The Protein Ontology (PRO) is designed as a formal and principled Open Biomedical Ontologies (OBO) Foundry ontology for proteins. The components of PRO extend from a classification of proteins on the basis of evolutionary relationships at the homeomorphic level to the representation of the multiple protein forms of a gene, including those resulting from alternative splicing, cleavage and/or posttranslational modifications. Focusing specifically on the TGF-beta signaling proteins, we describe the building, curation, usage and dissemination of PRO. PRO provides a framework (...) for the formal representation of protein classes and protein forms in the OBO Foundry. It is designed to enable data retrieval and integration and machine reasoning at the molecular level of proteins, thereby facilitating cross-species comparisons, pathway analysis, disease modeling and the generation of new hypotheses. (shrink)
Biomedical ontologies are emerging as critical tools in genomic and proteomic research where complex data in disparate resources need to be integrated. A number of ontologies exist that describe the properties that can be attributed to proteins; for example, protein functions are described by Gene Ontology, while human diseases are described by Disease Ontology. There is, however, a gap in the current set of ontologies—one that describes the protein entities themselves and their relationships. We have designed a PRotein Ontology (PRO) (...) to facilitate protein annotation and to guide new experiments. The components of PRO extend from the classification of proteins on the basis of evolutionary relationships to the representation of the multiple protein forms of a gene (products generated by genetic variation, alternative splicing, proteolytic cleavage, and other post-translational modification). PRO will allow the specification of relationships between PRO, GO and other OBO Foundry ontologies. Here we describe the initial development of PRO, illustrated using human proteins from the TGF-beta signaling pathway. (shrink)
The surface grammar of reports such as ‘I have a pain in my leg’ suggests that pains are objects which are spatially located in parts of the body. We show that the parallel construction is not available in Mandarin. Further, four philosophically important grammatical features of such reports cannot be reproduced. This suggests that arguments and puzzles surrounding such reports may be tracking artefacts of English, rather than philosophically significant features of the world.
It is often thought that sensible qualities such as colours do not exist as properties of physical objects. Focusing on the case of colour, I discuss two views: the Galilean view, according to which colours do not exist as qualities of physical objects, and the naive view, according to which colours are, as our perception presents them to be, qualities instantiated by physical objects. I argue that it is far from clear that the Galilean view is better than the naive (...) view. Given the arguments in this paper, the naive view ought to be taken seriously. The discussion here appeals especially to theorists who, like Goff, are already convinced that the quantitative language of physical science fails to capture all qualities. (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.
In _Sino-Theology and the Philosophy of History_ Leopold Leeb presents the ideas of an influential Chinese intellectual, Liu Xiaofeng, whose approach to the question of a Christian theology for China is both controversial and inspiring.
In the philosophy of mind, revelation is the claim that the nature of qualia is revealed in phenomenal experience. In the literature, revelation is often thought of as intuitive but in tension with physicalism. While mentions of revelation are frequent, there is room for further discussion of how precisely to formulate the thesis of revelation and what it exactly amounts to. Drawing on the work of David Lewis, this paper provides a detailed discussion on how the thesis of revelation, as (...) well as its incompatibility with physicalism, is to be understood. (shrink)
In this paper, we first propose a simple formal language to specify types of agents in terms of necessary conditions for their announcements. Based on this language, types of agents are treated as ‘first-class citizens’ and studied extensively in various dynamic epistemic frameworks which are suitable for reasoning about knowledge and agent types via announcements and questions. To demonstrate our approach, we discuss various versions of Smullyan’s Knights and Knaves puzzles, including the Hardest Logic Puzzle Ever (HLPE) proposed by Boolos (...) (in Harv Rev Philos 6:62–65, 1996). In particular, we formalize HLPE and verify a classic solution to it. Moreover, we propose a spectrum of new puzzles based on HLPE by considering subjective (knowledge-based) agent types and relaxing the implicit epistemic assumptions in the original puzzle. The new puzzles are harder than the previously proposed ones in the literature, in the sense that they require deeper epistemic reasoning. Surprisingly, we also show that a version of HLPE in which the agents do not know the others’ types does not have a solution at all. Our formalism paves the way for studying these new puzzles using automatic model checking techniques. (shrink)
Philosophers disagree about what the folk concept of pain is. This paper criticises existing theories of the folk concept of pain, i.e. the mental view, the bodily view, and the recently proposed polyeidic view. It puts forward an alternative proposal – the polysemy view – according to which pain terms like “sore,” “ache” and “hurt” are polysemous, where one sense refers to a mental state and another a bodily state, and the type of polysemy at issue reflects two distinct but (...) related concepts of pain. Implications with respect to issues in philosophy of pain are also drawn. (shrink)
This paper proposes a two-level modeling perspective which combines intrinsic 'betterness' and reason-based extrinsic preference, and develops its static and dynamic logic in tandem. Our technical results extend, integrate, and re-interpret earlier theorems on preference representation and update in the literature on preference change.
Two alternative accounts of quantum spontaneous symmetry breaking (SSB) are compared and one of them, the decompositional account in the algebraic approach, is argued to be superior for understanding quantum SSB. Two exactly solvable models are given as applications of our account -- the Weiss-Heisenberg model for ferromagnetism and the BCS model for superconductivity. Finally, the decompositional account is shown to be more conducive to the causal explanation of quantum SSB.
Most theories of slurs fall into one of two families: those which understand slurring terms to involve special descriptive/informational content (however conveyed), and those which understand them to encode special emotive/expressive content. Our view is that both offer essential insights, but that part of what sets slurs apart is use-theoretic content. In particular, we urge that slurring words belong at the intersection of a number of categories in a sociolinguistic register taxonomy, one that usually includes [+slang] and [+vulgar] and always (...) includes [-polite] and [+derogatory]. Thus, e.g., what distinguishes ‘Chinese’ from ‘chink’ is neither a peculiar sort of descriptive nor emotional content, but rather the fact that ‘chink’ is lexically marked as belonging to different registers than ‘Chinese’. It is, moreover, partly such facts which makes slurring ethically unacceptable. (shrink)
Globalization has changed almost every facet of life for people around the world, and today the flow of influence is no longer uni-directional. It is argued that East Asian societies are anchored in an indigenous form of hierarchical relationalism where social structure is produced by relational obligations of an ethical and normative nature that have slowed its traditional culture “melting into air” as prophesied by Marx. The successfully modernization of East Asia has involved hybridization, compartmentalization, and sequencing of traditional psychological (...) features of Confucianist societies such as delay of gratification and respect for education, paternalistic leadership, filial piety, and beliefs in harmony or benevolence. Features of hierarchical relationalism are adaptable to creating niches for East Asian societies that thrive under globalization as characterized by the paradoxical coupling of economic inequality in fact with discourses of equality in principle. Moral, ethical demands for enlightened leadership constrain East Asian elites to at least attempt to protect subordinates and protect societal well-being. A fundamental contribution of East Asia to global society may be in the articulation of how to ameliorate economic inequality using Confucian principles of hierarchical relationalism. (shrink)
Liu Ping discusses patriotism and nationalism in regard to culture and values and also the role of the prophetic voice in Chinese society. His provocative allegorical rewriting of a prophecy from the Biblical book of Amos, setting it in contemporary China, is pointedly political. Liu writes in the Chinese intellectual tradition of pointing out when a society or a country is on the brink of destruction.
In this paper, a criticism of the traditional theories of approximation and idealization is given as a summary of previous works. After identifying the real purpose and measure of idealization in the practice of science, it is argued that the best way to characterize idealization is not to formulate a logical model – something analogous to Hempel's D-N model for explanation – but to study its different guises in the praxis of science. A case study of it is then made (...) in thermostatistical physics. After a brief sketch of the theories for phase transitions and critical phenomena, I examine the various idealizations that go into the making of models at three difference levels. The intended result is to induce a deeper appreciation of the complexity and fruitfulness of idealization in the praxis of model-building, not to give an abstract theory of it. (shrink)
There are two accounts of how readers of unspaced writing systems know where to move their eyes: saccades are directed toward default targets ; or saccade lengths are adjusted dynamically, as a function of ongoing parafoveal processing. This article reports an eye-movement experiment supporting the latter hypothesis by demonstrating that the slope of the relationship between the saccade launch site on word N and the subsequent fixation landing site on word N + 1 is > 1, suggesting that saccades are (...) lengthened from launch sites that afford more parafoveal processing. This conclusion is then evaluated and confirmed via simulations using implementations of both hypotheses, with a discussion of these results for our understanding of saccadic targeting during reading and existing models of eye-movement control. (shrink)
In this paper, a multistable modified fourth-order autonomous Chua’s chaotic system is investigated. In addition to the dynamic characteristics of the third-order Chua’s chaotic system itself, what interests us is that this modified fourth-order autonomous Chua’s chaotic system has five different types of coexisting attractors: double-scroll, single band chaotic attractor, period-4 limit cycle, period-2 limit cycle, and period-1 limit cycle. Then, an inductorless modified fourth-order autonomous Chua’s chaotic circuit is proposed. The active elements as well as the synthetic inductor employed (...) in this circuit are designed using second-generation current conveyors. The reason for using CCIIs is that they have high conversion rate and operation speed, which enable the circuit to work at a higher frequency range. The Multisim simulations confirm the theoretical estimates of the performance of the proposed circuit. Finally, using RK-4 numerical algorithm of VHDL 32-bit IQ-Math floating-point number format, the inductorless modified fourth-order autonomous Chua’s chaotic system is implemented on FPGA for the development of embedded engineering applications based on chaos. The system is simulated and synthesized on Virtex-6 FPGA chip. The maximum operating frequency of modified Chua’s chaotic oscillator based on FPGA is 180.180 MHz. This study demonstrates that the hardware-based multistable modified fourth-order autonomous Chua’s chaotic system is a very good source of entropy and can be applied to various embedded systems based on chaos, including secure communication, cryptography, and random number generator. (shrink)
Servant leadership offers a compelling ideal of self-sacrificing individuals who put the needs of others before their own and cultivate a culture of growth in their organisations. Although the theory’s attempts to emphasise the moral, emotional and relational dimensions of leadership are laudable, it has primarily assumed a decontextualised view of leadership untouched by power. This article aims to problematise servant leadership by undertaking an intersectional analysis of an Asian cis-male heterosexual senior manager in Australia. Through in-depth interviews with the (...) manager and his staff, the article shows how his attempts to practice servant leadership were informed by intersecting power dynamics of race, gender, sexuality, age and class that subordinated him to white power. The findings demonstrate the ways servant leadership is necessarily embedded in wider power structures that shape who gets to be a “servant leader” and who remains merely a “servant”. (shrink)
Recent research in psycholinguistics suggests that language processing frequently involves mental imagery. This paper focuses on visual imagery and discusses two issues regarding the processing of polysemous words (i.e. words with multiple related meanings or senses) – co-predication and sense-relatedness. It aims to show how mental imagery can illuminate these two issues.
Review of: Sophia Roosth, Synthetic: How Life Got Made (University of Chicago Press, 2017); and Andrew S. Balmer, Katie Bulpin, and Susan Molyneux-Hodgson, Synthetic Biology: A Sociology of Changing Practices (Palgrave Macmillan, 2016).
Statements not only update our current knowledge, but also have other dynamic effects. In particular, suggestions or commands ?upgrade' our preferences by changing the current order among worlds. We present a complete logic of knowledge update plus preference upgrade that works with dynamic-epistemic-style reduction axioms. This system can model changing obligations, conflicting commands, or ?regret'. We then show how to derive reduction axioms from arbitrary definable relation changes. This style of analysis also has a product update version with preferences between (...) actions, as well as worlds. Some illustrations are presented involving defaults and obligations. We conclude that our dynamic framework is viable, while admitting a further extension to more numerical ?utility update'. (shrink)
On the one hand, Confucianism and Christianity advocate universal love for all humans on the ultimate basis of particular love for parents or for God respectively. On the other hand, they have to sacrifice the former for the latter in cases of conflict since they give top priority merely to the latter. In order to overcome this paradox in theory and realize the ideal of universal love in practice, they should transform their particularistic frameworks into universalistic ones and assign a (...) supreme position to their ideas of universal love for all humans, which imply in a potential way a modern, humanistic principle ‘respect the deserved rights of every human being’. (shrink)
The paper, as Part I of a two-part series, argues for a hybrid formulation of the semantic view of scientific theories. For stage-setting, it first reviews the elements of the model theory in mathematical logic (on whose foundation the semantic view rests), the syntactic and the semantic view, and the different notions of models used in the practice of science. The paper then argues for an integration of the notions into the semantic view, and thereby offers a hybrid semantic view, (...) which at once secures the view's logical foundations and enhances its applicability. The dilemma of either losing touch with the practice of science or yielding up the benefits of the model theory is thus avoided. (shrink)
A ‘community of minds’ has long been presumed to be a condition of possibility for genuine argumentative interactions. In part because of this disciplinary presupposition, argumentation scholars tend to exclude from their scope of inquiry conflict resolution among culturally heterogeneous and ideologically incompatible formations. Such a stance needs to be reexamined in view of recent developments in the on-going process of globalization. The unprecedented worldwide economic and financial integration has created for the first time a ‘generalized interest’ across national and (...) continental boundaries. The need to countercheck global market forces has given rise to calls for a ‘global legal/ethical system’ or even a ‘transnational public sphere.’ Non-Western interlocutors in general are willing to debate cross-cultural issues in Western terms. Increasingly, Western interlocutors are also seeking to justify Western positions in non-Western terms. This emerging situation renders it both necessary and possible to argue across the boundaries of communities that do not share the same cultural or rhetorical tradition. It also poses a host of theoretical and practical issues whose exploration and analysis should become a new focus of argumentation studies. (shrink)
Putnam and Burge have been viewed as launching a joint attack on individualism, the view that the content of one's psychological state is determined by what is in the head . Putnam argues that meanings are not in the head while Burge argues that beliefs are not in the head either, and both have come up with convincing arguments against individualism. It is generally conceived that Putnam's view is a version of physical externalism, which argues that factors in the physical (...) environment play a role in determining the meanings of natural kind terms. Burge, on the other hand, is regarded as following up Putnam's argument to bring in factors in the social environment for the determination of belief. Burge's view has been commonly referred to as 'social externalism.' The general consensus in the field is that physical externalism and social externalism are compatible views. Furthermore, both Putnam and Burge seem to endorse each other’s position for the most part. In this paper, however, I shall argue against this general view to show that the two theories are deep down incompatible. (shrink)
By introducing a flux-controlled memristor with quadratic nonlinearity into a 4D hyperchaotic system as a feedback term, a novel 5D hyperchaotic four-wing memristive system is derived in this paper. The HFWMS with multiline equilibrium and three positive Lyapunov exponents presented very complex dynamic characteristics, such as the existence of chaos, hyperchaos, limit cycles, and periods. The dynamic characteristics of the HFWMS are analyzed by using equilibria, phase portraits, poincare map, Lyapunov exponential spectrum, bifurcation diagram, and spectral entropy. Of particular interest (...) is that this novel system can generate two-wing hyperchaotic attractor under appropriate parameters and initial conditions. Moreover, the FPGA realization of the novel 5D HFWMS is reported, which prove that the system has complex dynamic behavior. Finally, synchronization of the 5D hyperchaotic system with different structures by active control and a secure signal masking application of the HFWMS are implemented based on numerical simulations and FPGA. This research demonstrates that the hardware-based design of the 5D HFWMS can be applied to various chaos-based embedded system applications including random number generation, cryptography, and secure communication. (shrink)
In this paper, we argue that symbols are conventional vehicles whose chief function is denotation, while models are epistemic vehicles, and their chief function is to show what their targets are like in the relevant aspects. And we explain why this is incompatible with the deflationary view on scientific modeling. Although the same object may serve both functions, the two vehicles are conceptually distinct and most models employ both elements. With the clarification of this point we offer an alternative account (...) to the deflationary view – the Hybrid Account; and we defend our account in contrast with deflationism. (shrink)