Morphological Computing as Logic Underlying Cognition in Human, Animal, and Intelligent Machine

This work examines the interconnections between logic, epistemology, and sciences within the Naturalist tradition. It presents a scheme that connects logic, mathematics, physics, chemistry, biology, and cognition, emphasizing scale-invariant, self-organizing dynamics across organizational tiers of nature. The inherent logic of agency exists in natural processes at various levels, under information exchanges. It applies to humans, animals, and artifactual agents. The common human-centric, natural language-based logic is an example of complex logic evolved by living organisms that already appears in the simplest form at the level of basal cognition of unicellular organisms. Thus, cognitive logic stems from the evolution of physical, chemical, and biological logic. In a computing nature framework with a self-organizing agency, innovative computational frameworks grounded in morphological/physical/natural computation can be used to explain the genesis of human-centered logic through the steps of naturalized logical processes at lower levels of organization. The Extended Evolutionary Synthesis of living agents is essential for understanding the emergence of human-level logic and the relationship between logic and information processing/computational epistemology. We conclude that more research is needed to elucidate the details of the mechanisms linking natural phenomena with the logic of agency in nature.Comment: 20 pages, no figure

Digestion, Habit, and Being at Home: Hegel and the Gut as Ambiguous Other

Recent work in the philosophy of biology argues that we must rethink the biological individual beyond the boundary of the species, given that a key part of our essential functioning is carried out by the bacteria in our intestines in a way that challenges any strictly genetic account of what is involved for the biological human. The gut is a kind of ambiguous other within our understanding of ourselves, particularly when we also consider the status of gastro-intestinal disorders. Hegel offers us theoretical tools to describe and understand our relationship to our gut. His description of our selves as continually mediated through otherness is strikingly compatible with the kind of structure contemporary biology presents us with. His accounts of digestion and habit, contextualized by his logic, help point toward an understanding of selfhood as porous and yet still capable of being sufficiently unified for us to make sense of ourselves, one which allows us to acknowledge otherness within us while still having enough unity for agency

Combining Luhmann and Actor-Network Theory to see Farm Enterprises as Self-organizing Systems

From a rural, sociological point of view no social theories have so far been able to grasp the ontological complexity and special character of a farm enterprise as an entity in a really satisfying way. The contention of this paper is that a combination of Luhmann’s theory of social systems and actor-network theory (ANT) of Latour, Callon, and Law offers a new and radical framework for understanding a farm as a self-organizing, heterogeneous system. Luhmann’s theory offers an approach to understand a farm as a self-organizing system (operating in meaning) that must produce and reproduce itself through demarcation from the surrounding world by selection of meaning. The meaning of the system is expressed through the goals, values, and the logic of the farming processes. His theory, however, is less useful when studying the heterogeneous character of a farm as a mixture of biology, sociology, technology, and economy. ANT offers an approach to focus on the heterogeneous network of interactions of human and non-human actors such as knowledge, technology, money, farmland, animals, plants, etc., and as to how these interactions depend on both the quality of the actors and the network context of interaction, but the theory is weak when it comes to explaining the self-organizing character of a farm enterprise

Practice-oriented controversies and borrowed epistemic credibility in current evolutionary biology: phylogeography as a case study

Although there is increasing recognition that theory and practice in science are intimately intertwined, philosophy of science perspectives on scientific controversies have been historically focused on theory rather than practice. As a step in the construction of frameworks for understanding controversies linked to scientific practices, here we introduce the notion of borrowed epistemic credibility (BEC), to describe the situation in which scientists, in order to garner support for their own stances, exploit similarities between tenets in their own field and accepted statements or positions properly developed within other areas of expertise. We illustrate the scope of application of our proposal with the analysis of a heavily methods-grounded, recent controversy in phylogeography, a biological subdiscipline concerned with the study of the historical causes of biogeographical variation through population genetics- and phylogenetics-based computer analyses of diversity in DNA sequences, both within species and between closely related taxa. Toward this end, we briefly summarize the arguments proposed by selected authors representing each side of the controversy: the ‘nested clade analysis’ school versus the ‘statistical phylogeography’ orientation. We claim that whereas both phylogeographic ‘research styles’ borrow epistemic credibility from sources such as formal logic, the familiarity of results from other scientific areas, the authority of prominent scientists, or the presumed superiority of quantitative vs. verbal reasoning, ‘theory’ plays essentially no role as a foundation of the controversy. Besides underscoring the importance of strictly methodological and other non-theoretical aspects of controversies in current evolutionary biology, our analysis suggests a perspective with potential usefulness for the re-examination of more general philosophy of biology issues, such as the nature of historical inference, rationality, justification, and objectivity

Combining Luhmann and Actor-Network Theory to see Farm Enterprises as Self-organizing Systems

From a rural, sociological point of view no social theories have so far been able to grasp the ontological complexity and special character of a farm enterprise as an entity in a really satisfying way. The contention of this paper is that a combination of Luhmann’s theory of social systems and the actor-network theory (ANT) of Latour, Callon, and Law offers a new and radical framework for understanding a farm as a self-organizing, heterogeneous system. Luhmann’s theory offers an approach to understand a farm as a self-organizing system (operating in meaning) that must produce and reproduce itself through demarcation from the surrounding world by selection of meaning. The meaning of the system is expressed through the goals, values, and logic of the farming processes. This theory is, however, less useful when studying the heterogeneous character of a farm as a mixture of biology, sociology, technology, and economy. ANT offers an approach to focus on the heterogeneous network of interactions of human and non-human actors, such as knowledge, technology, money, farmland, animals, plants, etc., and how these interactions depend on both the quality of the actors and the network context of interaction. But the theory is weak when it comes to explaining the self-organizing character of a farm enterprise. Using Peirce’s general semiotics as a platform, the two theories in combination open a new and radical framework for multidisciplinary studies of farm enterprises that may serve as a platform for communication between the different disciplines and approaches

Creation and Application of Various Tools for the Reconstruction, Curation, and Analysis of Genome-Scale Models of Metabolism

Systems biology uses mathematics tools, modeling, and analysis for holistic understanding and design of biological systems, allowing the investigation of metabolism and the generation of actionable hypotheses based on model analyses. Detailed here are several systems biology tools for model reconstruction, curation, analysis, and application through synthetic biology. The first, OptFill, is a holistic (whole model) and conservative (minimizing change) tool to aid in genome-scale model (GSM) reconstructions by filling metabolic gaps caused by lack of system knowledge. This is accomplished through Mixed Integer Linear Programming (MILP), one step of which may also be independently used as an additional curation tool. OptFill is applied to a GSM reconstruction of the melanized fungus Exophiala dermatitidis, which underwent various analyses investigating pigmentogenesis and similarity to human melanogenesis. Analysis suggest that carotenoids serve a currently unknown function in E. dermatitidis and that E. dermatitidis could serve as a model of human melanocytes for biomedical applications. Next, a new approach to dynamic Flux Balance Analysis (dFBA) is detailed, the Optimization- and Runge-Kutta- based Approach (ORKA). The ORKA is applied to the model plant Arabidopsis thaliana to show its ability to recreate in vivo observations. The analyzed model is more detailed than previous models, encompassing a larger time scale, modeling more tissues, and with higher accuracy. Finally, a pair of tools, the Eukaryotic Genetic Circuit Design (EuGeneCiD) and Modeling (EuGeneCiM) tools, is introduced which can aid in the design and modeling of synthetic biology applications hypothesized using systems biology. These tools bring a computational approach to synthetic biology, and are applied to Arabidopsis thaliana to design thousands of potential two-input genetic circuits which satisfy 27 different input and logic gate combinations. EuGeneCiM is further used to model a repressilator circuit. Efforts are ongoing to disseminate these tools to maximize their impact on the field of systems biology. Future research will include further investigation of E. dermatitidis through modeling and expanding my expertise to kinetic models of metabolism. Advisor: Rajib Sah

Quantum Biology

A critical assessment of the recent developments of molecular biology is presented. The thesis that they do not lead to a conceptual understanding of life and biological systems is defended. Maturana and Varela's concept of autopoiesis is briefly sketched and its logical circularity avoided by postulating the existence of underlying {\it living processes}, entailing amplification from the microscopic to the macroscopic scale, with increasing complexity in the passage from one scale to the other. Following such a line of thought, the currently accepted model of condensed matter, which is based on electrostatics and short-ranged forces, is criticized. It is suggested that the correct interpretation of quantum dispersion forces (van der Waals, hydrogen bonding, and so on) as quantum coherence effects hints at the necessity of including long-ranged forces (or mechanisms for them) in condensed matter theories of biological processes. Some quantum effects in biology are reviewed and quantum mechanics is acknowledged as conceptually important to biology since without it most (if not all) of the biological structures and signalling processes would not even exist. Moreover, it is suggested that long-range quantum coherent dynamics, including electron polarization, may be invoked to explain signal amplification process in biological systems in general

Canguilhem and the logic of life

In this paper we examine aspects of Canguilhem’s philosophy of biology, concerning the knowledge of life and its consequences on science and vitalism. His concept of life stems from the idea of a living individual, endowed with creative subjectivity and norms, a Kantian view which “disconcerts logic”. In contrast, two different approaches ground naturalistic perspectives to explore the logic of life (Jacob) and the logic of the living individual (Maturana and Varela) in the 1970s. Although Canguilhem is closer to the second, there are divergences; for example, unlike them, he does not dismiss vitalism, often referring to it in his work and even at times describing himself as a vitalist. The reason may lie in their different views of science

A Biologically Informed Hylomorphism

Although contemporary metaphysics has recently undergone a neo-Aristotelian revival wherein dispositions, or capacities are now commonplace in empirically grounded ontologies, being routinely utilised in theories of causality and modality, a central Aristotelian concept has yet to be given serious attention – the doctrine of hylomorphism. The reason for this is clear: while the Aristotelian ontological distinction between actuality and potentiality has proven to be a fruitful conceptual framework with which to model the operation of the natural world, the distinction between form and matter has yet to similarly earn its keep. In this chapter, I offer a first step toward showing that the hylomorphic framework is up to that task. To do so, I return to the birthplace of that doctrine - the biological realm. Utilising recent advances in developmental biology, I argue that the hylomorphic framework is an empirically adequate and conceptually rich explanatory schema with which to model the nature of organism