The three main approaches in statistical inference—classical statistics, Bayesian and likelihood—are in current use in phylogeny research. The three approaches are discussed and compared, with particular emphasis on theoretical properties illustrated by simple thought-experiments. The methods are problematic on axiomatic grounds, extra-mathematical grounds relating to the use of a prior or practical grounds. This essay aims to increase understanding of these limits among those with an interest in phylogeny.

The article analyses in detail the Meselson–Stahl experiment, identifying two novel difficulties for the crucial experiment account, namely, the fragility of the experimental results and the fact that the hypotheses under scrutiny were not mutually exclusive. The crucial experiment account is rejected in favour of an experimental-mechanistic account of the historical significance of the experiment, emphasizing that the experiment generated data about the biochemistry of DNA replication that is independent of the testing of the semi-conservative, conservative, and dispersive hypotheses. _1_ (...) Introduction _2_ The Meselson–Stahl Experiment _3_ Some Difficulties for the Crucial Experiment Account _3.1_ Additional experiments were required _3.2_ Simplicity considerations are unconvincing _3.3_ The fragility of the experimental results _3.4_ The problematic interpretation of falsifyng results _3.5_ Not all possible hypotheses considered or tested _3.6_ The tested hypotheses were not mutually exclusive _4_ The Historical and Scientific Significance of the Meselson–Stahl Experiment _4.1_ The challenge for the crucial experiment account _4.2_ A mechanistic perspective on the experiment _4.3_ The experimental design and its independence from theoretical speculations _4.4_ The advantages of a ‘bottom-up’ mechanistic account _5_ Conclusion. (shrink)

Phylogeography, a relatively new subdicipline of evolutionary biology that attempts to unify the fields of phylogenetics and population biology in an explicit geographical context, has hosted in recent years a highly polarized debate related to the purported benefits and limitations that qualitative versus quantitative methods might contribute or impose on inferential processes in evolutionary biology. Here we present a friendly, non-technical introduction to the conflicting methods underlying the controversy, and exemplify it with a balanced selection of quotes from the primary (...) biological literature, to invite the philosophy of biology community to pay attention to the elements that have played a primary role in its presumed resolution. We also present the basic features of our own metascientific take on the debate, and point out—as a preliminary step in preparation for upcoming, more detailed treatments—the importance that appeals to authority in fields external to phylogeography per se have played in the current status of this highly visible evolutionary biology dispute. (shrink)

The function and legitimacy of values in decision making is a critically important issue in the contemporary analysis of science. It is particularly relevant for some of the more application-oriented areas of science, specifically decision-oriented science in the field of regulation of technological risks. Our main objective in this paper is to assess the diversity of roles that non-cognitive values related to decision making can adopt in the kinds of scientific activity that underlie risk regulation. We start out, first, by (...) analyzing the issue of values with the help of a framework taken from the wider philosophical debate on science and values. Second, we study the principal conceptualizations used by scholars who have applied them to numerous case studies. Third, we appraise the links between those conceptualizations and learning processes in decision-oriented science. In this, we recur to the concept of methodological learning, i.e., learning about the best methodologies for generating knowledge that is useful for science-based regulatory decisions. The main result of our analysis is that non-cognitive values can contribute to methodological improvements in science in three principal ways: as basis for critical analysis, for contextualizing methodologies, and for establishing the burden of proof. (shrink)

We address some of the epistemological challenges highlighted by the Critical Data Studies literature by reference to some of the key debates in the philosophy of science concerning computational modeling and simulation. We provide a brief overview of these debates focusing particularly on what Paul Humphreys calls epistemic opacity. We argue that debates in Critical Data Studies and philosophy of science have neglected the problem of error management and error detection. This is an especially important feature of the epistemology of (...) Big Data. In “Error” section we explain the main characteristics of error detection and correction along with the relationship between error and path complexity in software. In this section we provide an overview of conventional statistical methods for error detection and review their limitations when faced with the high degree of conditionality inherent to modern software systems. (shrink)

In empirical modeling, an important desiderata for deeming theoretical entities and processes as real is that they can be reproducible in a statistical sense. Current day crises regarding replicability in science intertwines with the question of how statistical methods link data to statistical and substantive theories and models. Different answers to this question have important methodological consequences for inference, which are intertwined with a contrast between the ontological commitments of the two types of models. The key to untangling them is (...) the realization that behind every substantive model there is a statistical model that pertains exclusively to the probabilistic assumptions imposed on the data. It is not that the methodology determines whether to be a realist about entities and processes in a substantive field. It is rather that the substantive and statistical models refer to different entities and processes, and therefore call for different criteria of adequacy. (shrink)

The main objective of the paper is to propose a frequentist interpretation of probability in the context of model-based induction, anchored on the Strong Law of Large Numbers (SLLN) and justifiable on empirical grounds. It is argued that the prevailing views in philosophy of science concerning induction and the frequentist interpretation of probability are unduly influenced by enumerative induction, and the von Mises rendering, both of which are at odds with frequentist model-based induction that dominates current practice. The differences between (...) the two perspectives are brought out with a view to defend the model-based frequentist interpretation of probability against certain well-known charges, including [i] the circularity of its definition, [ii] its inability to assign ‘single event’ probabilities, and [iii] its reliance on ‘random samples’. It is argued that charges [i]–[ii] stem from misidentifying the frequentist ‘long-run’ with the von Mises collective. In contrast, the defining characteristic of the long-run metaphor associated with model-based induction is neither its temporal nor its physical dimension, but its repeatability (in principle); an attribute that renders it operational in practice. It is also argued that the notion of a statistical model can easily accommodate non-IID samples, rendering charge [iii] simply misinformed. (shrink)

This paper looks at an appeal to the authority of biomedical research that has recently been used by empirical economists to motivate and justify their methods. I argue that those who make this appeal mistake the nature of biomedical research. Randomised trials, which are said to have revolutionised biomedical research, are a central methodology, but according to only one paradigm. There is another paradigm at work in biomedical research, the inferentialist paradigm, in which randomised trials play no special role. I (...) outline the inferentialist alternative in broad strokes, apply it to a recent controversy in econometrics and draw some general conclusions concerning econometric methodology. (shrink)

The relevance of scientific knowledge for science and technology policy and regulation has led to a growing debate about the role of values. This article contributes to the clarification of what specific functions cognitive and noncognitive values adopt in knowledge generation and decisions, and what consequences the operation of values has for policy making and regulation. For our analysis, we differentiate between three different types of decision approaches, each of which shows a particular constellation of cognitive and noncognitive values. Our (...) objectives are to present a structured analysis of the varying functions that different kinds of values can adopt, as well as the value-related tensions and trade-offs they give rise to. We argue that the operation of noncognitive values in scientific knowledge generation, policy, and regulatory decision making can be understood as an enabling factor, rather than a limiting one. (shrink)

There are some philosophical questions that can be answered without attention to the social context in which evidence is produced and distributed.ing away from social context is an excellent way to ignore messy details and lay bare the underlying structure of the limits of inference. Idealization is entirely appropriate when one is essentially asking: In the best of all possible worlds, what am I entitled to infer? Yet, philosophers’ concerns often go beyond this domain. As an example I examine the (...) debate on mechanistic evidence and then reevaluate a canonical case study in this debate. I show that for the assessment of actual evidence, produced in a world that is far from ideal, omission of the social aspects of medical epistemology leads philosophers to draw the wrong lessons from cases they take as paradigmatic cases for their views. I close by arguing that social epistemology provides an avenue to incorporate these complications and provides the necessary framework to understand medical evidence. (shrink)

This paper surveys and critically assesses existing theories of evidence with respect to four desiderata. A good theory of evidence should be both a theory of evidential support (i.e., be informative about what kinds of facts speak in favour of a hypothesis), and of warrant (i.e., be informative about how strongly a given set of facts speaks in favour of the hypothesis), it should apply to the non-ideal cases in which scientists typically find themselves, and it should be ‘descriptively adequate’, (...) i.e., able to adequately represent typical episodes of evidentiary reasoning. The theories surveyed here—Bayesianism, hypotheticodeductivism,satisfaction theories, error statistics as well as Achinstein’s and Cartwright’s theories—are all found wanting in important respects. I finally argue that a deficiency all these theories have in common is a neglect or underplaying of the epistemic context in which the episode of evidentiary reasoning takes place.Este artículo describe y valora críticamente diversas teorías de la evidencia en relación a cuatro desiderata. Una buena teoría de la evidencia debería ser tanto una teoría sobre el apoyo evidencial [evidential support] (ser informativa sobre qué tipos de hechos hablan a favor de la hipótesis) como sobre la justificación [warrant]; debería aplicarse en las situaciones no ideales en las que normalmente se encuentran los científicos; y debería ser ‘descriptivamente adecuada’, esto es, capaz de representar correctamente episodios típicos de razonamiento evidencial. Las teorías aquí revisadas—bayesianismo, hipotético-deductivismo, teorías de la satisfacibilidad, la estadística del error, así como las propuestas de Achinstein y Cartwright—se consideran deficientes en aspectos básicos. Argumentaré que un defecto común en todas ellas es que olvidan, o minusvaloran, el contexto epistémico en el que el episodio de razonamiento evidencial tiene lugar. (shrink)

Philosophical theories of evidence have been on offer, but they are mostly evaluated in terms of all-or-none desiderata — if they fail to meet one of the desiderata, they are not a satisfactory theory. In this thesis, I aim to accomplish three missions. Firstly, I construct a new way of evaluating theories of evidence, which I call a tool-based view. Secondly, I analyse the nature of what I will call the various relevance-mediating vehicles that each theory of evidence employs. Thirdly, (...) I articulate the comparative core of evidential reasoning in the historical sciences, one which is overlooked in major theories of evidence. On the first mission, I endorse a meta-thesis of pluralism on theories of evidence, namely a tool-based view. I regard a theory of evidence as a purpose-specific and setting-sensitive tool which has its own strengths, difficulties and limitations. Among the major theories of evidence I have reviewed, I focus on Achinstein’s explanationist theory, Cartwright’s argument theory and Reiss’s inferentialist account, scrutinising and evaluating them against the purposes they set out and the scope of their applications. On the second mission, I note that there is no such thing as intrinsically ‘being evidence’. Rather, I hold that relevance-mediating vehicles configure data, materials or claims in such ways that some of them are labelled evidence. I identify the relevance-mediating vehicles that the theories of evidence employ. On the final mission, I argue that the likelihoodist account is an appropriate tool for explaining the evidential reasoning in poorly specified settings where likelihoods can be only imprecisely compared. Such settings, I believe, are typical in the historical sciences. Using the reconstruction of proto-sounds in historical linguistics as a case study, I formalise the rationale behind it by means of the law of likelihood. (shrink)

: Evidence claims depend on fallible assumptions. This paper discusses inferential robustness as a strategy for justifying evidence claims in spite of this fallibility. I argue that robustness can be understood as a means of establishing the partial security of evidence claims. An evidence claim is secure relative to an epistemic situation if it remains true in all scenarios that are epistemically possible relative to that epistemic situation.

Classical statistical inferences have been criticised for various reasons. To assess the soundness of such criticisms is a very important task because they are widely used in everyday scientific research. This is one of the reasons why the philosophy of statistics is an exciting field of study. In this paper, I focus on two such criticisms. The first one claims that the use of the p-value violates the principle of total evidence. It is a thesis that has been defended by (...) Elliott Sober and Bengt Autzen. The second one says that the result of classical tests does not only depend on the data but on the sampling plan of the experimenter also. The underlying criticism of course is that the sampling plan is not part of the evidence and that classical tests therefore violate PTE. The intentions of the experimenter should not affect the result of an inference. My aim is to show that both criticisms are unsound. Doing so, I hope to clarify the concept of p-value and the nature of the evidence in classical statistical tests. The point of my paper is to show that the identification of the evidence on which those criticisms rest is inadequate. (shrink)