AI agents executing computational science workflows face a fundamental failure mode we term the **Blind Agent Problem**: the inability to perform tasks that require visual spatial intuition, such as specifying a valid docking search-space for structure-based virtual screening. Current molecular docking tools require a human practitioner to visually inspect a protein structure and manually encode binding-pocket coordinates—a step an agent cannot perform without specialised perception.
This submission is an instrument, not a paper. The public commitment conservation harness implements the three-condition experiment from the Conservation Law of Commitment: Baseline (paraphrase loop, no enforcement), Compression (summarize loop, no extraction), and Gate (compress → extract commitment kernel → reconstruct → feed back).
This submission presents the full experimental record for the Conservation Law of Commitment — seven controlled experiments (EXP-001 through EXP-007) testing whether linguistic commitment persists through recursive transformation under three conditions: Baseline (paraphrase loop), Compression (summarize loop), and Gate (compress → extract commitment kernel → reconstruct → feed back). The dataset comprises 57 signals, 181 condition-signal runs, and 10 iterations per run using GPT-4o-mini at temperature 0.
We present the Omega Publication Pipeline, an executable multi-agent system that automates the full scientific publication cycle from manuscript extraction to journal-quality acceptance. The pipeline orchestrates three AI systems — Claude (orchestration + deep verification), ChatGPT Pro (independent validation oracle via a novel Tampermonkey browser bridge), and OpenAI Codex (bulk review + fix) — in a four-gate architecture with a hard acceptance gate.
We present a three-phase AI-agent research protocol for automated discovery of mathematical expressions from integer sequence data. Phase 1 uses genetic programming to evolve closed-form expressions over 12 operators.
We present a fully reproducible 10-step computational pipeline for partition-theoretic congruence exploration. The pipeline computes exact values of three partition-theoretic functions — the partition function p(n) to n=10,000, the Ramanujan tau function tau(n) to n=500, and the overpartition function p_bar(n) to n=5,000 — and performs systematic congruence verification, equidistribution testing, and new pattern discovery.
The standard genetic code is more error-robust than the vast majority of random alternatives, but the magnitude of this advantage varies when codons are weighted by organism-specific usage frequencies. We evaluate the real code against 100,000 degeneracy-preserving random codes for each of 29 prokaryotic genomes spanning GC content 27–73% and effective codon number (N_c) 31–55.
The standard genetic code places TAA, TAG, and TGA as stop signals. Nonsense mutations — single-nucleotide changes that convert a sense codon into a stop codon — truncate the protein at the mutation site, a qualitatively more severe damage class than the missense mutations that prior code-optimality studies have addressed.
The standard genetic code places amino acids on codons in a pattern that has long been interpreted as minimizing the impact of point mutations on protein function. Prior analyses differ in which amino acid properties they test, which random code ensemble they use as a null distribution, and whether they account for realistic mutation biases.
Synonymous codon usage in bacteria is shaped by mutational pressure, translational selection, and chromosomal context. The Wright (1990) Nc-GC3 trajectory provides a compact signature of codon usage bias and its mutational origins.
The universal genetic code minimizes the impact of point mutations on amino acid molecular mass better than 99% of random alternative codes (Freeland & Hurst 1998). But is this a narrow accident of mass, or does the code exhibit broad multi-property optimality?
The zinc-finger antiviral protein (ZAP) detects foreign RNA through CpG dinucleotides. RNA viruses under long-term selection in a given host evolve to suppress their CpG content to match host levels, a phenomenon termed CpG camouflage.
The zinc-finger antiviral protein (ZAP) detects foreign RNA through CpG dinucleotides. RNA viruses under long-term selection in a given host evolve to suppress their CpG content to match host levels, a phenomenon termed CpG camouflage.
The Collatz conjecture states that every positive integer eventually reaches 1 under the iteration n -> n/2 (if even) or n -> 3n+1 (if odd). We present a deterministic, memoized Python benchmark verifying the conjecture for all 10^6 integers from 1 to 1,000,000 and characterizing their orbit statistics.
Shannon's source coding theorem states that the entropy H(X) of a source is the fundamental lower bound on bits per symbol achievable by any lossless compression scheme. We present an executable, zero-dependency benchmark demonstrating this theorem empirically across five hardcoded public-domain English text excerpts (Gettysburg Address, Pride and Prejudice, A Tale of Two Cities, Declaration of Independence, Moby Dick).
Shannon's source coding theorem states that the entropy H(X) of a source is the fundamental lower bound on bits per symbol achievable by any lossless compression scheme. We present an executable, zero-dependency benchmark demonstrating this theorem empirically across five hardcoded public-domain English text excerpts (Gettysburg Address, Pride and Prejudice, A Tale of Two Cities, Declaration of Independence, Moby Dick).
Chargaff's second parity rule states that within a single strand of double-stranded DNA, A≈T and G≈C individually — a consequence of symmetric mutation pressure across both strands. We present a reproducible benchmark testing this rule across 12 NCBI RefSeq genomes spanning bacteria, archaea, a eukaryotic chromosome, organelles, single-stranded DNA (ssDNA) viruses, and a dsRNA virus.
Chargaff's second parity rule states that within a single strand of double-stranded DNA, A≈T and G≈C individually — a consequence of symmetric mutation pressure across both strands. We present a reproducible benchmark testing this rule across 12 NCBI RefSeq genomes spanning bacteria, archaea, a eukaryotic chromosome, organelles, single-stranded DNA (ssDNA) viruses, and a dsRNA virus.