Despite the promises made by molecular evolutionists since the early 1960s that phylogenies would be readily reconstructed using molecular data, the construction of molecular phylogenies has both retained many methodological problems of the past and brought up new ones of considerable epistemic relevance. The field is driven not only by changes in knowledge about the processes of molecular evolution, but also by an ever-present methodological anxiety manifested in the constant search for an increased objectivity—or in its converse, the avoidance of (...) subjectivity.This paper offers an exhaustive account of the methodological and conceptual difficulties embedded in each of the steps required to elaborate molecular phytogenies. The authors adopt a historical perspective on the field in order to follow the development of practices that seek to increase the objectivity of their methods and representations. These include the adoption and development of explicit criteria for evaluation of evidence, and of procedures associated with methods of statistical inference, quantification and automation. All these are linked to an increasing use of computers in research since the mid 1960s. We will show that the practices of objectivity described are highly dependent on the problems and tools of molecular phylogenetics. (shrink)

The role of scientific theories in classifying plants and animals is traced from Hennig's phylogenetics and the evolutionary taxonomy of Simpson and Mayr, through numerical phenetics, to present-day cladistics. Hennig limited biological classification to sister groups so that this one relation can be expressed unambiguously in classifications. Simpson and Mayr were willing to sacrifice precision in representation in order to include additional features of evolution in the construction of classifications. In order to make classifications more objective, precise and quantitative, numerical (...) pheneticists limited themselves to representing degrees of phenetic similarity. Finally, present-day cladists can be separated into phylogenetic cladists, who retain much of Hennig's theory of classification, and pattern cladists, who have stripped Hennig's system down to its bare essentials. (shrink)

We argue that the mathematization of science should be understood as a normative activity of advocating for a particular methodology with its own criteria for evaluating good research. As a case study, we examine the mathematization of taxonomic classification in systematic biology. We show how mathematization is a normative activity by contrasting its distinctive features in numerical taxonomy in the 1960s with an earlier reform advocated by Ernst Mayr starting in the 1940s. Both Mayr and the numerical taxonomists sought to (...) formalize the work of classification, but Mayr introduced a qualitative formalism based on human judgment for determining the taxonomic rank of populations, while the numerical taxonomists introduced a quantitative formalism based on automated procedures for computing classifications. The key contrast between Mayr and the numerical taxonomists is how they conceptualized the temporal structure of the workflow of classification, specifically where they allowed meta-level discourse about difficulties in producing the classification. (shrink)

The writings of Joseph Henry Woodger (1894–1981) are often taken to exemplify everything that was wrongheaded, misguided, and just plain wrong with early twentieth-century philosophy of biology. Over the years, commentators have said of Woodger: (a) that he was a fervent logical empiricist who tried to impose the explanatory gold standards of physics onto biology, (b) that his philosophical work was completely disconnected from biological science, (c) that he possessed no scientific or philosophical credentials, and (d) that his work was (...) disparaged – if not altogether ignored – by the biologists and philosophers of his era. In this paper, we provide the first systematic examination of Woodger’s oeuvre, and use it to demonstrate that the four preceding claims are false. We argue that Woodger’s ideas have exerted an important influence on biology and philosophy, and submit that the current consensus on his legacy stems from a highly selective reading of his works. By rehabilitating Woodger, we hope to show that there is no good reason to continue to disregard the numerous contributions to the philosophy of biology produced in the decades prior to the professionalization of the discipline. (shrink)

The use of molecules and reactions as evidence, markers and/or traits for evolutionary processes has a history more than a century long. Molecules have been used in studies of intra-specific variation and studies of similarity among species that do not necessarily result in the analysis of phylogenetic relations. Promoters of the use of molecular data have sustained the need for quantification as the main argument to make use of them. Moreover, quantification has allowed intensive statistical analysis, as a condition and (...) a product of increasing automation. All of these analyses are subject to the methodological anxiety characteristic of a community in search of objectivity. It is in this context that scientists compared and evaluated protein and nucleic acid sequence data with other types of molecular data – including immunological, electrophoretic and hybridization data. This paper argues that by looking at long-term historical processes, such as the use of molecular evidence in evolutionary biology, we gain valuable insights into the history of science. In that sense, it accompanies a growing concern among historians for big-pictures of science that incorporate the fruitful historical research on local cases of the last decades. (shrink)

What does it look like when a group of scientists set out to re-envision an entire field of biology in symbolic and formal terms? I analyze the founding and articulation of Numerical Taxonomy between 1950 and 1970, the period when it set out a radical new approach to classification and founded a tradition of mathematics in systematic biology. I argue that introducing mathematics in a comprehensive way also requires re-organizing the daily work of scientists in the field. Numerical taxonomists sought (...) to establish a mathematical method for classification that was universal to every type of organism, and I argue this intrinsically implicated them in a qualitative re-organization of the work of all systematists. I also discuss how Numerical Taxonomy’s re-organization of practice became entrenched across systematic biology even as opposing schools produced their own competing mathematical methods. In this way, the structure of the work process became more fundamental than the methodological theories that motivated it. (shrink)

The Development of Modern Taxonomy Taxonomy has a long history, going back to the ancient Greeks and to forerunners even less sophisticated in systematics. Our interest here is centered on modern taxonomy itself, and we shall largely ...

One of the principal difficulties in assessing Science as aProcess (Hull 1988) is determining the relationship between the various elements of Hull's theory. In particular, it is hard to understand precisely how conceptual selection is related to Hull's account of the social dynamics of science. This essay aims to clarify the relation between these aspects of his theory by examining his discussion of the``demic structure'' of science. I conclude that the social account cando significant explanatory work independently of the selectionistaccount. (...) Further, I maintain that Hull's treatment of the demicstructure of science points us toward an important set of issues insocial epistemology. If my reading of Science as a Process iscorrect, then most of Hull's critics (e.g., those who focus solelyon his account of conceptual selection) have ignored promisingaspects of his theory. (shrink)

This paper is based on my M.Sc. dissertation: ‘The Origins of Numerical Taxonomy’ 1985, submitted to the University of Leicester during the tenure of a D.E.S. State Studentship. For this work I drew extensively on interviews with Professors A. J. Cain, G. A. Harrison, R. R. Sokal and P. H. A. Sneath. I am very grateful to them for their time, interest and encouragement. Without the indefatigable assistance of Jon Harwood, this paper would never have been finished.

The twentieth century witnessed a dramatic increase in the use of statistics by biologists, including systematists. The modern synthesis and new systematics stimulated this development, particularly after World War II. The rise of "the statistical frame of mind " resulted in a rethinking of the relationship between biological and mathematical points of view, the roles of objectivity and subjectivity in systematic research, the implications of new computing technologies, and the place of systematics among the biological disciplines.

Hull's recent work in evolutionary epistemology is marred by a deep tension. While he maintains that conceptual and biological evolution are both driven by selection processes, he also claims that only the former is globally progressive. In this paper I formulate this tension and present four possible responses (including Hull's). I argue that Hull's position rests on the assumption that there is a goal which is sufficiently general to describe most scientific activity yet precise enough to guide research. Working from (...) within Hull's framework, I argue that a non-progressionist stance is both preferable and more consistent with Hull's basic commitments. (shrink)

During the early twentieth century, the Swiss Zoologist Adolf Naef (1883–1949) established himself as a leader in German comparative anatomy and higher level systematics. He is generally labeled an ‘idealistic morphologist’, although he himself called his research program ‘systematic morphology’. The idealistic morphology that flourished in German biology during the first half of the twentieth century was a rather heterogeneous movement, within which Adolf Naef worked out a special theoretical system of his own. Following a biographical sketch, we present an (...) English translation of a previously unpublished typescript from Naef’s estate, which Naef intended as the introduction to a textbook on Comparative Anatomy for which he was unable to find a publisher before his sudden death in 1949. The typescript contains Naef’s mature thoughts with unprecedented conciseness, focus, and clarity. The density of Naef’s text warrants a historical and contextual explication of its content. (shrink)

Community databases have become crucial to the collection, ordering and retrieval of data gathered on model organisms, as well as to the ways in which these data are interpreted and used across a range of research contexts. This paper analyses the impact of community databases on research practices in model organism biology by focusing on the history and current use of four community databases: FlyBase, Mouse Genome Informatics, WormBase and The Arabidopsis Information Resource. We discuss the standards used by the (...) curators of these databases for what counts as reliable evidence, acceptable terminology, appropriate experimental set-ups and adequate materials (e.g., specimens). On the one hand, these choices are informed by the collaborative research ethos characterising most model organism communities. On the other hand, the deployment of these standards in databases reinforces this ethos and gives it concrete and precise instantiations by shaping the skills, practices, values and background knowledge required of the database users. We conclude that the increasing reliance on community databases as vehicles to circulate data is having a major impact on how researchers conduct and communicate their research, which affects how they understand the biology of model organisms and its relation to the biology of other species. (shrink)

Biologists and historians often present natural history and molecular biology as distinct, perhaps conflicting, fields in biological research. Such accounts, although supported by abundant evidence, overlook important areas of overlap between these areas. Focusing upon examples drawn particularly from systematics and molecular evolution, I argue that naturalists and molecular biologists often share questions, methods, and forms of explanation. Acknowledging these interdisciplinary efforts provides a more balanced account of the development of biology during the post-World War II era.

When is conceptual change so significant that we should talk about a new theory, not a new version of the same theory? We address this problem here, starting from Gould’s discussion of the individuation of the Darwinian theory. He locates his position between two extremes: ‘minimalist’—a theory should be individuated merely by its insertion in a historical lineage—and ‘maximalist’—exhaustive lists of necessary and sufficient conditions are required for individuation. He imputes the minimalist position to Hull and attempts a reductio : (...) this position leads us to give the same ‘name’ to contradictory theories. Gould’s ‘structuralist’ position requires both ‘conceptual continuity’ and descent for individuation. Hull’s attempt to assimilate into his general selectionist framework Kuhn’s notion of ‘exemplar’ and the ‘semantic’ view of the structure of scientific theories can be used to counter Gould’s reductio , and also to integrate structuralist and population thinking about conceptual change. (shrink)

In this paper I consider the view that scientific change is the result of a selection process which has the same structure as that which drives natural selection. I argue that there are important differences between organic evolution and scientific growth. First, natural selection is much more constrained than scientific change; for example it is hard to populations of organisms to escape local maxima. Science progresses; it may not even make sense to say that biological evolution is progressive. Second, natural (...) selection depends for its power on the specifics of its domain, so I doubt that there is much point in seeing a selective regime in science as an instance of a more general family of selective regimes. Third, the replicator/interactor distinction fits scientific change much less well than biological evolution. But a family of selective theories of science can be identified ranging from the very ambitious to the very modest. Though the very ambitious programs of evolutionary epistemology are in trouble, there is space for one which is not a trivial redescription of what everyone already knows, but which is sensitive to the peculiarities of its domain. That selective theory explains important aspects of the community organization of science, an organization which is central to scientific progress. (shrink)

WE HAVE LEARNED in the preceding chapter that a revolutionary change of the species concept is in the making, a change which not only affects taxonomic procedure, but which also contributes considerably toward a better understanding of ...

The German tradition of considering species, and higher taxonomic entities, as individuals begins with the temporalization of natural history, thus pre-dating Darwin’s ‘Origin’ of 1859. In the tradition of German Naturphilosophie as developed by Friedrich Schelling, species came to be seen as parts of a complex whole that encompasses all (living) nature. Species were comprehended as dynamic entities that earn individuality by virtue of their irreversible passage through time. Species individuality was conceived in terms of species taxa forming a spatiotemporally (...) located relational system (complex whole), a conception of species that was easily assimilated to an evolutionary world view. However, the dynamics of an evolutionary process driven by variation and natural selection created a tension between continuity in nature as opposed to the discreteness and relative stasis of species. As a consequence, some authors such as Ernst Haeckel and Karl August Möbius denied the reality of species, while others explicitly linked the reality and individuality of species to their temporal duration. The mature conception of species as individuals, as formulated by Ludwig von Bertalanffy and adopted by Willi Hennig, is one of an historically conditioned, spatiotemporally located, causally integrated, dynamic yet transiently homeostatically stabilized relational system. (shrink)

Collecting, comparing, and computing molecular sequences are among the most prevalent practices in contemporary biological research. They represent a specific way of producing knowledge. This paper explores the historical development of these practices, focusing on the work of Margaret O. Dayhoff, Richard V. Eck, and Robert S. Ledley, who produced the first computer-based collection of protein sequences, published in book format in 1965 as the Atlas of Protein Sequence and Structure. While these practices are generally associated with the rise of (...) molecular evolution in the 1960s, this paper shows that they grew out of research agendas from the previous decade, including the biochemical investigation of the relations between the structures and function of proteins and the theoretical attempt to decipher the genetic code. It also shows how computers became essential for the handling and analysis of sequence data. Finally, this paper reflects on the relationships between experimenting and collecting as two distinct “ways of knowing” that were essential for the transformation of the life sciences in the twentieth century. (shrink)

In the last thirty years systematics has transformed itself from a discipline concerned with classification into a discipline concerned with reconstructing the evolutionary history of life. This transformation has been driven by cladistic analysis, a set of techniques for reconstructing evolutionary trees. Long interested in the large-scale structure of evolutionary history, cladistically oriented systematists have recently begun to apply "tree thinking" to problems near the species level. ¶ In any local ("non-dimensional") situation species are usually well-defined, but across space and (...) time the grouping of populations into species is often problematic. Three views of species are in common use today, the biological species concept, the evolutionary species concept, and the phylogenetic species concept. Each of these has strengths and weaknesses, but no matter which is applied, exact counts of the number of species in any extended area will always be ambiguous no matter how much factual information is available. This ambiguity arises because evolution is an historical process, and the grouping of organisms into species always depends to some extent upon expectations of the future behavior of those organisms and their descendants, expectations that cannot be evaluated in the present. The existence and special character of the species problem is itself one of the central pieces of evidence for evolution. (shrink)

David Hull's (1988c) model of science as a selection process suffers from a two-fold inability: (a) to ascertain when a lineage of theories has been established; i.e., when theories are descendants of older theories or are novelties, and what counts as a distinct lineage; and (b) to specify what the scientific analogue is of genotype and phenotype. This paper seeks to clarify these issues and to propose an abstract model of theories analogous to particulate genetic structure, in order to reconstruct (...) relationships of descent and identity. (shrink)

Despite the amount of work that has been produced on the subject over the years, the ‘transformation of cladistics’ is still a misunderstood episode in the history of comparative biology. Here, I analyze two outstanding, highly contrasting historiographic accounts on the matter, under the perspective of an influential dichotomy in the philosophy of science: the opposition between Scientific Realism and Empiricism. Placing special emphasis on the notion of ‘causal grounding’ of morphological characters in modern developmental biology’s theories, I arrive at (...) the conclusion that a ‘new transformation of cladistics’ is philosophically plausible. This ‘reformed’ understanding of ‘pattern cladistics’ entails retaining the interpretation of cladograms as ‘schemes of synapomorphies’, but in association to construing cladogram nodes as ‘developmental-genetic taxic homologies’, instead of ‘standard Darwinian ancestors’. The reinterpretation of pattern cladistics presented here additionally proposes to take Bas Van Fraassen’s ‘constructive empiricism’ as a philosophical stance that could properly support such analysis of developmental-genetic data for systematic purposes. The latter suggestion is justified through a reappraisal of previous ideas developed by prominent pattern cladists , which concerned a scientifically efficient ‘observable/non-observable distinction’ linked to the conceptual pair ‘ontogeny and phylogeny’. Finally, I argue that a robust articulation of Antirealist alternatives in systematics may provide a rational basis for its disciplinary separation from evolutionary biology, as well as for a critical reconsideration of the proper role of certain Scientific Realist positions, currently popular in comparative biology. (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)

Philosophers have distinguished a metaphysical category which they term "historical entities" or "continuants". Such particulars are spatiotemporally localized and develop continuously through time while retaining internal cohesiveness. Species, social groups and conceptual systems can be profitably treated as historical entities. No damage is done to preanalytic intuitions in treating social groups as historical entities; both biological species and conceptual systems can be construed as historical entities only by modifying the ordinary way of viewing both. However, if species and conceptual systems (...) are to "evolve", then they must be treated as historical entities. The type specimen method, which is used by systematists to individuate and name biological taxa, is set out and then extended to apply to scientific communities as social groups and conceptual systems. (shrink)

"Advocates of the evolutionary analogy claim that mechanisms governing scientific change are analogous to those at work in organic evolution - above all, natural selection. By referring to the works of the most influential proponents of evolutionary analogies (Toulmin, Campbell, Hull and, most notably, Kuhn) the authors discuss whether and to what extent their use of the analogy is appropriate. A careful and often illuminating perusal of the theoretical scope of the terms employed, as well as of the varying contexts (...) within which the analogy is appealed to in contemporary debates, leads to the conclusion that such general theories of selective processes are either too sketchy or eventually not persuasive, if not altogether based on flawed views of evolutionary biology. By clarifying what is at stake, the analysis carried out in the book sheds new light on one of the dominant theories of scientific progress. It also invites criticism, of course - but that is the very fuel of philosophical confrontation." - Stefano Gattei, IMT Institute for Advanced Studies, Lucca "This book presents a serious challenge to those, like David Hull, who seek to model scientific change as an evolutionary process. The authors point out that although there are similarities between the processes of scientific change and organic evolution, the dissimilarities present formidable difficulties to construing the relation as anything more than a weak analogy. Their argument employs what they call a 'type hierarchical' approach that promises to be a powerful tool for the classification of similarities between theories in all fields." - Michael Bradie, Department of Philosophy, Bowling Green State University "This is a most interesting discussion of the analogy between biological and scientific change. Particularly commendable is the close attention paid to the thinking of the late David Hull and his pathbreaking work on this issue." - Michael Ruse, History and Philosophy of Science, Florida State University. (shrink)

In Unifying Biology, Smocovitis offers a series of claimsregarding the relationship between key actors in the synthesisperiod of evolutionary studies and positivism, especially claimsentailing Joseph Henry Woodger and the Unity of Science Movement.This commentary examines Woodger''s possible relevance to key synthesis actors and challenges Smocovitis'' arguments for theexplanatory relevance of logical positivism, and positivism moregenerally, to synthesis history. Under scrutiny, these arguments areshort on evidence and subject to substantial conceptual confusion.Though plausible, Smocovitis'' minimal interpretation – that somegeneralised form of Comtean (...) positivism had a role in synthesishistory – requires more of an evidential basis and must engageexisting scholarship on epistemic reforms in the biological sciencesprior to the synthesis period. Smocovitis is right to investigateepistemology in the synthesis period of evolutionary studies and tolook for links to wider changes in science and philosophy. However,in its present form, Unifying Biology fails to support herbasic interpretation. (shrink)

The development of comparative biology has been of interest to philosophers and historians. Particular attention has been placed on the ‘war’ of the 1970s and 1980s, the apparent dispute among those who preferred this or that methodology. In this contribution we examine the history of comparative biology from the perspective of fundamentals rather than methodologies. Our examination is framed within the artificial—natural classification dichotomy, a viewpoint currently lost from view but worth resurrecting.

For more than two decades the philosopher of science David Hull has been involved with the community of biologists engaged in questions of taxonomical classification and evolution. In this book Hull uses this perspective to good advantage. By narrating the disputes, enmities, and alliances he has witnessed, he develops a theory of scientific change as a process operating according to a kind of natural selection of concepts.