The work is the presentation of a logical theory - Logic in Reality (LIR) - and of applications of that theory in natural science and philosophy, including ...

The mechanistic perspective has dominated biological disciplines such as biochemistry, physiology, cell and molecular biology, and neuroscience, especially during the 20th century. The primary strategy is reductionist: organisms are to be decomposed into component parts and operations at multiple levels. Researchers adopting this perspective have generated an enormous body of information about the mechanisms of life at scales ranging from the whole organism down to genetic and other molecular operations.

In many fields of biology, researchers explain a phenomenon by characterizing the responsible mechanism. This requires identifying the candidate mechanism, decomposing it into its parts and operations, recomposing it so as to understand how it is organized and its operations orchestrated to generate the phenomenon, and situating it in its environment. Mechanistic researchers have developed sophisticated tools for decomposing mechanisms but new approaches, including modeling, are increasingly being invoked to recompose mechanisms when they involve nonsequential organization of nonlinear operations. The (...) results often are dynamical mechanistic explanations. The steps in mechanistic research are illustrated using research on circadian rhythms. (shrink)

Panpsychism is the view that every concrete and unified thing has some form of phenomenal consciousness or experience. It is an age-old doctrine, which, to the surprise of many, has recently taken on new life. In philosophy of mind, it has been put forth as a simple and radical solution to the mind–body problem (Chalmers 1996, 2003;Strawson 2006; Nagel 1979, 2012). In metaphysics and philosophy of science, it has been put forth as a solution to the problem of accounting for (...) the intrinsic nature of the physical itself (Strawson 2006, Seager 2006). In this thesis, I show that panpsychism can also be defended on the basis of an argument from our (arguable) acquaintance with the nature of causation in agency. This argument has made frequent appearances throughout the history of philosophy, with philosophers such as Leibniz, Schopenhauer and James, and I construct and defend an updated version of it. Furthermore, I offer a solution to the combination problem: how can complex (human and animal-type) consciousness result from simple (fundamental particle-type) consciousness? This is generally regarded as the most serious problem facing contemporary panpsychism. I propose that mental combination can be construed as kind causal process culminating in a fusion, and show how this avoids the main difficulties with accounting for mental combination. (shrink)

Understanding a normative concept like oppression requires attention to not only its harms but also the causes of those harms. In other words, a complete understanding of such a concept requires a proper causal explanation. This causal explanation can also inform and constrain our moral response to such harms. Therefore, the conceptual explanatory framework that we use to inform our moral diagnosis and our moral response become significant. The first goal of this dissertation is to propose complexity theory as the (...) proper framework for not only explaining a social phenomenon like oppression but also understanding the proper sites for social change. The second goal of this dissertation is to answer three interrelated questions about how we should respond, morally, to a chronic and complex social problem like racial or gender inequality: (1) Why do the current interventions to address these problems fail? (2) Do social movements play any unique role in addressing these problems? (3) What is our individual responsibility to participate in social movements? In response, I argue that the explanatory frameworks that we choose to understand the cause(s) of social problems can be the source of the inadequacy of our intervention. I argue that a proper social and moral intervention needs to capture the complex and dynamic nature of the social world. I also show that changing the explanatory framework allows us to see the unique role social movements play in making effective and sustainable social change possible. Finally, I conclude supporting such movements is a moral imperative. (shrink)

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 organisms. (shrink)

In the last decade, Systems Biology has emerged as a conceptual and explanatory alternative to reductionist-based approaches in molecular biology. However, the foundations of this new discipline need to be fleshed out more carefully. In this paper, we claim that a relational ontology is a necessary tool to ground both the conceptual and explanatory aspects of Systems Biology. A relational ontology holds that relations are prior—both conceptually and explanatory—to entities, and that in the biological realm entities are defined primarily by (...) the context they are embedded within—and hence by the web of relations they are part of. (shrink)

Biochemists often adopt what may be called the “Strategy of Decomposition” for the causal discovery of biochemical pathway dynamic behaviours. This involves decomposing a pathway into a set of isolated parts, which are then analysed separately. It is assumed that knowledge gained of the isolated parts can then be used to explain the dynamic behaviours of the whole pathway. My thesis addresses the extent to which use of the Strategy of Decomposition is warranted. I evaluate two challenges contained in Bechtel (...) and Richardson’s Discovering Complexity. The first challenge is that pathways lack the ‘modular’ structure assumed in the Strategy of Decomposition. Bechtel and Richardson take biochemists to use a concept of modularity called ‘near decomposability’. The second challenge is that pathways have ‘Pathway Emergent’ behaviours. I reject both challenges. I show that near decomposability is the wrong type of modularity to apply to pathways, and that the occurrence of Pathway Emergence has not been established. I argue that an underlying problem with Bechtel and Richardson’s analyses is that they overstate the consequences of feedback and nonlinearity for the Strategy of Decomposition. Instead, the analysis of pathway modularity and emergence needs to be centered on the context-sensitivity of pathways’ ‘local causal laws’. I identify that the type of modularity assumed in the Strategy of Decomposition is ‘causal law modularity’, which requires the invariance of local causal laws. I also identify a necessary condition for Pathway Emergence: a pathway must manifest at least one local causal law that is not manifested by its isolated parts. I argue that the use of the Strategy of Decomposition may often be unwarranted. This is because the local causal laws of pathways are highly context-sensitive, and pathways might often not be causal law modular. This context-sensitivity also leaves open the possibility of Pathway Emergence. (shrink)

A number of areas of biology raise questions about what is of value in the natural environment and how we ought to behave towards it: conservation biology, environmental science, and ecology, to name a few. Based on my experience teaching students from these and similar majors, I argue that the field of environmental ethics has much to teach these students. They come to me with pent-up questions and a feeling that more is needed to fully engage in their subjects, and (...) I believe some exposure to environmental ethics can help focus their interests and goals. I identify three primary areas in which environmental ethics can con- tribute to their education. The first is an examination of who (or what) should be considered to be part of our moral community (i.e., the community to whom we owe direct duties). Is it humans only? Or does it include all sentient life? Or all life? Or ecosystems considered holistically? Often, readings implicitly assume one or more of these answers; the goal is to make the student more sensitive to these implicit claims and to get them to think about the different reasons that support them. The second area, related to the first, is the application of the different answers concerning the extent of the ethical community to real environmental issues and problems. Students need to be aware of how the different answers concerning the moral community can imply conflicting answers for how we should act in certain cases and to think about ways to move toward conflict resolution. The third area in which environmental ethics can contribute is a more conceptual one, focusing on central concepts such as biodiversity, sustainability, species, and ecosystems. Exploring and evaluating various meanings of these terms will make students more reflective and thoughtful citizens and biologists, sensitive to the implications that different conceptual choices make. (shrink)

Biochemical networks are often called upon to illustrate emergent properties of living systems. In this contribution, I question such emergentist claims by means of theoretical work on genetic regulatory models and random Boolean networks. If the existence of a critical connectivity Kc of such networks has often been coined “emergent” or “irreducible”, I propose on the contrary that the existence of a critical connectivity Kc is indeed mathematically explainable in network theory. This conclusion also applies to many other types of (...) formal networks and weakens the emergentist claim attached to bio-molecular networks, and by extension to living systems. (shrink)