Reconstructing the Past seeks to clarify and help resolve the vexing methodological issues that arise when biologists try to answer such questions as whether human beings are more closely related to chimps than they are to gorillas. It explores the case for considering the philosophical idea of simplicity/parsimony as a useful principle for evaluating taxonomic theories of evolutionary relationships. For the past two decades, evolutionists have been vigorously debating the appropriate methods that should be used in systematics, the field that (...) aims at reconstructing phylogenetic relationships among species. This debate over phylogenetic inference, Elliott Sober observes, raises broader questions of hypothesis testing and theory evaluation that run head on into long standing issues concerning simplicity/parsimony in the philosophy of science. Sober treats the problem of phylogenetic inference as a detailed case study in which the philosophical idea of simplicity/parsimony can be tested as a principle of theory evaluation. Bringing together philosophy and biology, as well as statistics, Sober builds a general framework for understanding the circumstances in which parsimony makes sense as a tool of phylogenetic inference. Along the way he provides a detailed critique of parsimony in the biological literature, exploring the strengths and limitations of both statistical and nonstatistical cladistic arguments. (shrink)

Philosophy of biology has a long and honourable history. Indeed, like most of the great intellectual achievements of the Western World, it goes back to the Greeks. However, until recently in this century, it was sadly neglected. With a few noteworthy exceptions, someone wishing to delve into the subject had to choose between extremes of insipid vitalism on the one hand, and sterile formalizations of the most elementary biological principles on the other. Whilst philosophy of physics pushed confidently ahead, the (...) philosophy of biology languished. In the past decade, however, things have changed dramatically. A number of energetic and thoughtful young philosophers have made real efforts to master the outlines and details of contemporary biology. They have shown that many stimulating problems emerge when analytic skills are turned towards the life-sciences, particularly if one does not feeI con strained to stay only with theoretical parts of biology, but can range over to more medical parts of the spectrum. At the same time, biology itself has had one of the most fruitful yet turbulent periods in its whole history, and more and more biologists have grown to see that many of the problems they face take them beyond the narrow confines of empiric al science: a broader perspective is needed. (shrink)

Brian Skyrms (1987, 1990, 1993, 1997) has discussed the role of dynamic coherence arguments in the theory of personal or subjective probability. In particular, Skryms (1997) both reviews and discusses the utility of martingale arguments in establishing the convergence of beliefs within the context of radical probabilism. The classical martingale converence theorem, however, assumes the countable additivity of the underlying probability measure; an assumption rejected by some subjectivists such as Bruno de Finetti (see, e.g., de Finetti 1930 and 1972). This (...) brief note has a very modest goal: to briefly consider the extent to which Skyrms’s argument can be extended to the finitely additive case. (shrink)

Several paleontologists have recently challenged the explanatory adequacy of the modern synthetic theory of evolution. Their position is that, contrary to the prevailing view that evolutionary change is gradual, the fossil record manifests long periods of species stasis (equilibrium) punctuated by periods of rapid species formation. And, they argue, this punctuated equilibria pattern challenges the gradualist, adaptationist and extrapolationist assumptions of the modern synthetic theory of evolution and supports a hierarchical, non-extrapolationist (non-reductionist) view of evolution. In this paper I argue (...) that the challenge rests on an inadequate characterization of the modern synthetic theory and that, even accepting punctuated equilibria and an irreducible evolutionary hierarchy, the modern synthetic theory is adequate to explain evolutionary change at all levels of the hierarchy. (shrink)

With this manifesto, John Dupré systematically attacks the ideal of scientific unity by showing how its underlying assumptions are at odds with the central conclusions of science itself.

INTRODUCTION I first read Charles Darwin's masterpiece, On the Origin of Species , some twenty years ago. At once I fell under its spell - an emotion which ...

Akaike’s framework for thinking about model selection in terms of the goal of predictive accuracy and his criterion for model selection have important philosophical implications. Scientists often test models whose truth values they already know, and they often decline to reject models that they know full well are false. Instrumentalism helps explain this pervasive feature of scientific practice, and Akaike’s framework helps provide instrumentalism with the epistemology it needs. Akaike’s criterion for model selection also throws light on the role of (...) parsimony considerations in hypothesis evaluation. I explain the basic ideas behind Akaike’s framework and criterion; several biological examples, including the use of maximum likelihood methods in phylogenetic inference, are considered. (shrink)

The `fact' of pluralism in science is nosurprise. Yet, if science is representing andexplaining the structure of the oneworld, why is there such a diversity ofrepresentations and explanations in somedomains? In this paper I consider severalphilosophical accounts of scientific pluralismthat explain the persistence of bothcompetitive and compatible alternatives. PaulSherman's `Levels of Analysis' account suggeststhat in biology competition betweenexplanations can be partitioned by the type ofquestion being investigated. I argue that thisaccount does not locate competition andcompatibility correctly. I then defend anintegrative (...) model for understanding pluralism. This view is based on taking seriously both thecomplexity and contingency of biologicalorganization and the idealized character ofbiological models. On this view, explanationbecomes, among other things, the location forthe integration of diverse models. I explicatemy argument by an analysis of explanations ofdivision of labor in social insects. (shrink)

Several paleontologists have recently challenged the explanatory adequacy of the modern synthetic theory of evolution. Their position is that, contrary to the prevailing view that evolutionary change is gradual, the fossil record manifests long periods of species stasis punctuated by periods of rapid species formation. And, they argue, this punctuated equilibria pattern challenges the gradualist, adaptationist and extrapolationist assumptions of the modern synthetic theory of evolution and supports a hierarchical, non-extrapolationist view of evolution. In this paper I argue that the (...) challenge rests on an inadequate characterization of the modern synthetic theory and that, even accepting punctuated equilibria and an irreducible evolutionary hierarchy, the modern synthetic theory is adequate to explain evolutionary change at all levels of the hierarchy. (shrink)

This paper contributes to the recently renewed debate over methodological individualism (MI) by carefully sorting out various individualist claims and by making use of recent work on reduction and explanation outside the social sciences. My major focus is on individualist claims about reduction and explanation. I argue that reductionist versions of MI fail for much the same reasons that mental predicates cannot be reduced to physical predicates and that attempts to establish reducibility by weakening the requirements for reduction also fail. (...) I consider and reject a number of explanatory theses, among them the claims that any adequate theory must refer only to individuals and that individualist theory suffices to explain fully. The latter claim, I argue, is not entailed by the supervenience of social facts on individual facts. Lastly, I argue that there is one individualist restriction on explanation which is far more plausible and significant than one would initially suspect. (shrink)

Advances in molecular biology have generally been taken to support the claim that biology is reducible to chemistry. I argue against that claim by looking in detail at a number of central results from molecular biology and showing that none of them supports reduction because (1) their basic predicates have multiple realizations, (2) their chemical realization is context-sensitive and (3) their explanations often presuppose biological facts rather than eliminate them. I then consider the heuristic and confirmational implications of irreducibility and (...) argue that purely biochemical approaches are likely to be unsound and to be unable to confirm an important range of statements. I conclude by sketching criteria for scientific unity that do not entail reducibility and yet leave an important place for identifying underlying mechanisms. Molecular biology, properly understood, provides an excellent paradigm of non-reductive unity between different explanatory levels. (shrink)

This paper argues that conceptualizing unity as "interconnection" (rather than reduction) provides a more fruitful and versatile framework for the philosophical study of scientific unification. Building on the work of Darden and Maull, Kitcher, and Kincaid, I treat unity as a relationship between fields: two fields become more integrated as the number and/or significance of interfield connections grow. Even when reduction fails, two theories or fields can be unified (integrated) in significant ways. I highlight two largely independent dimensions of unification. (...) Fields are theoretically unified to the extent that we understand how the ontologies, concepts, and generalizations of these fields are connected. (Reductionism is one form of theoretical unity, but not the only form). Fields are practically unified through heuristic connections (e.g., using the heuristics of one field to generate hypotheses in another field) and by the development of methods for integrating the qualitatively distinct bodies of data generated by the two fields. I discuss the relationship between paleontological and neontological systematics to illustrate the utility of conceptualizing unity as interconnection. (shrink)

This paper analyzes the generation and function of hitherto ignored or misrepresented interfield theories , theories which bridge two fields of science. Interfield theories are likely to be generated when two fields share an interest in explaining different aspects of the same phenomenon and when background knowledge already exists relating the two fields. The interfield theory functions to provide a solution to a characteristic type of theoretical problem: how are the relations between fields to be explained? In solving this problem (...) the interfield theory may provide answers to questions which arise in one field but cannot be answered within it alone, may focus attention on domain items not previously considered important, and may predict new domain items for one or both fields. Implications of this analysis for the problems of reduction and the unity and progress of science are mentioned. (shrink)

"Theoretical pluralism" obtains when there are good evidential reasons for accommodating multiple theories of the same domain. Issues of "relative significance" often arise in connection with the investigation of such domains. In this paper, I describe and give examples of theoretical pluralism and relative significance issues. Then I explain why theoretical pluralism so often obtains in biology--and why issues of relative significance arise--in terms of evolutionary contingencies and the paucity or lack of laws of biology. Finally, I turn from explanation (...) to justification, and raise questions about the purpose and value of concerns and disagreements about relative significance. (shrink)

Explores the development of the ideas of evolutionary biology, particularly as affected by the increasing understanding of genetics and of the chemical basis of inheritance.

The goal of cladistic systematics is to discern sister-group relations (cladistic relations) by the methods of cladistic analysis and to represent them explicitly and unambiguously in cladograms and cladistic classifications. Cladists have selected cladistic relations to represent for two reasons: cladistic relations can be discerned with reasonable certainty by the methods of cladistic analysis and they can be represented with relative ease in cladograms and classifications. Cladists argue that features of phylogeny other than cladistic relations cannot be discerned with sufficient (...) certainty to warrant attempting to represent them in either cladograms or classifications and could not be represented if they could. I argue that a better alternative is to work toward improving methods of cladistic analysis (or else to supplement them with other methods) so that such features of phylogeny can be discerned and to devise methods of representation capable of representing them in both cladograms and classifications. However, cladograms and classifications cannot represent everything about phylogeny. It is better to represent one or two aspects of phylogeny explicitly and unambiguously than nothing at all. (shrink)