How should we distinguish between selectable and circumstantial traits?

There is surprisingly little philosophical work on conceptually spelling out the difference between the traits on which natural selection may be said to act (e.g. "having a high running speed") and mere circumstantial traits (e.g. "happening to be in the path of a forest fire"). I label this issue the "selectable traits problem" and, in this paper, I propose a solution for it. I first show that, contrary to our first intuition, simply equating selectable traits with heritable ones is not an adequate solution. I then go on to argue that two recent philosophical solutions to this problem-due to Peter Godfrey-Smith and Pierrick Bourrat-are unconvincing because they cannot accommodate frequency-dependent selection. The way out of this difficulty is, I argue, to accept that extrinsic properties dependent on relations between intrinsic properties of the population members should also count as selectable traits. I then show that my proposal is legitimized by more than the simple accommodation of frequency-dependent selection.

Health and environment from adaptation to adaptivity: a situated relational account

The definitions and conceptualizations of health, and the management of healthcare have been challenged by the current global scenarios (e.g., new diseases, new geographical distribution of diseases, effects of climate change on health, etc.) and by the ongoing scholarship in humanities and science. In this paper we question the mainstream definition of health adopted by the WHO-'a state of complete physical, mental and social well-being and not merely the absence of disease or infirmity' (WHO in Preamble to the constitution of the World Health Organization as adopted by the international health conference, The World Health Organization, 1948)-and its role in providing tools to understand what health is in the contemporary context. More specifically, we argue that this context requires to take into account the role of the environment both in medical theory and in the healthcare practice. To do so, we analyse WHO documents dated 1984 and 1986 which define health as 'coping with the environment'. We develop the idea of 'coping with the environment', by focusing on two cardinal concepts: adaptation in public health and adaptivity in philosophy of biology. We argue that the notions of adaptation and adaptivity can be of major benefit for the characterization of health, and have practical implications. We explore some of these implications by discussing two recent case studies of adaptivity in public health, which can be valuable to further develop adaptive strategies in the current pandemic scenario: community-centred care and microbiologically healthier buildings.

Health as temporally extended: theoretical foundations and implications

This paper seeks to develop a theory of health that aligns with the shift in contemporary medical practice and research toward a temporally extended epidemiological view of health. The paper describes how such a theory is at the core of life course based approaches to health, and finds theoretical grounding in recent work in the philosophy of biology promulgating a process theory of life.

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.

A Note Against the Use of "Belonging To" Properties in Multilevel Selection Theory

In this short paper, I argue against what I call the "belonging to" interpretation of group selection in scenarios in which a group's fitness is defined as the per capita reproductive output of the individuals of the group. According to this interpretation, group selection acts on "belonging to" properties of individuals, i.e. on relational or contextual properties that all the individuals of a group share simply by belonging to that group; thus, if differences in the individuals' "belonging to" properties cause differences in their fitness, group selection sensu the "belonging to" interpretation is said to be at work. I argue that the main problem with the "belonging to" interpretation is that it confuses evolutionary changes due to differences in environmental quality with evolutionary changes due to selection. In other words, I argue that, in the majority of cases, this interpretation actually takes the "selection" out of the "group selection" notion it aims to interpret: by adopting this perspective, one implicitly commits to explaining the evolutionary change under consideration not by a kind of selection (be it individual or group selection), but by differences in the environmental quality experienced by individual types.

"Microbiota, symbiosis and individuality summer school" meeting report

How does microbiota research impact our understanding of biological individuality? We summarize the interdisciplinary summer school on "Microbiota, symbiosis and individuality: conceptual and philosophical issues" (July 2019), which was supported by a European Research Council starting grant project "Immunity, DEvelopment, and the Microbiota" (IDEM). The summer school centered around interdisciplinary group work on four facets of microbiota research: holobionts, individuality, causation, and human health. The conceptual discussion of cutting-edge empirical research provided new insights into microbiota and highlights the value of incorporating into meetings experts from other disciplines, such as philosophy and history of science. Video Abstract.

Explanatory goals and explanatory means in multilevel selection theory

It has become customary in multilevel selection theory to use the same terms (namely "multilevel selection 1" and "multilevel selection 2") to denote both two explanatory goals (explaining why certain individual- and, respectively, group-level traits spread) and two explanatory means (namely, two kinds of group selection we may appeal to in such explanations). This paper spells out some of the benefits that derive from avoiding this terminological conflation. I argue that keeping explanatory means and goals well apart allows us to see that, contrary to a popular recent idea, Price's equation and contextual analysis-the statistical methods most extensively used for measuring the effects of certain evolutionary factors (like individual selection, group selection etc.) on the change in the focal individual trait in multilevel selection scenarios-do not come with built-in notions of group selection and, therefore, the efficacy of these methods at analyzing various kinds of cases does not constitute a basis for deciding how group selection should best be defined. Moreover, contrary to another widely accepted idea, I argue that more than one type of group selection may serve as explanatory means when one's goal is that of explaining the evolution of individual traits in multilevel selection scenarios and I spell out how this explanatory role should be understood.

Drawing and the dynamic nature of living systems

Representing the dynamic nature of biological processes is a challenge. This article describes a collaborative project in which the authors – a philosopher of biology, an artist and a cell biologist – explore how best to represent the entire process of cell division in one connected image. This involved a series of group Drawing Labs, one-to-one sessions, and discussions between the authors. The drawings generated during the collaboration were then reviewed by four experts in cell division. We propose that such an approach has value, both in communicating the dynamic nature of biological processes and in generating new insights and hypotheses that can be tested by artists and scientists.

The harm of medical disorder as harm in the damage sense

Jerome Wakefield has argued that a disorder is a harmful dysfunction. This paper develops how Wakefield should construe harmful in his harmful dysfunction analysis (HDA). Recently, Neil Feit has argued that classic puzzles involved in analyzing harm render Wakefield's HDA better off without harm as a necessary condition. Whether or not one conceives of harm as comparative or non-comparative, the concern is that the HDA forces people to classify as mere dysfunction what they know to be a disorder. For instance, one can conceive of cases where simultaneous disorders prevent each other from being, in any traditional sense, actually harmful; in such cases, according to the HDA, neither would be a disorder. I argue that the sense of harm that Wakefield should employ in the HDA is dispositional, similar to the sense of harm used when describing a vile of poison: "Be careful! That's poison. It's harmful." I call this harm in the damage sense. Using this sense of harm enables the HDA to avoid Feit's arguments, and thus it should be preferred to other senses when analyzing harmful dysfunction.

Paleoanthropology's uses of the bipedal criterion

Bipedalism is one of the criteria that paleoanthropologists use in order to interpret the fossil record and to determine if a specimen belongs to the human lineage. In the context of such interpretations, bipedalism is considered to be a unique characteristic of this lineage that also marks its origin. This conception has largely remained unchallenged over the last decades, in spite of fossil discoveries that led to the emergence of bipedalism in the human lineage being shifted back by several millions of years. In this paper, I analyze the uses of this criterion in paleoanthropology and demonstrate that interpretative biases (such as underdetermined inferences and circular reasoning) are at play in interpretations of hominin remains. By discussing Darwin's hypotheses about the evolution of bipedalism, I identify major theoretical issues that need to be addressed in the current debates on hominin evolution. First, the assumption that "man alone has become a biped" (Darwin in The descent of man, and selection in relation to sex, John Murray, London, 1871) is analyzed in the light of recent empirical data. Three major issues are discussed: the definition of "man", i.e. "human", the uniqueness of human bipedalism, and the equivocal meaning of being a "biped". Then, I highlight some of Darwin's remarks that may be helpful for current debates in paleoanthropology, regarding natural selection in locomotor evolution, as well as taxonomic and phylogenetic significance of functional features. Finally, I analyze two examples of how fossil discoverers referred to Darwin in the recent years and discuss his role as an intellectual support.

In defence of biodiversity

The concept of biodiversity has played a central role within conservation biology over the last thirty years. Precisely how it should be understood, however, is a matter of ongoing debate. In this paper we defend what we call a classic multidimensional conception of biodiversity. We begin by introducing two arguments for eliminating the concept of biodiversity from conservation biology, both of which have been put forward in a recent paper by Santana (Biol Philos 29:761-780. doi:10.1007/s10539-014-9426-2, 2014). The first argument is against the concept's scientific usefulness. The other is against its value as a target of conservation. We show that neither of these objections is successful against the classic multidimensional conception of biodiversity. Biodiversity thus understood is important from a scientific perspective, because it plays important explanatory roles within contemporary ecology. Moreover, although it does not encompass all valuable features of the natural world, this does not show that we should abandon it as a target of conservation. Instead, biodiversity should be conceived as one of many grounds of value associated with ecosystems. This is consistent with concluding that a central aim of conservationists should be to protect biodiversity.

Molecular Phylogenetics and the Perennial Problem of Homology

The concept of homology has a long history, during much of which the issue has been how to reconcile similarity and common descent when these are not coextensive. Although thinking molecular phylogeneticists have learned not to say "percent homology," the problems are deeper than that and unresolved.

evoText: A new tool for analyzing the biological sciences

We introduce here evoText, a new tool for automated analysis of the literature in the biological sciences. evoText contains a database of hundreds of thousands of journal articles and an array of analysis tools for generating quantitative data on the nature and history of life science, especially ecology and evolutionary biology. This article describes the features of evoText, presents a variety of examples of the kinds of analyses that evoText can run, and offers a brief tutorial describing how to use it.

A Philosophical Perspective on Evolutionary Systems Biology

Evolutionary systems biology (ESB) is an emerging hybrid approach that integrates methods, models, and data from evolutionary and systems biology. Drawing on themes that arose at a cross-disciplinary meeting on ESB in 2013, we discuss in detail some of the explanatory friction that arises in the interaction between evolutionary and systems biology. These tensions appear because of different modeling approaches, diverse explanatory aims and strategies, and divergent views about the scope of the evolutionary synthesis. We locate these discussions in the context of long-running philosophical deliberations on explanation, modeling, and theoretical synthesis. We show how many of the issues central to ESB's progress can be understood as general philosophical problems. The benefits of addressing these philosophical issues feed back into philosophy too, because ESB provides excellent examples of scientific practice for the development of philosophy of science and philosophy of biology.

Methodology and Ontology in Microbiome Research

Research on the human microbiome has generated a staggering amount of sequence data, revealing variation in microbial diversity at the community, species (or phylotype), and genomic levels. In order to make this complexity more manageable and easier to interpret, new units-the metagenome, core microbiome, and enterotype-have been introduced in the scientific literature. Here, I argue that analytical tools and exploratory statistical methods, coupled with a translational imperative, are the primary drivers of this new ontology. By reducing the dimensionality of variation in the human microbiome, these new units render it more tractable and easier to interpret, and hence serve an important heuristic role. Nonetheless, there are several reasons to be cautious about these new categories prematurely "hardening" into natural units: a lack of constraints on what can be sequenced metagenomically, freedom of choice in taxonomic level in defining a "core microbiome," typological framing of some of the concepts, and possible reification of statistical constructs. Finally, lessons from the Human Genome Project have led to a translational imperative: a drive to derive results from the exploration of microbiome variation that can help to articulate the emerging paradigm of personalized genomic medicine (PGM). There is a tension between the typologizing inherent in much of this research and the personal in PGM.

Gould talking past Dawkins on the unit of selection issue

My general aim is to clarify the foundational difference between Stephen Jay Gould and Richard Dawkins concerning what biological entities are the units of selection in the process of evolution by natural selection. First, I recapitulate Gould's central objection to Dawkins's view that genes are the exclusive units of selection. According to Gould, it is absurd for Dawkins to think that genes are the exclusive units of selection when, after all, genes are not the exclusive interactors: those agents directly engaged with, directly impacted by, environmental pressures. Second, I argue that Gould's objection still goes through even when we take into consideration Sterelny and Kitcher's defense of gene selectionism in their admirable paper "The Return of the Gene." Third, I propose a strategy for defending Dawkins that I believe obviates Gould's objection. Drawing upon Elisabeth Lloyd's careful taxonomy of the various understandings of the unit of selection at play in the philosophy of biology literature, my proposal involves realizing that Dawkins endorses a different understanding of the unit of selection than Gould holds him to, an understanding that does not require genes to be the exclusive interactors.