Quantum Mechanics and Computation

In quantum computation non classical features such as superposition states and entanglement are used to solve problems in new ways, impossible on classical digital computers.We illustrate by Deutsch algorithm how a quantum computer can use superposition states to outperform any classical computer. We comment on the view of a quantum computer as a massive parallel computer and recall Amdahls law for a classical parallel computer. We argue that the view on quantum computation as a massive parallel computation disregards the presence of entanglement in a general quantum computation and the non classical way in which parallel results are combined to obtain the final output.     

Algebraic Self-Dualityc as the ”Ultimate Explanation”

Shahn Majids philosophy of physics is critically presented. In his view the postulate that the universe should be self-explaining implies that no fundamental theory of physics is complete unless it is self-dual. Majid shows that bicrossproduct Hopf algebras have this property. His philosophy is compared with other approaches to the ultimate explanation and briefly analyzed.     

On The Impossibility Of Empirical Controls Of Scientific Theories – From The Point Of View Of A Psychologist

Standard considerations of philosophy of science are reformulated in psychological terms and arguments, suggesting a fundamental change in life perspective: subjective experiences or introspective data are subject to motivational biases and therefore not admitted as objective empirical facts in science, However, we never experience objects or events of the external world, i.e., so called objective facts, but exclusively subjective percepts or mental events. They are merely assumed to, but may or may not be accurate or distorted mental representations of objects or events of an external world. Accordingly, the latter are theoretical constructs, i.e., constructs of the fictitious but most successful predictive (implicit) theory, called external world, which seems to be constructed from regularities observed in mental events and serves as a reference fiction for, erroneously called empirical, tests of predictions of scientific theories.Relevant Publication: Micko, H.C.: 2001, Psychologie: Von der Geistes – zur Naturwissenschaft – und weiter wohin? Erkenntnistheoretische Erwägungen vor und nach dem Aufkommen des philosophischen Konstruktivismus. Ztschr. f. Psychologie, 209: 54–68.     

Horizontal gene transfer from Eukarya to Bacteria and domain shuffling: the α-amylase model

-Amylases are present in all kingdoms of the living world. Despite strong conservation of the tertiary structure, only a few amino acids are conserved in interkingdom comparisons. Animal -amylases are characterized by several typical motifs and biochemical properties. A few cases of such -amylases have been previously reported in some eubacterial species. We screened the bacterial genomes available in the sequence databases for new occurrences of animal-like -amylases. Three novel cases were found, which belong to unrelated bacterial phyla: Chloroflexus aurantiacus, Microbulbifer degradans, and Thermobifida fusca. All the animal-like -amylases in Bacteria probably result from repeated horizontal gene transfer from animals. The M. degradans genome also contains bacterial-type and plant-type -amylases in addition to the animal-type one. Thus, this species exhibits -amylases of animal, plant, and bacterial origins. Moreover, the similarities in the extra C-terminal domains (different from both the -amylase domain C and the starch-binding domain), when present, also suggest interkingdom as well as intragenomic shuffling.Received 17 October 2003; accepted 6 November 2003     

Administration of the antitumor drug mitoguazone protects normal thymocytes against spontaneous and etoposide-induced apoptosis

The suggestion has been made that polyamines may be involved in the control of cell death, since exceedingly high or low levels induce apoptosis in different cell systems. For a deeper insight into the relationship between apoptosis and polyamine metabolism, we investigated in vitro the effect on rat thymocytes of mitoguazone (MGBG, which inhibits S-adenosylmethionine decarboxylase, i.e. a key enzyme in the polyamine biosynthetic pathway). Thymocytes were selected as an especially suitable model system, since they undergo spontaneous apoptosis in vivo and can be easily induced to apoptose in vitro by etoposide, used here as an apoptogenic agent. MGBG protected thymocytes from both spontaneous and drug-induced apoptosis, and this protective effect was associated with a decrease in polyamine oxidase activity and total polyamine levels.Received 7 July 2004; received after revision 2 September 2004; accepted 9 September 2004     

Novel aspects of glypican glycobiology

Mutations in glypican genes cause dysmorphic and overgrowth syndromes in men and mice, abnormal development in flies and worms, and defective gastrulation in zebrafish and ascidians. All glypican core proteins share a characteristic pattern of 14 conserved cysteine residues. Upstream from the C-terminal membrane anchorage are 3–4 heparan sulfate attachment sites. Cysteines in glypican-1 can become nitrosylated by nitric oxide in a copper-dependent reaction. When glypican-1 is exposed to ascorbate, nitric oxide is released and participates in deaminative cleavage of heparan sulfate at sites where the glucosamines have a free amino group. This process takes place while glypican-1 recycles via a nonclassical, caveolin-1-associated route. Glypicans are involved in growth factor signalling and transport, e.g. of polyamines. Cargo can be unloaded from heparan sulfate by nitric oxide-dependent degradation. How glypican and its degradation products and the cargo exit from the recycling route is an enigma.Received 27 November 2003; received after revision 8 January 2004; accepted 13 January 2004     

Angiogenesis and signal transduction in endothelial cells

Endothelial cells receive multiple information from their environment that eventually leads them to progress along all the stages of the process of formation of new vessels. Angiogenic signals promote endothelial cell proliferation, increased resistance to apoptosis, changes in proteolytic balance, cytoskeletal reorganization, migration and, finally, differentiation and formation of a new vascular lumen. We aim to review herein the main signaling cascades that become activated in angiogenic endothelial cells as well as the opportunities of modulating angiogenesis through pharmacological interference with these signaling mechanisms. We will deal mainly with the mitogen-activated protein kinases pathway, which is very important in the transduction of proliferation signals; the phosphatidylinositol-3-kinase/protein kinase B signaling system, particularly essential for the survival of the angiogenic endothelium; the small GTPases involved in cytoskeletal reorganization and migration; and the kinases associated to focal adhesions which contribute to integrate the pathways from the two main sources of angiogenic signals, i.e. growth factors and the extracellular matrix.Received 13 February 2004; received after revision 25 March 2004; accepted 19 April 2004     

Genesis of zircon and its constraints on interpretation of U-Pb age

Zircon U-Pb dating is the most commonly used method for isotopic geochronology. However, it has been a difficult issue when relating zircon U-Pb ages to metamorphic conditions in complex metamorphic rocks. Much progress has been made in the past decade with respect to the genesis of zircon and its constraints on interpretation of U-Pb age. Three methods have been proposed to link zircon U-Pb age to metamorphic conditions: ( i ) internal structure; ( ii ) trace element feature; (iii) mineral inclusion composition. Magmatic zircon shows typical oscillatory zoning and/or sector zoning, whereas metamorphic zircon has internal structures such as no zoned, weakly zoned, cloudy zoned, sector zoned, planar zoned, and patched zoned ones. Zircons formed in different geological environments generally have characteristic internal structures. Magmatic zircons from different rock types have variable trace element abundances, with a general trend of increasing trace element abundances in zircons from ultramafic through mafic to granitic rocks. Zircons formed under different metamorphic conditions have different trace element characteristics that can be used to relate their formation to metamorphic conditions. It is an effective way to relate zircon growth to certain P-T conditions by studying the trace element partitioning between coexisting metamorphic zircon and garnet in high-grade metamorphic rocks containing both zircon and garnet. Primary mineral inclusions in zircon can also provide unambiguous constraints on its formation conditions. Therefore, interpretation of zircon U-Pb ages can be constrained by its internal structure, trace element composition, mineral inclusion and so on.