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)

The current COVID-19 pandemic and the previous SARS/MERS outbreaks of 2003 and 2012 have resulted in a series of major global public health crises. We argue that in the interest of developing effective and safe vaccines and drugs and to better understand coronaviruses and associated disease mechenisms it is necessary to integrate the large and exponentially growing body of heterogeneous coronavirus data. Ontologies play an important role in standard-based knowledge and data representation, integration, sharing, and analysis. Accordingly, we initiated the (...) development of the community-based Coronavirus Infectious Disease Ontology in early 2020. -/- As an Open Biomedical Ontology (OBO) library ontology, CIDO is open source and interoperable with other existing OBO ontologies. CIDO is aligned with the Basic Formal Ontology and Viral Infectious Disease Ontology. CIDO has imported terms from over 30 OBO ontologies. For example, CIDO imports all SARS-CoV-2 protein terms from the Protein Ontology, COVID-19-related phenotype terms from the Human Phenotype Ontology, and over 100 COVID-19 terms for vaccines (both authorized and in clinical trial) from the Vaccine Ontology. CIDO systematically represents variants of SARS-CoV-2 viruses and over 300 amino acid substitutions therein, along with over 300 diagnostic kits and methods. CIDO also describes hundreds of host-coronavirus protein-protein interactions (PPIs) and the drugs that target proteins in these PPIs. CIDO has been used to model COVID-19 related phenomena in areas such as epidemiology. The scope of CIDO was evaluated by visual analysis supported by a summarization network method. CIDO has been used in various applications such as term standardization, inference, natural language processing (NLP) and clinical data integration. We have applied the amino acid variant knowledge present in CIDO to analyze differences between SARS-CoV-2 Delta and Omicron variants. CIDO's integrative host-coronavirus PPIs and drug-target knowledge has also been used to support drug repurposing for COVID-19 treatment. -/- CIDO represents entities and relations in the domain of coronavirus diseases with a special focus on COVID-19. It supports shared knowledge representation, data and metadata standardization and integration, and has been used in a range of applications. (shrink)

Current COVID-19 pandemic and previous SARS/MERS outbreaks have caused a series of major crises to global public health. We must integrate the large and exponentially growing amount of heterogeneous coronavirus data to better understand coronaviruses and associated disease mechanisms, in the interest of developing effective and safe vaccines and drugs. Ontologies have emerged to play an important role in standard knowledge and data representation, integration, sharing, and analysis. We have initiated the development of the community-based Coronavirus Infectious Disease Ontology (CIDO). (...) As an Open Biomedical Ontology (OBO) library ontology, CIDO is an open source and interoperable with other existing OBO ontologies. In this article, the general architecture and the design patterns of the CIDO are introduced, CIDO representation of coronaviruses, phenotypes, anti-coronavirus drugs and medical devices (e.g. ventilators) are illustrated, and an application of CIDO implemented to identify repurposable drug candidates for effective and safe COVID-19 treatment is presented. (shrink)

COVID-19 often manifests with different outcomes in different patients, highlighting the complexity of the host-pathogen interactions involved in manifestations of the disease at the molecular and cellular levels. In this paper, we propose a set of postulates and a framework for systematically understanding complex molecular host-pathogen interaction networks. Specifically, we first propose four host-pathogen interaction (HPI) postulates as the basis for understanding molecular and cellular host-pathogen interactions and their relations to disease outcomes. These four postulates cover the evolutionary dispositions involved (...) in HPIs, the dynamic nature of HPI outcomes, roles that HPI components may occupy leading to such outcomes, and HPI checkpoints that are critical for specific disease outcomes. Based on these postulates, an HPI Postulate and Ontology (HPIPO) framework is proposed to apply interoperable ontologies to systematically model and represent various granular details and knowledge within the scope of the HPI postulates, in a way that will support AI-ready data standardization, sharing, integration, and analysis. As a demonstration, the HPI postulates and the HPIPO framework were applied to study COVID-19 with the Coronavirus Infectious Disease Ontology (CIDO), leading to a novel approach to rational design of drug/vaccine cocktails aimed at interrupting processes occurring at critical host-coronavirus interaction checkpoints. Furthermore, the host-coronavirus protein-protein interactions (PPIs) relevant to COVID-19 were predicted and evaluated based on prior knowledge of curated PPIs and domain-domain interactions, and how such studies can be further explored with the HPI postulates and the HPIPO framework is discussed. (shrink)

The idea that technologies can change moral beliefs and practices is an old one. But how, exactly, does this happen? This paper builds on an emerging field of inquiry by developing a synoptic taxonomy of the mechanisms of techno-moral change. It argues that technology affects moral beliefs and practices in three main domains: decisional (how we make morally loaded decisions), relational (how we relate to others) and perceptual (how we perceive situations). It argues that across these three domains there are (...) six primary mechanisms of techno-moral change: (i) adding options; (ii) changing decision-making costs; (iii) enabling new relationships; (iv) changing the burdens and expectations within relationships; (v) changing the balance of power in relationships; and (vi) changing perception (information, mental models and metaphors). The paper also discusses the layered, interactive and second-order effects of these mechanisms. (shrink)

Essentialism in philosophy is the position that things, especially kinds of things, have essences, or sets of properties, that all members of the kind must have, and the combination of which only members of the kind do, in fact, have. It is usually thought to derive from classical Greek philosophy and in particular from Aristotle’s notion of “what it is to be” something. In biology, it has been claimed that pre-evolutionary views of living kinds, or as they are sometimes called, (...) “natu-ral kinds”, are essentialist. This static view of living things presumes that no tran-sition is possible in time or form between kinds, and that variation is regarded as accidental or inessential noise rather than important information about taxa. In contrast it is held that Darwinian, and post-Darwinian, biology relies upon varia-tion as important and inevitable properties of taxa, and that taxa are not, therefore, kinds but historical individuals. Recent attempts have been made to undercut this account, and to reinstitute essentialism in biological kind terms. Others argue that essentialism has not ever been a historical reality in biology and its predecessors. In this chapter, I shall outline the many meanings of the notion of essentialism in psychology and social science as well as science, and discuss pro- and anti-essentialist views, and some recent historical revisionism. It turns out that nobody was essentialist to speak of in the sense that is antievolutionary in biology, and that much confusion rests on treating the one word, “essence” as meaning a single notion when in fact there are many. I shall also discuss the philosophical implica-tions of essentialism, and what that means one way or the other for evolutionary biology. Teaching about evolution relies upon narratives of change in the ways the living world is conceived by biologists. This is a core narrative issue. (shrink)

The vision of natural kinds that is most common in the modern philosophy of biology, particularly with respect to the question whether species and other taxa are natural kinds, is based on a revision of the notion by Mill in A System of Logic. However, there was another conception that Whewell had previously captured well, which taxonomists have always employed, of kinds as being types that need not have necessary and sufficient characters and properties, or essences. These competing views employ (...) different approaches to scientific methodologies: Mill’s class-kinds are not formed by induction but by deduction, while Whewell’s type-kinds are inductive. More recently, phylogenetic kinds (clades, or monophyletic-kinds) are inductively projectible, and escape Mill’s strictures. Mill’s version represents a shift in the notions of kinds from the biological to the physical sciences. (shrink)

Ever since Darwin people have worried about the sceptical implications of evolution. If our minds are products of evolution like those of other animals, why suppose that the beliefs they produce are true, rather than merely useful? We consider this problem for beliefs in three different domains: religion, morality, and commonsense and scientific claims about matters of empirical fact. We identify replies to evolutionary scepticism that work in some domains but not in others. One reply is that evolution can be (...) expected to design systems that produce true beliefs in some domain. This reply works for commonsense beliefs and can be extended to scientific beliefs. But it does not work for moral or religious beliefs. An alternative reply which has been used defend moral beliefs is that their truth does not consist in their tracking some external state of affairs. Whether or not it is successful in the case of moral beliefs, this reply is less plausible for religious beliefs. So religious beliefs emerge as particularly vulnerable to evolutionary debunking. (shrink)

Few problems in the philosophy of evolutionary biology are more widely disseminated and discussed than the charge of Darwinian evolution being a tautology. The history is long and complex, and the issues are many, and despite the problem routinely being dismissed as an introductory-level issue, based on misunderstandings of evolution, it seems that few agree on what exactly these misunderstandings consist of. In this paper, I will try to comprehensively review the history and the issues. Then, I will try to (...) present the following “solution”, or, one might say, “dissolution”, of the problem, and consider the wider implications of formal, or schematic, explanations in science: yes, the principle of natural selection is a tautology, and so what? It is a promissory note for actual, physical, explanations in particular cases, and is none the worse for that. This is not a new argument, of course, but it does point up the importance of formal schematic models in science. (shrink)

Genes are thought to have evolved from long-lived and multiply-interactive molecules in the early stages of the origins of life. However, at that stage there were no replicators, and the distinction between interactors and replicators did not yet apply. Nevertheless, the process of evolution that proceeded from initial autocatalytic hypercycles to full organisms was a Darwinian process of selection of favourable variants. We distinguish therefore between Neo-Darwinian evolution and the related Weismannian and Central Dogma divisions, on the one hand, and (...) the more generic category of Darwinian evolution on the other. We argue that Hull’s and Dawkins’ replicator/interactor distinction of entities is a sufficient, but not necessary, condition for Darwinian evolution to take place. We conceive the origin of genes as a separation between different types of molecules in a thermodynamic state space, and employ a notion of reproducers. (shrink)

Abstract Charles Darwin, in his discussions with Asa Gray and in his published works, doubted whether God could so arrange it that exactly the desired contingent events would occur to cause particular outcomes by natural selection. In this paper, I argue that even a limited or neo-Leibnizian deity could have chosen a world that satisfied some arbitrary set of goals or functions in its outcomes and thus answer Darwin's conundrum. In more general terms, this supports the consistency of natural selection (...) with providentialism, and makes “theistic evolutionism” a coherent position to hold. (shrink)

To naturalize religion, we must identify what religion is, and what aspects of it we are trying to explain. In this paper, religious social institutional behavior is the explanatory target, and an explanatory hypothesis based on shared primate social dominance psychology is given. The argument is that various religious features, including the high status afforded the religious, and the high status afforded to deities, are an expression of this social dominance psychology in a context for which it did not evolve: (...) high-density populations made possible by agriculture. (shrink)

It is often noted that if someone has a tertiary degree in a scientific field who promotes an anti-science-establishment, antiscience, or pseudoscience agenda, they are very often engineers, dentists, surgeons or medical practitioners. While this does not mean that all members of these professions or disciplines are antiscience, of course, the higher frequency of pseudoscience among them is indicative of what I call the “deductivist mindset” regarding science itself. Opposing this is the “inductivist mindset”, a view that has been deprecated (...) among philosophers since Popper. Roughly, the deductivist mindset tends to see problems as questions that can be resolved by deduction from known theory or principle, while the inductivist sees problems as questions to be resolved by discovery. These form cognitive poles, which nobody ever purely instantiates, but a cognitive tendency to be a deductivist may explain why some people find results that conflict with prior theoretical commitments, whether scientific or not, unacceptable. The deductivist tends to be a cognitive conservative, where the inductivist tends to be a cognitive progressive, and the conservative mindset leads to a ressentiment about modernism, and hence about certain scientific results, more often, or so I shall argue in this chapter. (shrink)

The word 'reason' as used today is used ambiguous in its meaning. It may denote either of two mental faculties: a lower reason associated with discursive, linear thinking, and a higher reason associated with direct apprehension of first principles of mathematics and logic, and possibly also of moral and religious truths. These two faculties may be provisionally named Reason (higher reason) and rationality (lower reason). Common language and personal experience supply evidence of these being distinct faculties. So does classical philosophical (...) literature, the locus classicus being Plato's Divided Line analogy. -/- The effect of currently using a single word to denote both faculties not only produces confusion, but has had the effect of decreasing personal and cultural awareness of the higher faculty, Reason. Loss of a sense of Reason has arguably contributed to various psychological, social, moral, and spiritual problems of the modern age. This issue was also a central concern of 19th century Transcendentalists, who reacted to the radical empiricism of Locke. It would be advantageous to adopt consistent terms that make explicit a distinction between higher and lower reason. One possibility is to re-introduce the Greek philosophical terms nous and dianoia for the higher and lower reason, respectively. This discussion has certain parallels with the recent theories of McGilchrist (2009) concerning the increasingly left-brain hemisphere orientation of human culture. (shrink)

We argue that the logical outcome of the cladistics revolution in biological systematics, and the move towards rankless phylogenetic classification of nested monophyletic groups as formalized in the PhyloCode, is to eliminate the species rank along with all the others and simply name clades. We propose that the lowest level of formally named clade be the SNaRC, the Smallest Named and Registered Clade. The SNaRC is an epistemic level in the classification, not an ontic one. Naming stops at that level (...) because there is no currently acceptable evidence for clades within it, not because no smaller clades exist. Later, included clades may be named. They would then become the SNaRCs, while the original SNaRC would keep its original name. We argue that all theoretical tasks of biology, in evolution and ecology, as well as practical tasks such as conservation assessment, are better approached using this rankless phylogenetic approach. (shrink)

Artificial intelligence (AI) is increasingly expected to disrupt the ordinary functioning of society. From how we fight wars or govern society, to how we work and play, and from how we create to how we teach and learn, there is almost no field of human activity which is believed to be entirely immune from the impact of this emerging technology. This poses a multifaceted problem when it comes to designing and understanding regulatory responses to AI. This article aims to: (i) (...) defend the need for a novel conceptual model for understanding the systemic legal disruption caused by new technologies such as AI; (ii) to situate this model in relation to preceding debates about the interaction of regulation with new technologies (particularly the ‘cyberlaw’ and ‘robolaw’ debates); and (iii) to set out a detailed model for understanding the legal disruption precipitated by AI, examining both pathways stemming from new affordances that can give rise to a regulatory ‘disruptive moment’, as well as the Legal Development, Displacement or Destruction that can ensue. The article proposes that this model of legal disruption can be broadly generalisable to understanding the legal effects and challenges of other emerging technologies. (shrink)

John Clarke of Hull, one of the eighteenth century's staunchest proponents of psychological egoism, defended that theory in his Foundation of Morality in Theory and Practice. He did so mainly by opposing the objections to egoism in the first two editions of Francis Hutcheson's Inquiry into Virtue. But Clarke also produced a challenging, direct argument for egoism which, regrettably, has received virtually no scholarly attention. In this paper I give it some of the attention it merits. In addition to (...) reconstructing it and addressing interpretive issues about it, I show that it withstands a tempting objection. I also show that although Clarke's argument ultimately fails, to study it is instructive. It illuminates, for example, Hutcheson's likely intentions in a passage relevant to egoism. (shrink)

Ignorance is commonly assumed to be a lack of knowledge in Plato’s Socratic dialogues. I challenge that assumption. In the Protagoras, ignorance is conceived to be a substantive, structural psychic flaw—the soul’s domination by inferior elements that are by nature fit to be ruled. Ignorant people are characterized by both false beliefs about evaluative matters in specific situations and an enduring deception about their own psychic conditions. On my interpretation, akrasia, moral vices, and epistemic vices are products or forms of (...) ignorance, and a person who lacks knowledge is not necessarily ignorant. (shrink)

My task in this paper is to study Sartre’s ontology as a godless theology. The urgency of defending freedom and responsibility in the face of determinism called for an overarching first principle, a role that God used to play. I first show why such a principle is important and how Sartre filled the void that God had left with a solipsist consciousness. Then I characterize Sartre’s ontology of this consciousness as a “dualist monism”, explaining how it supports his radical conception (...) of freedom. Then, by assessing Sartre’s dualist monism through a theological lens, I disclose an inconsistency in his thought concerning the idea that the in-itself is a deterministic plenitude, which presumes a theos different from consciousness and hence threatens monism. Finally I argue that his inconsistency originates from the finitude of Sartre’s first principle and analyze this finitude by examining the modes of temporality it implies. The entire trajectory problematizes the practice of theo-logy, the idea that a theos stands at the origin of the “logic” (organization or intelligibility) of everything such that all must be conceived under the logos of the theos. While Sartre forcefully criticized the theology of the infinite, his was nonetheless a theology of finitude. (shrink)

It is widely taken that the first-order part of Frege's Begriffsschrift is complete. However, there does not seem to have been a formal verification of this received claim. The general concern is that Frege's system is one axiom short in the first-order predicate calculus comparing to, by now, the standard first-order theory. Yet Frege has one extra inference rule in his system. Then the question is whether Frege's first-order calculus is still deductively sufficient as far as the first-order completeness is (...) concerned. In this short note we confirm that the missing axiom is derivable from his stated axioms and inference rules, and hence the logic system in the Begriffsschrift is indeed first-order complete. (shrink)

This commentary focuses on explaining the intuition of revelation, an issue that Chalmers (2018) raises in his paper. I first sketch how the truth of revelation provides an explanation for the intuition of revelation, and then assess a physicalist proposal to explain the intuition that appeals to Derk Pereboom’s (2011, 2016, 2019) qualitative inaccuracy hypothesis.

This paper addresses the issue of finite versus countable additivity in Bayesian probability and decision theory -- in particular, Savage's theory of subjective expected utility and personal probability. I show that Savage's reason for not requiring countable additivity in his theory is inconclusive. The assessment leads to an analysis of various highly idealised assumptions commonly adopted in Bayesian theory, where I argue that a healthy dose of, what I call, conceptual realism is often helpful in understanding the interpretational value of (...) sophisticated mathematical structures employed in applied sciences like decision theory. In the last part, I introduce countable additivity into Savage's theory and explore some technical properties in relation to other axioms of the system. (shrink)

Can an agent deliberating about an action A hold a meaningful credence that she will do A? 'No', say some authors, for 'Deliberation Crowds Out Prediction' (DCOP). Others disagree, but we argue here that such disagreements are often terminological. We explain why DCOP holds in a Ramseyian operationalist model of credence, but show that it is trivial to extend this model so that DCOP fails. We then discuss a model due to Joyce, and show that Joyce's rejection of DCOP rests (...) on terminological choices about terms such as 'intention', 'prediction', and 'belief'. Once these choices are in view, they reveal underlying agreement between Joyce and the DCOP-favouring tradition that descends from Ramsey. Joyce's Evidential Autonomy Thesis (EAT) is effectively DCOP, in different terminological clothing. Both principles rest on the so-called 'transparency' of first-person present-tensed reflection on one's own mental states. (shrink)

In this paper, I transcend the abstract engagement of J. L. Austin's Speech Acts theory and explore their sociopolitical advantages, using the Nigerian social space as my primary experimental field. Nigerian social space is quite hierarchical and progresses along apparently asymmetrical lines of social relationship (in most cases). This in turn, accentuates some sort of power dynamics. In every communication, there is an implicit reinforcement of the social fabric as well as the power dynamic, either through one person's percep6of the (...) social status of the other or, of one's emphasis of power dynamic over the other. Austin's theory comes to the fore as a very laudable framework to map this interesting sociological facts. This work then, offers a philosophical contribution to an otherwise, sociological/anthropological fact. My job in this paper, is to explore a sociopolitical negotiation of Austin's theory in a multiethnic nation-state as Nigeria where hierarchy and power dynamics are heavily emphasized. This paper thus highlights the importance of the perlocutionary acts and the felicity conditions, and also accentuates their implications for social interactions and power dynamics in the Nigerian social space. (shrink)

This presentation of Aristotle's natural deduction system supplements earlier presentations and gives more historical evidence. Some fine-tunings resulted from conversations with Timothy Smiley, Charles Kahn, Josiah Gould, John Kearns,John Glanvillle, and William Parry.The criticism of Aristotle's theory of propositions found at the end of this 1974 presentation was retracted in Corcoran's 2009 HPL article "Aristotle's demonstrative logic".

As the aim of the responsible robotics initiative is to ensure that responsible practices are inculcated within each stage of design, development and use, this impetus is undergirded by the alignment of ethical and legal considerations towards socially beneficial ends. While every effort should be expended to ensure that issues of responsibility are addressed at each stage of technological progression, irresponsibility is inherent within the nature of robotics technologies from a theoretical perspective that threatens to thwart the endeavour. This is (...) because the concept of responsibility, despite being treated as such, is not monolithic: rather this seemingly unified concept consists of converging and confluent concepts that shape the idea of what we colloquially call responsibility. From a different perspective, robotics will be simultaneously responsible and irresponsible depending on the particular concept of responsibility that is foregrounded: an observation that cuts against the grain of the drive towards responsible robotics. This problem is further compounded by responsible design and development as contrasted to responsible use. From a different perspective, the difficulty in defining the concept of responsibility in robotics is because human responsibility is the main frame of reference. Robotic systems are increasingly expected to achieve the human-level performance, including the capacities associated with responsibility and other criteria which are necessary to act responsibly. This subsists within a larger phenomenon where the difference between humans and non-humans, be it animals or artificial systems, appears to be increasingly blurred, thereby disrupting orthodox understandings of responsibility. This paper seeks to supplement the responsible robotics impulse by proposing a complementary set of human rights directed specifically against the harms arising from robotic and artificial intelligence technologies. The relationship between responsibilities of the agent and the rights of the patient suggest that a rights regime is the other side of responsibility coin. The major distinction of this approach is to invert the power relationship: while human agents are perceived to control robotic patients, the prospect for this to become reversed is beginning. As robotic technologies become ever more sophisticated, and even genuinely complex, asserting human rights directly against robotic harms become increasingly important. Such an approach includes not only developing human rights that ‘protect’ humans but also ‘strengthen’ people against the challenges introduced by robotics and AI [This distinction parallels Berlin’s negative and positive concepts of liberty ], by emphasising the social and reflective character of the notion of humanness as well as the difference between the human and nonhuman. This will allow using the human frame of reference as constitutive of, rather than only subject to, the robotic and AI technologies, where it is human and not technology characteristics that shape the human rights framework in the first place. (shrink)

(Recipient of the 2020 Everett Mendelsohn Prize.) This article revisits the development of the protoplasm concept as it originally arose from critiques of the cell theory, and examines how the term “protoplasm” transformed from a botanical term of art in the 1840s to the so-called “living substance” and “the physical basis of life” two decades later. I show that there were two major shifts in biological materialism that needed to occur before protoplasm theory could be elevated to have equal status (...) with cell theory in the nineteenth century. First, I argue that biologists had to accept that life could inhere in matter alone, regardless of form. Second, I argue that in the 1840s, ideas of what formless, biological matter was capable of dramatically changed: going from a “coagulation paradigm” that had existed since Theophrastus, to a more robust conception of matter that was itself capable of movement and self-maintenance. In addition to revisiting Schleiden and Schwann’s original writings on cell theory, this article looks especially closely at Hugo von Mohl’s definition of the protoplasm concept in 1846, how it differed from his primordial utricle theory of cell structure two years earlier. This article draws on Lakoff and Johnson’s theory of “ontological metaphors” to show that the cell, primordial utricle, and protoplasm can be understood as material container, object, and substance, and that these overlapping distinctions help explain the chaotic and confusing early history of cell theory. (shrink)

In a recent paper, Reuter, Seinhold and Sytsma put forward an implicature account to explain the intuitive failure of the pain-in-mouth argument. They argue that utterances such as ‘There is tissue damage / a pain / an inflammation in my mouth’ carry the conversational implicature that there is something wrong with the speaker’s mouth. Appealing to new empirical data, this paper argues against the implicature account and for the entailment account, according to which pain reports using locative locutions, such as (...) ‘There is a pain in my mouth’, are intuitively understood as entailing corresponding predicative locutions, such as ‘My mouth hurts.’ On this latter account, the pain-in-mouth argument seems invalid because the conclusion is naturally understood as entailing something which cannot be inferred from the premisses. Implications for the philosophical debate about pain are also drawn. (shrink)

Since its proposition, the Knowledge Argument has been the center of debate in the Philosophy of the Mind, and many philosophers have proposed their rejections of it. This paper briefly looked at what Philip Goff characterized as the no-compromise response and the no propositional knowledge response before delving deep into a critique of Brian Loar's response to the Knowledge Argument. This paper accepts Brian Loar's critique of the semantic premise and his analysis of phenomenal concepts. However, after examining the implications (...) of Loar's response through conscious experience, this paper contends those implications conflict with simple intuitions and an analysis of the role of basic experiences in type-demonstrative referencing. It leads to new insights into the location of the dialectic of the Knowledge Argument being external to the brain. For the new dialectic of the Knowledge argument, I argue that a simpler Knowledge Argument provides an account of the referent of phenomenal concepts to be phenomenal properties (qualia), showing that Loar's response did not adequately reject the Knowledge Argument. (shrink)

Ad hoc concepts feature prominently in lexical pragmatics. A speaker can use a word or phrase to communicate an ad hoc concept that is different from the lexically encoded concept and the hearer can construct the intended ad hoc concept pragmatically during utterance comprehension. I argue that some philosophical concepts have origins as ad hoc concepts, and such concepts pose a challenge for experimental philosophy regarding these concepts. To illustrate this, I consider philosophers’ ‘what-it’s-like’-concepts and experimental philosophy of consciousness.

Host-microbiome interactions (HMIs) are critical for the modulation of biological processes and are associated with several diseases, and extensive HMI studies have generated large amounts of data. We propose that the logical representation of the knowledge derived from these data and the standardized representation of experimental variables and processes can foster integration of data and reproducibility of experiments and thereby further HMI knowledge discovery. A community-based Ontology of Host-Microbiome Interactions (OHMI) was developed following the OBO Foundry principles. OHMI leverages established (...) ontologies to create logically structured representations of microbiomes, microbial taxonomy, host species, host anatomical entities, and HMIs under different conditions and associated study protocols and types of data analysis and experimental results. (shrink)

Slurs are both derogatory and offensive, and they are said to exhibit “derogatory force” and “offensiveness.” Almost all theories of slurs, except the truth-conditional content theory and the invocational content theory, conflate these two features and use “derogatory force” and “offensiveness” interchangeably. This paper defends and explains the distinction between slurs’ derogatory force and offensiveness by fulfilling three goals. First, it distinguishes between slurs’ being derogatory and their being offensive with four arguments. For instance, ‘Monday’, a slur in the Bostonian (...) argot, is used to secretly derogate African Americans without causing offense. Second, this paper points out that many theories of slurs run into problems because they conflate derogatory force with offensiveness. For example, the prohibition theory’s account of offensiveness in terms of prohibitions struggles to explain why ‘Monday’ is derogatory when it is not a prohibited word in English. Third, this paper offers a new explanation of this distinction from the perspective of a speech act theory of slurs; derogatory force is different from offensiveness because they arise from two different kinds of speech acts that slurs are used to perform, i.e., the illocutionary act of derogation and the perlocutionary act of offending. This new explanation avoids the problems faced by other theories. (shrink)

The rigor and precision of Leibniz's "possible world" evolved into the concept of Turing machine, and with the birth of the first computer and the physical realization of Turing machine, human cognitive and intelligent activities were optimistically considered by cognitive scientists to be convertible into computational programs for simulation by machines. Cognitive science then formed the research agenda of "cognitive computationalism", and our Chinese scholars have responded to this general view that "the essence of cognition is computation" and that the (...) human brain and computers are merely formal systems for manipulating and processing symbols in their respective fields. Professor Hong Dingguo used the concepts of "manifest order" and "hidden order", Professor Jin Gulun used the philosophical categories of "constitutive theory" and "generative theory", and Liu Yuesheng used the concept of "cognition". Professor Hong Dingguo reinterpreted the relationship between the "real world" and the "possible world" by using the concepts of "manifest sequence" and "hidden sequence", Professor Jin Wulun used the philosophical categories of "composition theory" and "generation theory", and Professor Liu Yuesheng used the generalized information paradigm of "structural information" and "exchange information". "This provides a profound elucidation of the nature of cognitive logic and the process of human cognitive activities becoming symbols through coding and puts forward theoretical limits. The current theoretical dilemma and practical difficulty of cognitive science lies in the fact that it has developed algorithmic concepts in the Turing sense that can only model the explicitly sequential part of cognitive and intellectual activity, forming a constitutive atomic abstraction, or in our terms, classical "structural information", which cannot fully explain the inner mechanisms of human mental activity and its embodied flexibility, selectivity and self-emergence. Wu Xuemou's pan-system theory does not simply rely on logic and Turing machine algorithms, but models human intelligence by treating structural information as a complex large system composed of a collection of elements and a collection of relations (exchange information: five mutual eight chips), in order to break through the narrow path of seeking only the local consistency of the system as currently done; while Wang Dekui's exploration of the three-spin biological and physical path and Huang Zhanji's abandonment of the artificial means of logic to seek the large logical natural mechanisms and Mr. Zhou Liquan's proposal of a schema for successful communication using natural language on the basis of concepts such as context and implicit connotation ("Logic — A Theory of Correct Thinking and Successful Communication"), all reflect the milestones of Chinese scholars who seek to address the deeper issues of cognitive science. We believe that along this series of explorations, combined with new results in recent years in the fields of artificial life and evolutionary computation, a new research agenda in cognitive science will emerge. (shrink)

Since the early nineteenth century a membrane or wall has been central to the cell’s identity as the elementary unit of life. Yet the literally and metaphorically marginal status of the cell membrane made it the site of clashes over the definition of life and the proper way to study it. In this article I show how the modern cell membrane was conceived of by analogy to the first “artificial cell,” invented in 1864 by the chemist Moritz Traube (1826–1894), and (...) reimagined by the plant physiologist Wilhelm Pfeffer (1845–1920) as a precision osmometer. Pfeffer’s artificial cell osmometer became the conceptual and empirical basis for the law of dilute solutions in physical chemistry, but his use of an artificial analogue to theorize the existence of the plasma membrane as distinct from the cell wall prompted debate over whether biology ought to be more closely unified with the physical sciences, or whether it must remain independent as the science of life. By examining how the histories of plant physiology and physical chemistry intertwined through the artificial cell, I argue that modern biology relocated vitality from protoplasmic living matter to nonliving chemical substances—or, in broader cultural terms, that the disenchantment of life was accompanied by the (re)enchantment of ordinary matter. (shrink)

This paper offers a fine analysis of different versions of the well known sure-thing principle. We show that Savage's formal formulation of the principle, i.e., his second postulate (P2), is strictly stronger than what is intended originally.

Slurs are derogatory, and theories of slurs aim at explaining their “derogatory force”. This paper draws a distinction between the type derogatory force and the token derogatory force of slurs. To explain the type derogatory force is to explain why a slur is a derogatory word. By contrast, to explain the token derogatory force is to explain why an utterance of a slur is derogatory. This distinction will be defended by examples in which the type and the token derogatory force (...) come apart. Because of the distinction, an adequate theory of slurs must be plausible for both the type and the token derogatory force. However, I will argue that many theories fail to be plausible for both. In particular, Hom’s combinatorial externalism and the conventional implicature theory offer implausible accounts of the token derogatory force, whereas the prohibitionist theory is insufficient to explain the type derogatory force. (shrink)

This paper begins with Thomas Nagel's (1970) investigation of the possibility of altruism to further examine how to motivate altruism. When the pursuit of the gratification of one's own desires generally has an immediate causal efficacy, how can one also be motivated to care for others and to act towards the well-being of others? A successful motivational theory of altruism must explain how altruism is possible under all these motivational interferences. The paper will begin with an exposition of Nagel's proposal, (...) and see where it is insufficient with regard to this further issue. It will then introduce the views of Zhang Zai and Wang Fuzhi, and see which one could offer a better motivational theory of altruism. All three philosophers offer different insights on the role of human reason/reflection and human sentiments in moral motivation. The paper will end with a proposal for a socioethical moral program that incorporates both moral reason and moral sentiments as motivation. (shrink)

The Shape-of-a-Life phenomenon is widely recognized by philosophers of well-being: an upward life trajectory seems better than its downward equivalent if the sum of momentary well-being is held fixed. But what if we hold fixed the sum of momentary well-being in an upward trajectory, are certain ways to improve from the bad times better than the others? Velleman suggests that a redemptive trajectory is better than a bare upward trajectory. In this paper, I elaborate this proposal by developing a mediating (...) factor account of prudential redemption. I argue that, in redemptive trajectories, there is a mediating factor that bears certain relations with the negative and the positive events respectively, one that does not necessarily appear in bare upward trajectories. Prudential redemption, compared to mere improvement, can enhance a person’s lifetime well-being because a redeemed event is made less bad by virtue of the mediating factor. This result has implications for making decisions in the face of equally good options and for evaluating the rationality of honoring sunk costs. (shrink)

In "Experience as a Way of Knowing" (this journal), the author tries to create some troubles for philosophers who believe in "qualia" or "what it is like". I think the author has underestimated the complexity of the issues, and I will voice my concerns in five sections. Besides presenting my interpretation of the author's position and challenging it, I will (1) challenge the author's treatment of the knowledge argument, especially the author's treatment of "this is what it is like to (...) see red", (2) challenge the author's interpretation of "what-it-is-like" talk and the author's view that phenomenal properties are theoretical postulates, (3) challenge the author's rejection of "apparent properties", and (4) point out some issues with the author's interpretation of several authors who write about the knowledge argument. (shrink)

This presentation includes a complete bibliography of John Corcoran’s publications devoted at least in part to Aristotle’s logic. Sections I–IV list 20 articles, 43 abstracts, 3 books, and 10 reviews. It starts with two watershed articles published in 1972: the Philosophy & Phenomenological Research article that antedates Corcoran’s Aristotle’s studies and the Journal of Symbolic Logic article first reporting his original results; it ends with works published in 2015. A few of the items are annotated with endnotes connecting them (...) with other work. In addition, Section V “Discussions” is a nearly complete secondary bibliography of works describing, interpreting, extending, improving, supporting, and criticizing Corcoran’s work: 8 items published in the 1970s, 22 in the 1980s, 39 in the 1990s, 56 in the 2000s, and 65 in the current decade. The secondary bibliography is annotated with endnotes: some simply quoting from the cited item, but several answering criticisms and identifying errors. As is evident from the Acknowledgements sections, all of Corcoran’s publications benefited from correspondence with other scholars, most notably Timothy Smiley, Michael Scanlan, and Kevin Tracy. All of Corcoran’s Greek translations were done in consultation with two or more classicists. Corcoran never published a sentence without discussing it with his colleagues and students. REQUEST: Please send errors, omissions, and suggestions. I am especially interested in citations made in non-English publications. (shrink)

This paper calls for a re-appraisal of McGee's analysis of the semantics, logic and probabilities of indicative conditionals presented in his 1989 paper Conditional probabilities and compounds of conditionals. The probabilistic measures introduced by McGee are given a new axiomatisation built on the principle that the antecedent of a conditional is probabilistically independent of the conditional and a more transparent method of constructing such measures is provided. McGee's Dutch book argument is restructured to more clearly reveal that it introduces a (...) novel contribution to the epistemology of semantic indeterminacy, and shows that its more controversial implications are unavoidable if we want to maintain the Ramsey Test along with the standard laws of probability. Importantly, it is shown that the counterexamples that have been levelled at McGee's analysis|generating a rather wide consensus that it yields `unintuitive' or `wrong' probabilities for compounds |fail to strike at their intended target; for to honour the intuitions of the counterexamples one must either give up the Ramsey Test or the standard laws of probability. It will be argued that we need to give up neither if we take the counterexamples as further evidence that the indicative conditional sometimes allows for a non-epistemic `causal' interpretation alongside its usual epistemic interpretation. (shrink)

He drove a taxi. Now he drives a truck. So, must he be driving the truck right now? Must he, as long as he's working as a truck driver, keep driving his truck all day and all night? What do we speak of, when we speak of "now"? In this talk, some popular conceptions in the philosophy of time will be put under critical scrutiny: (1) The present (the "now") is an instant, a time point with no length; (2) the (...) "content" of the present is always an event, a happening, which constitutes a segment of a larger process; (3) what (time) is now, is determined by the passage of time (itself). The following points will be defended respectively: (1) The present may be a time period. "Now" is not an indivisible time-atom in the substantival sense. (2) What is now can be an event, a process, or a state. "Driving a truck now" – in the sense of being a truck driver – is neither an event nor something happening to him. (3) "Now", among other temporal concepts, is not a name for any thing, but schemata under which we understand ways things being themselves. There are variety of ways of being, and accordingly there are multiple aspects of now-ness. (shrink)

This short paper has two parts. First,we prove a generalisation of Aumann’s surprising impossibility result in the context of rational decision making. We then move, in the second part, to discuss the interpretational meaning of some formal setups of epistemic models, and we do so by means of presenting an interesting puzzle in epistemic logic. The aim is to highlight certain problematic aspects of these epistemic systems concerning first/third-person asymmetry which underlies both parts of the story. This asymmetry, we argue, (...) reveals certain limits of what epistemic models can be. (shrink)

Today, the lipid bilayer structure is nearly ubiquitous, taken for granted in even the most rudimentary introductions to cell biology. Yet the image of the lipid bilayer, built out of lipids with heads and tails, went from having obscure origins deep in colloid chemical theory in 1924 to being “obvious to any competent physical chemist” by 1935. This chapter examines how this schematic, strictly heuristic explanation of the idea of molecular orientation was developed within colloid physical chemistry, and how the (...) image was transformed into a reflection of the reality and agency of lipid molecules in the biological microworld. Whereas in physical and colloid chemistry these images considered secondary to instrumental measurement and mathematical modeling of surface phenomena, in biology the manipulable image of the lipid on paper became an essential tool for the molecularization of the cell. (shrink)