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)

Systems biologists often distance themselves from reductionist approaches and formulate their aim as understanding living systems “as a whole.” Yet, it is often unclear what kind of reductionism they have in mind, and in what sense their methodologies would offer a superior approach. To address these questions, we distinguish between two types of reductionism which we call “modular reductionism” and “bottom-up reductionism.” Much knowledge in molecular biology has been gained by decomposing living systems into functional modules or through detailed (...) studies of molecular processes. We ask whether systems biology provides novel ways to recompose these findings in the context of the system as a whole via computational simulations. As an example of computational integration of modules, we analyze the first whole-cell model of the bacterium M. genitalium. Secondly, we examine the attempt to recompose processes across different spatial scales via multi-scale cardiac models. Although these models rely on a number of idealizations and simplifying assumptions as well, we argue that they provide insight into the limitations of reductionist approaches. Whole-cell models can be used to discover properties arising at the interfaces of dynamically coupled processes within a biological system, thereby making more apparent what is lost through decomposition. Similarly, multi-scale modeling highlights the relevance of macroscale parameters and models and challenges the view that living systems can be understood “bottom-up.” Specifically, we point out that system-level properties constrain lower-scale processes. Thus, large-scale modeling reveals how living systems at the same time are more and less than the sum of the parts. (shrink)

This paper examines a looming reproducibility crisis in the core of the hard sciences. Namely, it concentrates on molecular modeling and simulation (MMS), a family of methods that predict properties of substances through computing interactions on a molecular level and that is widely popular in physics, chemistry, materials science, and engineering. The paper argues that in order to make quantitative predictions, sophisticated models are needed which have to be evaluated with complex simulation procedures that amalgamate theoretical, technological, (...) and social factors – leading to problems with reproducibility. Thus, for methodological reasons, the predictive success causes a reproducibility problem. (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)

Cancer biology features the ascription of normal functions to parts of cancers. At least some ascriptions of function in cancer biology track local normality of parts within the global abnormality of the aberration to which those parts belong. That is, cancer biologists identify as functions activities that, in some sense, parts of cancers are supposed to perform, despite cancers themselves having no purpose. The present paper provides a theory to accommodate these normal function ascriptions—I call it the Modeling Account (...) of Normal Function (MA). MA comprises two claims. First, normal functions are activities whose performance by the function-bearing part contributes to the self-maintenance of the whole system and, thereby, results in the continued presence of that part. Second, MA holds that models of system-level activities that are (partly) constitutive of self-maintenance are improved by including a representation of the relevant function-bearing part and by making reference to the activity/activities that part performs which contribute(s) to those system-level activities. I contrast MA with two other accounts that seek to explicate the ascription of normal functions in biology, namely, the organizational account and the selected effects account. Both struggle to extend to cancer biology. However, I offer ecumenical readings which allow them to recover some ascriptions of normal function to parts of cancers. So, though I contend that MA excels in this respect, the purpose of this paper is served if it provides materials for bridging the gap between cancer biology, philosophy of cancer, and the literature on function. (shrink)

Computational reproducibility possesses its own dynamics and narratives of crisis. Alongside the difficulties of computing as an ubiquitous yet complex scientific activity, computational reproducibility suffers from a naive expectancy of total reproducibility and a moral imperative to embrace the principles of free software as a non-negotiable epistemic virtue. We argue that the epistemic issues at stake in actual practices of computational reproducibility are best unveiled by focusing on software as a pivotal concept, one that is surprisingly often overlooked in accounts (...) of reproducibility issues. Software is not only about designing and coding but also about maintaining, supporting, distributing, licensing, and governance; it is not only about developers but also about users. We focus on openness debates among computational chemists involved in molecular modeling software packages as empirical grounding for our argument. We then identify and analyse four epistemic characteristics as key to the role of software in computational reproducibility. (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)

There are two fundamentally distinct kinds of biological theorizing. "Formal biology" focuses on the relations, captured in formal laws, among mathematically abstracted properties of abstract objects. Population genetics and theoretical mathematical ecology, which are cases of formal biology, thus share methods and goals with theoretical physics. "Compositional biology," on the other hand, is concerned with articulating the concrete structure, mechanisms, and function, through developmental and evolutionary time, of material parts and wholes. Molecular genetics, biochemistry, developmental biology, and physiology, which (...) are examples of compositional biology, are in serious need of philosophical attention. For example, the very concept of a "part" is understudied in both philosophy of biology and philosophy of science. ;My dissertation is an attempt to clarify the distinction between formal biology and compositional biology and, in so doing, provide a clear philosophical analysis, with case studies, of compositional biology. Given the social, economic, and medical importance of compositional biology, understanding it is urgent. For my investigation, I draw on the philosophical fields of metaphysics and epistemology, as well as philosophy of biology and philosophy of science. I suggest new ways of thinking about some classic philosophy of science issues, such as modeling, laws of nature, abstraction, explanation, and confirmation. I hint at the relevance of my study of two kinds of biological theorizing to debates concerning the disunity of science. (shrink)

Chemical visualizations and models are special kinds of situated, inductive arguments. In this paper, I examine several historical case studies—an archive of images from museums, special collections, and popular magazines—as examples of emergent practices of physical modeling as theoretical play which became the basis for molecular biology and structural chemistry. Specifically, I trace a legacy of visualization tools that starts with Archibald Scott Cooper and Friedrich Kekulé in the late 1800s, crystallizes as material manipulatives in Kekulé’s student Jacobus (...) Henricus Van’t Hoff and his folded paper “toys,” is legitimized in the California lab of Linus Pauling, and is glorified in the popular imaginary with James Watson and Francis Crick’s model of DNA. My tracing then follows several threads into contemporary modeling practices. I ultimately argue that modeling play, originally outside of the boundary of deductive, positivist science, is now an accepted mode of inductive reasoning in these related chemical fields. (shrink)

This Research Topic aimed at deepening our understanding of the levels and explanations that are of interest for cognitive sci- entists, neuroscientists, psychologists, behavioral scientists, and philosophers of science. Indeed, contemporary developments in neuroscience and psy- chology suggest that scientists are likely to deal with a multiplicity of levels, where each of the different levels entails laws of behavior appropriate to that level (Berntson et al., 2012). Also, gathering and modeling data at the different levels of analysis is not (...) suffi- cient: the integration of information across levels of analysis is a crucial issue. Given such state of affairs, a number of interesting questions arise. How can the autonomy of explanatory levels be properly understood in behavioral explanation? Is reductionism a satis- factory strategy? How can high-level and low-level models be constrained in order to be actually explanatory of both behav- ioral and neurological or molecular evidence? What is the kind of relationship between those models? (shrink)

The Protein Ontology (PRO) is designed as a formal and principled Open Biomedical Ontologies (OBO) Foundry ontology for proteins. The components of PRO extend from a classification of proteins on the basis of evolutionary relationships at the homeomorphic level to the representation of the multiple protein forms of a gene, including those resulting from alternative splicing, cleavage and/or posttranslational modifications. Focusing specifically on the TGF-beta signaling proteins, we describe the building, curation, usage and dissemination of PRO. PRO provides a framework (...) for the formal representation of protein classes and protein forms in the OBO Foundry. It is designed to enable data retrieval and integration and machine reasoning at the molecular level of proteins, thereby facilitating cross-species comparisons, pathway analysis, disease modeling and the generation of new hypotheses. (shrink)

Vaccine research, as well as the development, testing, clinical trials, and commercial uses of vaccines involve complex processes with various biological data that include gene and protein expression, analysis of molecular and cellular interactions, study of tissue and whole body responses, and extensive epidemiological modeling. Although many data resources are available to meet different aspects of vaccine needs, it remains a challenge how we are to standardize vaccine annotation, integrate data about varied vaccine types and resources, and support (...) advanced vaccine data analysis and inference. To address these problems, the community-based Vaccine Ontology (VO) has been developed through collaboration with vaccine researchers and many national and international centers and programs, including the National Center for Biomedical Ontology (NCBO), the Infectious Disease Ontology (IDO) Initiative, and the Ontology for Biomedical Investigations (OBI). VO utilizes the Basic Formal Ontology (BFO) as the top ontology and the Relation Ontology (RO) for definition of term relationships. VO is represented in the Web Ontology Language (OWL) and edited using the Protégé-OWL. Currently VO contains more than 2000 terms and relationships. VO emphasizes on classification of vaccines and vaccine components, vaccine quality and phenotypes, and host immune response to vaccines. These reflect different aspects of vaccine composition and biology and can thus be used to model individual vaccines. More than 200 licensed vaccines and many vaccine candidates in research or clinical trials have been modeled in VO. VO is being used for vaccine literature mining through collaboration with the National Center for Integrative Biomedical Informatics (NCIBI). Multiple VO applications will be presented. (shrink)

This book provides a critical reflection on automated science and addresses the question whether the computational tools we developed in last decades are changing the way we humans do science. More concretely: Can machines replace scientists in crucial aspects of scientific practice? The contributors to this book rethink and refine some of the main concepts by which science is understood, drawing a fascinating picture of the developments we expect over the next decades of human-machine co-evolution. The volume covers examples from (...) various fields and areas, such as molecular biology, climate modeling, clinical medicine, and artificial intelligence. The explosion of technological tools and drivers for scientific research calls for a renewed understanding of the human character of science. This book aims precisely to contribute to such a renewed understanding of science. (shrink)

The mantra that "the best way to predict the future is to invent it" (attributed to the computer scientist Alan Kay) exemplifies some of the expectations from the technical and innovative sides of biomedical research at present. However, for technical advancements to make real impacts both on patient health and genuine scientific understanding, quite a number of lingering challenges facing the entire spectrum from protein biology all the way to randomized controlled trials should start to be overcome. The proposal in (...) this chapter is that philosophy is essential in this process. By reviewing select examples from the history of science and philosophy, disciplines which were indistinguishable until the mid-nineteenth century, I argue that progress toward the many impasses in biomedicine can be achieved by emphasizing theoretical work (in the true sense of the word 'theory') as a vital foundation for experimental biology. Furthermore, a philosophical biology program that could provide a framework for theoretical investigations is outlined. (shrink)

Forty-two years ago, Capra published “The Tao of Physics” (Capra, 1975). In this book (page 17) he writes: “The exploration of the atomic and subatomic world in the twentieth century has …. necessitated a radical revision of many of our basic concepts” and that, unlike ‘classical’ physics, the sub-atomic and quantum “modern physics” shows resonances with Eastern thoughts and “leads us to a view of the world which is very similar to the views held by mystics of all ages and (...) traditions.“ This article stresses an analogous situation in biology with respect to a new theoretical approach for studying living systems, Integral Biomathics (IB), which also exhibits some resonances with Eastern thought. Stepping on earlier research in cybernetics1 and theoretical biology,2 IB has been developed since 2011 by over 100 scientists from a number of disciplines who have been exploring a substantial set of theoretical frameworks. From that effort, the need for a robust core model utilizing advanced mathematics and computation adequate for understanding the behavior of organisms as dynamic wholes was identified. At this end, the authors of this article have proposed WLIMES (Ehresmann and Simeonov, 2012), a formal theory for modeling living systems integrating both the Memory Evolutive Systems (Ehresmann and Vanbremeersch, 2007) and the Wandering Logic Intelligence (Simeonov, 2002b). Its principles will be recalled here with respect to their resonances to Eastern thought. (shrink)

This is a paper about the methodology of normative ethics. I claim that much work in normative ethics can be interpreted as modelling, the form of inquiry familiar from science, involving idealised representations. I begin with the anti-theory debate in ethics, and note that the debate utilises the vocabulary of scientific theories without recognising the role models play in science. I characterise modelling, and show that work with these characteristics is common in ethics. This establishes the plausibility of my interpretation. (...) Taking methodological inspiration from modelling in science gives us new tools for managing idealisations, and a new perspective on pluralism. I demonstrate why this interpretation is a fruitful way of interpreting ethics, by looking at three case studies. First, I return to the anti-theory debate and argue that modelling opens up a new middle ground. Second, I argue that a modelling lens offers a new way of understanding impossibility theorems in population ethics, and their bearing on ethics as a whole. Finally, I show how viewing our work as modelling can be deployed in debates within ethics, using the debate over prioritarianism as an example. I close with further methodological suggestions for those who choose to see themselves as modellers. I discuss the role of counterexamples, our responses to moral disagreement, and the training of new ethicists. (shrink)

In the last decade, the UK Government has attempted to implement improved processes and procedures in modelling and analysis in response to the Laidlaw report of 2012 and the Macpherson review of 2013. The Laidlaw report was commissioned after failings during the Intercity West Coast Rail (ICWC) Franchise procurement exercise by the Department for Transport (DfT) that led to a legal challenge of the analytical models used within the exercise. The Macpherson review looked into the quality assurance of Government analytical (...) models in the context of the experience with the Intercity West Coast franchise competition. This paper examines what progress has been made in the 8 years since the Laidlaw report in model building and best practise in government and proposes several recommendations for ways forward. This paper also discusses the Lords Science and Technology Committees of June 2020 that analysed the failings in the modelling of COVID. Despite going on to influence policy, many of the same issues raised within the Laidlaw and Macpherson Reports were also present in the Lords Science and Technology Committee enquiry. We examine the technical and organisational challenges to progress in this area and make recommendations for a way forward. (shrink)

ABSTRACT Is there something specific about modelling that distinguishes it from many other theoretical endeavours? We consider Michael Weisberg’s thesis that modelling is a form of indirect representation through a close examination of the historical roots of the Lotka–Volterra model. While Weisberg discusses only Volterra’s work, we also study Lotka’s very different design of the Lotka–Volterra model. We will argue that while there are elements of indirect representation in both Volterra’s and Lotka’s modelling approaches, they are largely due to two (...) other features of contemporary model construction processes that Weisberg does not explicitly consider: the methods-drivenness and outcome-orientedness of modelling. 1Introduction 2Modelling as Indirect Representation 3The Design of the Lotka–Volterra Model by Volterra 3.1Volterra’s method of hypothesis 3.2The construction of the Lotka–Volterra model by Volterra 4The Design of the Lotka–Volterra Model by Lotka 4.1Physical biology according to Lotka 4.2Lotka’s systems approach and the Lotka–Volterra model 5Philosophical Discussion: Strategies and Tools of Modelling 5.1Volterra’s path from the method of isolation to the method of hypothesis 5.2The template-based approach of Lotka 5.3Modelling: methods-driven and outcome-oriented 6Conclusion. (shrink)

Evolutionary anthropologists and archaeologists have been considerably successful in modelling the cumulative evolution of culture, of technological skills and knowledge in particular. Recently, one of these models has been introduced in the philosophy of science by De Cruz and De Smedt (Philos Stud 157:411–429, 2012), in an attempt to demonstrate that scientists may collectively come to hold more truth-approximating beliefs, despite the cognitive biases which they individually are known to be subject to. Here we identify a major shortcoming in that (...) attempt: De Cruz & De Smedt’s mathematical model makes one particularly strong tractability assumption that causes the model to largely miss its target (namely, truth accumulation in science), and that moreover conflicts with empirical observations. The second, more constructive part of the paper presents an alternative, agent-based model, which allows one to much better examine the conditions for scientific progress and decline. (shrink)

This essay replies to Michael Morreau and Erik J. Olsson’s ‘Learning from Ranters: The Effect of Information Resistance on the Epistemic Quality of Social Network Deliberation’. Morreau and Olsson use simulations to suggest that false ranters—agents who do not update their beliefs and only ever assert false claims—do not diminish the epistemic value of deliberation for other agents and can even be epistemically valuable. They argue conclude that “Our study suggests that including [false] ranters has little or no negative effect (...) on the epistemic value of social deliberation. Including them can even be epistemically beneficial. -/- I present concerns about their model and I enumerate some epistemic values that their discussion omits. I first raise two interrelated worries: (i.) The model is too simple; real-life irresponsible assertors do not speak uniformly falsely, for example. And tracking testifiers’ reliability demands cognitive resources. (ii.) In reality, we do not treat a person’s assertions that p as evidence that not p, especially not for all their assertions. I argue that these simplifications threat Morreau and Olsson conclusion. -/- I then enumerate epistemic values and disvalues that Morreau and Olsson do not discuss, but which bear on the value of false assertions and false ranters in their simulation and in real life. Candidate disvalues include: False beliefs of ranters; cognitive costs of discerning and recalling testifiers’ reliability; distrust; epistemic polarisatin; a prevalence of false assertion can impugn all testimony, including that of reliable testifiers. And candidate values include: a prevalence of true beliefs and assertions; attention being directed towards the right things; well-functioning trust relationships; believing people’s assertions; healthy discussion; epistemic respect; learning together. -/- . (shrink)

I argue that normative formal epistemology (NFE) is best understood as modelling, in the sense that this is the reconstruction of its methodology on which NFE is doing best. I focus on Bayesianism and show that it has the characteristics of modelling. But modelling is a scientific enterprise, while NFE is normative. I thus develop an account of normative models on which they are idealised representations put to normative purposes. Normative assumptions, such as the transitivity of comparative credence, are characterised (...) as modelling idealisations motivated normatively. I then survey the landscape of methodological options: what might formal epistemologists be up to? I argue the choice is essentially binary: modelling or theorising. If NFE is theorising it is doing very poorly: generating false claims with no clear methodology for separating out what is to be taken seriously. Modelling, by contrast, is a successful methodology precisely suited to the management of useful falsehoods. Regarding NFE as modelling is not costless, however. First, our normative inferences are less direct and are muddied by the presence of descriptive idealisations. Second, our models are purpose-specific and limited in their scope. I close with suggestions for how to adapt our practice. (shrink)

Economic models describe individuals in terms of underlying characteristics, such as taste for some good, sympathy level for another player, time discount rate, risk attitude, and so on. In real life, such characteristics change through experiences: taste for Mozart changes through listening to it, sympathy for another player through observing his moves, and so on. Models typically ignore change, not just for simplicity but also because it is unclear how to incorporate change. I introduce a general axiomatic framework for defining, (...) analysing and comparing rival models of change. I show that seemingly basic postulates on modelling change together have strong implications, like irrelevance of the order in which someone has his experiences and ‘linearity’ of change. This is a step towards placing the modelling of change on solid axiomatic grounds and enabling non-arbitrary incorporation of change into economic models. (shrink)

Bayesian models of legal arguments generally aim to produce a single integrated model, combining each of the legal arguments under consideration. This combined approach implicitly assumes that variables and their relationships can be represented without any contradiction or misalignment, and in a way that makes sense with respect to the competing argument narratives. This paper describes a novel approach to compare and ‘average’ Bayesian models of legal arguments that have been built independently and with no attempt to make them consistent (...) in terms of variables, causal assumptions or parameterization. The approach involves assessing whether competing models of legal arguments are explained or predict facts uncovered before or during the trial process. Those models that are more heavily disconfirmed by the facts are given lower weight, as model plausibility measures, in the Bayesian model comparison and averaging framework adopted. In this way a plurality of arguments is allowed yet a single judgement based on all arguments is possible and rational. (shrink)

The following considerations concern modelling Belief Dynamics (BD) not just in the sense of a formalization, but rather in the sense of building a computational model and implementing the corresponding data structures and algorithms of recomputing beliefs. The purpose of such a project is to illustrate some ideas about belief changes in a Web of Beliefs (WoB) to explore and deepen one's understanding of belief changes by trying to implement or improve corresponding algorithms.

This paper constructs a model of metaphysical indeterminacy that can accommodate a kind of ‘deep’ worldly indeterminacy that arguably arises in quantum mechanics via the Kochen-Specker theorem, and that is incompatible with prominent theories of metaphysical indeterminacy such as that in Barnes and Williams (2011). We construct a variant of Barnes and Williams's theory that avoids this problem. Our version builds on situation semantics and uses incomplete, local situations rather than possible worlds to build a model. We evaluate the resulting (...) theory and contrast it with similar alternatives, concluding that our model successfully captures deep indeterminacy. (shrink)

We introduce a number of logics to reason about collective propositional attitudes that are defined by means of the majority rule. It is well known that majoritarian aggregation is subject to irrationality, as the results in social choice theory and judgment aggregation show. The proposed logics for modelling collective attitudes are based on a substructural propositional logic that allows for circumventing inconsistent outcomes. Individual and collective propositional attitudes, such as beliefs, desires, obligations, are then modelled by means of minimal modalities (...) to ensure a number of basic principles. In this way, a viable consistent modelling of collective attitudes is obtained. (shrink)

Predictive processing theories are increasingly popular in philosophy of mind; such process theories often gain support from the Free Energy Principle (FEP)—a nor- mative principle for adaptive self-organized systems. Yet there is a current and much discussed debate about conflicting philosophical interpretations of FEP, e.g., repre- sentational versus non-representational. Here we argue that these different interpre- tations depend on implicit assumptions about what qualifies (or fails to qualify) as representational. We deploy the Free Energy Principle (FEP) instrumentally to dis- tinguish (...) four main notions of representation, which focus on organizational, struc- tural, content-related and functional aspects, respectively. The various ways that these different aspects matter in arriving at representational or non-representational interpretations of the Free Energy Principle are discussed. We also discuss how the Free Energy Principle may be seen as a unified view where terms that tradition- ally belong to different ontologies—e.g., notions of model and expectation versus notions of autopoiesis and synchronization—can be harmonized. However, rather than attempting to settle the representationalist versus non-representationalist debate and reveal something about what representations are simpliciter, this paper demon- strates how the Free Energy Principle may be used to reveal something about those partaking in the debate; namely, what our hidden assumptions about what represen- tations are—assumptions that act as sometimes antithetical starting points in this persistent philosophical debate. (shrink)

We show how to embed a framework for multilateral negotiation, in which a group of agents implement a sequence of deals concerning the exchange of a number of resources, into linear logic. In this model, multisets of goods, allocations of resources, preferences of agents, and deals are all modelled as formulas of linear logic. Whether or not a proposed deal is rational, given the preferences of the agents concerned, reduces to a question of provability, as does the question of whether (...) there exists a sequence of deals leading to an allocation with certain desirable properties, such as maximising social welfare. Thus, linear logic provides a formal basis for modelling convergence properties in distributed resource allocation. (shrink)

In this paper, I examine Reinforcement Learning modelling practice in psychiatry, in the context of alcohol use disorders. I argue that the epistemic roles RL currently plays in the development of psychiatric classification and search for explanations of clinically relevant phenomena are best appreciated in terms of Chang’s account of epistemic iteration, and by distinguishing mechanistic and aetiological modes of computational explanation.

Mathematical models provide explanations of limited power of specific aspects of phenomena. One way of articulating their limits here, without denying their essential powers, is in terms of contrastive explanation.

This dissertation examines aspects of the interplay between computing and scientific practice. The appropriate foundational framework for such an endeavour is rather real computability than the classical computability theory. This is so because physical sciences, engineering, and applied mathematics mostly employ functions defined in continuous domains. But, contrary to the case of computation over natural numbers, there is no universally accepted framework for real computation; rather, there are two incompatible approaches --computable analysis and BSS model--, both claiming to formalise algorithmic (...) computation and to offer foundations for scientific computing. -/- The dissertation consists of three parts. In the first part, we examine what notion of 'algorithmic computation' underlies each approach and how it is respectively formalised. It is argued that the very existence of the two rival frameworks indicates that 'algorithm' is not one unique concept in mathematics, but it is used in more than one way. We test this hypothesis for consistency with mathematical practice as well as with key foundational works that aim to define the term. As a result, new connections between certain subfields of mathematics and computer science are drawn, and a distinction between 'algorithms' and 'effective procedures' is proposed. -/- In the second part, we focus on the second goal of the two rival approaches to real computation; namely, to provide foundations for scientific computing. We examine both frameworks in detail, what idealisations they employ, and how they relate to floating-point arithmetic systems used in real computers. We explore limitations and advantages of both frameworks, and answer questions about which one is preferable for computational modelling and which one for addressing general computability issues. -/- In the third part, analog computing and its relation to analogue (physical) modelling in science are investigated. Based on some paradigmatic cases of the former, a certain view about the nature of computation is defended, and the indispensable role of representation in it is emphasized and accounted for. We also propose a novel account of the distinction between analog and digital computation and, based on it, we compare analog computational modelling to physical modelling. It is concluded that the two practices, despite their apparent similarities, are orthogonal. (shrink)

(1) An introduction to the principles of conceptual modelling, combinatorial heuristics and epistemological history; (2) the examination of a number of perennial epistemological-methodological schemata: conceptual spaces and blending theory; ars inveniendi and ars demonstrandi; the two modes of analysis and synthesis and their relationship to ars inveniendi; taxonomies and typologies as two fundamental epistemic structures; extended cognition, cognitio symbolica and model-based reasoning; (3) Plato’s notions of conceptual spaces, conceptual blending and hypothetical-analogical models (paradeigmata); (4) Ramon Llull’s concept analysis and combinatoric (...) spaces; (5) Gottfried Leibniz’s development of compositional analysis and synthesis as a general modelling method and a paradigm for ars inveniendi; (6) Fritz Zwicky’s revival of the morphological method of analysis and construction, and its subsequent computerised applications. (shrink)

Vehicle windshield wiper system increases the driving safety by contributing a clear shot viewing to the driver. In this paper, modelling, designing and simulation of a vehicle windshield wiper system with robust control theory is done successfully. H  loop shaping and robust pole placement controllers are used to improve the wiping speed by tracking a reference speed signals. The reference speed signals used in this paper are step and sine wave signals. Comparison of the H  loop shaping and (...) robust pole placement controllers based on the two reference signals is done and convincing results have been obtained. Finally the comparative results prove the effectiveness of the proposed H  Loop Shaping controller to improve the wiping mechanism for the given two reference signals. (shrink)

I will present the rationale followed for the conceptualization and the following development the Dual PECCS system that relies on the cognitively grounded heterogeneous proxytypes representational hypothesis. Such hypothesis allows integrating exemplars and prototype theories of categorization and has provided useful insights in the context of cognitive modelling for what concerns the typicality effects in categorization. As argued in [Chella et al., 2017] [Lieto et al., 2018b] [Lieto et al., 2018a] a pivotal role in this respect is played by the (...) use of the conceptual spaces framework and by its integration with a symbolic knowledge representation layer. (shrink)

I argue that there are no plausible non-representational explanations of episodes of hallucination. To make the discussion more specific, I focus on visual hallucinations in Charles Bonnet syndrome. I claim that the character of such hallucinatory experiences cannot be explained away non-representationally, for they cannot be taken as simple failures of cognizing or as failures of contact with external reality—such failures being the only genuinely non-representational explanations of hallucinations and cognitive errors in general. I briefly introduce a recent computational model (...) of hallucination, which relies on generative models in the brain, and argue that the model is a prime example of a representational explanation referring to representational mechanisms. The notion of the representational mechanism is elucidated, and it is argued that hallucinations—and other kinds of representations—cannot be exorcised from the cognitive sciences. (shrink)

The descriptions and theoretical laws scientists write down when they model a system are often false of any real system. And yet we commonly talk as if there were objects that satisfy the scientists’ assumptions and as if we may learn about their properties. Many attempt to make sense of this by taking the scientists’ descriptions and theoretical laws to define abstract or fictional entities. In this paper, I propose an alternative account of theoretical modelling that draws upon Kendall Walton’s (...) ‘make-believe’ theory of representation in art. I argue that this account allows us to understand theoretical modelling without positing any object of which scientists’ modelling assumptions are true. (shrink)

Culinary products have culinary value. That is, they have value qua culinary products. However, what is the nature of culinary value and what elements determine it? In the light of the central and universal role that culinary products play in our lives, offering a philosophical analysis of culinary value is a matter of interest. This paper attempts to do just this. It develops three different possible models of culinary value, two rather restricted ones and a third more encompassing one, rejects (...) the first two, and defends the third one. (shrink)

It is now increasingly accepted that many existing biological and medical ontologies can be improved by adopting tools and methods that bring a greater degree of logical and ontological rigor. In this chapter we will focus on the merits of a logically sound approach to ontologies from a methodological point of view. As we shall see, one crucial feature of a logically sound approach is that we have clear and functional definitions of the relational expressions such as ‘is a’ and (...) ‘part of ’. (shrink)

Cloud computing (ClC) has become a more popular computer paradigm in the preceding few years. Quality of Service (QoS) is becoming a crucial issue in service alteration because of the rapid growth in the number of cloud services. When evaluating cloud service functioning using several performance measures, the issue becomes more complex and non-trivial. It is therefore quite difficult and crucial for consumers to choose the best cloud service. The user's choices are provided in a quantifiable manner in the current (...) methods for choosing cloud services. Hence, this study attempts to achieve this objective through construction. decision-making framework so-called cloud services evaluator (CSsEv). The main indicator and its sub-indicators are formed as nodes at levels(n) in tree soft sets (TSSs). Thereafter Single Value Neutrosophic Sets (SVNSs) as branch of neutrosophic sets which conjunction with the Multi-Criteria Decision Making (MCDM) technique to facilitate analysis and evaluation process for the available Cloud services providers. Hence, entropy is employed to obtain indicators and sub_indicators weights and Complex Proportional Assessment utilizes these weights to facilitate the decision process of selecting optimal ClSPs. (shrink)

The continued development of General Circulation Models (GCMs) towards increasing resolution and complexity is a predominantly chosen strategy to advance climate science, resulting in channelling of research and funding to meet this aspiration. Yet many other modelling strategies have also been developed and can be used to understand past and present climates, to project future climates and ultimately to support decision-making. We argue that a plurality of climate modelling strategies and an equitable distribution of funding among them would be an (...) improvement on the current predominant strategy for informing policy making. To support our claim, we use a philosophy of science approach to compare increasing resolution and complexity of General Circulation Models with three alternate examples: the use of machine learning techniques, the physical climate storyline approach, and Earth System Models of Intermediate Complexity. We show that each of these strategies prioritises a particular set of methodological aims, among which are empirical agreement, realism, comprehensiveness, diversity of process representations, inclusion of the human dimension, reduction of computational expense, and intelligibility. Thus, each strategy may provide adequate information to support different specific kinds of research and decision questions. We conclude that, because climate decision-making consists of different kinds of questions, many modelling strategies are all potentially useful, and can be used in a complementary way. (shrink)

Modelling of Generancy is a book on Indian philosophy. In this book I have tried to express various problems of philosophy in mathematical language. I think mathematics is a language. Everything can be expressed in this language. With the help of mathematics, the published issues are understandable to all. No one has any objection to this. In the realm of knowledge all terms or words are considered categories. This category is again of three types: substance, quality and action. In another (...) way, this category is divided into five parts. These five parts are: Purusa, prakrti, jagat, jnana and karma. These five subjects are known as panchatattva. A total of fifty-five words, including these five words, are discussed in detail in the panchatattva. Fifty-five letters of the Sanskrit alphabet have been used to identify these fifty-five words. I think the problems of the present world are the problems of philosophy and knowledge. If this philosophy or knowledge can be expressed in the language of mathematics, then it will be useful for everyone to understand. Everyone will be aware of their responsibilities. That is what has been tried in this book. (shrink)

People often assume that everyone can be divided by sex/gender (that is, by physical and social characteristics having to do with maleness and femaleness) into two tidy categories: male and female. Careful thought, however, leads us to reject that simple ‘binary’ picture, since not all people fall precisely into one group or the other. But if we do not think of sex/gender in terms of those two categories, how else might we think of it? Here I consider four distinct models; (...) each model correctly captures some features of sex/gender, and so each is appropriate in some contexts. But the first three models are inadequate when tough questions arise, like whether trans women should be admitted as students at a women’s college or when it is appropriate for intersex athletes to compete in women’s athletic events. (‘Trans’ refers to the wide range of people who have an atypical gender identity for someone of their birth-assigned sex, and ‘intersex’ refers to people whose bodies naturally develop with markedly different physical sex characteristics than are paradigmatic of either men or women.) Such questions of inclusion and exclusion matter enormously to the people whose lives are affected by them, but ordinary notions of sex/gender offer few answers. The fourth model I describe is especially designed to make those hard decisions easier by providing a process to clarify what matters. (shrink)

Preference relations are intensively studied in Economics, but they are also approached in AI, Knowledge Representation, and Conceptual Modelling, as they provide a key concept in a variety of domains of application. In this paper, we propose an ontological foundation of preference relations to formalise their essential aspects across domains. Firstly, we shall discuss what is the ontological status of the relata of a preference relation. Secondly, we investigate the place of preference relations within a rich taxonomy of relations (e.g. (...) we ask whether they are internal or external, essential or contingent, descriptive or nondescriptive relations). Finally, we provide an ontological modelling of preference relation as a module of a foundational (or upper) ontology (viz. OntoUML). The aim of this paper is to provide a sharable foundational theory of preference relation that foster interoperability across the heterogeneous domains of application of preference relations. (shrink)

A key assumption fuelling optimism about the progress of Large Language Models (LLMs) in modelling the world is that the truth is systematic: true statements about the world form a whole that is not just consistent, in that it contains no contradictions, but cohesive, in that the truths are inferentially interlinked. This holds out the prospect that LLMs might rely on that systematicity to fill in gaps and correct inaccuracies in the training data: consistency and cohesiveness promise to facilitate progress (...) towards comprehensiveness in an LLM’s representation of the world. However, philosophers have identified reasons to doubt that the truth is systematic across all domains of thought, arguing that in normative domains, in particular, the truth is not necessarily systematic. I argue that insofar as the truth in normative domains is asystematic, this renders it correspondingly harder for LLMs to make progress, because they cannot rely on the consistency and cohesiveness of the truth to work towards comprehensiveness. And the less LLMs can rely on the systematicity of truth, the less we can rely on them to do our practical deliberation for us, as there is correspondingly more of a role for human agency in navigating asystematic normative domains. (shrink)

We show that linear logic can serve as an expressive framework in which to model a rich variety of combinatorial auction mechanisms. Due to its resource-sensitive nature, linear logic can easily represent bids in combinatorial auctions in which goods may be sold in multiple units, and we show how it naturally generalises several bidding languages familiar from the literature. Moreover, the winner determination problem, i.e., the problem of computing an allocation of goods to bidders producing a certain amount of revenue (...) for the auctioneer, can be modelled as the problem of finding a proof for a particular linear logic sequent. (shrink)

Until recently philosophy of physics has been overshadowed by the idea that the important philosophical issues that can be derived from physics are related only to fundamental theories, such as quantum mechanics and relativity. Applied fields of physics were deemed as unimportant. The argument for such a position lays in thinking that these applied fields of physics depend in their theoretical representations on fundamental theories and hence are reducible to these fundamental theories. It would be hard to defend such a (...) position, keeping in mind that applied fields of physics have a life of its own totally separate from fundamental physics and have in fact a lot to say to philosophers. The field of polymers is one of the branches of applied physics that has a lot to say to philosophers. It is a field of physics where theoreticians failed to present a coherent theory that can capture the different ways polymers can be built. This paper examines the difficulties that keep theoreticians away from having such a theory, revealing what kind of philosophical lessons polymers might have. The main thesis is: even in the cases where a theory predict the possibility of developing a specific type of polymers that was not previously known, the exact model that represent the outcome polymer theoretically will not be even in principle derivable from the theory that predicted its existence in the first place. (shrink)

A growing body of recent work in informal logic investigates the process of argumentation. Among other things, this work focuses on the ways in which individuals attempt to understand written or verbalised arguments in light of the fact that these are often presented in forms that are incomplete and unmarked. One of its aims is to develop general procedures for natural language argument recognition and reconstruction. Our aim here is to draw on this growing body of knowledge in informal logic (...) in order to take preliminary steps towards developing an architecture for computer systems that are able to recognise and reconstruct natural language arguments. This architecture aims to structure research of an applied and computational nature that strives to implement linguistic systems of various sorts, and to analyse problems in a way that both yields manageable and relatively independent components and also highlights how implementations can interact with existing resources from natural language processing. (shrink)

Global directional eliminativists deny that there is any global direction to time. This paper provides a way to understand everyday temporal assertions—assertions made outside the physics or metaphysics rooms, the truth of which appears to require that time has a global direction—on the assumption that global directional eliminativism is true.

The purpose of this article is to establish a connection between modelling practices and interpretive approaches in quantum mechanics, taking as a starting point the literature on scientific representation. Different types of modalities play different roles in scientific representation. I postulate that the way theoretical structures are interpreted in this respect affects the way models are constructed. In quantum mechanics, this would be the case in particular of initial conditions and observables. I examine two formulations of quantum mechanics, the standard (...) wave-function formulation and the consistent histories formulation, and show that they correspond to opposite stances, which confirms my approach. Finally, I examine possible strategies for deciding between these stances. (shrink)

In the view of my philosophical position “nominal conceptualism”, cognitive/knowledge agents, who are in some way aware of expressing the world based on their mental concepts, deal with their linguistic and/or symbolic expressions. In this paper I rely on nominal conceptualism to logically characterise agents’ concept-based descriptions of the world and analyse a fundamental logical system for conception representation.