Karola Stotz

(1963 - 2019)

Everyone has heard of ‘epigenetics’, but the term means different things to different researchers. Four important contemporary meanings are outlined in this paper. Epigenetics in its various senses has implications for development, heredity, and evolution, and also for medicine. Concerning development, it cements the vision of a reactive genome strongly coupled to its environment. Concerning heredity, both narrowly epigenetic and broader ‘exogenetic’ systems of inheritance play important roles in the construction of phenotypes. A thoroughly epigenetic model of development and evolution was Waddington’s aim when he introduced the term ‘epigenetics’ in the 1940s, but it has taken the modern development of molecular epigenetics to realize this aim. In the final sections of the paper we briefly outline some further implications of epigenetics for medicine and for the nature/nurture debate.

In their considered reviews both Thomas Pradeu and Lindell Bromham introduce important topics not sufficiently covered in our book. Pradeu asks us to enlarge on the epigenetic and ecological context of genes, particularly in the form of symbioses. We use the relationship between eukaryotes and their symbiotic organisms as a welcome opportunity to clarify our concept of the developmental niche, and its relationship to the developmental system. Bromham’s comments reveal that she is primarily interested in identifying macroevolutionary patterns. From her vantage point eco-evo-devo, the study of phenotypic plasticity, epigenetic and exogenetic inheritance, have not yet demonstrated the need for any revolutionary change in evolutionary thought. For us they highlight the extent to which proximate developmental mechanisms can inform ultimate biology

In the past century, nearly all of the biological sciences have been directly affected by discoveries and developments in genetics, a fast-evolving subject with important theoretical dimensions. In this rich and accessible book, Paul Griffiths and Karola Stotz show how the concept of the gene has evolved and diversified across the many fields that make up modern biology. By examining the molecular biology of the 'environment', they situate genetics in the developmental biology of whole organisms, and reveal how the molecular biosciences have undermined the nature/nurture distinction. Their discussion gives full weight to the revolutionary impacts of molecular biology, while rejecting 'genocentrism' and 'reductionism', and brings the topic right up to date with the philosophical implications of the most recent developments in genetics. Their book will be invaluable for those studying the philosophy of biology, genetics and other life sciences.

The interventionist account of causation offers a criterion to distinguish causes from non-causes. It also aims at defining various desirable properties of causal relationships, such as specificity, proportionality and stability. Here we apply an information-theoretic approach to these properties. We show that the interventionist criterion of causation is formally equivalent to non-zero specificity, and that there are natural, information-theoretic ways to explicate the distinction between potential and actual causal influence. We explicate the idea that the description of causes should be proportional to that of their effects. Then we draw a distinction between two ideas in the existing literature, the range of invariance of a causal relationship and its stability. The range of invariance is related to specificity and range of causal values. Stability concerns the effect of additional variables on the relationship between some focal pair of cause and effect variables. We show how to distinguish and measure the direct influence of background variables on the effect variable, and their influence on the relationship between the focal cause and the effect variable. Finally, we discuss the limitations of the information-theoretic approach, and offer prospects for complementary approaches.

Several authors have argued that causes differ in the degree to which they are ‘specific’ to their effects. Woodward has used this idea to enrich his influential interventionist theory of causal explanation. Here we propose a way to measure causal specificity using tools from information theory. We show that the specificity of a causal variable is not well-defined without a probability distribution over the states of that variable. We demonstrate the tractability and interest of our proposed measure by measuring the specificity of coding DNA and other factors in a simple model of the production of mRNA.

Integrating the study of human diversity into the human evolutionary sciences requires substantial revision of traditional conceptions of a shared human nature. This process may be made more difficult by entrenched, 'folkbiological' modes of thought. Earlier work by the authors suggests that biologically naive subjects hold an implicit theory according to which some traits are expressions of an animal's inner nature while others are imposed by its environment. In this paper, we report further studies that extend and refine our account of this aspect of folkbiology. We examine biologically naive subjects' judgments about whether traits of an animal are 'innate', 'in its DNA' or 'part of its nature'. Subjects do not understand these three descriptions to be equivalent. Both innate and in its DNA have the connotation that the trait is species-typical. This poses an obstacle to the assimilation of the biology of polymorphic and plastic traits by biologically naive audiences. Researchers themselves may not be immune to the continuing pull of folkbiological modes of thought.

Obesity is the focus of multiple lines of inquiry that have -- together and separately -- produced many deep insights into the physiology of weight gain and maintenance. We examine three such streams of research and show how they are oriented to obesity intervention through multilevel integrated approaches. The first research programme is concerned with the genetics and biochemistry of fat production, and it links metabolism, physiology, endocrinology and neurochemistry. The second account of obesity is developmental and draws together epigenetic and environmental explanations that can be embedded in an evolutionary framework. The third line of research focuses on the role of gut microbes in the production of obesity, and how microbial activities interact with host genetics, development and metabolism. These interwoven explanatory strategies are driven by an orientation to intervention, both for experimental and therapeutic outcomes. We connect the integrative and intervention-oriented aspects of obesity research through a discussion of translation, broadening the concept to capture the dynamic, iterative processes of scientific practice and therapy development. This system-oriented analysis of obesity research expands the philosophical scrutiny of contemporary developments in the biosciences and biomedicine, and has the potential to enrich philosophy of science and medicine.

Obesity is the focus of multiple lines of inquiry that have -- together and separately -- produced many deep insights into the physiology of weight gain and maintenance. We examine three such streams of research and show how they are oriented to obesity intervention through multilevel integrated approaches. The first research programme is concerned with the genetics and biochemistry of fat production, and it links metabolism, physiology, endocrinology and neurochemistry. The second account of obesity is developmental and draws together epigenetic and environmental explanations that can be embedded in an evolutionary framework. The third line of research focuses on the role of gut microbes in the production of obesity, and how microbial activities interact with host genetics, development and metabolism. These interwoven explanatory strategies are driven by an orientation to intervention, both for experimental and therapeutic outcomes. We connect the integrative and intervention-oriented aspects of obesity research through a discussion of translation, broadening the concept to capture the dynamic, iterative processes of scientific practice and therapy development. This system-oriented analysis of obesity research expands the philosophical scrutiny of contemporary developments in the biosciences and biomedicine, and has the potential to enrich philosophy of science and medicine.

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

The linear sequence specification of a gene product is not provided by the target DNA sequence alone but by the mechanisms of gene expressions. The main actors of these mechanisms, proteins and functional RNAs, relay environmental information to the genome with important consequences to sequence selection and processing. This `postgenomic' reality has implications for our understandings of development not as predetermined by genes but as an epigenetic process. Critics of genetic determinism have long argued that the activity of `genes' and hence their contribution to the phenotype depends on intra- and extraorganismal `environmental' elements. As will be shown here, even the mere physical existence of a `gene' is dependent on its phenotypic context.

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.

The Narrow Evolutionary Psychology Movement represents itself as a major reorientation of the social/behavioral sciences, a group of sciences previously dominated by something called the ‘Standard Social Science Model’. Narrow Evolutionary Psychology alleges that the SSSM treated the mind, and particularly those aspects of the mind that exhibit cultural variation, as devoid of any marks of its evolutionary history. Adherents of Narrow Evolutionary Psychology often suggest that the SSSM owed more to ideology than to evidence. It was the child of the 1960s, representing a politically motivated insistence on the possibility of changing social arrangements such as gender roles: " ‘Not so long ago jealousy was considered a pointless, archaic institution in need of reform. But like other denials of human nature from the 1960s, this bromide has not aged well.’ ) " This view of history does not ring true to those, like the authors, who have worked in traditions of evolutionary theorizing about the mind that have a continuous history through the 1960s and beyond: traditions such as evolutionary epistemology and psychoevolutionary research into emotion (Griffiths

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.

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.

Recent years have seen the development of an approach both to general philosophy and philosophy of science often referred to as ‘experimental philosophy’ or just ‘X-Phi’. Philosophers often make or presuppose empirical claims about how people would react to hypothetical cases, but their evidence for claims about what ‘we’ would say is usually very limited indeed. Philosophers of science have largely relied on their more or less intimate knowledge of their field of study to draw hypothetical conclusions about the state of scientific concepts and the nature of conceptual change in science. What they are lacking is some more objective quantitative data supporting their hypotheses. A growing number of philosophers , along with a few psychologists and anthropologists, have tried to remedy this situation by designing experiments aimed at systematically exploring people’s reactions to philosophically important thought experiments or scientists’ use of their scientific concepts. Many of the results have been surprising and some of the conclusions drawn from them have been more than a bit provocative. This symposium attempts to provide a window into this new field of philosophical inquiry and to show how experimental philosophy provides crucial tools for the philosopher and encourages two-way interactions between scientists and philosophers.Keywords: Experimental philosophy; Naturalism; Continuity thesis; Philosophy of science; Quantitative data

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.

In the last decade it has become en vogue for cognitive comparative psychologists to study animal behavior in an ‘integrated’ fashion to account for both the ‘innate’ and the ‘acquired’. We will argue that these studies, instead of really integrating the concepts of ‘nature’ and ‘nurture’, rather cement this old dichotomy. They combine empty nativist interpretation of behavior systems with blatantly environmentalist explanations of learning. We identify the main culprit as the failure to take development seriously. While in some areas of biology interest in the relationship between behavior and development has surged through topics such as extragenetic inheritance, niche construction, and phenotypic plasticity, this has gone almost completely unnoticed in the study of animal behavior in comparative psychology, and is frequently ignored in ethology too. The main aims of this paper are to clarify the relationship between the concepts of learning, experience, and development, and to investigate whether and how all three concepts can be usefully deployed in the study of animal behavior. This will require the full integration of the psychological study of behavior into biology, and of the idea of learning into a wider concept of experience. We lay out how, in a systems view of development, learning may just appear as one among many processes in which experience influences behavior. This new synthesis should help to overcome the age-old dualism between innate and acquired. It thereby opens up the possibility of developing scientifically more fruitful distinctions.

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

The historian Raphael Falk has described the gene as a ‘concept in tension’ (Falk 2000) – an idea pulled this way and that by the differing demands of different kinds of biological work. Several authors have suggested that in the light of contemporary molecular biology ‘gene’ is no more than a handy term which acquires a specific meaning only in a specific scientific context in which it occurs. Hence the best way to answer the question ‘what is a gene’, and the only way to provide a truly philosophical answer to that question is to outline the diversity of conceptions of the gene and the reasons for this diversity. In this essay we draw on the extensive literature in the history of biology to explain how the concept has changed over time in response to the changing demands of the biosciences . Finally, we outline some of the conceptions of the gene current today. The seeds of change are implicit in many of those current conceptions and the future of the gene concept looks set to be at as turbulent as the past.