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)

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)

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.

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)

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)

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)

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)

Many natural and biological phenomena can be depicted as networks. Theoretical and empirical analyses of networks have become prevalent. I discuss theoretical biases involved in the delineation of biological networks. The network perspective is shown to dissolve the distinction between regulatory architecture and regulatory state, consistent with the theoretical impossibility of distinguishing a priori between “program” and “data”. The evolutionary significance of the dynamics of trans-generational and inter-organism regulatory networks is explored and implications are presented for understanding the evolution of (...) the biological categories development-heredity; plasticity-evolvability; and epigenetic-genetic. (shrink)

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)