This chapter contains sections titled: Introduction The Scientific Method of Yore The Structure and Research Practices of Scientific Historiography of Nature Explanation and Confirmation in Scientific Historiography Narrative Explanation Common Cause Explanation References.

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)

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)

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 this paper I argue that we can best make sense of the practice of experimental evolutionary biology if we see it as investigating contingent, rather than lawlike, regularities. This understanding is contrasted with the experimental practice of certain areas of physics. However, this presents a problem for those who accept the Logical Positivist conception of law and its essential role in scientific explanation. I address this problem by arguing that the contingent regularities of evolutionary biology have a limited range (...) of nomic necessity and a limited range of explanatory power even though they lack the unlimited projectibility that has been seen by some as a hallmark of scientific laws. (shrink)

Variational evolutionary theory as advocated by Darwin is not a single theory, but a bundle of related but independent theories, namely: (a) variational evolution; (b) gradualism rather than large leaps; (c) processes of phyletic evolution and of speciation; (d) causes for the formation of varying individuals in populations and for the action of selective agents; and (e) all organisms evolved from a common ancestor. The first four are nomological-deductive explanations and the fifth is historical-narrative. Therefore evolutionary theory must be divided (...) into nomological and historical theories which are both testable against objective empirical observations. To be scientific, historical evolutionary theories must be based on well corroborated nomological theories, both evolutionary and functional. Nomological and general historical evolutionary theories are well tested and must be considered as strongly corroborated scientific theories. Opponents of evolutionary theory are concerned only with historical evolutionary theories, having little interest in nomological theory. Yet given a well corroborated nomological evolutionary theory, historical evolutionary theories follow automatically. If understood correctly, both forms of evolutionary theories stand on their own as corroborated scientific theories and should not be labeled as facts. (shrink)

Ernst Mayr’s concept of dual causality in biology with the two forms of causes continues to provide an essential foundation for the philosophy of biology. They are equivalent to functional and evolutionary causes with both required for full biological explanations. The natural sciences can be classified into nomological, historical nomological and historical dual causality, the last including only biology. Because evolutionary causality is unique to biology and must be included for all complete biological explanations, biology is autonomous from the physical (...) sciences. (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)

The primary purpose of this paper is to argue that biologists should stop citing Karl Popper on what a genuinely scientific theory is. Various ways in which biologists cite Popper on this matter are surveyed, including the use of Popper to settle debates on methodology in phylogenetic systematics. It is then argued that the received view on Popper—namely, that a genuinely scientific theory is an empirically falsifiable one—is seriously mistaken, that Popper’s real view was that genuinely scientific theories have the (...) form of statements of laws of nature. It is then argued that biology arguably has no genuine laws of its own. In place of Popperian falsifiability, it is suggested that a cluster class epistemic values approach (which subsumes empirical falsifiability) is the best solution to the demarcation problem between genuine science and pseudo- or non-science. (shrink)

That some propositions are testable, while others are not, was a fundamental idea in the philosophical program known as logical empiricism. That program is now widely thought to be defunct. Quine’s (1953) “Two Dogmas of Empiricism” and Hempel’s (1950) “Problems and Changes in the Empiricist Criterion of Meaning” are among its most notable epitaphs. Yet, as we know from Mark Twain’s comment on an obituary that he once had the pleasure of reading about himself, the report of a death can (...) be an exaggeration. The research program that began in Vienna and Berlin continues, even though many of the specific formulations that came out of those circles are flawed and need to be replaced. (shrink)

Evolutionary explanations are not only common in the biological sciences, but also widespread outside biology. But an account of how evolutionary explanations perform their explanatory work is still lacking. This paper develops such an account. I argue that available accounts of explanations in evolutionary science miss important parts of the role of history in evolutionary explanations. I argue that the historical part of evolutionary science should be taken as having genuine explanatory force, and that it provides how‐possibly explanations sensu Dray. (...) I propose an account of evolutionary explanations as comparative‐composite explanations consisting of two distinct kinds of explanations, one processual and one historical, that are connected via the explanandum's evolvability to show how the explanandum is the product of its evolutionary past. The account is both a reconstruction of how evolutionary explanations in biology work and a guideline specifying what kind of explanations evolutionary research programs should develop. (shrink)

No other branch of the philosophy of science is as backward as the philosophy of biology. When physicists or philosophers “explain biology,” they not only tend to use wrong terminologies but they usually throw away that which is typically biological. This error is second only to the even worse one of adopting vitalistic interpretations. Vitalism is now dead, as far as biologists are concerned, and a biologist can now talk about the differences between the philosophy of physics and the philosophy (...) of biology without being suspected of being a concealed vitalist. (shrink)

The ability to generalize from the known to the unknown is central to learning and inference. Two experiments explore the relationship between how a property is explained and how that property is generalized to novel species and artifacts. The experiments contrast the consequences of explaining a property mechanistically, by appeal to parts and processes, with the consequences of explaining the property functionally, by appeal to functions and goals. The findings suggest that properties that are explained functionally are more likely to (...) be generalized on the basis of shared functions, with a weaker relationship between mechanistic explanations and generalization on the basis of shared parts and processes. The influence of explanation type on generalization holds even though all participants are provided with the same mechanistic and functional information, and whether an explanation type is freely generated (Experiment 1), experimentally provided (Experiment 2), or experimentally induced (Experiment 2). The experiments also demonstrate that explanations and generalizations of a particular type (mechanistic or functional) can be experimentally induced by providing sample explanations of that type, with a comparable effect when the sample explanations come from the same domain or from a different domains. These results suggest that explanations serve as a guide to generalization, and contribute to a growing body of work supporting the value of distinguishing mechanistic and functional explanations. (shrink)

Historical explanations in evolutionary biology are commonly characterized as narrative explanations. Examples include explanations of the evolution of particular traits and explanations of macroevolutionary transitions. In this paper I present two case studies of explanations in accounts of pathogen evolution and host-pathogen coevolution, respectively, and argue that one of them is captured well by established accounts of time-sequenced narrative explanation. The other one differs from narrative explanations in important respects, even though it shares some characteristics with them as it is (...) also a population-level historical explanation. I thus argue that the second case represents a different kind of explanation that I call historical explanation of type phenomena. The main difference between the two kinds of explanation is the conceptualization of the explanandum phenomena as particulars or type phenomena, respectively. Narrative explanations explain particulars but also deal with generalization, regularities and type phenomena. Historical explanations of type phenomena, on the other hand, explain multiply realizable phenomena but also deal with particulars. The two kinds of explanation complement each other because they explain different aspects of evolution. (shrink)

Some adaptationist explanations are regarded as maximally solid and others fanciful just-so stories. Just-so stories are explanations based on very little evidence. Lack of evidence leads to circular-sounding reasoning: “this trait was shaped by selection in unseen ancestral populations and this selection must have occurred because the trait is present.” Well-supported adaptationist explanations include evidence that is not only abundant but selected from comparative, populational, and optimality perspectives, the three adaptationist subdisciplines. Each subdiscipline obtains its broad relevance in evolutionary biology (...) via assumptions that can only be tested with the methods of the other subdisciplines. However, even in the best-supported explanations, assumptions regarding variation, heritability, and fitness in unseen ancestral populations are always present. These assumptions are accepted given how well they would explain the data if they were true. This means that some degree of “circularity” is present in all evolutionary explanations. Evolutionary explanation corresponds not to a deductive structure, as biologists usually assert, but instead to ones such as abduction or induction. With these structures in mind, we show the way to a healthier view of “circularity” in evolutionary biology, and why integration across the comparative, populational, and optimality approaches is necessary. (shrink)

Deduction leads to causal explanation in phylogenetic inference when the evidence, the systematic character, is conceptualized as a transformation series. Also, the deductive entailment of modus tollens is satisfied when those kinds of events are operationalized as patristic difference. Arguments to the contrary are based largely on the premise that character-states are defined intensionally as objects, in terms of similarity relations. However, such relations leave biologists without epistemological access to the causal explanation and explanatory power of historical statements. Moreover, the (...) prediction-making to which those kinds of relations are limited in practice can lead to a category error—the mental conversion of an abstraction into a thing . The latter practices and problems characterize pattern cladistics, taxa being interpreted as homeostatic property cluster natural kinds, and other instrumentalist research programs. (shrink)

This article serves as an introduction to the laws-of-biology debate. After introducing the main issues in an introductory section, arguments for and against laws of biology are canvassed in Section 2. In Section 3, the debate is placed in wider epistemological context by engaging a group of scholars who have shifted the focus away from the question of whether there are laws of biology and toward offering good accounts of explanation(s) in the biological sciences. Section 4 introduces two relatively new (...) pieces of science – metabolic scaling theory and ecological stoichiometry – that have not been topics of much discussion by philosophers but are relevant because they have at least some of the hallmarks of laws of nature. Section 5 concludes by pointing out that discovering laws of biology, if any there be, will not necessarily answer the questions raised by the debate in the first place: we will still want to know how biology compares to other sciences, how to characterize its systems and processes, and whether accounts in terms of laws always or usually constitute adequate explanations in various sciences. (shrink)

As Aristotle stated, scientific explanation is based on deductive argument--yet, Wesley C. Salmon points out, not all deductive arguments are qualified explanations. The validity of the explanation must itself be examined. _Four Decades of Scientific Explanation_ provides a comprehensive account of the developments in scientific explanation that transpired in the last four decades of the twentieth century. It continues to stand as the most comprehensive treatment of the writings on the subject during these years. Building on the historic 1948 essay (...) by Carl G. Hempel and Paul Oppenheim, "Studies in the Logic of Explanation,” which introduced the deductive-nomological model on which most work on scientific explanation was based for the following four decades, Salmon goes beyond this model's inherent basis of describing empirical knowledge to tells us “not only _what,_ but also _why_.” Salmon examines the predominant models in chronological order and describes their development, refinement, and criticism or rejection. _Four Decades of Scientific Explanation_ underscores the need for a consensus of approach and ongoing evaluations of methodology in scientific explanation, with the goal of providing a better understanding of natural phenomena. (shrink)

The biological functions debate is a perennial topic in the philosophy of science. In the first full-length account of the nature and importance of biological functions for many years, Justin Garson presents an innovative new theory, the 'generalized selected effects theory of function', which seamlessly integrates evolutionary and developmental perspectives on biological functions. He develops the implications of the theory for contemporary debates in the philosophy of mind, the philosophy of medicine and psychiatry, the philosophy of biology, and biology itself, (...) addressing issues ranging from the nature of mental representation to our understanding of the function of the human genome. Clear, jargon-free, and engagingly written, with accessible examples and explanatory diagrams to illustrate the discussion, his book will be highly valuable for readers across philosophical and scientific disciplines. (shrink)

Is Popper's philosophy alive or dead? If we make a judgment based on recent discussion in academic philosophy of science, he definitely seems to be fading. Popper is still seen as an important historical figure, a key part of the grand drama of 20th century thinking about science. He is associated with an outlook, a mindset, and a general picture of scientific work. His name has bequeathed us an adjective, "Popperian," that is well established. But the adjective is used for (...) very general ideas that, according to most current philosophers, Popper did not develop convincingly. His detailed account is often seen as attractive on first impression, but full of holes that become bigger rather than smaller as discussion continues. The picture and the name remain, which is more than 1 most philosophers can hope for. But the name attaches more and more to a set of instincts and intuitions, less and less to views that are seeing ongoing philosophical development. Inside science itself, Popper's standing is quite different. He continues to be just about the only philosopher who can seize the imagination and command the loyalty of successful professional scientists. And he is popular within science not only for purposes of general commentary and public relations. Popper's philosophy is a resource drawn on by scientists in their internal debates about scientific matters. This has been especially marked in some parts of biology (Hull 1999). From the point of view of philosophers, this affection on the part of scientists may have an unflattering explanation. Popper offers a rather heroic view of the scientific character, featuring an appealing combination of creativity and hard-headedness. It is no surprise that scientists like to be described this way. It is no surprise that they prefer this picture to the one often (though inaccurately) associated with Hempel and Carnap – the scientist as a sort of logic-driven pattern-recognition machine. The same applies to the picture associated with Kuhn, who presents the normal scientist as a narrow-minded, indoctrinated member of a peculiar collective enterprise, an enterprise devoted to solving tiny puzzles most of the time but prone to occasional fits of crisis and chaos.. (shrink)

This paper explores the use of Popper's philosophy of science by cladists in their battle against evolutionary and numerical taxonomy. Three schools of biological systematics fiercely debated each other from the late 1960s: evolutionary taxonomy, phenetics or numerical taxonomy, and phylogenetic systematics or cladistics. The outcome of that debate was the victory of phylogenetic systematics/cladistics over the competing schools of thought. To bring about this "cladistic turn" in systematics, the cladists drew heavily on the philosopher K.R. Popper in order to (...) dress up phylogenetic systematics as a hypothetico-deductivist, indeed falsificationist, research program that would put an end to authoritarianism. As the case of the "cladistic revolution" demonstrates, scientists who turn to philosophy in defense of a research program read philosophers with an agenda in mind. That agenda is likely to distort the philosophical picture, as happened to Popper's philosophy of science at the hands of cladists. (shrink)