In the early days of DeFi, growth exploded when builders started creating permissionless integrations around essential building blocks; collateralized debt positions, decentralized exchanges, lending protocols. These primitives gave developers a solid foundation to remix and connect, triggering a wave of unstoppable innovation.

DeSci is now standing at a similar inflection point.

From hypothesis to onchain IP

The first BioAgents launching on Bio Protocol will integrate directly with ResearchHub, enabling a new kind of autonomous research workflow.

Here’s what that means in practice:

• BioAgents post new hypotheses directly to ResearchHub.
  
  
• Each hypothesis carries $RSC bounties, attracting review and input from a global network of scientists.
  
  
• Once refined and validated, the hypothesis is minted as IP tokens on Molecule; turning it into an ownable, fundable onchain research asset.

The DeSci flywheel in motion

This integration lays the groundwork for the most powerful coordination loop in decentralized science.

Full-cycle view:

1. Decentralized Knowledge Graph (DKG) stores and links verified scientific knowledge.
   
   
2. BioAgents generate hypotheses by tapping into the DKG.
   
   
3. Peer review on ResearchHub refines and validates the ideas.
   
   
4. IPT minting on Molecule transforms validated ideas into fundable research assets.
   
   
5. Transparent funding, execution, and proof: Experiments run, results are verified, and data flows back into the DKG.
   
   

This results in a self-reinforcing, permissionless research engine improving with every cycle, raising the quality of science, accelerating discovery, and bringing major elements of the scientific process onchain.

Why this matters

Just like DeFi primitives unlocked permissionless finance, DeSci primitives are unlocking permissionless science.

Hypotheses can surface daily, validation happens in the open, IP is tradable from day one, and the pursuit of truth becomes faster and more inclusive than ever before.

The debut of BioAgents marks the first turn of the hypothesis-to-IP flywheel. As these integrations deepen, the DeSci community will be able to follow an idea from its first spark to validated proof and with every step happening onchain.

Explore Bio Protocol, ResearchHub, and Molecule to see how these pieces fit together to power the next era of scientific breakthroughs.

Molecule Protocol V2 presents a comprehensive reimagining of how scientific intellectual property can be tokenized, governed, and monetized as blockchain-based Real World Assets (RWAs).

Molecule Protocol V2 builds on the current (V1) system by integrating traditional corporate structures with crypto tokens, enhancing compliance, tax efficiency, and investor appeal while preserving the ethos of decentralization.

V2 refines and merges the V1 structures (IP-NFTs for tokenizing IP (e.g., patents, data) and IPTs for collaboration) with traditional startups by putting IP-NFTs in corporations with equity available for qualified IPT contributors. That equity that controls the IP and project treasury, enhancing project accountability and upgrading the utility of the Molecule V1 Protocol to introduce a new DeSci asset class: IP RWAs.

The Genesis of a New Scientific Economy

The traditional scientific funding model is broken. With NIH budget cuts, biotech market drawdowns and the "Valley of Death" claiming countless promising research projects, the scientific community needs new pathways to financial sustainability. That's where Molecule comes in. Molecule is a fundamental reconstruction of how we think about scientific IP ownership and capital formation in the digital age.

Our journey began with a simple yet profound realization: what if we could make IP as liquid and tradeable as any digital asset, while maintaining the legal enforceability and compliance frameworks that institutional partners require? This question has guided our development of Molecule since its inception and continues with Protocol V2, which introduces a hybrid token-and-equity framework that bridges the gap between DeFi innovation and traditional biotech investment.

The Architecture of Scientific IP Liquidity

IP-NFT V2: Composable by Design

At the core of Protocol V2 lies our revolutionary IP RWA infrastructure, built with composability as its foundational principle. V2 enables developers and advanced science projects to tailor their use cases with unprecedented technical, legal, and financial flexibility with institution-grade asset creation.

The Token-to-Equity-to-RWA Revolution

Protocol V2 presents an innovative pathway mapping early stage crypto participation to blockchain-based, institution-grade, real-world assets. We're working on solving one of the most persistent challenges in crypto: how to provide real economic rights from project inception through to RWAs using the science project’s IP assets.

Phase 1: Token Acquisition
Contributors purchase IPTs (Intellectual Property Tokens), which could be through a non-profit organization established to support advanced scientific research (such as a BioDAO, most of which are non-profits) or on the open market.

Phase 2: Citizen-Led Science
Token holders can support the research by participating in the research for some projects and by locking their tokens to vote on the research direction and project milestones.

Phase 3: The Equity Bridge
When a project matures to the stage where it incorporates, contributors who want equity in the project corporation can undergo KYC and other qualifications depending on the project. Once legally qualified, contributors may obtain equity through project engagement. Institutional contributors, such as traditional biotech and venture capital firms, may also obtain project equity through capital contributions.

Phase 4: Revenue Distribution
Protocol V2 introduces sophisticated mechanisms for revenue-sharing. When projects begin generating revenue through licensing or product sales, they can tokenize those revenue streams, begin automated buyback-and-burn of their IPTs, or both. If projects ever sell their IP, e.g. to a biotech company or venture capital firm, they can compliantly distribute sales revenues to their equity holders.

This innovation allows us to provide economic benefits to both active contributors and passive investors. The revenue flows through separate, compliant instruments that can be distributed or sold according to the project’s governance decisions.

The Anatomy of Molecule Protocol V2

Each project operates through a carefully designed structure:

1. Project Corporation: Owns the IP-NFT and all associated intellectual property, providing familiar legal structures for institutional partners.
2. Non-Profit Issuer: A tax qualified organization that could issue IP tokens to contributors and investors.
3. IP-NFT Smart Contracts: Automate governance, treasury management, and revenue distribution according to predetermined rules.
4. On-Chain Treasury Governance: Each project maintains its own programmable treasury, governed by token holders through milestone-based disbursements. This creates accountability mechanisms where community members control funding release based on research progress, introducing unprecedented transparency to biotech R&D funding.

Market Context: DeSci's Explosive Growth

The timing for Protocol V2 couldn't be better. The DeSci ecosystem has reached a critical inflection point:

• Market Capitalization: The DeSci sector has grown to $1 billion in total market cap
• Daily Volume: Over $250 million in daily trading volume across ~30 active tokens
• Institutional Interest: Major exchanges like Coinbase and Binance are launching DeSci tokens, with BIO Protocol leading the charge
• Ecosystem Funding: Molecule's ecosystem has facilitated over $15 million in research funding across 35+ projects

This growth reflects growing recognition that traditional scientific funding models are inadequate for the pace of modern innovation. As NIH cuts threaten to reduce biomedical research funding by billions of dollars, DeSci offers a viable alternative that can mobilize global capital toward breakthrough research.

A New Social Contract for Science

At its essence, Protocol V2 represents a new social contract for scientific research—one where patients, researchers, funders, and communities share both risks and rewards in the pursuit of breakthrough therapies. By tokenizing science while maintaining legal compliance, we're creating markets for scientific innovation that can mobilize global capital toward humanity's greatest challenges.

The traditional "publish or perish" academic model has failed to adequately incentivize translational research. Our Protocol V2 framework creates sustainable business models for academic researchers while ensuring that successful therapeutics benefit all stakeholders, including the patients who need them most.

Implementation and Next Steps

Protocol V2 is currently in closed beta, with selected BioDAOs and research teams testing our infrastructure. For researchers, funders, and developers interested in participating in this next phase of DeSci evolution, we encourage you to join our community and reach out.

Conclusion: The Scientific Singularity Approaches

We believe we're approaching what we call the "Scientific Singularity"—a point where the combination of AI, blockchain, and decentralized funding mechanisms accelerates scientific discovery beyond current imagination. Protocol V2 is our contribution to this future: a legal, technical, and economic framework that makes scientific IP as liquid and programmable as any digital asset.

The challenges facing humanity, from aging and disease to climate change and resource scarcity, require unprecedented levels of collaboration and innovation. By tokenizing IP and creating markets for scientific advancement, we're building the infrastructure for a future where breakthrough discoveries can be funded by anyone, owned by communities, and deployed for maximum global benefit.

The future of science is decentralized, composable, transparent, and community-owned. Protocol V2 is how we get there.

To learn more about Molecule Protocol V2, or join our developer community, visit molecule.xyz or connect with us on Discord or Telegram. Together, we're building the future of scientific innovation.

‍

Hey DeSci, It's MIRA

Molecule has always embraced the transformative power of emerging technologies to reshape science - our web3 protocol stands as a testament to that belief. We see AI and large language models (LLMs) as a natural extension of this mission.

We’re happy to share with you MIRA v0, the release of a large language model developed to support researchers and newcomers to DeSci. MIRA v0 can answer questions related to DeSci & Molecule Products.

With MIRA, you can learn how to register your ideas on chain with Proof-of-Invention, mint your research project into IP-NFTs, explore tools available to fund your research, discover successful projects in the space and track the progress they’re making with their research. 

The answers are based on curated, audited and carefully written content. This first version represents both a technical and a learning step in how AI can be applied meaningfully within DeSci and Molecule Products.

Integrating AI into our tech stack

The choice to build MIRA was instinctive - there is no doubt in our minds that AI will significantly accelerate the pace of science. Naturally, our first step was defining a solid foundation on which our team, and others, can build meaningful AI tooling.  

Unlike general-purpose LLMs that use information from across the web, MIRA works within a defined, trusted set of live sources. One of our key design choices with MIRA was teaching it to recognize its limits. We spent some time iterating our base prompt, so the model avoids guessing when it lacks the right information. Instead of hallucinating answers, it redirects you to our domain experts. This reflects our belief that responsible AI should balance automation with human oversight.

To ensure high-quality responses, every answer links back to its original source, and we continuously evaluate MIRA’s performance through Langfuse. You can visit our Github for more.

What we’ve learned already

• MIRA v0 confirms that specialized, scoped AI models can help lower the barrier of entry to DeSci. 
• Researchers can benefit not only from accurate answers, but also from understanding where those answers come from and when the system simply doesn’t know. 
• We’ve also learned that conversational interfaces provide an accessible, familiar way to engage with DeSci and explore Molecule’s products.
  ‍

What's next?

We aim to evolve MIRA. We're exploring how AI systems, in their many forms, can serve researchers, patients, and decentralized science communities. Our goal is to understand how more advanced AI models can meaningfully contribute to our broader vision for DeSci. 

We are exploring how can AI - particularly agents - can enhance reasoning, signal detection, decision making and make more efficient complex workflows.

• Effective workflows can be improved by automating complex, fragmented processes in science, tradings, and IP tokenization. We’re beginning to explore agentic workflows to help coordinate actions and support decision-making.
  
• Augmenting human reasoning, pattern recognition, and decision-making in high-stakes, data-rich environments like scientific discovery and trading.

As part of this evolution, we’ll be integrating the next iterations of MIRA into our core products, the Molecule Screener and Molecule Labs, to test how it can create value for researchers and funders.

Use MIRA today

AI and LLMs are rapidly transforming the fabric of science, research, and innovation as we know it. This doesn't happen in a vaccum. We'd like you to get involved; have a conversation with MIRA to learn more about the DeSci ecosystem, the Molecule product suite and more.

Maria Sanmartín is a Senior Product Manager at Molecule. For feedback, questions or collabs, send her a message: maria@molecule.to.