Thomson was born at Glororum, Northumberland, England, the third child of Alexander Thomson and his wife, Janet, née Turnbull. After his father was killed in a hunting accident in 1830, the young Thomson and his mother went to live in Abbey St. Bathans, Berwickshire. He was educated at Wooler and Duns Academy, later spending some time attached to Marischal College, Aberdeen, and Edinburgh University before studying engineering at Peter Nicholson's School of Engineering at Newcastle-on-Tyne. Thomson arrived in the Malay Straits in 1838 and was employed by the East India Survey. In 1841 he was appointed Government Surveyor at Singapore and in 1844 became Superintendent of Roads and Public Works. He was responsible for the design and construction of a number of notable engineering works including bridges, roads, and hospitals. He conducted the allotment survey of Singapore, the topographical survey of the island of Singapore and its dependencies, and the marine survey of the Straits of Singapore and the east coasts of Johore and Penang. His outstanding achievement was the erection of the Horsburgh Lighthouse on Pedra Branca. In 1853 his health failed and he returned to England where he studied modern engineering techniques, and travelled widely through Britain and the Continent inspecting engineering works. Early in 1856 he emigrated to New Zealand, where he worked as Chief Surveyor of the Otago Province until 1873. From 1876 until 1879 he was Surveyor-General of New Zealand. He was also the original surveyor of the city ofInvercargill. From 1856 until 1858 Thomson surveyed and explored large sections of the interior of the South Island, covering most of the southern half of the island. Many names in the area bear witness to Thomson's Northumbrian background, though there is a widespread belief that the naming of many places was through a disagreement with the New Zealand surveying authorities. It has long been suggested that Thomson originally intended to give traditional Maori names to many places, but these names were refused. In response, Thomson gave prosaic Northumbrian names to many places, often simply in the form of a Northumbrian dialectic name for an animal. The Maniototo region around the town of Ranfurly, Central Otago is rife with such names as Kyeburn, Gimmerburn, Hoggetburn, and Wedderburn as a result, and the area is still occasionally referred to as "Thomson's Barnyard". Thomson was a founder of the Otago and Southland Institutes of New Zealand, to which he contributed numerous papers on scientific subjects including ethnological studies. Through his knowledge of Hindustani and Malay, he became interested in comparative linguistics and developed a theory ofracial diffusion based on philological evidence. He was also a keen amateur painter of landscapes, working mostly in oils. His paintings have little artistic merit but from a topographical viewpoint are of some interest today. Thomson married Jane Williamson of Dunedin in 1876. He died at his home in Invercargill on 16 October 1884. By marriage he was related to the Hall-Jones family, whose number included William Hall-Jones, a former Prime Minister of New Zealand. Thomson was responsible for the planning of the city of Invercargill in Southland, New Zealand and his mausoleum is in the St. John's Cemetery in Waikiwi, Invercargill. His descendants have written numerous books which contain authoritative information on his life in New Zealand. Thomson's great-grandson, John Hall-Jones, was a historian specializing in the history of southern New Zealand.
Legacy in Singapore
During his government service in Singapore, Thomson was responsible for many projects:
He made an elaborate survey of the Straits of Singapore, in conjunction with Captain Congalton who was largely responsible for clearing pirates from Malayan waters. He also surveyed Keppel Harbour. In 1829, he surveyed the Tombs of the Malayan Princes.
He carried out repairs and lowering of the Coleman Bridge.