I develop an account of homology and homoplasy drawing on their use in biological inference and explanation. Biologists call on homology and homoplasy to infer character states, support adaptationist explanations, identify evolutionary novelties and hypothesize phylogenetic relationships. In these contexts, the concepts must be understood phylogenetically and kept separate: as they play divergent roles, overlap between the two ought to be avoided. I use these considerations to criticize an otherwise attractive view defended by Gould, Hall, and Ramsey & Peterson. By (...) this view, homology and homoplasy can only be delineated qua some level of description, and some homoplasies (parallelisms) are counted as homologous. I develop an account which retains the first, but rejects the second, aspect of that view. I then characterize parallelisms and convergences in terms of their causal role. By the Strict Continuity account, homology and homoplasy are defined phylogenetically and without overlaps, meeting my restriction. Convergence and parallelisms are defined as two types of homoplasy: convergent homoplasies are largely constrained by external factors, while parallelisms are due to internal constraints. (shrink)

Stephen Jay Gould argued that replaying the “tape of life” would result in a radically different evolutionary outcome. Some biologists and philosophers, however, have pointed to convergent evolution as evidence for robust replicability in macroevolution. These authors interpret homoplasy, or the independent origination of similar biological forms, as evidence for the power of natural selection to guide form toward certain morphological attractors, notwithstanding the diversionary tendencies of drift and the constraints of phylogenetic inertia. In this paper, I consider the implications (...) of homoplasy for the debate over the nature of macroevolution. I argue that once the concepts of contingency and convergence are fleshed out, it becomes clear that many instances of homoplasy fail to negate Gould’s overarching thesis, and may in fact support a Gouldian view of life. My argument rests on the distinction between parallelism and convergence, which I defend against a recent challenge from developmental biology. I conclude that despite the difficulties in defining and identifying parallelism, the concept remains useful and relevant to the contingency controversy insofar as it underscores the common developmental origins of iterated evolution. (shrink)

In earlier work ( Cleland [2001] , [2002]), I sketched an account of the structure and justification of ‘prototypical’ historical natural science that distinguishes it from ‘classical’ experimental science. This article expands upon this work, focusing upon the close connection between explanation and justification in the historical natural sciences. I argue that confirmation and disconfirmation in these fields depends primarily upon the explanatory (versus predictive or retrodictive) success or failure of hypotheses vis-à-vis empirical evidence. The account of historical explanation that (...) I develop is a version of common cause explanation. Common cause explanation has long been vindicated by appealing to the principle of the common cause. Many philosophers of science (e.g., Sober and Tucker) find this principle problematic, however, because they believe that it is either purely methodological or strictly metaphysical. I defend a third possibility: the principle of the common cause derives its justification from a physically pervasive time asymmetry of causation (a.k.a. the asymmetry of overdetermination). I argue that explicating the principle of the common cause in terms of the asymmetry of overdetermination illuminates some otherwise puzzling features of the practices of historical natural scientists. (shrink)

David Lewis defends the thesis of the asymmetry of overdetermination: later affairs are seldom overdetermined by earlier affairs, but earlier affairs are usually overdetermined by later affairs. Recently, Carol Cleland has argued that since the distinctive methodologies of historical science and experimental science exploit different aspects of this asymmetry, the methodology of historical science is just as good, epistemically speaking, as that of experimental science. This paper shows, first, that Cleland's epistemological conclusion does not follow from the thesis of the (...) asymmetry of overdetermination, because overdetermination is compatible with epistemic underdetermination. The paper also shows, contra Cleland, that there is at least one interesting sense in which historical science is epistemically inferior to experimental science, after all, because local underdetermination problems are more widespread in historical than in experimental science. (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)

How can we know what really happened in the distant past in places like ancient Egypt, Mesopotamia, Palestine, Greece, and Rome, especially since the evidence is fragmentary and ancient cultures are so different from our own frame of reference? Scholars may examine historical documents and archaeological artifacts, and then make reasonable inferences. But in the final analysis there can be no absolute certainty about events far removed from present reality, and the past must be reconstructed by means of hypotheses that (...) coherently organize all available data. Knowledge claims about the past, and about many areas of science as well, rest on a network of interdependence between theory and evidence, and between interpretation and data. In this fascinating study of epistemology, philosopher Peter Kosso argues for a coherence model of epistemic justification. In the first part, the conceptual argument, he proposes a model of knowledge of the past. In the second part he presents three detailed case studies drawn from the work of historians and archaeologists. These studies are used to support and fine-tune the model outlined in the first part. Kosso presents many insights into the limits of knowledge and our ability to know the mental as well as the physical past. Historians, archaeologists, philosophers, and students interested in epistemology will find this accessible work to be of great value. (shrink)

The fate of optimality modeling is typically linked to that of adaptationism: the two are thought to stand or fall together (Gould and Lewontin, Proc Relig Soc Lond 205:581–598, 1979; Orzack and Sober, Am Nat 143(3):361–380, 1994). I argue here that this is mistaken. The debate over adaptationism has tended to focus on one particular use of optimality models, which I refer to here as their strong use. The strong use of an optimality model involves the claim that selection is (...) the only important influence on the evolutionary outcome in question and is thus linked to adaptationism. However, biologists seldom intend this strong use of optimality models. One common alternative that I term the weak use simply involves the claim that an optimality model accurately represents the role of selection in bringing about the outcome. This and other weaker uses of optimality models insulate the optimality approach from criticisms of adaptationism, and they account for the prominence of optimality modeling (broadly construed) in population biology. The centrality of these uses of optimality models ensures a continuing role for the optimality approach, regardless of the fate of adaptationism. (shrink)

This article deals with a type of functional explanation, viability explanation, that has been overlooked in recent philosophy of science. Viability explanations relate traits of organisms and their environments in terms of what an individual needs to survive and reproduce. I show that viability explanations are neither causal nor historical and that, therefore, they should be accounted for as a distinct type of explanation.

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)

Philosophers of evolutionary biology favor the so-called etiological concept of function according to which the function of a trait is its evolutionary purpose, defined as the effect for which that trait was favored by natural selection. We term this the selected effect (SE) analysis of function. An alternative account of function was introduced by Robert Cummins in a non-evolutionary and non-purposive context. Cummins''s account has received attention but little support from philosophers of biology. This paper will show that a similar (...) non-purposive concept of function, which we term causal role (CR) function, is crucial to certain research programs in evolutionary biology, and that philosophical criticisms of Cummins''s concept are ineffective in this scientific context. Specifically, we demonstrate that CR functions are a vital and ineliminable part of research in comparative and functional anatomy, and that biological categories used by anatomists are not defined by the application of SE functional analysis. Causal role functions are non-historically defined, but may themselves be used in an historical analysis. Furthermore, we show that a philosophical insistence on the primary of SE functions places practicing biologists in an untenable position, as such functions can rarely be demonstrated (in contrast to CR functions). Biologists who study the form and function of organismal design recognize that it is virtually impossible to identify the past action of selection on any particular structure retrospectively, a requirement for recognizing SE functions. (shrink)

Experimental research is commonly held up as the paradigm of "good" science. Although experiment plays many roles in science, its classical role is testing hypotheses in controlled laboratory settings. Historical science is sometimes held to be inferior on the grounds that its hypothesis cannot be tested by controlled laboratory experiments. Using contemporary examples from diverse scientific disciplines, this paper explores differences in practice between historical and experimental research vis-à-vis the testing of hypotheses. It rejects the claim that historical research is (...) epistemically inferior. For as I argue, scientists engage in two very different patterns of evidential reasoning and, although there is overlap, one pattern predominates in historical research and the other pattern predominates in classical experimental research. I show that these different patterns of reasoning are grounded in an objective and remarkably pervasive time asymmetry of nature. (shrink)

As a working hypothesis for philosophy of science, the unity of science thesis has been decisively challenged in all its standard formulations; it cannot be assumed that the sciences presuppose an orderly world, that they are united by the goal of systematically describing and explaining this order, or that they rely on distinctively scientific methodologies which, properly applied, produce domain-specific results that converge on a single coherent and comprehensive system of knowledge. I first delineate the scope of arguments against global (...) unity theses. However implausible old-style global unity theses may now seem, I argue that unifying strategies of a more local and contingent nature do play an important role in scientific inquiry. This is particularly clear in archaeology where, to establish evidential claims of any kind, practitioners must exploit a range of inter-field and inter-theory connections. At the same time, the robustness of these evidential claims depends on significant disunity between the sciences from which archaeologists draw background assumptions and auxiliary hypotheses. This juxtaposition of unity with disunity poses a challenge to standard positions in the debate about scientific unity. (shrink)

Function theorists routinely speculate that a viable function theory will be equally applicable to biological traits and artifacts. However, artifact function has received only the most cursory scrutiny in its own right. Closer scrutiny reveals that only a pluralist theory comprising two distinct notions of function--proper function and system function--will serve as an adequate general theory. The first section describes these two notions of function. The second section shows why both notions are necessary, by showing that attempts to do away (...) with one of them fail. This demonstration draws on examples from the artifactual realm to motivate major points of the argument. The third section is an outline of artifact function. It confirms the conclusions of the second section, and also begins the task of describing some of the special features of artifact function needing accommodation within the general theory. (shrink)

In the wake of the paleobiological revolution of the 1970s and 1980s, paleontologists continue to investigate far-reaching questions about how evolution works. Many of those questions have a philosophical dimension. How is macroevolution related to evolutionary changes within populations? Is evolutionary history contingent? How much can we know about the causes of evolutionary trends? How do paleontologists read the patterns in the fossil record to learn about the underlying evolutionary processes? Derek Turner explores these and other questions, introducing the reader (...) to exciting recent work in the philosophy of paleontology and to theoretical issues including punctuated equilibria and species selection. He also critically examines some of the major accomplishments and arguments of paleontologists of the last 40 years. (shrink)

The historical sciences, such as geology, evolutionary biology, and archaeology, appear to have no means to test hypotheses. However, on closer examination, reasoning in the historical sciences relies upon regularities, regularities that can be tested. I outline the role of regularities in the historical sciences, and in the process, blur the distinction between the historical sciences and the experimental sciences: all sciences deploy theories about the world in their investigations.

The vagaries of evidential reasoning in archaeology are notorious: the material traces that comprise the archaeological record are fragmentary and profoundly enigmatic, and the inferential gap that archaeologists must cross to constitute them as evidence of the cultural past is a peren­nial source of epistemic anxiety. And yet we know a great deal about the cultural past, including vast reaches of the past for which this material record is our only source of evidence. The contents of this record stand as (...) evidence only under interpretation, but however much a construct it is, archaeological evidence has a striking capacity to disrupt settled assump­tions, redirecting inquiry and expanding interpretive horizons in direc­tions no one could have anticipated. It is this capacity for constraining inference and interpretation that I am concerned to understand. I outline a model of evidential reasoning based on archaeological practice that integrates insights drawn from philosophical theories of confirmation, model building and hypothesis testing. Given growing interest in the uses of material evidence in fields that had been resolutely text-based, the archaeological principles of evidential reasoning may have much wider reach than this particular social/historical discipline. (shrink)

A number of philosophers and ‘evolutionary psychologists’ have argued that attacks on adaptationism in contemporary biology are misguided. These thinkers identify anti-adaptationism with advocacy of non-adaptive modes of explanation. They overlook the influence of anti-adaptationism in the development of more rigorous forms of adaptive explanation. Many biologists who reject adaptationism do not reject Darwinism. Instead, they have pioneered the contemporary historical turn in the study of adaptation. One real issue which remains unresolved amongst these methodological advances is the nature of (...) ‘phylogenetic inertia’. To what extent is an adaptive explanation needed for the persistence of a trait as well as its origin? (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)

How do historians, comparative linguists, biblical and textual critics and evolutionary biologists establish beliefs about the past? How do they know the past? This book presents a philosophical analysis of the disciplines that offer scientific knowledge of the past. Using the analytic tools of contemporary epistemology and philosophy of science the book covers such topics as evidence, theory, methodology, explanation, determination and underdetermination, coincidence, contingency and counterfactuals in historiography. Aviezer Tucker's central claim is that historiography as a scientific discipline should (...) be thought of as an effort to explain the evidence of past events. He also emphasizes the similarity between historiographic methodology to Darwinian evolutionary biology. This is an important, fresh approach to historiography and will be read by philosophers, historians and social scientists interested in the methodological foundations of their disciplines. (shrink)

Evolutionary biology, indeed any science that attempts to reconstruct prehistory, faces practical limitations on available data. These limitations create the problem of contrast failure: specific observations may fail to discriminate between rival evolutionary hypotheses. Assessing the risk of contrast failure provides a way to evaluate testing protocols in evolutionary science. Here I will argue that part of the methodological critique in the Spandrels paper involves diagnosing contrast failure problems. I then distinguish the problem of contrast failure from the more familiar (...) philosophical problem of underdetermination, and demonstrate how contrast failure arises in scientific practice with an investigation into Lewontin and White’s estimation of an adaptive landscape. (shrink)

I defend the view that many biological categories are defined by homology against a series of arguments designed to show that all biological categories are defined, at least in part, by selected function. I show that categories of homology are `abnormality inclusive'—something often alleged to be unique to selected function categories. I show that classifications by selected function are logically dependent on classifications by homology, but not vice-versa. Finally, I reject the view that biologists must use considerations of selected function (...) to abstract away from variation and pathology to form a canonical description of a class of biological systems. (shrink)

This fine collection of essays by a leading philosopher of science presents a defence of integrative pluralism as the best description for the complexity of scientific inquiry today. The tendency of some scientists to unify science by reducing all theories to a few fundamental laws of the most basic particles that populate our universe is ill-suited to the biological sciences, which study multi-component, multi-level, evolved complex systems. This integrative pluralism is the most efficient way to understand the different and complex (...) processes - historical and interactive - that generate biological phenomena. This book will be of interest to students and professionals in the philosophy of science. (shrink)

Scientists often make surprising claims about things that no one can observe. In physics, chemistry, and molecular biology, scientists can at least experiment on those unobservable entities, but what about researchers in fields such as paleobiology and geology who study prehistory, where no such experimentation is possible? Do scientists discover facts about the distant past or do they, in some sense, make prehistory? In this book Derek Turner argues that this problem has surprising and important consequences for the scientific realism (...) debate. His discussion covers some of the main positions in philosophy of science - realism, social constructivism, empiricism, and the natural ontological attitude - and shows how they relate to issues in paleobiology and geology. His original and thought-provoking book will be of wide interest to philosophers and scientists alike. (shrink)

I review the book “Making Prehistory: Historical Science and the Scientific Realism Debate” by Derek Turner. Turner suggests that philosophers should take seriously the historical sciences such as geology when considering philosophy of science issues. To that end, he explores the scientific realism debate with the historical sciences in mind. His conclusion is a view allied to that of Arthur Fine: a view Turner calls the natural historical attitude. While I find Turner’s motivations good, I find his characterisation of the (...) historical sciences unconvincing. I say why in a section at the end of the review. The result is that I am unpersuaded by his thesis. (shrink)

We discuss the scientific task of historical reconstruction and the problem of epistemic access. We argue that strong epistemic support for historical claims consists in the consilience of multiple independent lines of evidence, and analyze the impact hypothesis for the End-Cretaceous mass extinction to illustrate the accrual of epistemic support. Although there are elements of the impact hypothesis that enjoy strong epistemic support, the general conditions for this are strict, and help to clarify the difficulties associated with reconstructing the deep (...) past. (shrink)