The development of gene expression profiling and next-generation sequencing technologies have steered oncogenomics to the forefront of precision medicine. This created a need for harmonious cooperation between clinicians and researchers to increase access to precision oncology, despite multiple implementation challenges being encountered. The aim is to apply personalised treatment strategies early in cancer management, targeting tumour subtypes and actionable gene variants within the individual’s broader clinical risk profile and wellbeing. A knowledge-generating database linked to the South African Medical Research Council’s (...) Genomic Centre has been created for the application of personalised medicine, using an integrated service and research approach. Insights gained from patient experiences related to tumour heterogeneity, access to targeted therapies and incidental findings of pathogenic germline variants in tumour DNA, provided practice-changing evidence for the implementation of a cost-minimisation pathology-supported genetic testing strategy. Integrating clinical care with genomic research through data sharing advances personalised medicine and maximises precision oncology benefits. (shrink)

Plants belonging to the genus Salsola (Family: Chenopodiaceae) are common in the arid and semiarid regions of our planet with no less than 69 different Salsola species found in Namibia and the Republic of South Africa. This genus is used as a traditional medicine and aqueous extracts of Salsola have been used by Bushmen women as an oral contraceptive. Ingestion of the Namibian shrub Salsola tuberculatiformis Botsch. by pregnant Karakul sheep leads to prolonged gestation and fetal post‐maturity and, as a (...) result, the pelts of the new‐born karakul lambs are worthless. This initiated an investigation into the active agents in the plant, using the terminal enzyme in adrenal corticosteroidogenesis, cytochrome P450‐dependent 11β‐hydroxylase (P450c11), as a bioassay. Although the active fraction, S2, was extremely labile, partial structure determination suggested the presence of synephrine and a highly reactive aziridine. Therefore a more stable analogue, 2‐(4‐acetoxyphenyl)2‐chloro‐N‐methylethylammonium‐chloride (compound A), was synthesised, which, like the active plant extracts, inhibited adrenal steroidogenesis and acted as a contraceptive. In addition, compound A was stabilised by interaction with steroid‐binding globulins in plasma thus enhancing biological activity in vivo. These findings provided explanations for the complex biological effects of the shrub as well as a new insight into the mode of action of chemically labile plant products in vivo. BioEssays 25:612–619, 2003. © 2003 Wiley Periodicals, Inc. (shrink)

Some alethic pluralists maintain that there are two kinds of truths operant in our alethic discourse: a realist kind and an anti-realist kind. In this paper, we argue that such a binary conception cannot accommodate certain social truths, specifically truths about race. Most alethic pluralists surprisingly overlook the status of racial truths. Douglas Edwards is, however, an exception. In his version of alethic pluralism—Determination Pluralism—racial truths are superassertible (anti-realist) true rather than correspondence (realist) true. We argue that racial truths exhibit (...) features of both superassertibility (anti-realism) and correspondence (realism). This suggests a fuzzy boundary between realist and anti-realist kinds of truth. There may be a continuum rather than a dichotomy of truths. We conclude by sketching one way for alethic pluralists to accommodate such a notion. (shrink)

William Whewell’s 19th century philosophy of science is sometimes glossed over as a footnote to Kant. There is however a key feature of Whewell’s account worth noting. This is his appeal to Aristotle’s form/matter hylomorphism as a metaphor to explain how mind and world merge in successful scientific inquiry. Whewell’s hylomorphism suggests a middle way between rationalism and empiricism reminiscent of experience pragmatists like Steven Levine’s view that mind and world are entwined in experience. I argue however that Levine does (...) not adequately explain exactly how mind and world entwine. He could nonetheless do so if he appealed to Whewell’s hylomorphic metaphor. We may prefer a reductive metaphysical explanation, but I suggest that pragmatists only have recourse to metaphor in this case. Both reductive and metaphorical explanations can enjoy great explanatory power if they exhibit a suitable measure of what I will call sematic distance. Semantic distance measures how close or how far apart explanandum and explanans are from each other in meaning. Metaphorical explanation - as evident in Whewell’s hylomorphism and as detailed via the notion of semantic distance - presents a valuable new explanatory tool to those who hold that mind and world are entwined sans recourse to metaphysics. (shrink)

This qualitative study describes and interprets the lived experiences of African RomanCatholic Church seminarians. The interpretive lens employed was worldview, a conceptual tool extensively used in African-centred psychology. Sixteen Africanseminarians were purposely selected and interviewed in depthAdditional sources of data were reflexive notes and observation notes. Data were subjected tovarious iterative cycles of analysis. Participants described their difficulty in adjusting in theseminaries where teaching and living predominantly reflects a Western world view. Theyevidenced cognitive dissonance, emotional discomfort and feelings of marginalisation. (...) Thefindings point to the importance of acknowledging the world views and cultural heritage ofseminarians in their training. (shrink)

Inspired by Bas van Fraassen’s Stance Empiricism, Anjan Chakravartty has developed a pluralistic account of what he calls epistemic stances towards scientific ontology. In this paper, I examine whether Chakravartty’s stance pluralism can exclude epistemic stances that licence pseudo-scientific practices like those found in Scientology. I argue that it cannot. Chakravartty’s stance pluralism is therefore prone to a form of debilitating relativism. I consequently argue that we need (1) some ground or constraint in relation to which epistemic stances can be (...) ranked by degrees, and (2) some way to demarcate science from pseudo-science so that we know what epistemic stances are about. Regarding (1), I argue that empirical detectability can serve as the ground in relation to which epistemic stances are ranked by degrees. Regarding (2), I argue for ranking sciences on a continuum according to established institutional criteria, rather than attempting to draw a strict demarcation. (shrink)

For many physicists quantum theory contains strong conceptual difficulties, while for others the apparent conclusions about the reality of our physical world and the ways in which we discover that reality remain philosophically unacceptable. This book focuses on recent theoretical and experimental developments in the foundations of quantum physics, including topics such as the puzzles and paradoxes which appear when general relativity and quantum mechanics are combined; the emergence of classical properties from quantum mechanics; stochastic electrodynamics; EPR experiments and Bell's (...) Theorem; the consistent histories approach and the problem of datum uniqueness in quantum mechanics; non-local measurements and teleportation of quantum states; quantum non-demolition measurements in optics and matter wave properties observed by neutron, electron and atomic interferometry. Audience: This volume is intended for graduate students of physics and those interested in the foundations of quantum theory. (shrink)

I identify two versions of the scientific anti-realist’s selectionist explanation for the success of science: Bas van Fraassen’s original and K. Brad Wray’s newer interpretation. In Wray’s version, psycho-social factors internal to the scientific community – viz. scientists’ interests, goals, and preferences – explain the theory-selection practices that explain theory-success. I argue that, if Wray’s version were correct, then science should resemble art. In art, the artwork-selection practices that explain artwork-success appear faddish. They are prone to radical change over time. (...) Theory-selection practices that explain theory-success in science are however not faddish. They are mostly stable; that is, long-lived and consistent over time. This is because scientists (explicitly or implicitly) subscribe to what I will call the testability norm: scientific theories must make falsifiable claims about the external physical world. The testability norm and not psycho-sociology explains the theory-selection practices that explain theory-success in science. Contra Wray, scientific anti-realists can then maintain that the external physical world (as expressed in the testability norm) explains theory-success. (shrink)

William Whewell’s philosophy of science is often overlooked as a relic of 19th century Whiggism. I argue however that his view – suitably modified – can contribute to contemporary philosophy of science, particularly to debates around scientific progress. The reason Whewell’s view needs modification is that he makes the following problematic claim: as science progresses, it reveals necessarily truths and thereby grants a glimpse of the mind of God. Modifying Whewell’s view will involve reinventing his notion of necessary truth as (...) the pragmatist notion of superassertibility. And, if scientific progress does not uncover necessary truths, then it does not reveal the mind of God. The result is an outline of an account of scientific progress that is piecemeal and fallibilist in nature, yet at the same time maintains key Whewellian themes of consilience and the unity of science. (shrink)

Several complexity theorists draw a sharp and ontologically robust distinction between (merely) complicated systems and (genuinely) complex systems. I argue that this distinction does not hold. Upon fine-grained analysis, ostensibly complicated systems turn out to be complex systems. The purported boundary between the complicated and the complex appears to be vague rather than sharp. Systems are complex by degrees.

Quantum theory is one of the most fascinating and successful constructs in the intellectual history of mankind. Nonetheless, the theory has very shaky philosophical foundations. This book contains thoughtful discussions by eminent researchers of a spate of experimental techniques newly developed to test some of the stranger predictions of quantum physics. The advances considered include recent experiments in quantum optics, electron and ion interferometry, photon down conversion in nonlinear crystals, single trapped ions interacting with laser beams, atom-field coupling in micromaser (...) cavities, quantum computation, quantum cryptography, decoherence and macroscopic quantum effects, the quantum state diffusion model, quantum gravity, the quantum mechanics of cosmology and quantum non-locality along with the continuing debate surrounding the interpretation of quantum mechanics. -/- Audience: The book is intended for physicists, philosophers of science, mathematicians, graduate students and those interested in the foundations of quantum theory. (shrink)

This qualitative study describes and interprets the lived experiences of African Roman Catholic Church seminarians. The interpretive lens employed was world view, a conceptual tool extensively used in African-centred psychology. Sixteen African seminarians were purposely selected and interviewed in depth. Additional sources of data were reflexive notes and observation notes. Data were subjected to various iterative cycles of analysis. Participants described their difficulty in adjusting in the seminaries where teaching and living predominantly reflects a Western world view. They evidenced cognitive (...) dissonance, emotional discomfort and feelings of marginalisation. The findings point to the importance of acknowledging the world views and cultural heritage of seminarians in their training. (shrink)

Human beings are a marvel of evolved complexity. When we try to enhance poorly-understood complex evolved systems, our interventions often fail or backfire. It can appear as if there is a “wisdom of nature” which we ignore at our peril. A recognition of this reality can manifest as a vaguely normative intuition, to the effect that it is “hubristic” to try to improve on nature, or that biomedical therapy is ok while enhancement is morally suspect. We suggest that one root (...) of these moral intuitions may be fundamentally prudential rather than ethical. More importantly, we develop a practical heuristic, the “evolutionary optimality challenge”, for evaluating the plausibility that specific candidate biomedical interventions would be safe and effective. This heuristic recognizes the grain of truth contained in “nature knows best” attitudes while providing criteria for identifying the special cases where it may be feasible, with present or near-future technology, to enhance human nature. (shrink)

Paul Cilliers has developed a novel post-structural approach to complexity that has influenced several writers contributing to the current complexity literature. Concomitantly however, Cilliers advocates for modelling complex systems using connectionist neural networks (rather than analytic, rule-based models). In this paper, I argue that it is dilemmic to simultaneously hold these two positions. Cilliers’ post-structural interpretation of complexity states that models of complex systems are always contextual and provisional; there is no exclusive model of complex systems. This sentiment however appears (...) at odds with Cilliers’ promotion of connectionist neural networks as the best way to model complex systems. The lesson is that those who currently follow Cilliers’ post-structural approach to complexity cannot also develop a preferred model of complex systems, and those who currently advocate for some preferred model of complex systems cannot adopt the post-structural approach to complexity without giving up the purported objectivity and/or superiority of their preferred model. (shrink)

Douglas Edwards is arguably the most prominent contemporary advocate of moderate alethic pluralism. Significantly influenced by Crispin Wright and Michael Lynch, his work on the nature of truth has become widely discussed in the topical literature. Edwards labels his version of moderate alethic pluralism determination pluralism. At first blush, determination pluralism appears philosophically promising. The position deserves thoughtful consideration, particularly because of its capacity to accommodate the scope problem. I argue, however, that upon analysis the view is better understood as (...) a form of metaphysical dualism or what I will call meta-dualism. Furthermore, determination pluralists face a dilemma; there appears to be an instability at the core of their dualistic model. On the one horn of the dilemma, they need a clear metaphysical demarcation at the interface of their two necessary domains. On the other horn, they seem to need to a metaphysically vague boundary at the interface of their two necessary domains. Determination pluralism needs substantial revision. (shrink)

Prima facie, we make successful decisions as we act on and intervene in the world day-to-day. Epistemologists are often concerned with whether rationality is involved in such decision-making practices, and, if so, to what degree. Some, particularly in the post-structuralist tradition, argue that successful decision-making occurs via an existential leap into the unknown rather than via any determinant or criterion such as rationality. I call this view radical voluntarism (RV). Proponents of RV include those who subscribe to a view they (...) call Critical Complexity (CC). In this paper, I argue that CC presents a false dichotomy when it conceives of rationality in Cartesian – i.e. ideal and transcendental – terms, and then concludes that RV is the proper alternative. I then outline a pragmatist rationality informed by recent work in psychology on bounded rationality, ecological rationality, and specifically embodied rationality. Such a pragmatist rationality seems to be compatible with the tenets of post-structuralism, and can therefore replace RV in CC. (shrink)

Crossing the road within the traffic system is an example of an action human agents perform successfully day-to-day in complex systems. How do they perform such successful actions given that the behaviour of complex systems is often difficult to predict? The contemporary literature contains two contrasting approaches to the epistemology of complex systems: an analytic and a post-modern approach. We argue that neither approach adequately accounts for how successful action is possible in complex systems. Agents regularly perform successful actions without (...) obeying (explicit or implicit) algorithmic rules (as the analytic approach suggests) and without an existential leap to action (as the post-modern approach suggests). We offer an alternative: A common-sense pragmatist epistemology, one that focuses on the kind of actions making up most agents’ successful moment-to-moment actions in complex systems. Successful actions obtain when agents apply ceteris paribus rules-of-thumb during predictive and decisional practices while achieving some desired goal. (shrink)

Epistemic pluralists in the philosophy of science often argue that different epistemic perspectives in science are equally warranted. Sandra Mitchell – with her Integrative Pluralism (IP) – has notably advocated for this kind of epistemic pluralism. A problem arises for Mitchell however because she also wants to be an epistemological pluralist. She claims that, not only are different epistemic perspectives in science equally warranted in different contexts, but different understandings of these epistemic perspectives in science are also equally warranted in (...) different contexts. The problem is that Mitchell argues that her understanding of epistemic perspectives in science (IP) is the correct one, and it is dilemmic to then claim that there is more than one such understanding. As solution, I suggest that we abandon epistemological pluralism and instead follow Feyerabend in being opportunistic pluralists. We can adopt pluralism as a short-term strategy in the pursuit of a long-term unitary goal. This unitary goal is what philosophers of understanding call objectual understanding, the kind of understanding that Integrative Pluralism tacitly aspires to anyway. (shrink)

Stuart Kauffman has, in recent writings, developed a thought-provoking and influential argument for strong emergence. The outcome is his Theory of the Adjacent Possible (TAP). According to TAP, the biosphere constitutes a non-physical domain qualitatively distinct from the physical domain. The biosphere exhibits strongly emergent properties such as agency, meaning, value and creativity that cannot, in principle, be reduced to the physical. In this paper, I argue that TAP includes various (explicit or implicit) metaphysical commitments: commitments to (1) scientific realism, (...) (2) downward causation and teleology, and (3) modal realism. If TAP is to hang together as the kind of robust philosophical thesis it evidently aspires to be, it needs an account – an account that is currently absent – of its metaphysical commitments. It is however unclear how such an account can be developed since various dilemmas present themselves when one explores how subscribers to TAP might do so. (shrink)