A brief outline of the history and chemistry of the copper pthalocyanin-based Alcian blue dyes highlights the adverse effects of commercial secrecy and entrepreneurial dishonesty on the use of these valuable histochemical and biochemical reagents in the biological sciences. The acquisition of detailed and validated chemical structures required the avoidable expenditure of much time that otherwise would have been spent on new research. The combination of this chemical knowledge with experiments on isolated polyanions, using critical electrolyte concentration (CEC) techniques, established a molecular recognition paradigm of Alcian blue usage in histochemistry. New reagents (Cuprolinic and Cupromeronic blues) were synthesised to investigate and support the hypothesis that Alcian blue did not intercalate with DNA. They were made with the important additional aim of using them in electron microscopy of polynucleotides (in the case of Cuprolinic blue) and non-nucleotide polyanions, such as sulphated proteoglycans in extracellular matrices (in the case of Cupromeronic blue). The cationic groups of Alcian blue are easily removed in very mild conditions, producing insoluble blue pigment in situ (ingrain dying). This reaction underlies its unique capability to stain in repeated cycles, thus greatly amplifying sensitivity of detection of substrates present in very small amounts in tissues and on electrophoretic strips etc.