William Lawrence Tower’s work on the evolution of the Colorado Potato Beetle (_Leptinotarsa decemlineata_), documenting the environmental induction of mutation and speciation, made him a leading figure in experimental genetics during the first decade of the 20th century. His research program served as a model for other experimental evolution studies seeking to demonstrate the environmental modification of inheritance. Tower enjoyed the support of influential figures in the field, despite well-known problems that plagued Tower’s earlier academic career. The validity of his (...) genetic work, and other findings reported by Tower, were later challenged. The Tower affair illustrates how questionable and possibly fraudulent scientific practices can be tolerated to explore certain experimental directions and theoretical frameworks, particularly at the frontier of expanding disciplines. When needed, those explorations can be forestalled or extinguished by exploiting conspicuous vulnerabilities of rogue practitioners. In Tower’s case, both unrefuted allegations of scientific misconduct and personal problems dissolved his institutional support, leading to a swift ouster from academic science. Tower’s downfall discredited soft inheritance and neo-Lamarckian conceptions in the field of experimental genetics, facilitating the discipline’s embrace of a hard inheritance model that featured a hereditary material resistant to environmental modification. (shrink)

Recently improved understanding of evolutionary processes suggests that tree-based phylogenetic analyses of evolutionary change cannot adequately explain the divergent evolutionary histories of a great many genes and gene complexes. In particular, genetic diversity in the genomes of prokaryotes, phages, and plasmids cannot be fit into classic tree-like models of evolution. These findings entail the need for fundamental reform of our understanding of molecular evolution and the need to devise alternative apparatus for integrated analysis of these genomes. We advocate the development (...) of integrative phylogenomics for analyzing these genomes and their histories, with tools suited to analyzing the importance of lateral gene transfer (LGT) and of DNA evolution in extra-cellular mobile genetic elements (e.g., viruses, plasmids). These phenomena greatly increase the complexity of relationships among interacting genetic partners, as they exchange functional genetic units. We examine the ontology of functional genetic units, interacting genetic partners, and emergent genetic associations, argue that these three categories of entities are required for a successful integrated phylogenomics. We conclude with arguments to suggest that the proposed new perspective and associated tools are suitable, and perhaps required, as a replacement for the bifurcating trees that have dominated evolutionary thinking for the last 150 years. (shrink)

A decade after the completion of the Human Genome Project, the widespread appeal of personalized genomic medicine's vision and potential virtues for health care remains compelling. Advocates argue that our current medical regime “is in crisis as it is expensive, reactive, inefficient, and focused largely on one size fits all treatments for events of late stage disease.” What is revolutionary about this kind of medicine, its advocates maintain, is that it promises to resolve that crisis by simultaneously increasing the ability (...) to be “personalized,” “predictive,” “preventive,” and “participatory.” Some call personalized genomic medicine “P4 Medicine,” inscribing these cardinal virtues into the movement's name. All of these putative virtues have interesting implications for the future of health care. In this essay, we are especially interested in the claims that personalized medicine will lead to a more “participatory” or “patient‐centered” approach to health care, in which patients are “empowered” to take more personal control over their care. The rhetoric of patient empowerment is nothing new in health care, but personalized medicine is an interesting case study because it portrays empowerment as one of its key virtues and as a mechanism for fixing the health care “crisis.”. (shrink)

This article reviews current methods for evaluating models in the cognitive sciences, including theoretically based approaches, such as Bayes factors and minimum description length measures; simulation approaches, including model mimicry evaluations; and practical approaches, such as validation and generalization measures. This article argues that, although often useful in specific settings, most of these approaches are limited in their ability to give a general assessment of models. This article argues that hierarchical methods, generally, and hierarchical Bayesian methods, specifically, can provide a (...) more thorough evaluation of models in the cognitive sciences. This article presents two worked examples of hierarchical Bayesian analyses to demonstrate how the approach addresses key questions of descriptive adequacy, parameter interference, prediction, and generalization in principled and coherent ways. (shrink)

There are multiple formal characterizations of the natural numbers available. Despite being inter-derivable, they plausibly codify different possible applications of the naturals – doing basic arithmetic, counting, and ordering – as well as different philosophical conceptions of those numbers: structuralist, cardinal, and ordinal. Some influential philosophers of mathematics have argued for a non-egalitarian attitude according to which one of those characterizations is ‘more basic’ or ‘more fundamental’ than the others. This paper addresses two related issues. First, we review some of (...) these non-egalitarian arguments, lay out a laundry list of different, legitimate, notions of relative priority, and suggest that these arguments plausibly employ different such notions. Secondly, we argue that given a metaphysical-cum-epistemological gloss suggested by Frege's foundationalist epistemology, the ordinals are plausibly more basic than the cardinals. This is just one orientation to relative priority one could take, however. Ultimately, we subscribe to an egalitarian attitude towards these formal characterizations: they are, in some sense, equally ‘legitimate’. (shrink)

One of the more distinctive features of Bob Hale and Crispin Wright’s neologicism about arithmetic is their invocation of Frege’s Constraint – roughly, the requirement that the core empirical applications for a class of numbers be “built directly into” their formal characterization. In particular, they maintain that, if adopted, Frege’s Constraint adjudicates in favor of their preferred foundation – Hume’s Principle – and against alternatives, such as the Dedekind-Peano axioms. In what follows we establish two main claims. First, we show (...) that, if sound, Hale and Wright’s arguments for Frege’s Constraint at most establish a version on which the relevant application of the naturals is transitive counting – roughly, the counting procedure by which numerals are used to answer “how many”-questions. Second, we show that this version of Frege’s Constraint fails to adjudicate in favor of Hume’s Principle. If this is the version of Frege’s Constraint that a foundation for arithmetic must respect, then Hume’s Principle no more – and no less – meets the requirement than the Dedekind-Peano axioms do. (shrink)

Since the late 1980s, the human genetics and genomics research community has been promising to usher in a “new paradigm for health care”—one that uses molecular profiling to identify human genetic variants implicated in multifactorial health risks. After the completion of the Human Genome Project in 2003, a wide range of stakeholders became committed to this “paradigm shift,” creating a confluence of investment, advocacy, and enthusiasm that bears all the marks of a “scientific/intellectual social movement” within biomedicine. Proponents of this (...) movement usually offer four ways in which their approach to medical diagnosis and health care improves upon current practices, arguing that it is more “personalized,” “predictive,” “preventive,” and “participatory” than the medical status quo. Initially, it was personalization that seemed to best sum up the movement's appeal. By 2012, however, powerful opinion leaders were abandoning “personalized medicine” in favor of a new label: “precision medicine.” The new label received a decisive seal of approval when, in January 2015, President Obama unveiled plans for a national “precision medicine initiative” to promote the development and use of genomic tools in health care. (shrink)

This Element, written for researchers and students in philosophy and the behavioral sciences, reviews and critically assesses extant work on number concepts in developmental psychology and cognitive science. It has four main aims. First, it characterizes the core commitments of mainstream number cognition research, including the commitment to representationalism, the hypothesis that there exist certain number-specific cognitive systems, and the key milestones in the development of number cognition. Second, it provides a taxonomy of influential views within mainstream number cognition research, (...) along with the central challenges these views face. Third, it identifies and critically assesses a series of core philosophical assumptions often adopted by number cognition researchers. Finally, the Element articulates and defends a novel version of pluralism about number concepts. (shrink)

This chapter offers a high-level overview of the philosophy of cognitive science and an introduction to the Oxford Handbook of Philosophy of Cognitive Science. The philosophy of cognitive science emerged out of a set of common and overlapping interests among philosophers and scientists who study the mind. We identify five categories of issues that illustrate the best work in this broad field: (1) traditional philosophical issues about the mind that have been invigorated by research in cognitive science, (2) issues regarding (...) the practice of cognitive science and its foundational assumptions, (3) issues regarding the explication and clarification of core concepts in cognitive science, (4) first-order empirical issues where philosophers participate in the interdisciplinary investigation of particular psychological phenomena, (5) traditional philosophical issues that aren’t about the mind but that can be informed by a better understanding of how the mind works. (shrink)

Number words seemingly function both as adjectives attributing cardinality properties to collections, as in Frege’s ‘Jupiter has four moons’, and as names referring to numbers, as in Frege’s ‘The number of Jupiter’s moons is four’. This leads to what Thomas Hofweber calls Frege’s Other Puzzle: How can number words function as modifiers and as singular terms if neither adjectives nor names can serve multiple semantic functions? Whereas most philosophers deny that one of these uses is genuine, we instead argue that (...) number words, like many related expressions, are polymorphic, having multiple uses whose meanings are systematically related via type shifting. (shrink)

Aims: The Research Diagnostic Criteria for Temporomandi¬bular Disorders (RDC/TMD) Axis I diagnostic algorithms were demonstrated to be reliable but below target sensitivity and specificity. Empirical data supported Axis I algorithm revisions that were valid. Axis II instruments were shown to be both reliable and valid. An international consensus workshop was convened to obtain recommendations and finalization of new Axis I diagnostic algorithms and new Axis II instruments. Methods: A comprehensive search of published TMD diagnostic literature was followed by review and (...) consensus via a formal structured process by a panel of experts for revision of the RDC/TMD. Results: The recommended Diagnostic Criteria for TMD (DC/TMD) Axis I protocol includes both a valid screener for pain diagnoses and valid criteria for the most common pain-related TMDs and for one intra-articular disorder. The Axis II protocol retains selected RDC/TMD screening instruments augmented with new instruments to better assess the interactions between pain and psychosocial functioning. A comprehensive classification system is also presented. Conclusion: The recommended evidence-based DC/TMD protocol is appropriate for use in both the clinical and research settings. Simple Axis I and II screening tests augmented by validated Axis I and Axis II instruments allow for identification of simple to complex TMD patients. (shrink)

The philosophy of cognitive science is concerned with fundamental philosophical and theoretical questions connected to the sciences of the mind. How does the brain give rise to conscious experience? Does speaking a language change how we think? Is a genuinely intelligent computer possible? What features of the mind are innate? Advances in cognitive science have given philosophers important tools for addressing these sorts of questions; and cognitive scientists have, in turn, found themselves drawing upon insights from philosophy--insights that have often (...) taken their research in novel directions. The Oxford Handbook of Philosophy of Cognitive Science brings together twenty-one newly commissioned chapters by leading researchers in this rich and fast-growing area of philosophy. It is an indispensible resource for anyone who seeks to understand the implications of cognitive science for philosophy, and the role of philosophy within cognitive science. (shrink)

In this paper, we outline and critically evaluate Thomas Hofweber’s solution to a semantic puzzle he calls Frege’s Other Puzzle. After sketching the Puzzle and two traditional responses to it—the Substantival Strategy and the Adjectival Strategy—we outline Hofweber’s proposed version of Adjectivalism. We argue that two key components—the syntactic and semantic components—of Hofweber’s analysis both suffer from serious empirical difficulties. Ultimately, this suggests that an altogether different solution to Frege’s Other Puzzle is required.

Clarke and Beck import certain assumptions about the nature of numbers. Although these are widespread within research on number cognition, they are highly contentious among philosophers of mathematics. In this commentary, we isolate and critically evaluate one core assumption: the identity thesis.

A core commitment of Bob Hale and Crispin Wright’s neologicism is their invocation of Frege’s Constraint—roughly, the requirement that the core empirical applications for a class of numbers be “built directly into” their formal characterization. According to these neologicists, if legitimate, Frege’s Constraint adjudicates in favor of their preferred foundation—Hume’s Principle—and against alternatives, such as the Dedekind–Peano axioms. In this paper, we consider a recent argument for legitimating Frege’s Constraint due to Hale, according to which the primary empirical application of (...) the naturals is transitive counting, or answering ‘how many’-questions using numerals. We make two claims regarding Hale’s argument. First, it fails to legitimate Frege’s Constraint in virtue of resting on unsupported and highly contentious assumptions. Secondly, even if sound, Hale’s argument would vindicate a version of Frege’s Constraint which fails to adjudicate in favor of Hume’s Principle over alternative characterizations of the naturals. (shrink)

Hofweber (Ontology and the ambitions of metaphysics, Oxford University Press, 2016) argues for a thesis he calls “internalism” with respect to natural number discourse: no expressions purporting to refer to natural numbers in fact refer, and no apparent quantification over natural numbers actually involves quantification over natural numbers as objects. He argues that while internalism leaves open the question of whether other kinds of abstracta exist, it precludes the existence of natural numbers, thus establishing what he calls “restricted nominalism” about (...) natural numbers. We argue that Hofweber’s internalism fails to establish restricted nominalism. Not only is his primary argument for restricted nominalism invalid, the analysis of quantification proposed threatens to collapse internalism into either a traditional form of error theory or realism. (shrink)

While consensus exists among many practitioners of ethics consultation about the need for and identification of core competencies and standards, there has been virtually no attempt to determine how these competencies and standards are best taught and assessed. We believe that clinical ethics consultation has reached a state of sufficient maturity that expert practitioners can evaluate those who are new to the field. We will outline several steps that can facilitate the creation of a certification process for clinical ethics consultants, (...) assuring the competency and quality of consultation for the patients, families, and healthcare professionals who utilize ECSs. (shrink)

Disorders of consciousness (DOC) are a family of related neurological syndromes characterized by deficits of varying degrees of wakefulness (e.g., sleep–wake cycles and arousal) or awareness (e.g., reacting to stimuli, interacting with the environment). Although coma rarely persists for more than a few weeks, some patients remain in a subsequent vegetative state or a minimally conscious state for months or years. Caring for patients with DOC raises ethical questions, but the perspectives of healthcare providers on these questions remain poorly documented. (...) We conducted a qualitative study involving healthcare providers with different backgrounds. Semistructured interviews were used to explore attitudes toward ethical issues. We found that contextual (e.g., time, resource allocation) and relational aspects (e.g., communication process, families) shaped how ethical challenges surfaced and were managed. We call for greater awareness of contextual, institutional and social aspects and focus on these issues in training programs. (shrink)

The field of psychology, including cognitive science, is vexed by a crisis of confidence. Although the causes and solutions are varied, we focus here on a common logical problem in inference. The default mode of inference is significance testing, which has a free lunch property where researchers need not make detailed assumptions about the alternative to test the null hypothesis. We present the argument that there is no free lunch; that is, valid testing requires that researchers test the null against (...) a well-specified alternative. We show how this requirement follows from the basic tenets of conventional and Bayesian probability. Moreover, we show in both the conventional and Bayesian framework that not specifying the alternative may lead to rejections of the null hypothesis with scant evidence. We review both frequentist and Bayesian approaches to specifying alternatives, and we show how such specifications improve inference. The field of cognitive science will benefit because consideration of reasonable alternatives will undoubtedly sharpen the intellectual underpinnings of research. (shrink)

In the care of patients with disorders of consciousness (DOC), some ethical difficulties stem from the challenges of accurate diagnosis and the uncertainty of prognosis. Current neuroimaging research on these disorders could eventually improve the accuracy of diagnoses and prognoses and therefore change the context of end-of-life decision making. However, the perspective of healthcare professionals on these disorders remains poorly understood and may constitute an obstacle to the integration of research. We conducted a qualitative study involving healthcare professionals from an (...) acute care university medical center. A short questionnaire captured demographic data as well as the experience of participants with DOC patients. A semi-structured interview was used to explore attitudes toward ethical issues identified in a previous literature review. Qualitative content analysis of interviews was conducted with the NVivo software. Accurate diagnosis among DOC is often regarded as a challenge, but this was generally not the case for our participants because most reported high confidence in DOC diagnoses. However, participants reported struggling with prognosis, especially because of its essential role for end-of-life decision making and communication with families. Variability of opinion between healthcare professionals was reported and identified by some as a minor issue while others stressed how families struggle with different medical opinions. End-of-life decision making encompassed a large proportion of ethical challenges in these patients, and the removal of artificial nutrition and hydration created significant discomfort in a minority of participants. The concept of futility was subject to wide-ranging understandings with both favorable and unfavorable opinions. Our data suggest that to ensure the incorporation of new evidence-based advances, attention should be directed to the real-world practices and challenges of accurate diagnosis and prognosis. Given pervasive challenges in end-of-life care, we recommend improved training of healthcare professionals in the care of patients with DOC, particularly in end-of life care, understanding the context of decision making, and determining how to optimally integrate new neuroscience research on the care of patients with DOC. (shrink)

This chapter presents two models of priming. The primary task under consideration is the identification of words presented visually at threshold. The first model, REMI, is a model for long-term priming in implicit memory. It explains repetition priming effects by assuming that during study of a word some contextual information is added to the corresponding lexical trace. This contextual information stored during the study task will tend to match the contextual information present during the test task, leading subjects to prefer (...) studied words over non-studied words. The second model, ROUSE, is a model of short-term priming. ROUSE stands for Responding Optimally with Unknown Sources of Evidence, and it is able to explain an intricate pattern of results. (shrink)

Saul Kripke once noted that there is a tight connection between computation and de re knowledge of whatever the computation acts upon. For example, the Euclidean algorithm can produce knowledge of which number is the greatest common divisor of two numbers. Arguably, algorithms operate directly on syntactic items, such as strings, and on numbers and the like only via how the numbers are represented. So we broach matters of notation. The purpose of this article is to explore the relationship between (...) the notations acceptable for computation, the usual idealizations involved in theories of computability, flowing from Alan Turing’s monumental work, and de re propositional attitudes toward numbers and other mathematical objects. (shrink)

In January 2023, the Science and Security Board of the Bulletin of the Atomic Scientists moved the hands of the Doomsday Clock forward to 90 s before midnight.

The topic of epistemic normativity has come to the fore of recent work in epistemology, and so naturally, theories of knowledge, truth and justification have been increasingly held accountable to preserving normative epistemological platitudes. Central to discussions of epistemic normativity are questions about epistemic agency and epistemic value. Here, our aim is to take up some of these issues as they come to bear on the rather unconventional brand of epistemology that was defended by Richard Rorty. Our purpose is (...) to explore whether Rorty’s epistemology—or perhaps his replacement for epistemology—can preserve these normative platitudes about epistemic agency, responsibility, achievement, and the value of knowledge. Our conclusion is a negative one: that Rorty’s commitments leave him firmly at odds with some of the most plausible assumptions about epistemic agency and epistemic value. (shrink)

The COVID-19 pandemic prompted immense work on the investigation of the SARS-CoV-2 virus. Rapid, accurate, and consistent interpretation of generated data is thereby of fundamental concern. Ontologies––structured, controlled, vocabularies––are designed to support consistency of interpretation, and thereby to prevent the development of data silos. This paper describes how ontologies are serving this purpose in the COVID-19 research domain, by following principles of the Open Biological and Biomedical Ontology (OBO) Foundry and by reusing existing ontologies such as the Infectious Disease Ontology (...) (IDO) Core, which provides terminological content common to investigations of all infectious diseases. We report here on the development of an IDO extension, the Virus Infectious Disease Ontology (VIDO), a reference ontology covering viral infectious diseases. We motivate term and definition choices, showcase reuse of terms from existing OBO ontologies, illustrate how ontological decisions were motivated by relevant life science research, and connect VIDO to the Coronavirus Infectious Disease Ontology (CIDO). We next use terms from these ontologies to annotate selections from life science research on SARS-CoV-2, highlighting how ontologies employing a common upper-level vocabulary may be seamlessly interwoven. Finally, we outline future work, including bacteria and fungus infectious disease reference ontologies currently under development, then cite uses of VIDO and CIDO in host-pathogen data analytics, electronic health record annotation, and ontology conflict-resolution projects. (shrink)

The rapid growth of cultural evolutionary science, its expansion into numerous fields, its use of diverse methods, and several conceptual problems have outpaced corollary developments in theory and philosophy of science. This has led to concern, exemplified in results from a recent survey conducted with members of the Cultural Evolution Society, that the field lacks ‘knowledge synthesis’, is poorly supported by ‘theory’, has an ambiguous relation to biological evolution and uses key terms (e.g. ‘culture’, ‘social learning’, ‘cumulative culture’) in ways (...) that hamper operationalization in models, experiments and field studies. Although numerous review papers in the field represent and categorize its empirical findings, the field's theoretical challenges receive less critical attention even though challenges of a theoretical or conceptual nature underlie most of the problems identified by Cultural Evolution Society members. Guided by the heterogeneous ‘grand challenges’ emergent in this survey, this paper restates those challenges and adopts an organizational style requisite to discussion of them. The paper's goal is to contribute to increasing conceptual clarity and theoretical discernment around the most pressing challenges facing the field of cultural evolutionary science. It will be of most interest to cultural evolutionary scientists, theoreticians, philosophers of science and interdisciplinary researchers. (shrink)

> Wealthy nations must do much more, much faster. The United Nations General Assembly in September 2021 will bring countries together at a critical time for marshalling collective action to tackle the global environmental crisis. They will meet again at the biodiversity summit in Kunming, China, and the climate conference 26) in Glasgow, UK. Ahead of these pivotal meetings, we—the editors of health journals worldwide—call for urgent action to keep average global temperature increases below 1.5°C, halt the destruction of nature (...) and protect health. Health is already being harmed by global temperature increases and the destruction of the natural world, a state of affairs health professionals have been bringing attention to for decades.1 The science is unequivocal; a global increase of 1.5°C above the preindustrial average and the continued loss of biodiversity risk catastrophic harm to health that will be impossible to reverse.2 3 Despite the world’s necessary preoccupation with COVID-19, we cannot wait for the pandemic to pass to rapidly reduce emissions. Reflecting the severity of the moment, this editorial appears in health journals across the world. We are united in recognising that only fundamental and equitable changes to societies will reverse our current trajectory. The risks to health of increases above 1.5°C are now well established.2 Indeed, no temperature rise is ‘safe’. In the past 20 years, heat-related mortality among people aged over 65 has increased by more than 50%.4 Higher temperatures have brought increased dehydration and renal function loss, dermatological malignancies, tropical infections, adverse mental health outcomes, pregnancy complications, allergies, and cardiovascular and pulmonary morbidity and mortality.5 6 Harms disproportionately affect the most vulnerable, including children, older populations, ethnic minorities, poorer communities and those with underlying health problems.2 4 Global heating is also contributing to the decline in …. (shrink)

A critique of Rorty's own provocative political philosophy, as well as an in-depth look at both the issues concerning the relationship between the public and the private, and arguments on the role of reason in liberal political discourse generally.

Biological evolution provides a creative fount of complex and subtle adaptations, often surprising the scientists who discover them. However, because evolution is an algorithmic process that transcends the substrate in which it occurs, evolution’s creativity is not limited to nature. Indeed, many researchers in the field of digital evolution have observed their evolving algorithms and organisms subverting their intentions, exposing unrecognized bugs in their code, producing unexpected adaptations, or exhibiting outcomes uncannily convergent with ones in nature. Such stories routinely reveal (...) creativity by evolution in these digital worlds, but they rarely fit into the standard scientific narrative. Instead they are often treated as mere obstacles to be overcome, rather than results that warrant study in their own right. The stories themselves are traded among researchers through oral tradition, but that mode of information transmission is inefficient and prone to error and outright loss. Moreover, the fact that these stories tend to be shared only among practitioners means that many natural scientists do not realize how interesting and lifelike digital organisms are and how natural their evolution can be. To our knowledge, no collection of such anecdotes has been published before. This paper is the crowd-sourced product of researchers in the fields of artificial life and evolutionary computation who have provided first-hand accounts of such cases. It thus serves as a written, fact-checked collection of scientifically important and even entertaining stories. In doing so we also present here substantial evidence that the existence and importance of evolutionary surprises extends beyond the natural world, and may indeed be a universal property of all complex evolving systems. (shrink)

At the forefront of international concerns about global legislation and regulation, a host of noted environmentalists and business ethicists examine ethical issues in consumption from the points of view of environmental sustainability, economic development, and free enterprise.