Magister Artium - MA / This research investigates, within the framework of classical Sunni Islamic scholarship,what we might expect an Islamic opinion about evolution to be,bringing together an accurate and detailed understanding of evolutionary biology as the field stands today with a systematic consideration of the traditional Islamic sciences.The scope of the study encompasses the scholarly traditions recognized, at least by their respective adherents, to be part of Muslim orthodoxy – referred to in Islamic discourse as Ahl al-Sunnah wa al-Jamāʿah or more colloquially as “Sunni”. It covers the works of the scholars of the Ashʿarī, Māturīdī, and Salafī theological schools as well as the sources which they all draw upon – the Qur’ān, the Sunnah, and the opinions of the Salaf.The reason for this choice is that these traditions represent for most Muslims the “mainstream” of Islamic thinking, and therefore have a greater relevance for determining what a general Islamic perspective on evolution could be.The study first identifies and defines the methodological approaches of classical Sunni scholarship that have relevance to the question of an Islamic position on biological evolution. It also identifies and defines the issues within the field of Evolutionary Biology that need to be brought under scrutiny. The methods of classical Islamic Theology are then applied to the claims of Evolutionary Biology, drawing on traditional Islamic sources. The result of the study is an extrapolation of what an orthodox Islamic position towards biological evolution could be. Is Islam neutral towards the idea of biological evolution? Does it support it or categorically reject it? Can it accept certain aspects of Evolutionary Biology while rejecting others?Finally, the extrapolated “classical” Islamic position on evolution is compared with the writings of some contemporary Muslim scholars whose views run contrary to that extrapolation. Possible reasons for the discrepancy are explored.Such an interdisciplinary work should provide a valuable frame of reference for a more accurate analysis of the creation-evolution debate unfolding in the Muslim world today.

In this thesis, phylogenomic and comparative structural analyses of several widespread energy converting enzymes were performed. The focus was on the major subfamilies of the enzymes that process nucleoside triphosphates (ATP and GTP) and on some key enzymes of the electron transfer chains. First, we analyzed the P-loop GTPases, RadA/RecA recombinases, chaperone GroEL, branched-chain α-ketoacid dehydrogenase kinases, chaperone Hsc70, actins, and membrane pyrophosphatases. In the each inspected family we could identify (1) members which were potassium-dependent and/or contained K+ ions in the active site, and (2) potassium-independent enzymes with lysine or arginine residues as catalytic groups that occupy the positions of potassium ions in the homologous, K+-dependent enzymes. Based on the results of our analyses, we suggest that the appearance of the K+-binding sites could precede in evolution the recruitment of positively charged residues (lysine or arginine "fingers") with the latter providing more possibilities to control the enzyme reactions. Second, we have described the distinctive features of a phylogenetically separated subfamily of rotary membrane ATPases which we named N-ATPases. The N-ATPases have a specific operon organization with two additional subunits, absent in other rotary ATPases, and a complete set of Na+-binding ligands in the membrane c-subunits. We made a prediction, which was later confirmed, that these enzymes are capable of Na+ translocation across the membrane and may confer salt tolerance on marine prokaryotes. Third, phylogenomic analysis of the cytochrome bc complexes suggests that these enzyme complexes initially emerged within the bacteria and were then transferred to archaea via lateral gene transfer on several independent occasions. Our analysis indicates that the ancestral form of the cytochrome bc complex was a b6f-type complex; the fusion of the cytochrome b6 and the subunit IV to a "long" cytochrome b of the cytochrome bc1 complexes could have happened in different lineages independently. Fourth, our phylogenomic and comparative structural analyses of the cytochrome bc1 complex and of cytochrome c allowed us to trace how these enzymes became involved in triggering of apoptosis in Metazoa. We could trace the emergence of a specific cardiolipin-binding site within the cytochrome bc complex and the evolution of structural traits that account for the involvement of the cytochrome c as a trigger of apoptosis in vertebrates.