Philosophy and Science : The Place of Philosophy and Science in the Development of Knowledge and Understanding

This thesis examines the roles played by philosophy and science in the development of knowl-edge and understanding from ancient times to the present day. It is maintained that the sole contributor to this development has been science, philosophy for the most part acting as an impediment, contrary to the philosophically inspired myth that philosophy lays the groundwork for science, and consonant with the suspicions of most scientists who give thought to the matter. This thesis is expounded from two perspectives, the historical and the analytic. From the historical perspective, Part I of the thesis, the development of scientific ideas is traced in its philosophical context, principally that of the physical sciences from the time of Galileo, but also touching on the position of science in Greek thought. It is concluded that science effectively began with the scientific revolution of the seventeenth century, and pro-gressed from that time generally in opposition to philosophical dogma, and, once established, almost entirely independently of it. From the analytical perspective, Part II of the thesis, some recent and contemporary philosophical issues in the areas of epistemology, metaphysics and philosophy of mind, cen-tred principally on issues concerning the connection between mind and the world, are evalu-ated for their contributions to our current knowledge and understanding. The evaluation is that, by its resort to inappropriate terminology, for the most part philosophy generates confu-sion in matters that in everyday terms are inherently simple and in scientific terms are more complex than philosophers ever imagined—the issue of consciousness is given particular attention. The discussion devolves upon the view, also put forward by Rudolf Carnap in his later years, that controversy in these areas of philosophy arises largely from a confusion of theory with the referents of theory, of word with object, and from the consequent ideological commitment of philosophers to irreconcilable positions in the realist–idealist spectrum. The thesis maintains that although it is a scientific (that is, empirically based) fact that theories, concepts, percepts and the like are constructs of the human mind (suggesting an idealist view, and therefore a fact causing difficulty for realists), it does not follow that the referents of these constructs are themselves constructs of the human mind—indeed, the proposition that they are is without meaning (and hence the realism–idealism dualism is meaningless). This is because the referents of constructs are accessible only by means of those constructs, which do not speak of their own basis in the human mind—the reality of an object referred to depends on the empirical validity of the construct by which the reference is made (and, of course, it may not be real in this sense at all, but be an illusion or a deliberate fiction), not on some philosophical notion of reality. Thus, for example, while the theory of evolution is a human construct, there is no sense in which evolution can be spoken of as a human construct or oth-erwise—evolution is dealt with in its entirety through its theory. Such a resolution of age-old philosophical controversy reflects no more than the human condition (as epitomised by Neurath’s simile of “sailors who must rebuild their ship on the open sea”), which is fully en-compassed by the scientific approach, and from which there is no escape by means of any religious or philosophical construction

Smooth at one end and rough at the other: influence of object texture on grasping behaviour

© 2017, Springer-Verlag GmbH Germany. When picking up objects using a pinch grip, there are usually numerous places at which one could place the thumb and index finger. Yet, people seem to consistently place them at or close to the centre of mass (COM), presumably to minimize torque and therefore the required grip force. People also prefer to grasp objects by parallel surfaces and ones with higher friction coefficients (rough surfaces), to prevent the object from slipping when they lift it. Here, we examine the trade-off between friction and COM. Participants were asked to grasp and lift aluminium bars of which one end was polished and therefore smooth and the other was rough. Their finger positions were recorded to determine how they grasped the objects. The bars were oriented horizontally in the frontal plane, with the centre aligned with the participants’ body midline. The bars varied in the horizontal offset between the COM and the edge of the rough region. The offset could be 0, 1 or 2 cm. We expected participants to grasp closer to the rough area than the centre of the bar. Completely rough bars and completely smooth bars served as control conditions. The slipperiness of the surface that was grasped affected the height of the grasping points, indicating that participants adjusted their grasping behaviour to the slipperiness of the surface. However, the tendency to grasp closer to the rough area was minimal. This shows that the judged COM largely determines how an object is grasped. Friction has very limited influence

Urachus Fistula: A Rare First Presentation of Diverticulitis

Urachus fistulas are rare, especially in adulthood. In grown-ups urachus fistulas are usually a reflection of Crohn's disease. We present a patient in whom an urachus fistula was the first presentation of diverticulitis of the sigmoid colon. The need for proper preoperative diagnostic imaging is discussed

Grazing incidence synchrotron X-ray diffraction of marbles consolidated with diammonium hydrogen phosphate treatments : non-destructive probing of buried minerals

Diammonium hydrogen phosphate (DAP)-based consolidating treatments react with carbonatic stones and form calcium phosphates phases, whose composition depends on the availability of free calcium ions. In this work, an innovative non-destructive approach based on grazing incidence X-ray diffraction (GIXRD) with synchrotron radiation (SR) is used to investigate DAP-treated Carrara marble specimens and to study the influence of the substrate composition on the crystallization of calcium phosphate phases. The outcomes indicate that the presence of compositional micro-heterogeneity of Carrara marble favours the formation of specific phases. Dicalcium phosphate dihydrate, a calcium phosphate with a low Ca/P molar ratio, is formed on carbonatic phases with a low Ca amount, such as dolomite grains and Mg-containing veins. Furthermore, this study highlights the potentialities of SR-GIXRD as a powerful non-destructive tool for the diagnostic of Cultural Heritage objects since it allows investigating the conservation history of stone materials and their interaction with the environment

Merging microsatellite data: enhanced methodology and software to combine genotype data for linkage and association analysis

<p>Abstract</p> <p>Background</p> <p>Correctly merged data sets that have been independently genotyped can increase statistical power in linkage and association studies. However, alleles from microsatellite data sets genotyped with different experimental protocols or platforms cannot be accurately matched using base-pair size information alone. In a previous publication we introduced a statistical model for merging microsatellite data by matching allele frequencies between data sets. These methods are implemented in our software MicroMerge version 1 (v1). While MicroMerge v1 output can be analyzed by some genetic analysis programs, many programs can not analyze alignments that do not match alleles one-to-one between data sets. A consequence of such alignments is that codominant genotypes must often be analyzed as phenotypes. In this paper we describe several extensions that are implemented in MicroMerge version 2 (v2).</p> <p>Results</p> <p>Notably, MicroMerge v2 includes a new one-to-one alignment option that creates merged pedigree and locus files that can be handled by most genetic analysis software. Other features in MicroMerge v2 enhance the following aspects of control: 1) optimizing the algorithm for different merging scenarios, such as data sets with very different sample sizes or multiple data sets, 2) merging small data sets when a reliable set of allele frequencies are available, and 3) improving the quantity and 4) quality of merged data. We present results from simulated and real microsatellite genotype data sets, and conclude with an association analysis of three familial dyslipidemia (FD) study samples genotyped at different laboratories. Independent analysis of each FD data set did not yield consistent results, but analysis of the merged data sets identified strong association at locus D11S2002.</p> <p>Conclusion</p> <p>The MicroMerge v2 features will enable merging for a variety of genotype data sets, which in turn will facilitate meta-analyses for powering association analysis.</p

miRvestigator: web application to identify miRNAs responsible for co-regulated gene expression patterns discovered through transcriptome profiling

Transcriptome profiling studies have produced staggering numbers of gene co-expression signatures for a variety of biological systems. A significant fraction of these signatures will be partially or fully explained by miRNA-mediated targeted transcript degradation. miRvestigator takes as input lists of co-expressed genes from Caenorhabditis elegans, Drosophila melanogaster, G. gallus, Homo sapiens, Mus musculus or Rattus norvegicus and identifies the specific miRNAs that are likely to bind to 3′ un-translated region (UTR) sequences to mediate the observed co-regulation. The novelty of our approach is the miRvestigator hidden Markov model (HMM) algorithm which systematically computes a similarity P-value for each unique miRNA seed sequence from the miRNA database miRBase to an overrepresented sequence motif identified within the 3′-UTR of the query genes. We have made this miRNA discovery tool accessible to the community by integrating our HMM algorithm with a proven algorithm for de novo discovery of miRNA seed sequences and wrapping these algorithms into a user-friendly interface. Additionally, the miRvestigator web server also produces a list of putative miRNA binding sites within 3′-UTRs of the query transcripts to facilitate the design of validation experiments. The miRvestigator is freely available at http://mirvestigator.systemsbiology.net

Using NuRadioMC to study the performance of UHE radio neutrino detectors

NuRadioMC is an open-source, Python-based simulation and reconstruction framework for radio detectors of ultra-high energy neutrinos and cosmic rays. Its modular design makes NuRadioMC suitable for use with a range of past, current and future detectors. In addition, the recent deployment of a complete documentation as well as a pip release make NuRadioMC relatively easy to learn and use. Here, we outline the features currently available and under development in NuRadioMC, with a focus on its usage to simulate and study in-ice radio neutrino detectors