The objective of this paper is twofold. First, I present a framework called historical coherentism (Chang, 2004; Tal, 2016; Van fraassen 2008) and argue that it is the best epistemological framework available to tackle the problem of coordination, an epistemic conundrum that arises with every attempt to provide empirical content to scientific theories, models or statements. Second, I argue that the problem of coordination, which has so far been theorized only in the context of measurement practices (Reichenbach, 1927; Chang, 2001; (...) Tal, 2012; Van fraassen 2008), can be generalized beyond the philosophy of measurement. Specifically, it will be shown that the problem is embodied in classificatory practices and that, consequently, historical coherentism is well suited to analyze these practices as well as metrological ones. As a case study, I look at a contemporary debate in phylogenetics, regarding the evolutionary origin of a newly identified archaeal phylum called Methanonatronarchaeia. Exploring this debate through the lens of historical coherentism provides a detailed understanding of the dynamics of the field and a foothold for critical analyses of the standard rationale used by practitioners. (shrink)

Molecular clocks based upon amino acid sequences in proteins have played a major role in the clarification of evolutionary phylogenies. Creationist criticisms of these methods sometimes rely upon data that might initially seem to be paradoxical. For example, human cytochrome c differs from that of an alligator by 13 amino acids but differs by 14 amino acids from a much more closely related primate, Otolemur garnettii. The apparent anomaly is resolved by taking into consideration the variable substitution rate of cytochrome (...) c, particularly among primates. This paper traces some of the history of extensive research into the topic of rate heterogeneity in cytochrome c including data from cytochrome c pseudogenes. (shrink)

In this paper, we redefine the target of evolutionary explanations by proposing the “evosystem” as an alternative to populations, lineages and species. Evosystems account for changes in the distribution of heritable variation within individual Darwinian populations (evolution by natural selection, drift, or constructive neutral evolution), but also for changes in the networks of interactions within or between Darwinian populations and changes in the abiotic environment (whether these changes are caused by the organic entities or not). The evosystem can thereby become (...) a centerpiece for a redefined evolutionary science, that is, evolutionary studies, that apprehends through a single framework the variety of evolutionary processes that lie at various scales. To illustrate the importance of this broadened perspective on evolution, we use a case of antimicrobial resistance evolution: the spread of the blaNDM gene family and the related resistance to carbapenem antibiotics observed globally, and show how evolutionary studies can contribute to answering contemporary socially relevant challenges. (shrink)

Debate about the epistemic prowess of historical science has focused on local underdetermination problems generated by a lack of historical data; the prevalence of information loss over geological time, and the capacities of scientists to mitigate it. Drawing on Leonelli’s recent distinction between ‘phenomena-time’ and ‘data-time’ I argue that factors like data generation, curation and management significantly complexifies and undermines this: underdetermination is a bad way of framing the challenges historical scientists face. In doing so, I identify circumstances of epistemic (...) scarcity where underdetermination problems are particularly salient, and discuss cases where legacy data—data generated using differing technologies and systems of practice—are drawn upon to overcome underdetermination. This suggests that one source of overcoming underdetermination is our knowledge of science’s past. Further, data-time makes agnostic positions about the epistemic fortunes of scientists working under epistemic scarcity more plausible. But agnosticism seems to leave philosophers without much normative grip. So, I sketch an alternative approach: focusing on the strategies scientists adopt to maximize their epistemic power in light of the resources available to them. (shrink)

We identify a species of experiment—Kon-Tiki experiments—used to demonstrate the competence of a cause to produce a certain effect, and we examine their role in the historical sciences. We argue that Kon-Tiki experiments are used to test middle-range theory, to test assumptions within historical narratives, and to open new avenues of inquiry. We show how the results of Kon-Tiki experiments are involved in projective inferences, and we argue that reliance on projective inferences does not provide historical scientists with any special (...) protection against the problem of unconceived alternatives. (shrink)

Philosophers have usually highlighted how the weakness and paucity of historical evidence underdetermine the choice between rival historical explanations. Focusing underdetermination on the link between theory and evidence comes, I argue, with three assumptions: competing hypotheses are easy to generate, investigators agree on the constitution and interpretation of the evidence and a plurality of hypotheses is a useful evil to reach consensus. The last assumption implies that the sustained coexistence of incompatible hypotheses is considered as a scientific failure. I argue (...) that this negative vision of sustained disagreement has monistic undertones. By drawing from a case study in evolutionary biology, this paper defends a form of scientific pluralism. Firstly, I show that underdetermination is not only found at the inferential level but also at the level of the constitution and interpretation of the evidence, on the choice of investigative scaffolds and when interpreting background theories. Because of that, competing hypotheses exhibit a degree of methodological incommensurability. While catastrophic from a monistic standpoint, I defend that scientific pluralism gives a different, and I think richer, account of such situations. On the plus side, competing approaches benefit from their sustained coexistence and interaction. I argue that this generates direct and indirect epistemic goods independently of whether the controversy is solved. Scientific pluralism also shifts our attention from achieving consensus to managing disagreement. The challenge becomes to maintain the conditions for fruitful interactions in a community with incommensurable approaches and heterogeneous expertise. (shrink)

I offer four ways of distinguishing paleobiology from neontology, and from this develop a sketch of the philosophy of paleobiology. I then situate and describe the papers in the special issue Paleobiology and Philosophy, and reflect on the value and prospects of paleontology-focused philosophy.

This article is a study of the role and use of evidence in the evaluation of claims in the historical sciences. In order to do this, I develop a “snapshot” approach to Toulmin schemas. This framework is applied to the case of Archezoa, an initially supported then eventually rejected hypothesis in evolutionary biology. From this case study, I criticize Cleland’s “smoking gun” account of the methodology of the historical sciences. I argue that Toulmin schemas are conceptually precise tools that allow (...) for the building of enriched reconstructions of evidential reasoning. From the application of this framework, I discuss three ways in which the construction and use of facts in the historical sciences are theory-laden. Despite its inherent limits, TS are heuristically useful tools to identify epistemic moves that could be further investigated. It also sheds light on the positive roles of speculation in the historical sciences. Finally, I argue that it provides a context-specific and individuated understanding of hypothesis evaluation in the historical sciences. Overall, I think the application of Toulmin schemas to cases of evidential reasoning in the historical sciences is a promising descriptive and heuristic tool for philosophers of science. (shrink)

Cet article propose une étude conceptuelle d’une pratique scientifique. L’analyse phylogénétique, méthode phare en biologie de l’évolution, permet d’inférer les relations évolutives entre différentes espèces ou organismes. De nos jours, elle fait souvent intervenir l’usage de données moléculaires, dont les résultats sont appelés des phylogénies moléculaires. Comment caractériser cette pratique? Nous commençons par une présentation de la méthode, en la découpant en quatre étapes : l’identification puis l’alignement de séquences homologues ; la construction puis l’interprétation d’un arbre phylogénétique. Nous montrons (...) que l’analyse phylogénétique n’est pas une expérimentation, et donc n’appartient pas au « style de laboratoire », tel que défini par Hacking. Elle ne correspond pas non plus à une méthode typique des sciences historiques, telle que décrite par Cleland. Bien que la correspondance de l’analyse phylogénétique avec ces catégorisations ne soit que partielle, nous défendons l’utilité de chacune de ces confrontations pour souligner des aspects distincts de cette pratique. Nous remettons aussi en cause l’idée d’une séparation méthodologique nette entre sciences expérimentales et sciences historiques. (shrink)

Cet article propose une étude conceptuelle d’une pratique scientifique. L’analyse phylogénétique, méthode phare en biologie de l’évolution, permet d’inférer les relations évolutives entre différentes espèces ou organismes. De nos jours, elle fait souvent intervenir l’usage de données moléculaires, dont les résultats sont appelés des phylogénies moléculaires. Comment caractériser cette pratique? Nous commençons par une présentation de la méthode, en la découpant en quatre étapes : (1) l’identification puis (2) l’alignement de séquences homologues (descendants d’un ancêtre commun) ; (3) la construction (...) puis (4) l’interprétation d’un arbre phylogénétique. Nous montrons que l’analyse phylogénétique n’est pas une expérimentation, et donc n’appartient pas au « style de laboratoire », tel que défini par Hacking. Elle ne correspond pas non plus à une méthode typique des sciences historiques, telle que décrite par Cleland. Bien que la correspondance de l’analyse phylogénétique avec ces catégorisations ne soit que partielle, nous défendons l’utilité de chacune de ces confrontations pour souligner des aspects distincts de cette pratique. Nous remettons aussi en cause l’idée d’une séparation méthodologique nette entre sciences expérimentales et sciences historiques. (shrink)