Darwin’s classic ‘Origin of Species’ (Darwin 1859) described forces of selection acting upon individuals, but there remains a great deal of controversy about what exactly the status and definition of a biological individual is. Recently some authors have argued that the individual is dispensable – that an inability to pin it down is not problematic because little rests on it anyway. The aim of this paper is to show that there is a real problem of biological individuality, and an urgent (...) need to arbitrate over the current plethora of solutions to it. (shrink)

This article examines the revisionist role that current debates and philosophical positions on extended cognition might play for the historian of science, and uses as its case study August Kekulé’s formulation of the benzene molecule’s structure, including the dreams that Kekulé reported as the origin of his model. It builds on the notion of engaging philosophical positions through the historiography of nineteenth-century chemistry, but also examines some of the implications of the history of science for extended cognition. While an extended (...) cognition approach to Kekulé’s use of graphics and visual materials is promising, I argue that there is less usefulness for the idea of collective cognition. Instead I advocate using detailed historical studies to test theories of extended cognition. (shrink)

I begin by arguing that a consistent general naturalism must be understood in terms of methodological maxims rather than metaphysical doctrines. Some specific maxims are proposed. I then defend a generalized naturalism from the common objection that it is incapable of accounting for the normative aspects of human life, including those of scientific practice itself. Evolutionary naturalism, however, is criticized as being incapable of providing a sufficient explanation of categorical moral norms. Turning to the epistemological norms of science itself, particularly (...) those governing the empirical testing of specific models, I argue that these should be regarded as conditional rather than categorical and that, as such, can be given a naturalistic justification. The justification, however, is more cognitive than evolutionary. The historical development of science is found to be a better place for applying evolutionary ideas. After briefly considering the possibility of a naturalistic understanding of mathematics and logic, I turn to the problem of reconciling scientific realism with an evolutionary picture of scientific development. The solution, I suggest, is to understand scientific knowledge as being “perspectival” rather than absolutely objective. I first argue that scientific observation, whether by humans or instruments, is perspectival. This argument is extended to scientific theorizing which is regarded not as the formulation of universal laws of nature but as the construction of principles to be used in the construction of models to be applied to specific natural systems. The application of models, however, is argued to be not merely opportunistic but constrained by the methodological presumption that we live in a world with a definite causal structure even though we can understand it only from various perspectives. (shrink)

Exploring whether clades can reproduce leads to new perspectives on general accounts of biological development and individuation. Here we apply James Griesemer's general account of reproduction to clades. Griesemer's account of reproduction includes a requirement for development, raising the question of whether clades may bemeaningfully said to develop. We offer two illustrative examples of what clade development might look like, though evaluating these examples proves difficult due to the paucity of general accounts of development. This difficulty, however, is instructive about (...) what a general account of development should look like and how it may usefully be applied to research problems (further suggesting a means for evaluating general accounts of development). Reproduction also requires individuation of parent and offspring. We argue that there is no special problem of individuating older and younger clades. The vagaries involved with determining when clades begin, mature, and end are precisely the same as those that arise when the same questions are asked of cells, organisms, or species. Though the question of clade reproduction and selection may still be open, the process of discovery presents new insights into old problems. (shrink)

The theory of evolution by natural selection is, perhaps, the crowning intellectual achievement of the biological sciences. There is, however, considerable debate about which entity or entities are selected and what it is that fits them for that role. This article aims to clarify what is at issue in these debates by identifying four distinct, though often confused, concerns and then identifying how the debates on what constitute the units of selection depend to a significant degree on which of these (...) four questions a thinker regards as central. (shrink)

I argue that four of the fundamental claims of those calling themselves `genic pluralists'Philip Kitcher, Kim Sterelny, and Ken Watersare defective. First, they claim that once genic selectionism is recognized, the units of selection problems will be dissolved. Second, Sterelny and Kitcher claim that there are no targets of selection. Third, Sterelny, Kitcher, and Waters claim that they have a concept of genic causation that allows them to give independent genic causal accounts of all selection processes. I argue that each (...) one of these claims is either false or misleading. Moreover, the challenge that arises from the availability of genic causal accounts, namely, the inability to choose on rational grounds among genic and higher-level accounts, is unsupported. (shrink)

I analyze the importance of parts in the style of biological theorizing that I call compositional biology. I do this by investigating various aspects, including partitioning frames and explanatory accounts, of the theoretical perspectives that fall under and are guided by compositional biology. I ground this general examination in a comparative analysis of three different disciplines with their associated compositional theoretical perspectives: comparative morphology, functional morphology, and developmental biology. I glean data for this analysis from canonical textbooks and defend the (...) use of such texts for the philosophy of science. I end with a discussion of the importance of recognizing formal and compositional biology as two genuinely different ways of doing biology – the differences arising more from their distinct methodologies than from scientific discipline included or natural domain studied. Ultimately, developing a translation manual between the two styles would be desirable as they currently are, at times, in conflict. (shrink)

In this paper, I will conduct three interrelated analyses. First, I will develop an analysis of various concepts in the history of biology that used to refer to individual-level phenomena but were then reinterpreted by the Modern Synthesis in terms of populations. Second, I argue that a similar situation can be found in contemporary biological theory. While different approaches reflect on the causal role of developing organisms in evolution, proponents of the Modern Synthesis avoid any substantial change by reinterpreting and (...) explaining individual-level phenomena from a population perspective. Finally, I will approach this debate by advocating the statistical reading of natural selection, which holds that explanations by natural selection are statistical. I will argue that the above historical conceptual reinterpretations belong to a new explanatory strategy developed by the Modern Synthesis based on population thinking. The reinterpretation of concepts at the individual level is part of the explanatory framework of the Modern Synthesis and the empty role of development within this framework. Moreover, the statistical perspective adopted here allows for the integration of two explanatory models: population-statistical and individual-causal. Finally, I will argue that this pluralistic framework can help to define the explanatory scope of the different biological approaches in order to achieve a coherent integration of development into evolution without rejecting population thinking. (shrink)

Theoreticians that defend a form of realism regarding natural kinds minimally entertain the belief that the world features divisions into kinds and that the natural kind concept is a useful tool for philosophy of science. The objective of this paper is to challenge these assumptions. First, we challenge realism toward natural kinds by showing that the main arguments for their existence, which rely on the epistemic success of natural kinds, are unsatisfactory. Second, we show that, whether they exist or not, (...) natural kinds are expendable when it comes to describing and analyzing scientific explanations accurately. (shrink)

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

In recent years, the explanatory term “scaffold” has been gaining prominence in evolutionary biology. This notion has a long history in other areas, in particular, developmental psychology. In this paper, we connect these two traditions and identify a specific type of explanatory strategy shared between them, namely scaffolding explanations. We offer a new definition of “scaffold” anchored in the explanatory practices of evolutionary biologists and developmental psychologists that has yet to be clearly articulated. We conclude by offering a systematic overview (...) of the various dimensions of scaffolding explanations that further suggests both their usefulness and range of application. (shrink)

A theoretical framework is provided to explore teleonomy as a problem of self-causation, distinct from upward, downward and reticulate causation. Causality theories in biology are often formulated within hierarchy theories, where causation is conceptualized as running up or down the rungs of a ladder-like hierarchy or, more recently, as moving between multiple hierarchies. Research on the genealogy of cosmologies demonstrates that in addition to hierarchy theories, causality theories also depend upon ideas of time. This paper explores the roots and impact (...) of both time and hierarchy thinking on causal reasoning in the evolutionary sciences. Within evolutionary biology, the Neodarwinian synthesis adheres to a linear notion of time associated with linear hierarchies that portray upward causation. Eco-evo-devo schools recognize the importance of downward causation and consequently receive resistance from the standard view because downward causation is sometimes understood as backward causation, considered impossible by adherents of a linear time model. In contrast, downward causation works with a spatial or presential time notion. Hybridization, lateral gene transfer, infective heredity, symbiosis and symbiogenesis require recognition of reticulate causation occurring in both space and time, or spacetime, between distinct and interacting ontological hierarchies. Teleonomy is distinct from these types of causation because it invokes the problem of self-causation. By asking how the focal level in a hierarchy can persist through time, self-causation raises philosophical concerns on the nature of duration, identity and individuality. (shrink)

Elselijn Kingma argues that, in cases of mammalian placental pregnancy, the foster (roughly, the post-implantation embryo/foetus) is part of the gravida (the pregnant organism). But she does not consider the possibility of proper overlap. I show that this generates a number of serious problems for her argument and trace the oversight to a quite general issue within the literature on biological individuality. Doing so provides an opportunity to pull apart and clarify the relations between some importantly distinct questions concerning organismality (...) and organismic parthood, and to identify the implications that this has for those who want to draw on this literature when making metaphysical or mereological arguments. (shrink)

Applied Evolutionary Epistemology is a scientific-philosophical theory that defines evolution as the set of phenomena whereby units evolve at levels of ontological hierarchies by mechanisms and processes. This theory also provides a methodology to study evolution, namely, studying evolution involves identifying the units that evolve, the levels at which they evolve, and the mechanisms and processes whereby they evolve. Identifying units and levels of evolution in turn requires the development of ontological hierarchy theories, and examining mechanisms and processes necessitates theorizing (...) about causality. Together, hierarchy and causality theories explain how biorealities form and diversify with time. This paper analyzes how Applied EE redefines both hierarchy and causality theories in the light of the recent explosion of network approaches to causal reasoning associated with studies on reticulate and macroevolution. Causality theories have often been framed from within a rigid, ladder-like hierarchy theory where the rungs of the ladder represent the different levels, and the elements on the rungs represent the evolving units. Causality then is either defined reductionistically as an upward movement along the strands of a singular hierarchy, or holistically as a downward movement along that same hierarchy. Upward causation theories thereby analyze causal processes in time, i.e. over the course of natural history or phylogenetically, as Darwin and the founders of the Modern Synthesis intended. Downward causation theories analyze causal processes in space, ontogenetically or ecologically, as the current eco-evo-devo schools are evidencing. This work demonstrates how macroevolution and reticulate evolution theories add to the complexity by examining reticulate causal processes in space–time, and the interactional hierarchies that such studies bring forth introduce a new form of causation that is here called reticulate causation. Reticulate causation occurs between units and levels belonging to different as well as to the same ontological hierarchies. This article concludes that beyond recognizing the existence of multiple units, levels, and mechanisms or processes of evolution, also the existence of multiple kinds of evolutionary causation as well as the existence of multiple evolutionary hierarchies needs to be acknowledged. This furthermore implies that evolution is a pluralistic process divisible into different kinds. (shrink)

Contrary to the common-sense view and positivist aspirations, scientific concepts are often imprecise. Many of these concepts are ambiguous, vague, or have an under-specified meaning. In this paper, I discuss how imprecise concepts promote integration in biology and thus benefit science. Previous discussions of this issue focus on the concepts of molecular gene and evolutionary novelty. The concept of molecular gene helps biologists integrate explanatory practices, while the notion of evolutionary novelty helps them integrate research questions into an interdisciplinary problem (...) New directions in the philosophy of science, Springer, Dordrecht, 2014). In what follows, I compare molecular gene and evolutionary novelty to another imprecise concept, namely biological lineage. This concept promotes two other types of scientific integration: it helps biologists integrate theoretical principles and methodologies into different areas of biology. The concept of biological lineage facilitates these types of integration because it is broad and under-specified in ways that the concepts of molecular gene and evolutionary novelty are not. Hence, I use the concept of biological lineage as a case study to reveal types of integration that have been overlooked by philosophers. This case study also shows that even very imprecise concepts can be beneficial to scientific practice. (shrink)

info:eu-repo/semantics/publishedVersion.

This paper analyzes recent attempts to reject reproduction with lineage formation as a necessary condition for evolution by means of natural selection :560–570, 2008; Stud Hist Philos Sci Part C Stud Hist Philos Biol Biomed Sci 42:106–114, 2011; Bourrat in Biol Philos 29:517–538, 2014; Br J Philos Sci 66:883–903, 2015; Charbonneau in Philos Sci 81:727–740, 2014; Doolittle and Inkpen in Proc Natl Acad Sci 115:4006–4014, 2018). Building on the strengths of these attempts and avoiding their pitfalls, it is argued that (...) a robust formulation of evolution by natural selection without reproduction can be established. The main contribution of this paper is a reformulation of Lewontin’s three principles stating that minimal evolution by natural selection occurs when two conditions are met in a population: fitness-related variation and memory. Paradigmatic evolution by natural selection, which can generate adaptations, takes place when an additional condition is present, namely regeneration. (shrink)

Evolution by natural selection has been extended to several supraorganismic levels, but whether it can apply to ecosystems remains controversial on two main counts. First, local ecosystems are loosely individuated, so that it is unclear how they manifest heredity and fitness. Second, even if they did, the meta-ecosystem formed by this population of local ecosystems will also suffer from a very low degree of cohesion, which will jeopardize any ENS. We suggest a way to overcome both issues, focusing on ecosystem (...) properties rather than on ecosystemic individuals. First, we follow recent theoretical developments which deny the centrality of reproduction in ENS. This leads us to merge heredity and fitness in a single process, in which a local ecosystem causally influences its neighbors, in a way responsible for their phenotypic similarity. Second, we suggest that the resulting meta-ecosystem need not meet the criteria of individuality. Instead, the evolving meta-ecosystem is best understood as a homeostatic property cluster, i.e., a set of phenotypes that together evolve by ENS at the ecosystem level. We illustrate this conceptual framework with a hypothetical example of local ecosystems that vary in terms of stability, productivity, diversity, and complementarity between species. Finally, we stress that our property-based account of ecosystemic ENS can help understand evolution at other biological levels, such as early life evolution and holobionts. (shrink)

The hologenome concept of evolution is a hypothesis about the evolution of animals and plants. It asserts that the evolution of animals and plants was partially triggered by their interactions with their symbiotic microbiomes. In that vein, the hologenome concept posits that the holobiont (animal host + symbionts of the microbiome) is a unit of selection. -/- The hologenome concept has been severely criticized on the basis that selection on holobionts would only be possible if there were a tight transgenerational (...) host-genotype-to-symbiont-genotype connection. As our current evidence suggests that this is not the case for most of the symbiont species that compose the microbiome of animals and plants, the opportunity for holobiont selection is very low in relation to the opportunity for selection on each of the species that compose the host microbiome. Therefore, holobiont selection will always be disrupted ‘from below’, by selection on each of the species that compose the microbiome. -/- This thesis constitutes a conceptual effort to defend philosophically the hologenome concept. I argue that the criticism according to which holobiont selection requires tight transgenerational host-genotype-to-symbiont-genotype connection is grounded on a metaphysical view of the world according to which the biological hierarchy needs to be nested, such that each new level of selection includes every entity from below. Applied to hologenomes, it entails that the hologenome is a collection of genomes, and selection of hologenomes is assumed to entail cospeciation of the host with the species that constitute its microbiome. -/- Against that interpretation, I propose the ‘stability of traits’ account, according to which hologenome evolution is the result of the action of natural selection in a non-nested hierarchical world. In that vein, hologenome evolution does not entail cospeciation, and thus it does not require tight transgenerational host-genotype-to-symbiont-genotype connection. By embracing a multilevel selection perspective, I argue that hologenome evolution results from the simultaneous action of natural selection on each of the lineages that compose the microbiome, and on the assemblage composed by the host genome plus the functional traits of its microbiome. Hologenome selection occurs when the evolution of the traits of the microbiome result from their effects on the fitness of the host, and it can take the form of multilevel selection 1, or multilevel selection 2. In both cases, hologenome selection entails the evolution of microbiome traits, as well as evolution of the host genome, rather than cospeciation of lineages. (shrink)

Biologists are nearing the creation of the first fully synthetic eukaryotic genome. Does this mean that we still soon be able to create genomes that are parts of an existing genetic lineage? If so, it might be possible to bring back extinct species. But do genomes that are synthetically assembled, no matter how similar they are to native genomes, really belong to the genetic lineage on which they were modelled? This article will argue that they are situated within the same (...) genetic lineage. To see why requires closely examining whether material overlap between parents and offspring is a necessary feature of biological reproduction. The processes used to create synthetic genomes shows that these processes are a form of scaffolded reproduction because they use external machinery and take ownership of the material parts used to create synthetic genomes. Closely examining these processes also reveals, surprisingly, that ‘synthetic reproduction’ can take place between entities that don’t participate in the same biological lineages. 1Introduction2The Argument for Lineage-less Genomes3Synthetic Eukaryotic Chromosomes and Material Overlap4Biological Reproduction, Material, and Information5Synthetic Reproductive Processes and Their Implications. (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)

Holobionts, consisting of a host and diverse microbial symbionts, function as distinct biological entities anatomically, metabolically, immunologically, and developmentally. Symbionts can be transmitted from parent to offspring by a variety of vertical and horizontal methods. Holobionts can be considered levels of selection in evolution because they are well-defined interactors, replicators/reproducers, and manifestors of adaptation. An initial mathematical model is presented to help understand how holobionts evolve. The model offered combines the processes of horizontal symbiont transfer, within-host symbiont proliferation, vertical symbiont (...) transmission, and holobiont selection. The model offers equations for the population dynamics and evolution of holobionts whose hologenomes differ in gene copy number, not in allelic or loci identity. The model may readily be extended to include variation among holobionts in the gene identities of both symbionts and host. (shrink)

With an increasing number of ways to ‘assist’ reproduction, some bioethicists have started to wonder what it takes to become a genetic parent. It is widely agreed that sharing genes is not enough to substantiate the parent–offspring relation, but what is? Without a better understanding of the concept of reproduction, our thinking about parent–offspring relations and the ethical issues surrounding them risk being unprincipled. Here, I address that problem by offering a principled account of reproduction—the Overlap, Development and Persistence account—which (...) I believe best captures the meaning of ‘genetic parenthood’. (shrink)

Universal Darwinism provides a methodology to study the evolution of anatomical form and sociocultural behavior that centers on defining the units and levels of selection, and it identifies the conditions whereby natural selection operates. In previous work, I have examined how this selection-focused evolutionary epistemology may be universalized to include theories that associate with an extended synthesis. Applied evolutionary epistemology is a metatheoretical framework that understands any and all kinds of evolution as phenomena where units evolve by mechanisms at levels (...) of an ontological hierarchy; and it provides three heuristics to search for these units, levels and mechanisms. The heuristics are applicable to language and sociocultural evolution, and here, we give an in-depth analysis of how the unit-heuristic can be implemented into language origin and evolution studies. The importance of developing hierarchy theories is also more fully explained. (shrink)

Biological reproduction is a material process of intertwined, recursive propagule generation and development, assuming that development produces simple life cycles. Most organisms, however, have more or less complex life cycles. Here, I attempt to reconcile recent articulations of a reproducer account with traditional approaches to complex life cycles by generalizing genetic demarcation criteria for life cycle generations in terms of the “scaffolded” development of hybrid reproducers. I argue that scaffolding provides a general method for identifying developmental bottlenecks and suggests in (...) turn a new way of understanding developmental reaction norms. (shrink)

The definition of biological individuality is one of the most discussed topics in philosophy of biology, but current debate has focused almost exclusively on evolution-based accounts. Moreover, several participants in this debate consider the notions of a biological individual and an organism as equivalent. In this paper, I show that the debates would be considerably enriched and clarified if philosophers took into account two elements. First, physiological fields are crucial for the understanding of biological individuality. Second, the category of biological (...) individuals should be divided into two subcategories: physiological individuals and evolutionary individuals, which suggests that the notions of organism and biological individual should not be used interchangeably. I suggest that the combination of an evolutionary and a physiological perspective will enable biologists and philosophers to supply an account of biological individuality that will be both more comprehensive and more in accordance with scientific practices. (shrink)

That holobionts are units of selection squares poorly with the observation that microbes are often recruited from the environment, not passed down vertically from parent to offspring, as required for collective reproduction. The taxonomic makeup of a holobiont’s microbial community may vary over its lifetime and differ from that of conspecifics. In contrast, biochemical functions of the microbiota and contributions to host biology are more conserved, with taxonomically variable but functionally similar microbes recurring across generations and hosts. To save what (...) is of interest in holobiont thinking, we propose casting metabolic and developmental interaction patterns, rather than the taxa responsible for them, as units of selection. Such units need not directly reproduce or form parent-offspring lineages: their prior existence has created the conditions under which taxa with the genes necessary to carry out their steps have evolved in large numbers. These taxa or genes will reconstruct the original interaction patterns when favorable conditions occur. Interaction patterns will vary in ways that affect the likelihood of and circumstances under which such reconstruction occurs. Thus, they vary in fitness, and evolution by natural selection will occur at this level. It is on the persistence, reconstruction, and spread of such interaction patterns that students of holobiosis should concentrate, we suggest. This model also addresses other multi-species collectively beneficial interactions, such as biofilms or biogeochemical cycles maintaining all life. (shrink)

Cognitive niche theories consist in a theoretical framework that is proving extremely profitable in bridging evolutionary biology, philosophy, cognitive science, and anthropology by offering an inter-disciplinary ground, laden with novel approaches and debates. At the same time, cognitive niche theories are multiple, and differently related to niche theories in theoretical and evolutionary biology. The aim of this paper is to clarify the theoretical and epistemological relationships between cognitive and ecological niche theories. Also, by adopting a constructionist approach we will try (...) to explain the shift from ecological to cognitive niches and their actual and theoretical overlaps. In order to do so, we will take two concepts expressing loose forms of causation in the interaction between organisms and their environment: the biological notion of “enablement” and the psycho-cognitive one of “affordance”. (shrink)

Upshot: In our response we focus on five questions that point to important common themes in the commentaries: why start in wicked problems, what kind of system is a scientific perspective, what is the nature of second-order research processes, what does this mean for understanding interdisciplinary work, and how may polyocular research help make real-world decisions.

Context: The problems that are most in need of interdisciplinary collaboration are “wicked problems,” such as food crises, climate change mitigation, and sustainable development, with many relevant aspects, disagreement on what the problem is, and contradicting solutions. Such complex problems both require and challenge interdisciplinarity. Problem: The conventional methods of interdisciplinary research fall short in the case of wicked problems because they remain first-order science. Our aim is to present workable methods and research designs for doing second-order science in domains (...) where there are many different scientific knowledges on any complex problem. Method: We synthesize and elaborate a framework for second-order science in interdisciplinary research based on a number of earlier publications, experiences from large interdisciplinary research projects, and a perspectivist theory of science. Results: The second-order polyocular framework for interdisciplinary research is characterized by five principles. Second-order science of interdisciplinary research must: 1. draw on the observations of first-order perspectives, 2. address a shared dynamical object, 3. establish a shared problem, 4. rely on first-order perspectives to see themselves as perspectives, and 5. be based on other rules than first-order research. Implications: The perspectivist insights of second-order science provide a new way of understanding interdisciplinary research that leads to new polyocular methods and research designs. It also points to more reflexive ways of dealing with scientific expertise in democratic processes. The main challenge is that this is a paradigmatic shift, which demands that the involved disciplines, at least to some degree, subscribe to a perspectivist view. Constructivist content: Our perspectivist approach to science is based on the second-order cybernetics and systems theories of von Foerster, Maruyama, Maturana & Varela, and Luhmann, coupled with embodied theories of cognition and semiotics as a general theory of meaning from von Uexküll and Peirce. (shrink)

Scientific classification has long been recognized as involving a specific style of reasoning and doing research, and as occasionally affecting the development of scientific theories. However, the role played by classificatory activities in generating theories has not been closely investigated within the philosophy of science. I argue that classificatory systems can themselves become a form of theory, which I call classificatory theory, when they come to formalize and express the scientific significance of the elements being classified. This is particularly evident (...) in some of the classification practices used in contemporary experimental biology, such as bio-ontologies used to classify genomic data and typologies used to classify “normal” stages of development in developmental biology. In this paper, I explore some characteristics of classificatory theories and ways in which they differ from other types of scientific theories and other components of scientific epistemology, such as models and background assumptions. (shrink)

The article examines two cases of adoption of evolutionary ways of thinking by modern economists: Nelson and Winter’s (Evolutionary Theory of Economic Change, 1982), and evolutionary game theory (1990s and after). In both cases, the authors explicitly refer to natural selection in an economic context. I show that natural selection is taken in two different senses, which correspond to two general conceptions of the principle of natural selection, one of which contains reproduction and heredity as key elements, whereas the other (...) does not. (shrink)

Is knowledge in the natural sciences discovered or constructed? For objectivists, scientific knowledge is discovered through investigations into a mind-independent, natural world. For constructivists, such knowledge is produced through negotiations among members of a professional guild. I examine the clash between the two positions and propose that scientific knowledge is the concurrent outcome from investigations into a natural world and from consensus reached through negotiations of a professional guild. Specifically, I introduce the general methodological notion, instituting science, which incorporates both (...) the discovery and the construction processes in the generation of scientific knowledge. To that end, I use a case study from the biomedical sciences to illustrate the notion. I conclude with a discussion of how this methodological notion helps to address the debate between objectivists and constructivists over the generation of scientific knowledge, and of how it compares with others who have also attempted to address the debate. (shrink)

The semantic concept of information is one of the most important, and one of the most problematical concepts in biology. I suggest a broad definition of biological information: a source becomes an informational input when an interpreting receiver can react to the form of the source (and variations in this form) in a functional manner. The definition accommodates information stemming from environmental cues as well as from evolved signals, and calls for a comparison between information‐transmission in different types of inheritance (...) systems—the genetic, the epigenetic, the behavioral, and the cultural‐symbolic. This comparative perspective highlights the different ways in which information is acquired and transmitted, and the role that such information plays in heredity and evolution. Focusing on the special properties of the transfer of information, which are very different from those associated with the transfer of materials or energy, also helps to uncover interesting evolutionary effects and suggests better explanations for some aspects of the evolution of communication. (shrink)

The themes, problems and challenges of developmental systems theory as described in Cycles of Contingency are discussed. We argue in favor of a robust approach to philosophical and scientific problems of extended heredity and the integration of behavior, development, inheritance, and evolution. Problems with Sterelny's proposal to evaluate inheritance systems using his `Hoyle criteria' are discussed and critically evaluated. Additional support for a developmental systems perspective is sought in evolutionary studies of performance and behavior modulation of fitness.

In this paper, I will conduct three interrelated analyses. First, I will develop an analysis of various concepts in the history of biology that used to refer to individual-level phenomena but were then reinterpreted by the Modern Synthesis in terms of populations. Second, a similar situation can be found in contemporary evolutionary theory. While different approaches reflect on the causal role of developing organisms in evolution, proponents of the Modern Synthesis refrain from any substantial change by reinterpreting and explaining individual-level (...) phenomena from a population perspective. Finally, I will approach these historical and contemporary debates by arguing for the statistical reading of natural selection, which holds that explanations by natural selection are statistical. My main conclusion is that the historical conceptual reinterpretations belong to a new explanatory strategy developed by the Modern Synthesis based on population thinking. Adopting the statistical point of view has three advantages for the issues discussed in this paper. First, understanding historical conceptual change as part of an explanatory shift fits with the emergence of population biology as a discipline that employs statistical methods. Second, concerning current debates in evolutionary biology, the statisticalist reading can validate the goal of both sides of the dispute. It ascribes an invaluable role to the population statistical explanation of the MS and also commends the study of developmental and organismal causes of adaptive evolution. Finally, the division of explanatory roles in evolutionary biology, embarrassed by statisticalism, can be related to the different interpretations that important biological concepts have undergone throughout history and contemporary biology, i.e., that the division of explanatory roles allows for a division of conceptual interpretations. (shrink)

Mitochondrial replacement techniques (MRTs) are a new group of biotechnologies that aim to aid women whose eggs have disease-causing deleteriously mutated mitochondria to have genetically related healthy children. These techniques have also been used to aid women with poor oocyte quality and poor embryonic development, to have genetically related children. Remarkably, MRTs create humans with DNA from three sources: nuclear DNA from the intending mother and father, and mitochondrial DNA from the egg donor. In a recent publication Françoise Baylis argued (...) that MRTs are detrimental for genealogical research via mitochondrial DNA because they would obscure the lines of individual descent. In this paper, I argue that MRTs do not obscure genealogical research, but rather that MRT-conceived children can have two mitochondrial lineages. I argue for this position by showing that MRTs are reproductive in nature and, thus, they create genealogy. (shrink)

Immunology and its philosophy are a primary source for thinking about biological individuality. Through its discriminatory function, the immune system is believed to delineate organism and environment within one generation, thus defining the physiological individual. Based on the paradigmatic instantiations of immune systems, immune interactions and, thus, the physiological individual are believed to last only for one generation. However, in recent years, transgenerationally persisting immune responses have been reported in several phyla, but the consequences for physiological individuality have not yet (...) been explored. In this article, I will introduce an invertebrate immune system that is RNA-based and operates through a heritable silencing/licensing paradigm. I will discuss how such a perspective on immune systems can illuminate our conceptions of individuality. I will particularly introduce an account of immunological individuality that is not restricted to one generation. (shrink)

This article introduces a special issue on mechanisms in language evolution research. It describes processes relevant for the emergence of protolanguage and the transition thereof to modern language. Protolanguage is one of the key terms in the field of language evolution, used to designate a hypothesised intermediate stage in the emergence of language present in extinct hominins: qualitatively different from non-human primate communication in possessing some, but not all, of the features that characterise modern language. Much debate in language evolution (...) focuses on the exact delineation of these features, as well as the means whereby the transitions occurred: first from non-human primate communication systems to protolanguage, and then from protolanguage to modern language. In what follows, we first propose a comprehensive typology of protolanguage debates, taking into account the postulated structural organisation of protolanguage, its functions, and its communicative modality. This makes it possible to show how a specific focus on mechanisms and processes deemed relevant for the emergence of these features allows us to assess the explanatory scope of the existing theories of protolanguage. (shrink)

In this paper, I argue that the increasing data about non-genetic inheritance requires the construction of a new conceptual framework that should complement the inclusive approaches already discussed in the literature. More precisely, I hold that this framework should be epistemologically relevant for evolutionary biologists in capturing the limits of extended inheritance and in reassessing the boundaries of biological systems that transmit traits to their offspring. I outline the first elements of an organizational account of extended inheritance. In this account, (...) the category of inherited factors is neither restricted to genes nor extended to stable resources related to trans-generational similarities. Instead, it includes persisting constitutive elements appearing as difference makers for heterogeneous organizational constraints, namely for heterogeneous constitutive parts whose specific role is to harness flows of matter and energy across generations of clearly delimited extended organized systems. This both inclusive and restrictive framework opens an additional way to apprehend how extended inheritance may affect evolutionary trajectories. (shrink)

It is now widely accepted that microorganisms play many important roles in the lives of plants and animals. Every macroorganism has been shaped in some way by microorganisms. The recognition of the ubiquity and importance of microorganisms has led some to argue for a revolution in how we understand biological individuality and the primary units of natural selection. The term “holobiont” was introduced as a name for the biological unit made up by a host and all of its associated microorganisms, (...) and much of this new debate about biological individuality has focused on whether holobionts are integrated individuals or communities. In this paper, I show how parts of the holobiont can span both characterizations. I argue that most holobionts share more affinities with communities than they do with organisms, and that, except for maybe in rare cases, holobionts do not meet the criteria for being organisms, evolutionary individuals, or units of selection. (shrink)

The relation between method, concept and theory in science is complicated. I seek to shed light on that relation by considering an instance of it in systematics: The additional challenges phylogeneticists face when reconstructing phylogeny not at a single level, but simultaneously at multiple levels of the hierarchy. How does this complicate the task of phylogenetic inference, and how might it inform and shape the conceptual foundations of phylogenetics? This offers a lens through which the interplay of method, theory and (...) concepts may be understood in systematics, which, in turn, provides data for a more general account. (shrink)