Evolutionary distances in the twilight zone -- a rational kernel approach

Phylogenetic tree reconstruction is traditionally based on multiple sequence alignments (MSAs) and heavily depends on the validity of this information bottleneck. With increasing sequence divergence, the quality of MSAs decays quickly. Alignment-free methods, on the other hand, are based on abstract string comparisons and avoid potential alignment problems. However, in general they are not biologically motivated and ignore our knowledge about the evolution of sequences. Thus, it is still a major open question how to define an evolutionary distance metric between divergent sequences that makes use of indel information and known substitution models without the need for a multiple alignment. Here we propose a new evolutionary distance metric to close this gap. It uses finite-state transducers to create a biologically motivated similarity score which models substitutions and indels, and does not depend on a multiple sequence alignment. The sequence similarity score is defined in analogy to pairwise alignments and additionally has the positive semi-definite property. We describe its derivation and show in simulation studies and real-world examples that it is more accurate in reconstructing phylogenies than competing methods. The result is a new and accurate way of determining evolutionary distances in and beyond the twilight zone of sequence alignments that is suitable for large datasets.Comment: to appear in PLoS ON

The Rules of Ferrous Metallurgy : Genesis and Structure of a Field of Engineering Science, 1870–1914

The ways in which the sciences have been delineated and categorized throughout history provide insights into the formation, stabilization, and establishment of scientific systems of knowledge. The Dresdener school’s approach for explaining and categorizing the genesis of the engineering disciplines is still valid, but needs to be complemented by further-reaching methodological and theoretical reflections. Pierre Bourdieu’s theory of social practice is applied to the question of how individual agents succeed in influencing decisively a discipline’s changing object orientation, institutionalisation and self-reproduction. Through the accumulation of social, cultural and economic capital, they succeed in realising their own organisational ideas and scientific programs. Key concepts for the analysis include the struggle for power and resources, monopolies of interpretation, and the degree of autonomy. A case study from the Aachener Technische Hochschule shows that the consolidation of ferrous metallurgy can be conceived as a symbolical struggle between Fritz Wüst, professor for ferrous metallurgy, and the German Iron and Steel Institute, leading to a construction of a system of differences in which scientists accepted being scientists rather than entrepreneurs, and entrepreneurs accepted becoming entrepreneurs and renounced science