Metaphysical Explanation and the Inference to the Best Explanation (BA thesis)

Inference to the Best Explanation, roughly put, appeals to the explanatory power of a theory or hypothesis (relative to some data set) as constituting epistemic justification for it. Inference to the Best Explanation (henceforth IBE) is a tool widely employed among all reasoners alike, from the empirical sciences to ordinary life. Philosophical discussions do not differ in the usualness of explanatory appeals of this kind during serious argument. Often enough, the appeal is dialectically blocked, as many of our epistemic peers in philosophy offer reasons to be skeptical of IBE. Our aim with this monograph is to assess one worry that have been raised about this mode of inference: That explanatory power is not truth-conducive. We begin by discussing general features of inferences and then formulating IBE in detail. Afterward, we explicate and apply a canonical understanding of what an explanation is. This will lead to a certain understanding of explanatory power. We undergo a case study to defend the thesis that this kind of explanatory power is indeed epistemically irrelevant – unless, perhaps, when combined with other theoretical virtues. Our conclusion is that the measure what explanations are best requires taking other theoretical virtues into account, such as simplicity and unification. In this case, a complete assessment of IBE requires examining if, when, and how these alleged theoretical virtues are indeed truth-conducive

Diagnosing Discordance: Signal in Data, Conflict in Paradigms

I analyze recent debates between proponents of concatenation versus coalescence in phylogenetic inference. I argue that concatenation is the latest manifestation of a paradigm weaving through phylogenetics that has focused on a successive series of models thought to be justified by the “principle of total evidence.” I analyze the principle of total evidence as the main philosophical strand linking parsimony versus likelihood (1980s), character congruence versus consensus trees (1990s), and concatenation versus coalescence (2000–10s). My hope is to provide a foothold for philosophers to engage with contemporary phylogenetics, in the face of the discipline’s bewildering and rapidly expanding array of computational models. The basic idea of total evidence—include all data that is relevant to an analysis, that has signal with respect to the problem at hand—is extremely attractive at an intuitive level. However, the general intuition is less clear in the case that all relevant data are included in the overall study, but no single method employs the total dataset in one inferential step. Moreover, simulation studies demonstrate that there are cases in which excluding some data, even when that data provides signal, leads to a better result by a particular method. Each of these points is explored through analysis of the historical and contemporary debates

How to study adaptation (and why to do it that way)

Some adaptationist explanations are regarded as maximally solid and others fanciful just-so stories. Just-so stories are explanations based on very little evidence. Lack of evidence leads to circular-sounding reasoning: “this trait was shaped by selection in unseen ancestral populations and this selection must have occurred because the trait is present.” Well-supported adaptationist explanations include evidence that is not only abundant but selected from comparative, populational, and optimality perspectives, the three adaptationist subdisciplines. Each subdiscipline obtains its broad relevance in evolutionary biology via assumptions that can only be tested with the methods of the other subdisciplines. However, even in the best-supported explanations, assumptions regarding variation, heritability, and fitness in unseen ancestral populations are always present. These assumptions are accepted given how well they would explain the data if they were true. This means that some degree of “circularity” is present in all evolutionary explanations. Evolutionary explanation corresponds not to a deductive structure, as biologists usually assert, but instead to ones such as abduction or induction. With these structures in mind, we show the way to a healthier view of “circularity” in evolutionary biology, and why integration across the comparative, populational, and optimality approaches is necessary

Information-theoretic causal inference of lexical flow

This volume seeks to infer large phylogenetic networks from phonetically encoded lexical data and contribute in this way to the historical study of language varieties. The technical step that enables progress in this case is the use of causal inference algorithms. Sample sets of words from language varieties are preprocessed into automatically inferred cognate sets, and then modeled as information-theoretic variables based on an intuitive measure of cognate overlap. Causal inference is then applied to these variables in order to determine the existence and direction of influence among the varieties. The directed arcs in the resulting graph structures can be interpreted as reflecting the existence and directionality of lexical flow, a unified model which subsumes inheritance and borrowing as the two main ways of transmission that shape the basic lexicon of languages. A flow-based separation criterion and domain-specific directionality detection criteria are developed to make existing causal inference algorithms more robust against imperfect cognacy data, giving rise to two new algorithms. The Phylogenetic Lexical Flow Inference (PLFI) algorithm requires lexical features of proto-languages to be reconstructed in advance, but yields fully general phylogenetic networks, whereas the more complex Contact Lexical Flow Inference (CLFI) algorithm treats proto-languages as hidden common causes, and only returns hypotheses of historical contact situations between attested languages. The algorithms are evaluated both against a large lexical database of Northern Eurasia spanning many language families, and against simulated data generated by a new model of language contact that builds on the opening and closing of directional contact channels as primary evolutionary events. The algorithms are found to infer the existence of contacts very reliably, whereas the inference of directionality remains difficult. This currently limits the new algorithms to a role as exploratory tools for quickly detecting salient patterns in large lexical datasets, but it should soon be possible for the framework to be enhanced e.g. by confidence values for each directionality decision

How can we know whether fish feel pain? Epistemology of the scientific study of fish sentience

I start by defining sentience and giving an analysis of the epistemological problems that plague its scientific study; this consists mainly in justifying that the attribution of sentience is underdetermined by the data. Second I show that as a result of this situation of underdetermination, most of the types of arguments used to infer sentience from the data are inconclusive and lead to a stalemate. Third, I argue that the stalemates arise from a foundationalist epistemology which needlessly leads to skeptical conclusions; as an alternative, I propose to adopt a coherentist framework and defend a process of ‘epistemic iteration’ (Chang 2004) within that framework, which I argue gives us a way out of the underdetermination

Information-theoretic causal inference of lexical flow

This volume seeks to infer large phylogenetic networks from phonetically encoded lexical data and contribute in this way to the historical study of language varieties. The technical step that enables progress in this case is the use of causal inference algorithms. Sample sets of words from language varieties are preprocessed into automatically inferred cognate sets, and then modeled as information-theoretic variables based on an intuitive measure of cognate overlap. Causal inference is then applied to these variables in order to determine the existence and direction of influence among the varieties. The directed arcs in the resulting graph structures can be interpreted as reflecting the existence and directionality of lexical flow, a unified model which subsumes inheritance and borrowing as the two main ways of transmission that shape the basic lexicon of languages

A Beta-splitting model for evolutionary trees

In this article, we construct a generalization of the Blum-Fran\c{c}ois Beta-splitting model for evolutionary trees, which was itself inspired by Aldous' Beta-splitting model on cladograms. The novelty of our approach allows for asymmetric shares of diversification rates (or diversification `potential') between two sister species in an evolutionarily interpretable manner, as well as the addition of extinction to the model in a natural way. We describe the incremental evolutionary construction of a tree with n leaves by splitting or freezing extant lineages through the Generating, Organizing and Deleting processes. We then give the probability of any (binary rooted) tree under this model with no extinction, at several resolutions: ranked planar trees giving asymmetric roles to the first and second offspring species of a given species and keeping track of the order of the speciation events occurring during the creation of the tree, unranked planar trees, ranked non-planar trees and finally (unranked non-planar) trees. We also describe a continuous-time equivalent of the Generating, Organizing and Deleting processes where tree topology and branch-lengths are jointly modeled and provide code in SageMath/python for these algorithms.Comment: 23 pages, 3 figures, 1 tabl