zax.doi.bio/

About the Zax Institute

• Founder & Convener: Steven Randolph Ness
• Informal, unincorporated think‑tank backed by Zax Analytics
• Brings together structural biologists, computational scientists, theoreticians & curious learners
• Low overhead, high intellectual generosity; attribution is opt‑in

What We Do

• Pre‑publication sharing of papers, code snippets & prototype tools (AlphaFold, ESM, latent diffusion)
• Twice‑yearly “cognitive hackathons” producing GPU‑accelerated docking servers, novel assays & FAIR‑data workflows
• Monthly Fireside Seminars on topics from NP‑hard complexity in protein design to philosophy of science
• Mentorship via programs like How to Grow Almost Anything, guiding biohackers & student teams

Why It Matters

• Elevates structural biology (“form informs function”) alongside genomics
• Fosters open, cross‑disciplinary dialogue free from institutional red tape
• Enables seasoned experts to collaborate, innovate & mentor in a trusted, anonymous network

Join Us

• Public Discord (read‑only access for newcomers)
• Weekly email digest of highlights & upcoming events
• Invite‑a‑friend sponsorship to grow our diverse community

Passionate about proteins, puzzles or philosophy of science? Let’s connect!

Join Zax Discord

The Zax Institute — “a republic of curiosity, unconstrained by walls”

“Knowledge exists to be imparted.” — Ralph Waldo Emerson

The Zax Institute began with a simple problem: what do you do when leaving a well‑funded industrial research post does not diminish your hunger for discovery, yet traditional academic positions feel incompatible with your health, your schedule, or your preference for autonomy? Steven Randolph Ness answered by gathering long‑time collaborators—protein crystallographers from the early AutoDock era, computational theorists who cut their teeth on P ≠ NP, philosophers of science who read Kuhn by candlelight—into a distributed salon for idea exchange. The only membership fee is curiosity, the only dress code is respect.

“The scientist is not a person who gives the right answers. He’s one who asks the right questions.” — Claude Lévi‑Strauss

1. Our Ethos

• Radical Openness — We disseminate pre‑publication notebooks, datasets, and GPU Docker stacks because, recalling Louis Pasteur, “science knows no country.”
• Structural‑First Biology — Where funding cycles rush to Genomics 3.0, we proclaim Rosalind Franklin’s unspoken corollary: form illuminates function.
• Cross‑Disciplinary Pollination — A single Slack thread can drift from AlphaFold 3 contact‑map noise to Gödelian undecidability, echoing Richard Feynman’s conviction that “nature uses only the longest threads…”
• Anonymity as Freedom — Many contributors remain pseudonymous—Panthera, a senior pharma crystallographer; Birdo, an extremal‑combinatorics postdoc—so they may “speak what they think” (after Virginia Woolf) without institutional repercussion.
• Mentorship in Perpetuity — We re‑invest experience into programs like How to Grow Almost Anything because, as Maria Mitchell wrote in 1871, “we especially need imagination in science. It is not all mathematics, nor all logic, but it is somewhat beauty and poetry.”

2. What We Actually Do

• Literature Lightning‑Rounds

• Weekly Discord voice sessions where participants summarize one recent preprint in <5 minutes. “If you can’t explain it simply, you don’t understand it well enough.” — Albert Einstein

• Cognitive Hackathons (2× per year)

• 48‑hour sprints have birthed:

  • PlinderP - Collections of the abstracts and full text scientific papers associate with Plinder entries
  • CancerAI - Award winning project of the Cohere Hackathon
  • Infinite Purrfection - Award winning project of the Rhymesai hackathon

• Fireside Seminars (monthly)

• A 20‑minute primer (e.g., “Subset‑sum shadows in protein design”) followed by Socratic Q\&A. Karl Popper’s rule applies: “Our theories die in our stead.”

• Collaborative Preprint Sprints

• Ad‑hoc writing crews assemble in Overleaf; authorship order equals alphabetical order, because we heed Buckminster Fuller: “If you want to teach people a new way of thinking, don’t lecture—give them a tool.”

• ai.doi.bio Project

• An open‑markdown graph of structural papers linked to an in‑browser Mol* viewer. Alan Turing once dreamt of “machines that learn”; we add: machines that cite.

3. Research Vistas We’re Exploring

• Post‑AlphaFold Validation — How stable are transformer hallucinations at the bench? We echo Peter Medawar’s caution: “Theories are nets; only he who casts will catch.”
• Latent Diffusion for Macromolecular Conformations — Inspired by Claude Shannon’s channel capacity, we ask how many bits encode an allosteric landscape.
• P ≠ NP and Bio‑Designability — Might NP‑hard motifs in sequence space explain evolutionary bottlenecks? Donald Knuth reminds us: “Science is knowledge which we understand so well we can teach it to a computer.”
• Philosophy of Explanation — Reading Ian Hacking on “styles of reasoning,” we examine why protein‑folding narratives feel teleological—and how to avoid that trap.

4. Culture & Community

• Trust Via Craft — Code reviews double as social glue; your credibility is your pull‑request history.
• Diversity of Experience — Members span retirees from Vertex Pharmaceuticals, seasoned x-ray crystallographers, macromolecular methods developers to early‑career indie hackers in Lahore; we embody Jane Goodall’s plea: “What you do makes a difference, and you have to decide what kind of difference you want to make.”
• Playful Seriousness — Discord memes about Schrödinger’s ligand pepper long debates on Steven’s favorite koan: “Is rational number‑only physics plausible?” Katherine Johnson guides us: “Like what you do, and then you will do your best.”

5. Infrastructure & Support

• Funding — Core cloud credits and domain costs are underwritten by Zax Analytics, the data‑science firm founded by Steven’s wife.
• Legal Simplicity — We remain an unincorporated association; should grants require paperwork, we partner with fiscal sponsors. Henry David Thoreau: “Simplify, simplify.”
• Ethical Covenant — Default license GPLv3 + CC‑BY‑4.0; dual‑use discussions invoke Asilomar guidelines. We keep Margaret Mead’s reminder taped inside our Notion wiki: “Never doubt that a small group of thoughtful, committed citizens can change the world.”

6. How to Engage

• Grab a Seat in Discord

• First month read‑only; afterwards you can post.

• Subscribe to the Weekly Digest

• Perfect for colleagues who “don’t Discord.”

• Bring a Puzzle

• Code, data, philosophical thorn—anything that feeds the collective mind.

• Conference Badges

• Spot Steven wearing the green “Zax Institute” ribbon at ICML, NeurIPS, or ACS; conversation is collaboration’s seed.

“We are like dwarfs sitting on the shoulders of giants, so that we can see more than they.” — Bernard of Chartres

7. Closing Invitation

If you sense, as Carl Sagan did, that “somewhere, something incredible is waiting to be known,” yet you also feel that traditional silos have grown too narrow, you belong at the Zax Institute. Come share your half‑formed idea, your long‑formed skepticism, your pythonic daydream. Here, you’ll find peers who know that serious play is the shortest path to serious progress—and who cherish, above all, the privilege of thinking together.

Below is a draft “Philosophy” section for your site that weaves in Proudhon, Bakunin and Kropotkin’s key insights with the mission of the Zax Institute. Feel free to adapt the headings or tone to fit your design and audience.

Our Philosophical Roots

Since its founding, the Zax Institute has been guided by the conviction that knowledge advances fastest when barriers to sharing fall away, and when every contributor brings their full creativity to the table. This spirit echoes three 19th-century thinkers who first showed how radical decentralization and mutual aid could transform society:

Pierre-Joseph Proudhon (1809–1865)

– Proudhon coined the term “anarchism” and argued that true freedom arises when individuals and communities federate on the basis of mutual credit and voluntary cooperation. – At Zax, we mirror his idea of a “People’s Bank” by creating an open‐access repository of scientific data and models, where AI agents and researchers equally draw upon—and contribute to—a shared knowledge commons.

Mikhail Bakunin (1814–1876)

– Bakunin insisted on smashing every hierarchical barrier—from state bureaucracies to entrenched academic silos—and replacing them with bottom-up federations of self-organizing groups. – Likewise, our platform invites researchers, coders, and domain experts to form affinity clusters around topics (e.g. protein docking, molecular dynamics), each with the autonomy to innovate yet connected through our federated API layer.

Peter Kropotkin (1842–1921)

– Through his ethnographic work and The Conquest of Bread, Kropotkin showed that mutual aid is as natural to life (in biology and human societies) as competition. – At Zax, this translates into AI-facilitated collaboration: agents propose experiments, human experts refine them, and results feed back into the system—creating a self-reinforcing cycle of shared discovery that embodies “from each according to ability, to each according to need.”

What This Means for You

1. Decentralized Knowledge Networks Every dataset, model, or protocol can be forked, improved, and re-published—no gatekeepers, only peer-driven quality control.

2. Mutual-Aid Workflows When you submit a docking result or a novel lemma, the community (and our AI assistants) immediately build on it—no more reinventing the wheel, only amplifying your insight.

3. Federated Trust and Governance Inspired by Proudhon’s recallable delegates, we’re experimenting with transparent, reputation-based roles instead of fixed editorial boards, so the people doing the work shape its direction.

4. Prefigurative Research Just as Kropotkin urged building the future in the shell of the old, Zax hosts live “lab-in-canvas” sessions where you can prototype ideas with AI in real time—prefiguring the fully decentralized science ecosystem we all seek.

Contact

• Website: zax.doi.bio
• General inquiries: sness@sness.net
• Discord invite: email us “Let me in” with a one‑sentence bio.

“The future is already here—it’s just not evenly distributed.” — William Gibson Help us redistribute it.

<<<<<<< HEAD:index.md [I[O You can see some of our history in hackathons at the BiologyAI Discord Server (mail me for an invite when this expires)

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