Papers by Dr. Eric Werner
arXiv: Molecular Networks, 2012
Gynandromorphs are creatures where at least two di erent body sections are a di erent sex. Bilate... more Gynandromorphs are creatures where at least two di erent body sections are a di erent sex. Bilateral gynandromorphs are half male and half female. Here we develop a theory of gynandromorph ontogeny based on developmental control networks. The theory explains the embryogenesis of all known variations of gynandromorphs found in multicellular organisms. The theory also predicts a large variety of more subtle gynandromorphic morphologies yet to be discovered. The network theory of gynandromorph development has direct relevance to understanding sexual dimorphism (di erences in morphology between male and female organisms of the same species) and medical pathologies such as hemihyperplasia (asymmetric development of normally symmetric body parts in a unisexual individual). The network theory of gynandromorphs brings up fundamental open questions about developmental control in ontogeny. This in turn suggests a new theory of the origin and evolution of species that is based on cooperative i...
Distributed algorithms are presented that describe various degrees of cooperation between autonom... more Distributed algorithms are presented that describe various degrees of cooperation between autonomous agents. The algorithms generate styles of cooperation that cover a whole spectrum, from total cooperation, to complete self-interest, to absolute antagonism, to complete self-destruction and every mixture of these. A classification of cooperation styles is described. The algorithms act on the intentional states of the agents. To resolve goal conflicts, three compromise methods are considered: rank-based compromise using a simple ranking of goals, value-optimal compromise using costs and values with the branch-and-bound procedure, and a more efficient value-optimal compromise using a zero-one integer programming method that exploits goal dependencies.
This paper outlines a formal computational semantics and pragmatics of the major speech act types... more This paper outlines a formal computational semantics and pragmatics of the major speech act types. A theory of force is given that allows us to give a semantically and pragmaticaly motivated taxonomy of speech acts. The relevance of the communication theory to complex distributed artificial intellince, DAI, systems is described. Searle gives neither a formal semantics nor a formal pragmatics for speech act theory and thereby leaves his concept of force nebulous. By relating speech acts to the pragmatic transformations on the receivers informational, intentional and evaluative representational states, speech act theory can be integrated into a general theory of communication for agents situated in a social ecological space.
An early draft of an essay published in New Scientist: in response to a recent article on ending ... more An early draft of an essay published in New Scientist: in response to a recent article on ending cancer Eric Werner, University of Oxford 1 The authors of a recent article in the New Scientist describe promising new treatments of cancer (1). While these new approaches are good they have inherent limitations because they are based on what I consider to be a fundamentally mistaken perspective of how cancer works. The authors still have a gene-centered view of cancer that prevents a true understanding of how cancer develops and how cancer can be cured. The problem is that the very same genes said to cause cancer are also used in normal development. Hence, they cannot be the cause of the unique dynamical and morphological phenotypes that distinguish cancers from normal developing tissue and organs. That means we are still treating the effects and not the cause of cancer. Figure 1 Top: a stage of growth of a simulated exponential signaling cancer with linear growth. This kind of cancer is seen in bone cancer metastases. It can be stopped by interfering with the cell signaling or by changing the cancer network loops that are activated by the cell signaling.
In this essay the logical and conceptual foundations of distributed artificial intelligence and m... more In this essay the logical and conceptual foundations of distributed artificial intelligence and multi-agent systems are explored. An attempt is made to provide an introduction to some of the key concepts of the area. These include the notion of a changing social world of multiple agents. The agents have different dynamically changing, possible choices and abilities. The agents also have uncertainty or lack of 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 and meaning and their relationship to intentional and information states are investigated. The logic of agent abilities and intentions are motivated and formalized. The entropy of group plan states is defined.
What is reality? Why is there any- thing at all? How did the complex- ity of the universe arise? ... more What is reality? Why is there any- thing at all? How did the complex- ity of the universe arise? What do quantum mechanics and quantum computers have to do with all this?
Communication theory, semantics, Informational principles, complexity reflection principle, Shannon Communication theory and quantum mechanics are discussed.
--Science, Vol. 329. no. 5992, pp. 629 - 630
DOI: 10.1126/science.1192829.
What is the relation between the complexity of agents and the complexity of the goals that they ... more What is the relation between the complexity of agents and the complexity of the goals that they can achieve? It is argued on the basis of a fundamental con- servation of complexity principle that complex goals can only be achieved if either the agents or their environment has a complexity of matching stature. This has consequences for research programs in distributed artificial intelligence, robotics and connectionism. After presenting a qualitative theory of complexity of agent systems, we also critically investigate the claims and the realities behind reactive agents, the subsumption architecture (Brooks), and the view of plans as resources (Agre, Chapman, Suchman). Finally, the implications of the complexity conserva- tion principle for the foundations of cosmology and complexity of the universe are discussed. Puzzles appear whose possible solution relates the uncertainty principle of quantum mechanics with the second law of thermodynamics.
--This is a shortened and modified version originally Pub- lished as ”What Ants Cannot Do” in Lecture Notes in Computer Science, Peram, J., (editor), Springer Verlag, July 1996.
The in vivo and in silico understanding of genomes and networks in cellular and multicellular sy... more The in vivo and in silico understanding of genomes and networks in cellular and multicellular systems is essential for drug discovery for multicellular diseases. In silico methodologies, when integrated with in vivo engineering methods, lay the groundwork for understanding multicellular organisms and their genomes. The quest to construct a minimal cell can be followed by designed, minimal multicellular organisms. In silico multicellular systems biology will be essential in the design and construction of minimal genomes for minimal multicellular organisms. Advanced methodologies come to light that can aid drug discovery. These novel approaches include multicellular pharmacodynamics and networked multicellular pharmacodynamics.
FEBS Letters 579, pp 1779-1782 (March 21, 2005)
The in vivo and in silico understanding of genomes and networks in cellular and multicellular sys... more The in vivo and in silico understanding of genomes and networks in cellular and multicellular systems is essential for drug discovery for multicellular diseases. In silico methodologies when integrated with in vivo engineering methods, lay the groundwork for understanding of multicellular organisms and their genomes. The quest to construct a minimal cell will be followed by designed, minimal multicellular organisms. In silico multicellular systems biology will be essential in the design and construction of minimal genomes for minimal multicellular organisms. Advanced methodologies come to light that can aid drug discovery. These novel approaches include multicellular pharmacodynamics and networked multicellular pharmacodynamics.
cite: DDT Drug Discov Today, vol 8, no 24, pp 1121-1127, Dec 2003
We outline a unified account of intention, information, possibility and ability. We present funda... more We outline a unified account of intention, information, possibility and ability. We present fundamental principles relating information to ability and possibility. A formal description of information is given that relates information to possibility reduction. We distinguish a theory of possiblity from a theory of ability or can. We define the semantics and investigate the logic of the modal auxiliary can. Next we show how information creates abilities. We then develope a formal theory of intentional states and then relate intention to ability. Finally, a unified view of the interrelationships among intention, information, possiblity and ability is presented.
Introduction
Perhaps it is no accident that the field of distributed artificial intelligence must confront some of the most fundamental conceptual difficulties underlying the sciences. In the quest to design and build an artificial socially intelligent agent, that acts autonomously yet cooperatively, it might be expected that foundational issues of the most basic sort should arise. The concepts of information, possibility, ability and intention lie in the bedrock of science. These concepts are central to distributed artificial intelligence [Werner 88a, 89b, 90a, b], to robotics, to artificial intelligence and to the sciences in general. And yet, the meaning of these concepts and their interrelationships is still shrouded in mystery. In this paper we will attempt to clarify some of the basic relationships between information, capability and intentions. The emphasis is on the interrelationships abstracting away from the details.
cite: 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.
A short overview and perspective on present and future trends in bioin- formatics and systems bio... more A short overview and perspective on present and future trends in bioin- formatics and systems biology aimed at CEO's and decision makers in- volved in strategic development of biotechnology and pharmaceutical companies is presented. The emphasis is not on details; some reviews are cited for that, but rather on the vision of where we are heading and to assist the decision maker in strategic planning of research and development.
NewDrugs Magazine , Issue 3, March 2002.
A proof is presented that gene regulatory networks (GRNs) based solely on transcription factors c... more A proof is presented that gene regulatory networks (GRNs) based solely on transcription factors cannot control the development of complex multicellular life. GRNs alone cannot explain the evolution of multicellular life in the Cambrian Explosion. Networks are based on addressing systems which are used to construct network links. The more complex the network the greater the number of links and the larger the required address space. It has been assumed that combinations of transcription factors generate a large enough address space to form GRNs that are complex enough to control the development of complex multicellular life. However, it is shown in this article that transcription factors do not have sufficient combinatorial power to serve as the basis of an addressing system for regulatory control of genomes in the development of complex organisms. It is proven that given n transcription factor genes in a genome and address combinations of length k then there are at most n/k k-length transcription factor addresses in the address space. The complexity of embryonic development requires a corresponding complexity of control information in the cell and its genome. Therefore, a different addressing system must exist to form the complex control networks required for complex control systems. It is postulated that a new type of network evolved based on an RNA-DNA addressing system that utilized and subsumed the extant GRNs. These new developmental control networks are called CENES (for Control genes). The evolution of these new higher networks would explain how the Cambrian Explosion was possible. The architecture of these higher level networks may in fact be universal (modulo syntax) in the genomes of all multicellular life.
cite as: arXiv:1312.5565 [q-bio.MN]
Gynandromorphs are creatures where at least two different body sections are a different sex. Bila... more Gynandromorphs are creatures where at least two different body sections are a different sex. Bilateral gynandromorphs are half male and half female. Here we develop a theory of gynandromorph ontogeny based on developmental control networks. The theory explains the embryogenesis of all known variations of gynandromorphs found in multicellular organisms. The theory also predicts a large variety of more subtle gynandromorphic morphologies yet to be discovered. The network theory of gynandromorph development has direct relevance to understanding sexual dimorphism (differences in morphology between male and female organisms of the same species) and medical pathologies such as hemihyperplasia (asymmetric development of normally symmetric body parts in a unisexual individual). The network theory of gynandromorphs brings up fundamental open questions about developmental control in ontogeny. This in turn suggests a new theory of the origin and evolution of species that is based on cooperative interactions and conflicts between developmental control networks in the haploid genomes and epigenomes of potential sexual partners for reproduction. This network-based theory of the origin of species is a paradigmatic shift in our understanding of evolutionary processes that goes beyond gene-centered theories.
cite as: arXiv:1212.5439 [q-bio.MN]
In this paper we develop a formal computational theory of high-level linguistic communication tha... more In this paper we develop a formal computational theory of high-level linguistic communication that serves as foundation for understanding cooperative action in groups of autonomous agents. We do so by examining and describing how messages effect the planning process and thereby relating communication to the intentions of the agents. We start by developing an abstract formal theory of knowledge representation based on the concept of information. We distinguish two types of information: State information, which describes the agent's knowledge about its world (knowing that) and process information, which describes the agent's knowledge of how to achieve some goal (knowing how). These two types of information are then used to formally define the agent's representation of knowledge states including the agent's intentional states. We then show how situations and actions are related to the knowledge states. Using these relations we define a formal situation semantics for a propositional language. Based on this semantics, a formal pragmatic interpretation of the language is defined that formally describes how any given knowledge representational state is modified by a given message. Finally, using this theory of meaning of messages or speech acts, a theory of cooperation by means of communication is described.
We outline the global control architecture of genomes. A theory of genomic control information is... more We outline the global control architecture of genomes. A theory of genomic control information is presented. The concept of a developmental control network called a cene (for control gene) is introduced. We distinguish parts-genes from control genes or cenes. Cenes are interpreted and executed by the cell and, thereby, direct cell actions including communication, growth, division, differentiation and multi-cellular development. The cenome is the global developmental control network in the genome. The cenome is also a cene that consists of interlinked sub-cenes that guide the ontogeny of the organism. The complexity of organisms is linked to the complexity of the cenome. The relevance to ontogeny and evolution is mentioned. We introduce the concept of a universal cell and a universal genome.
An intriguing unanswered question about the evolution of bilateral animals with internal skeleton... more An intriguing unanswered question about the evolution of bilateral animals with internal skeletons is how an internal skeleton evolved in the first place. Computational modeling of the development of bilateral symmetric organisms suggests an answer to this question. Our hypothesis is that an internal skeleton may have evolved from a bilaterally symmetric ancestor with an external skeleton. By growing the organism inside-out an external skeleton becomes an internal skeleton. Our hypothesis is supported by a computational theory of bilateral symmetry that allows us to model and simulate this process. Inside-out development is achieved by an orientation switch. Given the development of two bilateral founder cells that generate a bilateral organism, a mutation that reverses the internal mirror orientation of those bilateral founder cells leads to inside-out development. The new orientation is epigenetically inherited by all progeny. A key insight is that each cell contained in the newly evolved organism with the internal skeleton develops according to the very same downstream developmental control network that directs the development of its exoskeletal ancestor. The networks and their genomes are are identical, but the interpretation is different because of the cell's inverted orientation. The result is inside-out bilateral symmetric development generating an inside-out organism with an internal skeleton.
This paper outlines a formal computational semantics and pragmatics of the major speech act types... more This paper outlines a formal computational semantics and pragmatics of the major speech act types. A theory of force is given that allows us to give a semantically and pragmatically motivated taxonomy of speech acts. The relevance of the communication theory to complex distributed artificial intelligence, DAI, systems is described.
In this paper we outline a formal semantics and pragmatics of speech acts based on an explicit formal theory of information and intention. A formal description of the notion of illocutionary force is given. We take a new look at Searle's classification of speech acts. In the process, we develop a deeper understanding of the rather vague notion of force.
COLING-88, Proceedings of the 12th International Conference on Computational Linguistics, Budapest, Hungary, pp. 744-749, 1988.
We present a general computational theory of cancer and its developmental dynamics. The theory is... more We present a general computational theory of cancer and its developmental dynamics. The theory is based on a theory of the architecture and function of developmental control networks which guide the formation of multicellular organisms. Cancer networks are special cases of developmental control networks. Cancer results from transformations of normal developmental networks. Our theory generates a natural classification of all possible cancers based on their network architecture. Each cancer network has a unique topology and semantics and developmental dynamics that result in distinct clinical tumor phenotypes. We apply this new theory with a series of proof of concept cases for all the basic cancer types. These cases have been computationally modeled, their behavior simulated and mathematically described using a multicellular systems biology approach. There are fascinating correspondences between the dynamic developmental phenotype of computationally modeled {\em in silico} cancers and natural {\em in vivo} cancers. The theory lays the foundation for a new research paradigm for understanding and investigating cancer. The theory of cancer networks implies that new diagnostic methods and new treatments to cure cancer will become possible.
A computational theory and model of the ontogeny and development of bilateral symmetry in multice... more A computational theory and model of the ontogeny and development of bilateral symmetry in multicellular organisms is presented. Understanding the origin and evolution of bilateral organisms requires an understanding of how bilateral symmetry develops, starting from a single cell. Bilateral symmetric growth of a multicellular organism from a single starter cell is explained as resulting from the opposite handedness and orientation along one axis in two daughter founder cells that are in equivalent developmental control network states. Several methods of establishing the initial orientation of the daughter cells (including oriented cell division and cell signaling) are discussed. The orientation states of the daughter cells are epigenetically inherited by their progeny. This results in mirror development with the two founding daughter cells generating complementary mirror image multicellular morphologies. The end product is a bilateral symmetric organism. The theory gives a unified explanation of diverse phenomena including symmetry breaking, situs inversus, gynandromorphs, inside-out growth, bilaterally symmetric cancers, and the rapid, punctuated evolution of bilaterally symmetric organisms in the Cambrian Explosion. The theory is supported by experimental results on early embryonic development. The theory makes precise testable predications.
Drafts by Dr. Eric Werner
Previously, in Internet of Life, Chp 1 [137], it was shown that if the interaction protocol betwe... more Previously, in Internet of Life, Chp 1 [137], it was shown that if the interaction protocol between parental genome networks is random then there is a loss of bilateral symmetry. Thus, a nonrandom meta-network, interaction protocol evolved as a precondition for the evolution of the first bilaterally symmetric organisms in the Precambrian more than 570 million years ago. In this chapter we investigate some of the consequence of nonran-dom interaction protocols for development and evolution. Computer simulations show that 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. Thus, at any given time, all cells in a given section are exclusively controlled by only one of the two parental haploid genome networks. The partition is dynamic with sections changing identity, splitting or merging as the organism develops. The developmental effects of later partition states are superposed on earlier developmental states leading to complex mixtures of ancestrally inherited phenotypes. Each protocol has an identifying meta-network signature. Different protocol signatures partition the developing organism differently leading to different morphologies and capacities both mental and physical. As protocols and developmental networks diverge new species and phyla can emerge. 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. Evidence for this new theory of development and evolution comes from computational multicellular experiments, human and animal development , malformations, teratology, hybrids and gynandromorphs. 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.
Uploads
Papers by Dr. Eric Werner
Communication theory, semantics, Informational principles, complexity reflection principle, Shannon Communication theory and quantum mechanics are discussed.
--Science, Vol. 329. no. 5992, pp. 629 - 630
DOI: 10.1126/science.1192829.
--This is a shortened and modified version originally Pub- lished as ”What Ants Cannot Do” in Lecture Notes in Computer Science, Peram, J., (editor), Springer Verlag, July 1996.
FEBS Letters 579, pp 1779-1782 (March 21, 2005)
cite: DDT Drug Discov Today, vol 8, no 24, pp 1121-1127, Dec 2003
Introduction
Perhaps it is no accident that the field of distributed artificial intelligence must confront some of the most fundamental conceptual difficulties underlying the sciences. In the quest to design and build an artificial socially intelligent agent, that acts autonomously yet cooperatively, it might be expected that foundational issues of the most basic sort should arise. The concepts of information, possibility, ability and intention lie in the bedrock of science. These concepts are central to distributed artificial intelligence [Werner 88a, 89b, 90a, b], to robotics, to artificial intelligence and to the sciences in general. And yet, the meaning of these concepts and their interrelationships is still shrouded in mystery. In this paper we will attempt to clarify some of the basic relationships between information, capability and intentions. The emphasis is on the interrelationships abstracting away from the details.
cite: 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.
NewDrugs Magazine , Issue 3, March 2002.
cite as: arXiv:1312.5565 [q-bio.MN]
cite as: arXiv:1212.5439 [q-bio.MN]
In this paper we outline a formal semantics and pragmatics of speech acts based on an explicit formal theory of information and intention. A formal description of the notion of illocutionary force is given. We take a new look at Searle's classification of speech acts. In the process, we develop a deeper understanding of the rather vague notion of force.
COLING-88, Proceedings of the 12th International Conference on Computational Linguistics, Budapest, Hungary, pp. 744-749, 1988.
Drafts by Dr. Eric Werner
Communication theory, semantics, Informational principles, complexity reflection principle, Shannon Communication theory and quantum mechanics are discussed.
--Science, Vol. 329. no. 5992, pp. 629 - 630
DOI: 10.1126/science.1192829.
--This is a shortened and modified version originally Pub- lished as ”What Ants Cannot Do” in Lecture Notes in Computer Science, Peram, J., (editor), Springer Verlag, July 1996.
FEBS Letters 579, pp 1779-1782 (March 21, 2005)
cite: DDT Drug Discov Today, vol 8, no 24, pp 1121-1127, Dec 2003
Introduction
Perhaps it is no accident that the field of distributed artificial intelligence must confront some of the most fundamental conceptual difficulties underlying the sciences. In the quest to design and build an artificial socially intelligent agent, that acts autonomously yet cooperatively, it might be expected that foundational issues of the most basic sort should arise. The concepts of information, possibility, ability and intention lie in the bedrock of science. These concepts are central to distributed artificial intelligence [Werner 88a, 89b, 90a, b], to robotics, to artificial intelligence and to the sciences in general. And yet, the meaning of these concepts and their interrelationships is still shrouded in mystery. In this paper we will attempt to clarify some of the basic relationships between information, capability and intentions. The emphasis is on the interrelationships abstracting away from the details.
cite: 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.
NewDrugs Magazine , Issue 3, March 2002.
cite as: arXiv:1312.5565 [q-bio.MN]
cite as: arXiv:1212.5439 [q-bio.MN]
In this paper we outline a formal semantics and pragmatics of speech acts based on an explicit formal theory of information and intention. A formal description of the notion of illocutionary force is given. We take a new look at Searle's classification of speech acts. In the process, we develop a deeper understanding of the rather vague notion of force.
COLING-88, Proceedings of the 12th International Conference on Computational Linguistics, Budapest, Hungary, pp. 744-749, 1988.
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. Several times I tried to get Oxford undergraduate students to come but they were intimidated by the ‘big apes’ in the room and by the high level of discussion. This was unfortunate since in my experience undergrads, precisely because of their lack of expertise, are more open to and often understand new ideas more easily than the specialists. 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 below 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.
Key Words: Cancer, tumor, cancer cure, cancer cell death, cancer cure protocol, cancer apoptosis protocol, cancer cell suicide, apoptosis, cancer CAD software, computational cancer modeling, cancer simulation, synthetic biology, cancer networks, CRISPR, genome editing, network design, network synthesis, cancer therapy, cancer network diagnosis, cancer network analysis, cancer epigenetics, epigenetic cancer treatment, cancer therapy