Showing papers on "Philosophy of biology published in 2019"

Philosophy of Science : A Contemporary Introduction

Abstract: Preface 1 WHY PHILOSOPHY OF SCIENCE? The relationship between science and philosophy Scientific questions and questions about science Modern science as philosophy Understanding science and understanding Western civilization 2 THE NATURE OF SCIENTIFIC EXPLANATION AND THE PHILOSOPHICAL PROBLEMS IT RAISES Defining scientific explanation Why do laws explain? Counter-examples and the pragmatics of explanation Causation and explanation Explaining why and explaining how Conclusion 3 SCIENTIFIC THEORIES, EPISTEMOLOGY AND METAPHYSICS Hypothetico-deductivism The problem of theoretical terms and the things they name Theories and models The epistemology of scientific testing Underdetermination 4 THE CHALLENGE OF HISTORY AND SOCIOLOGY OF SCIENCE A place for history? No place for first philosophy? From philosophy to history to relativism Could the earth really be flat? Bibliography Index

The meanings of 'function' in biology and the problematic case of de novo gene emergence.

Abstract: The word function has many different meanings in molecular biology. Here we explore the use of this word (and derivatives like functional) in research papers about de novo gene birth. Based on an analysis of 20 abstracts we propose a simple lexicon that, we believe, will help scientists and philosophers discuss the meaning of function more clearly.

What Biological Functions Are and Why They Matter

Abstract: The biological functions debate is a perennial topic in the philosophy of science. In the first full-length account of the nature and importance of biological functions for many years, Justin Garson presents an innovative new theory, the 'generalized selected effects theory of function', which seamlessly integrates evolutionary and developmental perspectives on biological functions. He develops the implications of the theory for contemporary debates in the philosophy of mind, the philosophy of medicine and psychiatry, the philosophy of biology, and biology itself, addressing issues ranging from the nature of mental representation to our understanding of the function of the human genome. Clear, jargon-free, and engagingly written, with accessible examples and explanatory diagrams to illustrate the discussion, his book will be highly valuable for readers across philosophical and scientific disciplines.

O Organism, Where Art Thou? Old and New Challenges for Organism-Centered Biology.

Abstract: This paper addresses theoretical challenges, still relevant today, that arose in the first decades of the twentieth century related to the concept of the organism. During this period, new insights into the plasticity and robustness of organisms as well as their complex interactions fueled calls, especially in the UK and in the German-speaking world, for grounding biological theory on the concept of the organism. This new organism-centered biology (OCB) understood organisms as the most important explanatory and methodological unit in biological investigations. At least three theoretical strands can be distinguished in this movement: Organicism, dialectical materialism, and (German) holistic biology. This paper shows that a major challenge of OCB was to describe the individual organism as a causally autonomous and discrete unit with consistent boundaries and, at the same time, as inextricably interwoven with its environment. In other words, OCB had to conciliate individualistic with anti-individualistic perspectives. This challenge was addressed by developing a concept of life that included functionalist and metabolic elements, as well as biochemical and physical ones. It allowed for specifying organisms as life forms that actively delimit themselves from the environment. Finally, this paper shows that the recent return to the concept of the organism, especially in the so-called “Extended Evolutionary Synthesis,” is challenged by similar anti-individualistic tendencies. However, in contrast to its early-twentieth-century forerunner, today’s organism-centered approaches have not yet offered a solution to this problem.

Philosophical bias is the one bias that science cannot avoid.

Abstract: Scientists seek to eliminate all forms of bias from their research. However, all scientists also make assumptions of a non-empirical nature about topics such as causality, determinism and reductionism when conducting research. Here, we argue that since these 'philosophical biases' cannot be avoided, they need to be debated critically by scientists and philosophers of science.

Reciprocal Causation and the Extended Evolutionary Synthesis

Abstract: Kevin Laland and colleagues have put forward a number of arguments motivating an extended evolutionary synthesis. Here I examine Laland et al.'s central concept of reciprocal causation. Reciprocal causation features in many arguments supporting an expanded evolutionary framework, yet few of these arguments are clearly delineated. Here I clarify the concept and make explicit three arguments in which it features. I identify where skeptics can—and are—pushing back against these arguments, and highlight what I see as the empirical, explanatory, and methodological issues at stake.

Measurement in biology is methodized by theory

Abstract: We characterize access to empirical objects in biology from a theoretical perspective. Unlike objects in current physical theories, biological objects are the result of a history and their variations continue to generate a history. This property is the starting point of our concept of measurement. We argue that biological measurement is relative to a natural history which is shared by the different objects subjected to the measurement and is more or less constrained by biologists. We call symmetrization the theoretical and often concrete operation which leads to considering biological objects as equivalent in a measurement. Last, we use our notion of measurement to analyze research strategies. Some strategies aim to bring biology closer to the epistemology of physical theories, by studying objects as similar as possible, while others build on biological diversity.

Immunology and individuality.

Abstract: Immunology and philosophy have a rich history of dialogue. Immunologists have long been influenced by ideas from philosophy, notably the concept of 'self', and many philosophers have explored the conceptual, theoretical and methodological foundations of immunology. Here, I discuss two aspects of this dialogue: biological individuality and immunogenicity.

A metaphysical approach to holobiont individuality: Holobionts as emergent individuals

Abstract: Holobionts are symbiotic assemblages composed by a host plus its microbiome. The status of holobionts as individuals has recently been a subject of continuous controversy, which has given rise to two main positions: on the one hand, holobiont advocates argue that holobionts are biological individuals; on the other, holobiont detractors argue that they are just mere chimeras or ecological communities, but not individuals. Both parties in the dispute develop their arguments from the framework of the philosophy of biology, in terms of what it takes for a “conglomerate” to be considered an interesting individual from a biological point of view. However, the debates about holobiont individuality have important ontological implications that have remained vaguely explored from a metaphysical framework. The purpose of this paper is to cover that gap by presenting a metaphysical approach to holobionts individuality. Drawing upon a conception of natural selection that puts the focus on the transgenerational recurrence of the traits and that supports the thesis that holobionts are units of selection, we argue that holobionts bear emergent traits and exert downward powers over the entities that compose them. In this vein, we argue, a reasonable argument can be made for conceiving holobionts as emergent biological individuals.

There Are No Ahistorical Theories of Function

Abstract: Theories of function are conventionally divided up into historical and ahistorical ones. Proponents of ahistorical theories often cite the ahistoricity of their accounts as a major virtue. Here, I argue that none of the mainstream “ahistorical” accounts are actually ahistorical. All of them embed, implicitly or explicitly, an appeal to history. In Boorse’s goal-contribution account, history is latent in the idea of statistical-typicality. In the propensity theory, history is implicit in the idea of a species’ natural habitat. In the causal role theory, history is required for making sense of dysfunction. I elaborate some consequences for the functions debate.

The Creativity of Natural Selection? Part II: The Synthesis and Since.

Abstract: This is the second of a two-part essay on the history of debates concerning the creativity of natural selection, from Darwin through the evolutionary synthesis and up to the present. In the first part, I focussed on the mid-late nineteenth century to the early twentieth, with special emphasis on early Darwinism and its critics, the self-styled “mutationists.” The second part focuses on the evolutionary synthesis and some of its critics, especially the “neutralists” and “neo-mutationists.” Like Stephen Gould, I consider the creativity of natural selection to be a key component of what has traditionally counted as “Darwinism.” I argue that the creativity of natural selection is best understood in terms of (1) selection initiating evolutionary change, and (2) selection directing evolutionary change, for example by creating the variation that it subsequently acts upon. I consider the respects in which both of these claims sound non-Darwinian, even though they have long been understood by supporters and critics alike to be virtually constitutive of Darwinism.

Health, ecology and the microbiome.

Abstract: Advances in microbiomics have changed the way in which many researchers think about health and disease. These changes have also raised a number of philosophical questions around these topics, such as the types of living systems to which these concepts can be applied. Here, I discuss the human microbiome from two perspectives: the first treats the microbiome as part of a larger system that includes the human; the second treats the microbiome as an independent ecosystem that provides services to humans. Drawing on the philosophy of medicine and ecology, I explore two questions: i) how can we make sense of disease and dysfunction in these two perspectives? ii) are these two perspectives complimentary or do they compete with each other?

Between biology and chemistry in the Enlightenment: how nutrition shapes vital organization. Buffon, Bonnet, C.F. Wolff.

Abstract: This paper seeks to characterize how the study of nutrition processes contributed to revisit the problem of vital organization in the late eighteenth century. It argues that focusing on nutrition leads to reformulate the problem of the relation between life and organization in terms of processes, rather than static or given structures. This nutrition-centered approach to life amounts to acknowledge the specific strategic role nutrition played in the development of a materialist approach to the generation of vital organization. The paper proposes a clarification of the multiple meanings of the concept of organization in the context of Enlightenment physiology and nascent biology, before focusing on the century long analogy between nutrition and generation. It shows how, by contrasting different uses of this analogy, nutrition was employed as a key vital phenomenon in the development of epigenetic theories of generation, i.e. how a nutritive modeling of generation was used in the undermining of preformationism. To this purpose I contrast two seemingly opposite theories of generation, Buffon’s and Bonnet’s, and show that despite the obvious metaphysical discontent, their views of generation share a common mechanical conceptual frame in which nutrition is conflated with growth and repair. I then turn to the role nutrition played in the epigenetic conception of generation in C. F. Wolff’s embryology and analyze this rival understanding of nutrition as an organizing process.

The Modern Synthesis: Theoretical or Institutional Event?

Abstract: This paper surveys questions about the nature of the Modern Synthesis as a historical event : was it rather theoretical than institutional? When and where did it actually happen? Who was involved? It argues that all answers to these questions are interrelated, and that systematic sets of answers define specific perspectives on the Modern Synthesis that are all complementary.

Life, time, and the organism: temporal registers in the construction of life forms

Abstract: In this paper we articulate how time and temporalities are involved in the making of living things. For these purposes, we draw on an instructive episode concerning Norfolk Horn sheep. We attend to historical debates over the nature of the breed, whether it is extinct or not, and whether presently living exemplars are faithful copies of those that came before. We argue that there are features to these debates that are important to understanding contemporary configurations of life, time, and the organism, especially as these are articulated within the field of synthetic biology. In particular, we highlight how organisms are configured within different material and semiotic assemblages that are always structured temporally. While we identify three distinct structures, namely the historical, phyletic, and molecular registers, we do not regard the list as exhaustive. We also highlight how these structures are related to the care and value invested in the organisms at issue. Finally, because we are interested ultimately in ways of producing time, our subject matter requires us to think about historiographical practice reflexively. This draws us into dialogue with other scholars interested in time, not just historians, but also philosophers and sociologists, and into conversations with them about time as always multiple and never an inert background.

Race and reference

Abstract: The biological race debate is at an impasse Issues surrounding hereditarianism aside, there is little empirical disagreement left between race naturalists and anti-realists about biological race The disagreement is now primarily semantic This would seem to uniquely qualify philosophers to contribute to the biological race debate However, philosophers of race are reluctant to focus on semantics, largely because of their worries about the ‘flight to reference’ In this paper, I show how philosophers can contribute to the debate without taking the flight to reference Drawing on the theory of reference literature and the history of meaning change in science, I develop some criteria for dealing with cases where there is uncertainty about reference I then apply these criteria to the biological race debate All of the criteria I develop for eliminating putative kinds are met in the case of ‘race’ as understood by twentieth century geneticist Theodosius Dobzhansky and his contemporary proponents, suggesting that we should eliminate it from our biological ontology

Ancient Genetics to Ancient Genomics:Celebrity and Credibility in Data-Driven Practice

Abstract: “Ancient DNA Research” is the practice of extracting, sequencing, and analyzing degraded DNA from dead organisms that are hundreds to thousands of years old. Today, many researchers are interested in adapting state-of-the-art molecular biological techniques and high-throughput sequencing technologies to optimize the recovery of DNA from fossils, then use it for studying evolutionary history. However, the recovery of DNA from fossils has also fueled the idea of resurrecting extinct species, especially as its emergence corresponded with the book and movie Jurassic Park in the 1990s. In this paper, I use historical material, interviews with scientists, and philosophical literature to argue that the search for DNA from fossils can be characterized as a data-driven and celebrity-driven practice. Philosophers have recently argued the need to seriously consider the role of data-driven inquiry in the sciences, and likewise, this history highlights the need to seriously consider the role of celebrity in shaping the kind of research that gets pursued, funded, and ultimately completed. On this point, this history highlights that the traditional philosophical and scientific distinctions between data-driven and hypothesis-driven research are not always useful for understanding the process and practice of science. Consequently, I argue that the celebrity status of a particular research practice can be considered as a “serious epistemic strategy” that researchers, as well as editors and funders, employ when making choices about their research and publication processes. This interplay between celebrity and methodology matters for the epistemology of science.

Realization in biology

Abstract: It is widely assumed that functional and dispositional properties are not identical to their physical base, but that there is some kind of asymmetrical ontological dependence between them. In this regard, a popular idea is that the former are realized by the latter, which, under the non-identity assumption, is generally understood to be a non-causal, constitutive relation. In this paper we examine two of the most widely accepted approaches to realization, the so-called 'flat view' and the 'dimensioned view', and we analyze their explanatory relevance in the light of a number of examples from the life sciences, paying special attention to developmental phenomena. Our conclusion is that the emphasis placed by modern-day biology on such properties as variability, evolvability, and a whole collection of phenomena like modularity, robustness, and developmental constraint or developmental bias requires the adoption of a much more dynamic perspective than traditional realization frameworks are able to capture.

Characterizing causality in cancer.

Abstract: Philosophers have explored the concept of causality for centuries. Here we argue that ideas about causality from philosophy can help scientists to better understand how cancerous tumors grow and spread in the body. After outlining six characteristics of causality that are relevant to cancer, we emphasize the importance of feedback loops and interactions between tumor-cell-intrinsic and tumor-cell-extrinsic factors for explaining the formation and dissemination of tumors.

From Biological Determination to Entangled Causation.

Abstract: Biologists and philosophers often use the language of determination in order to describe the nature of developmental phenomena. Accounts in terms of determination have often been reductionist. One common idea is that DNA is supposed to play a special explanatory role in developmental explanations, namely, that DNA is a developmental determinant. In this article we try to make sense of determination claims in developmental biology. Adopting a manipulationist approach, we shall first argue that the notion of developmental determinant is causal. We suggest that two different theses concerning developmental determination can be articulated: determination of occurrence and structural determination. We shall argue that, while the first thesis is problematic, the second, opportunely qualified, is feasible. Finally, we shall argue that an analysis of biological causation in terms of determination cannot account for entangled dynamics. Characterising causal entanglement as a particular kind of interactive causation whereby difference-making causes ascribable to different levels of biological organisation influence a particular ontogenetic outcome, we shall, via two illustrative examples, diagnose some potential limits of a reductionist, molecular and intra-level understanding of biological causation.

Is Psychopathy a Harmful Dysfunction

Abstract: In their paper “Is psychopathy a mental disease?”, Thomas Nadelhoffer and Walter Sinnott-Armstrong have argued that according to any plausible account of mental disorder, neural and psychological abnormalities correlated with psychopathy should be regarded as signs of a mental disorder. I oppose this conclusion by arguing that at least on a naturalistically grounded account, such as Wakefield’s ‘Harmful Dysfunction’ view, currently available empirical data and evolutionary considerations indicate that psychopathy is not a mental disorder.

Animal Behavior, Population Biology and the Modern Synthesis (1955–1985)

Abstract: This paper examines the history of animal behavior studies after the synthesis period. Three episodes are considered: the adoption of the theory of natural selection, the mathematization of ideas, and the spread of molecular methods in behavior studies. In these three episodes, students of behavior adopted practices and standards developed in population ecology and population genetics. While they borrowed tools and methods from these fields, they made distinct uses (inclusive fitness method, evolutionary theory of games, emphasis on individual selection) that set them relatively apart and led them to contribute, in their own way, to evolutionary theory. These episodes also highlight some limitations of “conjunction narratives” centered on the relation between a discipline and the modern synthesis. A trend in conjunction narratives is to interpret any development related to evolution in a discipline as an “extension,” an “integration,” or as a “delayed” synthesis. I here suggest that this can lead to underestimate discontinuities in the history of evolutionary biology.

Pluralization through epistemic competition: scientific change in times of data-intensive biology

Abstract: We present two case studies from contemporary biology in which we observe conflicts between established and emerging approaches. The first case study discusses the relation between molecular biology and systems biology regarding the explanation of cellular processes, while the second deals with phylogenetic systematics and the challenge posed by recent network approaches to established ideas of evolutionary processes. We show that the emergence of new fields is in both cases driven by the development of high-throughput data generation technologies and the transfer of modeling techniques from other fields. New and emerging views are characterized by different philosophies of nature, i.e. by different ontological and methodological assumptions and epistemic values and virtues. This results in a kind of conflict we call "epistemic competition" that manifests in two ways: On the one hand, opponents engage in mutual critique and defense of their fundamental assumptions. On the other hand, they compete for the acceptance and integration of the knowledge they provide by a broader scientific community. Despite an initial rhetoric of replacement, the views as well as the respective audiences come to be seen as more clearly distinct during the course of the debate. Hence, we observe-contrary to many other accounts of scientific change-that conflict results in the formation of new niches of research, leading to co-existence and perceived complementarity of approaches. Our model thus contributes to the understanding of the pluralization of the scientific landscape.

In What Sense Can There Be Evolution by Natural Selection Without Perfect Inheritance

Abstract: In Darwinian Population and Natural Selection, Peter Godfrey-Smith brought the topic of natural selection back to the forefront of philosophy of biology, highlighting different issues surrounding t...

El otro lado de la filosofía de la biología: una problematización de lo epistemológico como límite disciplinar

Abstract: The objective of this article is to problematize the assumption that the philosophy of biology constitutes a discipline limited to the epistemological analysis. To this end, the characteristics of a type of parallel analysis, carried out by more and more philosophers of biology, will be deepened: that which takes biological knowledge as a starting point to analyze philosophical problems. Throughout this development, the gnoseological parallels of these two types of analysis will be contemplated, and they will be put in relation with the criticisms of the philosophical assumption of a human exceptionality, made by the french philosopher Jean-Marie Schaeffer.

Code Biology, Peircean Biosemiotics, and Rosen’s Relational Biology

Abstract: The classical theories of the genetic code (the stereochemical theory and the coevolution theory) claimed that its coding rules were determined by chemistry—either by stereochemical affinities or by metabolic reactions—but the experimental evidence has revealed a totally different reality: it has shown that any codon can be associated with any amino acid, thus proving that there is no necessary link between them. The rules of the genetic code, in other words, obey the laws of physics and chemistry but are not determined by them. They are arbitrary, or conventional, rules. The result is that the genetic code is not a metaphorical entity, as implied by the classical theories, but a real code, because it is precisely the presence of arbitrary rules that divides a code from all other natural processes. In the past 20 years, furthermore, various independent discoveries have shown that many other organic codes exist in living systems, which means that the genetic code has not been an isolated case in the history of life. These experimental facts have one outstanding theoretical implication: they imply that in addition to the concept of information we must introduce in biology the concept of meaning, because we cannot have codes without meaning or meaning without codes. The problem is that at present we have two different theoretical frameworks for that purpose: one is Code Biology, where meaning is the result of coding, and the other is Peircean biosemiotics, where meaning is the result of interpretation. Recently, however, a third party has entered the scene, and it has been proposed that Robert Rosen’s relational biology can provide a bridge between Code Biology and Peircean biosemiotics.

The agent concept is a scientific tool : Samir Okasha: Agents and goals in evolution. Oxford: Oxford University Press, 2018, xiv+254pp, £30.00 HB

Abstract: Funding: European Research Council (grant 771387 ) and the Natural Environment Research Council (grant NE/K009524/1).

How Biological Technology Should Inform the Causal Selection Debate

Abstract: Waters’s (2007) actual difference making and Weber’s (2013, 2017) biological normality 6 approaches to causal selection have received many criticisms, some of which miss their tar7 get. Disagreement about whether Waters’s and Weber’s views succeed in providing criteria 8 that uniquely single out the gene as explanatorily significant in biology has led philosophers 9 to overlook a prior problem. Before one can address whether Waters’s and Weber’s views 10 successfully account for the explanatory significance of genes, one must ask whether either 11 view satisfactorily meets the necessary conditions for causal selection in the first place. An 12 adequate defense of causal selection must meet two desiderata. First, there must be an ex13 planatory property that sets some causes apart from others. Second, the property identified 14 must be one that is recognized by biologists as relevant to their domain(s) of inquiry. I argue 15 that both fall short of meeting the second condition. I demonstrate this by showing how 16 many of the biological technologies crucial to experimentation do not fit either view very 17 well. I offer a more adequate proposal that accommodates non-actual and artificial causal 18 variables. A consequence of my view is the following: When analyzing the causal selection 19 practices of biologists, philosophers should consider the explanatory targets relevant to a 20 research program—including ones whose explanans must appeal to biological technologies. 21 I then explain how this proposal can inform the existing debate between Weber (2017) and 22 Griffiths et al. (2015). 23