arithmetic-mean marker; repetitions include different occasions and some after90generations. Means are descriptive, not pooled confidence intervals or independent random samples. Some supplied confidence intervals do not contain their estimates; retained and flagged, never silently swapped or used as valid error bars. mu already divides by measured copy number; mu*C changes the estimand, does not remove all confounding and cannot disprove stalling. No sequence-level data republished."
  },
  "published_mismatch_kinetics": {
    "source": "Baranovskiy2022 Table2, all displayed values",
    "rows": [
      {
        "primer_end": "G-C",
        "kpol_per_s": 18.7,
        "kpol_SD": 0.41,
        "KD_mM": 0.218,
        "KD_SD_mM": 0.017,
        "efficiency_per_mM_s": 85.77981651376146,
        "kobs_at_0p05mM_per_s": 3.4888059701492535,
        "catalysis_slowdown": 1.0,
        "low_concentration_efficiency_ratio": 1.0,
        "slowdown_at_0p05mM": 1.0
      },
      {
        "primer_end": "T-C",
        "kpol_per_s": 0.492,
        "kpol_SD": 0.015,
        "KD_mM": 1.43,
        "KD_SD_mM": 0.14,
        "efficiency_per_mM_s": 0.3440559440559441,
        "kobs_at_0p05mM_per_s": 0.016621621621621622,
        "catalysis_slowdown": 38.00813008130081,
        "low_concentration_efficiency_ratio": 249.31938539568878,
        "slowdown_at_0p05mM": 209.89564373255672
      },
      {
        "primer_end": "T-G",
        "kpol_per_s": 1.74,
        "kpol_SD": 0.062,
        "KD_mM": 0.732,
        "KD_SD_mM": 0.088,
        "efficiency_per_mM_s": 2.377049180327869,
        "kobs_at_0p05mM_per_s": 0.11125319693094629,
        "catalysis_slowdown": 10.74712643678161,
        "low_concentration_efficiency_ratio": 36.08668142992723,
        "slowdown_at_0p05mM": 31.35915251329559
      }
    ],
    "reference_substrate_mM": 0.05,
    "limits": "Only displayed parameter means recomputed, no raw kinetic fit, no covariance available for ratio CI. Polalpha lacks intrinsic proofreading. The main paper rounds rates to3.5/.017 and reports206, whereas directly using the displayed parameters gives the stored ratio. No claim to reproduce the exact unrounded source fit."
  },
  "restart_model": {
    "parameters": {
      "initial_error": 0.05,
      "insertion_time": 1,
      "excision_time": 2,
      "right_extension_rate": 1,
      "right_excision_fraction": 0.01
    },
    "examples": [
      {
        "wrong_extension_rate": 0.001,
        "correction_rate": 0.0,
        "initial_error_probability": 0.05,
        "mean_completion_time": 51.95,
        "final_error_probability": 0.05,
        "expected_rejected_incorporations": 0.0,
        "activated_monomers_per_completion": 1.0,
        "completed_by_time10": 0.9499735292750612
      },
      {
        "wrong_extension_rate": 0.001,
        "correction_rate": 0.1,
        "initial_error_probability": 0.05,
        "mean_completion_time": 2.6802371457098197,
        "final_error_probability": 0.0005213538951281796,
        "expected_rejected_incorporations": 0.053134868158922835,
        "activated_monomers_per_completion": 1.0531348681589228,
        "completed_by_time10": 0.9679064609713355
      },
      {
        "wrong_extension_rate": 0.001,
        "correction_rate": 1.0,
        "initial_error_probability": 0.05,
        "mean_completion_time": 2.242353184882658,
        "final_error_probability": 5.310196997793378e-05,
        "expected_rejected_incorporations": 0.063101438958234,
        "activated_monomers_per_completion": 1.063101438958234,
        "completed_by_time10": 0.9929483252401958
      },
      {
        "wrong_extension_rate": 0.001,
        "correction_rate": 100.0,
        "initial_error_probability": 0.05,
        "mean_completion_time": 5.316834392883027,
        "final_error_probability": 1.0526199447269267e-06,
        "expected_rejected_incorporations": 1.105260941852748,
        "activated_monomers_per_completion": 2.105260941852748,
        "completed_by_time10": 0.8374508402043873
      },
      {
        "wrong_extension_rate": 1.0,
        "correction_rate": 0.0,
        "initial_error_probability": 0.05,
        "mean_completion_time": 2.0,
        "final_error_probability": 0.05,
        "expected_rejected_incorporations": 0.0,
        "activated_monomers_per_completion": 1.0,
        "completed_by_time10": 0.9995006007726127
      },
      {
        "wrong_extension_rate": 1.0,
        "correction_rate": 0.1,
        "initial_error_probability": 0.05,
        "mean_completion_time": 2.016574585635359,
        "final_error_probability": 0.045705675539929685,
        "expected_rejected_incorporations": 0.005524861878453039,
        "activated_monomers_per_completion": 1.0055248618784531,
        "completed_by_time10": 0.9990362344140709
      },
      {
        "wrong_extension_rate": 1.0,
        "correction_rate": 1.0,
        "initial_error_probability": 0.05,
        "mean_completion_time": 2.1068956677774926,
        "final_error_probability": 0.02589079723147911,
        "expected_rejected_incorporations": 0.03563188925916432,
        "activated_monomers_per_completion": 1.0356318892591643,
        "completed_by_time10": 0.9967597348191413
      },
      {
        "wrong_extension_rate": 1.0,
        "correction_rate": 100.0,
        "initial_error_probability": 0.05,
        "mean_completion_time": 5.309213951067153,
        "final_error_probability": 0.001041124414367517,
        "expected_rejected_incorporations": 1.1030713170223843,
        "activated_monomers_per_completion": 2.1030713170223843,
        "completed_by_time10": 0.8378203473154163
      }
    ],
    "checks": "All644cases compared renewal equations with independent4state absorbing CTMC mean, splitting probability, expected resets and finite-time survival.",
    "limits": "Chosen parameters, no biological calibration. Excised bases must be replaced and correct bases can be excised. Rate races use1/(forward+excision), not branch-conditioned1/rate. Fuel count assumes one activated monomer per incorporation attempt; not measured ATP burn, entropy production, natural selection simulation, or enzyme-design recommendation."
  },
  "shared_denominator": {
    "purpose": "Algebraic counterexample to treating a shared denominator correlation as unique evidence for stalling. Not a generative model or reanalysis of the actual full experimental noise.",
    "chosen_numerator": 1e-06,
    "copy_range": [
      5,
      150
    ],
    "limits": "Correct exposure normalization is necessary and is not itself a statistical mistake. This example does not show that the actual association is entirely artifactual."
  }
}