Research scientist Oxford Advanced Research Foundation
Publication List
Books
Noble, D., Chen, Z., Auffrey, C., Werner, E. The Selected Papers of Denis Noble, IPC Press, 2012.
Castelfranchi, C., and Werner, E., Artificial Social Systems, Springer Verlag, August 1994.
Werner, E., and Demazeau, Y., (eds.), Decentralized AI,Vol. 3, Elsevier Science Publishers, North Holland, 1992.
Werner, E., Logical Foundations of Distributed Artificial Intelligence, in preparation.
Werner, E., Computational Multicellular Systems Biology, in preparation.
Articles
Werner, E. “Conceptual Logical Foundations of Artificial Social Intelligence”, https://arxiv.org/abs/2505.07847 07 MAY 2025. Abstract: What makes a society possible at all? How is coordination and cooperation in social activity possible? What is the minimal mental architecture of a social agent? How is the information about the state of the world related to the agents intentions? How are the intentions of agents related? What role does communication play in this coordination process? This essay explores the conceptual and logical foundations of artificial social intelligence in the context of a society of multiple agents that communicate and cooperate to achieve some end. An attempt is made to provide an introduction to some of the key concepts, their formal definitions and their interrelationships. These include the notion of a changing social world of multiple agents. The logic of social intelligence goes beyond classical logic by linking information with strategic thought. A minimal architecture of social agents is presented. The agents have different dynamically changing, possible choices and abilities. The agents also have uncertainty, lacking perfect information about their physical state as well as their dynamic social state. The social state of an agent includes the intentional state of that agent, as well as, that agent’s representation of the intentional states of other agents. Furthermore, it includes the evaluations agents make of their physical and social condition. Communication, semantic and pragmatic meaning and their relationship to intention and information states are investigated. The logic of agent abilities and intentions are motivated and formalized. The entropy of group strategic states is defined.
Werner, E.. “AI-CAD-CRISPR Protocols to Crack the Cancer Code: Reverse Engineer Multicellular Life and Design in silico Brains with Natural Architectures“, September 2025, DOI:10.13140/RG.2.2.27761.95847, https://www.researchgate.net/publication/395391173_AI-CAD-CRISPR_Protocols_to_Crack_the_Cancer_Code_Reverse_Engineer_Multicellular_Life_and_Design_in_silico_Brains_with_Natural_Architectures Abstract: Generative CAD software is used to design, model and simulate multicellular development of cancers and their control networks. The designed genomes that encode the cancer networks can be saved as arbitrarily many, randomized, artificial DNA files. We then use those DNA files as data to train an AI-model to recognize the cancer networks in artificial genomes. Once trained, we set the AI-model on natural genomes of live cancer cells, like the HeLa cell. If the AI-model recognizes the cancer network, we then use the CAD software to edit the discovered cancer network and transform it into a cancer free network. Using that as a translation template, we can use CRISPR to edit out the corresponding actual cancer network in a live HeLa cancer cell, stopping cancer cell division. We will have halted the cancer by genome editing, not by drugs or radiation. Moreover, since cancer cells are controlled by the same code that regulates normal cell division, we have unlocked the syntax of the hidden code that controls the development of multicellular life. It sets the stage for decoding and understanding the semantics and pragmatics of multicellular systems, their evolution and design archi-tectures. This opens the door to modifying and designing living multicellular systems such as organs, animals and plants. If we use the regions of the genome that encode an animal brain and step-by-developmental-step translate it into software or hardware, then the final output is an in silico digital brain with the natural functional architecture of the animal brain. If the digital translation is a human brain, it has the natural social cooperative, mental capacities of humans. We can modify and/or merge the designs of different brains to extend and enhance any natural or artificial capacity, including reasoning, cooperativity, storage and processing. This article outlines strategies and protocols to make all this possible.
(Key Insight: Any nonrandom interaction protocol dynamically partitions the organism into two types of nonintersecting sections, one type controlled by the maternal and the other by the paternal haploid genome network. These protocols are the bedrock of social and sexual intercourse between male and female genomes. For any diploid species their haploid protocols must cooperate to generate a coherent, complete and consistent embryo. If the two haploid protocols of potential sex partners diverge too much, network disfunction causes developmental pathologies, miscarriage or unviability. Developmental networks and their meta-network protocols provide a fundamentally new explanatory framework for embryonic and post-embryonic development, developmental pathologies, animal and plant hybrids, heterosis, and evolutionary dynamics.)
Werner, E. “The internet of life, chapter 1: Universal nonrandom network protocols govern development and evolution of all bilaterians”. DOI: 10.13140/RG.2.2.30876.03207 Preprint 2020. PDF
(Key Insight: Universal protocols govern the interaction between the paternal and maternal haploid genomes (the genomes in sperm and egg). It is shown such protocols are a prerequisite for the development and evolution of all bilaterally symmetric sexually reproducing organisms. A conceptual paradigm shift, based on developmental networks and meta-networks, provides new, deep insight and understanding into how development and evolution work at lower and higher levels of genome interaction.)
(Key Insight: This is the unabridged version of the Science article “How central is the genome”. History behind this review: I initiated, organized, and held a weekly seminar in Balliol College, University of Oxford, together with the active participation of Denis Noble. I named it ‘The Conceptual Foundations of Systems Biology’ (CFSB) because I wanted to discuss fundamental problems at the foundations of biology. It brought together an interdisciplinary group of Oxford doctoral students, researchers, and professors with specialization in biology, computer science, mathematics, physics, the social sciences, and economics. The CFSB-Seminar lasted 6 years with weekly intense and profound discussions with regular members and invited speakers. It was a great, unique series that led to mutual trust and deeper understanding across the disciplines. The review was written at an early stage of the seminar and captures some of my initial ideas that were debated. Luckily at my behest all the meetings were recorded for future reference. Listening to those recordings makes one feel as if one is right there in the Massey Room in Balliol College, Oxford.)
Werner, E. “Iconoclastic thoughts on Spencer Brown’s Laws of Form”, Preprint, June 2019. DOI: 10.13140/RG.2.2.27611.00801 PDF
(Key Insight: Takes a critical view of Spencer Browns book ‘Laws of Form’ and compares it to religious texts.)
Werner, E. “The Coming CRISPR Wars: Or why genome editing can be more dangerous than nuclear weapons, Preprint, 2019, DOI: 10.13140/RG.2.2.17533.00485 PDF
(Key Point: Explores the extreme dangers of CRISPR-like editing of genomes including human, animal, plant and virus genomes.)
Werner, E. “Music and Distributed Programs”, Preprint, 2018, DOI: 10.13140/RG.2.2.26336.94724 PDF
(Key Insight: A critical conceptual analysis of misplaced views that the genome is like the keyboard of a piano that the cell plays. Instead I argue the genome is more like a distributed musical score (partitur) that controls how cells play to form an embryo. )
Werner, E. “Language, Mind and Society: A Critique of Previous Theories”, Preprint, DOI: 10.13140/RG.2.2.12923.77609, October 2018. Abstract-PDF
(Key Insight: A critical analysis of the dominant theories of human and animal communication)
Werner, E. “A Brief Conceptual History of Communication Theory for Distributed Social Agents in Social-Economic Ecologies.”, Preprint, DOI 10.13140/RG.2.2.22151.24487, October 2018. Abstract-PDF
(Key Insight: Informal background and history of my communication theory for social-economic ecologies)
Werner, E. “Viral Black Widow Protocols for Cancer Immunotherapy: Matching cancer cell signals with oncolytic virus receptors for complete and consistent cancer eradication”, Preprint, (August 2018) DOI: 10.13140/RG.2.2.10622.48968
(Key Insight: Similar to the T-cell Black Widow Protocol but replaces T-cells with oncolytic viruses. Cancer cell networks are transformed via CRISPR-Cas editing and Cancer-CAD software to express a unique “Kill me!” signal. The oncolytic virus is designed to only recognize the unique cancer signal. In effect it is a shotgun wedding between cancer cells and viruses such that the virus kills its mate. The result is cancer eradication without the side effects of standard cancer immunotherapy. The Viral Black Widow Protocol can be combined with the T-cell Black Widow Protocol if they target the same unique cancer signal. Then this polygamous relationship between the ‘male’ cancer cell and the female ‘T-cell’ and female ‘virus’ results in the females killing their cancer cell spouse.)
Werner, E. “The Black Widow Protocol for Coordinated Cancer Immunotherapy: Co-editing cancer cells and T-cells for minimal immunotherapeutic side effects”, Preprint, DOI: 10.13140/RG.2.2.21609.60002, July 2018. Abstract-PDF
(Key Insight: Unlike standard personalized T-cell immunotherapy, this is dual edit protocol to treat cancer. Cancer cells are edited to communicate unique “kill me!” signals to T-cells. In coordination, the T-cell receptors are co-edited to recognize and receive the unique “kill me!” signal sent by co-edited cancer cells. Thus after the ‘male’ cancer cell sends its signal to the ‘female’ T-cell, the Black Widow T-cell kills its mate. Most T-cell immunotherapies have moderate to deadly side effects because single-edit T-cells kill normal cells as well. This protocol was developed to avoid side effects by engineering a coordinated communication system between cancer cells and T-cells. )
Werner, E. “A Cancer Cell Suicide Protocol -Using cancer-CAD and CRISPR to edit cancer cell networks to induce cancer cell apoptosis”, Preprint, DOI: 10.13140/RG.2.2.29065.95848, July 2018. Abstract-PDF
(Key Insight: A protocol to cure cancer by having cancer cells destroy themselves. A method to cure cancer by digital and synthetic genome editing without surgery, drugs or radiation. )
Werner, E. “A Roadmap to Cure Cancer: Combining CRISPR genome editing with cancer network editing”, Preprint, DOI: 10.13140/RG.2.2.23272.37127, 2017. Abstract-PDF
(Key Insight: A protocol to cure cancer combines my cancer network paradigm with CRISPR genome editing. It opens a path to curing cancer by digital and synthetic genome editing without surgery, drugs or radiation. )
Werner, E. “A Roadmap to Create Synthetic Multicellular Life: Applications: Protocols to cure cancer, tissue regeneration, network-designed heterosis-hybrid vigor” Preprint, DOI: 10.13140/RG.2.2.25575.96160, 2017. Abstract-PDF
Werner, E., “Combinatorial Limits of Transcription Factors and Gene Regulatory Networks in Development and Evolution”. arXiv:1508.03531 [q-bio.MN], 2015, Abstract, pdf.
Werner, E., “What Transcription Factors Can’t Do: On the Combinatorial Limits of Gene Regulatory Networks” arXiv:1312.5565 [q-bio.MN], 2013. Abstract, pdf
Werner, E., “A Developmental Network Theory of Gynandromorphs, Sexual Dimorphism and Species Formation” arXiv:1212.5439 [q-bio.MN], 2012. Abstract, pdf
Werner, E., “How to Grow an Organism Inside-Out: Evolution of an internal skeleton from an external skeleton in bilateral organisms”, arXiv:1207.3624 [q-bio.TO], 2012. Abstract, pdf
Werner, E., “The Origin, Evolution and Development of Bilateral Symmetry in Multicellular Organisms”, arXiv:1207.3289 [q-bio.TO], 2012. Abstract, pdf
Werner, E, “Cancer Networks: A general theoretical and computational framework for understanding cancer”, arXiv:1110.5865v1 [q-bio.MN], Oct 26, 2011. Abstract, pdf
Werner, E., “On programs and Genomes”, arXiv:1110.5265v1 [q-bio.OT], Oct 24, 2011. Abstract , pdf
Werner, E., “Meaning in a Quantum Universe”, Science, Vol. 329. no. 5992, pp. 629 – 630
Werner, E., “Genome Semantics, In Silico Multicellular Systems and the Central Dogma”, FEBS Letters579, pp 1779-1782 (March 21, 2005).(Abstract)[PubMed]
Werner, E., “Systems biology: the new darling of drug discovery?”, DDT Drug Discov Today, Vol. 7, No. 18, September 2002.(Summary)[PubMed]
Werner, E., “Bioinformatics and Systems Biology: An Overview” NewDrugs Magazine , Issue 3, March 2002.(Abstract)
Werner, E., “The Self of Social Agents”, Human Cognition and Social Agent Technology, Dautenhahn, K., (ed.), “Advances in Consciousness Research”, John Benjamins Publishing Company, 1998.(Abstract)
Werner, E., “Logical Foundations of Distributed Artificial Intelligence”, Foundations of Distributed AI, G. O’Hare and N. Jennings (eds.), Wiley Publishers, 1996. (Abstract)
Werner, E., “What Ants Cannot Do”, Distributed Software Agents and Applications, Perram, J.W., and Müller, J.P., (eds.), Springer Verlag, 1996.(Abstract)
Kinny, D., Ljungberg, M., Rao, A., Sonnenberg, E., Tidhar, G., Werner, E., “Planned Team Activity”, Artificial Social Systems, Castelfranchi, C., and Werner, E., (eds.), Springer Verlag, 1994.
Werner, E., “On the Logic of Plans with Simultaneous Actions”, ECAI-92 Workshop on Beyond Sequential Planning, European Conference on Artificial Intelligence, 1994.
Werner, E. “Ontogeny of the Social Self”, Symposium on Social Simulation, University of Surrey, United Kingdom. (Abstract)
Werner, E., “The Design of Multi-Agent Systems”, Decentralized AI, Vol. 3, Werner, E., and Demazeau, Y., (eds.), Elsevier Science Publishers B.V. (North Holland), 1992. Abstract
Werner, E., “Integrating Social Rationality with Communication and Cooperation in Multi-Agent Systems”, FRIEND21 Workshop on Communication and Multi-Agents, Tokyo, Japan, 1991.
Werner, E., “Generating Cooperative and Non-Cooperative Behavior”, Proceedings of the FRIEND21 International Symposium on Next Generation Human Interface, Tokyo, Japan, 1991.
Werner, E., “A Unified View of Information, Intention and Ability”, Decentralized AI, vol. 2, Proceedings of the Second European Workshop on Modeling Autonomous Agents in Multiagent Worlds, Demazeau, Y. & Muelller, J-P., (eds.), Saint-Quentin en Yvelines, France. Elsevier Science Publishers, 1991. (Abstract)
Werner, E., “Making Systems Cooperative through Social Knowledge”, CKBS-90, A Working Conference On Cooperating Knowledge Based Systems, University of Keele, England, 1991.
Werner, E., “What Ants Cannot Do: On the Complexity of Multi-Agent Events”, IEE Colloquium on Intelligent Agents, Savoy Place, London, 1991. (Abstract)
Werner, E., “Planning and Uncertainty”, European Workshop on Planning, St. Augustine, F.R.G.. Also in Proceedings of the 10th UK Planning SIG, LOGICA, Cambridge, UK, 1991.
Kuenstliche Intelligenz, Proceedings of the 4th International GI Kongress, Munich, Germany. Published by Springer, 1991. (Abstract)
Werner, E. and Reinefeld, A., “Distributed Algorithms for Cooperating Agents”, DAI-90, Proceedings of the 10th International Workshop on Distributed Artificial Intelligence, Bandera, Texas, 1990. (Abstract-PDF)
Werner, E., “Distributed Cooperation Algorithms”, Decentralized AI, Proceedings of the 1st European Workshop on Modeling Autonomous Agents in a Multi-Agent World, Demazeau, Y. & Muelller, J-P., (eds.), Elsevier Science Publishers B.V. (North Holland), pp. 17-31, 1990.
Werner, E., “What Can Agents Do Together? A Semantics for Reasoning About Single and Multiagent Cooperative Ability”, ECAI-90, Proceedings of the 9th European Conference on Artificial Intelligence, Stockholm, Sweden, pp. 694-701, 1990. (Abstract)
Werner, E., “Cooperating Agents: A Unified Theory of Communication and Social Structure”, Distributed Artificial Intelligence, Vol. 2, L. Gasser and M. Huhns, eds., Morgan Kaufmann and Pitman Press, 1989. (Abstract)
Werner, E., “Distributed Artificial Intelligence: Report on the 1988 AAAI sponsored Workshop on DAI”, AI and Society, vol.3, pp. 260-267, Springer Press, London 1989.
Werner, E., “Semantics for Tensed Modal Logic”, WISBER Report B49, University of Hamburg, Hamburg, Germany, 1989.
Werner, E., “Communication in WISBER”, WISBER Report B51, University of Hamburg, Hamburg, Germany, 1989.
Werner, E., “Modal Logic of Games”, WISBER Report B48, University of Hamburg, Hamburg, Germany, 1989. (Abstract)
Werner, E., “Communication in Tarski, Possible World, and Situation Semantics”, WISBER Report, University of Hamburg, Hamburg, Germany, 1989. (Abstract)
Werner, E., “Temporal Modal Reasoning in Games”, WISBER Report M34, University of Hamburg, Hamburg, Germany, 1989.
Werner, E., “Two Ways of Representing Knowledge”, WISBER Report B44, University of Hamburg, Hamburg, Germany, 1989.
Werner, E., “A Formal Computational Semantics and Pragmatics of Speech Acts”, COLING-88, Proceedings of the 12th International Conference on Computational Linguistics, Budapest, Hungary, pp. 744-749, 1988. (Abstract)
Werner, E., “Socializing Robots: A Theory of Communication and Social Structure for Distributed Artificial Intelligence”, presented at the 8th AAAI Workshop on Distributed Artificial Intelligence, Lake Arrowhead, California, in: Les Gasser(ed.), Collected Draft Papers From the 1988 Workshop on Distributed Artificial Intelligence, Tech Report CRI-88-41, Computer Research Institute, University of Southern California, Los Angeles, CA, 1988.
Werner, E., “Social Intentions”, Panel on Interactions Among Intelligent Agents, ECAI-88, Proceedings of the 8th European Conference on Artificial Intelligence, Munich, Germany, pp. 719-723, 1988. Also appeared as WISBER report. (Abstract)
Werner, E., “Money Talk: Hierarchical Consultation Dialogue”, GWAI-88, Proceedings of the German Workshop on Artificial Intelligence, Eringerfeld, West Germany, pp. 211-215, 1988.
Werner, E., “Reasoning About Knowledge: Report on the TARK-88 Conference”, KI, vol. 3, Munich, Germany, pp. 18-19, 1988.
Werner, E., “Information, Intention, and Ability: Outline of a Unified Theory”, Presented at GWAI-88, German Workshop on Artificial Intelligence, WISBER Report Nr. B37, University of Hamburg, Hamburg, Germany, November 1988. (Abstract)
Werner, E., “Toward a Theory of Communication and Cooperation for Multiagent Planning”, Theoretical Aspects of Reasoning About Knowledge: Proceedings of the Second Conference, Morgan Kaufman Publishers, pp. 129-143, 1988. (Abstract)(PDF) (You may need the newest version of AcrobatReaderto view this pdf file.)