Aristotelian theory, as found in Michael Thompson and Philippa Foot, claims that to be good is to be good as a member of that kind. Moreover, Foot argues in effect that goodness admits of only the kind-based sort, obtaining solely in virtue of something’s satisfying kind-based standards. However, I contend that something can satisfy kind-relative standards but nonetheless be bad—I propose a hypothetical Ebola-like microbe that meets its kind-standards of being destructive for its own sake, but it would plausibly be (...) bad for doing so. In defending my counterexample, I respond to the Aristotelian contention that evaluations should only be made from “within” the standpoint of a particular lifeform conception, rather than an “external” one from which that kind itself can be judged to be bad. (shrink)

While in the humanities and social sciences at large we can observe posthumanist developments that engage with the microbiome, microbes are still not a major topic of discussion within environmental ethics. That the environmental ethics literature has not engaged extensively with this topic is surprising considering the range of theoretical challenges (and opportunities) it poses for environmental theorising. So, this paper is ‘looking through the microscope’ from an environmental ethics angle in order to see how these little beings challenge (...) what we consider to be ethically relevant and how we conduct moral theorising. Especially interesting is how a focus on microbes can simultaneously support and challenge individualist biocentric intuitions and theories, which attribute moral standing to (some) microbes. Accordingly, the main aim of this paper is to lay out crucial aspects of these challenges and present some initial arguments about why not all of them pose a serious threat to biocentric theorising—including biocentric theories of interspecies justice. The three challenges discussed are (1) the moral significance challenge, (2) the self-defence predicament, and (3) undermining individualist biocentric intuitions. (shrink)

This paper shows that the identity of living things is a composite reality. It also suggests that the immune system constitutes a unifying process for the organism.

Debates about obesity in bioethics tend to unfold in predictable epicycles between individual choices and behaviours and the oppressive socio-economic structures constraining them. Here, we argue that recent work from two cutting-edge research programmes in microbiology and social psychology can advance this conceptual stalemate in the literature. We begin in section 1 by discussing two promising lines of obesity research involving the human microbiome and relationship partners. Then, in section 2, we show how this research has made viable novel strategies (...) for fighting obesity, including microbial therapies and dyad-level interventions. Finally, in section 3, we consider objections to our account and conclude by arguing that attention to the most immediate features of our biological and social environment offers a middle ground solution, while also raising important new issues for bioethicists. (shrink)

Cooperation is rife in the microbial world, yet our best current theories of the evolution of cooperation were developed with multicellular animals in mind. Hamilton’s theory of inclusive fitness is an important case in point: applying the theory in a microbial setting is far from straightforward, as social evolution in microbes has a number of distinctive features that the theory was never intended to capture. In this article, I focus on the conceptual challenges posed by the project of extending (...) Hamilton’s theory to accommodate the effects of gene mobility. I begin by outlining the basics of the theory of inclusive fitness, emphasizing the role that the concept of relatedness is intended to play. I then provide a brief history of this concept, showing how, over the past fifty years, it has departed from the intuitive notion of genealogical kinship to encompass a range of generalized measures of genetic similarity. I proceed to argue that gene mobility forces a further revision of the concept. The reason in short is that, when the genes implicated in producing social behaviour are mobile, we cannot talk of an organism’s genotype simpliciter; we can talk only of an organism’s genotype at a particular stage in its life cycle. We must therefore ask: with respect to which stage(s) in the life cycle should relatedness be evaluated? For instance: is it genetic similarity at the time of social interaction that matters to the evolution of social behaviour, or is it genetic similarity at the time of reproduction? I argue that, strictly speaking, it is neither of these: what really matters to the evolution of social behaviour is diachronic genetic similarity between the producers of fitness benefits at the time they produce them and the recipients of those benefits at the end of their life-cycle. I close by discussing the implications of this result. The main payoff is that it makes room for a possible new mechanism for the evolution of altruism in microbes that does not require correlated interaction among bearers of the genes for altruism. The importance of this mechanism in nature remains an open empirical question. (shrink)

Philippe Huneman has recently questioned the widespread application of mechanistic models of scientific explanation based on the existence of structural explanations, i.e. explanations that account for the phenomenon to be explained in virtue of the mathematical properties of the system where the phenomenon obtains, rather than in terms of the mechanisms that causally produce the phenomenon. Structural explanations are very diverse, including cases like explanations in terms of bowtie structures, in terms of the topological properties of the system, or in (...) terms of equilibrium. The role of mathematics in bowtie structured systems and in topologically constrained systems has recently been examined in different papers. However, the specific role that mathematical properties play in equilibrium explanations requires further examination, as different authors defend different interpretations, some of them closer to the new-mechanistic approach than to the structural model advocated by Huneman. In this paper, we cover this gap by investigating the explanatory role that mathematics play in Blaser and Kirschner’s nested equilibrium model of the stability of persistent long-term human-microbe associations. We argue that their model is explanatory because: i) it provides a mathematical structure in the form of a set of differential equations that together satisfy an ESS; ii) that the nested nature of the ESSs makes the explanation of host-microbe persistent associations robust to any perturbation; iii) that this is so because the properties of the ESS directly mirror the properties of the biological system in a non-causal way. The combination of these three theses make equilibrium explanations look more similar to structural explanations than to causal-mechanistic explanation. (shrink)

The study of biodiversity spans many disciplines and includes data pertaining to species distributions and abundances, genetic sequences, trait measurements, and ecological niches, complemented by information on collection and measurement protocols. A review of the current landscape of metadata standards and ontologies in biodiversity science suggests that existing standards such as the Darwin Core terminology are inadequate for describing biodiversity data in a semantically meaningful and computationally useful way. Existing ontologies, such as the Gene Ontology and others in the Open (...) Biological and Biomedical Ontologies (OBO) Foundry library, provide a semantic structure but lack many of the necessary terms to describe biodiversity data in all its dimensions. In this paper, we describe the motivation for and ongoing development of a new Biological Collections Ontology, the Environment Ontology, and the Population and Community Ontology. These ontologies share the aim of improving data aggregation and integration across the biodiversity domain and can be used to describe physical samples and sampling processes (for example, collection, extraction, and preservation techniques), as well as biodiversity observations that involve no physical sampling. Together they encompass studies of: 1) individual organisms, including voucher specimens from ecological studies and museum specimens, 2) bulk or environmental samples (e.g., gut contents, soil, water) that include DNA, other molecules, and potentially many organisms, especially microbes, and 3) survey-based ecological observations. We discuss how these ontologies can be applied to biodiversity use cases that span genetic, organismal, and ecosystem levels of organization. We argue that if adopted as a standard and rigorously applied and enriched by the biodiversity community, these ontologies would significantly reduce barriers to data discovery, integration, and exchange among biodiversity resources and researchers. (shrink)

Dr Stockmann, the principal character in Henrik Ibsen's A Public Enemy, is a classic example of a whistle-blower who, upon detecting and disclosing a serious case of environmental pollution, quickly finds himself transformed from a public benefactor into a political outcast by those in power. If we submit the play to a 'second reading', however, it becomes clear that the ethical intricacies of whistle-blowing are interwoven with epistemological issues. Basically, the play is about the complex task of communicating scientific (notably (...) microbiological) data to lay audiences. This becomes even more apparent when we realise that Stockmann was a contemporary of real 'microbe hunters' such as Pasteur and Koch. The play's basic message is that epoch-making scientists (such as Pasteur and Koch) not only produced convincing and reliable data from a scientific point of view, but also acquired the skills and insights needed to enter into a dialogue with their cultural and societal environment. (shrink)

“Do Anthropocene narratives confuse an important distinction between the natural and the historical past?” asks Giuseppina D’Oro. D’Oro defends the view that the concept of the historical past is sui generis and distinct from that of the geological past against a new, Anthropocene-inspired challenge to the possibility of a humanistically oriented historiography. She argues that the historical past is not a short segment of geological time, the time of the human species on Earth, but the past investigated from the perspective (...) of a distinctive kind of interest, that of uncovering the norms which governed historical agents in different periods of time. The past for the Egyptologist, or for the Roman historian, is not the same past studied by the palaeontologist or the geologist, not because it is infinitesimal short in comparison to geological time, but because the questions asked by historians concerned with the Egyptian or Roman civilization are not the same kind of questions asked by empirically minded scientists. She argues that the accusation that the distinction between the historical and the natural/geological past, rests on unacceptable form of human exceptionalism is based on the conflation of the concept of the historical past with that of the human past and that keeping alive the nature/culture distinction has important implications for praxis. If the distinction between nature and culture is collapsed, and the corollary that historical agents are not distinct in kind from natural agents (such as yeast and microbes) is accepted, then “the anticipation of the future would become a mere spectator’s sport analogous to the activity of predicting the weather”: collapsing the nature culture distinction, D’Oro argues, undermines the possibility of political action against the very threat (climate change) that motivates Anthropocene narratives in the first instance. (shrink)

Synthetic biology is a field of research that concentrates on the design, construction, and modification of new biomolecular parts and metabolic pathways using engineering techniques and computational models. By employing knowledge of operational pathways from engineering and mathematics such as circuits, oscillators, and digital logic gates, it uses these to understand, model, rewire, and reprogram biological networks and modules. Standard biological parts with known functions are catalogued in a number of registries (e.g. Massachusetts Institute of Technology Registry of Standard Biological (...) Parts). Biological parts can then be selected from the catalogue and assembled in a variety of combinations to construct a system or pathway in a microbe. Through the innovative re-engineering of biological circuits and the optimization of certain metabolic pathways, biological modules can be designed to reprogram organisms to produce products or behaviors. Synthetic biology is what is known as a “platform technology”. That is, it generates highly transferrable theoretical models, engineering principles, and know-how that can be applied to create potential products in a wide variety of industries. Proponents suggest that applications of synthetic biology may be able to provide scientific and engineered solutions to a multitude of worldwide problems from health to energy. Synthetic biology research has already been successful in constructing microbial products which promise to offer cheaper pharmaceuticals such as the antimalarial synthetic drug artemisinin, engineered microbes capable of cleaning up oil spills, and the engineering of biosensors that can detect the presence of high concentrations of arsenic in drinking water. One of the potential benefits of synthetic biology research is in its application to biofuel production. It is this application which is the focus of this entry. The term “biofuel” has referred generally to all liquid fuels that are sourced from plant or plant byproducts and are used for energy necessary for transportation vehicles (Thompson 2012). Biofuels that are produced using synthetic biological techniques re-engineer microbes into biofuel factories are a subset of these. (shrink)

The way we farm, the kinds of backyards and landscapes we favor, and the way we control patterns of development are creating an invisible crisis through their affects upon soil ecology. The invisibility of soil ecosystems, the seemingly alien properties of the organisms that inhabit them, and the specialized knowledge required to understand them create obstacles to moral concern for these fountains of life. Our treatment of soils has reached the point of crisis. Obstacles to moral thinking about soils might (...) be overcome by supplying the moral imagination with a deeper understanding of our own biological identity as ecosystems analogous in organization and functions to soil ecosystems. Not only have microbes created the conditions necessary for human life, but they have shaped our evolutionary history and helped constitute the human genome. Our biological identity encompasses communities of microbes, such that humans (and all organisms) are most properly understood as ecosystems. For this reason, moral concern for humans implies moral concern for ecosystems. (shrink)

Research in infection biology aims to understand the complex nature of host–pathogen interactions. While this knowledge facilitates strategies for preventing and treating diseases, it can also be intentionally misused to cause harm. Such dual-use risk is potentially high for highly pathogenic microbes such as Risk Group-3 (RG3) bacteria and RG4 viruses, which could be used in bioterrorism attacks. However, other pathogens such as influenza virus (IV) and enterohemorrhagic Escherichia coli (EHEC), usually classified as RG2 pathogens, also demonstrate high dual-use (...) risk. As the currently approved therapeutics against these pathogens are not satisfactorily effective, previous outbreaks of these pathogens caused enormous public fear, media attention and economic burden. In this interdisciplinary review, we summarize the current perspectives of dual-use research on IV and EHEC, and further highlight the dual-use risk associated with evolutionary experiments with these infectious pathogens. We support the need to carry out experiments pertaining to pathogen evolution, including to gain predictive insights on their evolutionary trajectories, which cannot be otherwise achieved with stand-alone theoretical models and epidemiological data. However, we also advocate for increased awareness and assessment strategies to better quantify the risks-versus-benefits associated with such evolutionary experiments. In addition to building public trust in dual-use research, we propose that these approaches can be extended to other pathogens currently classified as low risk, but bearing high dual-use potential, given the particular pressing nature of their rapid evolutionary potential. (shrink)

Commensal and pathogenic organisms employ camouflage and mimicry to mediate mutualistic interactions and predator escape. However, the immune mechanisms accounting for the establishment and maintenance of symbiotic bacterial populations are poorly understood. A promising hypothesis suggests that molecular mimicry, a condition in which different organisms share common antigens, is a mechanism of establishing tolerance between commensals and their hosts. On this view, certain bacteria may mimic the structural features of some of their host’s T-cell receptors (TCRs), namely those that survive (...) thymic selection due to their lack of complementarity to self-antigens. With such “holoimmunity” the mimicking micro-organisms avoid immune recognition as the copied TCRs become mirror images of an extended super-organismal self, consisting of symbiotic and host antigens. Accordingly, analysis of genomic and metagenomic data suggests a tripartite mimicry between TCRs, self-antigens, and commensal antigens that would serve as the basis for immune tolerance between these populations. And conversely, in an autoimmune scenario, both symbiotic microbes and the mimicked host tissue would be targeted for immune destruction. (shrink)

“Indeed, we now know that the proportion of genetic sequences on earth that belongs to visible organisms is negligible. Furthermore, only 15% of the genetic sequences found in the samples from the environment and from feces analyzed in metagenomic studies belong to the three domains of microbes currently recognized in the tree-of-life framework – bacteria, archaea, and eukaryotes. Viruses contain another 15-30% of these genetic sequences.” This means that the majority of unidentified genetic sequences pose an unresolved problem. Where (...) do they come from? New genes suddenly appear, called ORFans (“orphan genes”) without any precursors. They may be produced by gene duplication, or fusion, or some other unknown process. Yet, Darwin’s tree of life concept would make it impossible to consider such processes. The transfer of genetic sequences from parasites to hosts could involve hundreds of genes for bacteria or viruses. But, as Raoult writes, “the current classification of the domains of life is based on the ribosome – the production apparatus of proteins – which does not exist in these viruses.” Adherence to the dogmatism of Darwin thus prevents these new discoveries, that overturn his century-and-a-half old teachings, from ever reaching the new generation of scientists. Raoult concludes, "Genetic research, in particular, must be free to find new models to explain, and enhance, twenty-first-century scientific discovery. Today, Darwin’s theory of evolution is more a hindrance than a help, because it has become a quasi-theological creed that is preventing the benefits of improved research from being fully realized.". (shrink)

According to a once influential view of selection, it consists of repeated cycles of replication and interaction. It has been argued that this view is wrong: replication is not necessary for evolution by natural selection. I analyze the nine most influential arguments for this claim and defend the replication–interaction conception of selection against these objections. In order to do so, however, the replication–interaction conception of selection needs to be modified significantly. My proposal is that replication is not the copying of (...) an entity, the replicator, but the copying of a property. Thus, we can have a replication process without there being a replicator that is being copied. (shrink)

In the last few years, the idea of human being has been enlarged from the individual closeness to morphogenetic openness. Concurrently with discovers and researches into invisible worlds that live with human beings – microbes, fungi, bacteria, etc. – a debate has opened up that agrees with recent positions in the field of ontology. The human being is capable of poietic openness and is defined by relations. Anyway, an absence of a rigorous conceptualisation of the individualising process remains latent (...) to the discourse. A classic principle of individualisation is probably incomplete. This paper brings into dialogue individualisation with singularisation through the manifestation process of expression in accordance with recent theoretical enactments of hybridisation processes. (shrink)

Internet and Biometric Web Based Business Management Decision Support MICROBE MOOC material prepared under IO1/A5 Development of the MICROBE personalized MOOCs content and teaching materials Prepared by: A. Kaklauskas, A. Banaitis, I. Ubarte Vilnius Gediminas Technical University, Lithuania Project No: 2020-1-LT01-KA203-078100.