John Scott was behind several scientific developments, including two methods of visualising connective tissues. His work in Taplow on differential staining of acid glycosaminoglycans by alcian blue salt solution, published with J Dorling in 1965 in the journal Histochemie, was listed in 1993 as a citation classic. He wrote nearly 260 articles, two books, was widely quoted in scientific literature and won many prizes, with several symposia and meetings held in his honour around the world.
In the 1970s, he synthesised cupromeronic blue with which to label and visualise polyanions for study by light and electron microscopy. He also developed a highly specific and sensitive assay for heparin, surrendering its commercial potential by releasing it freely into the public domain. This method was essential for many areas of modern medicine.
More recently he had worked on analysing the supra-molecular chemistry underlying a sliding proteoglycan-filament model he called the "shape module", a concept to unify and explain much of the morphological variability that had so long fascinated him. (Morphology deals with the study of the form and structure of organisms and their structural features.)
John Ernest Scott grew up in Macclesfield, Cheshire, into a poor working family, together with two sisters. He graduated from Manchester University in Chemistry and Physiology, and went on to gain an MSc and PhD. At university he shared digs with the journalist, Brian Redhead, who became a close friend.
He served in the RAF at Jurby on the Isle of Man (1956-58), and following the Munich disaster in 1958 was on standby for helping the Manchester United footballer Duncan Edwards with one of the earliest artificial kidneys. A chess player of international standard, he led Manchester University's team; his party trick was to play four people simultaneously, blindfolded. He was an avid music lover and attended performances around the world – many lifelong friends were made at these events. He also enjoyed jazz. He died on 12 July after a lengthy illness.