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.

On 10 & 11 June, the Molecule HQ transformed into a dynamic forum for the future of science, where real-world applications and visionary ideas in decentralized science took center stage.

This year’s gathering was marked by a clear sense of purpose and visible traction. Progress in decentralized clinical trials, tokenized IP frameworks, and new infrastructure tools was front and center in keynotes, panels, and discussions; highlighting how DeSci has been moving from theory to real-world impact.

Let’s look back at some of the key moments and takeaways from this year’s event.
‍

Paul Kohlhaas: Science needs a system upgrade

Molecule & BIO’s CEO Paul Kohlhaas opened the conference with a keynote that challenged the status quo. He called out the structural inefficiencies baked into traditional science, from funding bottlenecks to perverse incentives that disincentivize cures.

Drawing a line from Bitcoin’s challenge to centralized finance, Paul positioned DeSci as the necessary reinvention of the scientific ecosystem. He emphasized that the future of science is permissionless, built on open, decentralized infrastructure that anyone can contribute to.

Key highlights from his talk focused on how to scale DeSci sustainably. Paul stressed the importance of avoiding redundancy by encouraging collaboration across the ecosystem, rather than siloed replication. He advocated for building and sharing core primitives like tokenized IP, a concept pioneered by Molecule through the implementation of IP-NFT and IPTs, and DAO tooling, an area where BIO is actively supporting the growth of the BioDAO ecosystem, to create a stable foundation. He also called for a stronger focus on the demand side of science, ensuring projects deliver clear value to funders and end users. Finally, he highlighted AI’s growing role in accelerating discovery and the importance of metrics-based, data-driven development.

His message was clear: for DeSci to thrive, it must stay collaborative, accountable, and aligned with real impact.

Biotech bottlenecks, unpacked

In the panel "Breaking the Bottlenecks: What’s Stalling Biotech Innovation?" Kai Uwe Bindseiler, Chris Lewis, and Hannah Payette Peterson joined Shriya Bhat to dissect what’s holding biotech back.

They pointed to familiar blockers: slow tech transfer, funding gaps, risk-averse academic culture, and bureaucratic friction. However, the panel struck a hopeful tone. Cultural change, better support for early founders, and advances in AI were highlighted as ways to unlock stalled potential.

DeSci was framed as part of the solution by enabling faster funding, leaner coordination, and community-driven experimentation. Emerging areas like neurotech, preventative health, and longevity were highlighted as ripe for this model.

The message: change is possible, but it takes intentional shifts in both structure and mindset.

Molecule Labs launched at DeSci.Berlin

Kevin Noessler, Chief Product Officer at Molecule, unveiled Molecule Labs for the first time at DeSci.Berlin, marking a major leap forward for transparency in the DeSci ecosystem. The announcement was met with genuine excitement from the room, as attendees recognized the significance of what this unlocks for onchain science.

The platform brings scientific work onchain, turning static updates into dynamic, verifiable logs. With versioning, access control, and decentralized storage, project leads now can publish milestones in real time while communities track progress transparently. Built for BioDAOs and research teams, Molecule Labs streamlines data management, tokenization, and fundraising from a single hub. It also integrates with the DeSci Screener to align research milestones with crypto-native incentives.

Positioned as a “GitHub for DeSci” Molecule Labs lays the groundwork for a more open, accountable, and coordinated research ecosystem. Several projects, CLAW, HEMPY, VITARNA, and PSYMARK have already begun sharing progress updates through the platform.

DeSci from the Investor Seat

The panel "DeSci from the Investor Seat" featured moderator John Spies in conversation with Jakub Rusiecki, Patrick Mayr, and Dr. Georg Stricker, offering investors’ views on how DeSci fits into today’s evolving landscape.

They highlighted DeSci’s ability to bridge crypto-native models with real-world scientific outcomes.

A recurring theme was the need for better infrastructure to support growth and participation. Dr. Stricker noted that, like early open-source software, science needs a modern tech stack to scale. Genomics, consumer health, and AI-driven experimentation were seen as especially promising.

The next wave of success in DeSci, they suggested, will come from projects that combine scientific credibility with crypto-native coordination and deliver clear, measurable outcomes, from therapeutic breakthroughs to new models for funding and ownership.

Pitch, Vote, Build: Nucleate Pitch Competition

As part of the ongoing Molecule x Nucleate partnership, DeSci.Berlin 2025 hosted a high-energy pitch competition featuring four standout teams from Nucleate Germany’s Activator program. These early-stage biotech ventures, led by academic founders turned entrepreneurs, took to the stage to share bold visions; ranging from tumor avatars powered by AI (Oncera), to personalized deficiency monitoring (Keynostic), to low-cost early cancer detection (ExoSphere), and safer antifungal drug delivery (Aulixir Therapeutics).

With the crowd acting as jury, attendees casted live votes, ultimately selecting ExoSphere, pitched by Negar Shahmoradi, as the winner.

Blockchain infra for real-world science

The cross-chain panel brought together voices from Ethereum Foundation, Solana, Gnosis, MetaMask, and BIO. Dr. Friederike Ernst highlighted the misalignment between academic incentives and public good outcomes, arguing that DAOs offer a path to realign them.

Theodor Beutel cautioned against using blockchain for its own sake, urging focus on real problems. Tools like zk-tech, encryption, and modular coordination were seen as more immediately useful than fully onchain systems.

Patricia Albrecht shared how Solana’s Superteam model helps early-stage builders, while the panel emphasized that targeted experimentation, especially in areas like rare diseases, will define what scalable DeSci looks like.

Marco de Rossi laid out five areas where crypto infra adds value: discovery, problem definition, reproducibility, privacy, and incentives. The challenge now is stitching those Legos together with clear UX and clear intent.

Tokenized IP: building faster, sharing smarter

In the panel on tokenized IP, representatives from VitaDAO, ValleyDAO, and PsyDAO shared how BioDAOs are reshaping biotech fundraising and research ownership.

Each DAO outlined its distinct approach: ValleyDAO proactively scouts climate biotech projects, PsyDAO uses a cooperative token structure to decentralize decision-making, and VitaDAO blends inbound applications with a fellowship program to support early-stage ideas.

The discussion emphasized how tokenized IP accelerates funding, enables research pivots, and fosters better cultural alignment.

Examples included precision fermentation, preclinical RNA therapies launched with under $400k, and ethical frameworks in psychedelic research that honor indigenous rights while reducing due diligence costs.

Clinical trials, reimagined

One of the most grounded conversations happened in the decentralized clinical trials panel. Panelists from Molecule, Reputable Health, CerebrumDAO, Welshare, and Future4Care shared how token-based incentives, wearables, and remote diagnostics are reshaping clinical research.

It was discussed how teams are now running pilot trials in months, not years, with budgets under $100k, using tools like biomarker tracking, cognitive assessments, and privacy-aware recruitment to enable faster, more inclusive studies.

Stefan Adolf from Welshare stressed that decentralization alone isn’t a privacy solution, but paired with encryption, decentralized identifiers, and thoughtful UX, it puts control back in patients’ hands. While pharma hesitancy remains, the path forward is clear: transparency, speed, and community involvement are shifting the model.

Workshops at Westberlin Café

While the main stage brought the big ideas, the workshops at Westberlin Café were where builders rolled up their sleeves. These hands-on sessions gave participants practical tools, frameworks, and space to collaborate. Nour Karoui led a session on registering Proof of Innovation, while Paula Vulić shared strategies for marketing DeSci projects. Si Maclennan helped founders refine their messaging to better communicate complex ideas.

On Day 2, Sean Brennan and Aakaash Meduri from BIO explored how AI agents can speed up research workflows, and Edvard Hübinette and Erik Van Winkle walked through decentralized publishing. One of the most packed sessions covered tokenized clinical trial infrastructure, led by Aaron Weaver, Stefan Adolf, and Erik Van Winkle.

These workshops made one thing clear: DeSci doesn’t offer just a vision, but a toolkit ready to use.

That’s a Wrap on DeSci.Berlin 2025

DeSci.Berlin 2025 was a checkpoint in the movement that's been accelerating. The energy was high, and the vibe was extremely positive.

Beyond the insightful talks, dynamic panels and practical workshops, the heart of the event was in the connections; reuniting with old friends, meeting new ones, exchanging ideas, and co-creating what comes next. The spontaneous conversations, spirited debates, and brainstorms were just as impactful as anything on the stage.

To everyone who joined us at the Molecule HQ or tuned in from around the world: thank you. Your energy and contributions push this ecosystem forward.

Missed DeSci Berlin 2025? No worries. All main stage talks are being uploaded to the Molecule YouTube channel.
And if you want to relive the vibe or spot yourself in the crowd: browse the full event photo set.

Stay connected, keep building, and let’s carry this momentum into the next chapter of DeSci.

‍