The dangers of character reification for cladistic inference are explored. The identification and analysis of characters always involves theory-laden abstraction—there is no theory-free “view from nowhere.” Given theory-ladenness, and given a real world with actual objects and processes, how can we separate robustly real biological characters from uncritically reified characters? One way to avoid reification is through the employment of objectivity criteria that give us good methods for identifying robust primary homology statements. I identify six such criteria and explore each (...) with examples. Ultimately, it is important to minimize character reification, because poor character analysis leads to dismal cladograms, even when proper phylogenetic analysis is employed. Given the deep and systemic problems associated with character reification, it is ironic that philosophers have focused almost entirely on phylogenetic analysis and neglected character analysis. (shrink)

Species are generally considered to be the basic units of evolution, and hence to constitute spatio-temporally bounded entities. In addition, it has been argued that species also instantiate a natural kind. Evolution is fundamentally about change. The question then is how species can remain the same through evolutionary change. Proponents of the species qua individuals thesis individuate species through their unique evolutionary origin. Individuals, or spatio-temporally located particulars in general, can be bodies, objects, events, or processes, or a combination of (...) these. It is here argued that species are best understood as open or closed, causally integrated processual systems that also instantiate an historically conditioned homeostatic property cluster natural kind. (shrink)

The Darwinian concept of natural selection was conceived within a set of Newtonian background assumptions about systems dynamics. Mendelian genetics at first did not sit well with the gradualist assumptions of the Darwinian theory. Eventually, however, Mendelism and Darwinism were fused by reformulating natural selection in statistical terms. This reflected a shift to a more probabilistic set of background assumptions based upon Boltzmannian systems dynamics. Recent developments in molecular genetics and paleontology have put pressure on Darwinism once again. Current work (...) on self-organizing systems may provide a stimulus not only for increased problem solving within the Darwinian tradition, especially with respect to origins of life, developmental genetics, phylogenetic pattern, and energy-flow ecology, but for deeper understanding of the very phenomenon of natural selection itself. Since self-organizational phenomena depend deeply on stochastic processes, self-organizational systems dynamics advance the probability revolution. In our view, natural selection is an emergent phenomenon of physical and chemical selection. These developments suggest that natural selection may be grounded in physical law more deeply than is allowed by advocates of the autonomy of biology, while still making it possible to deny, with autonomists, that evolutionary explanations can be modeled in terms of a deductive relationship between laws and cases. We explore the relationship between, chance, self-organization, and selection as sources of order in biological systems in order to make these points. (shrink)

In a 1993 paper, I argued that empirical treatments of the epistemologyused by scientists in experimental work are too abstract in practice tocounter relativist efforts to explain the outcome of scientificcontroversies by reference to sociological forces. This was because, atthe rarefied level at which the methodology of scientists is treated byphilosophers, multiple mutually inconsistent instantiations of theprinciples described by philosophers are employed by contestingscientists. These multiple construals change within a scientificcommunity over short time frames, and these different versions ofscientific methodology (...) can determine the outcome of a controversy. Iillustrated with a comparatively detailed analysis of the methodologyused by biologists debating the existence of an entity called thebacterial mesosome between the mid-1950s and the mid-1970s. This 1993piece has drawn several critiques in the philosophical literature. Inthis present piece I respond to these critiques and argue that they failto address the core argument of the original paper, and I reflectfurther on the methodologies of philosophers of science pursuingempirical or `naturalistic' epistemology. (shrink)

David Hull's analysis of conceptual change in science, as presentedin his book, Science as a Process (1988), provides a useful framework for understanding one of the scientific controversies in which he actively and constructively intervened, the units of selectiondebates in evolutionary biology. What follows is a brief overview ofthose debates and some reflections on them.

: This paper offers a preliminary analysis of conceptual change between event concepts. It begins with a brief review of the major findings of cognitive studies on event knowledge. The script model proposed by Schank and Abelson was the first attempt to represent event knowledge. Subsequent cognitive studies indicated that event knowledge is organized in the form of dimensional organizations in which temporally successive actions are related causally. This paper proposes a frame representation to capture and outline the internal structure (...) of event concepts, in particular, their causal connections. The frame representation offers an effective method to analyze the relations between event concepts, and to expose the unique cognitive mechanisms behind conceptual change involved event concepts. Finally this paper shows that the frame representation of event concepts is instrumental to understanding an important historical episode of conceptual change in the context of nineteenth-century optics. (shrink)

ABSTRACT I propose a division of the literature on natural kinds into metaphysical worries, semantic worries, and methodological worries. I argue that the latter set of worries, which concern how classification influences scientific practices, should occupy centre stage in philosophy of science discussions about natural kinds. I apply this methodological framework to the problems of classifying chemical species and nanomaterials. I show that classification in nanoscience differs from classification in chemistry because the latter relies heavily on compositional identity, whereas the (...) former must consider additional properties, namely, size, shape, and surface chemistry. I use this difference to argue for a scale-dependent theory of scientific classification. _1_ Introduction _2_ The Methodological Problem of Kinds _3_ Chemical Kindhood: Reactivity, Microstructure, and the Structure–Property Paradigm _4_ Scale-Dependence and Nanoscale Kinds _5_ Conclusion. (shrink)

It is time to escape the constraints of the Systematics Wars narrative and pursue new questions that are better positioned to establish the relevance of the field in this time period to broader issues in the history of biology and history of science. To date, the underlying assumptions of the Systematics Wars narrative have led historians to prioritize theory over practice and the conflicts of a few leading theorists over the less-polarized interactions of systematists at large. We show how shifting (...) to a practice-oriented view of methodology, centered on the trajectory of mathematization in systematics, demonstrates problems with the common view that one camp straightforwardly “won” over the other. In particular, we critique David Hull’s historical account in Science as a Process by demonstrating exactly the sort of intermediate level of positive sharing between phenetic and cladistic theories that undermines their mutually exclusive individuality as conceptual systems over time. It is misleading, or at least inadequate, to treat them simply as holistically opposed theories that can only interact by competition to the death. Looking to the future, we suggest that the concept of workflow provides an important new perspective on the history of mathematization and computerization in biology after World War II. (shrink)

Biological individuality is a major topic of discussion in biology and philosophy of biology. Recently, several objections have been raised against traditional accounts of biological individuality, including the objections of monism, theory-centrism, ahistoricity, disciplinary isolationism, and the multiplication of conceptual uncertainties. In this introduction, I will examine the current philosophical landscape about biological individuality, and show how the contributions gathered in this special issue address these five objections. Overall, the aim of this issue is to offer a more diverse, unifying, (...) and scientifically informed conception of what a biological individual is. (shrink)

The topic of this paper is external versus internal explanations, first, of the genesis of evolutionary theory and, second, its reception. Victorian England was highly competitive and individualistic. So was the view of society promulgated by Malthus and the theory of evolution set out by Charles Darwin and A.R. Wallace. The fact that Darwin and Wallace independently produced a theory of evolution that was just as competitive and individualistic as the society in which they lived is taken as evidence for (...) the impact that society has on science. The same conclusion is reached with respect to the reception of evolutionary theory. Because Darwin's contemporaries lived in such a competitive and individualistic society, they were prone to accept a theory that exhibited these same characteristics. The trouble is that Darwin and Wallace did not live in anything like the same society and did not formulate the same theory. Although the character of Victorian society may have influenced the acceptance of evolutionary theory, it was not the competitive, individualistic theory that Darwin and Wallace set out but a warmer, more comforting theory. (shrink)

What is the epistemic position that a scientist must be in vis-à-vis a proposition, p, to be in a good enough epistemic position to assert that p to a fellow scientist within the scientific process? My aim is to provide an answer to this question and, more generally, to connect the epistemological debates about the epistemic norms of assertion to the debates about the nature of the scientific process. The question is important because science is a collaborative enterprise based on (...) a division of labor. It has even been suggested that such collaboration is a part of the scientific method. However, scientific collaboration depends upon communication between scientists—that is, intra-scientific testimony. After distinguishing some different kinds of intra-scientific testimony, I provide a specific proposal for an epistemic norm of assertion that generally governs such testimony. I argue that the proposal aligns with the requirements of three scientific virtues—replicability, revisability, and accountability. The discussion of replicability considers a prominent debate in the social and cognitive sciences. In conclusion, I consider some of the wider questions raised by characterizing scientific collaboration, division of labor, and more generally, scientific method via intra-scientific testimony. (shrink)

In the past 150 years there have been many attempts to draw parallels between cultural and biological evolution. Most of these attempts were flawed due to lack of knowledge and false ideas about evolution. In recent decades these shortcomings have been cleared away, thus triggering a renewed interest in the subject. This paper offers a critical survey of the main issues and arguments in that discussion. The paper starts with an explication of the Darwinian algorithm of evolution. It is argued (...) that this ‘formula’ is substrate-neutral, which means that biological evolution might not be the only Darwinian process. Other dynamic systems could evolve as well provided that certain conditions are met. In the case of human culture this seems to be the case. The paper then focuses on the notion of niche construction. It is argued that niche construction plays a crucial role in human evolution because it has altered the sources of natural selection and thus the path of evolution. Next two approaches to cultural evolution are discussed: sociobiology and memetics. I will argue that both approaches have flaws because they either underestimate the influence of culture or they stretch analogies too far. Finally two common objections against the idea of cultural evolution are addressed: Lamarckian inheritance and the issue of guided variation. I will argue that although cultural evolution differs from biological evolution in several respects, these discrepancies do not jeopardize the claim that cultural evolution is essentially Darwinian. (shrink)

Aside from his remarkable studies in psychology and the social sciences, Donald Thomas Campbell (1916–1996) made significant contributions to philosophy, particularly philosophy of science,epistemology, and ethics. His name and his work are inseparably linked with the evolutionary approach to explaining human knowledge (evolutionary epistemology). He was an indefatigable supporter of the naturalistic turn in philosophy and has strongly influenced the discussion of moral issues (evolutionary ethics). The aim of this paper is to briefly characterize Campbells work and to discuss its (...) philosophical implications. In particular, I show its relevance to some current debates in the intersection of biology and philosophy. In fact, philosophy of biology would look poorer without Campbells influence. The present paper is not a hagiography but an attempt to evaluate and critically discuss the meaning of Campbells work for philosophy of biology and to encourage scholars working in this field to read and re-read this work which is both challenging and inspiring. (shrink)

The biological species (biospecies) concept applies only to sexually reproducing species, which means that until sexual reproduction evolved, there were no biospecies. On the universal tree of life, biospecies concepts therefore apply only to a relatively small number of clades, notably plants andanimals. I argue that it is useful to treat the various ways of being a species (species modes) as traits of clades. By extension from biospecies to the other concepts intended to capture the natural realities of what keeps (...) taxa distinct, we can treat other modes as traits also, and so come to understand that theplurality of species concepts reflects the biological realities of monophyletic groups.We should expect that specialists in different organisms will tend to favour those concepts that best represent the intrinsic mechanisms that keep taxa distinct in their clades. I will address the question whether modes ofreproduction such as asexual and sexual reproduction are natural classes, given that they are paraphyletic in most clades. (shrink)

David Hull has demonstrated a marvelous ability to annoy everyone who caresabout science (or should), by forcing us to confront deep truths about howscience works. Credit, priority, precularities, and process weave together tomake the very fabric of science. As Hull's studies reveal, the story is bothmessier and more irritating than those limited by a single disciplinaryperspective generally admit. By itself history is interesting enough, andphilosophy valuable enough. But taken together, they do so much in tellingus about science and by puncturing (...) the comfortable popular illusion abouthow science works. Ultimately, David Hull shows by his example thathistory and philosophy of science can make science better. I agree, and withits focus on the history of science in particular, this paper explores why. (shrink)

Building on work by Popper, Schweber, Nozick, Sober, and others in a still-growing literature, I explore here the conceptual kinship between Adam Smith''s ''invisible hand'' and Darwinian natural selection. I review the historical ties, and examine Ullman -Margalit''s ''constraints'' on invisible-hand accounts, which I later re-apply to natural selection, bringing home the close relationship. These theories share a ''parent'' principle, itself neither biological no politico-economic, that collective order and well-being can emerge parsimoniously from the dispersed action of individuals. The invisible (...) hand operates on ''memes'' the way natural selection operates on genes. Like Darwin''s concept, it brings together traditional opposites, ''nature'' and ''selection,'' forming a saltation-mitigating transition between biological instinct and full-blown conscious design. Herschel''s criterion of confirmation, which Darwin long strove to satisfy, is itself an invisible hand-like meme – a ''Midas effect'' revealing and rewarding the fittest theories, Darwin''s and Smith''s emphatically among them. (shrink)

There are many things that philosophy of biology might be. But, given the existence of a professional philosophy of biology that is arguably a progressive research program and, as such, unrivaled, it makes sense to define philosophy of biology more narrowly than the totality of intersecting concerns biologists and philosophers (let alone other scholars) might have. The reasons for the success of the “new” philosophy of biology remain poorly understood. I reflect on what Dutch and Flemish, and, more generally, European (...) philosophers of biology could do to improve the situation of their discipline locally, regionally, and internationally, paying particular attention to the lessons to be learned from the “Science Wars.”. (shrink)

Karl Popper has been one of the few philosophers of sciences who has influenced scientists. I evaluate Popper's influence on our understanding of evolutionary theory from his earliest publications to the present. Popper concluded that three sorts of statements in evolutionary biology are not genuine laws of nature. I take him to be right on this score. Popper's later distinction between evolutionary theory as a metaphysical research program and as a scientific theory led more than one scientist to misunderstand his (...) position on evolutionary theory as a scientific theory. In his later work Popper also introduced what he took to be improvements of evolutionary theory. Thus far these improvements have had almost no influence on evolutionary biology. I conclude by examining the influence of Popper on the reception of cladistic analysis. (shrink)

Ontological understanding of biological units (i.e. what kinds of things are they) is crucial to their use in experimental design, analysis, and interpretation. Conceptualizing fundamental units in biology as individuals or classes is important for subsequent development of discovery operations. While the criteria for diagnosing individuals are acknowledged, temporal boundedness is often misinterpreted and temporal minima are applied to units in question. This results in misdiagnosis or abandonment of ontological interpretation altogether. Biological units such as areas of endemism in biogeography (...) and species in evolutionary biology fall victim to such problems. Our goal here is to address the misconception that biological individuals such as species and areas of endemism have a temporal minimum. Areas of endemism can persist within small temporal boundaries in the context of metapopulation dynamics, island biogeography, and range expansion and contraction. Similarly, lineage reticulation illustrates examples of short-lived species. Here, examples of known entities are provided to illustrate their persistence on short time scales in attempt to rescue future interpretation of biological units from ontological misdiagnosis, elucidate the philosophical individuality of areas of endemism and species with short lifespans, and provide justification for the “snapshot in time” diagnostic approach. (shrink)

The current widespread belief that taxonomic methods used before Darwin were essentialist is ill-founded. The essentialist method developed by followers of Plato and Aristotle required definitions to state properties that are always present. Polythetic groups do not obey that requirement, whatever may have been the ontological beliefs of the taxonomist recognizing such groups. Two distinct methods of forming higher taxa, by chaining and by examplar, were widely used in the period between Linnaeus and Darwin, and both generated polythetic groups. Philosopher (...) William Whewell congratulated pre-Darwinian taxonomists for not adhering to the rigid ideal of definition used in the mathematical sciences. What he called the method of types is here called the method of exemplars because typology has been equated with essentialism, whereas the use of a type species as the reference point or prototype for a higher category was a practice inconsistent with essentialism. The story that the essentialism of philosophers dominated the development of systematics may prove to be a myth. (shrink)

Yellowstone National Park poses critical issues in biology and philosophy. Among these are (1) how to value nature, especially at the ecosystem level, and whether to let nature take its course or employ hands-on scientific management; (2) the meaning of natural as this operates in park policy; (3) establishing biological claims on th scale of regional systems; (4) the interplay of natural and cultural history, involving both native and European Americans; (5) and sociopolitical forces as determinants in biological discovery. Alston (...) Chase's strident Playing God in Yellowstone is critized and used as a test of David Hull's naturalistic philosophy of biology. Biology and philosophy in Yellowstone ought to combine for an appropriate environmental ethic. (shrink)

I propose a new perspective on the study of scientific revolutions. This is a transformation from an object-only perspective to an ontological perspective that properly treats objects and processes as distinct kinds. I begin my analysis by identifying an object bias in the study of scientific revolutions, where it takes the form of representing scientific revolutions as changes in classification of physical objects. I further explore the origins of this object bias. Findings from developmental psychology indicate that children cannot distinguish (...) processes from objects until the age of 7, but they have already developed a core system of object knowledge as early as 4 months of age. The persistence of this core system is responsible for the object bias among mature adults, i.e., the tendency to apply knowledge of physical objects to temporal processes. In light of the distinction between physical objects and temporal processes, I redraw the picture of the Copernican revolution. Rather than seeing it as a taxonomic shift from a geocentric to a heliocentric cosmology, we should understand it as a transformation from a conceptual system that was built around an object concept to one that was built around a process concept. (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)

Materialists argue that there is no place for God in the universe. Chance and contingency are all that structure our world. However, the materialists’ dismissal of subjectivity manifests a flawed metaphysics that invalidates their arguments against God. In this essay I explore the following: (1) How does personal metaphysics affect one's ability to do science? (2) Are the materialist arguments about contingency used to dismiss the importance of our place in the universe valid? (3) What are the implications of subjectivity (...) on belief and science? To answer the first question, I examine the later years of Sir Alfred Russel Wallace, one of the cofounders of evolution through natural selection with Darwin. His belief in nineteenth–century spiritualism profoundly affected his standing in the scientific community. I describe the effect of spiritualism on Wallace's science. To answer the second question, I use my own work in mathematical modeling of evolutionary processes to show that randomness, and contingency at one level, can actually be nearly deterministic at another. I demonstrate how arguments about chance and contingency do not imply anything relevant about whether there is a designer behind the universe. To answer the third question I begin by exploring a paradox of consciousness and show how the existence of subjective truths may provide a paradigm for sustaining a rational belief in God. These questions form the framework of a structured belief in a creator while yet embracing what science has to offer about the development of life on our planet. (shrink)

Co-authorship of papers is very common in most areas of science, and it has increased as the complexity of research has strengthened the need for scientific collaboration. But the fact that papers have more than an author tends to complicate the attribution of merit to individual scientists. I argue that collaboration does not necessarily entail co-authorship, but that in many cases the latter is an option that individual authors might not choose, at least in principle: each author might publish in (...) a separate way her own contribution to the collaborative project in which she has taken part, or papers could explicitly state what the contribution of each individual author has been. I ask, hence, why it is that scientists prefer to ‘pool’ their contributions instead of keeping them separate, if what they pursue in their professional careers is individual recognition. My answer is based on the view of the scientific paper as a piece of argumentation, following an inferentialist approach to scientific knowledge. A few empirical predictions from the model presented here are suggested in the conclusions. (shrink)

David Hull: a memoir Content Type Journal Article DOI 10.1007/s10539-010-9236-0 Authors Michael Ruse, Department of Philosophy, Florida State University, Tallahassee, FL 32306, USA Journal Biology and Philosophy Online ISSN 1572-8404 Print ISSN 0169-3867.

This paper discusses the reception of Darwinian evolutionary theory and sociobiology in Japan. Darwinism was introduced into Japan in the late 19th century and Japanese people readily accepted the concept of evolution because, lacking Christianity, there was no religious opposition. However, the theory of evolution was treated as a kind of social scientific tool, i.e., social Spencerism and eugenics. Although evolutionary biology was developed during the late 19th and the early 20th century, orthodox Darwinian theory was neglected for a long (...) time. In the mid 1980s, sociobiology was introduced but it was ignored and criticized by a large part of the ecologist-evolutionist community in Japan. This hostile attitude was due to the absence of Darwinism among these scientists. Compared with the reception of sociobiology in English-speaking countries, there were both similarities and differences in Japan. (shrink)

In 1987, George Soros introduced his concepts of reflexivity and fallibility and has further developed and applied these concepts over subsequent decades. This paper attempts to build on Soros's framework, provide his concepts with a more precise definition, and put them in the context of recent thinking on complex adaptive systems. The paper proposes that systems can be classified along a ‘spectrum of complexity’ and that under specific conditions not only social systems but also natural and artificial systems can be (...) considered ‘complex reflexive.’ The epistemological challenges associated with scientifically understanding a phenomenon stem not from whether its domain is social, natural, or artificial, but where it falls along this spectrum. Reflexive systems present particular challenges; however, evolutionary model-dependent realism provides a bridge between Soros and Popper and a potential path forward for economics. (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.

The history of biological systematics documents a continuing tension between classifications in terms of nested hierarchies congruent with branching diagrams (the ‘Tree of Life’) versus reticulated relations. The recognition of conflicting character distribution led to the dissolution of the scala naturae into reticulated systems, which were then transformed into phylogenetic trees by the addition of a vertical axis. The cladistic revolution in systematics resulted in a representation of phylogeny as a strictly bifurcating pattern (cladogram). Due to the ubiquity of character (...) conflict—at the genetic or morphological level, or at any level in between—some characters will necessarily have to be discarded ( qua noise) in favor of others in support of a strictly bifurcating phylogenetic tree. Pattern analysts will seek maximal congruence in the distribution of characters (ultimately of any kind) relative to a branching tree-topology; process explainers will call such tree-topologies into question by reference to incompatible evolutionary processes. Pattern analysts will argue that process explanations must not be brought to bear on pattern reconstruction; process explainers will insist that the reconstructed pattern requires a process explanation to become scientifically relevant, i.e., relevant to evolutionary theory. The core question driving the current debate about the adequacy of the ‘Tree of Life’ metaphor seems to be whether the systematic dichotomization of the living world is an adequate representation of the complex evolutionary history of global biodiversity. In ‘Questioning the Tree of Life’, it seems beneficial to draw at least four conceptual distinctions: pattern reconstruction versus process explanation as different epistemological approaches to the study of phylogeny; open versus closed systems as expressions of different kinds of population (species) structures; phylogenetic trees versus cladograms as representations of evolutionary processes versus patterns of relationships; and genes versus species as expressions of different levels of causal integration and evolutionary transformation. (shrink)