Bayesian model selection has frequently been the focus of philosophical inquiry (e.g., Forster, Br J Philos Sci 46:399–424, 1995; Bandyopadhyay and Boik, Philos Sci 66:S390–S402, 1999; Dowe et al., Br J Philos Sci 58:709–754, 2007). This paper argues that Bayesian model selection procedures are very diverse in their inferential target and their justification, and substantiates this claim by means of case studies on three selected procedures: MML, BIC and DIC. Hence, there is no tight link between Bayesian model selection and (...) Bayesian philosophy. Consequently, arguments for or against Bayesian reasoning based on properties of Bayesian model selection procedures should be treated with great caution. (shrink)

Geologists, Paleontologists and other historical scientists are frequently concerned with narrative explanations targeting single cases. I show that two distinct explanatory strategies are employed in narratives, simple and complex. A simple narrative has minimal causal detail and is embedded in a regularity, whereas a complex narrative is more detailed and not embedded. The distinction is illustrated through two case studies: the ‘snowball earth’ explanation of Neoproterozoic glaciation and recent attempts to explain gigantism in Sauropods. This distinction is revelatory of historical (...) science. I argue that at least sometimes which strategy is appropriate is not a pragmatic issue, but turns on the nature of the target. Moreover, the distinction reveals a counterintuitive pattern of progress in some historical explanation: shifting from simple to complex. Sometimes, historical scientists rightly abandon simple, unified explanations in favour of disunified, complex narratives. Finally I compare narrative and mechanistic explanation, arguing that mechanistic approaches are inappropriate for complex narrative explanations. (shrink)

The comparative method grants epistemic access to the biological past. Comparing lineages provides empirical traction on both hypotheses about particular lineages and models of trait evolution. Understanding this evidential role is important. Although philosophers have recently turned their attention to relations of descent, little work exists exploring the status of evidence from convergences. I argue that, where they exist, convergences play a central role in the confirmation of adaptive hypotheses. I focus on ‘analogous inferences’, show how such inferences ought to (...) be analysed and suggest three methods for strengthening their evidential weight. 1 Introduction2 Analogous Inferences2.1 Adaptive explanations and analogies2.2 Analogous inferences2.3 Scope, grain, and specificity3 Parallel Modelling, Integrated Explanations, and Convergent Modelling3.1 Parallel modelling3.2 Integrated explanations3.1 Convergent modelling4 Conclusion. (shrink)

Probability ratio and likelihood ratio measures of inductive support and related notions have appeared as theoretical tools for probabilistic approaches in the philosophy of science, the psychology of reasoning, and artificial intelligence. In an effort of conceptual clarification, several authors have pursued axiomatic foundations for these two families of measures. Such results have been criticized, however, as relying on unduly demanding or poorly motivated mathematical assumptions. We provide two novel theorems showing that probability ratio and likelihood ratio measures can be (...) axiomatized in a way that overcomes these difficulties. (shrink)

It can often be heard in the hallways, and occasionally read in print, that reliabilism runs into special trouble regarding lottery cases. My main aim in this paper is to argue that this is not so. Nevertheless, lottery cases do force us to pay close attention to the relation between justification and probability.

I analyze two recent parsimony arguments that have been offered to break the current impasse in the chimpanzee mindreading controversy, the ‘logical problem’ argument from Povinelli, Penn, and Vonk, and Sober's attempt to apply model selection criteria in support of the mindreading hypothesis. I argue that Sober's approach fails to adequately rebut the ‘logical problem’. However, applying model selection criteria to chimpanzees' own mental models of behavior does yield a response to the ‘logical problem’ and reveals an adaptive advantage of (...) mindreading models and a potential solution to a paradox raised by Whiten. (shrink)

Current empirical studies of moral behavior of healthcare professionals are almost entirely focused on self-reports, usually collected under the assumption that an ethical disposition characterizes individuals across various contexts. It is well known, however, that individuals adjust their behavior to what they see being done by those in their peer group. That presents a methodological challenge to traditional research within a community of peers because the behavior of each individual is both the result of norms and a contributor to the (...) norms of others. Computer simulations can be used to address this methodological challenge. A Markov replicator model that runs on an Excel spreadsheet was used to investigate a community with four agent types in the dental community: devious practitioners, ethical practitioners who avoid involvement in the poor ethics of others, ethical practitioners who accept it as part of their professional responsibility to challenge colleagues who act unprofessionally, and those who enforce ethical standards. A panel of leaders in the profession independently estimated parameters for the model and criteria for a possible distribution of agent types in the community. The simulation converged on distributions of the agent types that were very similar to the expectations of the panel. The simulation suggests the following characteristics of such moral communities: The structure of such communities is robust across a wide distribution. It appears that reduction in unethical behavior is more sensitive to the way ethical practitioners interact with each other than to sanctions the enforcement community imposes on unethical practitioners, and that large external interventions will be short lived. (shrink)

Inductive reasoning aims at constructing rules and models of general applicability from a restricted set of observations. Induction is a keystone in natural sciences, and it influences diverse application fields such as engineering, medicine and economics. More generally, induction plays a major role in the way humans learn and operate in their everyday life. The level of reliability that a model achieves depends on how informative the observations are relative to the flexibility of the process by which the model is (...) constructed. When the process is articulated so that the model can incorporate descriptive details and subtleties, a large set of informative observations are required to reliably tune the model, whereas models obtained from simple procedures can be tuned with fewer observations. This article introduces the concept of “dominance”, which refers to the situation in which a reduced subset of observations suffices to reconstruct the model. A mathematical framework is presented to quantify the reliability of learning procedures as a function of the size of the subset of dominant observations. Although limited in scope, we believe that our study can contribute to the understanding of some fundamental mechanisms by which knowledge is generated from observations in inductive reasoning. (shrink)

What sort of evidence can confer the strongest support to a hypothesis? A natural answer is that the evidence entails the hypothesis. Roush claims that the likelihood ratio measure of degree of incremental support can deliver this intuitively natural result, and regards it as unifying “[the] account of induction and deduction in the only way that makes sense”. In this paper, we highlight a difficulty in the treatment of this case, and question the great significance that is attached to this (...) measure and its alleged capacity to accommodate the logicality requirement. We contrast the likelihood ratio measure with other measures, and argue that problems still emerge in light of tensions with plausible requirements for confirmation measures more generally. (shrink)

In this paper, I examine a contextualist thesis that has been little discussed in comparison with contextualism about knowledge, namely contextualism about evidential support. This seems surprising since, prima facie, evidential support statements seem shifty in a way parallel to knowledge ascriptions. I examine but reject the suggestion that contrastivism about evidential support is motivated by arguments analogous to those used to motivate contrastivism about knowledge including sceptical closure arguments, the nature of inquiry, the existence of explicitly contrastive evidential support (...) statements, and the intuitive shiftiness of some binary evidential support statements. I end by discussing the relations between contextualism about evidential support, evidence and knowledge. In particular, I argue that my discussion of contrastivism about evidential support undermines Neta's contextualist view about evidence, and his broader suggestion that the shiftiness of evidence statements explains the shiftiness of knowledge ascriptions. (shrink)

This essay analyzes and develops recent views about explanation in biology. Philosophers of biology have parted with the received deductive-nomological model of scientific explanation primarily by attempting to capture actual biological theorizing and practice. This includes an endorsement of different kinds of explanation (e.g., mathematical and causal-mechanistic), a joint study of discovery and explanation, and an abandonment of models of theory reduction in favor of accounts of explanatory reduction. Of particular current interest are philosophical accounts of complex explanations that appeal (...) to different levels of organismal organization and use contributions from different biological disciplines. The essay lays out one model that views explanatory integration across different disciplines as being structured by scientific problems. I emphasize the philosophical need to take the explanatory aims pursued by different groups of scientists into account, as explanatory aims determine whether different explanations are competing or complementary and govern the dynamics of scientific practice, including interdisciplinary research. I distinguish different kinds of pluralism that philosophers have endorsed in the context of explanation in biology, and draw several implications for science education, especially the need to teach science as an interdisciplinary and dynamic practice guided by scientific problems and explanatory aims. (shrink)

In recent controversies about Intelligent Design Creationism (IDC), the principle of methodological naturalism (MN) has played an important role. In this paper, an often neglected distinction is made between two different conceptions of MN, each with its respective rationale and with a different view on the proper role of MN in science. According to one popular conception, MN is a self-imposed or intrinsic limitation of science, which means that science is simply not equipped to deal with claims of the supernatural (...) (Intrinsic MN or IMN). Alternatively, we will defend MN as a provisory and empirically grounded attitude of scientists, which is justified in virtue of the consistent success of naturalistic explanations and the lack of success of supernatural explanations in the history of science (Provisory MN or PMN). Science does have a bearing on supernatural hypotheses, and its verdict is uniformly negative. We will discuss five arguments that have been proposed in support of IMN: the argument from the definition of science, the argument from lawful regularity, the science stopper argument, the argument from procedural necessity, and the testability argument. We conclude that IMN, because of its philosophical flaws, proves to be an ill-advised strategy to counter the claims of IDC. Evolutionary scientists are on firmer ground if they discard supernatural explanations on purely evidential grounds, instead of ruling them out by philosophical fiat. (shrink)

A book review of R. Paul Thompson's "A Remarkable Journey: The Story of Evolution.

In Ockham's Razors: A User's Guide, Elliott Sober argues that parsimony considerations are epistemically relevant on the grounds that certain methods of model selection, such as the Akaike Information Criterion, exhibit good asymptotic behaviour and take the number of adjustable parameters in a model into account. I raise some worries about this form of argument.

Promotion is the relation between an act and a desire that obtains when the act advances or serves the desire. Under what conditions does an act promote a desire? Probabilistic accounts of promotion, the most prominent accounts, analyze promotion in terms of an increase in the probability of the desire’s satisfaction. In this paper, we clarify the promotion relation and explain why probabilistic accounts are attractive. Then we identify two questions probabilistic accounts must answer: the Baseline Question and the Interpretation (...) Question. We discuss and reject the three answers to the Baseline Question found in the literature, and explain the challenge future attempts at answering this question will face. Proponents of probabilistic accounts have not adequately addressed the Interpretation Question. We survey three answers to this question, finding each unsatisfactory. We conclude that no satisfactory probabilistic account has yet been offered, and that there are significant hurdles to providing one in the future. (shrink)

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.

Elliott Sober is both an empiricist and an instrumentalist. His empiricism rests on a principle called actualism, whereas his instrumentalism violates this. This violation generates a tension in his work. We argue that Sober is committed to a conflicting methodological imperative because of this tension. Our argument illuminates the contemporary debate between realism and empiricism which is increasingly focused on the application of scientific inference to testing scientific theories. Sober’s position illustrates how the principle of actualism drives a wedge between (...) two conceptions of scientific inference and at the same time brings to the surface a deep conflict between empiricism and instrumentalism. (shrink)

The paper examines the claim that significance testing violates the Principle of Total Evidence. I argue that p-values violate PTE for two-sided tests but satisfy PTE for one-sided tests invoking a sufficient test statistic independent of the preferred theory of evidence. While the focus of the paper is to evaluate a particular claim about the relationship of significance testing and PTE, I clarify the reading of this methodological principle along the way.

We examine the claim that the methodology of psychology leads to a bias in animal cognition research against attributing “anthropomorphic” properties to animals . This charge is examined in light of a debate on the role of folk psychology between primatologists who emphasize similarities between humans and other apes, and those who emphasize differences. We argue that while in practice there is sometimes bias, either in the formulation of the null hypothesis or in the preference of Type-II errors over Type-I (...) errors, the bias is not the result of proper use of the Neyman and Pearson hypothesis testing method. Psychologists’ preference for false negatives over false positives cannot justify a preference for avoiding anthropomorphic errors over anthropectic errors. (shrink)

Among philosophical analyses of Darwin’s Origin, a standard view says the theory presented there had no concrete observational consequences against which it might be checked. I challenge this idea with a new analysis of Darwin’s principal geographical distribution observations and how they connect to his common ancestry hypothesis.

Extreme Permissivism is the view that a body of evidence could rationally permit both the attitude of belief and disbelief towards a proposition. This paper puts forward a new argument against Extreme Permissivism, which improves on a similar style of argument due to Roger White (2005, 2014). White’s argument is built around the principle that the support relation between evidence and a hypothesis is objective: so that if evidence E makes it rational for an agent to believe a hypothesis H, (...) then E makes it rational to believe H, for all agents. In this paper, I construct a new argument against Extreme Permissivism that appeals to a logically weaker, less demanding view about evidential support, Relational Objectivity: whether a body of evidence E is more likely if H is true than if H is false is an objective matter and does not depend on how any agent interprets the relationship between E and H. Relational Objectivity is solely concerned with the conditional probabilities called likelihoods and does not put substantive constraints on an agent’s prior and posterior credences. For this reason, the presented argument avoids the standard permissivist criticism levelled against White’s argument. (shrink)

These preprints were automatically compiled into a PDF from the collection of papers deposited in PhilSci-Archive in conjunction with the PSA 2018.

The ?Dimensioned? view analyzes (multiple) realization in terms of compositional relation, and the ?Flat? view analyzes (multiple) realization in terms of causal-functional mechanism. The two different analyses of realization lead to the disagreement about whether realization is transitive. The two views, perhaps not surprisingly, have different consequences on testing for multiple realization, and prescribe different ?reconstructions? for the evidential significance of observation for multiple realization. I examine the differences between the two views on testing for multiple realization within a model-selection (...) theoretical framework. I claim that the model-selection theoretical framework provides a ground to discuss and assess evidence for multiple realization. (shrink)

This chapter offers a critique of intelligent design arguments against evolution and a philosophical discussion of the nature of science, drawing several lessons for the teaching of evolution and for science education in general. I discuss why Behe’s irreducible complexity argument fails, and why his portrayal of organismal systems as machines is detrimental to biology education and any under-standing of how organismal evolution is possible. The idea that the evolution of complex organismal features is too unlikely to have occurred by (...) random mutation and selection (as recently promoted by Dembski) is very widespread, but it is easy to show students why such small probability arguments are fallacious. While intelligent design proponents have claimed that the exclusion of supernatural causes mandated by scientific methods is dogmatically presupposed by science, scientists have an empirical justification for using such methods. This justification is instructive for my discussion of how to demarcate science from pseudoscience. I argue that there is no universal account of the nature of science, but that the criteria used to judge an intellectual approach vary across historical periods and have to be specific to the scientific domain. Moreover, intellectual approaches have to be construed as practices based on institutional factors and values, and to be evaluated in terms of the activities of their practitioners. Science educators should not just teach scientific facts, but present science as a practice and make students reflect on the nature of science, as this gives them a better appreciation of the ways in which intelligent design falls short of actual science. (shrink)

This paper investigates the degree to which information theory, and the derived uses that make it work as a metaphor of our age, can be helpful in thinking about God’s immanence and transcendance. We ask when it is possible to say that a consciousness has to be behind the information we encounter. If God is to be thought about as a communicator of information, we need to ask whether a communication system has to pre-exist to the divine and impose itself (...) to God. If we want God to be Creator, and not someone who would work like a human being, ‘creating’ will mean sustaining in being as much the channel, the material system, as the message. Is information control? It seems that God’s actions are not going to be informational control of everything. To clarify the issue, we attempt to distinguish two kinds of ‘genialities’ in nature, as a way to evaluate the likelihood of God from nature. We investigate concepts and images of God, in terms of the history of ideas but also in terms of philosophical theology, metaphysics, and religious ontology. (shrink)

This book examines the philosophical conception of abductive reasoning as developed by Charles S. Peirce, the founder of American pragmatism. It explores the historical and systematic connections of Peirce's original ideas and debates about their interpretations. Abduction is understood in a broad sense which covers the discovery and pursuit of hypotheses and inference to the best explanation. The analysis presents fresh insights into this notion of reasoning, which derives from effects to causes or from surprising observations to explanatory theories. The (...) author outlines some logical and AI approaches to abduction as well as studies various kinds of inverse problems in astronomy, physics, medicine, biology, and human sciences to provide examples of retroductions and abductions. The discussion covers also everyday examples with the implication of this notion in detective stories, one of Peirce’s own favorite themes. The author uses Bayesian probabilities to argue that explanatory abduction is a method of confirmation. He uses his own account of truth approximation to reformulate abduction as inference which leads to the truthlikeness of its conclusion. This allows a powerful abductive defense of scientific realism. This up-to-date survey and defense of the Peircean view of abduction may very well help researchers, students, and philosophers better understand the logic of truth-seeking. (shrink)

David Hume was clearly a critic of religion. It is still debated, however, whether or not he was an atheist who denied the existence of God. According to some interpretations he was a theist of some kind and others claim he was an agnostic who simply suspends any belief on this issue. This essay argues that Hume’s theory of belief tells against any theistic interpretation – including the weaker, “attenuated” accounts. It then turns to the case for the view that (...) Hume’s criticisms of theism were limited to the “soft” skeptical (agnostic) aim of discrediting theist arguments, and shows that he is committed to a “harder” skeptical view that denies the theist hypothesis (in all its forms). Hume’s atheistic commitments are, the paper concludes, entirely consistent with his mitigated skeptical principles. (shrink)

There is an active research program currently underway, which treats cancer progression as an evolutionary process. This contribution investigates the ways that cancer progression is like and unlike evolution in other contexts. The aim is to take a multi-level perspective on cancer, investigating the levels at which selection may be acting, the unit or target of selection, the relative roles of selection and drift, and the idea that cancer progression may be a by-product of selection at other levels of organization.

Evolutionary biology is a field currently animated by much discussion concerning its conceptual foundations. On the one hand, we have supporters of a classical view of evolutionary theory, whose backbone is provided by population genetics and the so-called Modern Synthesis (MS). On the other hand, a number of researchers are calling for an Extended Synthe- sis (ES) that takes seriously both the limitations of the MS (such as its inability to incorporate developmental biology) and recent empirical and theoretical research on (...) issues such as evolvability, modularity, and self-organization. In this article, I engage in an in-depth commentary of an influential paper by population geneticist Michael Lynch, which I take to be the best defense of the MS-population genetics position published so far. I show why I think that Lynch’s arguments are wanting and propose a modification of evolutionary theory that retains but greatly expands on population genetics. (shrink)

Finding out why we have beliefs and desires is important for a thorough understanding of the nature of our minds (and those of other animals). It is therefore unsurprising that several accounts have been presented that are meant to answer this question. At least in the philosophical literature, the most widely accepted of these are due to Kim Sterelny and Peter Godfrey-Smith, who argue that beliefs and desires evolved due to their enabling us to be behaviourally flexible in a way (...) that reflexes do not—which, they claim, is beneficial in epistemically complex environments. However, as I try to make clear in this paper, upon closer consideration, this kind of account turns out to be theoretically implausible. In the main, this is because it fails to give due credit to the powers of reflex-driven organisms, which can in fact be just as flexible in their behaviour as ones that are belief/desire-driven. In order to improve on this account, I therefore propose that beliefs and desires evolved, not due to their enabling us to do something completely different from what reflexive organisms can do, but rather due to their enabling us to do the same things better. Specifically, I argue that beliefs and desires evolved for making the generation of behaviour more efficient, since they can simplify the necessary cognitive labour considerably. I end by considering various implications of this account. (shrink)

This paper addresses the general problem of how to rationally choose an algorithm for phylogenetic inference. Specifically, the controversy between maximum likelihood (ML) and maximum parsimony (MP) perspectives is reframed within the philosophical issue of theory choice. A Kuhnian approach in which rationality is bounded and value-laden is offered and construed through the notion of a Style of Modeling. A Style is divided into four stages: collecting remnant models, constructing models of taxonomical identity, implementing modeling algorithms, and finally inferring and (...) confirming evolutionary trees or cladograms. The identification and investigation of styles is useful for exploring sociological and epistemological issues such as individuating scientific communities and assessing the rationality of algorithm choice. Regarding the last point, this paper suggests that the values motivating ML and MP perspectives are justified but only contextually; these algorithms also have normative force because they can be therapeutic by allowing us to rationally choose among several competing trees, nonetheless this force is limited and cannot be used in order to decide the controversy tout court. (shrink)

Forster presented some interesting examples having to do with distinguishing the direction of causal influence between two variables, which he argued are counterexamples to the likelihood theory of evidence. In this paper, we refute Forster's arguments by carefully examining one of the alleged counterexamples. We argue that the example is not convincing as it relies on dubious intuitions that likelihoodists have forcefully criticized. More importantly, we show that contrary to Forster's contention, the consilience-based methodology he favored is accountable within the (...) framework of the LTE. (shrink)

Systematics based solely on structuralist principles is non-science because it is derived from first principles that are inconsistent in dealing with both synchronic and diachronic aspects of evolution, and its evolutionary models involve hidden causes, and unnameable and unobservable entities. Structuralist phylogenetics emulates axiomatic mathematics through emphasis on deduction, and “hypotheses” and “mapped trait changes” that are actually lemmas and theorems. Sister-group-only evolutionary trees have no caulistic element of scientific realism. This results in a degenerate systematics based on patterns of (...) fact or evidence being treated as so fundamental that all other data may be mapped to the cladogram, resulting in an apparently well-supported classification that is devoid of evolutionary theory. Structuralism in systematics is based on a non-ultrametric analysis of sister-group informative data that cannot detect or model a named taxon giving rise to a named taxon, resulting in classifications that do not reflect macroevolutionary changes unless they are sister lineages. Conservation efforts are negatively affected through epistemological extinction of scientific names. Evolutionary systematics is a viable alternative, involving both deduction and induction, hypothesis and theory, developing trees with both synchronic and diachronic dimensions often inferring nameable ancestral taxa, and resulting in classifications that advance evolutionary theory and explanations for particular groups. (shrink)

Debunking arguments in ethics contend that our moral beliefs have dubious evolutionary, cultural, or psychological origins—hence concluding that we should doubt such beliefs. Debates about debunking are often couched in coarse-grained terms—about whether our moral beliefs are justified or not, for instance. In this paper, I propose a more detailed Bayesian analysis of debunking arguments, which proceeds in the fine-grained framework of rational confidence. Such analysis promises several payoffs: it highlights how debunking arguments don’t affect all agents, but rather only (...) those agents who updated on their intuitions using a specific range of evidentiary weights; it underscores how the debunkers shouldn’t conclude that we should reduce confidence beyond some threshold, but rather only that we should reduce confidence by some amount; and it proposes a method of integrating different kinds of evidence—about the kinds of epistemic flaws at play, about the different possible origins of our moral beliefs, about the background normative assumptions we’re entitled to make—in order to arrive at a rational moral credence in light of debunking. (shrink)

A scientific explanatory project, part-whole explanation, and a kind of science, part-whole science are premised on identifying, investigating, and using parts and wholes. In the biological sciences, mechanistic, structuralist, and historical explanations are part-whole explanations. Each expresses different norms, explananda, and aims. Each is associated with a distinct partitioning frame for abstracting kinds of parts. These three explanatory projects can be complemented in order to provide an integrative vision of the whole system, as is shown for a detailed case study: (...) the tetrapod limb. My diagnosis of part-whole explanation in the biological sciences as well as in other domains exploring evolved, complex, and integrated systems (e.g., psychology and cognitive science) cross-cuts standard philosophical categories of explanation: causal explanation and explanation as unification. Part-whole explanation is itself one essential aspect of part-whole science. (shrink)

Selectionist evolutionary theory has often been faulted for not making novel predictions that are surprising, risky, and correct. I argue that it in fact exhibits the theoretical virtue of predictive capacity in addition to two other virtues: explanatory unification and model fitting. Two case studies show the predictive capacity of selectionist evolutionary theory: parallel evolutionary change in E. coli, and the origin of eukaryotic cells through endosymbiosis.

The dangers of character reification for cladistic inference are explored. The identification and analysis of characters always involves theory-laden abstraction—there is no theory-free “view from nowhere.” Given theory-ladenness, and given a real world with actual objects and processes, how can we separate robustly real biological characters from uncritically reified characters? One way to avoid reification is through the employment of objectivity criteria that give us good methods for identifying robust primary homology statements. I identify six such criteria and explore each (...) with examples. Ultimately, it is important to minimize character reification, because poor character analysis leads to dismal cladograms, even when proper phylogenetic analysis is employed. Given the deep and systemic problems associated with character reification, it is ironic that philosophers have focused almost entirely on phylogenetic analysis and neglected character analysis. (shrink)

We argued that explanatoriness is evidentially irrelevant in the following sense: Let H be a hypothesis, O an observation, and E the proposition that H would explain O if H and O were true. Then our claim is that Pr = Pr. We defended this screening-off thesis by discussing an example concerning smoking and cancer. Climenhaga argues that SOT is mistaken because it delivers the wrong verdict about a slightly different smoking-and-cancer case. He also considers a variant of SOT, called (...) “SOT*”, and contends that it too gives the wrong result. We here reply to Climenhaga’s arguments and suggest that SOT provides a criticism of the widely held theory of inference called “inference to the best explanation”. (shrink)

The vision of natural kinds that is most common in the modern philosophy of biology, particularly with respect to the question whether species and other taxa are natural kinds, is based on a revision of the notion by Mill in A System of Logic. However, there was another conception that Whewell had previously captured well, which taxonomists have always employed, of kinds as being types that need not have necessary and sufficient characters and properties, or essences. These competing views employ (...) different approaches to scientific methodologies: Mill’s class-kinds are not formed by induction but by deduction, while Whewell’s type-kinds are inductive. More recently, phylogenetic kinds (clades, or monophyletic-kinds) are inductively projectible, and escape Mill’s strictures. Mill’s version represents a shift in the notions of kinds from the biological to the physical sciences. (shrink)

I aim to provide some evidence that Husserl’s description of perceptual updating actually fits very nicely into the Bayesian Brain paradigm, articulated by Karl Friston and others, and that that paradigm, in turn, can be taken as an excellent example of “Neurophenomenology”. The apparently un-phenomenological Helmholtzian component of the Bayesian Brain paradigm, according to which what one consciously seems to see is a product of unconscious causal reasoning to the best explanation of one’s sensory stimulations, can be finessed, I claim, (...) in a way that makes it compatible with a phenomenological orientation. I begin by roughly characterizing the Bayesian Brain paradigm as it relates to perceptual cognition. I then show how Husserl’s descriptions of the conscious perceptual process relate to the paradigm. I conclude with some considerations about how to understand the relation between conscious and unconscious brain process in the present case and in relation to Neurophenomenology generally. (shrink)

In evolutionary biology changes in population structure are explained by citing trait fitness distribution. I distinguish three interpretations of fitness explanations—the Two‐Factor Model, the Single‐Factor Model, and the Statistical Interpretation—and argue for the last of these. These interpretations differ in their degrees of causal commitment. The first two hold that trait fitness distribution causes population change. Trait fitness explanations, according to these interpretations, are causal explanations. The last maintains that trait fitness distribution correlates with population change but does not cause (...) it. My defense of the Statistical Interpretation relies on a distinctive feature of causation. Causes conform to the Sure Thing Principle. Trait fitness distributions, I argue, do not. *Received July 2009; revised October 2009. †To contact the author, please write to: Department of Philosophy/Institute for the History, Philosophy of Science and Technology, University of Toronto, Victoria College, 91 Charles Street West, Toronto, ON M5S 1K7, Canada; e‐mail: [email protected]. (shrink)

In this paper we consider the problem of how to measure the strength of statistical evidence from the perspective of evidence amalgamation operations. We begin with a fundamental measurement amalgamation principle : for any measurement, the inputs and outputs of an amalgamation procedure must be on the same scale, and this scale must have a meaningful interpretation vis a vis the object of measurement. Using the p value as a candidate evidence measure, we examine various commonly used approaches to amalgamation (...) of evidence across similar studies, including standard forms of meta-analysis. We show that none of these methods satisfies MAP. Thus an underlying measurement problem remains. We argue that a successful approach to evidence amalgamation necessitates a solution to the problem of evidence measurement, and we suggest some lines of reasoning that might guide further work towards this end. (shrink)

Common ancestry is a central feature of the theory of evolution, yet it is not clear what “common ancestry” actually means; nor is it clear how it is related to other terms such as “the Tree of Life” and “the last universal common ancestor”. I argue these terms describe three distinct hypotheses ordered in a logical way: that there is a Tree of Life is a claim about the pattern of evolutionary history, that there is a last universal common ancestor (...) is an ontological claim about the existence of an entity of a specific kind, and that there is universal common ancestry is a claim about a causal pattern in the history of life. With these generalizations in mind, I argue that the existence of a Tree of Life entails a last universal common ancestor, which would entail universal common ancestry, but neither of the converse entailments hold. This allows us to make sense of the debates surrounding the Tree, as well as our lack of knowledge about the last universal common ancestor, while still maintaining the uncontroversial truth of universal common ancestry. (shrink)

Phylogenetic trees are meant to represent the genealogical history of life and apparently derive their justification from the existence of the tree of life and the fact that evolutionary processes are treelike. However, there are a number of problems for these assumptions. Here it is argued that once we understand the important role that phylogenetic trees play as models that contain idealizations, we can accept these criticisms and deny the reality of the tree while justifying the continued use of trees (...) in phylogenetic theory and preserving nearly all of what defenders of trees have called the “importance of tree thinking.”. (shrink)

A phylogeny that allows for lateral gene transfer (LGT) can be thought of as a strictly branching tree (all of whose branches are vertical) to which lateral branches have been added. Given that the goal of phylogenetics is to depict evolutionary history, we should look for the best supported phylogenetic network and not restrict ourselves to considering trees. However, the obvious extensions of popular tree-based methods such as maximum parsimony and maximum likelihood face a serious problem—if we judge networks by (...) fit to data alone, networks that have lateral branches will always fit the data at least as well as any network that restricts itself to vertical branches. This is analogous to the well-studied problem of overfitting data in the curve-fitting problem. Analogous problems often have analogous solutions and we propose to treat network inference as a case of model selection and use the Akaike Information Criterion (AIC). Strictly tree-like networks are more parsimonious than those that postulate lateral as well as vertical branches. This leads to the conclusion that we should not always infer LGT events whenever it would improve our fit-to-data, but should do so only when the improved fit is larger than the penalty for adding extra lateral branches. (shrink)

Mind Association 2017Elliott Sober’s first book, Simplicity, defends the view that the simplicity of a theory or hypothesis is a measure of its informativeness – roughly, simpler theories require less new information to be added to them to answer relevant questions of interest. While this measure of simplicity is question-relative, it is still what you might call a global view of simplicity – simplicity means the same thing across different scientific problems and it is always an epistemic virtue. Ockham’s Razor (...) is just good scientific reasoning. Sober’s 1988 book Reconstructing the Past: Parsimony, Evolution, and Inference argues against this global conception of simplicity and replaces it with a local one. Here, in one context parsimony means one thing while in another context it may mean something different. Similarly, whether the more parsimonious hypothesis is to be preferred is also a local matter; it... (shrink)

Charles Stein discovered a paradox in 1955 that many statisticians think is of fundamental importance. Here we explore its philosophical implications. We outline the nature of Stein’s result and of subsequent work on shrinkage estimators; then we describe how these results are related to Bayesianism and to model selection criteria like AIC. We also discuss their bearing on scientific realism and instrumentalism. We argue that results concerning shrinkage estimators underwrite a surprising form of holistic pragmatism.