Mixtures Recomposition by Neural Nets: A Multidisciplinary Overview.

Artificial Neural Networks (ANNs) are transforming how we understand chemical mixtures, providing an expressive view of the chemical space and multiscale processes. Their hybridization with physical knowledge can bridge the gap between predictivity and understanding of the underlying processes. This overview explores recent progress in ANNs, particularly their potential in the 'recomposition' of chemical mixtures. Graph-based representations reveal patterns among mixture components, and deep learning models excel in capturing complexity and symmetries when compared to traditional Quantitative Structure-Property Relationship models. Key components, such as Hamiltonian networks and convolution operations, play a central role in representing multiscale mixtures. The integration of ANNs with Chemical Reaction Networks and Physics-Informed Neural Networks for inverse chemical kinetic problems is also examined. The combination of sensors with ANNs shows promise in optical and biomimetic applications. A common ground is identified in the context of statistical physics, where ANN-based methods iteratively adapt their models by blending their initial states with training data. The concept of mixture recomposition unveils a reciprocal inspiration between ANNs and reactive mixtures, highlighting learning behaviors influenced by the training environment.

Hierarchical network structure as the source of hierarchical dynamics (power-law frequency spectra) in living and non-living systems: How state-trait continua (body plans, personalities) emerge from first principles in biophysics.

Living systems are hierarchical control systems that display a small world network structure. In such structures, many smaller clusters are nested within fewer larger ones, producing a fractal-like structure with a 'power-law' cluster size distribution (a mereology). Just like their structure, the dynamics of living systems shows fractal-like qualities: the timeseries of inner message passing and overt behavior contain high frequencies or 'states' (treble) that are nested within lower frequencies or 'traits' (bass), producing a power-law frequency spectrum that is known as a 'state-trait continuum' in the behavioral sciences. Here, we argue that the power-law dynamics of living systems results from their power-law network structure: organisms 'vertically encode' the deep spatiotemporal structure of their (anticipated) environments, to the effect that many small clusters near the base of the hierarchy produce high frequency signal changes and fewer larger clusters at its top produce ultra-low frequencies. Such ultra-low frequencies exert a tonic regulatory pressure that produces morphological as well as behavioral traits (i.e., body plans and personalities). Nested-modular structure causes higher frequencies to be embedded within lower frequencies, producing a power-law state-trait continuum. At the heart of such dynamics lies the need for efficient energy dissipation through networks of coupled oscillators, which also governs the dynamics of non-living systems (e.q., earthquakes, stock market fluctuations). Since hierarchical structure produces hierarchical dynamics, the development and collapse of hierarchical structure (e.g., during maturation and disease) should leave specific traces in system dynamics (shifts in lower frequencies, i.e. morphological and behavioral traits) that may serve as early warning signs to system failure. The applications of this idea range from (bio)physics and phylogenesis to ontogenesis and clinical medicine.

When do parts form wholes? Integrated information as the restriction on mereological composition.

Under what conditions are material objects, such as particles, parts of a whole object? This is the composition question and is a longstanding open question in philosophy. Existing attempts to specify a non-trivial restriction on composition tend to be vague and face serious counterexamples. Consequently, two extreme answers have become mainstream: composition (the forming of a whole by its parts) happens under no or all conditions. In this paper, we provide a self-contained introduction to the integrated information theory (IIT) of consciousness. We show that IIT specifies a non-trivial restriction on composition: composition happens when integrated information is maximized. We compare the IIT restriction to existing proposals and argue that the IIT restriction has significant advantages, especially in response to the problems of vagueness and counterexamples. An appendix provides an introduction to calculating parts and wholes with a simple system.

The Mereotopology of Pregnancy.

Consider the following two metaphysical questions about pregnancy: (1) When does a new organism of a certain kind start to exist? (2) What is the mereological and topological relationship between the pregnant organism and with what it is pregnant? Despite assumptions made in the literature, I take these questions to be independent of each other, such that an answer to one does not provide an answer to the other. I argue that the way to connect them is via a maximality principle that prevents one organism being a proper part of another organism of the same kind. That being said, such a maximality principle need not be held, and may not apply in the case of pregnancy. The aims of this paper are thus to distinguish and connect these metaphysical questions, in order to outline a taxonomy of rival mereotopological models of pregnancy that result from the various combinations of their answers.

The Bundle Theory Approach to Relational Quantum Mechanics.

The present essay provides a new metaphysical interpretation of Relational Quantum Mechanics (RQM) in terms of mereological bundle theory. The essential idea is to claim that a physical system in RQM can be defined as a mereological fusion of properties whose values may vary for different observers. Abandoning the Aristotelian tradition centered on the notion of substance, I claim that RQM embraces an ontology of properties that finds its roots in the heritage of David Hume. To this regard, defining what kind of concrete physical objects populate the world according to RQM, I argue that this theoretical framework can be made compatible with (i) a property-oriented ontology, in which the notion of object can be easily defined, and (ii) moderate structural realism, a philosophical position where relations and relata are both fundamental. Finally, I conclude that under this reading relational quantum mechanics should be included among the full-fledged realist interpretations of quantum theory.

Possible Objects: Topological Approaches to Individuation.

We think of the world around us as divided into physical objects like toasters and daisies, rather than solely as a smear of properties like yellow and smooth. How do we single out these objects? One theory of object concepts uses part-of relations and relations of connectedness. According to this proposal, an object is a connected spatial item of maximal extent: Any other connected item that overlaps (i.e., shares a part with) the object must be a part of that object. This article reports four experiments that test this proposal. Participants see descriptions or diagrams of spatial items that vary across trials in their relative positions. In separate experiments, participants decide whether the items are physical objects, whether they are wholes, or how many objects are present. All experiments find support for connectedness as a contributor to object status, but they find little support for maximality. The results suggest that maximality is not a necessary feature of wholes or of objects.

Holobionts: Ecological communities, hybrids, or biological individuals? A metaphysical perspective on multispecies systems.

Holobionts are symbiotic assemblages composed by a macrobe host (animal or plant) plus its symbiotic microbiota. In recent years, the ontological status of holobionts has created a great amount of controversy among philosophers and biologists: are holobionts biological individuals or are they rather ecological communities of independent individuals that interact together? Chiu and Eberl have recently developed an eco-immunity account of the holobiont wherein holobionts are neither biological individuals nor ecological communities, but hybrids between a host and its microbiota. According to their account, the microbiota is not a proper part of the holobiont. Yet, it should be regarded as a set of scaffolds that support the individuality of the host. In this paper, we approach Chiu and Eberl's account from a metaphysical perspective and argue that, contrary to what the authors claim, the eco-immunity account entails that the microorganisms that compose the host's microbiota are proper parts of the holobiont. Second, we argue that by claiming that holobionts are hybrids, and therefore, not biological individuals, the authors seem to be assuming a controversial position about the ontology of hybrids, which are conventionally characterized as a type of biological individual. In doing so, our paper aligns with the contemporary tendency to incorporate metaphysical resources to shed light on current biological debates and builds on that to provide additional support to the consideration of holobionts as biological individuals from an eco-immunity perspective.

The Organism as a Whole in an Analysis of Death.

Although death statutes permitting physicians to declare brain death are relatively uniform throughout the United States, academic debate persists over the equivalency of human death and brain death. Alan Shewmon showed that the formerly accepted integration rationale was conceptually incomplete by showing that brain-dead patients demonstrated a degree of integration. We provide a more complete rationale for the equivalency of human death and brain death by defending a deeper understanding of the organism as a whole (OaaW) and by using a novel strategy with shared objectives to justify death determination criteria. Our OaaW account describes different types of OaaW, defining human death as the loss of status as a human OaaW. We defend human death as similar to nonhuman death in terms of wakefulness, but also distinct in terms of the sui generis properties, particularly conscious awareness. We thereby defend the equivalency of brain death and human death using a resulting neurocentric rationale.

Consciousness and topologically structured phenomenal spaces.

There are strong reasons to believe that our conscious inner life is structured, suggested both by introspection as well as scientific psychology. One of the most salient structural characteristics of conscious experiences is known as unity of consciousness. In this contribution, we wish to demonstrate how features of experience that pertain to the unity of consciousness could be made precise in terms of mathematical relations that hold between phenomenal objects. Based on phenomenological considerations, we first outline three such features. These are (i) environmental embedding, (ii) the mutual constraint between local and global representations, and (iii) a top-down process of object formation in consciousness. We then introduce a formal model based on the notion of phenomenal space, defined in terms of a set of quasi-elementary and extended entities. We describe the structure of phenomenal space by appealing to mereological and topological concepts, and we outline a projector-based calculus to account for the idea that the structure of phenomenal space is ultimately dynamical. Using the above concepts, one could approach the mind-matter problem by relating environmentally embedded agents to topologically well-defined objects that result from decompositions of phenomenal space. We conclude our discussion by putting it into the context of some recent conceptual questions that appear in cognitive science and consciousness studies. We opt for the possibility to regard the phenomenon of consciousness not in terms of a singular transition that happens between "brain" and "mind" but rather in terms of a series of transitions between structured layers of experience.

Facet Theory and the Mapping Sentence As Hermeneutically Consistent Structured Meta-Ontology and Structured Meta-Mereology.

When behavior is interpreted in a reliable manner (i.e., robustly across different situations and times) its explained meaning may be seen to possess hermeneutic consistency. In this essay I present an evaluation of the hermeneutic consistency that I propose may be present when the research tool known as the mapping sentence is used to create generic structural ontologies. I also claim that theoretical and empirical validity is a likely result of employing the mapping sentence in research design and interpretation. These claims are non-contentious within the realm of quantitative psychological and behavioral research. However, I extend the scope of both facet theory based research and claims for its structural utility, reliability and validity to philosophical and qualitative investigations. I assert that the hermeneutic consistency of a structural ontology is a product of a structural representation's ontological components and the mereological relationships between these ontological sub-units: the mapping sentence seminally allows for the depiction of such structure.

An Applied Mereology of the City: Unifying Science and Philosophy for Urban Planning.

Based on their research showing that growing cities follow basic principles, two theoretical physicists, Luis Bettencourt and Geoffrey West, call for researchers and professionals to contribute to a grand theory of urban sustainability. In their research, they develop a 'science of the city' to help urban planners address problems that arise from population increases. Although they provide valuable insights for understanding urban sustainability issues, they do not give planners a manageable way to approach such problems. I argue that developing an applied mereology to understand the concept of 'city identity' gives planners a theoretical device for addressing urban affairs, including ethical concerns. In turn, I devise a model of city identity to show how a 'philosophy of the city' contributes to a grand theory of urban sustainability.