Papers by Andrée Ehresmann
Integral Biomathics, 2012
Leslie S. Smith, Neuroscience and Natural Computing, UK [email protected] 2 _______________... more Leslie S. Smith, Neuroscience and Natural Computing, UK [email protected] 2 ______________________________________________________________________________ Note: This White Paper is not a concise report on the research program we seek to elaborate in INBIOSA. It has been conceived as a 'living' document, progressively developed along the months by discussions among scientists with differing formations and states of mind. We have chosen to respect their personalities, at the risk of some lack of homogeneity and repetitions between different passages. Also, incompleteness, inconsistences and antagonisms could not be completely avoided.
The INBIOSA project brings together a group of experts across many disciplines who believe that s... more The INBIOSA project brings together a group of experts across many disciplines who believe that science requires a revolutionary transformative step in order to address many of the vexing challenges presented by the world. It is INBIOSA’s purpose to enable the focused collaboration of an interdisciplinary community of original thinkers.
This paper sets out the case for support for this effort. The focus of the transformative research program proposal is biology-centric. We admit that biology to date has been more fact-oriented and less theoretical than physics. However, the key leverageable idea is that careful extension of the science of living systems can be more effectively applied to some of our most vexing modern problems than the prevailing scheme, derived from abstractions in physics. While these have some universal application and demonstrate computational advantages, they are not theoretically mandated for the living. A new set of mathematical abstractions derived from biology can now be similarly extended. This is made possible by leveraging new formal tools to understand abstraction and enable computability. [The latter has a much expanded meaning in our context from the one known and used in computer science and biology today, that is "by rote algorithmic means", since it is not known if a living system is computable in this sense (Mossio et al., 2009).] Two major challenges constitute the effort.
The first challenge is to design an original general system of abstractions within the biological domain. The initial issue is descriptive leading to the explanatory. There has not yet been a serious formal examination of the abstractions of the biological domain. What is used today is an amalgam; much is inherited from physics (via the bridging abstractions of chemistry) and there are many new abstractions from advances in mathematics (incentivized by the need for more capable computational analyses). Interspersed are abstractions, concepts and underlying assumptions “native” to biology and distinct from the mechanical language of physics and computation as we know them. A pressing agenda should be to single out the most concrete and at the same time the most fundamental process-units in biology and to recruit them into the descriptive domain. Therefore, the first challenge is to build a coherent formal system of abstractions and operations that is truly native to living systems.
Nothing will be thrown away, but many common methods will be philosophically recast, just as in physics relativity subsumed and reinterpreted Newtonian mechanics.
This step is required because we need a comprehensible, formal system to apply in many domains. Emphasis should be placed on the distinction between multi-perspective analysis and synthesis and on what could be the basic terms or tools needed.
The second challenge is relatively simple: the actual application of this set of biology-centric ways and means to cross-disciplinary problems. In its early stages, this will seem to be a “new science”.
This White Paper sets out the case of continuing support of Information and Communication Technology (ICT) for transformative research in biology and information processing centered on paradigm changes in the epistemological, ontological, mathematical and computational bases of the science of living systems. Today, curiously, living systems cannot be said to be anything more than dissipative structures organized internally by genetic information. There is not anything substantially different from abiotic systems other than the empirical nature of their robustness. We believe that there are other new and unique properties and patterns comprehensible at this bio-logical level. The report lays out a fundamental set of approaches to articulate these properties and patterns, and is composed as follows.
Sections 1 through 4 (preamble, introduction, motivation and major biomathematical problems) are incipient. Section 5 describes the issues affecting Integral Biomathics and Section 6 -- the aspects of the Grand Challenge we face with this project. Section 7 contemplates the effort to formalize a General Theory of Living Systems (GTLS) from what we have today. The goal is to have a formal system, equivalent to that which exists in the physics community. Here we define how to perceive the role of time in biology. Section 8 describes the initial efforts to apply this general theory of living systems in many domains, with special emphasis on cross-disciplinary problems and multiple domains spanning both “hard” and “soft” sciences. The expected result is a coherent collection of integrated mathematical techniques. Section 9 discusses the first two test cases, project proposals, of our approach. They are designed to demonstrate the ability of our approach to address “wicked problems” which span across physics, chemistry, biology, societies and societal dynamics. The solutions require integrated measurable results at multiple levels known as “grand challenges” to existing methods. Finally, Section 10 adheres to an appeal for action, advocating the necessity for further long-term support of the INBIOSA program.
The report is concluded with preliminary non-exclusive list of challenging research themes to address, as well as required administrative actions. The efforts described in the ten sections of this White Paper will proceed concurrently. Collectively, they describe a program that can be managed and measured as it progresses.
Keywords: integral biomathics, theoretical biology, biological mathematics, theoretical physics, endophysics, semiotics, observer-participation, developmental biology, neuroscience, natural computing, biocomputing, category theory, logic, positivism, scientific revolution, determinism, non-deterministic chaos, first-person perspective, complementarity, emergence, complexity, holism, reductionism, information, information integration, communication, change, development, hierarchies, scale and hyperscale, self-organization, autopoiesis, internalism, mechanicism, vagueness, class identity, individual identity, biological time, mind-body problem, non-locality, virtualization, distribution, genetic transcoding, neural systems, memory, cognition, consciousness, quantum effects in biology, life.
The aim of the uCepCortex project is to develop an exocortex based on Ubiquitous Complex Event Pr... more The aim of the uCepCortex project is to develop an exocortex based on Ubiquitous Complex Event Processing (U-CEP) as an Artificial Cognitive System and to investigate how to enhance human cognitive abilities, manage assistive robots, and their cooperation with humans via an exocortex system. A reference model and reference architecture are needed to realize the connection of humans and robots to the knowledge from a global event cloud by an exocortex as a preprocessor for relevant or subscribed complex event patterns. Here, using the theory of Memory Evolutive Systems (MES), we propose a mathematical model NBS for neuro-bio-systems which identifies the characteristics necessary for intelligent handling of U-CEP. These characteristics are extended to obtain a reference model for neuro-bio-ICT-systems in which human cognitive activities are enhanced by an exocortex with the above properties.
Lecture Notes in Computer Science, 2015
Progress in Biophysics and Molecular Biology, 2015
The paper discusses how neural and mental processes correlate for developing cognitive abilities ... more The paper discusses how neural and mental processes correlate for developing cognitive abilities like memory or spatial representation and allowing the emergence of higher cognitive processes up to embodied cognition, consciousness and creativity. It is done via the presentation of MENS (for Memory Evolutive Neural System), a mathematical methodology, based on category theory, which encompasses the neural and mental systems and analyzes their dynamics in the process of 'becoming'. Using the categorical notion of a colimit, it describes the generation of mental objects through the iterative binding of distributed synchronous assemblies of neurons, and presents a new rationale of spatial representation in the hippocampus (Gómez-Ramirez and Sanz, 2011). An important result is that the degeneracy of the neural code (Edelman, 1989) is the property allowing for the formation of mental objects and cognitive processes of increasing complexity order, with multiple neuronal realizabilities; it is essential "to explain certain empirical phenomena like productivity and systematicity of thought and thinking (Aydede 2010)". Rather than restricting the discourse to linguistics or philosophy of mind, the formal methods used in MENS lead to precise notions of Compositionality, Productivity and Systematicity, which overcome the dichotomic debate of classicism vs. connectionism and their multiple facets. It also allows developing the naturalized phenomenology approach asked for by Varela (1996) which "seeks articulations by mutual constraints between phenomena present in experience and the correlative field of phenomena established by the cognitive sciences", while avoiding their pitfalls.
AIP Conference Proceedings
Evolution is marked by the emergence of new objects and interactions. Pursuing our preceding work... more Evolution is marked by the emergence of new objects and interactions. Pursuing our preceding work on Memory Evolutive Systems (MES cf. our Internet site), we propose a general mathematical model for this process, based on Category Theory. Its main characteristics is the Multiplicity Principle (MP) which asserts the existence of complex objects with several possible configurations. The MP entails the
Application of the model MES introduced by A. Ehresmann and J.-P. Vanbremeersch for multi-scale s... more Application of the model MES introduced by A. Ehresmann and J.-P. Vanbremeersch for multi-scale self-organized systems to design.
Monade, dyade et triade sont comme trois manières d’appréhender la relation comme chiffre intime ... more Monade, dyade et triade sont comme trois manières d’appréhender la relation comme chiffre intime de la réalité sous ses différentes modalités matérielles, organiques, culturelles et métaphysiques. Le parcours proposé est organisé autour de trois lieux qui ont trait à la théologique et à la métaphysique, aux sciences et philosophies des sciences, enfin à la culture et à l’identité. Au cours de cette exploration de la réalité, la relation se donne à voir comme tenue et différentiation à deux et à trois. Enfin, l’expérience montre que, quand des chercheurs venus d’horizons divers se disposent à une rencontre interdisciplinaire, alors se met en place une dynamique d’ouverture, d’écoute et de questionnement. Alors, la proximité des intervenants se révèle bien plus profonde que ne laissait supposer l’écart de leur spécialité respective.
Lecture Notes in Computer Science, 2013
Lecture Notes in Computer Science, 2011
This paper discusses the rebirth of the old quest for the principles of biology along the discour... more This paper discusses the rebirth of the old quest for the principles of biology along the discourse line of machine-organism disanalogy and within the context of biocomputation from a modern perspective. It reviews some new attempts to revise the existing body of research and enhance it with new developments in some promising fields of mathematics and computation. The major challenge is that the latter are expected to also answer the need for a new framework, a new language and a new methodology capable of closing the existing gap between the different levels of complex system organization.
International Journal of General Systems, 2004
ABSTRACT The aim of the paper is to compare two different approaches to the modeling of complex n... more ABSTRACT The aim of the paper is to compare two different approaches to the modeling of complex natural systems, in particular of their hierarchical organization with higher-order structures and their emergence processes. These approaches are, respectively, the hyperstructures (HS) of Baas and the memory evolutive systems (MES) of Ehresmann and Vanbremeersch. The HS are “structural” while MES, based on category theory, take dynamics more into account. It is shown how the dynamical organization and mechanisms developed for MES rely on simple ideas of a philosophical nature, that might be disengaged from the categorical setting and extended to the general frame of HS.
Bulletin of Mathematical Biology, 1987
Biosystems, 1997
The aim of this paper is to evaluate the role of symmetry and symmetrybreaking processes on the c... more The aim of this paper is to evaluate the role of symmetry and symmetrybreaking processes on the complex information processing developed by hierarchical evolutionary natural systems, such as biological, neural, social or cultural systems. The study is conducted in the frame of the Memory Evolutive Systems, which give a mathematical model of these systems. The dynamics of a MES is modulated by the competition between a net of internal regulation centers, which act apart but encode overlapping strategies which have to be equilibrated The main characteristics of these systems, at the root of their complexity and adaptability, is a symmetry-breaking in the passage from a higher (or macro) level to a lower (or micro) level: several disparate subsystems with different comportments at the micro level can be undistinguishable at the higher macro level because of a similar macro behavior (Multiplicity Principle). It is responsible for the development of a dialectics between heterogeneous regulation centers, and for the emergence in time of more and more complex objects. An application to neural systems vindicates an emergentist dynamical reduction of mental states to physical states.
Axiomathes, 2009
We comment on the preceding reviews of our book “Memory Evolutive Systems”, discussing the improv... more We comment on the preceding reviews of our book “Memory Evolutive Systems”, discussing the improvements proposed by some of the reviewers and answering to critics of others, in particular on the use of category theory for modeling living systems.
Axiomathes, 2006
ABSTRACT Robert Rosen has proposed several characteristics to distinguish “simple” physical syste... more ABSTRACT Robert Rosen has proposed several characteristics to distinguish “simple” physical systems (or “mechanisms”) from “complex” systems, such as living systems, which he calls “organisms”. The Memory Evolutive Systems (MES) introduced by the authors in preceding papers are shown to provide a mathematical model, based on category theory, which satisfies his characteristics of organisms, in particular the merger of the Aristotelian causes. Moreover they identify the condition for the emergence of objects and systems of increasing complexity. As an application, the cognitive system of an animal is modeled by the “MES of cat-neurons” obtained by successive complexifications of his neural system, in which the emergence of higher order cognitive processes gives support to Mario Bunge’s “emergentist monism.”
Integral Biomathics, 2012
Leslie S. Smith, Neuroscience and Natural Computing, UK [email protected] 2 _______________... more Leslie S. Smith, Neuroscience and Natural Computing, UK [email protected] 2 ______________________________________________________________________________ Note: This White Paper is not a concise report on the research program we seek to elaborate in INBIOSA. It has been conceived as a 'living' document, progressively developed along the months by discussions among scientists with differing formations and states of mind. We have chosen to respect their personalities, at the risk of some lack of homogeneity and repetitions between different passages. Also, incompleteness, inconsistences and antagonisms could not be completely avoided.
Drafts by Andrée Ehresmann
The goal of this paper is to advance an extensible theory of living systems using an approach to ... more The goal of this paper is to advance an extensible theory of living systems using an approach to biomathematics and biocomputation that suitably addresses self-organized, self-referential and anticipatory systems with multi-temporal multi-agents. Our first step is to provide foundations for modelling of emergent and evolving dynamic multi-level organic complexes and their sustentative processes in artificial and natural life systems. Main applications are in life sciences, medicine, ecology and astrobiology, as well as robotics, industrial automation, man-machine interface and creative design. Since 2011 over 100 scientists from a number of disciplines have been exploring a substantial set of theoretical frameworks for a comprehensive theory of life known as Integral Biomathics. That effort identified the need for a robust core model of organisms as dynamic wholes, using advanced and adequately computable mathematics. The work described here for that core combines the advantages of a situation and context aware multivalent computational logic for active self-organizing networks, Wandering Logic Intelligence (WLI), and a multi-scale dynamic category theory, Memory Evolutive Systems (MES), hence WLIMES. This is presented to the modeller via a formal augmented reality language as a first step towards practical modelling and simulation of multi-level living systems. Initial work focuses on the design and implementation of this visual language and calculus (VLC) and its graphical user interface. The results will be integrated within the current methodology and practices of theoretical biology and (personalized) medicine to deepen and to enhance the holistic understanding of life.
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Papers by Andrée Ehresmann
This paper sets out the case for support for this effort. The focus of the transformative research program proposal is biology-centric. We admit that biology to date has been more fact-oriented and less theoretical than physics. However, the key leverageable idea is that careful extension of the science of living systems can be more effectively applied to some of our most vexing modern problems than the prevailing scheme, derived from abstractions in physics. While these have some universal application and demonstrate computational advantages, they are not theoretically mandated for the living. A new set of mathematical abstractions derived from biology can now be similarly extended. This is made possible by leveraging new formal tools to understand abstraction and enable computability. [The latter has a much expanded meaning in our context from the one known and used in computer science and biology today, that is "by rote algorithmic means", since it is not known if a living system is computable in this sense (Mossio et al., 2009).] Two major challenges constitute the effort.
The first challenge is to design an original general system of abstractions within the biological domain. The initial issue is descriptive leading to the explanatory. There has not yet been a serious formal examination of the abstractions of the biological domain. What is used today is an amalgam; much is inherited from physics (via the bridging abstractions of chemistry) and there are many new abstractions from advances in mathematics (incentivized by the need for more capable computational analyses). Interspersed are abstractions, concepts and underlying assumptions “native” to biology and distinct from the mechanical language of physics and computation as we know them. A pressing agenda should be to single out the most concrete and at the same time the most fundamental process-units in biology and to recruit them into the descriptive domain. Therefore, the first challenge is to build a coherent formal system of abstractions and operations that is truly native to living systems.
Nothing will be thrown away, but many common methods will be philosophically recast, just as in physics relativity subsumed and reinterpreted Newtonian mechanics.
This step is required because we need a comprehensible, formal system to apply in many domains. Emphasis should be placed on the distinction between multi-perspective analysis and synthesis and on what could be the basic terms or tools needed.
The second challenge is relatively simple: the actual application of this set of biology-centric ways and means to cross-disciplinary problems. In its early stages, this will seem to be a “new science”.
This White Paper sets out the case of continuing support of Information and Communication Technology (ICT) for transformative research in biology and information processing centered on paradigm changes in the epistemological, ontological, mathematical and computational bases of the science of living systems. Today, curiously, living systems cannot be said to be anything more than dissipative structures organized internally by genetic information. There is not anything substantially different from abiotic systems other than the empirical nature of their robustness. We believe that there are other new and unique properties and patterns comprehensible at this bio-logical level. The report lays out a fundamental set of approaches to articulate these properties and patterns, and is composed as follows.
Sections 1 through 4 (preamble, introduction, motivation and major biomathematical problems) are incipient. Section 5 describes the issues affecting Integral Biomathics and Section 6 -- the aspects of the Grand Challenge we face with this project. Section 7 contemplates the effort to formalize a General Theory of Living Systems (GTLS) from what we have today. The goal is to have a formal system, equivalent to that which exists in the physics community. Here we define how to perceive the role of time in biology. Section 8 describes the initial efforts to apply this general theory of living systems in many domains, with special emphasis on cross-disciplinary problems and multiple domains spanning both “hard” and “soft” sciences. The expected result is a coherent collection of integrated mathematical techniques. Section 9 discusses the first two test cases, project proposals, of our approach. They are designed to demonstrate the ability of our approach to address “wicked problems” which span across physics, chemistry, biology, societies and societal dynamics. The solutions require integrated measurable results at multiple levels known as “grand challenges” to existing methods. Finally, Section 10 adheres to an appeal for action, advocating the necessity for further long-term support of the INBIOSA program.
The report is concluded with preliminary non-exclusive list of challenging research themes to address, as well as required administrative actions. The efforts described in the ten sections of this White Paper will proceed concurrently. Collectively, they describe a program that can be managed and measured as it progresses.
Keywords: integral biomathics, theoretical biology, biological mathematics, theoretical physics, endophysics, semiotics, observer-participation, developmental biology, neuroscience, natural computing, biocomputing, category theory, logic, positivism, scientific revolution, determinism, non-deterministic chaos, first-person perspective, complementarity, emergence, complexity, holism, reductionism, information, information integration, communication, change, development, hierarchies, scale and hyperscale, self-organization, autopoiesis, internalism, mechanicism, vagueness, class identity, individual identity, biological time, mind-body problem, non-locality, virtualization, distribution, genetic transcoding, neural systems, memory, cognition, consciousness, quantum effects in biology, life.
Drafts by Andrée Ehresmann
This paper sets out the case for support for this effort. The focus of the transformative research program proposal is biology-centric. We admit that biology to date has been more fact-oriented and less theoretical than physics. However, the key leverageable idea is that careful extension of the science of living systems can be more effectively applied to some of our most vexing modern problems than the prevailing scheme, derived from abstractions in physics. While these have some universal application and demonstrate computational advantages, they are not theoretically mandated for the living. A new set of mathematical abstractions derived from biology can now be similarly extended. This is made possible by leveraging new formal tools to understand abstraction and enable computability. [The latter has a much expanded meaning in our context from the one known and used in computer science and biology today, that is "by rote algorithmic means", since it is not known if a living system is computable in this sense (Mossio et al., 2009).] Two major challenges constitute the effort.
The first challenge is to design an original general system of abstractions within the biological domain. The initial issue is descriptive leading to the explanatory. There has not yet been a serious formal examination of the abstractions of the biological domain. What is used today is an amalgam; much is inherited from physics (via the bridging abstractions of chemistry) and there are many new abstractions from advances in mathematics (incentivized by the need for more capable computational analyses). Interspersed are abstractions, concepts and underlying assumptions “native” to biology and distinct from the mechanical language of physics and computation as we know them. A pressing agenda should be to single out the most concrete and at the same time the most fundamental process-units in biology and to recruit them into the descriptive domain. Therefore, the first challenge is to build a coherent formal system of abstractions and operations that is truly native to living systems.
Nothing will be thrown away, but many common methods will be philosophically recast, just as in physics relativity subsumed and reinterpreted Newtonian mechanics.
This step is required because we need a comprehensible, formal system to apply in many domains. Emphasis should be placed on the distinction between multi-perspective analysis and synthesis and on what could be the basic terms or tools needed.
The second challenge is relatively simple: the actual application of this set of biology-centric ways and means to cross-disciplinary problems. In its early stages, this will seem to be a “new science”.
This White Paper sets out the case of continuing support of Information and Communication Technology (ICT) for transformative research in biology and information processing centered on paradigm changes in the epistemological, ontological, mathematical and computational bases of the science of living systems. Today, curiously, living systems cannot be said to be anything more than dissipative structures organized internally by genetic information. There is not anything substantially different from abiotic systems other than the empirical nature of their robustness. We believe that there are other new and unique properties and patterns comprehensible at this bio-logical level. The report lays out a fundamental set of approaches to articulate these properties and patterns, and is composed as follows.
Sections 1 through 4 (preamble, introduction, motivation and major biomathematical problems) are incipient. Section 5 describes the issues affecting Integral Biomathics and Section 6 -- the aspects of the Grand Challenge we face with this project. Section 7 contemplates the effort to formalize a General Theory of Living Systems (GTLS) from what we have today. The goal is to have a formal system, equivalent to that which exists in the physics community. Here we define how to perceive the role of time in biology. Section 8 describes the initial efforts to apply this general theory of living systems in many domains, with special emphasis on cross-disciplinary problems and multiple domains spanning both “hard” and “soft” sciences. The expected result is a coherent collection of integrated mathematical techniques. Section 9 discusses the first two test cases, project proposals, of our approach. They are designed to demonstrate the ability of our approach to address “wicked problems” which span across physics, chemistry, biology, societies and societal dynamics. The solutions require integrated measurable results at multiple levels known as “grand challenges” to existing methods. Finally, Section 10 adheres to an appeal for action, advocating the necessity for further long-term support of the INBIOSA program.
The report is concluded with preliminary non-exclusive list of challenging research themes to address, as well as required administrative actions. The efforts described in the ten sections of this White Paper will proceed concurrently. Collectively, they describe a program that can be managed and measured as it progresses.
Keywords: integral biomathics, theoretical biology, biological mathematics, theoretical physics, endophysics, semiotics, observer-participation, developmental biology, neuroscience, natural computing, biocomputing, category theory, logic, positivism, scientific revolution, determinism, non-deterministic chaos, first-person perspective, complementarity, emergence, complexity, holism, reductionism, information, information integration, communication, change, development, hierarchies, scale and hyperscale, self-organization, autopoiesis, internalism, mechanicism, vagueness, class identity, individual identity, biological time, mind-body problem, non-locality, virtualization, distribution, genetic transcoding, neural systems, memory, cognition, consciousness, quantum effects in biology, life.