At the beginning of this special issue of Acta Biotheoretica carrying the above title, we present a brief overview on currently important topics that have been brought up during the last "European Conference on Mathematical and Theoretical Biology" in Edinburgh. After emphasizing the need for a "synthetic biology" also from the side of theory, model building and analysis, we survey most plenary talks of this Conference and a selected series of eigth review articles, which are mainly related to corresponding minisymposia, reflecting the current state of the art and the lively discussion within this interdisciplinary field.