We often hear how scientists have discovered that a certain human trait – or a trait of another type of organism – is innate, genetic, heritable, inherited, naturally selected etc. All these claims have something in common: they all declare a trait to have significant organism internal (for instance genetic) causes that are present in the organism at its birth. I call claims like these “nativist claims”. Nativist claims are important. They shape our overall understanding of what we are, what (...) we can do and what is good for us. They also impact our practical decision making. For instance, we know that certain types of genes increase the risk of certain diseases, and increasingly this has an effect on healthcare practices. Many people believe that in the matter of children’s education we should consider the fact that many cognitive abilities are highly heritable. Associations between genetics and aggressive behavior have been taken to be alleviating circumstances in criminal sentencing. It is therefore important to correctly understand the content and implications of nativist claims. In this doctoral thesis I analyze, by philosophical means, the content of different kinds of nativist claim. What does it mean that some psychological tendency is innate? What does it mean that intelligence is 50% heritable? How (if at all) do genes come to carry information about the traits of an organism – they are nothing like the information carriers familiar to us, such as newspapers, e-mails, secret codes, and audio files. This thesis emphasizes two things. Firstly, I demonstrate, that in different scientific contexts these words ('innate', 'genetically caused' etc.) can mean very different things. Therefore, the implications of a given nativist claim in one scientific context can be remarkably different from another nativist claim’s implications in some other scientific context. Secondly, I explain how the development of innate, heritable and genetically caused traits can be determined in different and often unexpected ways by our environment and experiences. I demonstrate that the content of a concept that is considered innate by cognitive scientists can be determined by what the organism that possesses the concept has experienced. I also show that even a trait which is 100% heritable can at the same time be a socially constructed trait. (shrink)

In this article, we discuss epistemological limitations relating to the use of ethnoracial categories in biomedical research as devised by the Office of Management and Budget’s institutional guidelines. We argue that the obligation to use ethnoracial categories in genomics research should be abandoned. First, we outline how conceptual imprecision in the definition of ethnoracial categories can generate epistemic uncertainty in medical research and practice. Second, we focus on the use of ethnoracial categories in medical genetics, particularly genomics-based precision medicine, where (...) ethnoracial identity is understood as a proxy for medically relevant differences among individuals. Notably, extensive criticisms have been made already against the genetic interpretation of races, but, nonetheless, the concept of race remains a key element of contemporary genomics. This motivates us to explore possible reasons why such criticisms may have been ineffective in redirecting attention to other (non-race-based) ways of controlling for human variability. We contend that popular arguments against the idea that human races have a genetic basis, though convincing in many respects, are not sufficient to exclude the pragmatic use of race and ethnicity as proxies for genetic variability related to complex phenotypes. Finally, we provide two further arguments to support the idea that ethnoracial categories are unlikely to provide meaningful insights into medical genetics, which implies that even the interpretation of race as a useful tool to stratify disease risk is unwarranted. (shrink)

Most psychological research aims to uncover generalizations about the mind that hold across subjects. Philosophical discussions of scientific explanation have focused on such generalizations, but in doing so, have often overlooked an important phenomenon: variation. Variation is ubiquitous in psychology and many other domains, and an important target of explanation in its own right. Here I characterize explananda that concern individual differences and formulate an account of what it takes to explain them. I argue that the notion of actual difference (...) making, the only causal concept in the literature that explicitly addresses variation, cannot be used to ground such an account. Instead, I propose a view on which explaining individual differences involves identifying causes that could be intervened on to reduce the variability in the population. This account provides criteria of success for explaining variation and deepens our understanding of causal explanation. (shrink)

Recent trends in psychiatry involve a transition from categorical to dimensional frameworks, in which the boundary between health and pathology is understood as a difference in degree rather than as a difference in kind. A major tenet of dimensional approaches is that no qualitative distinction can be made between health and pathology. As a consequence, these approaches tend to characterize such a threshold as pragmatic or conventional in nature. However, dimensional approaches to psychopathology raise several epistemological and ontological issues. First, (...) we review major sources of evidence usually recruited in support of the dimensional trend (focusing on clinical observation and biological data), and we show that these are connected to different conceptualizations of how dimensional traits extend across health and pathology. Second, we criticize two unquestioned assumptions that stand at the core of the dimensional trend: a) that there is continuity from health to pathology at the symptomatic level; b) that such continuity reflects an underlying continuity in the genetic liability for pathological conditions. Third, we argue against the idea of a conventional threshold by showing that such a view implies a linear relationship between the genotype and the phenotype. Fourth, drawing on epigenetics and developmental biology, we offer a characterization of mental disorders as stable and dynamic constellations of multi-level variables that differ qualitatively from ‘healthy states’. We conclude by showing that our account has several theoretical advantages over both categorical and dimensional approaches. Notably, it provides crucial insights into psychological development over time and individual differences, with major implications in terms of intervention and clinical decision-making. (shrink)

Organoids and organs-on-a-chip are currently the two major families of 3D advanced organotypic in vitro culture systems, aimed at reconstituting miniaturized models of physiological and pathological states of human organs. Both share the tenets of the so-called “three-dimensional thinking”, a Systems Physiology approach focused on recapitulating the dynamic interactions between cells and their microenvironment. We first review the arguments underlying the “paradigm shift” toward three-dimensional thinking in the in vitro culture community. Then, through a historically informed account of the technical (...) affordances and the epistemic commitments of these two approaches, we highlight how they embody two distinct experimental cultures. We finally argue that the current systematic effort for their integration requires not only innovative “synergistic” engineering solutions, but also conceptual integration between different perspectives on biological causality. (shrink)

This paper introduces the reconstitutor as a comprehensive unit of heredity within the context of evolutionary research. A reconstitutor is the structure resulting from a set of relationships between different elements or processes that are actively involved in the recreation of a specific phenotypic variant in each generation regardless of the biomolecular basis of the elements or whether they stand in a continuous line of ancestry. Firstly, we justify the necessity of introducing the reconstitutor by showing the limitations of other (...) evolutionary conceptions of the unit of heredity, such as the replicator, the reproducer, and the Darwinian individual. We argue that these conceptions are based on the requirement of lineage formation, which we argue to be unnecessary for the existence of evolutionary heredity. In the second part, we introduce the reconstitutor, which we base on the concept of Stability of Traits, and illustrate how it covers cases of hereditary phenomena not covered by the previous accounts. Secondly, we illustrate how the reconstitutor could serve as a platform to rethink ecological inheritance and other forms of inheritance that have been recently introduced under the song/singer model of evolution. (shrink)

Causation has multiple distinct meanings in genetics. One reason for this is meaning slippage between two concepts of the gene: Mendelian and molecular. Another reason is that a variety of genetic methods address different kinds of causal relationships. Some genetic studies address causes of traits in individuals, which can only be assessed when single genes follow predictable inheritance patterns that reliably cause a trait. A second sense concerns the causes of trait differences within a population. Whereas some single genes can (...) be said to cause population-level differences, most often these claims concern the effects of many genes. Polygenic traits can be understood using heritability estimates, which estimate the relative influences of genetic and environmental differences to trait differences within a population. Attempts to understand the molecular mechanisms underlying polygenic traits have been developed, although causal inference based on these results remains controversial. Genetic variation has also recently been leveraged as a randomizing factor to identify environmental causes of trait differences. This technique—Mendelian randomization—offers some solutions to traditional epidemiological challenges, although it is limited to the study of environments with known genetic influences. (shrink)

Recent studies demonstrating epigenetic and developmental sensitivity to early environments, as exemplified by fields like the Developmental Origins of Health and Disease (DOHaD) and environmental epigenetics, are bringing new data and models to bear on debates about race, genetics, and society. Here, we first survey the historical prominence of models of environmental determinism in early formulations of racial thinking to illustrate how notions of direct environmental effects on bodies have been used to naturalize racial hierarchy and inequalities in the past. (...) Next, we conduct a scoping review of postgenomic work in environmental epigenetics and DOHaD that looks at the role of race/ethnicity in human health (2000–2021). Although there is substantial heterogeneity in how race is conceptualized and interpreted across studies, we observe practices that may unwittingly encourage typological thinking, including: using DNA methylation as a novel marker of racial classification; neglect of variation and reversibility within supposedly homogenous racial groups; and a tendency to label and reify whole groups as pathologized or impaired. Even in the very different politico-economic and epistemic context of contemporary postgenomic science, these trends echo deeply held beliefs in Western thinking which claimed that different environments shape different bodies and then used this logic to argue for essential differences between Europeans and non-Europeans. We conclude with a series of suggestions on interpreting and reporting findings in these fields that we feel will help researchers harness this work to benefit disadvantaged groups while avoiding the inadvertent dissemination of new and old forms of stigma or prejudice. (shrink)

The identity and the existence of genes has been challenged by postgenomic discoveries. Specifically, the consideration of molecular and cellular phenomena in which genes are embedded has proved relevant for their understanding. In response to these challenges, I will argue that the complexity of genetic phenomena supports the weak emergence of genes from the DNA. In Section 2, I will expose what genes are taken to be in the postgenomic world. In Section 3, I will present the relevant account of (...) emergence. I consider weak emergence as in Franklin and Knox, for which a phenomenon is emergent when it displays novelty and robustness. In Section 4, I will argue that genes are weakly emergent since they are novel, improving explanations, and robust in respect to some perturbations. Then, I will conclude in Section 5 that genes’ emergence is a way to allow genes’ flexibility and context dependency, without compromising their existence. (shrink)

According to the standard model of cosmology, Λ\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\Lambda $$\end{document}CDM, the mass-energy budget of the current stage of the universe is not dominated by the luminous matter that we are familiar with, but instead by some form of dark matter (and dark energy). It is thus tempting to adopt scientific realism about dark matter. However, there are barely any constraints on the myriad of possible properties of this entity—it is not even certain (...) that it is a form of matter. In light of this underdetermination I advocate caution: we should not (yet) be dark matter realists. The “not(-yet)-realism” that I have in mind is different from Hacking’s (Philos Sci 56 (4), 555–581, 1989) anti-realism, in that it is semantic rather than epistemological. It also differs from the semantic anti-realism of logical empiricism, in that it is naturalistic, such that it may only be temporary and does not automatically apply to all other unobservables (or even just to all other astronomical unobservables, as with Hacking’s anti-realism). The argument is illustrated with the analogy of the much longer history of the concept of a gene, as the current state of the concept of dark matter resembles in some relevant ways that of the early concept of genes. (shrink)

The rapid development of CRISPR-based gene editing has been accompanied by a polarized governance debate about the status of CRISPR-edited crops as genetically modified organisms. This article argues that the polarization around the governance of gene editing partly reflects a failure of public engagement with the current state of research in genomics and postgenomics. CRISPR-based gene-editing technology has become embedded in a narrow narrative about the ease and precision of the technique that presents the gene as a stable object under (...) technological control. By tracing the considerably destabilized scientific understanding of the gene in genomics and postgenomics, this article highlights that this publicly mediated ontology strategically avoids positioning the “ease of CRISPR-based editing” in the wider context of the “complexity of the gene.” While this strategic narrowness of CRISPR narratives aims to create public support for gene-editing technologies, we argue that it stands in the way of socially desirable anticipatory governance and open public dialogue about societal promises and the unintended consequences of gene editing. In addressing the polarization surrounding CRISPR-based editing technology, the article emphasizes the need for engagement with the complex state of postgenomic science that avoids strategic simplifications of the scientific literature in promoting or opposing the commercial use of the gene-editing technology. (shrink)

The Frame Problem is the problem of how one can design a machine to use information so as to behave competently, with respect to the kinds of tasks a genuinely intelligent agent can reliably, effectively perform. I will argue that the way the Frame Problem is standardly interpreted, and so the strategies considered for attempting to solve it, must be updated. We must replace overly simplistic and reductionist assumptions with more sophisticated and plausible ones. In particular, the standard interpretation assumes (...) that mental processes are identical to certain kinds of computational processes, and so solving the Frame Problem is a matter of finding a computational architecture that can effectively represent relations of semantic relevance. Instead, we must take seriously the possibility that the way in which intelligent agents use information is inherently different. Whereas intelligent agents are plausibly genuinely causally sensitive to semantic properties as such (to what they perceive, desire, believe intend, etc.), computational systems can only be causally sensitive to the formal features that represent these properties. Indeed, it is this very substitution of formal generalizations for genuinely semantic ones that is responsible for the way current AI systems are brittle, inflexible, and highly specialized. What we need is a more sophisticated way of investigating the relationship between computational information processing and genuinely semantic information use, so that these two senses of using information are not conflated, but instead the question of how they are related to one another can be studied directly. I apply the generative methodology I have developed elsewhere for cognitive science and AI research (Miracchi, 2017, 2019a) to show how the Frame Problem can be appropriately updated. (shrink)

In this dissertation, I address the question of how to construct scientific theories of emotions that are both conceptually sound and empirically fruitful. To do this, I offer an analysis of the main challenges scientific theories of emotions face, and I propose a meta-theoretical framework to construct scientific concepts of emotions as explications of folk emotion concepts. Part I discusses the main challenges theories of emotions in psychology and neuroscience encounter. The first states that a proper scientific theory of emotions (...) must explain all and only the phenomena under the vernacular term ‘emotion’ with a common set of conceptual resources and under an overarching generic concept of emotion. The second demands that each emotion category corresponds to well-coordinated sets of neural, physiological, and behavioral patterns of responses. I argue that none of the best contemporary theories of emotions in psychology and neuroscience overcomes these challenges. As a result, a new theory of emotions is required. In Part II, I develop the meta-theoretical framework to construct a theory of emotions that overcomes the challenges above. First, I propose a pluralistic account of scientific kinds based on different patterns of projection that various disciplines may take to justify inductive inferences. These are essentialist, historical, and social patterns. Each of these patterns provides a framework to construct different types of scientific concepts. I argue that among the frameworks for scientific kinds available, the one that is best suited to explicate emotion concepts is a functional framework. Consequently, I conclude by recommending scientists pursue functionalist theories of emotions over essentialist, historical, or social theories. (shrink)

One of the defining features of the classical gene was its position. In molecular genetics, positions are defined instead as nucleotide numbers and there is no clear correspondence with its classical counterpart. However, the classical gene position did not simply disappear with the development of the molecular approach, but survived in the lab associated to different genetic practices. The survival of classical gene position would illustrate Waters’ view about the practical persistence of the genetic approach beyond reductionism and anti-reductionist claims. (...) We show instead that at the level of laboratory practices there are also reductive processes, operating through the rise and fall of different techniques. Molecular markers made the concept of classical gene position practically dispensable, leading us to rethink whether it had any causal role or was just a mere heuristic. (shrink)

Our technological lifeworld has become an info-computational media populated by data and algorithms, an artificial environment for life and shared experiences. In this chapter, I tried to sketch three new assumptions for bioethics – it is hardly possible to substantiate ethical guidelines or an idea of normativity in an aprioristic manner; moral status is a function of data entities, not something solely human; agency is plural and thus is shared or sometimes delegated – in order to chart a proposal for (...) a posthuman bioethics. Posthuman is perhaps not the best expression available, but it covers the idea of a shift from a world centered on self-contained and exclusively human agency to a more comprehensive and relational way of thinking. The “posthuman” label should be understood as a rebuttal of biocentrism and anthropocentrism by moving closer to conceptions we encounter in population ethics or in discourse about biosocial and technical systems. Posthuman bioethics is “environmentalist” without losing the humanistic stance. The question regarding how suitable an infocentric bioethics is in practice remains to be settled. The moral principles in bioethics could be reconceived as relying on these new assumptions, in a postindividualistic manner that accepts formal primacy of causal digital artifacts in affording actions in a world of ambient algorithmic intelligence. (shrink)

This paper challenges the common assumption that some phenotypic traits are quantitative while others are qualitative. The distinction between these two kinds of traits is widely influential in biological and biomedical research as well as in scientific education and communication. This is probably due to both historical and epistemological reasons. However, the quantitative/qualitative distinction involves a variety of simplifications on the genetic causes of phenotypic variability and on the development of complex traits. Here, I examine three cases from the life (...) sciences that show inconsistencies in the distinction: Mendelian traits, Mendelian diseases, and polygenic mental disorders. I show that these traits can be framed both quantitatively and qualitatively depending, for instance, on the methods through which they are investigated and on specific epistemic purposes. This suggests that the received view of quantitative and qualitative traits has a limited heuristic power—limited to some local contexts or to the specific methodologies adopted. Throughout the paper, I provide directions for framing phenotypes beyond the quantitative/qualitative distinction. I conclude by pointing at the necessity of developing a principled characterisation of what phenotypic traits, in general, are. (shrink)

The interventionist account provides us with several notions permitting the qualification of causal relationships. In recent years, there has been a push toward formalizing these notions using information theory. In this paper, I discuss one of them, namely causal specificity. The notion of causal specificity is ambiguous as it can refer to at least two different concepts. After having presented these, I show that current attempts to formalize causal specificity in information theoretic terms have mostly focused on one of these (...) two concepts. I then propose and apply a new information-theoretic measure which captures the other concept. (shrink)

Bourrat and Griffiths :33, 2018) have recently argued that most of the evidence presented by holobiont defenders to support the thesis that holobionts are evolutionary individuals is not to the point and is not even adequate to discriminate multispecies evolutionary individuals from other multispecies assemblages that would not be considered evolutionary individuals by most holobiont defenders. They further argue that an adequate criterion to distinguish the two categories is fitness alignment, presenting the notion of fitness boundedness as a criterion that (...) allows divorcing true multispecies evolutionary individuals from other multispecies assemblages and provides an adequate criterion to single out genuine evolutionary multispecies assemblages. A consequence of their criterion is that holobionts, as conventionally defined by hologenome defenders, are not evolutionary individuals except in very rare cases, and for very specific host-symbiont associations. This paper is a critical response to Bourrat and Griffiths’ arguments and a defence of the arguments presented by holobiont defenders. Drawing upon the case of the hologenomic basis of the evolution of sanguivory in vampire bats, I argue that Bourrat and Griffiths overlook some aspects of the biological nature of the microbiome that justifies the thesis that holobionts are evolutionarily different to other multispecies assemblages. I argue that the hologenome theory of evolution should not define the hologenome as a collection of genomes, but as the sum of the host genome plus some traits of the microbiome which together constitute an evolutionary individual, a conception I refer to as the stability of traits conception of the hologenome. Based on that conception I argue that the evidence presented by holobiont defenders is to the point, and supports the thesis that holobionts are evolutionary individuals. In this sense, the paper offers an account of the holobiont that aims to foster a dialogue between hologenome advocates and hologenome critics. (shrink)

Metaphysical investigation often proceeds by way of linguistic meaning. This tradition relies on an assumption about meanings, namely that they can be given in terms of referential relations and truth. Chomsky and others have illustrated the difficulty with this externalist hypothesis regarding natural language meanings, which implies that natural languages are ill‐suited for the purposes of metaphysical investigation. In reply to this discordance between the features of natural languages and the goals of metaphysical investigation, metaphysicians propose that we look to (...) the invented languages used to express our best scientific theories as metaphysical guides, in the hope that these languages are better behaved. I argue that this retreat is beset with similar troubles for the metaphysician. In particular, I argue that central terms in the field of biology, namely ‘gene’ and ‘species’, exhibit a kind of lexical flexibility that renders them, much like their natural language counterparts, ill‐suited for the metaphysician's aims. (shrink)

The philosophical problem of personal identity has been widely discussed in contemporary analytic philosophy. The disputes over identity throughout time abound in references to thought experiments, excluding any connection to practical problems or to scientific knowledge and biotechnological practices. Nevertheless, some real cases challenge the pure metaphysical formulation of the problem and also show how science has an indubitable impact on the issue of identity. I will discuss the case of approximately 500 children who were appropriated during the most recent (...) Argentinian dictatorship (1976–1983), as well as their restitution thanks to Abuelas de Plaza de Mayo’s fight and certain genetics outcomes. I will examine an alleged notion of genetic identity thought to have stemmed from the restitution phenomenon; and I will argue against some criticisms to that notion departing from contemporary philosophy of biology and philosophy of science. Particularly, I will discuss if a genetic stance of personal individual identity can be considered as supported by contemporary biological knowledge; and if a pluralistic perspective on scientific practice that appraises the role of values allows us to maintain the reference to DNA regarding identity but overcoming aforementioned criticisms. (shrink)

Binding specificity is a centrally important concept in molecular biology, yet it has received little philosophical attention. Here I aim to remedy this by analyzing binding specificity as a causal property. I focus on the concept’s role in drug design, where it is highly prized and hence directly studied. From a causal perspective, understanding why binding specificity is a valuable property of drugs contributes to an understanding of causal selection—of how and why scientists distinguish between causes, not just causes from (...) noncauses. In particular, the specificity of drugs is precisely what underwrites their value as experimental interventions on biological processes. (shrink)

We develop a conceptual framework that connects biological heredity and organization. We refer to heredity as the cross-generation conservation of functional elements, defined as constraints subject to organizational closure. While hereditary objects are functional constituents of biological systems, any other entity that is stable across generations—and possibly involved in the recurrence of phenotypes—belongs to their environment. The central outcome of the organizational perspective consists in extending the scope of heredity beyond the genetic domain without merging it with the broad category (...) of cross-generation stability. After discussing some implications, we conclude with a reflection on the relationship between stability and variation. 1Introduction2From Extended Heredity to Cross-generation Stability 2.1Extending the scope of heredity: A brief state of the art2.2Rethinking heredity: Conceptual challenges3Biological Heredity in Light of Organization 3.1Biological organization within organisms and beyond3.2Extending organization in time3.3What is biological heredity?4Implications and Objections 4.1Heredity as a specific kind of cross-generation stability4.2Heredity at various levels of description4.3Non-functional and dysfunctional objects5Conclusions: From Conservation to Variation. (shrink)

A crucial question for a process view of life is how to identify a process and how to follow it through time. The genidentity view can contribute decisively to this project. It says that the identity through time of an entity X is given by a well-identified series of continuous states of affairs. Genidentity helps address the problem of diachronic identity in the living world. This chapter describes the centrality of the concept of genidentity for David Hull and proposes an (...) extension of Hull’s view to the ubiquitous phenomenon of symbiosis. Finally, using immunology as a key example, it shows that the genidentity view suggests that the main interest of a process approach is epistemological rather than ontological and that its principal claim is one of priority, namely that processes precede and define things, and not vice versa. (shrink)

Recently, several critics of the multiple realizability thesis have argued that philosophers have tended to accept the thesis on too weak grounds. On the one hand, the analytic challenge has problematized how philosophers have treated the multiple realization relation itself, claiming that assessment of the sameness of function and the relevant difference of realizers has been uncritical. On the other hand, it is argued that the purported evidence of the thesis is often left empirically unverified. This paper provides a novel (...) strategy to answer these worries by introducing a role for multiple realizability in the context of biological engineering. In the field of synthetic biology, bioengineers redesign the evolutionary realizations of biological functions, even constructing artificial chemical surrogates in the laboratory. I show how in the rational design approach to biological engineering, multiple realizability can function as a design heuristic in which the sameness of function and difference of realizers can be controlled. Although practically motivated, this engineering approach has also a theoretical, exploratory component that can be used to study the empirical limitations of multiple realizability. Successful realization of the engineering designs would amount to a concrete demonstration of multiple realizability, taking evidence for MRT beyond what is readily found in nature. (shrink)

These preprints were automatically compiled into a PDF from the collection of papers deposited in PhilSci-Archive in conjunction with the PSA 2018.

“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)

Heritability estimates obtained from genome-wide association studies are much lower than those of traditional quantitative methods. This phenomenon has been called the “missing heritability problem.” By analyzing and comparing GWAS and traditional quantitative methods, we first show that the estimates obtained from the latter involve some terms other than additive genetic variance, while the estimates from the former do not. Second, GWAS, when used to estimate heritability, do not take into account additive epigenetic factors transmitted across generations, while traditional quantitative (...) methods do. Given these two points we show that the missing heritability problem can largely be dissolved. (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)

Kyle Stanford has recently given substance to the problem of unconceived alternatives, which challenges the reliability of inference to the best explanation (IBE) in remote domains of nature. Conjoined with the view that IBE is the central inferential tool at our disposal in investigating these domains, the problem of unconceived alternatives leads to scientific anti-realism. We argue that, at least within the biological community, scientists are now and have long been aware of the dangers of IBE. We re-analyze the nineteenth-century (...) study of inheritance and development (Stanford’s case study) and extend it into the twentieth century, focusing in particular on both classical Mendelian genetics and the studies by Avery et al. on the chemical nature of the hereditary substance. Our extended case studies show the preference of the biological community for a different methodological standard: the vera causa ideal, which requires that purported causes be shown on non-explanatory grounds to exist and be competent to produce their effects. On this basis, we defend a prospective realism about the biological sciences. (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)

Griffiths and Russell D. Gray (1994, 1997, 2001) have argued that the fundamental unit of analysis in developmental systems theory should be a process – the life cycle – and not a set of developmental resources and interactions between those resources. The key concepts of developmental systems theory, epigenesis and developmental dynamics, both also suggest a process view of the units of development. This chapter explores in more depth the features of developmental systems theory that favour treating processes as fundamental (...) in biology and examines the continuity between developmental systems theory and ideas about process in the work of several major figures in early 20th century biology, most notable C.H Waddington. (shrink)

The biological sciences have always proven a fertile ground for philosophical analysis, one from which has grown a rich tradition stemming from Aristotle and flowering with Darwin. And although contemporary philosophy is increasingly becoming conceptually entwined with the study of the empirical sciences with the data of the latter now being regularly utilised in the establishment and defence of the frameworks of the former, a practice especially prominent in the philosophy of physics, the development of that tradition hasn’t received the (...) wider attention it so thoroughly deserves. This review will briefly introduce some recent significant topics of debate within the philosophy of biology, focusing on those whose metaphysical themes (in everything from composition to causation) are likely to be of wide-reaching, cross-disciplinary interest. (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)

In this chapter we examine the relationship between biological information, the key biological concept of specificity, and recent philosophical work on causation. We begin by showing how talk of information in the molecular biosciences grew out of efforts to understand the sources of biological specificity. We then introduce the idea of ‘causal specificity’ from recent work on causation in philosophy, and our own, information theoretic measure of causal specificity. Biological specificity, we argue, is simple the causal specificity of certain biological (...) processes. This, we suggest, means that causal relationships in biology are ‘informational’ relationships simply when they are highly specific relationships. Biological information can be identified with the storage, transmission and exercise of biological specificity. It has been argued that causal relationships should not be regarded as informational relationship unless they are ‘arbitrary’. We argue that, whilst arbitrariness is an important feature of many causal relationships in living systems, it should not be used in this way to delimit biological information. Finally, we argue that biological specificity, and hence biological information, is not confined to nucleic acids but distributed among a wide range of entities and processes. (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)

The present thesis explores some metaphysical issues concerning biochemical kinds and the relations between chemical and biological properties and phenomena. The main result of this thesis is that there is something sui generis about biochemical kinds. This result is motivated by two theoretical steps. The first is characterising biochemical functions as weakly emergent from the chemical structure [Chapter 3, Chapter 6]. The second is via an account for which biochemical kinds are natural categories [Chapter 4, Chapter 7]. The thesis comprises (...) four parts. Part I [Chapter 1, Chapter 2] aims to offer the methodological and conceptual tools that underpin this research. Chapter 1 presents the debate on the unity of science and the motivation of the research. Chapter 2 presents the account of natural kinds that will be used throughout the thesis. Part II [Chapter 3, Chapter 4] offers a detailed metaphysical analysis of the molecular gene. Chapter 3 argues that molecular genes are weakly emergent from nucleic acids. Chapter 4 argues that the category "molecular gene" can be deemed a natural kind, following the account presented in Chapter 2. Part III [Chapter 5, Chapter 6, Chapter 7] explores some of the themes related to biochemical kinds and generalises some of the results from Part II. Chapter 5 considers biochemical functions and how functional attribution should be interpreted for biochemical molecules. Chapter 6 considers the relation between biochemical functions and structure, spelt in terms of weak emergence and explores unity in biochemistry. Chapter 7 considers the topic of biochemical kinds per se and argues that biochemical kinds are natural categories. Part IV [Chapter 8] elucidates the main outcome and the implications that this research can have for future discussion in the philosophy and metaphysics of biochemistry and the unity of science. (shrink)

What is a gene? Does it represent a natural kind, or is it just a tool for genomics? A clear answer to these questions has been challenged by postgenomic discoveries. In response, I will argue that the gene can be deemed a natural kind as it satisfies some requirements for genuine kindhood. Specifically, natural kinds are projectible categories in our best scientific theories, and they represent nodes in the causal network of the world (as in Khalidi. Natural Categories and Human (...) Kinds: Classification in the Natural and Social Sciences. Cambridge University Press, Cambridge, 2013; Khalidi. Synthese 195: 1379–1396, 2018; Khalidi. Are Sexes Natural Kinds, In: Dasgupta S, Weslake B (eds) Current Controversies in Philoso-phy of Science. Routledge, New York, 2020; Khalidi. Philos Sci 88:1–21, 2021). In Sect. 2, I will present a brief history of the gene and the controversy over its status. In Sect. 3, I will introduce the account of natural kinds considered in this paper. In Sect. 4, I will first present the relevant definition of genes and how they can be classified. Then, I will argue that the gene can be considered a natural kind as it satisfies the criteria for natural kindhood. Section 5 concludes. (shrink)

The concept of causal specificity is drawing considerable attention from philosophers of biology. It became the rationale for rejecting (and occasionally, accepting) a thesis of causal parity of developmental factors. This literature assumes that attributing specificity to causal relations is at least in principle a straightforward (if not systematic) task. However, the parity debate in philosophy of biology seems to be stuck at a point where it is not the biological details that will help move forward. In this paper, I (...) take a step back to reexamine the very idea of causal specificity and its intended role in the parity dispute in philosophy of biology. I contend that the idea of causal specificity across variations as currently discussed in the literature is irreducibly twofold in nature: it is about two independent components that are not mutually entailed. I show this to be the source of prior complications with the notion of specificity itself that ultimately affect the purposes for which it is often invoked, notably to settle the parity dispute. (shrink)

A number of biologists and philosophers have noted the diversity of interpretations of evolvability in contemporary evolutionary research. Different clusters of research defined by co-citation patterns or shared methodological orientation sometimes concentrate on distinct conceptions of evolvability. We examine five different activities where the notion of evolvability plays conceptual roles in evolutionary biological investigation: setting a research agenda, characterization, explanation, prediction, and control. Our analysis of representative examples demonstrates how different conceptual roles of evolvability are quasi-independent and yet exhibit important (...) relationships across scientific activities. It also provides us with the resources to detail two distinct strategies for how evolvability can help to synthesize disparate areas of research and thereby potentially serve as a unifying concept in evolutionary biology. (shrink)

This article sets the stage for a genealogy of the postgenomic body. It starts with the current transformative views of epigenetics and microbiomics to offer a more pluralistic history in which the ethical problem of how to live with a permeable body – that is plasticity as a form of life – is pervasive in traditions pre-dating and coexisting with modern biomedicine (particularly humoralism in its several ramifications). To challenge universalizing narratives, I draw on genealogical method to illuminate the unequal (...) distribution of plasticity across gender and ethnic groups. Finally, after analysing postgenomics as a different thought-style to genomics, I outline some of its implications for notions of plasticity. I argue that postgenomic plasticity is neither a modernistic plasticity of instrumental control of the body nor a postmodernist celebration of endless potentialities. It is instead closer to an alter-modernistic view that disrupts clear boundaries between openness and determination, individual and community. (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)

Biologists and philosophers of science have recently called for an extension of evolutionary theory. This so-called ‘extended evolutionary synthesis’ seeks to integrate developmental processes, extra-genetic forms of inheritance, and niche construction into evolutionary theory in a central way. While there is often agreement in evolutionary biology over the existence of these phenomena, their explanatory relevance is questioned. Advocates of EES posit that their perspective offers better explanations than those provided by ‘standard evolutionary theory’. Still, why this would be the case (...) is unclear. Usually, such claims assume that EES’s superior explanatory status arises from the pluralist structure of EES, its different problem agenda, and a growing body of evidence for the evolutionary relevance of developmental phenomena. However, what is usually neglected in this debate is a discussion of what the explanatory standards of EES actually are, and how they differ from prevailing standards in SET. In other words, what is considered to be a good explanation in EES versus SET? To answer this question, we present a theoretical framework that evaluates the explanatory power of different evolutionary explanations of the same phenomena. This account is able to identify criteria for why and when evolutionary explanations of EES are better than those of SET. Such evaluations will enable evolutionary biology to find potential grounds for theoretical integration. (shrink)

Current debates about the integration of traditional and academic ecological knowledge struggle with a dilemma of division and assimilation. On the one hand, the emphasis on differences between traditional and academic perspectives has been criticized as creating an artificial divide that brands TEK as “non-scientific” and contributes to its marginalization. On the other hand, there has been increased concern about inadequate assimilation of Indigenous and other traditional perspectives into scientific practices that disregards the holistic nature and values of TEK. The (...) aim of this article is to develop a practice-based account of the epistemic relations between TEK and AEK that avoids both horns of the dilemma. While relations between TEK and AEK are often described in terms of the “holistic” nature of the former and the “mechanistic” character of the latter, we argue that a simple holism–mechanism divide misrepresents the epistemic resources of both TEK and AEK. Based on the literature on mechanistic explanations in philosophy of science, we argue that holders of TEK are perfectly capable of identifying mechanisms that underlie ecological phenomena while AEK often relies on non-mechanistic strategies of dealing with ecological complexity. Instead of generic characterizations of knowledge systems as either mechanistic or holistic, we propose to approach epistemic relations between knowledge systems by analyzing their heuristics in practice. (shrink)

This is an introduction to a collection of articles on the conceptual history of epigenesis, from Aristotle to Harvey, Cavendish, Kant and Erasmus Darwin, moving into nineteenth-century biology with Wolff, Blumenbach and His, and onto the twentieth century and current issues, with Waddington and epigenetics. The purpose of the topical collection is to emphasize how epigenesis marks the point of intersection of a theory of biological development and a theory of active matter. We also wish to show that the concept (...) of epigenesis existed prior to biological theorization and that it continues to permeate thinking about development in recent biological debates. (shrink)