The isChemist Protocol

Preamble: A Stance on the Central Science

The ancient Greeks had a word: logos. It signifies not just "word" or "reason," but the intelligible, underlying principle of the cosmos. The Enlightenment was a project to apply this principle—to replace dogma with verifiable truth and superstition with structured inquiry.

Chemistry is the central science, the bridge between the quantum world of physics and the emergent complexity of biology. It is uniquely positioned to understand and manipulate the logos of matter itself.

Yet, modern science is beset by a crisis of its own making: a focus on the symbols of progress (publications, metrics) over the substance of truth. We face a reproducibility crisis, perverse incentives, and a deluge of low-signal work. This is a new scholasticism, a retreat from the Enlightenment's core mandate.

The isChemist Protocol is a stance against this. It is a commitment to a set of principles for conducting research and building tools in a way that is legible, durable, and true to the logos. It is a personal and professional standard for those who seek to build, not merely to publish.

Principle I: Verifiable Truth

All scientific artifacts—figures, tables, and analyses—must be generated by a single, executable script that runs directly on the ground-truth data.

1. No manual intervention. There will be NO manual editing of figures in Illustrator. NO copying and pasting of data into Excel. The path from raw computational output or experimental data to final publication-ready asset must be fully automated and auditable.
2. Open code, open data. All code used for analysis is to be open-sourced. Wherever possible, the raw data it operates on should be made available in a public repository.
3. Environment as code. Full reproducibility requires a defined environment. Projects must use a dependency management system (e.g., pyproject.toml, pnpm-lock.yaml) and, for complex systems, containerization (e.g., Docker) to ensure that the analysis can be rerun by anyone, anywhere, at any time.

Principle II: Enduring Utility

Our work must result in an artifact that has intrinsic, enduring value outside the context of academic publishing. This artifact is the source of truth. The paper is its manifest.

1. The artifact is the end. The primary output of our work is a durable artifact. This can be:
   • A software tool: A piece of well-engineered code that solves a real problem for others.
   • A body of verifiable knowledge: A foundational insight, a new dataset, or a definitive negative result, all produced by a fully auditable and reproducible process as mandated by Principle I.
2. The paper is a pointer. The paper is not the artifact. It is a human-readable document that describes the artifact, explains its significance, and points to its canonical location (e.g., a code repository, a data archive). Its purpose is dissemination and context, not self-justification.
3. Demonstrated value precedes publication. We do not produce an artifact in order to write a paper. We write a paper because we have produced an artifact of demonstrated value. For a tool, this means it has users or a clear, validated use case. For knowledge, this means it is sufficiently robust and significant to serve as a reliable foundation for future work. The act of publishing is the final step of sharing a completed work, not the goal of the work itself.

Principle III: Agentic Inquiry

This principle defines the character of the agent. It is a framework for navigating the scientific world with purpose and integrity, grounded in the belief that the individual is the ultimate locus of discovery.

1. Assume good faith. We engage with the ideas of others from a position of intellectual charity. We critique the work, not the person. We seek to understand before we seek to be understood. This is the bedrock of productive scientific discourse.
2. Internal locus of responsibility. You are the architect of your work. The pursuit of knowledge is an act of personal agency, not of passive compliance. A mentor's role is to sharpen your mind, not to direct your hands. The responsibility for the quality and integrity of your work is yours alone.
3. Principled dissent from convention. We recognize that systemic incentives may diverge from the path of genuine discovery. Where convention conflicts with the principles of this protocol, we adhere to the protocol. Our work is judged against the enduring standards of verifiable truth and utility, not the transient metrics of a flawed system. We build what is right, not what is merely rewarded.
4. Commitment to the logos. Our work builds upon the axiom that an objective reality exists and is knowable. We therefore produce auditable, verifiable models and maps of that reality, not self-contained rhetorical artifacts.

Engineering Principles

Inspired by the pragmatism of John Carmack and the directness of George Hotz.

• Code is a liability, not an asset. Every line you write is a maintenance burden. The best code is no code. The second best is simple, obvious code that you can delete without fear.
• Clarity is king. Explicit is better than implicit. A newcomer should be able to trace the data flow without a debugger. Avoid magic. Favor simple functions and clear data structures.
• Data shapes code. The quality of your code is downstream of the quality of your data structures. Get the data right first. Think in terms of transformations on immutable data.
• Ship, measure, iterate. A working v1 in the hands of users is infinitely more valuable than a perfect v2 that exists only in your head. We build robust systems that allow for rapid, safe iteration.

Project Index

The following works resulted from adhering to the isChemist Protocol.

Adoption

Projects adhering to this protocol should include the following badge in their README.md:

[![isChemist Protocol v1.0.0](https://img.shields.io/badge/protocol-isChemist%20v1.0.0-blueviolet)](https://github.com/ischemist/protocol)