RÉSUMÉMalgré son usage très répandu, l'inférence à la meilleure explication a souvent été considérée avec suspicion par des théoriciens d'allégeances diverses. On lui a reproché à maintes reprises defaire reposer son recours à la simplicité et ses autres vertus explicatives sur des présuppositions métaphysiques douteuses. J'aborde ces questions, dans le présent article, dans le contexte d'une discussion large de l'usage de l'IME pour fonder notre croyance au monde extérieur. Distinguant entre la légitimité et l'efficacité de l'IME, je soutiendrai qu'elle constitue (...) bien une forme légitime d'inférence, mais que son efficacité dépend de la fonction de la théorie de la connaissance qui la supporte. (shrink)

Metaphysicians frequently appeal to the idea that theoretical simplicity is truth conducive in metaphysics, in the sense that, all other things being equal, simpler metaphysical theories are more likely to be true. In this paper I defend the notion that theoretical simplicity is truth conducive in metaphysics, against several recent objections. I do not give any direct arguments for the thesis that simplicity is truth conducive in metaphysics, since I am aware of no such arguments. I do argue, however, that (...) there is no special problem with the notion that simplicity is truth conducive in metaphysics. More specifically, I argue that if you accept the idea that simplicity is truth conducive in science, then it would be objectionably arbitrary to reject the idea that simplicity is truth conducive in metaphysics. (shrink)

The idea that simplicity matters in science is as old as science itself, with the much cited example of Ockham's Razor, 'entia non sunt multiplicanda praeter necessitatem': entities are not to be multiplied beyond necessity. A problem with Ockham's razor is that nearly everybody seems to accept it, but few are able to define its exact meaning and to make it operational in a non-arbitrary way. Using a multidisciplinary perspective including philosophers, mathematicians, econometricians and economists, this 2002 monograph examines simplicity (...) by asking six questions: what is meant by simplicity? How is simplicity measured? Is there an optimum trade-off between simplicity and goodness-of-fit? What is the relation between simplicity and empirical modelling? What is the relation between simplicity and prediction? What is the connection between simplicity and convenience? The book concludes with reflections on simplicity by Nobel Laureates in Economics. (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)

Here we challenge the orthodoxy according to which abduction is an a posteriori mode of inference. We start by providing a case study illustrating how abduction can justify a philosophical claim not justifiable by empirical evidence alone. While many grant abduction's epistemic value, nearly all assume that abductive justification is a posteriori, on grounds that our belief in abduction's epistemic value depends on empirical evidence about how the world contingently is. Contra this assumption, we argue, first, that our belief in (...) abduction’s epistemic value is not and could not be justified a posteriori, and second, that attention to the roles experience plays in abductive justification supports taking abduction to be an a priori mode of inference. We close by highlighting how our strategy for establishing the a priority of abduction positively contrasts with strategies in Bonjour (1998), Swinburne (2001), and Peacocke (2004) aiming to establish the a priority of certain ampliative modes of inference or abductive principles. (shrink)

Path-dependence offers a promising way of understanding the role historicity plays in explanation, namely, how the past states of a process can matter in the explanation of a given outcome. The two main existing accounts of path-dependence have sought to present it either in terms of dynamic landscapes or branching trees. However, the notions of landscape and tree both have serious limitations and have been criticized. The framework of causal networks is both more fundamental and more general that that of (...) landscapes and trees. Within this framework, I propose that historicity in networks should be understood as symmetry breaking. History matters when an asymmetric bias towards an outcome emerges in a causal network. This permits a quantitative measure for how path-dependence can occur in degrees, and offers suggestive insights into how historicity is intertwined both with causal structure and complexity. (shrink)

In this paper, I sketch an argument for the view that we cannot know (or have good reasons to believe) that God exists. Some call this view “strong agnosticism” but I prefer the term “skeptheism” in order to clearly distinguish between two distinct epistemic attitudes with respect to the existence of God, namely, agnosticism and skepticism. For the skeptheist, we cannot know (or have good reasons to believe) that God exists, since there can be neither conceptual (a priori) nor empirical (...) (a posteriori) evidence for the existence of God. (shrink)

According to one large family of views, scientific explanations explain a phenomenon (such as an event or a regularity) by subsuming it under a general representation, model, prototype, or schema (see Bechtel, W., & Abrahamsen, A. (2005). Explanation: A mechanist alternative. Studies in History and Philosophy of Biological and Biomedical Sciences, 36(2), 421–441; Churchland, P. M. (1989). A neurocomputational perspective: The nature of mind and the structure of science. Cambridge: MIT Press; Darden (2006); Hempel, C. G. (1965). Aspects of scientific (...) explanation. In C. G. Hempel (Ed.), Aspects of scientific explanation (pp. 331–496). New York: Free Press; Kitcher (1989); Machamer, P., Darden, L., & Craver, C. F. (2000). Thinking about mechanisms. Philosophy of Science, 67(1), 1–25). My concern is with the minimal suggestion that an adequate philosophical theory of scientific explanation can limit its attention to the format or structure with which theories are represented. The representational subsumption view is a plausible hypothesis about the psychology of understanding. It is also a plausible claim about how scientists present their knowledge to the world. However, one cannot address the central questions for a philosophical theory of scientific explanation without turning one’s attention from the structure of representations to the basic commitments about the worldly structures that plausibly count as explanatory. A philosophical theory of scientific explanation should achieve two goals. The first is explanatory demarcation. It should show how explanation relates with other scientific achievements, such as control, description, measurement, prediction, and taxonomy. The second is explanatory normativity. It should say when putative explanations succeed and fail. One cannot achieve these goals without undertaking commitments about the kinds of ontic structures that plausibly count as explanatory. Representations convey explanatory information about a phenomenon when and only when they describe the ontic explanations for those phenomena. (shrink)

In this paper, I argue that, other things being equal, simpler arguments are better. In other words, I argue that, other things being equal, it is rational to prefer simpler arguments over less simple ones. I sketch three arguments in support of this claim: an argument from mathematical proofs, an argument from scientific theories, and an argument from the conjunction rule.

The Humean argument concerning miracles says that one should always think it more likely that anyone who testifies to a miracle is lying or deluded than that the alleged miracle actually occurred, and so should always reject any single report of it. A longstanding and widely accepted objection is that even if this is right, the concurring and non-collusive testimony of many witnesses should make it rational to believe in whatever miracle they all report. I argue that on the contrary, (...) even multiple reports from non-collusive witnesses lack the sort of independence that could make trouble for Hume. (shrink)

According to Grice's “Modified Occam's Razor”, in case of uncertainty between the implicature account and the polysemy account of word uses it is parsimonious to opt for the former. However, it is widely agreed that uses can be partially conventionalised by repetition. This fact, I argue, raises a serious problem for MOR as a methodological principle, but also for the substantial notion of implicature in lexical pragmatics. In order to overcome these problems, I propose to reinterpret implicatures in terms of (...) implicature-like effects delivered by non-inferential processes. (shrink)

Many biological investigations are organized around a small group of species, often referred to as ‘model organisms’, such as the fruit fly Drosophila melanogaster. The terms ‘model’ and ‘modelling’ also occur in biology in association with mathematical and mechanistic theorizing, as in the Lotka–Volterra model of predator-prey dynamics. What is the relation between theoretical models and model organisms? Are these models in the same sense? We offer an account on which the two practices are shown to have different epistemic characters. (...) Theoretical modelling is grounded in explicit and known analogies between model and target. By contrast, inferences from model organisms are empirical extrapolations. Often such extrapolation is based on shared ancestry, sometimes in conjunction with other empirical information. One implication is that such inferences are unique to biology, whereas theoretical models are common across many disciplines. We close by discussing the diversity of uses to which model organisms are put, suggesting how these relate to our overall account. 1 Introduction2 Volterra and Theoretical Modelling3 Drosophila as a Model Organism4 Generalizing from Work on Model Organisms5 Phylogenetic Inference and Model Organisms6 Further Roles of Model Organisms6.1 Preparative experimentation6.2 Model organisms as paradigms6.3 Model organisms as theoretical models6.4 Inspiration for engineers6.5 Anchoring a research community7 Conclusion. (shrink)

In the past five years, there have been a series of papers in the journal Evolution debating the relative significance of two theories of evolution, a neo-Fisherian and a neo-Wrightian theory, where the neo-Fisherians make explicit appeal to parsimony. My aim in this paper is to determine how we can make sense of such an appeal. One interpretation of parsimony takes it that a theory that contains fewer entities or processes, (however we demarcate these) is more parsimonious. On the account (...) that I defend here, parsimony is a ‘local’ virtue. Scientists’ appeals to parsimony are not necessarily an appeal to a theory’s simplicity in the sense of it’s positing fewer mechanisms. Rather, parsimony may be proxy for greater probability or likelihood. I argue that the neo-Fisherians appeal is best understood on this interpretation. And indeed, if we interpret parsimony as either prior probability or likelihood, then we can make better sense of Coyne et al. argument that Wright’s three phase process operates relatively infrequently. (shrink)

Discussions of the functions of biological traits generally take the notion of a trait for granted. Defining this notion is a non-trivial problem. Different approaches to function place different constraints on adequate accounts of the notion of a trait. Accounts of function based on engineering-style analyses allow trait boundaries to be a matter of human interest. Accounts of function based on natural selection have typically been taken to require trait boundaries that are objectively real. After canvassing problems raised by each (...) approach, I conclude with some facts that satisfactory notions of trait must respect. (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)

This article discusses the role of simplicity and the notion of a best balance of simplicity and strength within the best systems account (BSA) of laws of nature. The article explores whether there is anything in scientific practice that corresponds to the notion of simplicity or to the trade-off between simplicity and strength to which the BSA appeals. Various theoretical rationales for simplicity preferences and their bearing on the identification of laws are also explored. It is concluded that there are (...) a number of issues about the role of simplicity within the BSA and its relation to strength that need to be addressed before the BSA can be regarded as an adequate account of laws. 1 Introduction2 The Best Systems Account3 The Trade-Off between Simplicity and Strength: Preliminary Considerations4 Alternative Conceptions of the Relationship between Simplicity and Strength5 Two Roles for Simplicity6 Simplicity in the Best Systems Account: Curve-Fitting7 Simplicity as a Corrective for Overfitting8 Descriptive Simplicity in the Best Systems Account?9 Simplicity as Due to Human Intellectual Limitations10 Summary11 Concluding Remarks. (shrink)

We begin by considering two principles, each having the form causal completeness ergo screening-off. The first concerns a common cause of two or more effects; the second describes an intermediate link in a causal chain. They are logically independent of each other, each is independent of Reichenbach's principle of the common cause, and each is a consequence of the causal Markov condition. Simple examples show that causal incompleteness means that screening-off may fail to obtain. We derive a stronger result: in (...) a rather general setting, if the composite cause C1 & C2 & … & Cn screens-off one event from another, then each of the n component causes C1, C2, …, Cn must fail to screen-off. The idea that a cause may be ordinally invariant in its impact on different effects is defined; it plays an important role in establishing this no-go theorem. Along the way, we describe how composite and component causes can all screen-off when ordinal invariance fails. We argue that this theorem is relevant to assessing the plausibility of the two screening-off principles. The discovery of incomplete causes that screen-off is not evidence that causal completeness must engender screening-off. Formal and epistemic analogies between screening-off and determinism are discussed. (shrink)

de Queiroz (1995), Griffiths (1999) and LaPorte (2004) offer a new version of essentialism called "historical essentialism". According to this version of essentialism, relations of common ancestry are essential features of biological taxa. The main type of argument for this essentialism proposed by Griffiths (1999) and LaPorte (2004) is that the dominant school of classification, cladism, defines biological taxa in terms of common ancestry. The goal of this paper is to show that this argument for historical essentialism is unsatisfactory: cladism (...) does not assume that relations of common ancestry are essential attributes of biological taxa. Therefore, historical essentialism is not justified by cladism. (shrink)

Charles Lyell’s Principles of Geology is widely regarded as one of the great works of 19th century science, and one of the most influential works in the entire history of the earth sciences. Yet the standard critical interpretation of the Principles makes such high regard and influence look puzzling at best. We are told, for instance, that Lyell’s argument rests on a contentious a priori methodological distinction between scientific and non-scientific explanations, the former featuring observed causes at their present intensities, (...) the latter featuring anything else. 2 We are also told that Lyell simply assumes a priori that. (shrink)

Abductivists claim that explanatory considerations (e.g., simplicity, parsimony, explanatory breadth, etc.) favor belief in the external world over skeptical hypotheses involving evil demons and brains in vats. After showing how most versions of abductivism succumb fairly easily to obvious and fatal objections, I explain how rationalist versions of abductivism can avoid these difficulties. I then discuss the most pressing challenges facing abductivist appeals to the a priori and offer suggestions on how to overcome them.

In a formal theory of induction, inductive inferences are licensed by universal schemas. In a material theory of induction, inductive inferences are licensed by facts. With this change in the conception of the nature of induction, I argue that the celebrated “problem of induction” can no longer be set up and is thereby dissolved. Attempts to recreate the problem in the material theory of induction fail. They require relations of inductive support to conform to an unsustainable, hierarchical empiricism.

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)

In “Spandrels,” Gould and Lewontin criticized what they took to be an all-too-common conviction, namely, that adaptation to current environments determines organic form. They stressed instead the importance of history. In this paper, we elaborate upon their concerns by appealing to other writings in which those issues are treated in greater detail. Gould and Lewontin’s combined emphasis on history was three-fold. First, evolution by natural selection does not start from scratch, but always refashions preexisting forms. Second, preexisting forms are refashioned (...) by the selection of whatever mutational variations happen to arise: the historical order of mutations needs to be taken into account. Third, the order of environments and selection pressures also needs to be taken into account. (shrink)

This article argues that a particular notion of rationality, more exactly a specific notion of legitimate inference, is presupposed by much work in the social sciences to their detriment. The author describes the notion of rationality he has in mind, explains why it is misguided, identifies where and how it affects social research, and illustrates why that research is weaker as a result. The notion of legitimate inference the author has in mind is one that believes inferences are guided by (...) principles that are formal, universal and a priori—that is, that make no substantive, domain-specific empirical assumptions about the world. The author briefly provides a variety of reasons to be skeptical about such principles. Those reasons extend from broad philosophical considerations to quasi-empirical evidence. The author then argues that this notion of inference is involved with both the practice and the content of the social sciences in various ways. In terms of practice, this notion of inference lies behind the way statistical testing is generally done in the social sciences. In terms of content, the author argues that this notion of rationality is invoked, for example, in game theory and in rational expectations macroeconomics. In all cases, use of the formal rationality notion leads social scientists to put more faith in their results than is warranted and thus is an obstacle to doing better social science. (shrink)

Maximum Parsimony (MP) and Maximum Likelihood (ML) are two methods for evaluating which phlogenetic tree is best supported by data on the characteristics of leaf objects (which may be species, populations, or individual organisms). MP has been criticized for assuming that evolution proceeds parsimoniously -- that if a lineage begins in state i and ends in state j, the way it got from i to j is by the smallest number of changes. MP has been criticized for needing to assume (...) some model or other of the evolutionary process even though biologists often do not know what that process really is. This paper critically evaluates both criticisms. (shrink)

The paper criticizes the attempt to account for the direction of causation in terms of objective statistical asymmetries, such as those of the fork asymmetry. Following Ramsey, I argue that the most plausible way to account for causal asymmetry is to regard it as "put in by hand", that is as a feature that agents project onto the world. Its temporal orientation stems from that of ourselves as agents. The crucial statistical asymmetry is an anthropocentric one, namely that we take (...) our actions to be statistically independent of everything except (what we come to call) their effects. I argue that this account explains the intuitive plausibility of Reichenbach's principle of the common cause. (shrink)

If a parsimony criterion may be used to choose between theories that make different predictions, may the same criterion be used to choose between theories that are predictively equivalent? The work of the statistician H. Akaike (1973) is discussed in connection with this question. The results are applied to two examples in which parsimony has been invoked to choose between philosophical theories-Shoemaker's (1969) discussion of the possibility of time without change and the discussion by Smart (1959) and Brandt and Kim (...) (1967) of mind/body dualism and the identity theory. (shrink)

When two causally independent processes each have a quantity that increases monotonically (either deterministically or in probabilistic expectation), the two quantities will be correlated, thus providing a counterexample to Reichenbach's principle of the common cause. Several philosophers have denied this, but I argue that their efforts to save the principle are unsuccessful. Still, one salvage attempt does suggest a weaker principle that avoids the initial counterexample. However, even this weakened principle is mistaken, as can be seen by exploring the concepts (...) of homology and homoplasy used in evolutionary biology. I argue that the kernel of truth in the principle of the common cause is to be found by separating metaphysical and epistemological issues; as far as the epistemology is concerned, the Likelihood Principle is central. (shrink)

Recent work on inference to the best explanation has come to an impasse regarding the proper way to coordinate the theoretical virtues in explanatory inference with probabilistic confirmation theory, and in particular with aspects of Bayes's Theorem. I argue that the theoretical virtues are best conceived heuristically and that such a conception gives us the resources to explicate the virtues in terms of ceteris paribus theorems. Contrary to some Bayesians, this is not equivalent to identifying the virtues with likelihoods or (...) priors per se; the virtues may be more accessible epistemically than likelihoods or priors. I then prove a ceteris paribus theorem regarding theoretical consilience, use it to correct a recent application of Reichenbach's common cause principle, and apply it to a test case of scientific reasoning. Explanation and confirmation The heuristic conception of theoretical virtues Abduction and the accessibility of explanatory power Evidential and theoretical consilience A test case: gravitational lensing Conclusion Thus natural science appears completely to lose from sight the large and general questions; but all the more splendid is the success when, groping in the thicket of special questions, we suddenly find a small opening that allows a hitherto undreamt of outlook on the whole. (L. Boltzmann, Theoretical Physics and Philosophical Problems). (shrink)

The paper provides a formal proof that efficient estimates of parameters, which vary as as little as possible when measurements are repeated, may be expected to provide more accurate predictions. The definition of predictive accuracy is motivated by the work of Akaike (1973). Surprisingly, the same explanation provides a novel solution for a well known problem for standard theories of scientific confirmation — the Ravens Paradox. This is significant in light of the fact that standard Bayesian analyses of the paradox (...) fail to account for the predictive utility of universal laws like All ravens are black. (shrink)

Almost all commentators acknowledge that among the grounds on which scientists perform theory-choices are criteria of simplicity. In general, simplicity is regarded either as only a logico-empirical quality of a theory, diagnostic of the theory's future predictive success, or as a purely aesthetic or otherwise extra-empirical property of it. This paper attempts to demonstrate that the simplicity-criteria applied in scientific practice include both a logico-empirical and a quasi-aesthetic criterion: to conflate these in an account of scientists' theory-choice is to court (...) confusion. (shrink)

Despite the platitude that analytic philosophy is deeply concerned with language, philosophers of science have paid little attention to methodological issues that arise within historical linguistics. I broach this topic by arguing that many inferences in historical linguistics conform to Reichenbach's common cause principle (CCP). Although the scope of CCP is narrower than many have thought, inferences about the genealogies of languages are particularly apt for reconstruction using CCP. Quantitative approaches to language comparison are readily understood as methods for detecting (...) the correlations that serve as premises for common cause inferences, and potential sources of error in historical linguistics correspond to well-known limitations of CCP. (shrink)

Traditional analyses of the curve fitting problem maintain that the data do not indicate what form the fitted curve should take. Rather, this issue is said to be settled by prior probabilities, by simplicity, or by a background theory. In this paper, we describe a result due to Akaike [1973], which shows how the data can underwrite an inference concerning the curve's form based on an estimate of how predictively accurate it will be. We argue that this approach throws light (...) on the theoretical virtues of parsimoniousness, unification, and non ad hocness, on the dispute about Bayesianism, and on empiricism and scientific realism. * Both of us gratefully acknowledge support from the Graduate School at the University of Wisconsin-Madison, and NSF grant DIR-8822278 (M.F.) and NSF grant SBE-9212294 (E.S.). Special thanks go to A. W. F. Edwards.William Harper. Martin Leckey. Brian Skyrms, and especially Peter Turney for helpful comments on an earlier draft. (shrink)

What Do the Data Tell Us? Justification of scientific theories is a three-place relation between data, theories, and background knowledge. Though this should be a commonplace, many methodologies in science neglect it. The article will elucidate the significance and function of our background knowledge in epistemic justification and their consequences for different scientific methodologies. It is argued that there is no simple and at the same time acceptable statistical algorithm that justifies a given theory merely on the basis of certain (...) data. And even if we think to know the probability of a theory, that does not decide whether we should accept it or not. (shrink)

The idea that the changing entropy of a system is relevant to explaining why we know more about the system's past than about its future has been criticized on several fronts. This paper assesses the criticisms and clarifies the epistemology of the inference problem. It deploys a Markov process model to investigate the relationship between entropy and temporally asymmetric inference.

Neanderthal extinction is a matter of intense debate. It has been suggested that demography (as opposed to environment or competition) could alone provide a sufficient explanation for the phenomenon. We argue that demography cannot be a ‘stand-alone’ or ‘alternative’ explanation of token extinctions as demographic features are entangled with competitive and environmental factors, and further because demography should not be conflated with neutrality.

The longstanding species problem in biology has a history that suggests a solution, and that history is not the received history found in many texts written by biologists or philosophers. The notion of species as the division into subordinate groups of any generic predicate was the staple of logic from Aristotle through the middle ages until quite recently. However, the biological species concept during the same period was at first subtly and then overtly different. Unlike the logic sense, which relied (...) on definitions of the essence of both genus and species, biological species from the time of Epicurus were consistently considered to involve a reproductive element: in short, living species relied not on essential definitions, but on the generative cause, which might not be definable. I term this the generative conception of species: species were the generation by reproduction of form. This undercuts the claim that species before Darwin were essentialist, and divorces the notion of a type from that of essence. In fact, as late as the end of the nineteenth century, logicians explicitly treated biological “species” as a homonym only of logical essentialist species, and permitted considerable deviation from the type or form. At every point, species in logic were thought to be a subset, in effect, of some more general notion. I sketch a history of both philosophical and biological traditions of the species concept, before turning to the current conceptions. These are reconsidered in the light of this history, and in particular Mayr’s changing views are shown to be somewhat Whiggish, historiographically. Of the many touted biological species concepts, only one of which (Mayr’s) is called _the_ Biological Species Concept, none appears to capture all the relevant facts, intuitions, and operational requirements of biology. Cladistic conceptions, however, have much in common with the older philosophical literature, in that the natural group of cladism is the clade, or monophyletic group. After considering the Individuality Thesis, and the metaphysics of species, we see that species are the most particular terminal taxa in a clade, and that they are “defined” in terms of the particular synapomorphies, or evolved characters, that are causally responsible for keeping the lineages that organisms form distinct from one another. In this way, we can remain within the generative conception of species that has been in play for over two millennia, and yet avoid the pitfalls of prior attempts to find a universal conception of species. (shrink)

The task of Philosophy in Science (PinS) is to use philosophical tools to help solve scientific problems. This article describes how I stumbled into this line of work and then addressed several topics in philosophy of biology—units of selection, cladistic parsimony, robustness and trade-offs in model building, adaptationism, and evidence for common ancestry—often in collaboration with scientists. I conclude by offering advice for would-be PinS practitioners.

Cladism, today the dominant school of systematics in biology, includes a classification component – the view that classification ought to reflect phylogeny only, such that all and only taxa are monophyletic (i.e. consist of an ancestor and all its descendants) - and a metaphysical component – the view that all and only real groups or kinds of organisms are monophyletic. For the most part these are seen as amounting to much the same thing, but I argue they can and should (...) be distinguished, in particular that cladists about classification need not accept the typically cladist view about real groups or kinds. Cladists about classification can and should adopt an explanatory criterion for the reality of groups or kinds, on which being monophyletic is neither necessary nor sufficient for being real or natural. Thus the line of reasoning that has rightly led to cladism becoming dominant within systematics, and the attractive line of reasoning in the philosophical literature that advocates a more liberal approach to natural kinds, are seen to be, contrary to appearances, compatible. (shrink)

In this article, I will provide a critical overview of the form of non-deductive reasoning commonly known as “Inference to the Best Explanation” (IBE). Roughly speaking, according to IBE, we ought to infer the hypothesis that provides the best explanation of our evidence. In section 2, I survey some contemporary formulations of IBE and highlight some of its putative applications. In section 3, I distinguish IBE from C.S. Peirce’s notion of abduction. After underlining some of the essential elements of IBE, (...) the rest of the entry is organized around an examination of various problems that IBE confronts, along with some extant attempts to address these problems. In section 4, I consider the question of when a fact requires an explanation, since presumably IBE applies only in cases where some explanation is called for. In section 5, I consider the difficult question of how we ought to understand IBE in light of the fact that among philosophers, there is significant disagreement about what constitutes an explanation. In section 6, I consider different strategies for justifying the truth-conduciveness of the explanatory virtues, e.g., simplicity, unification, scope, etc., criteria which play an indispensable role in any given application of IBE. In section 7, I survey some of the most recent literature on IBE, much of which consists of investigations of the status of IBE from the standpoint of the Bayesian philosophy of science. (shrink)

The no-free-lunch theorems promote a skeptical conclusion that all possible machine learning algorithms equally lack justification. But how could this leave room for a learning theory, that shows that some algorithms are better than others? Drawing parallels to the philosophy of induction, we point out that the no-free-lunch results presuppose a conception of learning algorithms as purely data-driven. On this conception, every algorithm must have an inherent inductive bias, that wants justification. We argue that many standard learning algorithms should rather (...) be understood as model-dependent: in each application they also require for input a model, representing a bias. Generic algorithms themselves, they can be given a model-relative justification. (shrink)

Three competing ‘methods’ have been endorsed for inferring phylogenetic hypotheses: parsimony, likelihood, and Bayesianism. The latter two have been claimed superior because they take into account rates of sequence substitution. Can rates of substitution be justified on its own accord in inferences of explanatory hypotheses? Answering this question requires addressing four issues: (1) the aim of scientific inquiry, (2) the nature of why-questions, (3) explanatory hypotheses as answers to why-questions, and (4) acknowledging that neither parsimony, likelihood, nor Bayesianism are inferential (...) actions leading to explanatory hypotheses. The aim of scientific inquiry is to acquire causal understanding of effects. Observation statements of organismal characters lead to implicit or explicit why-questions. Those questions, conveyed in data matrices, assume the truth of observation statements, which is contrary to subsequently invoking substitution rates within inferences to phylogenetic hypotheses. Inferences of explanatory hypotheses are abductive in form, such that some version of an evolutionary theory(ies) is/are included or implied. If rates of sequence evolution are to be considered, it must be done prior to, rather than within abduction, which requires renaming those putatively-shared nucleotides subject to substitution rates. There are, however, no epistemic grounds for renaming characters to accommodate rates, calling into question the legitimacy of causally accounting for sequence data. (shrink)

Darwin famously held that his use of the term "chance" in evolutionary theory merely "serves to acknowledge plainly our ignorance of the causes of each particular variation". Is this a tenable view today? Or should we revise our thinking about chance in evolution in light of the more advanced, quantitative models of Neo-Darwinian theory, which make substantial use of statistical reasoning and the concept of probability? Is determinism still a viable metaphysical doctrine about biological reality after the quantum revolution in (...) physics, or dowe have to abandon it in favor of an objective indeterminism? In light of such reflections, what is the relevant interpretation of probability in evolutionary theory? Do biologists use the concept of probability because they are finite cognitive agents or because the evolutionary process is fundamentally probabilistic? In this paper, I will show that we do not yet fully understand the nature of chance in evolution. (shrink)

Within eighteenth-century debates on animal cognition we can distinguish at least three main theoretical positions: (i) Buffon’s mechanism, (ii) Reimarus’ theory of instincts, and (iii) the sensationalism of Condillac and Leroy. In this paper, I adopt a philosophical perspective on this debate and argue that in order to fully understand the justification Buffon, Reimarus, Condillac, and Leroy gave for their respective theories, we must pay special attention to the theoretical virtues these naturalists alluded to while justifying their position. These theoretical (...) virtues have received little to no attention in the literature on eighteenth-century animal cognition, but figure prominently in the justification of the mechanist, instinctive, and sensationalist theories of animal behavior. Through my philosophical study of the role of theoretical virtues in eighteenth-century debates on animal cognition, we obtain a deeper understanding of how theoretical virtues were conceptualized in eighteenth-century science and how they influenced the justification of theories of animal cognition. (shrink)