Since the last decades of the twentieth and the beginning of the twenty-first century, the use of metaphysics by philosophers when approaching conceptual problems in biology has increased. Some philosophers call this tendency in philosophy of biology ‘Metaphysics of Biology’. In this paper, I aim at characterizing Metaphysics of Biology by paying attention to the diverse ways philosophers use metaphysics when addressing conceptual problems in biology. I will claim that there are two different modes of doing Metaphysics of Biology, namely (...) Metaphysics for Biology and Metaphysics in Biology. (shrink)

A general view in philosophy of science says that the appropriateness of an object to act as a surrogate depends on the user’s decision to utilize it as such. This paper challenges this claim by examining the role of surrogative reasoning in high-throughput sequencing technologies as they are used in contemporary microbiome science. Drawing on this, we argue that, in technology-driven surrogates, knowledge about the type of inference practically permitted and epistemically justified by the surrogate constrains their use and thus (...) puts a limit to the user’s intentions to use any object as a surrogate for what they please. Ignoring this leads to a serious epistemic misalignment, which ultimately prevents surrogative reasoning. Thus, we conclude that knowledge about the type of surrogate reasoning that the technologies being used allow is fundamental to avoid misinterpreting the consequences of the data obtained with them, the hypothesis this data supports, and what these technologies are surrogates of. (shrink)

Bourrat and Griffiths :33, 2018) have recently argued that most of the evidence presented by holobiont defenders to support the thesis that holobionts are evolutionary individuals is not to the point and is not even adequate to discriminate multispecies evolutionary individuals from other multispecies assemblages that would not be considered evolutionary individuals by most holobiont defenders. They further argue that an adequate criterion to distinguish the two categories is fitness alignment, presenting the notion of fitness boundedness as a criterion that (...) allows divorcing true multispecies evolutionary individuals from other multispecies assemblages and provides an adequate criterion to single out genuine evolutionary multispecies assemblages. A consequence of their criterion is that holobionts, as conventionally defined by hologenome defenders, are not evolutionary individuals except in very rare cases, and for very specific host-symbiont associations. This paper is a critical response to Bourrat and Griffiths’ arguments and a defence of the arguments presented by holobiont defenders. Drawing upon the case of the hologenomic basis of the evolution of sanguivory in vampire bats, I argue that Bourrat and Griffiths overlook some aspects of the biological nature of the microbiome that justifies the thesis that holobionts are evolutionarily different to other multispecies assemblages. I argue that the hologenome theory of evolution should not define the hologenome as a collection of genomes, but as the sum of the host genome plus some traits of the microbiome which together constitute an evolutionary individual, a conception I refer to as the stability of traits conception of the hologenome. Based on that conception I argue that the evidence presented by holobiont defenders is to the point, and supports the thesis that holobionts are evolutionary individuals. In this sense, the paper offers an account of the holobiont that aims to foster a dialogue between hologenome advocates and hologenome critics. (shrink)

This paper addresses the topic of determinism in contemporary microbiome research. I distinguish two types of deterministic claims about the microbiome, and I show evidence that both types of claims are present in the contemporary literature. First, the idea that the host genetics determines the composition of the microbiome which I call “host-microbiome determinism”. Second, the idea that the genetics of the holobiont (the individual unit composed by a host plus its microbiome) determines the expression of certain phenotypic traits, which (...) I call “microbiome-phenotype determinism”. Drawing on the stability of traits conception of individuality (Suárez in Hist Philos Life Sci 42:11, 2020) I argue that none of these deterministic hypotheses is grounded on our current knowledge of how the holobiont is transgenerationally assembled, nor how it expresses its phenotypic traits. (shrink)

I investigate the intrinsic/extrinsic nature of stemness in muscle stem cells (MSC) by relying on recent research on quiescence, with the aim of shedding light on the nature of dispositions and deriving some consequences about stem cells. First, I argue why the study of quiescence is the best available way to establish any claim about the intrinsicness/extrinsicness of stemness at least is some stem cells. Drawing on that, I argue that MSC’s stem capacities result from the combination of intrinsic cues (...) plus extrinsic factors from the stem cell niche, making stemness an extrinsic disposition in MSC. Importantly, it is shown that the niche allows the instantiation of stemness in MSC by acting as a masker of its manifestation. This shows that stemness is, at least in MSC, what I call an extrinsically structurally masked disposition (SMD); that is, a disposition whose instantiation requires, as a condition of possibility, the interaction between the bearer and a masker. Finally, I conclude by suggesting some potential consequences of this observation for the philosophical study of dispositions and for stem cell research. (shrink)

Cognitive biases can lead to misinterpretations of human and non-human biology and behavior. The concept of the Umwelt describes phylogenetic contrasts in the sensory realms of different species and has important implications for evolutionary studies of cognition (including biases) and social behavior. It has recently been suggested that the microbiome (the diverse network of microorganisms in a given environment, including those within a host organism such as humans) has an influential role in host behavior and health. In this paper, we (...) discuss the host’s microbiome in relation to cognitive biases and the concept of the Umwelt. Failing to consider the role of host–microbiome (collectively termed a “holobiont”) interactions in a given behavior, may underpin a potentially important cognitive bias – which we refer to as the Holobiont Blindspot. We also suggest that microbially mediated behavioral responses could augment our understanding of the Umwelt. For example, the potential role of the microbiome in perception and action could be an important component of the system that gives rise to the Umwelt. We also discuss whether microbial symbionts could be considered in System 1 thinking – that is, decisions driven by perception, intuition and associative memory. Recognizing Holobiont Blindspots and considering the microbiome as a key factor in the Umwelt and System 1 thinking has the potential to advance studies of cognition. Furthermore, investigating Holobiont Blindspots could have important implications for our understanding of social behaviors and mental health. Indeed, the way we think about how we think may need to be revisited. (shrink)

The Problem of Biological Individuality is the problem of how to count organisms. Whilst counting organisms may seem easy, the biological world is full of difficult cases such as colonial siphonophores and aspen tree groves. One of the main solutions to the Problem of Biological Individuality is the Physiological Approach. Drawing on an argument made by Eric Olson in the personal identity debate, I argue that the Physiological Approach faces a metaphysical problem - the ‘Foetus Problem’. This paper illustrates how (...) metaphysics can contribute to debates about organisms in the philosophy of biology. (shrink)

The Problem of Biological Individuality is the problem of how to count organisms. Whilst counting organisms may seem easy, the biological world is full of difficult cases such as colonial siphonophores and aspen tree groves. One of the main solutions to the Problem of Biological Individuality is the Physiological Approach. Drawing on an argument made by Eric Olson in the personal identity debate, I argue that the Physiological Approach faces a metaphysical problem - the ‘Foetus Problem’. This paper illustrates how (...) metaphysics can contribute to debates about organisms in the philosophy of biology. (shrink)

Dietary changes can alter the human microbiome with potential detrimental consequences for health. Given that environment, health, and evolution are interconnected, we ask: Could diet‐driven microbiome perturbations have consequences that extend beyond their immediate impact on human health? We address this question in the context of the urgent health challenges posed by global climate change. Drawing on recent studies, we propose that not only can diet‐driven microbiome changes lead to dysbiosis, they can also shape life‐history traits and fuel human evolution. (...) We posit that dietary shifts prompt mismatched microbiome‐host genetics configurations that modulate human longevity and reproductive success. These mismatches can also induce a heritable intra‐holobiont stress response, which encourages the holobiont to re‐establish equilibrium within the changed nutritional environment. Thus, while mismatches between climate change‐related genetic and epigenetic configurations within the holobiont increase the risk and severity of diseases, they may also affect life‐history traits and facilitate adaptive responses. These propositions form a framework that can help systematize and address climate‐related dietary challenges for policy and health interventions. (shrink)

The units or levels of selection debate concerns the question of what kind of biological systems are stable enough that part of their evolution is a result of the process of natural selection acting at their level. Traditionally, the debate has concerned at least two different, though related, questions: the question of the level at which interaction with the environment occurs, and the question of the level at which reproduction occurs. In recent years, biologists and philosophers have discussed a new (...) aspect of this debate, namely the possibility that certain multi-species consortia formed by a host and its microbiome may act as a unit of selection. This thesis, however, has not been without criticism, as it is doubtful that such consortia could meet the conditions required to achieve the degree of stability that would allow them to experience natural selection. The purpose of this paper is to systematically examine such criticisms and to defend the thesis that the holobiont/hologenome can act as a genuine level of selection both in the form of an interactor and in the form of a reproducer. To do so, it will be argued that the microbiome should be characterized in functional rather than taxonomic terms. (shrink)