Throughout the biological and biomedical sciences there is a growing need for, prescriptive ‘minimum information’ (MI) checklists specifying the key information to include when reporting experimental results are beginning to find favor with experimentalists, analysts, publishers and funders alike. Such checklists aim to ensure that methods, data, analyses and results are described to a level sufficient to support the unambiguous interpretation, sophisticated search, reanalysis and experimental corroboration and reuse of data sets, facilitating the extraction of maximum value from data sets (...) them. However, such ‘minimum information’ MI checklists are usually developed independently by groups working within representatives of particular biologically- or technologically-delineated domains. Consequently, an overview of the full range of checklists can be difficult to establish without intensive searching, and even tracking thetheir individual evolution of single checklists may be a non-trivial exercise. Checklists are also inevitably partially redundant when measured one against another, and where they overlap is far from straightforward. Furthermore, conflicts in scope and arbitrary decisions on wording and sub-structuring make integration difficult. This presents inhibit their use in combination. Overall, these issues present significant difficulties for the users of checklists, especially those in areas such as systems biology, who routinely combine information from multiple biological domains and technology platforms. To address all of the above, we present MIBBI (Minimum Information for Biological and Biomedical Investigations); a web-based communal resource for such checklists, designed to act as a ‘one-stop shop’ for those exploring the range of extant checklist projects, and to foster collaborative, integrative development and ultimately promote gradual integration of checklists. (shrink)

Methodological critique of the sociological theory "spontaneous cooperation" to explain the revolution in Germany in 1989. This approach represented the german sociologists Dieter Opp and Detlef Pollack. The author reconstructs the two statements. Opp's approach is logically inconsistent. This approach is also unfit for scientific prediction, but Opp says the possibility of prediction is a necessary criterion for a scientific theory. Pollack's systemtheoretical approach ignores the really existing organized resistance of the subversive groups in Leipzig, for example the "Working group (...) for human rights" or the "Working group for Justice". Miracle or surprise chance are scientifically anacceptable models to explain a revolution. Both economically and politically offered the capitalist welfare state more for the workers than the socialism. So people noticed socialism as a system with more work for less prosperity and without civil rights, as a system of "exploitation by inefficiency" (Elsenhans). The author describes the revolution as a result of very effective collaboration between people, who willing to take risks and wanted to emigrate from the GDR to West, and the subversive groups, that could organize the revolutionary resistance. - This is a possible interpretation of the revolution from the interaction of transition-theory and voice-and-exit-theory (Hirschman). (shrink)

Simple claims with the verb ‘seem’, as well as the specific sensory verbs, ‘look’, ‘sound’, etc., require the speaker to have some relevant kind of perceptual acquaintance (Pearson, 2013; Ninan, 2014). But different forms of these reports differ in their perceptual requirements. For example, the copy raising (CR) report, ‘Tom seems like he’s cooking’ requires the speaker to have seen Tom, while its expletive subject (ES) variant, ‘It seems like Tom is cooking’, does not (Rogers, 1972; Asudeh and Toivonen, 2012). (...) This contrast has led some theorists to hold that the matrix subject in CR constructions is uniformly interpreted as the perceptual source (p-source) (Asudeh and Toivonen, 2012; Rett and Hyams, 2014). Others, based on examples of CR reports that seem not to require perception of the referent of the matrix subject, have taken the p-source interpretation instead to be non-uniform across CR reports (Landau, 2011; Doran, 2015). We reconsider these theoretical approaches to copy raising in light of new experimental work probing the sensitivity of these requirements to the matrix verb, the embedded ‘like’-clause, and the context. While we find some motivation for a non-uniform p-source analysis, it comes from importantly different cases than those others have relied on. Furthermore, our findings cast doubt on the prevalent assumption that the perceptual requirements of CR reports are to be captured solely by the presence or absence of the p-source interpretation. We suggest that the data motivating a non-uniform p-source view are better captured by an alternative approach, which makes use of a more minimal evidential source role, in place of the perceptual source role. We close by considering the relationship between English copy raising and evidential constructions cross-linguistically. (shrink)

In theoretical work about the language of personal taste, the canonical example is the simple predicate of personal taste, 'tasty'. We can also express the same positive gustatory evaluation with the complex expression, 'taste good'. But there is a challenge for an analysis of 'taste good': While it can be used equivalently with 'tasty', it need not be (for instance, imagine it used by someone who can identify good wines by taste but doesn't enjoy them). This kind of two-faced behavior (...) systematically arises with complex sensory-evaluative predicates, including those with other appearance verbs, such as 'look splendid' and 'sound nice'. I examine two strategies for capturing these different uses: one that posits an ambiguity in appearance verbs, and one that does not. The former is in line with an approach to 'look'-statements prominent in work in philosophy of perception, and I consider how the motivation given in that tradition carries over to the present context. I then show how the data used to support the verbal ambiguity approach can equally be captured on the second strategy, which appeals only to independently-motivated flexibility in adjective meaning. I close by discussing some considerations that are relevant for choosing between the two options. (shrink)

Assertions about appearances license inferences about the speaker's perceptual experience. For instance, if I assert, 'Tom looks like he's cooking', you will infer both that I am visually acquainted with Tom (what I call the "individual acquaintance inference"), and that I am visually acquainted with evidence that Tom is cooking (what I call the "evidential acquaintance inference"). By contrast, if I assert, 'It looks like Tom is cooking', only the latter inference is licensed. I develop an account of the acquaintance (...) inferences of appearance assertions building on two main previous lines of research: first, the copy raising literature, which has aimed to account for individual acquaintance inferences through the "perceptual source" semantic role; second, the subjectivity literature, which has focused on the status of acquaintance inferences with predicates of personal taste, but hasn't given much attention to the added complexities introduced by appearance language. I begin by developing what I take to be the most empirically-sound version of a perceptual source analysis. I then show how its insights can be maintained, while however taking anything about perception out of the truth conditions of appearance sentences. This, together with the assumption that appearance assertions express experiential attitudes, allows us to capture the acquaintance inferences of bare appearance assertions without making incorrect predictions about the behavior of appearance verbs in embedded environments. (shrink)

Conceptual engineering involves revising our concepts. It can be pursued as a specific philosophical methodology, but is also common in ordinary, non-philosophical, contexts. How does our capacity for conceptual engineering fit into human cognitive life more broadly? I hold that conceptual engineering is best understood alongside practices of conceptual exploration, examples of which include conceptual supposition (i.e., suppositional reasoning about alternative concepts), and conceptual comparison (i.e., comparisons between possible concept choices). Whereas in conceptual engineering we aim to change the concepts (...) we use, in conceptual exploration, we reason about conceptual possibilities. I approach conceptual exploration via the linguistic tools we use to communicate about concepts, using metalinguistic negotiation, convention-shifting conditionals, and metalinguistic comparatives as my key examples. I present a linguistic framework incorporating conventions that can account for this communication in a unified way. Furthermore, I argue that conceptual exploration helps undermine skepticism about conceptual engineering itself. (shrink)

Faultless disagreement and faultless retraction have been taken to motivate relativism for predicates of personal taste, like ‘tasty’. Less attention has been devoted to the question of what aspect of their meaning underlies this relativist behavior. This paper illustrates these same phenomena with a new category of expressions: appearance predicates, like ‘tastes vegan’ and ‘looks blue’. Appearance predicates and predicates of personal taste both fall into the broader category of experiential predicates. Approaching predicates of personal taste from this angle suggests (...) that their relativist behavior is due to their experience-sensitivity, rather than their evaluative meaning. Furthermore, appearance predicates hold interest beyond what they can teach us about predicates of personal taste. Examination of a variety of uses of appearance predicates reveals that they give rise to relativist behavior for a variety of reasons—including some that apply also to other types of expressions, such as epistemic modals and comparative terms. This paper thus serves both to probe the source of relativist behavior in discourse about personal taste, as well as to map out this kind of behavior in the rich and under-explored discourse about appearances. (shrink)

We offer a novel account of metalinguistic comparatives, such as 'Al is more wise than clever'. On our view, metalinguistic comparatives express comparative commitments to conventions. Thus, 'Al is more wise than clever' expresses that the speaker has a stronger commitment to a convention on which Al is wise than to a convention on which she is clever. This view avoids problems facing previous approaches to metalinguistic comparatives. It also fits within a broader framework—independently motivated by metalinguistic negotiations and convention-shiftingexpressions— (...) that gives linguistic conventions a role in the semantics. (shrink)

This paper focuses on the phenomenology of awareness and the second reduction.

An English translation of Pierre Bayle's posthumous last book, Entretiens de Maxime et de Themiste (1707), in which Bayle defends his skeptical position on the problem of the evil. This book is often cited and attacked by G.W. Leibniz in his Theodicy (1710). Over one hundred pages of original philosophical and historical material introduce the translation, providing it with context and establishing the work's importance.

This paper focuses on liberation as the experience of pervasive radiance.

Some assertions give rise to the acquaintance inference: the inference that the speaker is acquainted with some individual. Discussion of the acquaintance inference has previously focused on assertions about aesthetic matters and personal tastes (e.g. 'The cake is tasty'), but it also arises with reports about how things seem (e.g. 'Tom seems like he's cooking'). 'Seem'-reports give rise to puzzling acquaintance behavior, with no analogue in the previously-discussed domains. In particular, these reports call for a distinction between the specific acquaintance (...) inference (that the speaker is acquainted with a specific individual) and the general acquaintance inference (that the speaker is acquainted with something or other of relevance). We frame a novel empirical generalization -- the specific with stage-level generalization -- that systematizes the observed behavior, in terms of the semantics of the embedded 'like'-clause. We present supporting experimental work, and explain why the generalization makes sense given the evidential role of 'seem'-reports. Finally, we discuss the relevance of this result for extant proposals about the semantics of 'seem'-reports. More modestly, it fills a gap in previous theories by identifying which reports get which of two possible interpretations; more radically, it suggests a revision of the kind of explanation that should be given for the acquaintance behavior in question. (shrink)

This paper focuses on the path of appearance and awareness.

This paper focuses on mystical humanism as magical realism.

In ordinary conversation, speakers disagree not only about worldly facts, but also about how to use language to describe the world. For example, disagreement about whether Buffalo is in the American Midwest, whether Pluto is a planet, or whether someone has been canceled, can persist even with agreement about all the relevant facts. The speakers may still engage in “metalinguistic negotiation”—disputing what to mean by “Midwest”, “planet”, or “cancel”. I first motivate an approach to metalinguistic negotiation that generalizes a Stalnakerian (...) theory of communication by including linguistic commitments in the conversational common ground. Then, I turn to cases where the very status of a disagreement as metalinguistic or factual is unclear or contested. For example, after the publication of the New York Times Magazine’s 1619 Project, some responses claimed to identify factual errors, while others took those same “errors” to be matters of interpretation. I’ll consider how to extend our theorizing about metalinguistic negotiation to this type of (even more) “meta” disagreement, using the discussion following the 1619 Project as a case study. On my view, in most such cases, there will be a metalinguistic negotiation going on. Still, I explain several ways in which, despite a dispute being metalinguistic, the factualist side can sometimes receive important vindication. I also discuss why it can make sense for speakers to contest the status of a dispute. (shrink)

This paper describes subjectivity as the manifestation of the primordial awareness field.

This paper focuses on the phenomenology of symbolic transmissions.

This paper describes the non dual relationship between the visible and the invisible.

This paper focuses on the radiance of awareness.

This paper uses a schema for infinite regress arguments to provide a solution to the problem of the infinite regress of justification. The solution turns on the falsity of two claims: that a belief is justified only if some belief is a reason for it, and that the reason relation is transitive.

This paper reviews the hole argument as an argument against spacetime substantivalism. After a careful presentation of the argument itself, I critically review possible responses.

Is calculation possible without language? Or is the human ability for arithmetic dependent on the language faculty? To clarify the relation between language and arithmetic, we studied numerical cognition in speakers of Mundurukú, an Amazonian language with a very small lexicon of number words. Although the Mundurukú lack words for numbers beyond 5, they are able to compare and add large approximate numbers that are far beyond their naming range. However, they fail in exact arithmetic with numbers larger than 4 (...) or 5. Our results imply a distinction between a nonverbal system of number approximation and a language-based counting system for exact number and arithmetic. (shrink)

I argue, through appeal to the distinction between analysis and decomposition described by Dummett, that Wittgenstein employs both of those notions in the Tractatus. I then bring this interpretation to bear upon the issue of propositional unity, where I formulate an objection to the views of both Leonard Linksy and José Zalabardo. I show that both Linsky and Zalabardo fail to acknowledge the distinction between analysis and decomposition present in the Tractatus, and that they consequently mischaracterise Wittgenstein’s position with respect (...) to propositional unity. (shrink)

This paper focuses on Heidegger's presentation of becoming self liberated.

This paper focuses on the phenomenology of essence and appearance in Merleau Ponty.

This paper focuses on the realm of omnipotence from a Lacanian viewpoint.

This paper focuses on awareness and movement in dzogchen.

This paper focuses on the phenomenology of timeless awareness.

This paper focuses on the phenomenology of healing within the awareness field.

This paper focuses on the phenomenology of the experiential awareness field.

This paper focuses in detail on the practice of meditation as becoming aware of awareness as a field vast and multidimensional.

This paper focuses on deathlessness awareness.

This paper focuses on the appearance of emptiness through time.

Empirical philosophers of science aim to base their philosophical theories on observations of scientific practice. But since there is far too much science to observe it all, how can we form and test hypotheses about science that are sufficiently rigorous and broad in scope, while avoiding the pitfalls of bias and subjectivity in our methods? Part of the answer, we claim, lies in the computational tools of the digital humanities, which allow us to analyze large volumes of scientific literature. Here (...) we advocate for the use of these methods by addressing a number of large-scale, justificatory concerns—specifically, about the epistemic value of journal articles as evidence for what happens elsewhere in science, and about the ability of DH tools to extract this evidence. Far from ignoring the gap between scientific literature and the rest of scientific practice, effective use of DH tools requires critical reflection about these relationships. (shrink)

In this paper, I argue for a novel reading of Spinoza’s position in his exchangewith Boyle about Boyle’s experiment with nitre. Boyle claimed to have shownthrough experiments that nitre ceased to be nitre after heating. Spinozadisagreed and proposed the alternative hypothesis that nitre has changed itsstate and not its nature. Spinoza’s position was construed in the literature asrational scepticism denying that experiments can yield knowledge ofessences because all sensory experience is underdetermined and open tomultiple interpretations. I argue for an alternative (...) reading of Spinoza’sposition which focuses on Bacon’s notion of crucial instance. According tothis reading, Spinoza did not deny the possibility of knowing byexperimentation whether nitre has changed its nature, he asked for a crucialinstance, i.e. an experiment that would refute the hypothesis that nitre haschanged merely its state. Spinoza’s argumentative strategy shows that,contrary to the mainstream reading, the representational content of sensoryideas can be determined even if it does not represent the essence of theobject: we can know with absolute, rather than merely moral, certaintywhether nitre ceased to be nitre without knowing what nitre is. (shrink)

This paper focuses on the unfolding of awareness as embodiment of luminous spaceousness.

This paper focuses on the hermeneutic of reading text and hearing text.

This paper focuses on meditation as natural luminousity.

We make some remarks on the mathematics and metaphysics of the hole argument, in response to a recent article in this journal by Weatherall ([2018]). Broadly speaking, we defend the mainstream philosophical literature from the claim that correct usage of the mathematics of general relativity `blocks' the argument.

In this paper I offer an argument against one important version of panentheism, that is, mereological panentheism. Although panentheism has proven difficult to define, I provide a working definition of the view, and proceed to argue that given this way of thinking about the doctrine, mereological accounts of panentheism have serious theological drawbacks. I then explore some of these theological drawbacks. In a concluding section I give some reasons for thinking that the classical theistic alternative to panentheism is preferable, all (...) things considered. (shrink)

The mapping of numbers onto space is fundamental to measurement and to mathematics. Is this mapping a cultural invention or a universal intuition shared by all humans regardless of culture and education? We probed number-space mappings in the Mundurucu, an Amazonian indigene group with a reduced numerical lexicon and little or no formal education. At all ages, the Mundurucu mapped symbolic and nonsymbolic numbers onto a logarithmic scale, whereas Western adults used linear mapping with small or symbolic numbers and logarithmic (...) mapping when numbers were presented nonsymbolically under conditions that discouraged counting. This indicates that the mapping of numbers onto space is a universal intuition and that this initial intuition of number is logarithmic. The concept of a linear number line appears to be a cultural invention that fails to develop in the absence of formal education. (shrink)

Two extremely detailed accounts of temporal experience can be found in the work of C. D. Broad. These accounts have been subject to considerable criticism. I argue that, when we look more carefully at Broad’s work, we find that much of this criticism fails to find its target. I show that the objection that ultimately proves troubling for Broad stems from his commitment to two principles: i) the Thin-PSA, and ii) the ‘Overlap’ claim. I use this result to demonstrate that (...) we can learn two extremely important lessons from Broad’s work on temporal experience. -/- The first lesson is that there is a structural problem facing any account that commits to these two principles. This is significant given that a number of recent accounts of temporal experience are so committed. The second lesson is that the problem facing these accounts stems only from commitment to the Thin-PSA and ‘Overlap’, rather than to commitment to a particular conception of how experiences are to be individuated. This, I argue, gives us reason to reject Tye’s recent claim that the problems facing accounts of temporal experience can be dissolved simply by making stipulations about how experiences are to be individuated. (shrink)

This paper explores the form of Marx’s and Engels’s critique in German Ideology. Against traditional claims, it argues that Marx and Engels, working on the manuscripts of 1845–47, were not concerned with establishing their own theory of society and history, but with the quarrel with Young-Hegelians and “true socialists” instead. Focusing on the polemical character of German Ideology, one is able to trace the working process of Marx and Engels. For this purpose, it is analysed how the concept of ideology (...) and the scheme of something acquiring independent existence are used throughout the manuscripts. Hence it becomes clear that Marx’s and Engels’s critique is not coherent, but has internal frictions. Utilising concepts and schemes of argumentation in the way of tools, varied in detail by context, they formed their own assumptions and critical replies. Marx and Engels developed the polemics of German Ideology in a strikingly dynamic manner. (shrink)

Binding specificity is a centrally important concept in molecular biology, yet it has received little philosophical attention. Here I aim to remedy this by analyzing binding specificity as a causal property. I focus on the concept’s role in drug design, where it is highly prized and hence directly studied. From a causal perspective, understanding why binding specificity is a valuable property of drugs contributes to an understanding of causal selection—of how and why scientists distinguish between causes, not just causes from (...) noncauses. In particular, the specificity of drugs is precisely what underwrites their value as experimental interventions on biological processes. (shrink)

Jacques Monod (1971) argued that certain molecular processes rely critically on the property of chemical arbitrariness, which he claimed allows those processes to “transcend the laws of chemistry”. It seems natural, as some philosophers have done, to interpret this in modal terms: a biological relationship is chemically arbitrary if it is possible, within the constraints of chemical “law”, for that relationship to have been otherwise than it is. But while modality is certainly important for understanding chemical arbitrariness, understanding its biological (...) role also requires an account of the concrete causal-functional features that distinguish arbitrary from non-arbitrary phenomena. In this paper I elaborate on this under-emphasised aspect by offering a general account of these features: arbitrary relations are instantiated by mechanisms that involve molecular adapters, which causally couple two properties or processes which would otherwise be uncorrelated. Additionally, adapters work by acting as intermediate rather than cooperating causes. (shrink)

Ontologies, as the term is used in informatics, are structured vocabularies comprised of human- and computer-interpretable terms and relations that represent entities and relationships. Within informatics fields, ontologies play an important role in knowledge and data standardization, representation, integra- tion, sharing and analysis. They have also become a foundation of artificial intelligence (AI) research. In what follows, we outline the Coronavirus Infectious Disease Ontology (CIDO), which covers multiple areas in the domain of coronavirus diseases, including etiology, transmission, epidemiology, pathogenesis, diagnosis, (...) prevention, and treatment. We emphasize CIDO development relevant to COVID-19. (shrink)

Theophrastus' treatise "Metaphysics" contains a compact and critical reconstruction of unsolved systematic problems of classical Greek philosophy. It is primarily about fundamental problems of ontology and natural philosophy, such as the question of the interdependence of principles and perceptible phenomena or the plausibility of teleology as a methodical principle of the explanation of nature. The aim of the critical Greek-German edition (with introduction and commentary) is to make visible the systematic significance of Theophrastus' critique of metaphysics.

The aim of this paper is to assess the relevance of somatic evolution by natural selection to our understanding of cancer development. I do so in two steps. In the first part of the paper, I ask to what extent cancer cells meet the formal requirements for evolution by natural selection, relying on Godfrey-Smith’s (2009) framework of Darwinian populations. I argue that although they meet the minimal requirements for natural selection, cancer cells are not paradigmatic Darwinian populations. In the second (...) part of the paper, I examine the most important examples of adaptation in cancer cells. I argue that they are not significant accumulations of evolutionary changes, and that as a consequence natural selection plays a lesser role in their explanation. Their explanation, I argue, is best sought in the previously existing wiring of the healthy cells. (shrink)