The Protein Ontology (PRO; http://proconsortium.org) formally defines protein entities and explicitly represents their major forms and interrelations. Protein entities represented in PRO corresponding to single amino acid chains are categorized by level of specificity into family, gene, sequence and modification metaclasses, and there is a separate metaclass for protein complexes. All metaclasses also have organism-specific derivatives. PRO complements established sequence databases such as UniProtKB, and interoperates with other biomedical and biological ontologies such as the Gene Ontology (GO). PRO relates to (...) UniProtKB in that PRO’s organism-specific classes of proteins encoded by a specific gene correspond to entities documented in UniProtKB entries. PRO relates to the GO in that PRO’s representations of organism-specific protein complexes are subclasses of the organism-agnostic protein complex terms in the GO Cellular Component Ontology. The past few years have seen growth and changes to the PRO, as well as new points of access to the data and new applications of PRO in immunology and proteomics. Here we describe some of these developments. (shrink)

In this essay I argue that Thomas Aquinas is not as naively optimistic about the noetic effects of sin as is often portrayed by standard neo-Calvinist objections. Still, his metaphysics of the human person requires some development to better explain the mind’s impairment by sin, a development made possible by the work of Bernard Lonergan and the resulting Lonergan/Aquinas (L/A) model of the noetic effects of sin.

Ethics edifies to the extent it takes seriously the munus propheticum Jesu Christi. Though many assume ethical action indicates behaviour realising Jesus Christ, this is problematic because it implies he is otherwise mute and absent. Paul Lehmann offers a refreshing alternative when he argues that the principal concern of ethics is alignment with all that God in Christ is doing now to make and keep human life human. Lehmann thus recasts the question ‘What am I to do?’ by taking seriously (...) the presence and activity of the One who summons human beings to participate in his work. In a manner consistent with the christological foundations of Dietrich Bonhoeffer’s Ethics , Lehmann’s proposals evoke an ethic shaped by and subject to the self-disclosure and radiance of the triune God. (shrink)

This invaluable resource is the first one-volume, in-depth, comprehensive history of modern science ever published.

A critical evaluation of Deane-Peter Baker’s use of Charles Taylor to overcome perceived inadequacies in Reformed epistemology. Baker claims that a successful response to the de jure objection must provide motivation for the unbeliever to seriously consider the truth of Christianity, but this very test is undone by Taylor’s A Secular Age.

This paper concludes a special feature of Sustainability Science that explores a broad range of social value theoretical traditions, such as religious studies, social psychology, indigenous knowledge, economics, sociology, and philosophy. We introduce a novel transdisciplinary conceptual framework that revolves around concepts of 'lenses' and 'tensions' to help navigate value diversity. First, we consider the notion of lenses: perspectives on value and valuation along diverse dimensions that describe what values focus on, how their sociality is envisioned, and what epistemic and (...) procedural assumptions are made. We characterise fourteen of such dimensions. This provides a foundation for exploration of seven areas of tension, between: (1) the values of individuals vs collectives; (2) values as discrete and held vs embedded and constructed; (3) value as static or changeable; (4) valuation as descriptive vs normative and transformative; (5) social vs relational values; (6) different rationalities and their relation to value integration; (7) degrees of acknowledgment of the role of power in navigating value conflicts. In doing so, we embrace the 'mess' of diversity, yet also provide a framework to organise this mess and support and encourage active transdisciplinary collaboration. We identify key research areas where such collaborations can be harnessed for sustainability transformation. Here it is crucial to understand how certain social value lenses are privileged over others and build capacity in decision-making for understanding and drawing on multiple value, epistemic and procedural lenses. (shrink)

This paper concludes a special feature of Sustainability Science that explores a broad range of social value theoretical traditions, such as religious studies, social psychology, indigenous knowledge, economics, sociology, and philosophy. We introduce a novel transdisciplinary conceptual framework that revolves around concepts of ‘lenses’ and ‘tensions’ to help navigate value diversity. First, we consider the notion of lenses: perspectives on value and valuation along diverse dimensions that describe what values focus on, how their sociality is envisioned, and what epistemic and (...) procedural assumptions are made. We characterise fourteen of such dimensions. This provides a foundation for exploration of seven areas of tension, between: (1) the values of individuals vs collectives; (2) values as discrete and held vs embedded and constructed; (3) value as static or changeable; (4) valuation as descriptive vs normative and transformative; (5) social vs relational values; (6) different rationalities and their relation to value integration; (7) degrees of acknowledgment of the role of power in navigating value conflicts. In doing so, we embrace the ‘mess’ of diversity, yet also provide a framework to organise this mess and support and encourage active transdisciplinary collaboration. We identify key research areas where such collaborations can be harnessed for sustainability transformation. Here it is crucial to understand how certain social value lenses are privileged over others and build capacity in decision-making for understanding and drawing on multiple value, epistemic and procedural lenses. (shrink)

Rationale: Deep brain stimulation (DBS) of the hippocampus is proposed for enhancement of memory impaired by injury or disease. Many pre-clinical DBS paradigms can be addressed in epilepsy patients undergoing intracranial monitoring for seizure localization, since they already have electrodes implanted in brain areas of interest. Even though epilepsy is usually not a memory disorder targeted by DBS, the studies can nevertheless model other memory-impacting disorders, such as Traumatic Brain Injury (TBI). Methods: Human patients undergoing Phase II invasive monitoring for (...) intractable epilepsy were implanted with depth electrodes capable of recording neurophysiological signals. Subjects performed a delayed-match-to-sample (DMS) memory task while hippocampal ensembles from CA1 and CA3 cell layers were recorded to estimate a multi-input, multi-output (MIMO) model of CA3-to-CA1 neural encoding and a memory decoding model (MDM) to decode memory information from CA3 and CA1 neuronal signals. After model estimation, subjects again performed the DMS task while either MIMO-based or MDM-based patterned stimulation was delivered to CA1 electrode sites during the encoding phase of the DMS trials. Each subject was sorted (post hoc) by prior experience of repeated and/or mild-to-moderate brain injury (RMBI), TBI, or no history (control) and scored for percentage successful delayed recognition (DR) recall on stimulated vs. non-stimulated DMS trials. The subject’s medical history was unknown to the experimenters until after individual subject memory retention results were scored. Results: When examined compared to control subjects, both TBI and RMBI subjects showed increased memory retention in response to both MIMO and MDM-based hippocampal stimulation. Furthermore, effects of stimulation were also greater in subjects who were evaluated as having pre-existing mild-to-moderate memory impairment. Conclusion: These results show that hippocampal stimulation for memory facilitation was more beneficial for subjects who had previously suffered a brain injury (other than epilepsy), compared to control (epilepsy) subjects who had not suffered a brain injury. This study demonstrates that the epilepsy/intracranial recording model can be extended to test the ability of DBS to restore memory function in subjects who previously suffered a brain injury other than epilepsy, and support further investigation into the beneficial effect of DBS in TBI patients. (shrink)

In this paper I outline the main features of Karen Bennett’s (Australasian Journal of Philosophy 1–21, 2011) non-classical mereology, and identify its methodological costs. I argue that Bennett’s mereology cannot account for the composition of structural universals because it cannot explain the mereological difference between isomeric universals, such as being butane and being isobutane. I consider responses, which come at costs to the view.

Sonja Plischke’s Die Seleukiden und Iran is an attempt to study Seleucid empire building in Iran. In view of the fact that indigenous written sources from Iran are practically absent, Plischke decided to include Babylonia in this work, since the written cuneiform evidence from that region is fairly abundant. She detects some general tendencies—such as religious policy and the general wish to connect the different parts of the empire—supported by a personal conception of Seleucid kingship, beside more specific treatment of (...) different regions. In my view, the Seleucids probably did not pay sufficient attention to the East, so that their control weakened. I take the opportunity to discuss the Babylonian sources, correct errors in Plischke’s use of them, and adduce some new publications. (shrink)

The four short works in Untimely Meditations were published by Nietzsche between 1873 and 1876.They deal with such broad topics as the relationship between popular and genuine culture, strategies for cultural reform, the task of philosophy, the nature of education, and the relationship between art, science and life. They also include Nietzsche's earliest statement of his own understanding of human selfhood as a process of endlessly 'becoming who one is'. As Daniel Breazeale shows in his introduction to this new edition (...) of R. J. Hollingdale's translation of the essays, these four early texts are key documents for understanding the development of Nietzsche's thought and clearly anticipate many of the themes of his later writings. Nietzsche himself always cherished his Untimely Meditations and believed that they provide valuable evidence of his 'becoming and self-overcoming' and constitute a 'public pledge' concerning his own distinctive task as a philosopher. (shrink)

This paper challenges historically preconceived notions surrounding a minor’s ability to make medical decisions, arguing that federal health law should be reformed to allow minors with capacity as young as age 12 to consent to their own Centers for Diseases Control and Prevention (CDC)-approved COVID-19 vaccinations. This proposal aligns with and expands upon current exceptions to limitations on adolescent decision-making. This analysis reviews the historic and current anti-vaccination sentiment, examines legal precedence and rationale, outlines supporting ethical arguments regarding adolescent decision-making, (...) and offers rebuttals to anticipated ethical counterarguments. (shrink)

(1980). Verbaliser‐Imager Learning Style and Children's Recall of Information Presented in Pictorial versus Written Form. Educational Studies: Vol. 6, No. 2, pp. 141-145.

In this chapter, Hankinson discusses Aristotle's conceptions of nature, change, and potentiality; the four causes, spontaneity, and chance; teleology and hypothetical necessity; and also Aristotle's account of action, freedom, and responsibility. The choice facing Greek philosopher‐scientists is simple: show how a structured, regular world could arise out of undirected processes, or pursue a teleological explanation, insisting on the activity of divine intelligence in the cosmos. Aristotle, Hankinson writes, pursues a middle way between these options, although, ultimately, Aristotle takes the whole (...) structure of the cosmos to be teleologically organized. Aristotle rejects Plato's metaphysics of perfect hypostasized forms and divinely directed teleology: relying heavily on his concept of phusis or nature, Aristotle makes teleology an internal principle governing the development of natural objects. Aristotle distinguishes four causes or causal factors in explanation: matter, form, agent, and end, and he distinguishes sharply between regular natural events that can be explained by means of these causes, and chance events, which do not admit full explanation. (shrink)

In this chapter, Hankinson discusses the origins of syncretism, or the growing convergence of Platonism, Aristotelianism, and Stoicism, focusing mainly on the Old Academy Platonists Speusippus and Xenocrates, the empiricist Stoic Posidonius, the lapsed sceptic Antiochus, and the orthodox Aristotelian Alexander of Aphrodisias. Hankinson also discusses Eudorus, Philo of Larissa, and Plutarch, as well as briefly noting the influential Primer on Plato's Doctrines by Alcinous. The importance of the Old Academy is its influence upon the development of later Platonic tradition; (...) Proclus, for instance, credits Xenocrates with a distinction between transcendent and immanent causation that became a central feature of Middle Platonism. Posidonius, a Stoic and Cicero's philosophical mentor, is important to the growing convergence of the schools because he introduced Platonism and Aristotelianism into his account of Stoicism, while Antiochus, a product of Philo of Larissa's sceptical Academy, pursued an eclectic Platonism. Alexander of Aphrodisias was the leading Peripatetic of Alexandria, around the second century ad; he revived an orthodox Aristotelianism, accepting Aristotle's four causes doctrine, and identifying Fate as an efficient cause. (shrink)

Open peer commentary on the article “A Cybernetic Approach to Contextual Teaching and Learning” by Philip Baron. Upshot: I consider implications of Baron’s article on change in university education. In particular, I address the problem of why change happens with difficulty and how the principles and practices of second-order cybernetics that Baron discusses are applicable beyond South Africa to a wide range of situations.