Darwinism without populations: a more inclusive understanding of the "Survival of the Fittest"

Evolvability: filling the explanatory gap between adaptedness and the long-term mathematical conception of fitness

The new foundation for the propensity interpretation of fitness (PIF), developed by Pence and Ramsey (Br J Philos Sci 64:851-881, 2013), describes fitness as a probability distribution that encompasses all possible daughter populations to which the organism may give rise, including daughter populations in which traits might change and the possible environments that members of the daughter populations might encounter. This long-term definition of fitness is general enough to avoid counterexamples faced by previous mathematical conceptions of PIF. However, there seem to be downsides to its generality: the ecological role of fitness involves describing the degree of adaptedness between an organism and the specific environment it inhabits. When all possible changes in traits and all possible environments that a daughter population may encounter are included in the concept, it becomes difficult to see how fitness can fulfill this role. In this paper, we argue that this is a feature of Pence and Ramsey's view rather than a bug: long-term fitness accommodates evolvability considerations, which concern the role that variation plays in evolutionary processes. Building on the foundations, we show that Pence and Ramsey's fitness-F-can be partitioned into fourths: adaptedness, robustness of adaptedness, and two facets of evolvability. Conceptualizing these last three components forces us to consider the role played by grains of description of both organisms and the environment when thinking about long-term fitness. They track the possibility that there could be a change in type in a daughter population as a way of responding to environmental challenges, or that the type persists in the face of novel environments. We argue that these components are just as salient as adaptedness for long-term fitness. Together, this decomposition of F provides a more accurate picture of the factors involved in long-term evolutionary success.

Gaia as Solaris: An Alternative Default Evolutionary Trajectory

Now that we know that Earth-like planets are ubiquitous in the universe, as well as that most of them are much older than the Earth, it is justified to ask to what extent evolutionary outcomes on other such planets are similar, or indeed commensurable, to the outcomes we perceive around us. In order to assess the degree of specialty or mediocrity of our trajectory of biospheric evolution, we need to take into account recent advances in theoretical astrobiology, in particular (i) establishing the history of habitable planets' formation in the Galaxy, and (ii) understanding the crucial importance of "Gaian" feedback loops and temporal windows for the interaction of early life with its physical environment. Hereby we consider an alternative macroevolutionary pathway that may result in tight functional integration of all sub-planetary ecosystems, eventually giving rise to a true superorganism at the biospheric level. The blueprint for a possible outcome of this scenario has been masterfully provided by the great Polish novelist Stanisław Lem in his 1961 novel Solaris. In fact, Solaris offers such a persuasive and powerful case for an "extremely strong" Gaia hypothesis that it is, arguably, high time to investigate it in a discursive astrobiological and philosophical context. In addition to novel predictions in the domain of potentially detectable biosignatures, some additional cognitive and heuristic benefits of studying such extreme cases of functional integration are briefly discussed.

The Epistemic Revolution Induced by Microbiome Studies: An Interdisciplinary View

Simple Summary

This interdisciplinary study, conducted by experts in evolutionary biology, ecology, ecosystem studies, arts, medicine, forensic analyses, agriculture, law, and philosophy of science describe how microbiome studies are convergently affecting the concepts and practices of diverse fields and practices, that now consider microbiomes within their legitimate scope. Consequently, it describes what seems to be an ongoing pluridisciplinary epistemic revolution, with the potential to fundamentally change how we understand the world through an ecologization of pre-existing concepts, a greater focus on interactions, the use of multi-scalar interaction networks as explanatory frameworks, the reconceptualization of the usual definitions of individuals, and a de-anthropocentrification of our perception of phenomena.

Abstract

Many separate fields and practices nowadays consider microbes as part of their legitimate focus. Therefore, microbiome studies may act as unexpected unifying forces across very different disciplines. Here, we summarize how microbiomes appear as novel major biological players, offer new artistic frontiers, new uses from medicine to laws, and inspire novel ontologies. We identify several convergent emerging themes across ecosystem studies, microbial and evolutionary ecology, arts, medicine, forensic analyses, law and philosophy of science, as well as some outstanding issues raised by microbiome studies across these disciplines and practices. An ‘epistemic revolution induced by microbiome studies’ seems to be ongoing, characterized by four features: (i) an ecologization of pre-existing concepts within disciplines, (ii) a growing interest in systemic analyses of the investigated or represented phenomena and a greater focus on interactions as their root causes, (iii) the intent to use openly multi-scalar interaction networks as an explanatory framework to investigate phenomena to acknowledge the causal effects of microbiomes, (iv) a reconceptualization of the usual definitions of which individuals are worth considering as an explanans or as an explanandum by a given field, which result in a fifth strong trend, namely (v) a de-anthropocentrification of our perception of the world.

Modeling the evolution of interconnected processes: It is the song and the singers: Tracking units of selection with interaction networks

Recently, Doolittle and Inkpen formulated a thought provoking theory, asserting that evolution by natural selection was responsible for the sideways evolution of two radically different kinds of selective units (also called Domains). The former entities, termed singers, correspond to the usual objects studied by evolutionary biologists (gene, genomes, individuals, species, etc.), whereas the later, termed songs, correspond to re-produced biological and ecosystemic functions, processes, information, and memes. Singers perform songs through selected patterns of interactions, meaning that a wealth of critical phenomena might receive novel evolutionary explanations. However, this theory did not provide an empirical approach to study evolution in such a broadened context. Here, we show that analyzing songs and singers, using patterns of interaction networks as a common ontology for both, offers a novel, actionable, inclusive and mathematical way to analyze not only the re-production but also the evolution and fitness of biological and ecosystemic interconnected processes.

What Is a Hologenomic Adaptation? Emergent Individuality and Inter-Identity in Multispecies Systems

Contemporary biological research has suggested that some host-microbiome multispecies systems (referred to as "holobionts") can in certain circumstances evolve as unique biological individual, thus being a unit of selection in evolution. If this is so, then it is arguably the case that some biological adaptations have evolved at the level of the multispecies system, what we call hologenomic adaptations. However, no research has yet been devoted to investigating their nature, or how these adaptations can be distinguished from adaptations at the species-level (genomic adaptations). In this paper, we cover this gap by investigating the nature of hologenomic adaptations. By drawing on the case of the evolution of sanguivory diet in vampire bats, we argue that a trait constitutes a hologenomic adaptation when its evolution can only be explained if the holobiont is considered the biological individual that manifests this adaptation, while the bacterial taxa that bear the trait are only opportunistic beneficiaries of it. We then use the philosophical notions of emergence and inter-identity to explain the nature of this form of individuality and argue why it is special of holobionts. Overall, our paper illustrates how the use of philosophical concepts can illuminate scientific discussions, in the trend of what has recently been called metaphysics of biology.

Making Evolutionary Sense of Gaia

The Gaia hypothesis in a strong and frequently criticized form assumes that global homeostatic mechanisms have evolved by natural selection favoring the maintenance of conditions suitable for life. Traditional neoDarwinists hold this to be impossible in theory. But the hypothesis does make sense if one treats the clade that comprises the biological component of Gaia as an individual and allows differential persistence - as well as differential reproduction - to be an outcome of evolution by natural selection. Recent developments in theoretical and experimental evolutionary biology may justify both maneuvers.

Multispecies individuals

We assess the arguments for recognising functionally integrated multispecies consortia as genuine biological individuals, including cases of so-called 'holobionts'. We provide two examples in which the same core biochemical processes that sustain life are distributed across a consortium of individuals of different species. Although the same chemistry features in both examples, proponents of the holobiont as unit of evolution would recognize one of the two cases as a multispecies individual whilst they would consider the other as a compelling case of ecological dependence between separate individuals. Some widely used arguments in support of the 'holobiont' concept apply equally to both cases, suggesting that those arguments have misidentified what is at stake when seeking to identify a new level of biological individuality. One important aspect of biological individuality is evolutionary individuality. In line with other work on the evolution of individuality, we show that our cases can be distinguished by focusing on the fitness alignment between the partners of the consortia. We conclude that much of the evidence currently presented for the ubiquity and importance of multi-species individuals is simply not to the point, at least unless the issue of biological individuality is firmly divorced from the question of evolutionary individuality.

Processes and patterns of interaction as units of selection: An introduction to ITSNTS thinking

Many practicing biologists accept that nothing in their discipline makes sense except in the light of evolution, and that natural selection is evolution's principal sense-maker. But what natural selection actually is (a force or a statistical outcome, for example) and the levels of the biological hierarchy (genes, organisms, species, or even ecosystems) at which it operates directly are still actively disputed among philosophers and theoretical biologists. Most formulations of evolution by natural selection emphasize the differential reproduction of entities at one or the other of these levels. Some also recognize differential persistence, but in either case the focus is on lineages of material things: even species can be thought of as spatiotemporally restricted, if dispersed, physical beings. Few consider-as "units of selection" in their own right-the processes implemented by genes, cells, species, or communities. "It's the song not the singer" (ITSNTS) theory does that, also claiming that evolution by natural selection of processes is more easily understood and explained as differential persistence than as differential reproduction. ITSNTS was formulated as a response to the observation that the collective functions of microbial communities (the songs) are more stably conserved and ecologically relevant than are the taxa that implement them (the singers). It aims to serve as a useful corrective to claims that "holobionts" (microbes and their animal or plant hosts) are aggregate "units of selection," claims that often conflate meanings of that latter term. But ITSNS also seems broadly applicable, for example, to the evolution of global biogeochemical cycles and the definition of ecosystem function.

Stability-based sorting: The forgotten process behind (not only) biological evolution

Natural selection is considered to be the main process that drives biological evolution. It requires selected entities to originate dependent upon one another by the means of reproduction or copying, and for the progeny to inherit the qualities of their ancestors. However, natural selection is a manifestation of a more general persistence principle, whose temporal consequences we propose to name "stability-based sorting" (SBS). Sorting based on static stability, i.e., SBS in its strict sense and usual conception, favours characters that increase the persistence of their holders and act on all material and immaterial entities. Sorted entities could originate independently from each other, are not required to propagate and need not exhibit heredity. Natural selection is a specific form of SBS-sorting based on dynamic stability. It requires some form of heredity and is based on competition for the largest difference between the speed of generating its own copies and their expiration. SBS in its strict sense and selection thus have markedly different evolutionary consequences that are stressed in this paper. In contrast to selection, which is opportunistic, SBS is able to accumulate even momentarily detrimental characters that are advantageous for the long-term persistence of sorted entities. However, it lacks the amplification effect based on the preferential propagation of holders of advantageous characters. Thus, it works slower than selection and normally is unable to create complex adaptations. From a long-term perspective, SBS is a decisive force in evolution-especially macroevolution. SBS offers a new explanation for numerous evolutionary phenomena, including broad distribution and persistence of sexuality, altruistic behaviour, horizontal gene transfer, patterns of evolutionary stasis, planetary homeostasis, increasing ecosystem resistance to disturbances, and the universal decline of disparity in the evolution of metazoan lineages. SBS acts on all levels in all biotic and abiotic systems. It could be the only truly universal evolutionary process, and an explanatory framework based on SBS could provide new insight into the evolution of complex abiotic and biotic systems.

Missing concepts in natural selection theory reconstructions

The concept of fitness has generated a lot of discussion in philosophy of biology. There is, however, relative agreement about the need to distinguish at least two uses of the term: ecological fitness on the one hand, and population genetics fitness on the other. The goal of this paper is to give an explication of the concept of ecological fitness by providing a reconstruction of the theory of natural selection in which this concept was framed, that is, based on the way the theory was put to use in Darwin's main texts. I will contend that this reconstruction enables us to account for the current use of the theory of natural selection. The framework presupposed in the analysis will be that of metatheoretical structuralism. This framework will provide both a better understanding of the nature of ecological fitness and a more complete reconstruction of the theory. In particular, it will provide what I think is a better way of understanding how the concept of fitness is applied through heterogeneous cases. One of the major advantages of my way of thinking about natural selection theory is that it would not have the peculiar metatheoretical status that it has in other available views. I will argue that in order to achieve these goals it is necessary to make several concepts explicit, concepts that are frequently omitted in usual reconstructions.

Being human is a gut feeling

Some metagenomic studies have suggested that less than 10% of the cells that comprise our bodies are Homo sapiens cells. The remaining 90% are bacterial cells. The description of this so-called human microbiome is of great interest and importance for several reasons. For one, it helps us redefine what a biological individual is. We suggest that a human individual is now best described as a super-individual in which a large number of different species (including Homo sapiens) coexist. New concepts of biological individuality must extend beyond the traditional limitations of our own skin to include our resident microbes. Besides its important contributions to science, microbiome research raises philosophical questions that strike close to home. What is left of Homo sapiens? If most of our cells are not Homo sapiens cells, what does it mean to be an individual human being? In this paper, we argue that the biological individual is determined by the amount of functional integration among its constitutive parts, a definition that applies perfectly to Homo sapiens and its microbiome.