The ecological rationality of explanatory reasoning

There is growing evidence that explanatory considerations influence how people change their degrees of belief in light of new information. Recent studies indicate that this influence is systematic and may result from people’s following a probabilistic update rule. While formally very similar to Bayes’ rule, the rule or rules people appear to follow are different from, and inconsistent with, that better-known update rule. This raises the question of the normative status of those updating procedures. Is the role explanation plays in people’s updating their degrees of belief a bias? Or are people right to update on the basis of explanatory considerations, in that this offers benefits that could not be had otherwise? Various philosophers have argued that any reasoning at deviance with Bayesian principles is to be rejected, and so explanatory reasoning, insofar as it deviates from Bayes’ rule, can only be fallacious. We challenge this claim by showing how the kind of explanation-based update rules to which people seem to adhere make it easier to strike the best balance between being fast learners and being accurate learners. Borrowing from the literature on ecological rationality, we argue that what counts as the best balance is intrinsically context-sensitive, and that a main advantage of explanatory update rules is that, unlike Bayes’ rule, they have an adjustable parameter which can be fine-tuned per context. The main methodology to be used is agent-based optimization, which also allows us to take an evolutionary perspective on explanatory reasoning.     

Catching the WAVE: The Weight-Adjusting Account of Values and Evidence

It is commonly argued that values “fill the logical gap” of underdetermination of theory by evidence, namely, values affect our choice between two or more theories that fit the same evidence. The underdetermination model, however, does not exhaust the roles values play in evidential reasoning. I introduce WAVE – a novel account of the logical relations between values and evidence. WAVE states that values influence evidential reasoning by adjusting evidential weights. I argue that the weight-adjusting role of values is distinct from their underdetermination gap-filling role. Values adjust weights in three ways. First, values affect our trust in the testimony of others. Second, values influence the evidential thresholds required for justified epistemic judgments. Third, values influence the relative weight of a certain type of evidence within a body of multimodal discordant evidence. WAVE explains, from an epistemic perspective, rather than psychological, how smokers, for example, can find the same evidence about the dangers of smoking less persuasive than non-smokers. WAVE allows for a wider effect of values on our accepted scientific theories and beliefs than the effect for which the underdetermination model allows alone; therefore, science studies scholars must consider WAVE in their research and analysis of evidential case studies.     

Styles of reasoning: A pluralist view

Styles of reasoning are important devices to understand scientific practice. As I use the concept, a style of reasoning is a pattern of inferential relations that are used to select, interpret, and support evidence for scientific results. In this paper, I defend the view that there is a plurality of styles of reasoning: different domains of science often invoke different styles. I argue that this plurality is an important source of disunity in scientific practice, and it provides additional arguments in support of the disunity claim. I also contrast Ian Hacking’s broad characterization of styles of reasoning with a narrow understanding that I favor. Drawing on examples from molecular biology, chemistry and mathematics, I argue that differences in style of reasoning lead to differences in the way the relevant results are obtained and interpreted. The result is a pluralist view about styles of reasoning that is sensitive to nuances of inferential relations in scientific activity.     

Feyerabend,truth, and relativisms: Footnotes to the Italian debate

There is a substantial literature on Feyerabend's relativism—including a few papers in this collection—but fewer specific studies of the ways that his writings and ideas have been taken up among the non-academic public. This is odd, given his obvious interest in the lives and concerns of persons who were not ‘intellectuals’—a term that, for him, had a pejorative ring to it. It is also odd, given the abundance of evidence of how Feyerabend's relativism played a role in a specific national and cultural context—namely, contemporary Italian debates about relativism. This paper offers a study of how Feyerabend's ideas have been deployed by Italian intellectuals and cultural commentators—including the current Pope—and critically assesses them.     

Ptolemy and the meta-helikôn

In his Harmonics, Ptolemy constructs a complex set of theoretically ‘correct’ forms of musical scale, represented as sequences of ratios, on the basis of mathematical principles and reasoning. But he insists that their credentials will not have been established until they have been submitted to the judgement of the ear. They cannot be audibly instantiated with the necessary accuracy without the help of specially designed instruments, which Ptolemy describes in detail, discussing the uses to which each can be put and cataloguing its limitations. The best known of these instruments is the monochord, but there are several more complex devices. This paper discusses one such instrument which is known from no other source, ancient or modern, whose design was prompted by the geometrical construction known as the helikôn. It has several remarkable peculiarities. I examine its design, its purposes, and the merits and shortcomings which Ptolemy attributes to it. An appendix describes an instrument I have built to Ptolemy’s specifications (possibly the first of its kind since the second century bc), in an attempt to find out how satisfactorily such a bizarre contraption will work; and it explains how various practical problems can be resolved.     

Eliminative abduction: examples from medicine

Peter Lipton argues that inference to the best explanation (IBE) involves the selection of a hypothesis on the basis of its loveliness. I argue that in optimal cases of IBE we may be able to eliminate all but one of the hypotheses. In such cases we have a form of eliminative induction takes place, which I call ‘Holmesian inference’. I argue that Lipton’s example in which Ignaz Semmelweis identified a cause of puerperal fever better illustrates Holmesian inference than Liptonian IBE. I consider in detail the conditions under which Holmesian inference is possible and conclude by considering the epistemological relations between Holmesian inference and Liptonian IBE.     

CHFR: a key checkpoint component implicated in a wide range of cancers

CHFR (Checkpoint with Forkhead-associated and RING finger domains) has been implicated in a checkpoint regulating entry into mitosis. However, the details underlying its roles and regulation are unclear due to conflicting lines of evidence supporting different notions of its functions. We provide here an overview of how CHFR is thought to contribute towards regulating mitotic entry and present possible explanations for contradictory observations published on the functions and regulation of CHFR. Furthermore, we survey key data showing correlations between promoter hypermethylation or down-regulation of CHFR and cancers, with a view on the likely reasons why different extents of correlations have been reported. Lastly, we explore the possibilities of exploiting CHFR promoter hypermethylation status in diagnostics and therapeutics for cancer patients. With keen interest currently focused on the association between hypermethylation of CHFR and cancers, details of how CHFR functions require further study to reveal how its absence might possibly contribute to tumorigenesis.     

Computer models and the evidence of anthropogenic climate change: An epistemology of variety-of-evidence inferences and robustness analysis

To study climate change, scientists employ computer models, which approximate target systems with various levels of skill. Given the imperfection of climate models, how do scientists use simulations to generate knowledge about the causes of observed climate change? Addressing a similar question in the context of biological modelling, Levins (1966) proposed an account grounded in robustness analysis. Recent philosophical discussions dispute the confirmatory power of robustness, raising the question of how the results of computer modelling studies contribute to the body of evidence supporting hypotheses about climate change. Expanding on Staley’s (2004) distinction between evidential strength and security, and Lloyd’s (2015) argument connecting variety-of-evidence inferences and robustness analysis, I address this question with respect to recent challenges to the epistemology robustness analysis. Applying this epistemology to case studies of climate change, I argue that, despite imperfections in climate models, and epistemic constraints on variety-of-evidence reasoning and robustness analysis, this framework accounts for the strength and security of evidence supporting climatological inferences, including the finding that global warming is occurring and its primary causes are anthropogenic.     

Everettian quantum mechanics and physical probability: Against the principle of “State Supervenience”

Everettian quantum mechanics faces the challenge of how to make sense of probability and probabilistic reasoning in a setting where there is typically no unique outcome of measurements. Wallace has built on a proof by Deutsch to argue that a notion of probability can be recovered in the many worlds setting. In particular, Wallace argues that a rational agent has to assign probabilities in accordance with the Born rule. This argument relies on a rationality constraint that Wallace calls state supervenience. I argue that state supervenience is not defensible as a rationality constraint for Everettian agents unless we already invoke probabilistic notions.     

Henri Poincaré and bruno de finetti: Conventions and scientific reasoning

In his account of probable reasoning, Poincaré used the concept, or at least the language, of conventions. In particular, he claimed that the prior probabilities essential for inverse probable reasoning are determined conventionally. This paper investigates, in the light of Poincaré's well known claim about the conventionality of metric geometry, what this could mean, and how it is related to other views about the determination of prior probabilities. Particular attention is paid to the similarities and differences between Poincaré's conventionalism as it applies to probabilities and de Finetti's subjectivism. The aim of the paper is to suggest that in accounts of the development of ideas about probable reasoning, particularly those customarily described as Bayesian, Poincaré's discussion deserves more attention than it has so far received.     

Qualitative novelty in seventeenth-century science: Hydrostatics from Stevin to Pascal

Two works on hydrostatics, by Simon Stevin in 1586 and by Blaise Pascal in 1654, are analysed and compared. The contrast between the two serves to highlight aspects of the qualitative novelty involved in changes within science in the first half of the seventeenth century. Stevin attempted to derive his theory from unproblematic postulates drawn from common sense but failed to achieve his goal insofar as he needed to incorporate assumptions involved in his engineering practice but not sanctioned by his postulates. Pascal's theory went beyond common sense by introducing a novel concept, pressure. Theoretical reflection on novel experiments was involved in the construction of the new concept and experiment also provided important evidence for the theory that deployed it. The new experimental reasoning was qualitatively different from the Euclidean style of reasoning adopted by Stevin. The fact that a conceptualization of a technical sense of pressure adequate for hydrostatics was far from obvious is evident from the work of those, such as Galileo and Descartes, who did not make significant moves in that direction.     

The emergence of objectivity: Fleck,Foucault, Kuhn and Hacking

The analytical notions of ‘thought style’, ‘paradigm’, ‘episteme’ and ‘style of reasoning’ are some of the most popular frameworks in the history and philosophy of science. Although their proponents, Ludwik Fleck, Thomas Kuhn, Michel Foucault, and Ian Hacking, are all part of the same philosophical tradition that closely connects history and philosophy, the extent to which they share similar assumptions and objectives is still under debate. In the first part of the paper, I shall argue that, despite the fact that these four thinkers disagree on certain assumptions, their frameworks have the same explanatory goal – to understand how objectivity is possible. I shall present this goal as a necessary element of a common project -- that of historicising Kant's a priori. In the second part of the paper, I shall make an instrumental use of the insights of these four thinkers to form a new model for studying objectivity. I shall also propose a layered diagram that allows the differences between the frameworks to be mapped, while acknowledging their similarities. This diagram will show that the frameworks of style of reasoning and episteme illuminate conditions of possibility that lie at a deeper level than those considered by thought styles and paradigms.     

Extracellular proteins as enterobacterial thermometers

Biological thermometers are cellular components or structures which sense increasing temperatures, interaction of the thermometer and the thermal stress bringing about the switching-on of inducible responses, with gradually enhanced levels of response induction following gradually increasing temperatures. In enterobacteria, for studies of such thermometers, generally induction of heat shock protein (HSP) synthesis has been examined, with experimental studies aiming to establish (often indirectly) how the temperature changes which initiate HSP synthesis are sensed; numerous other processes and responses show graded induction as temperature is increased, and how the temperature changes which induce these are sensed is also of interest. Several classes of intracellular component and structure have been proposed as enterobacterial thermometers, with the ribosome and the DnaK chaperone being the most favoured, although for many of the proposed intracellular thermometers, most of the evidence for their functioning in this way is indirect. In contrast to the above, the studies reviewed here firmly establish that for four distinct stress responses, which are switched-on gradually as temperature increases, temperature changes are sensed by extracellular components (extracellular sensing components, ESCs) i.e. there is firm and direct evidence for the occurrence of extracellular thermometers. All four thermometers described here are proteins, which appear to be distinct and different from each other, and on sensing thermal stress are activated by it to four distinct extracellular induction components (EICs), which interact with receptors on the surface of organisms to induce the appropriate responses. It is predicted that many other temperature-induced processes, including the synthesis of HSPs, will be switched-on following the activation of similar extracellular thermometers by thermal stimuli.     

Varieties of noise: Analogical reasoning in synthetic biology

The picture of synthetic biology as a kind of engineering science has largely created the public understanding of this novel field, covering both its promises and risks. In this paper, we will argue that the actual situation is more nuanced and complex. Synthetic biology is a highly interdisciplinary field of research located at the interface of physics, chemistry, biology, and computational science. All of these fields provide concepts, metaphors, mathematical tools, and models, which are typically utilized by synthetic biologists by drawing analogies between the different fields of inquiry. We will study analogical reasoning in synthetic biology through the emergence of the functional meaning of noise, which marks an important shift in how engineering concepts are employed in this field. The notion of noise serves also to highlight the differences between the two branches of synthetic biology: the basic science-oriented branch and the engineering-oriented branch, which differ from each other in the way they draw analogies to various other fields of study. Moreover, we show that fixing the mapping between a source domain and the target domain seems not to be the goal of analogical reasoning in actual scientific practice.     

The tragedy of the canon; or,path dependence in the history and philosophy of science

We have previously argued that historical cases must be rendered canonical before they can plausibly serve as evidence for philosophical claims, where canonicity is established through a process of negotiation among historians and philosophers of science (Bolinska and Martin, 2020). Here, we extend this proposal by exploring how that negotiation might take place in practice. The working stock of historical examples that philosophers tend to employ has long been established informally, and, as a result, somewhat haphazardly. The composition of the historical canon of philosophy of science is therefore path dependent, and cases often become stock examples for reasons tangential to their appropriateness for the purposes at hand. We show how the lack of rigor around the canonization of case studies has muddied the waters in selected philosophical debates. This, in turn, lays the groundwork for proposing ways in which they can be improved.     

Reconciling theories of chaperonin accelerated folding with experimental evidence

For the last 20 years, a large volume of experimental and theoretical work has been undertaken to understand how chaperones like GroEL can assist protein folding in the cell. The most accepted explanation appears to be the simplest: GroEL, like most other chaperones, helps proteins fold by preventing aggregation. However, evidence suggests that, under some conditions, GroEL can play a more active role by accelerating protein folding. A large number of models have been proposed to explain how this could occur. Focused experiments have been designed and carried out using different protein substrates with conclusions that support many different mechanisms. In the current article, we attempt to see the forest through the trees. We review all suggested mechanisms for chaperonin-mediated folding and weigh the plausibility of each in light of what we now know about the most stringent, essential, GroEL-dependent protein substrates.     

Knowledge transfer across scientific disciplines

Thomas Kuhn suggested that symbolic generalizations are applied to concrete systems by a process involving exemplars and analogical reasoning. Using the related concepts of theoretical and formal templates, I argue that the process of applying templates can in some cases be made explicit and that we do not need to rely on similarity relations and tacit knowledge. In so doing I show how some formal models can be transferred from one scientific field to another. Examples include scale-free networks, the Lotka-Volterra model from biology, and the Goodwin model in economics. I also argue that this explicit approach has advantages over the more psychologically oriented approach of Kuhn and explain the sense in which templates do and do not produce unification.     

Exemplification and the use-values of cases and case studies

This paper provides an account of the ‘use-value’ of case-based research by showing how social scientists exploit cases, and case studies, in a variety of practices of inference and extension. The critical basis for making such extensions relies on the power of a case, or the account given of a case (the case-study account), to exemplify certain features of the social world in ways which prove valuable for further analysis: either of the same case, or in many domains beyond the original case study. Framing use-values in terms of exemplification compares favourably with understanding reasoning beyond the case either as a form of analogical reasoning or in taking cases as experimentable objects.     

The problem of confirmation in the Everett interpretation

I argue that the Oxford school Everett interpretation is internally incoherent, because we cannot claim that in an Everettian universe the kinds of reasoning we have used to arrive at our beliefs about quantum mechanics would lead us to form true beliefs. I show that in an Everettian context, the experimental evidence that we have available could not provide empirical confirmation for quantum mechanics, and moreover that we would not even be able to establish reference to the theoretical entities of quantum mechanics. I then consider a range of existing Everettian approaches to the probability problem and show that they do not succeed in overcoming this incoherence.     

Regulation of self-renewal and differentiation by the intestinal stem cell niche

The gastrointestinal epithelium is a highly organised tissue that is constantly being renewed. In order to maintain homeostasis, the balance between intestinal stem cell (ISC) self-renewal and differentiation must be carefully regulated. In this review, we describe how the intestinal stem cell niche provides a unique environment to regulate self-renewal and differentiation of ISCs. It has traditionally been believed that the mesenchymal myofibroblasts play an important role in the crosstalk between ISCs and the niche. However, recent evidence in Drosophila and in vertebrates suggests that epithelial cells also contribute to the niche. We discuss the multiple signalling pathways that are utilised to regulate stemness within the niche, including members of the Wnt, BMP and Hedgehog pathways, and how aberrations in these signals lead to disruption of the normal crypt–villus axis. Finally, we also discuss how CDX1 and inhibition of the Notch pathway are important in specifying enterocyte and goblet cell differentiation respectively.