Exploring what a scientific metaphysics grounded in biological practices could look like and how it might impact the way we investigate the world around us, the contributors to From Biological Practice to Scientific Metaphysics review and discuss long-held objections to metaphysics by natural scientists. They illuminate how, in order to learn about the world as it truly is, we must look not only at what scientists say but also what they do.

What methodological approaches do research programs use to investigate the world? Elisabeth Lloyd’s Logic of Research Questions (LRQ) characterizes such approaches in terms of the questions that the researchers ask and causal factors they consider. She uses the Logic of Research Questions Framework to criticize adaptationist programs in evolutionary biology for dogmatically assuming selection explanations of the traits of organisms. I argue that Lloyd’s general criticism of methodological adaptationism is an artefact of the impoverished LRQ. My Ordered Factors Proposal extends (...) the LRQ to characterize approaches with sequences of questions and factors. I highlight the importance that ordering one’s investigation plays in approaches at the level of adaptationism by analyzing two research programs in community ecology: competitionists and neutralists. Competitionists and neutralists take opposed starting points and use explanatory and developmental heuristics to consider more factors in due time. On the Ordered Factors Proposal, these approaches are not only the ecological factors they are open to considering but also the order in which they will consider them. My disagreement with Lloyd’s over how to characterize methodological approaches reflects different views about methodological monism and pluralism. (shrink)

Two strategies for using a model as “null” are distinguished. Null modeling evaluates whether a process is causally responsible for a pattern by testing it against a null model. Baseline modeling measures the relative significance of various processes responsible for a pattern by detecting deviations from a baseline model. When these strategies are conflated, models are illegitimately privileged as accepted until rejected. I illustrate this using the neutral theory of ecology and draw general lessons from this case. First, scientists cannot (...) draw certain conclusions using null modeling. Second, these conclusions follow using baseline modeling, but doing so requires more evidence. (shrink)

Neutral Theory is controversial in ecology. Ecologists and philosophers have diagnosed the source of the controversy as: its false assumption that individuals in different species within the same trophic level are ecologically equivalent, its conflict with Competition Theory and the adaptation of species, its role as a null hypothesis, and as a Lakatosian research programme. In this paper, I show why we should instead understand the conflict at the level of research programs which involve more than theory. The Neutralist and (...) Competitionist research programs borrow and construct theories, models, and experiments for various aims and given their home ecological systems. I present a holistic and pragmatic view of the controversy that foregrounds the interrelation between many kinds of practices and decisions in ecological research. (shrink)

We evaluate a common reasoning strategy used in community ecology and comparative psychology for selecting between competing hypotheses. This strategy labels one hypothesis as a “null” on the grounds of its simplicity and epistemically privileges it as accepted until rejected. We argue that this strategy is unjustified. The asymmetrical treatment of statistical null hypotheses is justified through the experimental and mathematical contexts in which they are used, but these contexts are missing in the case of the “pseudo-null hypotheses” found in (...) our case studies. Moreover, statistical nulls are often not epistemically privileged in practice over their alternatives because failing to reject the null is usually a negative result about the alternative, experimental hypothesis. Scientists should eschew the appeal to pseudo-nulls. It is a rhetorical strategy that glosses over a commitment to valuing simplicity over other epistemic virtues in the name of good scientific and statistical methodology. (shrink)

The ecologist today finds scarce ground safe from controversy. Decisions must be made about what combination of data, goals, methods, and theories offers them the foundations and tools they need to construct and defend their research. When push comes to shove, ecologists often turn to philosophy to justify why it is their approach that is scientific. Karl Popper’s image of science as bold conjectures and heroic refutations is routinely enlisted to justify testing hypotheses over merely confirming them. One of the (...) most controversial theories in contemporary science is the Neutral Theory of Ecology. Its chief developer and proponent, Stephen Hubbell, presents the neutral theory as a bold conjecture that has so far escaped refutation. Critics of the neutral theory claim that it already stands refuted, despite what the dogmatic neutralists say. We see the controversy through a Popperian lens. But Popper’s is an impoverished philosophy of science that distorts contemporary ecology. -/- The controversy surrounding the neutral theory actually rests on a methodological fault. There is a strong but messy historical link between the concepts of being neutral and being null in biology, and Hubbell perpetuates this when he claims that the neutral theory is supplies the appropriate null for testing alternative theories. What method is being followed here? There are three contenders: -/- Null hypothesis testing tests for whether a there is a pattern to be explained. Null modeling tests for whether a process is causally relevant to a pattern. Baseline modeling apportions relative responsibility to multiple processes each relevant to a pattern. -/- Whether the neutral theory supplies an appropriate “null” depends upon whether null hypothesis, null modeling, or baseline model is intended. These methods prescribe distinct inference patterns. If they are null hypothesis testing or null modeling, the neutralists’s reasoning is invalid. If they are baseline modeling, the justification of a crucial assumption remains opaque. Either way, the neutral-null connection is being exploited rhetorically to privilege the neutral theory over its rivals. Clarifying the reasoning immunizes us against the rhetoric and foregrounds the underlying virtues of the neutralist approach to ecology. -/- The Popperian lens distorts theoretical development as dogmatism. Lakatos’s view of science as the development of research programmes clarifies the epistemology of the neutral theory. Focusing philosophical attention on the neutralist research programme illuminates (1) the synchronic uses of the neutral theory to make predictions and give descriptions and explanations; (2) its diachronic development in response to theoretical innovation and confrontation with data; (3) its complex relationships to alternative theories. For example, baseline modeling is now seen to be its primary explanatory heuristic. The justification for baseline modeling with the neutral theory, previously hidden from view, is seen in the logic of in the neutralist research programme. (shrink)

Numerous scholarly works focus solely on scientific metaphysics or biological practice, but few attempt to bridge the two subjects. This volume, the latest in the Minnesota Studies in the Philosophy of Science series, explores what a scientific metaphysics grounded in biological practices could look like and how it might impact the way we investigate the world around us. From Biological Practice to Scientific Metaphysics examines how to reconcile the methods of biological practice with the methods of metaphysical cosmology, notably regarding (...) the origins of life. The contributors take up a wide range of traditional metaphysics and philosophy of science topics, including natural kinds, medicine, ecology, genetics, scientific pluralism, reductionism, operationalism, mechanisms, the nature of information, and more. Many of the chapters represent the first philosophical treatments of significant biological practices. From causality and complexity to niche constructions and inference, the contributors review and discuss long-held objections to metaphysics by natural scientists. They illuminate how, in order to learn about the world as it truly is, we must look not only at what scientists say but also what they do: for ontology cannot be read directly from scientific claims. (shrink)

An analysis of two heuristic strategies for the development of mechanistic models, illustrated with historical examples from the life sciences. In Discovering Complexity, William Bechtel and Robert Richardson examine two heuristics that guided the development of mechanistic models in the life sciences: decomposition and localization. Drawing on historical cases from disciplines including cell biology, cognitive neuroscience, and genetics, they identify a number of "choice points" that life scientists confront in developing mechanistic explanations and show how different choices result in (...) divergent explanatory models. Describing decomposition as the attempt to differentiate functional and structural components of a system and localization as the assignment of responsibility for specific functions to specific structures, Bechtel and Richardson examine the usefulness of these heuristics as well as their fallibility—the sometimes false assumption underlying them that nature is significantly decomposable and hierarchically organized. When Discovering Complexity was originally published in 1993, few philosophers of science perceived the centrality of seeking mechanisms to explain phenomena in biology, relying instead on the model of nomological explanation advanced by the logical positivists (a model Bechtel and Richardson found to be utterly inapplicable to the examples from the life sciences in their study). Since then, mechanism and mechanistic explanation have become widely discussed. In a substantive new introduction to this MIT Press edition of their book, Bechtel and Richardson examine both philosophical and scientific developments in research on mechanistic models since 1993. (shrink)

The economically deprived come into contact with the criminal court system in disproportionate number. This collection of original, interactive essays, written from a variety of ideological perspectives, explores some of the more troubling questions and ethical dilemmas inherent in this situation. The contributors, including well-known legal and political philosophers Philip Pettit, George Fletcher, and Jeremy Waldron, examine issues such as heightened vulnerability, indigent representation, and rotten social background defenses.

We offer an account of the generic use of the term “porn”, as seen in recent usages such as “food porn” and “real estate porn”. We offer a definition adapted from earlier accounts of sexual pornography. On our account, a representation is used as generic porn when it is engaged with primarily for the sake of a gratifying reaction, freed from the usual costs and consequences of engaging with the represented content. We demonstrate the usefulness of the concept of generic (...) porn by using it to isolate a new type of such porn: moral outrage porn. Moral outrage porn is representations of moral outrage, engaged with primarily for the sake of the resulting gratification, freed from the usual costs and consequences of engaging with morally outrageous content. Moral outrage porn is dangerous because it encourages the instrumentalization of one’s empirical and moral beliefs, manipulating their content for the sake of gratification. Finally, we suggest that when using porn is wrong, it is often wrong because it instrumentalizes what ought not to be instrumentalized. (shrink)

The generative entrenchment of an entity is a measure of how much of the generated structure or activity of a complex system depends upon the presence or activity of that entity. It is argued that entities with higher degrees of generative entrenchment are more conservative in evolutionary changes of such systems. A variety of models of complex structures incorporating the effects of generative entrenchment are presented and we demonstrate their relevance in analyzing and explaining a variety of developmental and evolutionary (...) phenomena, both on a macroscopic developmental and evolutionary scale, and using models and strategies pioneered by Kauffman, on the more microscopic scale appropriate to the analysis of the structure and behavior of gene control networks. The resulting picture suggests that generative entrenchment acts as a powerful and constructive developmental constraint on the course of evolutionary processes. Since virtually any system exhibits varying degrees of generative entrenchment among its parts and activities, these studies and results have in addition broad potential application for the analysis of generative structures in other areas. (shrink)

Since children are considered incapable ofgiving informed consent to participate inresearch, regulations require that bothparental permission and the assent of thepotential child subject be obtained. Assent andpermission are uniquely bound together, eachserving a different purpose. Parentalpermission protects the child from assumingunreasonable risks. Assent demonstrates respectfor the child and his developing autonomy. Inorder to give meaningful assent, the child mustunderstand that procedures will be performed,voluntarily choose to undergo the procedures,and communicate this choice. Understanding theelements of informed consent has been theparadigm for (...) assessing capacity to give assent.This method leaves the youngest, leastcognitively mature children vulnerable towaiver of assent and forced researchparticipation. Voluntariness can also becompromised by the influence of authorityfigures who can exert undue influence andcoerce children to participate in research. This paper discusses factors that may influencethe decision to give assent/permission,potential parent-child conflict in theassent/permission process and how it isresolved, and potential parental undueinfluence on research participation. Theseissues are illustrated with quotations drawnfrom a larger qualitative study of parentalpermission and child assent (data notpresented). We suggest a developmentalapproach, viewing assent as a continuum rangingfrom mere affirmation in the youngest childrento the equivalent of the informed consentprocess in the mature adolescent. (shrink)

The study of Social Issues in Management (SIM) has exhausted its primary analytic framework based on corporate social performance (social science), business ethics (philosophy), and stakeholder theory (organizational science), and needs to move to a new paradigmatic level based on the natural sciences. Doing so would expand research horizons to include cosmological perspectives (astrophysics), evolutionary theory (biology, genetics, ecology), and non-sectarian spirituality concepts (theological naturalism, cognitive neuroscience). Absent this shift, SIM studies risk increasing irrelevance for scholars and business practitioners.

Biological ontologies are used to organize, curate, and interpret the vast quantities of data arising from biological experiments. While this works well when using a single ontology, integrating multiple ontologies can be problematic, as they are developed independently, which can lead to incompatibilities. The Open Biological and Biomedical Ontologies Foundry was created to address this by facilitating the development, harmonization, application, and sharing of ontologies, guided by a set of overarching principles. One challenge in reaching these goals was that the (...) OBO principles were not originally encoded in a precise fashion, and interpretation was subjective. Here we show how we have addressed this by formally encoding the OBO principles as operational rules and implementing a suite of automated validation checks and a dashboard for objectively evaluating each ontology’s compliance with each principle. This entailed a substantial effort to curate metadata across all ontologies and to coordinate with individual stakeholders. We have applied these checks across the full OBO suite of ontologies, revealing areas where individual ontologies require changes to conform to our principles. Our work demonstrates how a sizable federated community can be organized and evaluated on objective criteria that help improve overall quality and interoperability, which is vital for the sustenance of the OBO project and towards the overall goals of making data FAIR. Competing Interest StatementThe authors have declared no competing interest. (shrink)

Is Goodness Without God Good Enough contains a lively debate between William Lane Craig and Paul Kurtz on the relationship between God and ethics, followed by seven new essays that both comment on the debate and advance the broader discussion of this important issue. Written in an accessible style by eminent scholars, this book will appeal to students and academics alike.

We explore the crucial role of diagrams in scientific reasoning, especially reasoning directed at developing mechanistic explanations of biological phenomena. We offer a case study focusing on one research project that resulted in a published paper advancing a new understanding of the mechanism by which the central circadian oscillator in Synechococcus elongatus controls gene expression. By examining how the diagrams prepared for the paper developed over the course of multiple drafts, we show how the process of generating a new explanation (...) vitally involved the development and integration of multiple versions of different types of diagrams, and how reasoning about the mechanism proceeded in tandem with the development of the diagrams used to represent it. (shrink)

Institutional review board delays may hinder the successful completion of federally funded research in the U.S. military. When this happens, time-sensitive, mission-relevant questions go unanswered. Research participants face unnecessary burdens and risks if delays squeeze recruitment timelines, resulting in inadequate sample sizes for definitive analyses. More broadly, military members are exposed to untested or undertested interventions, implemented by well-intentioned leaders who bypass the research process altogether. To illustrate, we offer two case examples. We posit that IRB delays often appear in (...) the service of managing institutional risk, rather than protecting research participants. Regulators may see more risk associated with moving quickly than risk related to delay, choosing to err on the side of bureaucracy. The authors of this article, all of whom are military-funded researchers, government stakeholders, and/or human subject protection experts, offer feasible recommendations to improv... (shrink)

Parts I through III of this paper will examine several, increasingly comprehensive forms of aggregation, ranging from insurance reimbursement “lock-in” programs to PDMPs to completely unified electronic medical records. Each part will advocate for the adoption of these aggregation systems and provide suggestions for effective implementation in the fight against opioid misuse. All PDMPs are not made equal, however, and Part II will, therefore, focus on several elements — mandating prescriber usage, streamlining the user interface, ensuring timely data uploads, creating (...) a national data repository, mitigating privacy concerns, and training doctors on how to respond to perceived doctor-shopping — that can make these systems more effective. In each part, we will also discuss the privacy concerns of aggregating data, ranging from minimal to significant, and highlight the unique role of stigma in motivating these concerns. In Part IV, we will conclude by suggesting remedial steps to offset this loss of privacy and to combat the stigma around SUDs and mental health disorders in general. (shrink)

Contributors: Sabina Leonelli Nancy J. Nersessian Michel Janssen Jacob G. Foster James A. Evans Mark A. Bedau Marshall Abrams Gilbert B. Tostevin Salikoko S. Mufwene Massimo Maiocchi Joseph D. Martin Paul E. Smaldino Claes Andersson Anton Törnberg Petter Törnberg Beyond the Meme assembles interdisciplinary perspectives on cultural evolution, providing a nuanced understanding of it as a process in which dynamic structures interact on different scales of size and time. The volume demonstrates how a thick understanding of change in culture emerges (...) from multiple disciplinary vantage points, each of which is required to understand cultural evolution in all its complexity. (shrink)

DNA topoisomerase II (topo II) is involved in chromosome structure and function, although its exact location and role in mitosis are somewhat controversial. This is due in part to the varied reports of its localization on mitotic chromosomes, which has been described at different times as uniformly distributed, axial on the chromosome arms and predominantly centromeric. These disparate results are probably due to several factors, including use of different preparation and fixation techniques, species differences and changes in distribution during the (...) cell cycle. Recently, several papers have re‐investigated the distribution of topo II on chromosomes as a function of cell cycle and species(1–3). The new studies suggest that Topo II has a dynamic pattern of distribution on the chromosomes, in general becoming axial as chromosomes condense during prophase and then concentrating at centromeres during metaphase. These experiments suggest a novel role for topo II in centromere structure and function. (shrink)

Cognitive agents, whether human or computer, that engage in natural-language discourse and that have beliefs about the beliefs of other cognitive agents must be able to represent objects the way they believe them to be and the way they believe others believe them to be. They must be able to represent other cognitive agents both as objects of beliefs and as agents of beliefs. They must be able to represent their own beliefs, and they must be able to represent beliefs (...) as objects of beliefs. These requirements raise questions about the number of tokens of the belief representation language needed to represent believers and propositions in their normal roles and in their roles as objects of beliefs. In this paper, we explicate the relations among nodes, mental tokens, concepts, actual objects, concepts in the belief spaces of an agent and the agent's model of other agents, concepts of other cognitive agents, and propositions. We extend, deepen, and clarify our theory of intensional knowledge representation for natural-language processing, as presented in previous papers and in light of objections raised by others. The essential claim is that tokens in a knowledge-representation system represent only intensions and not extensions. We are pursuing this investigation by building CASSIE, a computer model of a cognitive agent and, to the extent she works, a cognitive agent herself. CASSIE's mind is implemented in the SNePS knowledge-representation and reasoning system. (shrink)

Considerable controversy has recently arisen regarding the patenting of medical and surgical processes in the United States. One such patent, viz. for a "chevron" incision used in ophthalmologic surgery, has especially occasioned heated response including a major, condemnatory ethics policy statement from the American Medical Association as well as federal legislation denying patent protection for most uses of a patented medical or surgical procedure. This article identifies and discusses the major legal, ethical and public policy considerations offered by proponents and (...) opponents of such patents. The existing literature divides up into those who favor such patents essentially without qualification, and those who condemn and wish to outlaw them. We advance a compromise position where administrative and legislative action is called for to provide more specific guidelines regarding the patentability of such processes by the Patent and Trademark Office. Our position, in sum, will be that too much is at stake in this complicated area for either the blanket prohibition, or wholesale, uncritical acceptance, of the patenting of medical and surgical processes or techniques. (shrink)

Michael Weisberg has given us a lovely book on models. It has very broad coverage of issues intersecting the nature of models and their use, an extensive consideration of long ignored “concrete” models with a rich case study, a discussion and classification of the many diverse kinds of models, and a particularly groundbreaking and innovative discussion of similarity concerning how models relate to the world. Included are insightful discussions of increasingly used “agent based” models, and the conjoint use of multiple (...) models in looking for robust results. Weisberg fills in some discussions with modeling and simulation results of his own.In addition, he considers and critiques other recent competing views on models, including the increasingly popular “models as fictions” account. His discussion is clear and technically precise without being needlessly so, and his distinctions are useful. The scientist is more likely to recognize his objects than the semantic theorist, and that is how it .. (shrink)

We examined how the cultural dimension of universalism–particularism influences managers’ attitudes toward relational favoritism. Paradoxically, we found in a survey study that Brazilian and Chinese managers perceived more negative consequences of relational favoritism than did American managers—even though the Brazilians and the Chinese perceived stronger particularistic cultural norms in their countries than Americans did in the United States. We attribute this pattern of results to “cultural reflexivity”—the ability of people from transforming economies to be culturally self-critical during a period of (...) dramatic societal change. This pattern of results also emerged in a scenario study in which we asked these same Brazilian, Chinese, and American participants to assess managerial succession decisions made by a General Manager. We varied the scenarios so that the promoted manager was either a colleague with no pre-existing relation with the GM or a colleague who was a relative, a close friend, from the same town, or from the same school. Consistent with the results of the survey study, we found that perceived cultural norms of particularism were negatively related to perceptions of fairness. In other words, Brazilians and Chinese, even while living in more particularistic cultures, were more harsh in judging relational favoritism. We conclude with a discussion on the implications of these paradoxical relationships. (shrink)

This study explores the relationship between decision-making styles and moral judgements to understand how maximizers and satisficers differ in their analysis of ethical dilemmas. It also explores the linkage between decision-making styles and the moral reasoning perspectives of absolutism and relativism, investigating if ethical ideologies play a mediating role in how maximizers and satisficers evaluate ethical situations. In order to test these relationships, data is collected from a sample of 187 upper level business students. Results indicate that maximizers are significantly (...) more likely than satisficers to judge ethically ambiguous actions as immoral. Underlying this effect, maximizers (vs. satisficers) have a more idealistic ethical ideology. (shrink)

Grace and human response -- The common good -- Conscience -- Faithfully practicing virtue -- Our bodies and our issues -- Responsible sexuality -- Social justice -- Conclusion : and, in the end ....