There is consensus within the chemosciences that olfactory perception is of the molecular structure of chemical compounds, yet within philosophical theories of smell there is little agreement about the nature of smell. The paper critically assesses the current state of debate regarding smells within philosophy in the hopes of setting it upon firm scientific footing. The theories to be covered are: Naïve Realism, Hedonic Theories, Process Theory, Odor Theories, and non-Objectivist Theories. The aforementioned theories will be evaluated (...) based on their explanations of the (a) the olfactory quality of a smell, (b) smells as distal entities, and (c) our experience of smells as intentional objects. The paper concludes with a defense of Molecular Structure Theory that demonstrating its superiority in accounting for each of these three aspects of smell. (shrink)

The type-level abstraction is a formal way to represent molecular structures in biological practice. Graphical representations of molecular structures of biological objects are also used to identify functional processes of things. This paper will reveal that category theory is a formal mathematical language not only to visualize molecular structures of biological objects as type-level abstraction formally but also to understand how to infer biological functions from the molecular structures of biological objects. Category theory is (...) a toolkit to understand biological knowledge at the type-level formally, not individual token-level, as well as typical heuristic strategies in molecular biology. (shrink)

Today, the lipid bilayer structure is nearly ubiquitous, taken for granted in even the most rudimentary introductions to cell biology. Yet the image of the lipid bilayer, built out of lipids with heads and tails, went from having obscure origins deep in colloid chemical theory in 1924 to being “obvious to any competent physical chemist” by 1935. This chapter examines how this schematic, strictly heuristic explanation of the idea of molecular orientation was developed within colloid physical chemistry, (...) and how the image was transformed into a reflection of the reality and agency of lipid molecules in the biological microworld. Whereas in physical and colloid chemistry these images considered secondary to instrumental measurement and mathematical modeling of surface phenomena, in biology the manipulable image of the lipid on paper became an essential tool for the molecularization of the cell. (shrink)

We perceive smells as perduring complex entities within a distal array that might be conceived of as smellscapes. However, the philosophical orthodoxy of Odor Theories has been to deny that smells are perceived as having a distal location. Recent challenges have been mounted to Odor Theories’ veracity in handling the timescale of olfactory perception, how it individuates odors as a distal entities, and their claim that olfactory perception is not spatial. The paper does not aim to dispute these criticisms. Rather, (...) what will be shown is that Molecular Structure Theory, a refinement of Odor Theory, can be further developed to handle these challenges. The theory is further refined by focusing on distal perception that requires considering the perceptual object as mereologically complex persisting odor against a background scene conceived of as a smellscape. What will be offered is an expansion of Molecular Structure Theory to account for distal smell perception within natural environments. (shrink)

It is arguably the case that olfactory system contains two senses that share the same type of stimuli, sensory transduction mechanism, and processing centers. Yet, orthonasal and retronasal olfaction differ in their types of perceptible objects as individuated by their sensory qualities. What will be explored in this paper is how the account of orthonasal smell developed in the Molecular Structure Theory of smell can be expanded for retronasal olfaction (Young, 2016, 2019a-b, 2020). By considering the object (...) of olfactory perception to be the molecular structure of chemical compounds composing odor plumes, Molecular Structure Theory provides a means for determining an odor’s olfactory quality, how odors can be identified and individuated, and how we perceive smellscapes. Surveying the differences between orthonasal and retronasal olfaction provides the basis for the central argument of the paper that the perceptible objects we refer to as smells and individuated on the basis of their olfactory qualities are only relative to orthonasal olfaction. Retronasal olfaction it is speculatively concluded might play an essential role in our perception of flavorful objects. (shrink)

Are living organisms--as Descartes argued--just machines? Or is the nature of life such that it can never be fully explained by mechanistic models? In this thought-provoking and controversial book, eminent geophysicist Walter M. Elsasser argues that the behavior of living organisms cannot be reduced to physico-chemical causality. Suggesting that molecular biology today is at the same point as Newtonian physics on the eve of the quantum revolution, Elsasser lays the foundation for a theoretical biology that points the way toward (...) a natural philosophy of organic life. Explicitly repudiating "vitalism" (the notion that the laws of nature need to be modified when applied to living organisms), Elsasser argues instead that the structural complexity of even a single living cell is "transcomputational"--that is, beyond the power of any imaginable system to compute. Beginning from this insight, Elsasser leads the reader through a step-by-step process that ultimately arrives at the conclusion that living and non-living matter are separated by "a no-man's land of irrationality." Trained in Germany as a physicist, Elsasser first pondered the implications of quantum mechanics for biology as early as 1951. The more closely he studied the inherent complexity of life, the more skeptical he became of the reductionist view of organisms as tiny machines. "An organism," he concluded, "is a source of causal chains which cannot be traced beyond a terminal point because they are lost in the unfathomable complexity of the organism." Like the physicist who works within the bounds of an unfathomable universe, Elsasser argues, the biologist must seek answers within a system that is no less unfathomable. (shrink)

This paper examines the adequacy of causal graph theory as a tool for modeling biological phenomena and formalizing biological explanations. I point out that the causal graph approach reaches it limits when it comes to modeling biological phenomena that involve complex spatial and structural relations. Using a case study from molecular biology, DNA-binding and -recognition of proteins, I argue that causal graph models fail to adequately represent and explain causal phenomena in this field. The inadequacy of these models (...) is due to their failure to include relevant spatial and structural information in a way that does not render the model non-explanatory, unmanageable, or inconsistent with basic assumptions of causal graph theory. (shrink)

Whether or not quantum physics can account for molecular structure is a matter of considerable controversy. Three of the problems raised in this regard are the problems of molecular structure. We argue that these problems are just special cases of the measurement problem of quantum mechanics: insofar as the measurement problem is solved, the problems of molecular structure are resolved as well. In addition, we explore one consequence of our argument: that claims about the (...) reduction or emergence of molecular structure cannot be settled independently of the choice of a particular resolution to the measurement problem. Specifically, we consider how three standard putative solutions to the measurement problem inform our under- standing of a molecule in isolation, as well as of chemistry’s relation to quantum physics. (shrink)

One of the most plausible and widely discussed examples of strong emergence is molecular structure. The only detailed account of it, which has been very influential, is due to Robin Hendry and is formulated in terms of downward causation. This paper explains Hendry’s account of the strong emergence of molecular structure and argues that it is coherent only if one assumes a diachronic reflexive notion of downward causation. However, in the context of this notion of downward (...) causation, the strong emergence of molecular structure faces three challenges that have not been met and which have so far remained unnoticed. First, the putative empirical evidence presented for the strong emergence of molecular structure equally undermines supervenience, which is one of the main tenets of strong emergence. Secondly, it is ambiguous how the assumption of determinate nuclear positions is invoked for the support of strong emergence, as the role of this assumption in Hendry’s argument can be interpreted in more than one way. Lastly, there are understandings of causation which render the postulation of a downward causal relation between a molecule’s structure and its quantum mechanical entities, untenable. (shrink)

In the author’s previous contribution to this journal (Rosen 2015), a phenomenological string theory was proposed based on qualitative topology and hypercomplex numbers. The current paper takes this further by delving into the ancient Chinese origin of phenomenological string theory. First, we discover a connection between the Klein bottle, which is crucial to the theory, and the Ho-t’u, a Chinese number archetype central to Taoist cosmology. The two structures are seen to mirror each other in expressing the (...) psychophysical (phenomenological) action pattern at the heart of microphysics. But tackling the question of quantum gravity requires that a whole family of topological dimensions be brought into play. What we find in engaging with these structures is a closely related family of Taoist forebears that, in concert with their successors, provide a blueprint for cosmic evolution. Whereas conventional string theory accounts for the generation of nature’s fundamental forces via a notion of symmetry breaking that is essentially static and thus unable to explain cosmogony successfully, phenomenological/Taoist string theory entails the dialectical interplay of symmetry and asymmetry inherent in the principle of synsymmetry. This dynamic concept of cosmic change is elaborated on in the three concluding sections of the paper. Here, a detailed analysis of cosmogony is offered, first in terms of the theory of dimensional development and its Taoist (yin-yang) counterpart, then in terms of the evolution of the elemental force particles through cycles of expansion and contraction in a spiraling universe. The paper closes by considering the role of the analyst per se in the further evolution of the cosmos. (shrink)

The Mystery of Human Consciousness: Atomic Origins and Universal Inquiry -/- Human beings are, at their core, atomic in nature. Every cell in our body is composed of atoms arranged in complex molecular structures, forming tissues, organs, and ultimately, the human brain. Yet, despite being made of the same fundamental particles as the rest of the universe, humans possess something extraordinary: consciousness, intelligence, and the ability to study the very laws that govern existence. This paradox raises profound philosophical, scientific, (...) and metaphysical questions. -/- The Atomic Nature of Humans -/- Modern science confirms that all matter, including living organisms, is composed of atoms. These atoms, governed by the laws of physics and chemistry, interact in predictable ways. The human brain, a highly sophisticated network of neurons, functions through electrical and biochemical processes, yet it gives rise to thoughts, emotions, and self-awareness. How do these atomic interactions lead to the emergence of consciousness? This remains one of the greatest mysteries in both science and philosophy. -/- The Drive to Study Natural Laws -/- Despite being bound by the same physical principles as the rest of nature, human intelligence seeks to understand and manipulate these laws. This drive has led to remarkable advancements in physics, medicine, engineering, and philosophy. The question arises: why do humans have this intellectual curiosity? Is it purely an evolutionary adaptation for survival, or is there a deeper reason for our need to understand the universe? -/- One possible explanation is that consciousness is an emergent property of complex systems. The human brain, with its intricate network of neurons, may reach a threshold of complexity that enables self-awareness and abstract thought. However, some argue that intelligence and consciousness cannot be fully explained by physical interactions alone, suggesting the influence of a deeper, possibly universal, intelligence guiding human evolution. -/- The Paradox of Consciousness and Physical Laws -/- If the mind is purely a product of atomic interactions, it raises an important paradox: how can something that follows deterministic physical laws experience free will and creativity? This dilemma has led scientists and philosophers to explore theories that go beyond classical physics, such as quantum mechanics, which suggests that subatomic particles behave in ways that are not strictly deterministic. Some speculate that consciousness itself may be linked to quantum processes, bridging the gap between the physical and the metaphysical. -/- Implications for Human Understanding -/- The mystery of human consciousness challenges both science and philosophy. If intelligence and self-awareness are purely emergent properties of atomic interactions, then the potential for artificial intelligence to reach human-like consciousness remains an open question. On the other hand, if consciousness is guided by a universal intelligence, as some theories suggest, it implies a deeper purpose to human existence beyond mere physical survival. -/- Furthermore, this discussion aligns with the principle that human decision-making follows natural laws, as proposed by the universal law of balance in nature. If consciousness arises through a balance of atomic and energetic interactions, then understanding this balance could provide insights into optimizing human thought, behavior, and societal progress. -/- Conclusion -/- The study of human consciousness, rooted in atomic nature yet capable of self-awareness, is one of the most profound inquiries in human history. Whether it can be fully explained through scientific investigation or requires a broader metaphysical perspective remains an open question. Regardless of the answer, the human drive to understand the universe is a testament to the mystery and wonder of our existence. Perhaps, in unlocking the secrets of consciousness, we may come closer to understanding our true place in the cosmos. -/- . (shrink)

In this article I examine several related views expressed by Robin Hendry concerning molecular structure, emergence and chemical bonding. There is a long-standing problem in the philosophy of chemistry arising from the fact that molecular structure cannot be strictly derived from quantum mechanics. Two or more compounds which share a molecular formula, but which differ with respect to their structures, have identical Hamiltonian operators within the quantum mechanical formalism. As a consequence, the properties of all (...) such isomers yield precisely the same calculated quantities such as their energies, dipole moments etc. The only means through which the difference between the isomers can be recovered is to build their structures into the quantum mechanical calculations, something that is carried out by the application of the Born-Oppenheimer approximation. Consequently, it has been argued by many authors that molecular structure is written in ‘by hand’ rather than derived. Robin Hendry is one such author, but he goes a great deal further by proposing that this situation implies the existence of emergence and downward causation. In the current article I argue that there are alternative explanations which render emergence and downward causation redundant. Such an alternative lies in the notion of quantum decoherence and the appeal to work in the foundations of physics, which posits that the various isomers exist as a superposition until their wavefunctions are collapsed either by observation or by interacting with their environment. Hendry also alludes to a debate among chemists as to whether chemical bonds are real or not, in the sense of directional connections between two or more nuclei in any given molecule. I reject this view and propose that the structural and energetic views of chemical bonding, that have been discussed by some philosophers of chemistry including Hendry, do not refer to any essential ontological differences. I agree that chemists view bonding in a more realistic fashion and may consider bonds to be in some senses real, while physicists may consider bonding in more abstract energetic terms. However, I do not believe that such differences in scientific practice and attitudes should be considered to offer a window as to the ontological status of bonding or whether bonding is real. Finally, I discuss the kinetic energy school of chemical bonding which would seem to challenge any notion of bonds as directional entities, since bonding is no longer regarded as being primarily due to the build-up of electron density between nuclei. (shrink)

Precision medicine and molecular systems medicine (MSM) are highly utilized and successful approaches to improve understanding, diagnosis, and treatment of many diseases from bench-to-bedside. Especially in the COVID-19 pandemic, molecular techniques and biotechnological innovation have proven to be of utmost importance for rapid developments in disease diagnostics and treatment, including DNA and RNA sequencing technology, treatment with drugs and natural products and vaccine development. The COVID-19 crisis, however, has also demonstrated the need for systemic thinking and transdisciplinarity and (...) the limits of MSM: the neglect of the bio-psycho-social systemic nature of humans and their context as the object of individual therapeutic and population-oriented interventions. COVID-19 illustrates how a medical problem requires a transdisciplinary approach in epidemiology, pathology, internal medicine, public health, environmental medicine, and socio-economic modeling. Regarding the need for conceptual integration of these different kinds of knowledge we suggest the application of general system theory (GST). This approach endorses an organism-centered view on health and disease, which according to Ludwig von Bertalanffy who was the founder of GST, we call Organismal Systems Medicine (OSM). We argue that systems science offers wider applications in the field of pathology and can contribute to an integrative systems medicine by (i) integration of evidence across functional and structural differentially scaled subsystems, (ii) conceptualization of complex multilevel systems, and (iii) suggesting mechanisms and non-linear relationships underlying the observed phenomena. We underline these points with a proposal on multi-level systems pathology including neurophysiology, endocrinology, immune system, genetics, and general metabolism. An integration of these areas is necessary to understand excess mortality rates and polypharmacological treatments. In the pandemic era this multi-level systems pathology is most important to assess potential vaccines, their effectiveness, short-, and long-time adverse effects. We further argue that these conceptual frameworks are not only valid in the COVID-19 era but also important to be integrated in a medicinal curriculum. (shrink)

Why are computers so smart these days? And why are humans apparently still a bit smarter? Does this have something to do with the difference between data and meaning? Does this in turn mean that at least some abstract entities, such as numbers, exist independently of human thought? Wouldn’t that require an expansion of our scientific world view? And would that at all be compatible with what we know about our world from physics and chemistry, philosophy, psychology, neuroscience and the (...) theory of evolution? Finally, what would this tell us about ethical and aesthetic value theories? These and related questions will be discussed in this book. We will find that the difference between data and meaning, i.e. quantitative and qualitative information, does indeed appear to be of central importance for understanding both artificial and natural intelligence. And then the independent existence of abstract entities not only appears to be a particularly promising hypothesis, but also one that is entirely compatible with the sum of our scientific knowledge, especially with regard to value theories. The book thus arrives at the exploration of a scientifically tenable, panpsychistically inspired, objective idealism that can be derived from our most fundamental intuitions as subjects that perceive qualities, but that can also take into account the structuring of the world already at the micro-scale, found in the modern natural sciences. The result is a Platonic, but in a second step also a scientific realism and a naturalism in the sense that it is informed by the natural sciences in terms of an inductive metaphysics. An objective idealism, not in a rationalistic maximum form, but in a pragmatic minimum form; without eternal truths, but dependent on the continued philosophical-scientific and also philosophicalsocial dialog. The proposed model could offer interesting solutions to a number of problems at and near the mind/matter boundary: Proposals are being considered for the interpretation of quantum mechanics, the problem of molecular symmetry, the neuronal code and the binding problem in neuroscience, mental causation, a more holistic understanding of mental processes, and so on and so forth. However, the extent to which the model threatens to promise far too much is also being discussed. In sum, the core question is how we can imagine human thinking beyond physically conceived information processing. An alternative model of human thinking is then put up for discussion, for which not only machine-like cognitive performance, but above all the intentional perception of qualitative information, i.e. of abstract entities, would be central, as well as the free, ultimately creative linking of patterns of quantitative information (signals, data) with such qualities (meanings). (shrink)

(v.3) In this paper it is argued that Barad's Agential Realism, an approach to quantum mechanics originating in the philosophy of Niels Bohr, can be the basis of a 'theory of everything' consistent with a proposal of Wheeler that 'observer-participancy is the foundation of everything'. On the one hand, agential realism can be grounded in models of self- organisation such as the hypercycles of Eigen, while on the other agential realism, by virtue of the 'discursive practices' that constitute one (...) aspect of the theory, implies the possibility of the generation of physical phenomena through acts of specification originating at a more fundamental level. This kind of order stems from the association of persisting structures with special mechanisms for sustaining such structures. Included in phenomena that may be generated by these mechanisms are the origin and evolution of life, and human capacities such as mathematical and musical intuition. (shrink)

The neutral theory often is presented as a theory of "noise" or silent changes at an isolated "molecular level", relevant to marking the steady pace of divergence, but not to the origin of biological structure, function, or complexity. Nevertheless, precisely these issues can be addressed in neutral models, such as those elaborated here in regard to scrambled ciliate genes, gRNA-mediated RNA editing, the transition from self-splicing to spliceosomal splicing, and the retention of duplicate genes. All of (...) these are instances of a more general scheme of "constructive neutral evolution" that invokes biased variation, epistatic interactions, and excess capacities to account for a complex series of steps giving rise to novel structures or operations. The directional and constructive outcomes of these models are not due to neutral allele fixations per se, but to these other factors. Neutral models of this type may help to clarify the poorly understood role of non-selective factors in evolutionary innovation and directionality. (shrink)

The maturation of the physical image has made apparent the limits of our scientific understanding of fundamental reality. These limitations serve as motivation for a new form of metaphysical inquiry that restricts itself to broadly scientific methods. Contributing towards this goal we combine the mathematical universe hypothesis as developed by Max Tegmark with the axioms of Stewart Shapiro’s structure theory. The result is a theory we call the Theory of the Structural Multiverse (TSM). The focus is (...) on informal theory development and constraint satisfaction. Some empirical consequences of the theory are worked out, in particular the feasibility of a predictive observer selection effect. The explanatory, unifying, and generative powers of the theory are found to substantially support the theory. The TSM is demonstrated to be an empirically significant scientific theory that is foundational to and continuous with the rest of the scientific image. (shrink)

While many different mechanisms contribute to the generation of spatial order in biological development, the formation of morphogenetic fields which in turn direct cell responses giving rise to pattern and form are of major importance and essential for embryogenesis and regeneration. Most likely the fields represent concentration patterns of substances produced by molecular kinetics. Short range autocatalytic activation in conjunction with longer range “lateral” inhibition or depletion effects is capable of generating such patterns (Gierer and Meinhardt, 1972). Non-linear reactions (...) are required, and mathematical criteria were derived to design molecular models capable of pattern generation. The classical embryological feature of proportion regulation can be incorporated into the models. The conditions are mathematically necessary for the simplest two-factor case, and are likely to be a fair approximation in multi-component systems in which activation and inhibition are systems parameters subsuming the action of several agents. Gradients, symmetric and periodic patterns, in one or two dimensions, stable or pulsing in time, can be generated on this basis. Our basic concept of autocatalysis in conjunction with lateral inhibition accounts for self-regulatory biological features, including the reproducible formation of structures from near-uniform initial conditions as required by the logic of the generation cycle. Real tissue form, for instance that of budding Hydra, may often be traced back to local curvature arising within an initially relatively flat cell sheet, the position of evagination being determined by morphogenetic fields. Shell theory developed for architecture may also be applied to such biological processes. (shrink)

Computational Functionalism is a subfield of philosophy of mind most relevant to the subject of cognitive science as well as to artificial intelligence (AI). The analysis of this paper focuses on Hilary Putnam’s and Gualtiero Piccinini’s standpoints regarding the molecular understanding of computation. Finally, Putnam’s argument of the functionalism in notion of the mental states is based on the positive definition of those states by their functions, while Piccinini, and on the other hand suggest that an understanding of the (...) mechanism of computation will go a long way to explaining cognition. This research also points out shortcomings of functionalism in their theories especially in regards to connectivity with physicality of AI structures. Therefore, the paper identifies the following gaps: The first gap holds that although both theorists have important insights, the two approaches put forward by the respective theorists are flawed and a better proposal is required, then a new proposal is suggested In identifying these gaps, the paper seeks to contribute to the literature by arguing for the need to develop a composite of the two theorists. The results show that the big ideas are important in present-day AI debate and analysis, which helps to explain the mind as computation. (shrink)

All theory makes assumptions about the nature of reality (either implicitly or explicitly) and such ontological assumptions necessarily regulate how one studies the things and events under investigation. Successful study is inex- tricably dependent upon an adequate ontology. As Bryant neatly puts it, "Effective application, in turn, is connected with adequate working assumptions about the constitution of society. Argument about the constitution of society is thus not a recondite activity which most sociologists [and organi- sation theorists] can safely ignore" (...) (1995: 58, interpolation added). The central concern in this paper is with the ontological underpinnings of much of the current literature in organisation studies in respect of struc- ture and culture. It will be argued that conflation of irreducible and causally-efficacious strata of social reality in the shape of social structure and culture permeates much of the current literature, thus rendering analysis of the interplay between them and their relationship with human agency diffi- cult to elucidate. The ontological underpinnings of organisational analysis have arguably turned full circle from the depth of social reality acknowl- edged by functionalism, structural Marxism and systems theory to the generic endorsement of Giddens’ structuration theory. As will be argued, Giddens’ theory entails a depthless ontology, which necessarily precludes methodological prescription. (shrink)

Without directly addressing the Demarcation Problem for logic—the problem of distinguishing logical vocabulary from others—we focus on distinctive aspects of logical vocabulary in pursuit of a second goal in the philosophy of logic, namely, proposing criteria for the justification of logical rules. Our preferred approach has three components. Two of these are effectively Belnap’s, but with a twist. We agree with Belnap’s response to Prior’s challenge to inferentialist characterisations of the meanings of logical constants. Belnap argued that for a logical (...) constant to exist, its rules must be conservative over a previously given consequence relation and guarantee the uniqueness of the constant. The twist is that we require logical vocabulary to be provably conservative, not over a previously given formal consequence relation, but over a previously given meaningful vocabulary of a language. Uniqueness is also a feature defined in terms of provability: if two syntactically distinguished expressions are governed by the same rules, then formulas with them as main operators are interderivable. Belnap’s criteria are not only those for the existence of a logical constant, but more: they are what distinguishes logical vocabulary from all other expressions. It is the defining mark of a logical constant that it is provably conservative over the fragment of the language which excludes it and that its rules guarantee its uniqueness. The third component is the topic neutrality of logic. The provable conservativeness of logic over a previously given vocabulary of a language is motivated, in part, by appeal to molecularism in the theory of meaning. Molecularity is a feature endorsed by the theory of meaning as a whole, so it does not distinguish logical constants from other expressions. The same is true for conservativeness. We argue that molecularity, and hence conservativeness, are implicit presuppositions of speakers’ use of language: the addition of new vocabulary to a language is presupposed to be conservative. But this presupposition is one that we should be able reflectively to endorse (such as when attempting a rational reconstruction of the use of the vocabulary). Thus, where conservativeness is found to fail, this defect should be remedied and the use of the vocabulary corrected (as in classical negation) or excised altogether (as in pejoratives). We go on to characterise a notion of topic neutrality, which we argue applies to logical vocabulary. We then note that reflective endorsement of the conservativeness of a topic neutral vocabulary requires a proof that the vocabulary is conservative relative to any base vocabulary. Thus we require that logical vocabulary be demonstrably conservative. Allying this requirement, distinctive of logic, to a general consideration about the commitments of assertion yields a mode of justification for logical constants akin to some conceptions of Harmony, i.e., to the idea that the consequences of assertion of a logical complex need to be warranted by the grounds and ought to be the strongest consequences warranted by the grounds. Intuitionistic logic acquires a somewhat familiar justification but emanating from a new motivation. (shrink)

Modern physics describes the mechanics of the Universe. We have discovered a new foundation for physics, which explains the components of the Universe with precision and depth. We quantify the existence of Aether, subatomic particles, and the force laws. Some aspects of the theory derive from the Standard Model, but much is unique. A key discovery from this new foundation is a mathematically correct Unified Force Theory. Other fundamental discoveries follow, including the origin of the fine structure (...) constant and subatomic particle g-factors, a slight correction of neutron magnetic moment, a geometrical structure for charge, the quantification of electromagnetic charge as separate from electrostatic charge, a more precise meaning of spin, the quantification of space-resonance in five dimensions, and a new system of quantum units. The Aether quantifies as a fabric of quantum rotating magnetic fields with electromagnetic, electrostatic, and gravitational dipole structures. Subatomic particles quantify as angular momentum encapsulated in a quantum, rotating magnetic field. All quantum, atomic, and molecular processes can be precisely modeled, leading to discrete physics with new understandings and insights. (shrink)

As Jaegwon Kim points out in his excellent new book, “reductionism” has become something of a pejorative term in philosophy and related disciplines. But originally (eg, as expressed in Ernest Nagel’s 1961 The Structure of Science) reduction was supposed to be a form of explanation, and one may wonder whether it is reasonable to reject in principle the advances in knowledge which such explanations may offer. Nagel’s own view, illustrated famously by the reduction of thermodynamics to statistical mechanics, was (...) that reduction is a relation between theories: theory A is reduced to theory B by formulating “bridge laws” which link the terminology of the theories, and using them to derive A from B. (An additional reductive claim is that Aphenomena are identical with certain B-phenomena—as when the temperature of a gas is identified with its mean molecular kinetic energy—but this kind of identity claim is, strictly speaking, independent of the claim about theories.) Applied to the case of mental states and brain states, a reduction would provide explanatory relations between psychology and neuroscience, normally supplemented with the claim that mental properties are identical with physical properties in the brain. (shrink)

While structural equations modeling is increasingly used in philosophical theorizing about causation, it remains unclear what it takes for a particular structural equations model to be correct. To the extent that this issue has been addressed, the consensus appears to be that it takes a certain family of causal counterfactuals being true. I argue that this account faces difficulties in securing the independent manipulability of the structural determination relations represented in a correct structural equations model. I then offer an alternate (...) understanding of structural determination, and I demonstrate that this theory guarantees that structural determination relations are independently manipulable. The account provides a straightforward way of understanding hypothetical interventions, as well as a criterion for distinguishing hypothetical changes in the values of variables which constitute interventions from those which do not. It additionally affords a semantics for causal counterfactual conditionals which is able to yield a clean solution to a problem case for the standard ‘closest possible world’ semantics. (shrink)

n this article the author develops a critique of reductionism in biological sciences from three different points of view. The first is related to the problem of reduction in the context of scientific theories. More specifically, reduction deals with a special form of intertheoretic relationship between molecular biology and the rest of biology. The second meaning of reductionism has to do with the significance of its genetic outfit for the ontogeny of an organism, i.e. its development from zygote to (...) its final or adult structure and function. Third, closely related to this more biological topic are questions about the anthropological consequences of the application of reductionistic methodologies for the explanation and evaluation of human behaviour. (shrink)

The theory of mind debate has reached a “hybrid consensus” concerning the status of theory-theory and simulation-theory. Extant hybrid models either specify co-dependency and implementation relations, or distribute mentalizing tasks according to folk-psychological categories. By relying on a non-developmental framework these models fail to capture the central connection between simulation and theory. I propose a “dynamic” hybrid that is informed by recent work on the nature of similarity cognition. I claim that Gentner’s model of (...) class='Hi'>structure-mapping allows us to understand simulation as a process in which psychological representations are aligned, causing the spontaneous abstraction of theoretical generalizations about the psychological domain. (shrink)

This book (in German) on "Physics, life and mind" is on the physical foundations of modern biology. The basic features of living systems, reproduction, mutation and metabolism, can be explained in terms of molecular processes involving nucleic acids as genetic material, and proteins as catalysts. The generation of structure and form in each generation results from spatiotemporal gene regulation in conjunction with the de novo formation of spatial order in which interplays of activation and inhibition play a crucial (...) part. Brain functions can be understood in terms of information processing in neural networks. Fundamental limitations of explanations of biological phenomena on the basis of physics are expected for the relation between neural and mental states, which may not be fully decodable by finite procedures. A complete algorithmic theory of the human mind encompassing all, including self-referential, aspects appears to be impossible even in principle, not only in practice. The range and limitations of explanations of life on the basis of physical laws and processes reflect the scope and limits of science in general. In contrast to the notions in circulation in the 19th century, modern science is open at the metatheoretical level to different philosophical, cultural and religious interpretations of man and the universe. -/- . (shrink)

Abstract This paper introduces a novel paradigm for aging that reinterprets biological senescence as a progressive decoherence of biological resonance fields, rather than a simple accumulation of cellular damage. Aging, we argue, is fundamentally an entropic phenomenon, where systemic synchronization breaks down across molecular, cellular, and cognitive scales, leading to loss of energy efficiency, structural deterioration, and perceptual time compression. Integrating quantum decoherence theory, resonance dynamics, and nonlinear thermodynamics, we propose that longevity is not merely a function of (...) genetic or biochemical integrity, but of coherence maintenance across biological oscillatory systems. Specifically, we examine how phase stability within metabolic cycles, mitochondrial function, neural oscillations, and epigenetic regulation directly correlates with both subjective time perception and lifespan extension. -/- We further explore whether time itself is an emergent property of coherence gradients, and whether interventions aimed at restoring biological phase-locking could modulate perceived time, slow down biological aging, and enhance cognitive efficiency. Experimental methodologies for validating this hypothesis are outlined, including: • Molecular phase-locking studies to analyze coherence shifts in aging cells. • Neurological synchrony measurements to assess time perception dilation as a function of cognitive coherence. • Metabolic oscillation modeling to determine whether biological time scales can be artificially extended. If aging is indeed a decoherence-driven loss of informational structure, then the implications extend beyond biology into cosmology, AI development, and theoretical physics. Understanding and modulating coherence fields may offer a new frontier in both longevity research and the very nature of how organisms experience time. (shrink)

This book is the fifth volume in the series of Collected Papers on Advancing Uncertain Combinatorics through Graphization, Hyperization, and Uncertainization: Fuzzy, Neutrosophic, Soft, Rough, and Beyond. This volume specifically delves into the concept of Various SuperHyperConcepts, building on the foundational advancements introduced in previous volumes. The series aims to explore the ongoing evolution of uncertain combinatorics through innovative methodologies such as graphization, hyperization, and uncertainization. These approaches integrate and extend core concepts from fuzzy, neutrosophic, soft, and rough set theories, (...) providing robust frameworks to model and analyze the inherent complexity of real-world uncertainties. At the heart of this series lies combinatorics and set theory—cornerstones of mathematics that address the study of counting, arrangements, and the relationships between collections under defined rules. Traditionally, combinatorics has excelled in solving problems involving uncertainty, while advancements in set theory have expanded its scope to include powerful constructs like fuzzy and neutrosophic sets. These advanced sets bring new dimensions to uncertainty modeling by capturing not just binary truth but also indeterminacy and falsity. In this fifth volume, the exploration of Various SuperHyperConcepts provides an innovative lens to address uncertainty, complexity, and hierarchical relationships. It synthesizes key methodologies introduced in earlier volumes, such as hyperization and neutrosophic extensions, while advancing new theories and applications. From pioneering hyperstructures to applications in advanced decision-making, language modeling, and neural networks, this book represents a significant leap forward in uncertain combinatorics and its practical implications across disciplines. -/- The book is structured into 17 chapters, each contributing unique perspectives and advancements in the realm of Various SuperHyperConcepts and their related frameworks: Chapter 1 introduces the concept of Body-Mind-Soul-Spirit Fluidity within psychology and phenomenology, while examining established social science frameworks like PDCA and DMAIC. It extends these frameworks using Neutrosophic Sets, a flexible extension of Fuzzy Sets, to improve their adaptability for mathematical and programming applications. The chapter emphasizes the potential of Neutrosophic theory to address multi-dimensional challenges in social sciences. Chapter 2 delves into the theoretical foundation of Hyperfunctions and their generalizations, such as Hyperrandomness and Hyperdecision-Making. It explores higher-order frameworks like Weak Hyperstructures, Hypergraphs, and Cognitive Hypermaps, aiming to establish their versatility in addressing multi-layered problems and setting a foundation for further studies. Chapter 3 extends traditional decision-making methodologies into HyperDecision-Making and n-SuperHyperDecision-Making. By building on approaches like MCDM and TOPSIS, this chapter develops frameworks capable of addressing complex decision-making scenarios, emphasizing their applicability in dynamic, multi-objective contexts. Chapter 4 explores integrating uncertainty frameworks, including Fuzzy, Neutrosophic, and Plithogenic Sets, into Large Language Models (LLMs). It proposes innovative models like Large Uncertain Language Models and Natural Uncertain Language Processing, integrating hierarchical and generalized structures to advance the handling of uncertainty in linguistic representation and processing. Chapter 5 introduces the Natural n-Superhyper Plithogenic Language by synthesizing natural language, plithogenic frameworks, and superhyperstructures. This innovative construct seeks to address challenges in advanced linguistic and structural modeling, blending attributes of uncertainty, complexity, and hierarchical abstraction. Chapter 6 defines mathematical extensions such as NeutroHyperstructures and AntiHyperstructures using the Neutrosophic Triplet framework. It formalizes structures like neutro-superhyperstructures, advancing classical frameworks into higher-dimensional realms. Chapter 7 explores the extension of Binary Code, Gray Code, and Floorplans through hyperstructures and superhyperstructures. It highlights their iterative and hierarchical applications, demonstrating their adaptability for complex data encoding and geometric arrangement challenges. Chapter 8 investigates the Neutrosophic TwoFold SuperhyperAlgebra, combining classical algebraic operations with neutrosophic components. This chapter expands upon existing algebraic structures like Hyperalgebra and AntiAlgebra, exploring hybrid frameworks for advanced mathematical modeling. Chapter 9 introduces Hyper Z-Numbers and SuperHyper Z-Numbers by extending the traditional Z-Number framework with hyperstructures. These extensions aim to represent uncertain information in more complex and multidimensional contexts. Chapter 10 revisits category theory through the lens of hypercategories and superhypercategories. By incorporating hierarchical and iterative abstractions, this chapter extends the foundational principles of category theory to more complex and layered structures. Chapter 11 formalizes the concept of n-SuperHyperBranch-width and its theoretical properties. By extending hypergraphs into superhypergraphs, the chapter explores recursive structures and their potential for representing intricate hierarchical relationships. Chapter 12 examines superhyperstructures of partitions, integrals, and spaces, proposing a framework for advancing mathematical abstraction. It highlights the potential applications of these generalizations in addressing hierarchical and multi-layered problems. Chapter 13 revisits Rough, HyperRough, and SuperHyperRough Sets, introducing new concepts like Tree-HyperRough Sets. The chapter connects these frameworks to advanced approaches for modeling uncertainty and complex relationships. Chapter 14 explores Plithogenic SuperHyperStructures and their applications in decision-making, control, and neuro systems. By integrating these advanced frameworks, the chapter proposes innovative directions for extending existing systems to handle multi-attribute and contradictory properties. Chapter 15 focuses on superhypergraphs, expanding hypergraph concepts to model complex structural types like arboreal and molecular superhypergraphs. It introduces Generalized n-th Powersets as a unifying framework for broader mathematical applications, while also touching on hyperlanguage processing. Chapter 16 defines NeutroHypergeometry and AntiHypergeometry as extensions of classical geometric structures. Using the Geometric Neutrosophic Triplet, the chapter demonstrates the flexibility of these frameworks in representing multi-dimensional and uncertain relationships. Chapter 17 establishes the theoretical groundwork for SuperHyperGraph Neural Networks and Plithogenic Graph Neural Networks. By integrating advanced graph structures, this chapter opens pathways for applying neural networks to more intricate and uncertain data representations. (shrink)

The recent advent of high-resolution imaging and force spectroscopy using atomic force mi- croscopy (AFM) in organic and inorganic solutions opens the way to imaging a wide variety of surfaces and their solvent structure. However, to take full advantage of the high resolution and provide signicant new analytical capability, a detailed understanding of the background contrast mechanisms that lead to atomic and molecular resolution is critical. Without a theory that connects the measured force to atomic models of (...) the surface and tip of the microscope, the information that can be distilled from these measurements is limited. Molecular dynamics simulations show that the forces acting on the microscope tip result from the direct interaction between a tip and a surface and are entirely due to the structure of water around the tip and surface. (shrink)

Symmetries play a major role in physics, in particular since the work by E. Noether and H. Weyl in the first half of last century. Herein, we briefly review their role by recalling how symmetry changes allow to conceptually move from classical to relativistic and quantum physics. We then introduce our ongoing theoretical analysis in biology and show that symmetries play a radically different role in this discipline, when compared to those in current physics. By this comparison, we stress that (...) symmetries must be understood in relation to conservation and stability properties, as represented in the theories. We posit that the dynamics of biological organisms, in their various levels of organization, are not just processes, but permanent (extended, in our terminology) critical transitions and, thus, symmetry changes. Within the limits of a relative structural stability (or interval of viability), variability is at the core of these transitions. (shrink)

This paper argues that the theory of structured propositions is not undermined by the Russell-Myhill paradox. I develop a theory of structured propositions in which the Russell-Myhill paradox doesn't arise: the theory does not involve ramification or compromises to the underlying logic, but rather rejects common assumptions, encoded in the notation of the $\lambda$-calculus, about what properties and relations can be built. I argue that the structuralist had independent reasons to reject these underlying assumptions. The theory (...) is given both a diagrammatic representation, and a logical representation in a novel language. In the latter half of the paper I turn to some technical questions concerning the treatment of quantification, and demonstrate various equivalences between the diagrammatic and logical representations, and a fragment of the $\lambda$-calculus. (shrink)

Alasia Nuti’s recent book Injustice and the Reproduction of History: Structural Inequalities, Gender and Redress puts forward a compelling vision of contemporary duties to redress past wrongdoing, grounded in the idea of “historical-structural-injustice”, constituted by the “structural reproduction of an unjust history over time and through changes”. Such an approach promises to transcend the familiar scholarly divide between “backward-looking” and “forward-looking” models, and allow for a reparative approach that focuses specifically on those past wrongs that impact the present, while retaining (...) a significant focus on the historical. While Nuti’s work is perhaps the most sophisticated treatment of structural injustice to date, this paper argues that an exclusive concentration on historical-structural-injustices neglects some aspects and some acts of wrongdoing that call out for present-day redress. What is needed, therefore, is a pluralist theory that can accept the pressing force in the present of historical-structural-injustices, whilst also making room for past-regarding duties that either do not fit, or are not best conceptualized in terms of, this approach, without being overwhelmed by the sheer scale of historic injustice. (shrink)

We model scientific theories as Bayesian networks. Nodes carry credences and function as abstract representations of propositions within the structure. Directed links carry conditional probabilities and represent connections between those propositions. Updating is Bayesian across the network as a whole. The impact of evidence at one point within a scientific theory can have a very different impact on the network than does evidence of the same strength at a different point. A Bayesian model allows us to envisage and (...) analyze the differential impact of evidence and credence change at different points within a single network and across different theoretical structures. (shrink)

Physical theories are complex and necessary tools for gaining new knowledge about their areas of application. A distinction is made between abstract and practical theories. The last are constantly being improved in the cognitive activity of professional physicists and studied by future physicists. A variant of the philosophy of physics based on a modified structural-nominative reconstruction of practical theories is proposed. Readers should decide whether this option is useful for their understanding of the philosophy of physics, as well as other (...) philosophies of particular sciences. (shrink)

It is exhibited that mature scientific economical theory is a set of propositions that describe the relationship between theoretical objects of two types - basic objects and derivative ones. The set of basic objects makes up the aggregate of initial idealizations (the Fundamental Theoretical Scheme or FTS) with no direct reference to experimental data. The derivative theoretical objects are formed from the basic ones according to certain rules. The sets of derivative objects form partial theoretical schemes or PTS. Any (...) mature economics scientific theory grows due to transitions, in order to describe each new experimental situation, from FTS to PTS. Each PTS construction from the FTS represents a problem that cannot be reduced to a strict algorithm. (shrink)

A strong motivation for the human genome project was to relate biological features to the structure and function of small sets of genes, and ideally to individual genes. However, it is now increasingly realized that many problems require a "systems" approach emphasizing the interplay of large numbers of genes, and the involvement of complex networks of gene regulation. This implies a new emphasis on integrative, systems theoretical approaches. It may be called 'holistic' if the term is used without irrational (...) overtones, in the general sense of directing attention to integrated features of organs and organisms. In the history of biology, seemingly conflicting reductionist and holistic notions have alternated, with bottom-up as well as top-down approaches eventually contributing to the solutions of basic problems. By now, there is no doubt that biological features and phenomena are rooted in physico-chemical processes of the molecules involved; and yet, integrated systems aspects are becoming more and more relevant in developmental biology, brain and behavioural science, and socio-biology. -/- . (shrink)

The layers of a solvent liquid flowing around a moving molecule have a finite thickness corresponding to the finite dimensions of the solvent molecules. Taking this feature into account leads to a modification of Stokes’ laws of the relation between friction and viscosity in continuous media. We derive the observed order of magnitude of the microfriction, for rotation as well as translation, and its approximately correct dependence on the radii of moving and solvent molecules.

Structural analogies connect Williamson’s epistemology and action theory: for example, action is the direction-of-fit mirror image of knowledge, and knowledge stands to belief as action stands to intention. These structural analogies, for Williamson, are meant to illuminate more generally how ‘mirrors’ reversing direction of fit should be understood as connecting the spectrum of our cognitive and practically oriented mental states. This paper has two central aims, one negative and the other positive. The negative aim is to highlight some intractable (...) problems with Williamson’s preferred analogical picture, which links the cognitive and the practical through the nexus of direction-of-fit mirroring. The positive aim of the paper is to propose a better alternative. In particular, we show that an achievement-theoretic proposal captures what is in common across the range of attitudes that exhibit the kind of structure that knowledge-belief, action-desire/intention do, while at the same time avoiding the problems shown to face Williamson’s proposed picture. Moreover, we draw attention to several key theoretical benefits of embracing our proposed achievement-theoretic picture, including some of the key benefits of the knowledge-first programme that Williamson’s own analogies were designed to secure. (shrink)

This unpublished paper, written in 2005 in the PhD philosophy program at Notre Dame, argues that algebraic structural realism faces a potentially fatal difficulty raised by the existence of inequivalent representations in quantum field theory.

This paper argues that the future of capabilities approach lies on the theoretical development of the democratic political structure. For this purpose, we take into account Martha Nussbaum’s late theoretical works. Firstly, we argue that the capability approach can be divided into two main models: the top down and the bottom up. Nussbaum, for example, endorses a top-down model, which it begins from an abstractive theory of partial justice and then draws the issue of institutional implementation. On the (...) other hand, Amartya Sem advocates the bottom-up model, which starts from the immanent demands of justice from public sphere and then up to normative and abstract questions (like his “idea of justice”). In the second part of this paper, we present Nussbaum’s partial theory of justice, arguing that it is mainly composed by four issues: (a) the elaboration of the list of capabilities, (b) the process of normative evaluation, (c) arguments for stability, (d) the implementation of the model. About this last topic, we argue in the third part that the current theoretical advance of the capabilities approach lies on the issue of the democratic political structure. In other words, the future of capabilities approach depends on the interaction between its own theory and a theory of democracy. Finally, in the last section we provide a re-elaboration of Nussbaum’s threshold level of capabilities (the list) in order to make it more adherent with the democratic political structure. (shrink)

Lukács is widely recognized as being the first critical theorist to have explicitly developed the idea of a “standpoint theory”. According to such a theory, members of oppressed groups enjoy an epistemic privilege regarding the nature of their oppression. However, there is no agreement regarding what precise argument Lukács offers for his claims regarding the alleged epistemic privilege of the working class. Additionally, it remains unclear whether later feminist standpoint theories share any continuity with Lukács’s argument. In this (...) analysis, I identify four arguments for the epistemic privilege of oppressed groups that could be attributed to Lukács. I argue that, although Lukács does not consistently endorse any specific argument, the most promising interpretation suggests that epistemic privilege arises from a contradiction between the norms that guide the self-understanding of such groups and the effects of the social practices they are socially obligated to engage in. (shrink)

Set-theoretic and category-theoretic foundations represent different perspectives on mathematical subject matter. In particular, category-theoretic language focusses on properties that can be determined up to isomorphism within a category, whereas set theory admits of properties determined by the internal structure of the membership relation. Various objections have been raised against this aspect of set theory in the category-theoretic literature. In this article, we advocate a methodological pluralism concerning the two foundational languages, and provide a theory that fruitfully (...) interrelates a `structural' perspective to a set-theoretic one. We present a set-theoretic system that is able to talk about structures more naturally, and argue that it provides an important perspective on plausibly structural properties such as cardinality. We conclude the language of set theory can provide useful information about the notion of mathematical structure. (shrink)

Set-theoretic and category-theoretic foundations represent different perspectives on mathematical subject matter. In particular, category-theoretic language focusses on properties that can be determined up to isomorphism within a category, whereas set theory admits of properties determined by the internal structure of the membership relation. Various objections have been raised against this aspect of set theory in the category-theoretic literature. In this article, we advocate a methodological pluralism concerning the two foundational languages, and provide a theory that fruitfully (...) interrelates a ‘structural’ perspective to a set-theoretic one. We present a set-theoretic system that is able to talk about structures more naturally, and argue that it provides an important perspective on plausibly structural properties such as cardinality. We conclude the language of set theory can provide useful information about the notion of mathematical structure. (shrink)

Decision-making under normative uncertainty requires an agent to aggregate the assessments of options given by rival normative theories into a single assessment that tells her what to do in light of her uncertainty. But what if the assessments of rival theories differ not just in their content but in their structure -- e.g., some are merely ordinal while others are cardinal? This paper describes and evaluates three general approaches to this "problem of structural diversity": structural enrichment, structural depletion, and (...) multi-stage aggregation. All three approaches have notable drawbacks, but I tentatively defend multi-stage aggregation as least bad of the three. (shrink)

Theorising the interplay of structure and agency is the quintessential focus of sociological endeavour. This paper aims to be part of that continuing endeavour, arguing for a stratified social ontology, where structure and agency are held to be irreducible to each other and causally efficacious, yet necessarily interdependent. It thus aims not to be part of that on-going journey in search of the 'ontological holy grail'. Instead, it offers a way of linking structure and agency which enables (...) the practical education researcher concretely to examine their relative interplay over time. The methodological key to teasing out their relative interplay is held to be analytical dualism. It will be argued that such a methodological device is precluded by Giddens' structuration theory. (shrink)

Bernard Lonergan has argued for a theory of cognition that is transcendentally secure, that is, one such that any plausible attempt to refute it must presuppose its correctness, and one that also grounds a correct metaphysics and ontology. His proposal combines an identity theory of knowledge with an intentional relation between knower and known. It depends in a crucial way upon an appropriation of one’s own cognitional motives and acts, that is, upon “knowing one’s own knowing.” I argue (...) that because of conflicts between the identity and intentionality components of the theory, rational self-appropriation cannot, as Lonergan claims, be an iteration of just the same acts by which we acquire other sorts of knowledge. I propose an amended theory in which the relation between intending-subject and intended-object of first-level cognition becomes, in RSA, a numerical identity of knower and known and of the epistemic and the ontological. (shrink)