Philosophy of chemistry and the image of science

The philosophical analysis of chemistry has advanced at such a pace during the last dozen years that the existence of philosophy of chemistry as an autonomous discipline cannot be doubted any more. The present paper will attempt to analyse the experience of philosophy of chemistry at the, so to say, meta-level. Philosophers of chemistry have especially stressed that all sciences need not be similar to physics. They have tried to argue for chemistry as its own type of science and for a pluralistic understanding of science in general. However, when stressing the specific character of chemistry, philosophers do not always analyse the question ‘What is science?’ theoretically. It is obvious that a ‘monistic’ understanding of science should not be based simply on physics as the epitome of science, regarding it as a historical accident that physics has obtained this status. The author’s point is that the philosophical and methodological image of science should not be chosen arbitrarily; instead, it should be theoretically elaborated as an idealization (theoretical model) substantiated on the historical practice of science. It is argued that although physics has, in a sense, justifiably obtained the status of a paradigm of science, chemistry, which is not simply a physical science, but a discipline with a dual character, is also relevant for elaborating a theoretical model of science. The theoretical model of science is a good tool for examining various issues in philosophy of chemistry as well as in philosophy of science or science studies generally.     

The cold case: Are rhinoviruses perfectly adapted pathogens?

Rhinoviruses, which cause common cold, belong to the Picornaviridae family, small non-enveloped viruses (diameter 15-30 nm) containing a single-stranded RNA genome (about 7 kb). Over 100 different rhinoviral serotypes have been identified thus far, establishing rhinoviruses as the most diverse group of Picornaviridae. Based on receptor binding properties, rhinoviruses are divided into two classes: the major group binding to intracellular adhesion molecule-1 and the minor group binding to the very low density lipoprotein receptors. Interactions between virus and the receptor molecules cause a conformational change in the capsid, which is a prerequisite for viral uptake. Rhinoviruses trigger a chemokine response upon infection that may lead to exacerbation of the symptoms of common cold, i.e. asthma and inflammation. The following review aims to summarize the knowledge about rhinoviral infections and discusses therapeutical approaches against this almost perfectly adapted pathogen.     

Global Optimization in Any Minkowski Metric: A Permutation-Translation Simulated Annealing Algorithm for Multidimensional Scaling

It is well known that considering a non-Euclidean Minkowski metric in Multidimensional Scaling, either for the distance model or for the loss function, increases the computational problem of local minima considerably. In this paper, we propose an algorithm in which both the loss function and the composition rule can be considered in any Minkowski metric, using a multivariate randomly alternating Simulated Annealing procedure with permutation and translation phases. The algorithm has been implemented in Fortran and tested over classical and simulated data matrices with sizes up to 200 objects. A study has been carried out with some of the common loss functions to determine the most suitable values for the main parameters. The experimental results confirm the theoretical expectation that Simulated Annealing is a suitable strategy to deal by itself with the optimization problems in Multidimensional Scaling, in particular for City-Block, Euclidean and Infinity metrics.     

A non-commutative time-frequency tomography

The characterization of non-stationary signal requires joint time and frequency information. However, time and frequency are a pair of non-commuting variables that cannot constitute a joint probability density in the time-frequency plane. The time-frequency distributions have difficult interpretation problems arising from negative and complex values or spurious components. In this paper, we get time-frequency information from the marginal distributions in rotated directions in the time-frequency plane. The rigorous probability interpretation of the marginal distributions is without any ambiguities. This time-frequency transformation is similar to the computerized axial tomography (CT or CAT) and is applied to signal analysis and signal detection and reveals a lot of advantages especially in the signal detection of the low signal/noise (S/N).     

Mutations in the gene encoding the basal body protein RPGRIP1L, a nephrocystin-4 interactor, cause Joubert syndrome

Protein-protein interaction analyses have uncovered a ciliary and basal body protein network that, when disrupted, can result in nephronophthisis (NPHP), Leber congenital amaurosis, Senior-L?ken syndrome (SLSN) or Joubert syndrome (JBTS). However, details of the molecular mechanisms underlying these disorders remain poorly understood. RPGRIP1-like protein (RPGRIP1L) is a homolog of RPGRIP1 (RPGR-interacting protein 1), a ciliary protein defective in Leber congenital amaurosis. We show that RPGRIP1L interacts with nephrocystin-4 and that mutations in the gene encoding nephrocystin-4 (NPHP4) that are known to cause SLSN disrupt this interaction. RPGRIP1L is ubiquitously expressed, and its protein product localizes to basal bodies. Therefore, we analyzed RPGRIP1L as a candidate gene for JBTS and identified loss-of-function mutations in three families with typical JBTS, including the characteristic mid-hindbrain malformation. This work identifies RPGRIP1L as a gene responsible for JBTS and establishes a central role for cilia and basal bodies in the pathophysiology of this disorder.