Advocates of an ‘extended evolutionary synthesis’ have claimed that standard evolutionary theory fails to accommodate epigenetic inheritance. The opponents of the extended synthesis argue that the evidence for epigenetic inheritance causing adaptive evolution in nature is insufficient. We suggest that the ambiguity surrounding the conception of the gene represents a background semantic issue in the debate. Starting from Haig’s gene-selectionist framework and Griffiths and Neumann-Held’s notion of the evolutionary gene, we define senses of ‘gene’, ‘environment’, and ‘phenotype’ in a way (...) that makes them consistent with gene-centric evolutionary theory. We argue that the evolutionary gene, when being materialized, need not be restricted to nucleic acids but can encompass other heritable units such as epialleles. If the evolutionary gene is understood more broadly, and the notions of environment and phenotype are defined accordingly, current evolutionary theory does not require a major conceptual change in order to incorporate the mechanisms of epigenetic inheritance. _1_ Introduction _2_ The Gene-centric Evolutionary Theory and the ‘Evolutionary Gene’ _2.1_ The evolutionary gene _2.2_ Genes, phenotypes, and environments _3_ Epigenetic Inheritance and the Gene-Centred Framework _3.1_ Treating the gene as the sole heritable material? _3.2_ Epigenetics and phenotypic plasticity _4_ Conclusion. (shrink)

What is the role of the environment, and of the information it provides, in cognition? More specifically, may there be a role for certain artefacts to play in this context? These are questions that motivate "4E" theories of cognition (as being embodied, embedded, extended, enactive). In his take on that family of views, Hajo Greif first defends and refines a concept of information as primarily natural, environmentally embedded in character, which had been eclipsed by information-processing views of cognition. He continues (...) with an inquiry into the cognitive bearing of some artefacts that are sometimes referred to as 'intelligent environments'. Without necessarily having much to do with Artificial Intelligence, such artefacts may ultimately modify our informational environments. -/- With respect to human cognition, the most notable effect of digital computers is not that they might be able, or become able, to think but that they alter the way we perceive, think and act. (shrink)

We describe an approach to measuring biological information where ‘information’ is understood in the sense found in Francis Crick’s foundational contributions to molecular biology. Genes contain information in this sense, but so do epigenetic factors, as many biologists have recognized. The term ‘epigenetic’ is ambiguous, and we introduce a distinction between epigenetic and exogenetic inheritance to clarify one aspect of this ambiguity. These three heredity systems play complementary roles in supplying information for development. -/- We then consider the evolutionary significance (...) of the three inheritance systems. Whilst the genetic inheritance system was the key innovation in the evolution of heredity, in modern organisms the three systems each play important and complementary roles in heredity and evolution. -/- Our focus in the earlier part of the paper is on ‘proximate biology’, where information is a substantial causal factor that causes organisms to develop and causes offspring to resemble their parents. But much philosophical work has focused on information in ‘ultimate biology’. Ultimate information is a way of talking about the evolutionary design of the mechanisms of development and inheritance. We conclude by clarifying the relationship between the two. Ultimate information is not a causal factor that acts in development or heredity, but it can help to explain the evolution of proximate information, which is. (shrink)

All disciplines must define their basic units and core processes. In evolutionary biology, the core process is natural selection and the basic unit of selection and adaptation is the individual. To operationalize the theory of natural selection we must count individuals, as they are the bearers of fitness. While canonical individuals have often been taken to be multicellular organisms, the hierarchy of life shows that new kinds of individuals have evolved. A variety of criteria have been used to define biological (...) individuality. Some criteria rely on the presence/absence of a particular property while others advocate an approach that reflects the process of natural selection. The plethora of approaches to classifying individuality has resulted in confusion regarding how to study individuality in a given taxon. (shrink)

It is now widely accepted that a scientifically credible conception of human nature must reject the folkbiological idea of a fixed, inner essence that makes us human. We argue here that to understand human nature is to understand the plastic process of human development and the diversity it produces. Drawing on the framework of developmental systems theory and the idea of developmental niche construction we argue that human nature is not embodied in only one input to development, such as the (...) genome, and that it should not be confined to universal or typical human characteristics. Both similarities and certain classes of differences are explained by a human developmental system that reaches well out into the 'environment'. We point to a significant overlap between our account and the ‘Life History Trait Cluster’ account of Grant Ramsey, and defend the developmental systems account against the accusation that trying to encompass developmental plasticity and human diversity leads to an unmanageably complex account of human nature. (shrink)

In the article titled ‘A new perspective on the race debate’，Robin O. Andreasen argues that contrary to popular scientific belief, human races are biologically real—it is just that we are wrong about them. Andreasen calls her contemporary biological concept of race ‘the cladistic race concept’ (or CRC). Her theory uses theory from cladistics—a systematic school founded by entomologist Willi Hennig in 1950—to define human races genealogically as cladistic subspecies. In this paper I will argue that despite its promise as a (...) biological definition of human races, Andreasen's CRC is unconvincing. In particular, I will show that the central problem of the CRC is its attempt to apply cladistics below the species level. In other words, there is good reason to think that cladistic subspecies are not real, and therefore, they cannot be the target of a realist concept of race. (shrink)

Modularity has been the subject of intense debate in the cognitive sciences for more than 2 decades. In some cases, misunderstandings have impeded conceptual progress. Here the authors identify arguments about modularity that either have been abandoned or were never held by proponents of modular views of the mind. The authors review arguments that purport to undermine modularity, with particular attention on cognitive architecture, development, genetics, and evolution. The authors propose that modularity, cleanly defined, provides a useful framework for directing (...) research and resolving debates about individual cognitive systems and the nature of human evolved cognition. Modularity is a fundamental property of living things at every level of organization; it might prove indispensable for understanding the structure of the mind as well. (shrink)

Philosophers and historians of biology have argued that genes are conceptualized differently in different fields of biology and that these differences influence both the conduct of research and the interpretation of research by audiences outside the field in which the research was conducted. In this paper we report the results of a questionnaire study of how genes are conceptualized by biological scientists at the University of Sydney, Australia. The results provide tentative support for some hypotheses about conceptual differences between different (...) fields of biological research. (shrink)

A consensus exists among contemporary philosophers of biology about the history of their field. According to the received view, mainstream philosophy of science in the 1930s, 40s, and 50s focused on physics and general epistemology, neglecting analyses of the 'special sciences', including biology. The subdiscipline of philosophy of biology emerged (and could only have emerged) after the decline of logical positivism in the 1960s and 70s. In this article, I present bibliometric data from four major philosophy of science journals (Erkenntnis, (...) Philosophy of Science, Synthese, and the British Journal for the Philosophy of Science), covering 1930-59, which challenge this view. (shrink)

In this paper, I propose two theses, and then examine what the consequences of those theses are for discussions of reduction and emergence. The first thesis is that what have traditionally been seen as robust, reductions of one theory or one branch of science by another more fundamental one are a largely a myth. Although there are such reductions in the physical sciences, they are quite rare, and depend on special requirements. In the biological sciences, these prima facie sweeping reductions (...) fade away, like the body of the famous Cheshire cat, leaving only a smile.... The second thesis is that the "smiles" are fragmentary patchy explanations, and though patchy and fragmentary, they are very important, potentially Nobel-prize winning advances. To get the best grasp of these "smiles," I want to argue that, we need to return to the roots of discussions and analyses of scientific explanation more generally, and not focus mainly on reduction models, though three conditions based on earlier reduction models are retained in the present analysis. I briefly review the scientific explanation literature as it relates to reduction, and then offer my account of explanation. The account of scientific explanation I present is one I have discussed before, but in this paper I try to simplify it, and characterize it as involving field elements and a preferred causal model system abbreviated as FE and PCMS. In an important sense, this FE and PCMS analysis locates an "explanation" in a typical scientific research article. This FE and PCMS account is illustrated using a recent set of neurogenetic papers on two kinds of worm foraging behaviors: solitary and social feeding. One of the preferred model systems from a 2002 Nature article in this set is used to exemplify the FE and PCMS analysis, which is shown to have both reductive and nonreductive aspects. The paper closes with a brief discussion of how this FE and PCMS approach differs from and is congruent with Bickle's "ruthless reductionism" and the recently revived mechanistic philosophy of science of Machamer, Darden, and Craver. (shrink)

Developmental systems theory (DST) is a wholeheartedly epigenetic approach to development, inheritance and evolution. The developmental system of an organism is the entire matrix of resources that are needed to reproduce the life cycle. The range of developmental resources that are properly described as being inherited, and which are subject to natural selection, is far wider than has traditionally been allowed. Evolution acts on this extended set of developmental resources. From a developmental systems perspective, development does not proceed according to (...) a preformed plan; what is inherited is much more than DNA; and evolution is change not only in gene frequencies, but in entire developmental systems. (shrink)

Whether collective agency is a coherent concept depends on the theory of agency that we choose to adopt. We argue that the enactive theory of agency developed by Barandiaran, Di Paolo and Rohde (2009) provides a principled way of grounding agency in biological organisms. However the importance of biological embodiment for the enactive approach might lead one to be skeptical as to whether artificial systems or collectives of individuals could instantiate genuine agency. To explore this issue we contrast the concept (...) of collective agency with multi-agent systems and multi-system agents, and argue that genuinely collective agents instantiate agency at both the collective level and at the level of the component parts. Developing the enactive model, we propose understanding agency – both at the level of the individual and of the collective – as spectra that are constituted by dimensions that vary across time. Finally, we consider whether collectives that are not merely metaphorically ‘agents’ but rather are genuinely agentive also instantiate subjectivity at the collective level. We propose that investigations using the perceptual crossing paradigm suggest that a shared lived perspective can indeed emerge but this should not be conflated with a collective first-person perspective, for which material integration in a living body may be required. (shrink)

According to the proponents of Developmental Systems Theory and the Causal Parity Thesis, the privileging of the genome as “first among equals” with respect to the development of phenotypic traits is more a reflection of our own heuristic prejudice than of ontology - the underlying causal structures responsible for that specified development no more single out the genome as primary than they do other broadly “environmental” factors. Parting with the methodology of the popular responses to the Thesis, this paper offers (...) a novel criterion for ‘causal primacy’, one that is grounded in the ontology of the unique causal role of dispositional properties. This paper argues that, if the genome is conceptualised as realising dispositional properties that are “directed toward” phenotypic traits, the parity of ‘causal roles’ between genetic and extra-genetic factors is no longer apparent, and further, that the causal primacy of the genome is both plausible and defensible. (shrink)

Ethological theories usually attribute semantic content to animal signals. To account for this fact, many biologists and philosophers appeal to some version of teleosemantics. However, this picture has recently came under attack: while mainstream teleosemantics assumes that representational systems must cooperate, some biologists and philosophers argue that in certain cases signaling can evolve within systems lacking common interest. In this paper I defend the standard view from this objection.

Since van Fraassen first put forward the suggestive idea that many philosophical positions should be construed as ‘stances’ rather than factual beliefs, there have been various attempts to spell out precisely what a philosophical stance might be, and on what basis one should be adopted. In this paper I defend a particular account of stances, the view that they are pragmatically justified perspectives or ways of seeing the world, and compare it to some other accounts that have been offered. In (...) Sect. 2 I consider van Fraassen’s argument for construing empiricism as a stance, and look at some responses to it. In Sect. 3 I outline my conception of stances as perspectives or ways of seeing, and explain how stances so understood may be justified. I illustrate this conception by way of a discussion of the model pluralist position with respect to the units of selection debate in biology, and suggest that on the model pluralist view different perspectives on the units of selection, such as the gene’s eye view, are in fact van Fraassian stances. In Sect. 4 I discuss the view put forward by Teller and Chakravartty among others that stances should be understood as epistemic policies, and argue that it is consistent with the conception of stances as perspectives. In the final section I criticise Rowbottom’s attempt to assimilate stances to Kuhnian paradigms. I argue that he has overlooked some important disanalogies between stances and paradigms, so that the comparison obscures more than it reveals. (shrink)

Minimal genetic pre-formationism is defended, in that primacy is ascribed to DNA in the structuring of molecules through molecular codes. This together with the importance of such codes for stability and variation in living systems makes DNA categorically different from other causal factors. It is argued that post-transcriptional and post-translational processing in protein synthesis does not rob DNA of this structuring role. Notions of structuring causal powers that may vary in degree, of arbitrary molecular codes that are more or less (...) realized, of partial templating and of genetic information as a subspecies of mechanistic information are brought in to support this and to rival causal and semantic notions of information. It is concluded that the primacy of genes in their structuring of molecules goes together with parity between genes and non-genetic causal factors in regulation of living systems. This is seen to hold independently of the radical reconceptualization of organism cum environment that has been suggested in developmental systems theory. (shrink)

Integrative and naturalistic philosophy of mind can both learn from and contribute to the contemporary cognitive sciences of dreaming. Two related phenomena concerning self-representation in dreams demonstrate the need to bring disparate fields together. In most dreams, the protagonist or dream self who experiences and actively participates in dream events is or represents the dreamer: but in an intriguing minority of cases, self-representation in dreams is displaced, disrupted, or even absent. Working from dream reports in established databanks, we examine two (...) key forms of polymorphism of self-representation: dreams in which I take an external visuospatial perspective on myself, and those in which I take someone else's perspective on events. In remembering my past experiences or imagining future or possible experiences when awake, I sometimes see myself from an external or 'observer' perspective. By relating the issue of perspective in dreams to established research traditions in the study of memory and imagery, and noting the flexibility of perspective in dreams, we identify new lines of enquiry. In other dreams, the dreamer does not appear to figure at all, and the first person perspective on dream events is occupied by someone else, some other person or character. We call these puzzling cases 'vicarious dreams' and assess some potential ways to make sense of them. Questions about self-representation and perspectives in dreams are intriguing in their own right and pose empirical and conceptual problems about the nature of self-representation with implications beyond the case of dreaming. (shrink)

In this article, I argue that the use of scientific models that attribute intentional content to complex systems bears a striking similarity to the way in which statistical descriptions are used. To demonstrate this, I compare and contrast an intentional model with a statistical model, and argue that key similarities between the two give us compelling reasons to consider both as a type of phenomenological model. I then demonstrate how intentional descriptions play an important role in scientific methodology as a (...) type of phenomenal model, and argue that this makes them as essential as any other model of this type. (shrink)

It is often said that there is just one “objective” tree of life: a single accurate branching hierarchy of species reflecting order of descent. For any two species there is a single correct answer as to whether one is a “daughter” of the other, whether the two are “sister species” by virtue of their descent from a common parental species, whether they belong to a family line that excludes any given third species, and so on. This position is not right. (...) We may whittle a tree of life, paring troublesome branches, in order to portray an ordering that admits of no legitimate dissent. But the history of life can sustain many legitimate arrangements of the same branches of species. The same can be said about other taxonomically relevant groups besides species, such as “Least Inclusive Taxonomic Units” (LITUs), so the basic claim survives even if we abandon traditional species. Similarly, the claim survives even if we distinguish between synchronic and diachronic groups, even if we consider polytomies, even if we distinguish between models and the world modeled, and even if we recognize an objective world. Nor is the claim merely an epistemic one. (shrink)

Two controversies exist regarding the appropriate characterization of hierarchical and adaptive evolution in natural populations. In biology, there is the Wright-Fisher controversy over the relative roles of random genetic drift, natural selection, population structure, and interdemic selection in adaptive evolution begun by Sewall Wright and Ronald Aylmer Fisher. There is also the Units of Selection debate, spanning both the biological and the philosophical literature and including the impassioned group-selection debate. Why do these two discourses exist separately, and interact relatively little? (...) We postulate that the reason for this schism can be found in the differing focus of each controversy, a deep difference itself determined by distinct general styles of scientific research guiding each discourse. That is, the Wright-Fisher debate focuses on adaptive process, and tends to be instructed by the mathematical modeling style, while the focus of the Units of Selection controversy is adaptive product, and is typically guided by the function style. The differences between the two discourses can be usefully tracked by examining their interpretations of two contested strategies for theorizing hierarchical selection: horizontal and vertical averaging. (shrink)

The comparative method grants epistemic access to the biological past. Comparing lineages provides empirical traction on both hypotheses about particular lineages and models of trait evolution. Understanding this evidential role is important. Although philosophers have recently turned their attention to relations of descent, little work exists exploring the status of evidence from convergences. I argue that, where they exist, convergences play a central role in the confirmation of adaptive hypotheses. I focus on ‘analogous inferences’, show how such inferences ought to (...) be analysed and suggest three methods for strengthening their evidential weight. 1 Introduction2 Analogous Inferences2.1 Adaptive explanations and analogies2.2 Analogous inferences2.3 Scope, grain, and specificity3 Parallel Modelling, Integrated Explanations, and Convergent Modelling3.1 Parallel modelling3.2 Integrated explanations3.1 Convergent modelling4 Conclusion. (shrink)

There are many ways that biological theory can inform ethical discussions of genetic engineering and biomedical enhancement. In this essay, we highlight some of these potential contributions, and along the way provide a synthetic overview of the papers that comprise this special issue. We begin by comparing and contrasting genetic engineering with programs of selective breeding that led to the domestication of plants and animals, and we consider how genetic engineering differs from other contemporary biotechnologies such as embryo selection. We (...) go on to consider the implications of genetic engineering for human nature, human evolution, and persistence of the human species. Finally, we question whether genetic interventions warrant the extraordinary ethical scrutiny they are often given, and we show how the misleading “genetic blueprint” metaphor has imposed a faulty structure on the enhancement debate. We conclude by considering the nature of biological development and the sobering limits it places on what genetic engineering can reasonably hope to achieve. (shrink)

A central idea of developmental systems theory is ‘parity’ or ‘symmetry’ between genes and non-genetic factors of development. The precise content of this idea remains controversial, with different authors stressing different aspects and little explicit comparisons among the various interpretations. Here I characterise and assess several influential versions of parity.

The problem of plant individuality is something which has vexed botanists throughout the ages, with fashion swinging back and forth from treating plants as communities of individuals (Darwin 1800 ; Braun and Stone 1853 ; Münch 1938 ) to treating them as organisms in their own right, and although the latter view has dominated mainstream thought most recently (Harper 1977 ; Cook 1985 ; Ariew and Lewontin 2004 ), a lively debate conducted mostly in Scandinavian journals proves that the issues (...) are far from being resolved (Tuomi and Vuorisalo 1989b ; Fagerström 1992 ; Pan and Price 2001 ). In this paper I settle the matter once and for all, by showing which elements of each side are correct. (shrink)

Our aim in the present paper is to approach the nature of life from the perspective of autonomy, showing that this perspective can be helpful for overcoming the traditional Cartesian gap between the physical and cognitive domains. We first argue that, although the phenomenon of life manifests itself as highly complex and multidimensional, requiring various levels of description, individual organisms constitute the core of this multifarious phenomenology. Thereafter, our discussion focuses on the nature of the organization of individual living entities, (...) proposing autonomy as the main concept to grasp it. In the second part of the article we show how autonomy is also fundamental to explaining major evolutionary transitions, in an attempt to rethink evolution from the point of view of the organizational structure of the entities/organisms involved. This gives further support to the idea of autonomy not only as a key to understanding life in general but also the complex expressions of it that we observe on our planet. Finally, we suggest a possible general principle that underlies those evolutionary transitions, which allow for the open-ended redefinition of autonomous systems: namely, the relative dynamic decoupling that must be articulated among distinct parts, modules or modes of operation in these systems. (shrink)

Andrew Bourke’s Principles of Social Evolution identifies three stages that characterize an evolutionary transition in individuality and deploys inclusive fitness theory to explain each stage. The third stage, social group transformation, has hitherto received relatively little attention from inclusive fitness theorists. In this review, I first discuss Bourke’s “virtual dominance” hypothesis for the evolution of the germ line. I then contrast Bourke’s inclusive fitness approach to the major transitions with the multi-level approach developed by Richard Michod, Samir Okasha and others. (...) I suggest that, rather than choosing between these approaches, we should exploit the strengths of both. Finally, I stress the need for a firmer conceptual grasp of the nature of social group transformation. (shrink)

The disagreement between philosophers about the scientific worth of the evolutionary behavioral sciences (evolutionary psychology, human behavioral ecology, etc.) is in part due to the fact that critics and advocates of these sciences characterize them very differently. In this article, by analyzing quantitatively the citations made in the articles published in Evolution & Human Behavior between January 2000 and December 2002, we provide some evidence that undermines the characterization of the evolutionary behavioral sciences put forward by their critics.

Darwin’s classic ‘Origin of Species’ (Darwin 1859) described forces of selection acting upon individuals, but there remains a great deal of controversy about what exactly the status and definition of a biological individual is. Recently some authors have argued that the individual is dispensable – that an inability to pin it down is not problematic because little rests on it anyway. The aim of this paper is to show that there is a real problem of biological individuality, and an urgent (...) need to arbitrate over the current plethora of solutions to it. (shrink)

Philosophy of biology, perhaps more than any other philosophy of science, is a discipline in flux. What counts as consensus and key arguments in certain areas changes rapidly.The publication of Contemporary Debates in Philosophy of Biology (2010 Wiley-Blackwell) is reviewed and is used as a catalyst to a discussion of the recent expansion of subjects and perspectives in the philosophy of biology as well as their diverse epistemological and methodological commitments.

S. Oyama’s prominent account of the Parity Thesis states that one cannot distinguish in a meaningful way between nature-based (i.e. gene-based) and nurture-based (i.e. environment-based) characteristics in development because the information necessary for the resulting characteristics is contained at both levels. Oyama as well as P. E. Griffiths and K. Stotz argue that the Parity Thesis has far-reaching implications for developmental psychology in that both nativist and interactionist developmental accounts of psychological capacities that presuppose a substantial nature/nurture dichotomy are inadequate. (...) We argue that well-motivated abandoning of the nature/nurture dichotomy, as advocated in converging versions of the Parity Thesis in biology, does not necessarily entail abandoning the distinction between biologically given abilities necessary for the development of higher psychological capacities and the learning process they enable. Thus, contrary to the claims of the aforementioned authors, developmental psychologists need not discard a substantial distinction between innate (biologically given) characteristics and those acquired by learning, even if they accept the Parity Thesis. We suggest a two-stage account of development: the first stage is maturational and involves interaction of genetic, epigenetic and environmental causes, resulting in the endogenous biological ‘machinery’ (e.g. language acquisition device), responsible for learning in the subsequent stage of the developmental process by determining the organism’s responses to the environment. This account retains the crux of nativism (the endogenous biological structure determines the way the organism learns/responds to an environment) whilst adopting the developmentalist view of biology by characterizing environments as distinctly different in terms of structure and function in two developmental stages. (shrink)

Recent theories in cognitive science have begun to focus on the active role of organisms in shaping their own environment, and the role of these environmental resources for cognition. Approaches such as situated, embedded, ecological, distributed and particularly extended cognition look beyond ‘what is inside your head’ to the old Gibsonian question of ‘what your head is inside of’ and with which it forms a wider whole—its internal and external cognitive niche. Since these views have been treated as a radical (...) departure from the received view of cognition, their proponents have looked for support to similar extended views within (the philosophy of) biology, most notably the theory of niche construction. This paper argues that there is an even closer and more fruitful parallel with developmental systems theory and developmental niche construction. These ask not ‘what is inside the genes you inherited’, but ‘what the inherited genes are inside of’ and with which they form a wider whole—their internal and external ontogenetic niche, understood as the set of epigenetic, social, ecological, epistemic and symbolic legacies inherited by the organism as necessary developmental resources. To the cognizing agent, the epistemic niche presents itself not just as a partially self-engineered selective niche, as the niche construction paradigm will have it, but even more so as a partially self-engineered ontogenetic niche, a problem-solving resource and scaffold for individual development and learning. This move should be beneficial for coming to grips with our own (including cognitive) nature: what is most distinctive about humans is their developmentally plastic brains immersed into a well-engineered, cumulatively constructed cognitive–developmental niche. (shrink)

The dissertation criticizes two analogical applications of Darwinism to the spheres of mind and culture: the Darwinian approach to creativity and memetics. These theories rely on three basic analogies: the ontological analogy states that the basic ontological units of culture are so-called memes, which are replicators like genes; the origination analogy states that novelty in human creativity emerges in a "blind" Darwinian manner; and the explanatory units of selection analogy states that memes are "egoistic" and that they can spread independently (...) of our mind. The detailed philosophical analysis offered in the dissertation shows that these three analogies rely on either wrong or trivial statements: they provide either wrong or no new descriptions or explanations of the phenomena at hand. In Chapter One, I introduce the diverse ways, in which contemporary Darwinism is used today outside of evolutionary biology. Chapter Two explains what it means to claim that something evolves in a Darwinian manner. Chapter Three to Five address each of the three analogies separately. Darwinism applied to culture and mind, at least in the way discussed in this study, is not a dangerous idea. It leads either to wrong claims or to a re-telling in Darwinian terms of what we have already known. (shrink)

The ‘marketplace of ideas’ is an influential metaphor with widespread currency in debates about freedom of speech. We explore a number of ways competition between ideas might be described as occurring in a marketplace and find that none support the use of the metaphor. We suggest that an alternative metaphor, that of the ‘garden of ideas’, may offer more productive insights into issues surrounding the regulation of speech.

Biologists rely heavily on the language of information, coding, and transmission that is commonplace in the field of information theory developed by Claude Shannon, but there is open debate about whether such language is anything more than facile metaphor. Philosophers of biology have argued that when biologists talk about information in genes and in evolution, they are not talking about the sort of information that Shannon’s theory addresses. First, philosophers have suggested that Shannon’s theory is only useful for developing a (...) shallow notion of correlation, the so-called causal sense of information. Second, they typically argue that in genetics and evolutionary biology, information language is used in a semantic sense, whereas semantics are deliberately omitted from Shannon’s theory. Neither critique is well-founded. Here we propose an alternative to the causal and semantic senses of information: a transmission sense of information, in which an object X conveys information if the function of X is to reduce, by virtue of its sequence properties, uncertainty on the part of an agent who observes X. The transmission sense not only captures much of what biologists intend when they talk about information in genes, but also brings Shannon’s theory back to the fore. By taking the viewpoint of a communications engineer and focusing on the decision problem of how information is to be packaged for transport, this approach resolves several problems that have plagued the information concept in biology, and highlights a number of important features of the way that information is encoded, stored, and transmitted as genetic sequence. (shrink)

This paper assesses Sarkar's ([2003]) deflationary account of genetic information. On Sarkar's account, genes carry information about proteins because protein synthesis exemplifies what Sarkar calls a ‘formal information system’. Furthermore, genes are informationally privileged over non-genetic factors of development because only genes enter into arbitrary relations to their products (in virtue of the alleged arbitrariness of the genetic code). I argue that the deflationary theory does not capture four essential features of the ordinary concept of genetic information: intentionality, exclusiveness, asymmetry, (...) and causal relevance. It is therefore further removed from what is customarily meant by genetic information than Sarkar admits. Moreover, I argue that it is questionable whether the account succeeds in demonstrating that information is theoretically useful in molecular genetics. Introduction Sarkar's Information System The Pre-theoretic Features of Genetic Information 3.1 Intentionality 3.2 Exclusiveness 3.3 Asymmetry 3.4 Causal relevance Theoretical Usefulness Conclusion CiteULike Connotea Del.icio.us What's this? (shrink)

College of Medicine, University of South Alabama Mobile, AL 36688-0002, USA wbp501{at}jaguar1.usouthal.edu ' + u + '@' + d + ' '//--> Abstract Recent work in viral genomics has shown that bacteriophages exhibit a high degree of mosaicism, which is most likely due to a long history of prolific horizontal gene transfer (HGT). Given these findings, we argue that each of the most plausible attempts to properly classify bacteriophages into distinct species fail. Mayr's biological species concept fails because there is (...) no useful viral analog to sexual reproduction. Phenetic species concepts fail because they obscure the mosaicism and the rich reticulated viral histories. Phylogenetic species concepts, even when extended to take into account reticulation, fail because there is no non-arbitrary distinction between recombination events that create a new viral species and those that do not. There is good reason to think that bacteriophages, arguably the Earth's most abundant biological agent, evolve without forming species. Introduction The Biology of Viruses 2.1 Bacteriophage life cycles 2.2 Mechanisms of HGT The Species Problem and Species Concepts 3.1 Phenetic species concepts 3.2 The biological species concept 3.3 Phylogenetic species concepts 3.4 The ecological species concept 3.5 Homeostatic property cluster species Viruses and Species Taxonomy Reticular Phylogenies Conclusion CiteULike Connotea Del.icio.us What's this? (shrink)

Most models of generational succession in sexually reproducing populations necessarily move back and forth between genic and genotypic spaces. We show that transitions between and within these spaces are usually hidden by unstated assumptions about processes in these spaces. We also examine a widely endorsed claim regarding the mathematical equivalence of kin-, group-, individual-, and allelic-selection models made by Lee Dugatkin and Kern Reeve. We show that the claimed mathematical equivalence of the models does not hold. *Received January 2007; revised (...) April 2008. †To contact the authors, please write to: Elisabeth Lloyd, Department of History and Philosophy of Science, 130 Goodbody Hall, Indiana University, Bloomington, IN 47405; e-mail: [email protected]; Richard Lewontin, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138; Marcus Feldman, Department of Biological Sciences, Stanford University, Stanford, CA 94305; e-mail: [email protected]. (shrink)

This chapter offers a review of standard views about the requirements for natural selection to shape evolution and for the sorts of ‘units’ on which selection might operate. It then summarizes traditional arguments for genic selectionism, i.e., the view that selection operates primarily on genes (e.g., those of G. C. Williams, Richard Dawkins, and David Hull) and traditional counterarguments (e.g., those of William Wimsatt, Richard Lewontin, and Elliott Sober, and a diffuse group based on life history strategies). It then offers (...) a series of responses to the arguments, based on more contemporary considerations from molecular genetics, offered by Carmen Sapienza. A key issue raised by Sapienza concerns the degree to which a small number of genes might be able to control much of the variation relevant to selection operating on such selectively critical organs as hearts. The response to these arguments suggests that selection acts on many levels at once and that sporadic selection, acting with strong effects, can act successively on different key traits (and genes) while maintaining a balance among many potentially conflicting demands faced by organisms within an evolving lineage. (shrink)

We argue that philosophical and historical research can constitute a ‘Biohumanities’ which deepens our understanding of biology itself; engages in constructive 'science criticism'; helps formulate new 'visions of biology'; and facilitates 'critical science communication'. We illustrate these ideas with two recent 'experimental philosophy' studies of the concept of the gene and of the concept of innateness conducted by ourselves and collaborators.

Philosophical discussion of molecular and developmental biology began in the late 1960s with the use of genetics as a test case for models of theory reduction. With this exception, the theory of natural selection remained the main focus of philosophy of biology until the late 1970s. It was controversies in evolutionary theory over punctuated equilibrium and adaptationism that first led philosophers to examine the concept of developmental constraint. Developmental biology also gained in prominence in the 1980s as part of a (...) broader interest in the new sciences of self-organization and complexity. The current literature in the philosophy of molecular and developmental biology has grown out of these earlier discussions under the influence of twenty years of rapid and exciting growth of empirical knowledge. Philosophers have examined the concepts of genetic information and genetic program, competing definitions of the gene itself and competing accounts of the role of the gene as a developmental cause. The debate over the relationship between development and evolution has been enriched by theories and results from the new field of 'evolutionary developmental biology'. Future developments seem likely to include an exchange of ideas with the philosophy of psychology, where debates over the concept of innateness have created an interest in genetics and development. (shrink)

David Papineau’s model of scientific reduction, contrary to his intent, appears to enable a naturalist realist account of the primitive normativity involved in a biological adaptation’s being “for” this or that (say the eye’s being for seeing). By disabling the crucial anti-naturalist arguments against any such reduction, his model would support a cognitivist semantics for normative claims like “The heart is for pumping blood, and defective if it doesn’t.” No moral claim would follow, certainly. Nonetheless, by thus “pressing from below” (...) we may learn something about moral normativity. For instance, suppose non-cognitivists like Mackie are right that the semantics of normative claims should be “unified”: if the semantics of moral claims is non-cognitivist, so too is that of all normative claims. Then, assuming that a naturalist reduction does yield a sound cognitivist account of the primitive normativity, it would follow that our semantics of moral claims is cognitivist as well. (shrink)

Throughout his career David Hull has sought to bring the philosophy of science into closer contact with science and especially with biological science (Hull 1969, 1997b). This effort has taken many forms. Sometimes it has meant ‘either explaining basic biology to philosophers or explaining basic philosophy to biologists’ (Hull 1996, p. 77). The first of these tasks, simple as it sounds, has been responsible for revolutionary changes. It is well known that traditional philosophy of science, modeled as it was on (...) theoretical physics, proved inadequate when philosophers turned their attention to biological science. Biological examples have driven major revisions of accounts of reduction (Hull 1974; Schaffner 1993, Ch. 9), laws of nature (Beatty et al. 1997), theories (Lloyd 1988) and natural kinds (Wilson 1999, Part III). Nor is explaining basic philosophy to biologists a task to be looked down upon. It is useful, not because philosophy has all the answers, but because scientists must think about how to do science, that is doing philosophy of science and scientists frequently reinvent philosophical views with known flaws. Early in his career Hull found biological systematists in the grip of a crude operationalism about scientific concepts and said so in the pages of Systematic Zoology (Hull 1968). For the next thirty years, as biologists debated the nature of species and the correct principles of classification, Hull added a philosophical note at the same congresses and in the same journals (Hull 1970, 1976, 1980, 1997a, 1999). (shrink)

I analyze the importance of parts in the style of biological theorizing that I call compositional biology. I do this by investigating various aspects, including partitioning frames and explanatory accounts, of the theoretical perspectives that fall under and are guided by compositional biology. I ground this general examination in a comparative analysis of three different disciplines with their associated compositional theoretical perspectives: comparative morphology, functional morphology, and developmental biology. I glean data for this analysis from canonical textbooks and defend the (...) use of such texts for the philosophy of science. I end with a discussion of the importance of recognizing formal and compositional biology as two genuinely different ways of doing biology – the differences arising more from their distinct methodologies than from scientific discipline included or natural domain studied. Ultimately, developing a translation manual between the two styles would be desirable as they currently are, at times, in conflict. (shrink)

This notice provides a critical discussion of some of the issues from Alex Rosenberg’s Darwinian Reductionism, in particular proper functions and the relationship of proximate and ultimate biology, developmental programs and genocentrism, biological laws, the principle of natural selection as a fundamental law, genetic determinism, and the definition of “reductionism.”.

The concept of niche (setting, context, habitat, environment) has been little studied by ontologists, in spite of its wide application in a variety of disciplines from evolutionary biology to economics. What follows is a first formal theory of this concept, a theory of the relations between objects and their niches. The theory builds upon existing work on mereology, topology, and the theory of spatial location as tools of formal ontology. It will be illustrated above all by means of simple biological (...) examples, but the concept of niche should be understood as being, like concepts such as part, boundary, and location, a structural concept that is applicable in principle to a wide range of different domains. (shrink)

Mendelian genes have become molecular genes, with increasing puzzlement about locating them, due to increasing complexity in genomic webworks. Genome science finds modular and conserved units of inheritance, identified as homologous genes. Such genes are cybernetic, transmitting information over generations; this too requires multi-leveled analysis, from DNA transcription to development and reproduction of the whole organism. Genes are conserved; genes are also dynamic and creative in evolutionary speciation—most remarkably producing humans capable of wondering about what genes are.

The theory and practice of contemporary comparative biology and phylogeny reconstruction (systematics) emphasizes algorithmic aspects but neglects a concern for the evidence. The character data used in systematics to formulate hypotheses of relationships in many ways constitute a black box, subject to uncritical assessment and social influence. Concerned that such a state of affairs leaves systematics and the phylogenetic theories it generates severely underdetermined, we investigate the nature of the criteria of homology and their application to character conceptualization in the (...) context of transformationist and generative paradigms. Noting the potential for indeterminacy in character conceptualization, we conclude that character congruence (the coherence of character statements) relative to a hierarchy is a necessary, but not a sufficient, condition for phylogeny reconstruction. Specifically, it is insufficient due to the lack of causal grounding of character hypotheses. Conceptualizing characters as homeostatic property cluster natural kinds is in accordance with the empirical practice of systematists. It also accounts for the lack of sharpness in character conceptualization, yet requires character identification and re-identification to be tied to causal processes. (shrink)