Multilevel research strategies characterize contemporary molecular inquiry into biological systems. We outline conceptual, methodological, and explanatory dimensions of these multilevel strategies in microbial ecology, systems biology, protein research, and developmental biology. This review of emerging lines of inquiry in these fields suggests that multilevel research in molecular life sciences has significant implications for philosophical understandings of explanation, modeling, and representation.

The discovery and ongoing investigation of microRNAs suggest important conceptual and methodological lessons for philosophers and historians of biology. This paper provides an account of miRNA research and the shift from viewing these tiny regulatory entities as minor curiosities to seeing them as major players in the post-transcriptional regulation of genes. Conceptually, the study of miRNAs is part of a broader change in understandings of genetic regulation, in which simple switch-like mechanisms were reinterpreted as aspects of complex cellular and genome-wide (...) processes. Among them are the activities of small RNAs, previously regarded as non-functional. Methodologically, the miRNA story suggests new ways of characterizing biological research that should prove helpful to philosophers of science who seek to develop more pluralistic, pragmatic models of scientific inquiry. miRNA research displays iterative movements between multiple modes of investigation that include not only the proposal and testing of hypotheses but also exploratory, technology-oriented and question-driven modes of research. As an exemplary story of scientific discovery and development, the miRNA case illustrates transitions from genetics to genomics and systems biology, and it shows how diverse configurations of research practice are related to major scientific advances. (shrink)

Microbial model systems have a long history of fruitful use in fields that include evolution and ecology. In order to develop further insight into modelling practice, we examine how the competitive exclusion and coexistence of competing species have been modelled mathematically and materially over the course of a long research history. In particular, we investigate how microbial models of these dynamics interact with mathematical or computational models of the same phenomena. Our cases illuminate the ways in which microbial systems and (...) equations work as models, and what happens when they generate inconsistent findings about shared targets. We reveal an iterative strategy of comparative modelling in different media, and suggest reasons why microbial models have a special degree of epistemic tractability in multimodel inquiry. (shrink)

Thomas Kuhn had little to say about scientific change in biological science, and biologists are ambivalent about how applicable his framework is for their disciplines. We apply Kuhn’s account of paradigm change to evolutionary microbiology, where key Darwinian tenets are being challenged by two decades of findings from molecular phylogenetics. The chief culprit is lateral gene transfer, which undermines the role of vertical descent and the representation of evolutionary history as a tree of life. To assess Kuhn’s relevance to this (...) controversy, we add a social analysis of the scientists involved to the historical and philosophical debates. We conclude that while Kuhn’s account may capture aspects of the pattern of an episode of scientific change, he has little to say about how the process of generating new understandings is occurring in evolutionary microbiology. Once Kuhn’s application is limited to that of an initial investigative probe into how scientific problem-solving occurs, his disciplinary scope becomes broader. (shrink)

The types of cetacean cultural behavior patterns described (primarily food-related and communication-related) reflect a very different research focus than that found in primatology, where dietary variation and food processing is emphasized and other potentially patterns have (until recently) been relatively neglected. The lack of behavioral research in all but a few cetacean species is also notable, as it mirrors a bias in primatology towards only a few genera.

Recent discoveries of geographical patterns in microbial distribution are undermining microbiology’s exclusively ecological explanations of biogeography and their fundamental assumption that ‘everything is everywhere: but the environment selects’. This statement was generally promulgated by Dutch microbiologist Martinus Wilhelm Beijerinck early in the twentieth century and specifically articulated in 1934 by his compatriot, Lourens G. M. Baas Becking. The persistence of this precept throughout twentieth-century microbiology raises a number of issues in relation to its formulation and widespread acceptance. This paper will (...) trace the conceptual history of Beijerinck’s claim that ‘everything is everywhere’ in relation to a more general account of its theoretical, experimental and institutional context. His principle also needs to be situated in relationship to plant and animal biogeography, which, this paper will argue, forms a continuum of thought with microbial biogeography. Finally, a brief overview of the contemporary microbiological research challenging ‘everything is everywhere’ reveals that philosophical issues from Beijerinck’s era of microbiology still provoke intense discussion in twenty-first century investigations of microbial biogeography. (shrink)

Human microbiome research makes causal connections between entire microbial communities and a wide array of traits that range from physiological diseases to psychological states. To evaluate these causal claims, we first examine a well-known single-microbe causal explanation: of Helicobacter pylori causing ulcers. This apparently straightforward causal explanation is not so simple, however. It does not achieve a key explanatory standard in microbiology, of Koch’s postulates, which rely on manipulations of single-microorganism cultures to infer causal relationships to disease. When Koch’s postulates (...) are framed by an interventionist causal framework, it is clearer what the H. pylori explanation achieves and where its explanatory strengths lie. After assessing this ‘simple’, single-microbe case, we apply the interventionist framework to two key areas of microbiome research, in which obesity and mental health states are purportedly explained by microbiomes. Despite the experimental data available, interventionist criteria for explanation show that many of the causal claims generated by microbiome research are weak or misleading. We focus on the stability, specificity and proportionality of proposed microbiome causal explanations, and evaluate how effectively these dimensions of causal explanation are achieved in some promising avenues of research. We suggest some conceptual and explanatory strategies to improve how causal claims about microbiomes are made. (shrink)

Human microbiome research makes causal connections between entire microbial communities and a wide array of traits that range from physiological diseases to psychological states. To evaluate these causal claims, we first examine a well-known single-microbe causal explanation: of Helicobacter pylori causing ulcers. This apparently straightforward causal explanation is not so simple, however. It does not achieve a key explanatory standard in microbiology, of Koch’s postulates, which rely on manipulations of single-microorganism cultures to infer causal relationships to disease. When Koch’s postulates (...) are framed by an interventionist causal framework, it is clearer what the H. pylori explanation achieves and where its explanatory strengths lie. After assessing this ‘simple’, single-microbe case, we apply the interventionist framework to two key areas of microbiome research, in which obesity and mental health states are purportedly explained by microbiomes. Despite the experimental data available, interventionist criteria for explanation show that many of the causal claims generated by microbiome research are weak or misleading. We focus on the stability, specificity and proportionality of proposed microbiome causal explanations, and evaluate how effectively these dimensions of causal explanation are achieved in some promising avenues of research. We suggest some conceptual and explanatory strategies to improve how causal claims about microbiomes are made. (shrink)

Human microbiome research makes causal connections between entire microbial communities and a wide array of traits that range from physiological diseases to psychological states. To evaluate these causal claims, we first examine a well-known single-microbe causal explanation: of Helicobacter pylori causing ulcers. This apparently straightforward causal explanation is not so simple, however. It does not achieve a key explanatory standard in microbiology, of Koch’s postulates, which rely on manipulations of single-microorganism cultures to infer causal relationships to disease. When Koch’s postulates (...) are framed by an interventionist causal framework, it is clearer what the H. pylori explanation achieves and where its explanatory strengths lie. After assessing this ‘simple’, single-microbe case, we apply the interventionist framework to two key areas of microbiome research, in which obesity and mental health states are purportedly explained by microbiomes. Despite the experimental data available, interventionist criteria for explanation show that many of the causal claims generated by microbiome research are weak or misleading. We focus on the stability, specificity and proportionality of proposed microbiome causal explanations, and evaluate how effectively these dimensions of causal explanation are achieved in some promising avenues of research. We suggest some conceptual and explanatory strategies to improve how causal claims about microbiomes are made. (shrink)

Metagenomics is an emerging microbial systems science that is based on the large-scale analysis of the DNA of microbial communities in their natural environments. Studies of metagenomes are revealing the vast scope of biodiversity in a wide range of environments, as well as new functional capacities of individual cells and communities, and the complex evolutionary relationships between them. Our examination of this science focuses on the ontological implications of these studies of metagenomes and metaorganisms, and what they mean for common (...) sense and philosophical understandings of multicellularity, individuality and organism. We show how metagenomics requires us to think in different ways about what human beings are and what their relation to the microbial world is. Metagenomics could also transform the way in which evolutionary processes are understood, with the most basic relationship between cells from both similar and different organisms being far more cooperative and less antagonistic than is widely assumed. In addition to raising fundamental questions about biological ontology, metagenomics generates possibilities for powerful technologies addressed to issues of climate, health and conservation. We conclude with reflections about process-oriented versus entity-oriented analysis in light of current trends towards systems approaches. (shrink)

This commentary focuses on the authors’ treatment of Koch’s postulates. It argues in favour of a modification of Koch’s postulates and their analysis in terms of necessary and sufficient conditions. This leads to a criticism of the authors’ treatment of the C. difficile case, and to query the need for the criteria of specificity and proportionality.

This commentary focuses on the authors’ treatment of Koch’s postulates. It argues in favour of a modification of Koch’s postulates and their analysis in terms of necessary and sufficient conditions. This leads to a criticism of the authors’ treatment of the C. difficile case, and to query the need for the criteria of specificity and proportionality.

Much is being written these days about integration, its desirability and even its necessity when complex research problems are to be addressed. Seldom, however, do we hear much about the failure of such efforts. Because integration is an ongoing activity rather than a final achievement, and because today’s literature about integration consists mostly of manifesto statements rather than precise descriptions, an examination of unsuccessful integration could be illuminating to understand better how it works. This paper will examine the case of (...) prokaryote phylogeny and its apparent failure to achieve integration within broader tree-of-life accounts of evolutionary history. Despite the fact that integrated databases exist of molecules pertinent to the phylogenetic reconstruction of all lineages of life, and even though the same methods can be used to construct phylogenies wherever the organisms fall on the tree of life, prokaryote phylogeny remains at best only partly integrated within tree-of-life efforts. I will examine why integration does not occur, compare it with integrative practices in animal and other eukaryote phylogeny, and reflect on whether there might be different expectations of what integration should achieve. Finally, I will draw some general conclusions about integration and its function as a ‘meta-heuristic’ in the normative commitments guiding scientific practice. (shrink)

The eukaryote cell is one of the most radical innovations in the history of life, and the circumstances of its emergence are still deeply contested. This paper will outline the recent history of attempts to reveal these origins, with special attention to the argumentative strategies used to support claims about the first eukaryote cell. I will focus on two general models of eukaryogenesis: the phagotrophy model and the syntrophy model. As their labels indicate, they are based on claims about metabolic (...) relationships. The first foregrounds the ability to consume other organisms; the second the ability to enter into symbiotic metabolic arrangements. More importantly, however, the first model argues for the autogenous or self-generated origins of the eukaryote cell, and the second for its exogenous or externally generated origins. Framing cell evolution this way leads each model to assert different priorities in regard to cell-biological versus molecular evidence, cellular versus environmental influences, plausibility versus evolutionary probability, and irreducibility versus the continuity of cell types. My examination of these issues will conclude with broader reflections on the implications of eukaryogenesis studies for a philosophical understanding of scientific contestation. (shrink)

Ecology is usually described as the study of organisms interacting with one another and their environments. From this view of ecology, viruses – not usually considered to be organisms – would merely be part of the environment. Since the late 1980s, however, a growing stream of micrographic, experimental, molecular, and model-based (theoretical) research has been investigating how and why viruses should be understood as ecological actors of the most important sort. Viruses, especially phage, have been revealed as participants in the (...) planet's most crucial food webs, even though viruses technically consume nothing (they do not metabolize by themselves). Even more impressively, viruses have been identified as regulators of planetary biogeochemistry, in which they control cycles such as carbon, nitrogen and phosphorus – cycles on which all life depends. Although much biogeochemical research black-boxes the entities filling functional roles, it is useful to focus a little more closely to understand how viruses can be held responsible for the global processes of life. This paper will give a brief overview of the history of virus ecology and tease out the implications of large-scale ecological modelling with viruses. This analysis suggests that viruses should be conceptualized as ecological actors that are at least comparable and possibly equal to organismal actors. Ecological agency can therefore be distinguished from standard interpretations of biological agency. (shrink)

Although the cell is commonly addressed as the unit of life, historians and philosophers have devoted relatively little attention to this concept in comparison to other fundamental concepts of biology such as the gene or species. As a partial remedy to this neglect, we introduce the cell as a major point of connection between various disciplinary approaches, epistemic strategies, technological vectors and overarching biological processes such as metabolism, growth, reproduction and evolution. We suggest that the role of the cell as (...) a nexus forms the basis for a new philosophical and historical appreciation of cell biology. This perspective focuses less on the cell as a well-defined, stable object and places more emphasis on its role as a mediator of fundamental biological processes. (shrink)

Health research increasingly relies on organized collections of health data and biological samples. There are many types of sample and data collections that are used for health research, though these are collected for many purposes, not all of which are health-related. These collections exist under different jurisdictional and regulatory arrangements and include: 1) Population biobanks, cohort studies, and genome databases 2) Clinical and public health data 3) Direct-to-consumer genetic testing 4) Social media 5) Fitness trackers, health apps, and biometric data (...) sensors Population biobanks, cohort studies, and genome databases Clinical and public health data Direct-to-consumer genetic testing Social media Fitness trackers, health apps, and biometric data sensors Ethical, legal, and social challenges of such collections are well recognized, but there has been limited attention to the broader societal implications of the existence of these collections. Although health research conducted using these collections is broadly recognized as beneficent, secondary uses of these data and samples may be controversial. We examine both documented and hypothetical scenarios of secondary uses of health data and samples. In particular, we focus on the use of health data for purposes of: Forensic investigations Civil lawsuits Identification of victims of mass casualty events Denial of entry for border security and immigration Making health resource rationing decisions Facilitating human rights abuses in autocratic regimes Forensic investigations Civil lawsuits Identification of victims of mass casualty events Denial of entry for border security and immigration Making health resource rationing decisions Facilitating human rights abuses in autocratic regimes Current safeguards relating to the use of health data and samples include research ethics oversight and privacy laws. These safeguards have a strong focus on informed consent and anonymization, which are aimed at the protection of the individual research subject. They are not intended to address broader societal implications of health data and sample collections. As such, existing arrangements are insufficient to protect against subversion of health databases for non-sanctioned secondary uses, or to provide guidance for reasonable but controversial secondary uses. We are concerned that existing debate in the scholarly literature and beyond has not sufficiently recognized the secondary data uses we outline in this paper. Our main purpose, therefore, is to raise awareness of the potential for unforeseen and unintended consequences, in particular negative consequences, of the increased availability and development of health data collections for research, by providing a comprehensive review of documented and hypothetical non-health research uses of such data. (shrink)

Background Policy decisions about childhood vaccination require consideration of multiple, sometimes conflicting, public health and ethical imperatives. Examples of these decisions are whether vaccination should be mandatory and, if so, whether to allow for non-medical exemptions. In this article we argue that these policy decisions go beyond typical public health mandates and therefore require democratic input.Methods We report on the design, implementation, and results of a deliberative public forum convened over four days in Ontario, Canada, on the topic of childhood (...) vaccination.Results 25 participants completed all four days of deliberation and collectively developed 20 policy recommendations on issues relating to mandatory vaccinations and exemptions, communication about vaccines and vaccination, and AEFI (adverse events following immunization) compensation and reporting. Notable recommendations include unanimous support for mandatory childhood vaccination in Ontario, the need for broad educational communication about vaccination, and the development of a no-fault compensation scheme for AEFIs. There was persistent disagreement among deliberants about the form of exemptions from vaccination (conscience, religious beliefs) that should be permissible, as well as appropriate consequences if parents do not vaccinate their children.Conclusions We conclude that conducting deliberative democratic processes on topics that are polarizing and controversial is viable and should be further developed and implemented to support democratically legitimate and trustworthy policy about childhood vaccination. (shrink)

This book is a rich blend of analyses by leading experts from various cultures and disciplines. A compact introduction to a complex field, it illustrates biotechnology's profound impact upon the environment and society. Moreover, it underscores the vital relevance of cultural values. This book empowers readers to more critically assess biotechnology's value and effectiveness within both specific cultural and global contexts.

This book is a collection of secondary essays on America's most important philosophic thinkers—statesmen, judges, writers, educators, and activists—from the colonial period to the present. Each essay is a comprehensive introduction to the thought of a noted American on the fundamental meaning of the American regime.

We report two experiments in which participants had to judge the time of occurrence of a stimulus relative to a clock. The experiments were based on the control condition used by Libet, Gleason, Wright, and Pearl [Libet, B., Gleason, C. A., Wright, E. W., & Pearl, D. K. . Time of conscious intention to act in relation to onset of cerebral activities : The unconscious initiation of a freely voluntary act. Brain 106, 623–642] to correct for any bias in the (...) estimation of the time at which an endogenous event, the conscious intention to perform a movement, occurred. Participants’ responses were affected systematically by the sensory modality of the stimulus and by the speed of the clock. Such findings demonstrate the variability in judging the time at which an exogenous event occurs and, by extension, suggest that such variability may also apply to the judging the time of occurrence of endogenous events. The reliability of participants’ estimations of when they formed the conscious intention to perform a movement in Libet et al.’s study is therefore questionable. (shrink)