John Halliday Scott was born at Edinburgh, Scotland, on 28 December 1851, the son of Marion Shaw Lidderdale and her husband, Andrew Scott, a writer to the signet. He was baptised John Lidderdale Scott but later changed his middle name to Halliday. He was educated at the Edinburgh Institution and the University of Edinburgh, where he graduated MB and CM in 1874. He worked as a house surgeon for six months each at the Edinburgh Royal Infirmary and the Stirling Royal Infirmary, and then for the next 18 months as a demonstrator in anatomy at the University of Edinburgh. In 1877 he gained his MRCS and the same year took the degree of MD at Edinburgh university, winning a gold medal for his thesis on the nervous system of the dog. He was elected a fellow of the Royal Society of Edinburgh in 1880.
In 1877 Scott was selected from 25 applicants for the chair in anatomy and physiology at the University of Otago Medical School, New Zealand. The first professor, Millen Coughtrey, had been unsuccessful in obtaining recognition in Britain for the school, and subsequently resigned in December 1876. Scott arrived in New Zealand on the Ringarooma on 29 July 1877. His salary was £600 per annum, plus student fees of three guineas each. He was not allowed to practise privately. He was also appointed to the honorary medical staff of Dunedin Hospital, a position he held until 1883 when he found his teaching duties occupied him full time.
At first there were only five students. It is doubtful that he would have applied for the position at all if he had known that the medical school to which he was to come was really non-existent, that he was to be the sole staff member, and that the school was inadequately financed and poorly housed. However, Scott was possessed of an inflexible sense of duty and strong determination. He gave the fledgeling medical school his full loyalty and set about establishing it on a proper basis within the meagre budget which the university's finances would allow.
In this he was aided by the fact that his appointment immediately solved the vital question of recognition: the University of Edinburgh recognised the classes of its former teacher and the other British medical schools soon followed suit. Medical instruction in Dunedin was limited to the first two years of what was then a four-year course, with students going on to a British medical school for the remainder of their training. Realising that if it were to be successful the Otago Medical School would have to teach a full medical curriculum, in 1881 Scott presented a plan for a complete medical course. His proposal was adopted in 1883, and in 1885 lectureships were established in a range of medical subjects, although Scott remained for some years the only professor at the school. The first student graduated Bachelor of Medicine of the University of New Zealand in 1887.
Scott taught anatomy on the sound principles he had learnt in Edinburgh, with a very firm grounding in osteology. With the assistance of only one porter he gave practical instruction in the dissecting room. Although his specialist training was entirely in anatomy he continued to teach physiology as well until 1905, when a separate chair of physiology was established. He was a meticulous teacher and strict disciplinarian, scathing of students who did not reach his high standards. His lectures, always simple and clear, were timed to the minute. But his students admired him for the quality of his teaching and the interest he took in their subsequent careers.
During the summer vacation of 1882–83 Scott went to Britain, and there, at Cheltenham, Gloucestershire, on 18 January 1883, he married Helen Gardner Bealey, daughter of John Bealey, who had been an early runholder in Canterbury. They were to have three sons and two daughters.
Scott was a competent watercolour artist. He joined the Otago Art Society on his arrival in Dunedin and was its secretary for over 30 years – from 1881 until his death. He was represented at the New Zealand and South Seas Exhibition in Dunedin in 1889–90, and later at the National Centennial Exhibition of New Zealand Art in 1940 with 'Moeraki boulders, 1889', his best-known work. He painted his own diagrams for anatomical teaching, which were of such quality that they were still in use 30 years after his death.
He was also a member of the Otago Institute and served a term as its president. Convinced of the necessity for a university to be involved in research, he undertook a major project on Polynesian osteology, which was published in 1893 in the Transactions and Proceedings of the New Zealand Institute. In this paper, 'Contribution to the osteology of the aborigines of New Zealand and of the Chatham Islands', he recorded more than 70 measurements in each of over 80 Maori skulls. It was a monumental work which remains the most comprehensive on its subject a century later.
In 1891 the University of Otago established a faculty of medicine and Scott was appointed the dean. This made him the principal administrator of the medical school: a position he already held in practice if not in name. In 1896 he was organising secretary of the Intercolonial Medical Congress of Australasia held in Dunedin, and carried out this task with the same efficiency and meticulous attention to detail with which he administered the medical school. Neither as professor nor as dean did he ever have any clerical assistance. He was his own efficient secretary and preferred it that way, being poor at delegating and liking to keep everything in his own hands. In addition, he was ever mindful of the university's stretched finances; a secretary's salary could be better spent on other things.
The achievements of the Otago Medical School were confirmed by the high standards reached by its former students in both undergraduate and postgraduate study in Britain. However, the school had many detractors in New Zealand. Criticism came to a head in 1894 when, in response to complaints from the Wellington branch of the New Zealand Medical Association about the standards of teaching and facilities at the school, the senate of the University of New Zealand set up a special committee of inquiry. Its findings were a complete vindication of Professor Scott and the medical school. By 1913, his last year at the school, there were 140 students and New Zealand graduates formed approximately one-seventh of the medical profession in New Zealand.
In the last few months of his life Scott had a succession of small strokes, causing muscular weakness and some speech loss. Although this made teaching difficult he persevered to the last. He died at Dunedin on 25 February 1914, aged 62. His wife, Helen Scott, had died in 1899. He had lived to see two of their sons qualify in medicine in Edinburgh and practise in New Zealand.
John Scott was an exemplary teacher, yet he failed to keep up with progress in his subject. He became increasingly conservative. To the end he was teaching the anatomy he had learnt in Edinburgh 40 years earlier, and teaching it in the same way. Almost single-handedly, however, he transformed the University of Otago Medical School from an institution having only nominal existence into a flourishing and productive seat of medical learning.