Although the justification for using cladistic parsimony to infer phylogenetic trees has been extensively discussed, much less attention has been paid to the use of cladistic parsimony to reconstruct the character states of the ancestral species postulated by an inferred phylogenetic tree. These two problems differ in terms of both their inputs and their outputs, as shown in the following table. In the former, one begins with data on the character states of extant species and tries to find the best (...) supported phylogenetic tree. In the latter, one begins with the tree that is most firmly supported by characteristics C1, C2,... Cn-1; one then takes some new characteristic Cn and records the character states of Cn that attach to the tree’s interior nodes, which represent common ancestors. In both cases, cladistic parsimony solves the problem by finding the hypothesis that requires the fewest changes in character state that are needed to explain the observations. (shrink)

This volume consists of the first of the John Dewey Lectures delivered under the auspices of Columbia University's Philosophy Department as well as other essays by the author. Intended to clarify the meaning of the philosophical doctrines propounded by Professor Quine in 'Word and Objects', the essays included herein both support and expand those doctrines.

The book includes chapters on forms of natural realism, theories of perceptual experience, representationalism, the argument from illusion, phenomenological senses, types of perceptual content, the representationalist/intentionalist thesis, and adverbialist accounts of perceptual experience. The ideas of Austin, Dretske, Heidegger, Millikan, Putnam, and Robinson are considered among others and the reader is given an invaluable philosophical framework within which to consider the issues.

The philosophical issues raised by perception make it one of the central topics in the philosophical tradition. Debate about the nature of perceptual knowledge and the objects of perception comprises a thread that runs through the history of philosophy. In some historical periods the major issues have been predominantly epistemological and related to scepticism, but an adequate understanding of perception is important more widely, especially for metaphysics and the philosophy of mind. For this reason Barry Maund provides an account of (...) the major issues in the philosophy of perception that highlights the importance of a good theory of perception in a range of philosophical fields, while also seeking to be sensitive to the historical dimension of the subject. The work presents chapters on forms of natural realism; theories of perceptual experience; representationalism; the argument from illusion; phenomenological senses; types of perceptual content; the representationalist/intentionalist thesis; and adverbialist accounts of perceptual experience. The ideas of, among others, Austin, Dretske, Heidegger, Millikan, Putnam and Robinson are considered and the reader is given a philosophical framework within which to consider the issues. (shrink)

I adopt a cladistic view of species, and explore the possibility that there exists an equally valuable cladistic view of organismic traits. This suggestion seems to run counter to the stress on functional views of biological traits in recent work in philosophy and psychology. I show how the tension between these two views can be defused with a multilevel view of biological explanation. Despite the attractions of this compromise, I conclude that we must reject it, and adopt an essentially cladistic (...) conception of biological traits. (shrink)

In his new foreword to this edition, Hilary Putnam forcefully rejects these nativist claims.

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)

Homology is a natural kind term and a precise account of what homology is has to come out of theories about the role of homologues in evolution and development. Definitions of homology are discussed with respect to the question as to whether they are able to give a non-circular account of the correspondence or sameness referred to by homology. It is argued that standard accounts tie homology to operational criteria or specific research projects, but are not yet able to offer (...) a concept of homology that does not presuppose a version of homology or a comparable notion of sameness. This is the case for phylogenetic definitions that trace structures back to the common ancestor as well as for developmental approaches such as Wagner's biological homology concept. In contrast, molecular homology is able to offer a definition of homology in genes and proteins that explicates homology by reference to more basic notions. Molecular correspondence originates by means of specific features of causal processes. It is speculated that further understanding of morphogenesis might enable biologists to give a theoretically deeper definition of homology along similar lines: an account which makes reference to the concrete mechanisms that operate in organisms. (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)

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)

"Legend is overdue for replacement, and an adequate replacement must attend to the process of science as carefully as Hull has done. I share his vision of a serious account of the social and intellectual dynamics of science that will avoid both the rosy blur of Legend and the facile charms of relativism.... Because of [Hull's] deep concern with the ways in which research is actually done, Science as a Process begins an important project in the study of science. It (...) is one of a distinguished series of books, which Hull himself edits."—Philip Kitcher, Nature "In Science as a Process, [David Hull] argues that the tension between cooperation and competition is exactly what makes science so successful.... Hull takes an unusual approach to his subject. He applies the rules of evolution in nature to the evolution of science, arguing that the same kinds of forces responsible for shaping the rise and demise of species also act on the development of scientific ideas."—Natalie Angier, New York Times Book Review "By far the most professional and thorough case in favour of an evolutionary philosophy of science ever to have been made. It contains excellent short histories of evolutionary biology and of systematics (the science of classifying living things); an important and original account of modern systematic controversy; a counter-attack against the philosophical critics of evolutionary philosophy; social-psychological evidence, collected by Hull himself, to show that science does have the character demanded by his philosophy; and a philosophical analysis of evolution which is general enough to apply to both biological and historical change."—Mark Ridley, Times Literary Supplement "Hull is primarily interested in how social interactions within the scientific community can help or hinder the process by which new theories and techniques get accepted.... The claim that science is a process for selecting out the best new ideas is not a new one, but Hull tells us exactly how scientists go about it, and he is prepared to accept that at least to some extent, the social activities of the scientists promoting a new idea can affect its chances of being accepted."—Peter J. Bowler, Archives of Natural History "I have been doing philosophy of science now for twenty-five years, and whilst I would never have claimed that I knew everything, I felt that I had a really good handle on the nature of science, Again and again, Hull was able to show me just how incomplete my understanding was.... Moreover, [Science as a Process] is one of the most compulsively readable books that I have ever encountered."—Michael Ruse, Biology and Philosophy. (shrink)

Argues for the primacy of the phylogenetic system as the general reference system in biology. This book, first published in 1966, generated significant controversy and opened possibilities for evolutionary biology.

" Because characters and the conception of characters are central to all studies of evolution, and because evolution is the central organizing principle of biology, this book will appeal to a wide cross-section of biologists.

Do the sciences aim to uncover the structure of nature, or are they ultimately a practical means of controlling our environment? In Instrumental Biology, or the Disunity of Science, Alexander Rosenberg argues that while physics and chemistry can develop laws that reveal the structure of natural phenomena, biology is fated to be a practical, instrumental discipline. Because of the complexity produced by natural selection, and because of the limits on human cognition, scientists are prevented from uncovering the basic structure of (...) biological phenomena. Consequently, biology and all of the disciplines that rest upon it--psychology and the other human sciences--must aim at most to provide practical tools for coping with the natural world rather than a complete theoretical understanding of it. (shrink)

Certain lines of reasoning common in evolutionary taxonomy have been termed viciously circular. They are quite obviously not logically circular. They do give the superficial appearance of epistemological circularity. This appearance arises from the method of successive approximation used by evolutionary taxonomists. It is argued that this method is not epistemologically circular, even when the only evidence that the taxonomist has to go on is the phenetic similarity of contemporary forms. The important criticism of evolutionary taxonomy is rather that in (...) the absence of fossil evidence phyletic reconstructions are not warranted. It is argued that this charge stems initially from a misunderstanding of the kind of certainty possible in empirical science. When this criticism is couched in appropriate terms, it may be seen to have some force. Many phyletic inferences are not as warranted as one might wish. However, there is a great deal of difference between arguing that a line of reasoning is unwarranted and arguing that it is viciously circular. (shrink)

A word, phrase, or sentence is ambiguous if it has more than one meaning. The word 'light', for example, can mean not very heavy or not very dark. Words like 'light', 'note', 'bear' and 'over' are lexically ambiguous. They induce ambiguity in phrases or sentences in which they occur, such as 'light suit' and 'The duchess can't bear children'. However, phrases and sentences can be ambiguous even if none of their constituents is. The phrase 'porcelain egg container' is structurally ambiguous, (...) as is the sentence 'The police shot the rioters with guns'. Ambiguity can have both a lexical and a structural basis, as with sentences like 'I left her behind for you' and 'He saw her duck'. (shrink)