The field of the philosophy of biology is flourishing in its aim to evaluate and rethink the view inherited from the previous century ---the Modern Synthesis. Different research areas and theories have come to the fore in the last decades in order to account for different biological phenomena that, in the first instance, fall beyond the explanatory scope of the Modern Synthesis. This thesis is anchored and motivated by this revolt in the philosophy of biology. -/- The central target in (...) this context is the possibility of naturalizing teleology, a classical nightmare for the history of biology itself. This requires, principally, understanding the causes of teleological explanations without assuming an unfashioned backward causation of sorts. As the riddles of teleological explanations are about their temporal dimension, I analyze different temporal scales of biological processes: evolutionary, developmental, and physiological. -/- The first one is the one defended in the context of the Modern Synthesis. As expected, one of the aims of this thesis is to evaluate the adequacy of an evolutionary account of teleological explanation. The scrutiny is negative. Evolutionary explanations in the context of the Modern Synthesis lack the necessary causal roots to naturalize teleology. Concerning the physiological scale, a long tradition pushed up by Kant and the organicist movement in the 20th century allows us to better understand how teleological explanations can be naturalized in physiological process. The key notions in this temporal scale are self-organization and the recursive, looped character of physiological process. While the physiological scale may be suitably accounted by contemporaries views, such as Autonomous Systems Theory, different central teleological phenomena remain unexplained from a purely physiological perspective. In particular, different issues concerning the (adaptive) construction of organism ---such as plasticity, robustness, variation, novelty, inheritance--- deserve an ontogenetic analysis. -/- The principal aim of this thesis is to provide a theory of teleological development that falls beyond the Modern Synthesis' framework and is prompted by different insights from the history of biology. I call it Agential Teleosemantics. It rests on two central pillars. First, that developmental processes, beyond any gene-centered stance, can be understood in informational terms; i.e. developmental processes are about the interaction of developmental resources conveying biological information. The second ingredient is agentivity, namely the idea that development is regulated by an agentive system according to the adaptiveness of the phenotypic outcomes produced. The role of agency in Agential Teleosemantic is equivalent to the role of genes in the Modern Synthesis: it is responsible for explaining the order and the adaptive complexity in the living realm. -/- The second target of this thesis regards the possibility of naturalizing intentional explanations in cognitive science. The central project involved in such an aim is known as teleosemantics. Classical teleosemantics however is etiological: it explains the teleofunctions of representational systems in terms of evolutionary processes. The different disputes in the contemporary philosophy of biology provide two insights to analyze teleosemantics in cognitive science. First, the challenges against the Modern Synthesis must be extended to the evolutionary approach of etiological teleosemantics. Second, as Agential Teleosemantics suggests an alternative source for teleofunctions ---ontogeny, I offer an attempt to integrate Agential Teleosemantics into cognitive science in order to provide an alternative teleosemantic project to understand intentional explanations in cognitive science. (shrink)

The longstanding species problem in biology has a history that suggests a solution, and that history is not the received history found in many texts written by biologists or philosophers. The notion of species as the division into subordinate groups of any generic predicate was the staple of logic from Aristotle through the middle ages until quite recently. However, the biological species concept during the same period was at first subtly and then overtly different. Unlike the logic sense, which relied (...) on definitions of the essence of both genus and species, biological species from the time of Epicurus were consistently considered to involve a reproductive element: in short, living species relied not on essential definitions, but on the generative cause, which might not be definable. I term this the generative conception of species: species were the generation by reproduction of form. This undercuts the claim that species before Darwin were essentialist, and divorces the notion of a type from that of essence. In fact, as late as the end of the nineteenth century, logicians explicitly treated biological “species” as a homonym only of logical essentialist species, and permitted considerable deviation from the type or form. At every point, species in logic were thought to be a subset, in effect, of some more general notion. I sketch a history of both philosophical and biological traditions of the species concept, before turning to the current conceptions. These are reconsidered in the light of this history, and in particular Mayr’s changing views are shown to be somewhat Whiggish, historiographically. Of the many touted biological species concepts, only one of which (Mayr’s) is called _the_ Biological Species Concept, none appears to capture all the relevant facts, intuitions, and operational requirements of biology. Cladistic conceptions, however, have much in common with the older philosophical literature, in that the natural group of cladism is the clade, or monophyletic group. After considering the Individuality Thesis, and the metaphysics of species, we see that species are the most particular terminal taxa in a clade, and that they are “defined” in terms of the particular synapomorphies, or evolved characters, that are causally responsible for keeping the lineages that organisms form distinct from one another. In this way, we can remain within the generative conception of species that has been in play for over two millennia, and yet avoid the pitfalls of prior attempts to find a universal conception of species. (shrink)

In this paper, I discuss the neo-Aristotelian approaches, which usually reinterpret Aristotle’s ideas on form and/or borrow the notion of formal cause without engaging with the broader implications of Aristotle’s metaphysics. In opposition to these approaches, I claim that biosemiotics can propose an alternative view on life’s form. Specifically, I examine the proposals to replace the formal cause with gene-centrism, functionalism, and structuralism. After critically addressing these approaches, I discuss the problems of reconciling Aristotelianism with the modern view of life’s (...) organization. I claim that the notion of the final cause proposes a cosmological hierarchy and that this is the main problem with applying the formal cause to biology. An alternative categorization of conceptualizing life’s form involves the processual identity, relational property clusters, and context-dependent transmission of representational units. The third category points to a semiotic basis of the form of life. In this context, I offer to readjust the focus of the problem of matter-form duality by pointing out that form is primarily an issue of the subject-object relation. Biosemiotics helps to understand the constructive role of symbolic representation in living systems, which is crucial to extend the analysis of the form from cognitive representations to external phenomena. Emergence of subjectivity and perspectivity of interactions are key elements to bridge the form and actual processes within a non-hylomorphic account. To demonstrate transitions from the physical influence of shapes to the organic recognition of forms, I address the biological studies on the synchronization of coincidental inputs and enzyme specificity. (shrink)

The concept of information and its relation to biosemiotics is a major area of contention among biosemioticians. Biosemioticians influenced by von Uexküll, Sebeok, Bateson and Peirce are critical of the way the concept as developed in information science has been applied to biology, while others believe that for biosemiotics to gain acceptance it will have to embrace information science and distance biosemiotics from Peirce’s philosophical work. Here I will defend the influence of Peirce on biosemiotics, arguing that information science and (...) biosemiotics as these were originally formulated are radically opposed research traditions. Failure to appreciate this will undermine the challenge of biosemiotics and other anti-reductionist traditions to mainstream science with its reductionist ambition to explain everything through physics. However, for this challenge to be successful, it will be necessary to respond to criticisms of Peircian ideas, jettisoning ideas that are no longer defensible and integrating ideas allied to his anti-reductionist agenda. Here I will argue that the natural philosophy of Gilbert Simondon, offering a searching critique of the application of the new concept of information and cybernetics to the life and human sciences, provides the means to defend and advance Peirce’s core ideas and thereby defend post-reductionist biosemiotics. (shrink)

In this paper I first offer a systematic outline of a series of conceptual novelties in the life-sciences that have favoured, over the last three decades, the emergence of a more social view of biology. I focus in particular on three areas of investigation: (1) technical changes in evolutionary literature that have provoked a rethinking of the possibility of altruism, morality and prosocial behaviours in evolution; (2) changes in neuroscience, from an understanding of the brain as an isolated data processor (...) to the ultrasocial and multiply connected social brain of contemporary neuroscience; and (3) changes in molecular biology, from the view of the gene as an autonomous master of development to the ‘reactive genome’ of the new emerging field of molecular epigenetics. In the second section I reflect on the possible implications for the social sciences of this novel biosocial terrain and argue that the postgenomic language of extended epigenetic inheritance and blurring of the nature/nurture boundaries will be as provocative for neo-Darwinism as it is for the social sciences as we have known them. Signs of a new biosocial language are emerging in several social-science disciplines and this may represent an exciting theoretical novelty for twenty-first social theory. (shrink)

The role of the body in cognition is acknowledged across a variety of disciplines, even if the precise nature and scope of that contribution remain contentious. As a result, most philosophers working on embodiment—e.g. those in embodied cognition, enactivism, and ‘4e’ cognition—interact with the life sciences as part of their interdisciplinary agenda. Despite this, a detailed engagement with emerging findings in epigenetics and post-genomic biology has been missing from proponents of this embodied turn. Surveying this research provides an opportunity to (...) rethink the relationship between embodiment and genetics, and we argue that the balance of current epigenetic research favours the extension of an enactivist approach to mind and life, rather than the extended functionalist view of embodied cognition associated with Andy Clark and Mike Wheeler, which is more substrate neutral. (shrink)

“What is a gene?” is an important philosophical question that has been asked over and over. This paper approaches this question by understanding it as the individuation problem of genes, because it implies the problem of identifying genes and identifying a gene presupposes individuating the gene. I argue that there are at least two levels of the individuation of genes. The transgenic technique can individuate “a gene” as an individual while the technique of gene mapping in classical genetics can only (...) individuate “a gene” as a type or a kind. The two levels of individuation involve different techniques, different objects that are individuated, and different references of the term “gene”. Based on the two levels of individuation, I discuss important philosophical implications including the relationship between individuality and individuation and that between individuals and kinds in experimental contexts. I also suggest a new gene conception, calling it “the transgenic conception of the gene.”. (shrink)

Ongoing empirical discoveries in molecular biology have generated novel conceptual challenges and perspectives. Philosophers of biology have reacted to these trends when investigating the practice of molecular biology and contributed to scientific debates on methodological and conceptual matters. This article reviews some major philosophical issues in molecular biology. First, philosophical accounts of mechanistic explanation yield a notion of explanation in the context of molecular biology that does not have to rely on laws of nature and comports well with molecular discovery. (...) Second, reductionism continues to be debated and increasingly be rejected by scientists. Philosophers have likewise moved away from reduction toward integration across fields or integrative explanations covering several levels of organization. Third, although the gene concept has undergone substantial transformation and even fragmentation, it still enjoys widespread use by molecular biologists, which has prompted philosophers to understand the empirical reasons for this. At the same time, it has been argued the notion of ‘genetic information’ is largely an empty metaphor, which generates the illusion of explanatory understanding without offering an adequate explanation of molecular and developmental mechanisms. (shrink)

Genetic determinism can be described as the attribution of the formation of traits to genes, where genes are ascribed more causal power than what scientific consensus suggests. Belief in genetic determinism is an educational problem because it contradicts scientific knowledge, and is a societal problem because it has the potential to foster intolerant attitudes such as racism and prejudice against sexual orientation. In this article, we begin by investigating the very nature of belief in genetic determinism. Then, we investigate whether (...) knowledge of genetics and genomics is associated with beliefs in genetic determinism. Finally, we explore the extent to which social factors such as gender, education, and religiosity are associated with genetic determinism. Methodologically, we gathered and analyzed data on beliefs in genetic determinism, knowledge of genetics and genomics, and social variables using the “Public Understanding and Attitudes towards Genetics and Genomics” instrument. Our analyses of PUGGS responses from a sample of Brazilian university freshmen undergraduates indicated that belief in genetic determinism was best characterized as a construct built up by two dimensions or belief systems: beliefs concerning social traits and beliefs concerning biological traits; levels of belief in genetic determination of social traits were low, which contradicts prior work; associations between knowledge of genetics and genomics and levels of belief in genetic determinism were low; and social factors such as age and religiosity had stronger associations with beliefs in genetic determinism than knowledge. Although our study design precludes causal inferences, our results raise questions about whether enhancing genetic literacy will decrease or prevent beliefs in genetic determinism. (shrink)

This paper uses formal Darwinism as elaborated by Alan Grafen to articulate an explanatory pluralism that casts light upon two strands of controversies running across evolutionary biology, viz., the place of organisms versus genes, and the role of adaptation. Formal Darwinism shows that natural selection can be viewed either physics-style, as a dynamics of alleles, or in the style of economics as an optimizing process. After presenting such pluralism, I argue first that whereas population genetics does not support optimization, optimality (...) can still be taken as a default hypothesis when modeling evolutionary processes; and second, that organisms have an explanatory role in evolutionary theory, since they are involved in the economic perspective of optimization. Finally, in order to ask whether the Modern Synthesis can indeed provide a theory of organisms, I apply a Kantian-inspired theoretical view of organisms (underlying much developmental modeling), according to which they are both designed entities and subjects of intrinsic circular processes involving the whole organism and its parts. I first show that the design aspect is accountable for in terms of the Modern Synthesis understood in the formal Darwinism framework. I then question whether the latter aspect of organisms can also be ultimately captured in the same framework, and to this purpose devise an empirical test relying on an assessment of the relative weight of genetic elements in developmental and functional gene regulatory networks. (shrink)

Bennett and Hacker criticize a number of neuroscientists and philosophers for attributing capacities which belong to the human being as a whole, like perceiving or deciding, to a “part” of the human being, viz. the brain. They call this type of mistake the “mereological fallacy”. Interestingly, the authors say that these capacities cannot be ascribed to the mind either. They reject not only materialistic monism but also Cartesian dualism, arguing that many predicates describing human life do not refer to physical (...) or mental properties, nor to the sum of such properties. I agree with this important principle and with the critique of the mereological fallacy which it underpins, but I have two objections to the authors’ view. Firstly, I think that the brain is not literally a part of the human being, as suggested. Secondly, Bennett and Hacker do not offer an account of body and mind which explains in a systematic way how the domain of phenomena which transcends the mental and the physical relates to the mental and the physical. I first argue that Helmuth Plessner’s philosophical anthropology provides the kind of account we need. Then, drawing on Plessner, I present an alternative view of the mereological relationships between brain and human being. My criticism does not undercut Bennett and Hacker’s diagnosis of the mereological fallacy but rather gives it a more solid philosophical–anthropological foundation. (shrink)

In spite of being ubiquitous in life sciences, the concept of information is harshly criticized. Uses of the concept other than those derived from Shannon's theory are denounced as pernicious metaphors. We perform a computational experiment to explore whether Shannon's information is adequate to describe the uses of said concept in commonplace scientific practice. Our results show that semantic sequences do not have unique complexity values different from the value of meaningless sequences. This result suggests that quantitative theoretical frameworks do (...) not account fully for the complex phenomenon that the term “information” refers to. We propose a restructuring of the concept into two related, but independent notions, and conclude that a complete theory of biological information must account completely not only for both notions, but also for the relationship between them. (shrink)

Although it may seem like a truism to assert that biology is the science that studies organisms, during the second half of the twentieth century the organism category disappeared from biological theory. Over the past decade, however, biology has begun to witness the return of the organism as a fundamental explanatory concept. There are three major causes: (a) the realization that the Modern Synthesis does not provide a fully satisfactory understanding of evolution; (b) the growing awareness of the limits of (...) reductionism in molecular biology; and (c) the renewed interest in the nature of life as a genuine scientific problem. This essay examines these recent developments and considers the new epistemological roles being played by the organism in each of them. It also reflects on what the present resurgence of the organism means for the philosophy of biology. (shrink)

First the ‘Weismann barrier’ and later on Francis Crick’s ‘central dogma’ of molecular biology nourished the gene-centric paradigm of life, i.e., the conception of the gene/genome as a ‘central source’ from which hereditary specificity unidirectionally flows or radiates into cellular biochemistry and development. Today, due to advances in molecular genetics and epigenetics, such as the discovery of complex post-genomic and epigenetic processes in which genes are causally integrated, many theorists argue that a gene-centric conception of the organism has become problematic. (...) Here, we first explore the causal implications of the following two central dogma-related issues: (1) widespread reverse transcription—arguing for an extension from ‘DNA-genome’ to RNA-encompassing ‘NA-genome’ and, thus, from traditional DNA-centrism to a broader ‘NA-centrism’; and (2) the absence of a mechanism of reverse translation—arguing for the ‘structural primacy’ of NA-sequence over protein in cellular biochemistry. Secondly, we explore whether this latter conclusion can be extended to a ‘functional primacy’ of NA-sequence over protein in cellular biochemistry, which would imply a limited kind of ‘gene/NA-centrism’ confined to the subcellular level of NA/protein-based biochemistry. Finally, we explore the conditions—and their (non)fulfilment—for a more generalised form of gene-centrism extendable to higher levels of biological organisation. We conclude that the higher we go in the biological hierarchy, the more dubious gene-centric claims become. (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.

In this paper I use a case study—the discovery of the chaperon function exerted by proteins in the various steps of the hereditary process—to re-discuss the question whether the nucleic acids are the sole repositories of relevant information as assumed in the information theory of heredity. The evidence I here present of a crucial role for molecular chaperones in the folding of nascent proteins, as well as in DNA duplication, RNA folding and gene control, suggests that the family of proteins (...) acting as molecular chaperones provides information that is complementary to that stored in the nucleic acids, and equally important. A re-evaluation of the role of proteins in the hereditary process is in order away from the gene-centric approach of the information theory of heredity, to which neo-Darwinian evolutionists adhere. (shrink)

Voles are attracting attention because genetic variation at a single locus appears to have a profound impact on a complex social behavior, namely monogamy. After briefly reviewing the state of the most relevant scientific literature, I examine the way that this research gets taken up by the popular media, by scientists, and by the notable philosopher of neuroscience Patricia Churchland and interpreted as having deeply revisionary implications for how we ordinarily understand ourselves as persons. We have all these big questions (...) we would like to resolve about free will, consciousness, our understanding of persons, and the nature of morality and there is a tendency to ask more of neuroscience than it can yet answer. I do not deny that advances in neuroscience may eventually bear on important philosophical issues. However, it is not at all clear that this research has many of the sweeping implications being claimed for it and, in communicating science responsibly to the public, there is reason to be cautious about suggesting that it does. (shrink)

Biological atomism postulates that all life is composed of elementary and indivisible vital units. The activity of a living organism is thus conceived as the result of the activities and interactions of its elementary constituents, each of which individually already exhibits all the attributes proper to life. This paper surveys some of the key episodes in the history of biological atomism, and situates cell theory within this tradition. The atomistic foundations of cell theory are subsequently dissected and discussed, together with (...) the theory’s conceptual development and eventual consolidation. This paper then examines the major criticisms that have been waged against cell theory, and argues that these too can be interpreted through the prism of biological atomism as attempts to relocate the true biological atom away from the cell to a level of organization above or below it. Overall, biological atomism provides a useful perspective through which to examine the history and philosophy of cell theory, and it also opens up a new way of thinking about the epistemic decomposition of living organisms that significantly departs from the physicochemical reductionism of mechanistic biology. (shrink)

Modularity has become a central and remarkably useful concept in evolutionary developmental biology, offering an explanation of how independent, interacting units make possible developmental events and evolutionary changes. These modules exist at several different levels of organization, from genes to signal transduction pathways to cell populations. Cell populations, which are multicellular modules, provide an opportunity both to clarify our notion of modularity and to reexamine such central concepts as cell-to-cell communication. Rosine Chandebois’s work on “cell sociology” is reframed in the (...) language of modularity in order to show how groups of cells maintain their collective identity during development and how signaling information from the group’s environment is received by the constituent cells. In a “test case” for our account of multicellular modules, we consider the vertebrate neural crest, a migratory cell population made up of several subpopulations. The neural crest proves yet again to be a complex case, showing the importance of taking into account both developmental and evolutionary transformations of multicellular modules. (shrink)

The comprehension of living organisms in all their complexity poses a major challenge to the biological sciences. Recently, systems biology has been proposed as a new candidate in the development of such a comprehension. The main objective of this paper is to address what systems biology is and how it is practised. To this end, the basic tools of a systems biological approach are explored and illustrated. In addition, it is questioned whether systems biology ‘revolutionizes’ molecular biology and ‘transcends’ its (...) assumed reductionism. The strength of this claim appears to depend on how molecular and systems biology are characterised and on how reductionism is interpreted. Doing credit to molecular biology and to methodological reductionism, it is argued that the distinction between molecular and systems biology is gradual rather than sharp. As such, the classical challenge in biology to manage, interpret and integrate biological data into functional wholes is further intensified by systems biology’s use of modelling and bioinformatics, and by its scale enlargement. (shrink)

According to a recent suggestion, the names of gene taxa should be conceived of as referring to individuals with concrete genes as their parts, just as the names of biological species are often understood as denoting individuals with organisms as their parts. Although prima facie this suggestion might advance the debate on gene concepts in a similar way as the species-are-individuals thesis advanced the debate on species concepts, I argue that the principal arguments in support of the gene-individuality thesis are (...) much less compelling than the parallel arguments in the species case. In addition, I argue that the notion of biological function invoked in the gene-individuality thesis (selected effect) is not the one that biologists actually use when individuating genes. Contra the gene-individuality thesis, I argue that gene names refer to kinds, defined primarily (though not exclusively) by causal-role functions. (shrink)

This paper explores the issue of life and its relevance to nursing, through Aristotle's philosophy and an Aristotelian interpretation of Nightingale's Notes on Nursing. Life as process and becoming has ontological status in Aristotle's philosophy and this dynamism is particularly relevant for nursing. The paper presents aspects of Aristotle's philosophy of life: his account of life as inherent powers of the individual, his analysis of change and time, and his understanding of sickness and health as qualitative states of living beings. (...) It is shown how the Greek medical‐philosophical tradition, continued by Galenic medicine and hygiene into modern time, influenced Nightingale's nursing. Individuals' life‐maintaining metabolic relations to their surroundings are investigated through Aristotle and modern philosophy of biology and through Nightingale's nursing emphasis on the patient's relation to her or his immediate surroundings. It is argued that Nightingale's concern is really the processes of individual life, which in sickness necessitate temporally continuous nursing observation. Humans' radical dependency on their surroundings is actualized as interpersonal interdependency. The paper argues that the end of nursing care, the telos for which sake it is practised, is inherent in the individual course of the patients' life. When life processes are affected by sickness, infirmity, medical interventions or mental suffering, individuals need competent help to live – and to live as well as possible. It is suggested that the special responsibility of nursing is to facilitate, relieve and protect individual life continuously during such times. (shrink)

In the mid-1990s, the company Human Genome Sciences submitted three potentially revolutionary patent applications to the US Patent and Trademark Office, each of which claimed the entire genome sequence of a microorganism. The patent examiners, however, objected to these applications, and after negotiation they were eventually re-written to resemble more traditional gene patents. In this paper, which is based on a study of the patent examination files, we examine the reasons why these patent applications were unsuccessful in their original form. (...) We show that with respect to utility and novelty, the patent attorney’s case built on an understanding of the genome as a computer-related invention. The patent examiners did not object to the patenting of complete genome sequences as computer-related inventions on moral grounds or in terms of the distinction between a discovery and an invention. Instead, their objections were based on classification, rules and procedure. Rather than patent examiners having a notion of a genome that should not be patented, the notion of a ‘genome’, and the ways in which it may be different from a ‘gene’, played no role in these debates. We discuss the consequences of our findings for patenting in the biosciences. (shrink)

Although biologists and philosophers of science generally agree that genes cannot determine the forms of biological and psychological traits, students, journalists, politicians, and other members of the general public nonetheless continue to embrace genetic determinism. This article identifies some of the concerns typically raised by individuals when they first encounter the systems perspective that biologists and philosophers of science now favor over genetic determinism, and uses arguments informed by that perspective to address those concerns. No definitive statements can yet be (...) made about why genetic determinism has proven so resilient in the face of empirical evidence pointing up its deficiencies, but conveying the essential interdependence of 'nature' and 'nurture' to the general public will likely require deployment of the arguments that systems theorists ordinarily use to reject genetic determinism. In addition, the elaboration of new metaphors that focus attention on the dynamic nature of trait construction will likely prove valuable, because re-conceptualizing notions like 'genes' and 'nature' will probably be one of the most effective ways to help students and the general public abandon the genetic determinism that biologists now recognize as indefensible. (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.

I show that gene regulation networks are qualitatively consistent and therefore sufficiently similar to linearly seperable connectionist networks to warrant that the connectionist framework be applied to gene regulation. On this view, natural selection designs gene regulation networks to overcome the difficulty of development. I offer some general lessons about their evolvability that can be learned by examining the generic features of connectionist networks.

If the question ``What is a gene?'' proves to be worth asking it must be able to elicit an answer which both recognizes and address the reasons why the concept of the gene ever seemed to be something worth getting excited about in the first place as well analyzing and evaluating the latest develops in the molecular biology of DNA. Each of the preceding papers fails to do one of these and sufferrs the consequences. Where Rolston responds to the apparent (...) failure of molecular biology to make good on the desideratum of the classical gene by veering off into fanciful talk about ``cybernetic genes,'' Griffiths and Stotz lose themselves in the molecular fine print and forget to ask themselves why ``genes'' should be of any special interst anyway. (shrink)

Essentialism is widely regarded as a mistaken view of biological kinds, such as species. After recounting why (sections 2-3), we provide a brief survey of the chief responses to the “death of essentialism” in the philosophy of biology (section 4). We then develop one of these responses, the claim that biological kinds are homeostatic property clusters (sections 5-6) illustrating this view with several novel examples (section 7). Although this view was first expressed 20 years ago, and has received recent discussion (...) and critique, it remains underdeveloped and is often misrepresented by its critics (section 8). (shrink)

The social, behavioral, and a good chunk of the biological sciences concern the nature of individual agency, where our paradigm for an individual is a human being. Theories of economic behavior, of mental function and dysfunction, and of ontogenetic development, for example, are theories of how such individuals act, and of what internal and external factors are determinative of that action. Such theories construe individuals in distinctive ways.

David Waldron Smithers was, among other things, a physician and a pioneer of cancer radiotherapy and a well-respected figure in British medicine and public health. From the 1940s until his retirement from medical practice in 1973, he was the director of the Radiotherapy Department at the Royal Marsden Hospital and London University Chair of Radiotherapy at the Institute of Cancer Research. Using massive amounts of clinical observations, which he interpreted from an organicist viewpoint, and his impressive synthetic thinking, he proposed (...) a coherent alternative perspective to the somatic mutation theory (SMT) which was then, and still is, the dominant theory of cancer. The purpose of this essay is to acquaint the modern audience with his seminal paper, published in 1962, because it deserves to be recognized as a true classic. In it, he examined the lack of fit between clinical observations and the SMT and proposed the rejection of this reductionist perspective. In addition, he built an organicist alternative in which carcinogenesis is seen as a problem of biological organization. His conceptual contribution to the cancer problem has inspired us and other authors over the last two decades. His essay “Cancer: An Attack on Cytologism,” originally published in The Lancet in 1962, is available as supplementary material in the online version of this article. (shrink)

The Darwinian theory of evolution is itself evolving and this book presents the details of the core of modern Darwinism and its latest developmental directions. The authors present current scientific work addressing theoretical problems and challenges in four sections, beginning with the concepts of evolution theory, its processes of variation, heredity, selection, adaptation and function, and its patterns of character, species, descent and life. The second part of this book scrutinizes Darwinism in the philosophy of science and its usefulness in (...) understanding ecosystems, whilst the third section deals with its application in disciplines beyond the biological sciences, including evolutionary psychology and evolutionary economics, Darwinian morality and phylolinguistics. The final section addresses anti-Darwinism, the creationist view and issues around teaching evolution in secondary schools. The reader learns how current experimental biology is opening important perspectives on the sources of variation, and thus of the very power of natural selection. This work examines numerous examples of the extension of the principle of natural selection and provides the opportunity to critically reflect on a rich theory, on the methodological rigour that presides in its extensions and exportations, and on the necessity to measure its advantages and also its limits. Scholars interested in modern Darwinism and scientific research, its concepts, research programs and controversies will find this book an excellent read, and those considering how Darwinism might evolve, how it can apply to the human sciences and other disciplines beyond its origins will find it particularly valuable. Originally produced in French (Les Mondes Darwiniens), the scope and usefulness of the book have led to the production of this English text, to reach a wider audience. This book is a milestone in the impressive penetration by Francophone scholars into the world of Darwinian science, its historiography and philosophy over the last two decades. Alex Rosenberg, R. Taylor Cole Professor of Philosophy, Duke University Until now this useful and comprehensive handbook has only been available to francophones. Thanks to this invaluable new translation, this collection of insightful and original essays can reach the global audience it deserves. Tim Lewens, University of Cambridge. (shrink)

The paper analyzes the early theory building process of Thomas Hunt Morgan from the 1910s to the 1930s and the introduction of the invisible gene as a main explanatory unit of heredity. Morgan’s work marks the transition between two different styles of thought. In the early 1900s, he shifted from an embryological study of the development of the organism to a study of the mechanism of genetic inheritance and gene action. According to his contemporaries as well as to historiography, Morgan (...) separated genetics from embryology, and the gene from the whole organism. Other scholars identified an underlying embryological focus in Morgan’s work throughout his career. Our paper aims to clarify the debate by concentrating on Morgan’s theory building—characterized by his confidence in the power of experimental methods, and carefully avoiding any ontological commitment towards the gene—and on the continuity of the questions to be addressed by both embryology and genetics. (shrink)

There has been a long-standing opposition to genetically modified organisms worldwide. Some studies have tried to identify the deep-lying philosophical, conceptual as well as psychological motivations for this opposition. Philosophical essentialism, psychological essentialism, and vitalism have been proposed as possible candidates. I approach the plausibility of the claim that these notions are related to GMO opposition from a historical perspective. Vitalism and philosophical essentialism have been associated with anti-GMO stance on account of their purported hostility to species and organismic mutability. (...) I show that vitalism has often been associated to various mutabilist theories, whereas the case for philosophical essentialism as motivating GMO opposition depends on the now discredited Essentialism Story that had constructed essentialism as a predominant view in pre-Darwinian science. Further, as philosophical essentialism taken seriously is incompatible with the reality of genetic engineering, it is unlikely to be a reason for opposition. Psychological essentialism, involving an instinctive repulsion from the practice of manipulating what is thought to be the essence of living beings, is a more likely reason for resistance to transgenesis. Yet even here, historical considerations are crucial. Not only lay people tend to essentialize genes, but scientists themselves can be shown to have been complicit in essentialist tendencies. From the advent of modern genetics, the imagery of the all-powerful genes, often depicted by scientists themselves metaphorically as material counterparts of the now obsolete vitalistic agent, has permeated the language of leading scientific figures, whose influence in shaping public opinion should not be downplayed. Enthusiasm for genetic engineering and the abhorrence from it might both derive from the same unrealistic image of the essential gene, the revision of which thus holding out the hope for transcending the present impasse of the GMO controversy. (shrink)

The rise of molecular epigenetics over the last few years promises to bring the discourse about the sociality and susceptibility to environmental influences of the brain to an entirely new level. Epigenetics deals with molecular mechanisms such as gene expression, which may embed in the organism “memories” of social experiences and environmental exposures. These changes in gene expression may be transmitted across generations without changes in the DNA sequence. Epigenetics is the most advanced example of the new postgenomic and context-dependent (...) view of the gene that is making its way into contemporary biology. In my article I will use the current emergence of epigenetics and its link with neuroscience research as an example of the new, and in a way unprecedented sociality of contemporary biology. After a review of the most important developments of epigenetic research, and some of its links with neuroscience, in the second part I reflect on the novel challenges that epigenetics presents for the social sciences for a re-conceptualization of the link between the biological and the social in a postgenomic age. Although epigenetics remains a contested, hyped, and often uncritical terrain, I claim that especially when conceptualized in broader non-genecentric frameworks,. (shrink)

Methodological reductionists practice ‘wannabe reductionism’. They claim that one should pursue reductionism, but never propose how. I integrate two strains in prior work to do so. Three kinds of activities are pursued as “reductionist”. “Successional reduction” and inter-level mechanistic explanation are legitimate and powerful strategies. Eliminativism is generally ill-conceived. Specific problem-solving heuristics for constructing inter-level mechanistic explanations show why and when they can provide powerful and fruitful tools and insights, but sometimes lead to erroneous results. I show how traditional metaphysical (...) approaches fail to engage how science is done. The methods used do so, and support a pragmatic and non-eliminativist realism. (shrink)

Griffiths and Stotz’s Genetics and Philosophy: An Introduction offers a very good overview of scientific and philosophical issues raised by present-day genetics. Examining, in particular, the questions of how a “gene” should be defined and what a gene does from a causal point of view, the authors explore the different domains of the life sciences in which genetics has come to play a decisive role, from Mendelian genetics to molecular genetics, behavioural genetics, and evolution. In this review, I highlight what (...) I consider as the two main theses of the book, namely: genes are better conceived as tools; genes become causes only in a context. I situate these two theses in the wider perspective of developmental systems theory. This leads me to emphasize that Griffiths and Stotz reflect very well an on going process in genetics, which I call the “epigenetization” of genetics, i.e., the growing interest in the complex processes by which gene activation is regulated. I then make a factual objection, which is that Griffiths and Stotz have almost entirely neglected the perspective of ecological developmental biology, and more precisely recent work on developmental symbioses, and I suggest that this omission is unfortunate in so far as an examination of developmental symbioses would have considerably strengthened Griffiths and Stotz’s own conclusions. (shrink)

This inaugural handbook documents the distinctive research field that utilizes history and philosophy in investigation of theoretical, curricular and pedagogical issues in the teaching of science and mathematics. It is contributed to by 130 researchers from 30 countries; it provides a logically structured, fully referenced guide to the ways in which science and mathematics education is, informed by the history and philosophy of these disciplines, as well as by the philosophy of education more generally. The first handbook to cover the (...) field, it lays down a much-needed marker of progress to date and provides a platform for informed and coherent future analysis and research of the subject. -/- The publication comes at a time of heightened worldwide concern over the standard of science and mathematics education, attended by fierce debate over how best to reform curricula and enliven student engagement in the subjects There is a growing recognition among educators and policy makers that the learning of science must dovetail with learning about science; this handbook is uniquely positioned as a locus for the discussion. -/- The handbook features sections on pedagogical, theoretical, national, and biographical research, setting the literature of each tradition in its historical context. Each chapter engages in an assessment of the strengths and weakness of the research addressed, and suggests potentially fruitful avenues of future research. A key element of the handbook’s broader analytical framework is its identification and examination of unnoticed philosophical assumptions in science and mathematics research. It reminds readers at a crucial juncture that there has been a long and rich tradition of historical and philosophical engagements with science and mathematics teaching, and that lessons can be learnt from these engagements for the resolution of current theoretical, curricular and pedagogical questions that face teachers and administrators. (shrink)

The somatic mutation theory has been the prevailing paradigm in cancer research for the last 50 years. Its premises are: (1) cancer is derived from a single somatic cell that has accumulated multiple DNA mutations, (2) the default state of cell proliferation in metazoa is quiescence, and (3) cancer is a disease of cell proliferation caused by mutations in genes that control proliferation and the cell cycle. From this compelling simplicity, an increasingly complicated picture has emerged as more than 100 (...) oncogenes and 30 tumor suppressor genes have been identified. To accommodate this complexity, additional ad hoc explanations have been postulated. After a critical review of the data gathered from this perspective, an alternative research program has been proposed. It is based on the tissue organization field theory, the premises of which are that carcinogenesis represents a problem of tissue organization, comparable to organogenesis, and that proliferation is the default state of all cells. The merits of these competing theories are evaluated herein. BioEssays 26:1097–1107, 2004. © 2004 Wiley Periodicals, Inc. (shrink)

Radically new or unexpected findings in a science demand an openness to new concepts and styles of explanation. The time is more than ripe for asking ourselves what we have learned from the research program of comparative genomics. Where not long ago the human genome was expected to reveal a close association of complexity with the quantitative expansion of the roster of unique genes, more recent findings, especially in relation to comparisons between human and chimp, have raised the bracing possibility (...) that when it comes to complexity, it may be that `less is more'. But `less is more' is not the only observation or inference that follows from the data. The idea of `progressive detachment' will be introduced and set forth as the most perspicuous conceptual resource for unifying and interpreting the overall findings from comparative genomics to date. (shrink)

The topic of this paper is social constructivist doctrines about the nature of scientific knowledge. I don't propose to review all the many accounts that have either claimed this designation or had it ascribed to them. Rather I shall try to consider in a very general way what sense should be made of the underlying idea, and then illustrate some of the central points with two central examples from biology. The first thing to say is that, on the face of (...) it, some doctrine of the social construction of science must self-evidently be true. The notion of science as progressing through the efforts of solitary geniuses may have had some plausibility in the seventeenth century, but it has none today. Science is a massively cooperative, social, enterprise. And surely it is constructed. Scientific knowledge doesn't grow on trees; it is produced through hard work by human agents. Putting these two banal points together we conclude that science is socially constructed. (shrink)

Recently the terms “codes” and “information” as used in the context of molecular biology have been the subject of much discussion. Here I propose that a variety of structural realism can assist us in rethinking the concepts of DNA codes and information apart from semantic criteria. Using the genetic code as a theoretical backdrop, a necessary distinction is made between codes qua symbolic representations and information qua structure that accords with data. Structural attractors are also shown to be entailed by (...) the mapping relation that any DNA code is a part of (as the domain). In this framework, these attractors are higher-order informational structures that obviate any “DNA-centric” reductionism. In addition to the implications that are discussed, this approach validates the array of coding systems now recognized in molecular biology. (shrink)

Experimental philosophy of science gathers empirical data on how key scientific concepts are understood by particular scientific communities. In this paper we briefly describe two recent studies in experimental philosophy of biology, one investigating the concept of the gene, the other the concept of innateness. The use of experimental methods reveals facts about these concepts that would not be accessible using the traditional method of intuitions about possible cases. It also contributes to the study of conceptual change in science, which (...) we understand as the result of a form of conceptual ecology, in which concepts become adapted to specific epistemic niches. (shrink)

There is ongoing controversy as to whether the genome is a representing system. Although it is widely recognised that DNA carries information, both correlating with and coding for various outcomes, neither of these implies that the genome has semantic properties like correctness or satisfaction conditions, In the Scope of Logic, Methodology, and the Philosophy of Sciences, Vol. II. Kluwer, Dordrecht, pp. 387–400). Here a modified version of teleosemantics is applied to the genome to show that it does indeed have semantic (...) properties – there is representation in the genome. The account differs in three respects from previous attempts to apply teleosemantics to genes. It emphasises the role of the consumer of representations. It rejects the standard assumption that genetic representation can be used to explain the course of an organism’s development. And it identifies the explanatory role played by representational properties of the genome. A striking consequence of this account is that other inheritance systems could also be representational. Thus, a version of the parity thesis is accepted. However, the criteria for being an inheritance system are demanding, so semantic properties are not ubiquitous. (shrink)

We outline three very different concepts of the gene—instrumental, nominal, and postgenomic. The instrumental gene has a critical role in the construction and interpretation of experiments in which the relationship between genotype and phenotype is explored via hybridization between organisms or directly between nucleic acid molecules. It also plays an important theoretical role in the foundations of disciplines such as quantitative genetics and population genetics. The nominal gene is a critical practical tool, allowing stable communication between bioscientists in a wide (...) range of fields grounded in well-defined sequences of nucleotides, but this concept does not embody major theoretical insights into genome structure or function. The post-genomic gene embodies the continuing project of understanding how genome structure supports genome function, but with a deflationary picture of the gene as a structural unit. This final concept of the gene poses a significant challenge to conventional assumptions about the relationship between genome structure and function, and between genotype and phenotype. (shrink)

I begin with a rather unpromising dispute that Nozick once had with Ian Hacking in the pages of the London Review of Books, in which both vied with one another in their enthusiasm to repudiate the thesis that some human people or peoples are closer than others to animality. I shall attempt to show that one can build, on the basis of Nozick’s discussion of rationality, a defense of the view that the capacity tor language places human rationality out of (...) reach of a comparison with animals. The difference rests, paradoxically, on the human capacity tor irratianality. Irrationality depends on the capacity tor language, which allows the detachment of explicit thoughts from their underlying dynamic implementation; these, in turn, condition the essential disputability of principles of rationality. That is what places every human potentially -- if not actually -- on the other side of an unbridgeable gulf that separates us from other animals. (shrink)

It has been widely received that one of Gregor Mendel’s most important contributions to the history of genetics is his novel work on developmental information (for example, the proposal of the famous Mendelian ratios like 1:2:1, 3:1, and 9:3:3:1). This view is well evidenced by the fact that much of early Mendelians’ work in the 1900s focuses on the retrodiction (viz. the re-analysis of the pre-exist data with Mendel’s approach). However, there is no consensus on what Mendel meant by development (...) (Entwicklung). Nor is there an agreement on the interpretation of Mendel’s laws of developmental series (Entwicklungsreihe). This chapter revisits Mendel’s notions of development and developmental series. Firstly, I argue that Mendel’s use of development is greatly influenced by Gärtner’s. Secondly, I show Mendel’s work on developmental series are novel and important for its new ways of experimentation, conceputalisation, and analysis. Thirdly, I argue that Mendel’s laws of developmental information were not about heredity. (shrink)