Alan Love

Philosophical analyses of individuals in biology have focused on theories of individuality that derive from evolutionary theory, understood as a fundamental framework that governs all of biology. Less attention has been given to how individuals are determined in experimental practice. The author uses the problem agenda of growth in developmental biology to argue that individuation practices are guided by structured problems, which leads to variable and divergent conceptualizations of what qualifies as an individual. The result is a pluralist perspective on biological individuality in which different kinds of individuals are counted, compared, detected, or tracked in practice. The problem-relative nature of individuation dissolves the so-called problem of biological individuality and captures more accurately how biologists engage in successful practices that contribute to the manipulation, prediction, and explanation of biological individuals.

Many philosophers have explored the extensive use of non-universal generalizations in different sciences for inductive and explanatory purposes, analyzing properties such as how widely a generalization holds in space and time. In the present paper, we concentrate on developmental biology to distinguish and characterize two common approaches to scientific generalization—mechanism generalization and principle generalization. The former approach seeks detailed descriptions of causal relationships among specific types of biological entities that produce a characteristic phenomenon across some range of different biological entities; the latter approach abstractly describes relations or interactions that occur during ontogeny and are exemplified in a wide variety of different biological entities. These two approaches to generalization correspond to different investigative aims. Our analysis shows why each approach is sought in a research context, thereby accounting for how practices of inquiry are structured. It also diagnoses problematic assumptions in prior discussions, such as abstraction always being correlated positively with generalizations of wide scope.

James Griesemer has delivered groundbreaking analyses of evolutionary biology for four decades using a combination of historical, sociological, and philosophical tools. A primary area of interest has been the relationship between evolution and development. In “What Salamander Biologists Have Taught Us About Evo–Devo,” Griesemer explores David Wake’s taxon-based research for understanding evolutionary processes that was facilitated by a distinctive kind of multi-dimensional model (a model clade). By introducing new analytic categories, such as packages of problems and phenomena or the notion of selective export, Griesemer advances our comprehension of how biologists strategically generalize across different domains and levels of organization while keeping in view historical contingency, ultimately showing how multidisciplinary communities of inquiry mind the gap between development and evolution.

Philosophers and psychologists alike have long debated the etiology of beliefs about human agency. Recently, empirical investigations have shown that lay beliefs about free will and determinism represent stable and important individual differences. Despite a perennial interest in the sources of agentic belief, genetic and environmental influences on such beliefs have never been studied. We administered a battery of items assessing these beliefs to a unique sample of 394 adoptive and biological families with adult offspring to investigate the origins of agentic beliefs and their relationships. We found significant differences between adopted and biological offspring and between the parents of such children, particularly in beliefs about determinism. Biometric modeling revealed especially surprising results: unlike the vast majority of traits studied in family designs, agentic beliefs appear to be weakly or not at all heritable. Since genetic factors might be regarded as typical of the “initial conditions” in philosophical thought experiments about free will and determinism, it is especially ironic that beliefs about free will and determinism may be among the traits least influenced by genetic differences.

Scientists often rely on proxies when they identify or measure new or complex phenomena. However, these tools are frequently seen as epistemologically inferior because they are indirect and make it difficult to properly control for confounding factors. This view implies two methodological norms. First, if possible, proxies should be replaced with more direct and better-controlled tools. Second, if proxies cannot be replaced, they should be improved by increasing control over confounding factors. We evaluate this view by examining functional genomics, a field in which proxies are abundant. Analysing work from the largest contemporary initiative in functional genomics (ENCODE), we observe that researchers do not follow these methodological norms. Instead, they continue using the same proxies and even combine them to produce novel insights or measurements. This potentially paradoxical finding can be explained if we recognise that proxies have a “generativity” that is appreciated and leveraged by the researchers working with them. Proxies in functional genomics form a dynamic toolkit that equips researchers to discover unexpected insights and ask new questions. Our analysis thereby contributes to a better understanding of the epistemic roles that proxies play in scientific practice.

Evolutionary developmental biology (Evo-devo) is a loose conglomeration of research programs in the life sciences with two main axes: (a) the evolution of development, or inquiry into the pattern and processes of how ontogeny varies and changes over time; and, (b) the developmental basis of evolution, or inquiry into the causal impact of ontogenetic processes on evolutionary trajectories—both in terms of constraint and facilitation. Philosophical issues are found along both axes surrounding concepts such as evolvability, novelty, and modularity. The developmental basis of evolution has garnered much attention because it speaks to the possibility of revising a standard construal of evolutionary theory, but the evolution of development harbors its own conceptual questions. This article addresses the heterogeneity of Evo-devo’s conglomerate structure (including disagreements over its individuation), as well as the concepts and controversies of philosophical interest pertaining to the evolution of development and the developmental basis of evolution. Future research will benefit from a shift away from global theorizing toward the scientific practices of Evo-devo.

Multilevel research strategies characterize contemporary molecular inquiry into biological systems. We outline conceptual, methodological, and explanatory dimensions of these multilevel strategies in microbial ecology, systems biology, protein research, and developmental biology. This review of emerging lines of inquiry in these fields suggests that multilevel research in molecular life sciences has significant implications for philosophical understandings of explanation, modeling, and representation.

Many biologists and philosophers have worried that importing models of reasoning from the physical sciences obscures our understanding of reasoning in the life sciences. In this paper we discuss one example that partially validates this concern: part-whole reductive explanations. Biology and physics tend to incorporate different models of temporality in part-whole reductive explanations. This results from differential emphases on compositional and causal facets of reductive explanations, which have not been distinguished reliably in prior philosophical analyses. Keeping these two facets distinct facilitates the identifi cation of two further aspects of reductive explanation: intrinsicality and fundamentality. Our account provides resources for discriminating between different types of reductive explanation and suggests a new approach to comprehending similarities and differences in the explanatory reasoning found in biology and physics.

The intersection of development and evolution has always harbored conceptual issues, but many of these are on display in contemporary evolutionary developmental biology (evo-devo). These issues include: (1) the precise constitution of evo-devo, with its focus on both the evolution of development and the developmental basis of evolution, and how it fits within evolutionary theory; (2) the nature of evo-devo model systems that comprise the material of comparative and experimental research; (3) the puzzle of how to understand the widely used notion of 'conserved mechanisms'; (4) the definition of evolutionary novelties and expectations for how to explain them; and (5) the demand of interdisciplinary collaboration that derives from investigating complex phenomena at key moments in the history of life, such as the fin-limb transition. This Element treats these conceptual issues with close attention to both empirical detail and scientific practice to offer new perspectives on evolution and development. This title is also available as Open Access on Cambridge Core.

Although random mutation is central to models of evolutionary change, a lack of clarity remains regarding the conceptual possibilities for thinking about the nature and role of mutation in evolution. We distinguish several claims at the intersection of mutation, evolution, and directionality and then characterize a previously unrecognized category: complex conditioned mutation. Empirical evidence in support of this category suggests that the historically famous fluctuation test should be revisited, and new experiments should be undertaken with emerging experimental techniques to facilitate detecting mutation rates within specific loci at an ultra‐high, individual base pair resolution.

“To arrange in or analyse into classes according to shared qualities or characteristics; to make a formal or systematic classification” (OED). For many, classification provokes images of dull cataloging and arcane knowledge. However, in the eighteenth century it was neither dull nor arcane and had momentous import for natural philosophers and everyday individuals alike. Susannah Gibson has captured this expertly in her new book, and the subtitle accents the stakes: How Eighteenth-Century Science Disrupted the Natural Order. Although originating out of a doctoral dissertation, this is not a dense monograph. Instead, Gibson targets a wider academic audience using compelling vignettes in digestible chapters with compact endnotes and helpful suggestions for further reading. On the whole, the book is a success, though more illuminating in some places than others.

The inapplicability of variations on theory reduction in the context of genetics and their irrelevance to ongoing research has led to an anti-reductionist consensus in philosophy of biology. One response to this situation is to focus on forms of reductive explanation that better correspond to actual scientific reasoning (e.g. part–whole relations). Working from this perspective, we explore three different aspects (intrinsicality, fundamentality, and temporality) that arise from distinct facets of reductive explanation: composition and causation. Concentrating on these aspects generates new forms of reductive explanation and conditions for their success or failure in biology and other sciences. This analysis is illustrated using the case of protein folding in molecular biology, which demonstrates its applicability and relevance, as well as illuminating the complexity of reductive reasoning in a specific biological context

Nobody wants unnatural kinds. Just as we prefer all natural ingredients in our food, so also we prefer natural kinds in our ontology and epistemology. Philosophers contrast natural with merely “conventional” kinds, and scientists advocate for natural rather than artificial classification systems. A central plank of the desired naturalness is “mind independence”—the property of existing independent of human interests and desires. Natural kinds are discovered, not made. They reflect the structure of the world (“nature’s joints”) and for this reason justify the practice of inductive inference. Conventional kinds, by contrast, are dependent on human classificatory activities. They are created with an end in view and therefore lack “a real existence in nature” (J. S. Mill, A System of Logic, Ratiocinative and Inductive [London: Longmans, 1843], 1:165). Since their existence is dependent on human activities, nominal kinds need not track nature’s joints. Because scientists are interested in groupings that really exist in nature—not those fabricated for human purposes—their classificatory practices aim to achieve natural-kind classifications. Achieving these classifications is crucial to the success of science.

The concept of teleonomy has been attracting renewed attention recently. This is based on the idea that teleonomy provides a useful conceptual replacement for teleology, and even that it constitutes an indispensable resource for thinking biologically about purposes. However, both these claims are open to question. We review the history of teleological thinking from Greek antiquity to the modern period to illuminate the tensions and ambiguities that emerged when forms of teleological reasoning interacted with major developments in biological thought. This sets the stage for an examination of Pittendrigh’s (Adaptation, natural selection, and behavior. In: Roe A, Simpson GG (eds) Behavior and evolution. Yale University Press, New Haven, pp 390–416, 1958) introduction of “teleonomy” and its early uptake in the work of prominent biologists. We then explore why teleonomy subsequently foundered and consider whether the term may yet have significance for discussions of goal-directedness in evolutionary biology and philosophy of science. This involves clarifying the relationship between teleonomy and teleological explanation, as well as asking how the concept of teleonomy impinges on research at the frontiers of evolutionary theory.

Contributors: Sabina Leonelli Nancy J. Nersessian Michel Janssen Jacob G. Foster James A. Evans Mark A. Bedau Marshall Abrams Gilbert B. Tostevin Salikoko S. Mufwene Massimo Maiocchi Joseph D. Martin Paul E. Smaldino Claes Andersson Anton Törnberg Petter Törnberg Beyond the Meme assembles interdisciplinary perspectives on cultural evolution, providing a nuanced understanding of it as a process in which dynamic structures interact on different scales of size and time. The volume demonstrates how a thick understanding of change in culture emerges from multiple disciplinary vantage points, each of which is required to understand cultural evolution in all its complexity.

The ongoing debate about a “replication crisis” has put scientific failure in the spotlight, not only in psychological research and the social sciences but also in the life sciences. However, despite this increased salience of failure in research, the concept itself has so far received little attention in the literature (for an exception, see Ref. 1). The lack of a systematic perspective on scientific failure—a daily experience for researchers—hampers our understanding of this complex phenomenon and the development of efficient policies and measures to address it. Without a better grasp of the multiple dimensions of scientific failure, there is a risk that necessary measures will be neglected or that inadequate policies will be adopted because different kinds of failures require different responses. Developing a basic taxonomy of scientific failure will help to identify connections between different types of failures and benefit the formulation of policy measures for improving replicability.

John Bonner managed a long and productive career that balanced specialized inquiry into cellular slime molds with general investigations of big questions in evolutionary biology, such as the origins of multicellular development and the evolution of complexity. This commentary engages with his final paper (“The evolution of evolution”), which argues that the evolutionary process has changed through the history of life. In particular, Bonner emphasizes the possibility that natural selection plays different roles at different size scales. I identify some underlying assumptions in his argument and evaluate its cogency to both foster future discussion and emulate the intellectual example set by Bonner over a lifetime. This endeavor is important beyond Bonner's own theoretical disposition because similar issues are visible in controversies about the possibility of an extended evolutionary synthesis.

The fact that genes and environment contribute differentially to variation in human behaviors, traits and attitudes is central to the field of behavior genetics. Perceptions about these differential contributions may affect ideas about human agency. We surveyed two independent samples (N = 301 and N = 740) to assess beliefs about free will, determinism, political orientation, and the relative contribution of genes and environment to 21 human traits. We find that lay estimates of genetic influence on these traits cluster into four distinct groups, which differentially predict beliefs about human agency, political orientation, and religiosity. Despite apparent ideological associations with these beliefs, the correspondence between mean lay estimates and published heritability estimates for the surveyed traits is large (r = .77). Belief in genetic determinism emerges as a modest predictor of accuracy in these lay estimates. Additionally, educated mothers with multiple children emerge as particularly accurate in their estimates of the genetic contribution to these traits.

The concept of evolvability—the capacity of a population to produce and maintain evolutionarily relevant variation—has become increasingly prominent in evolutionary biology. Paleontology has a long history of investigating questions of evolvability, but paleontological thinking has tended to neglect recent discussions, because many tools used in the current evolvability literature are challenging to apply to the fossil record. The fundamental difficulty is how to disentangle whether the causes of evolutionary patterns arise from variational properties of traits or lineages rather than being due to selection and ecological success. Despite these obstacles, the fossil record offers unique and growing sources of data that capture evolutionary patterns of sustained duration and significance otherwise inaccessible to evolutionary biologists. Additionally, there exist a variety of strategic possibilities for combining prominent neontological approaches to evolvability with those from paleontology. We illustrate three of these possibilities with quantitative genetics, evolutionary developmental biology, and phylogenetic models of macroevolution. In conclusion, we provide a methodological schema that focuses on the conceptualization, measurement, and testing of hypotheses to motivate and provide guidance for future empirical and theoretical studies of evolvability in the fossil record.