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Thomson strongly urged by the leading men of science in Great Britain to send out a roomy and well-equipped vessel, in order to make a series of soundings and dredgings in the three great ocean basins, to ascertain the temperature and character of the water, to collect specimens of the fauna and flora on the surface and from all possible depths, and to study as far as possible certain rarely visited oceanic islands—in fact, to make a somewhat devious voyage of circumnavigation, which was expressly guided by the desire to increase scientific knowledge. The Challenger, a corvette of 2,306 tons, was specially fitted up and placed under command of Captain (now Sir George) Nares, with a naval surveying staff. Thomson, who had been granted leave of absence by his university, was appointed chief of the civilian scientific staff (six in number), and the vessel left Sheerness on 7 Dec. 1872. They crossed the Atlantic from the Canary Isles to the West Indies, when after skirting its American side as far north as Halifax they recrossed to Madeira by the Azores. Then they sailed southward of the Cape de Verde Islands and St. Paul's Rocks to Fernando Noronha and the Brazil coast, crossing the southern Atlantic by way of Tristan da Cunha to the Cape of Good Hope. From this they made for the Antarctic Ocean by way of the Crozets and Kerguelen land, and reached the ice-pack a little south of the Antarctic circle, beyond which it was unsafe to venture in an ordinary vessel. Thence they proceeded to Australia, and after touching at Melbourne and Sydney, sailed for Fiji. A devious course took them through the Australasian islands, and they then visited Japan and the Sandwich Islands. After sailing due south to the tropic of Capricorn, they took an easterly course to Valparaiso, and made their way into the southern Atlantic through the Magellan Strait. After calling at Montevideo they visited the Canaries, and returned to England by a variation of their former route, arriving at Spithead on 24 May 1876, having travelled in this remarkable voyage 68,890 nautical miles, and having made observations by soundings at 362 stations. An enormous mass of material had been obtained for study, and Thomson (who received the honour of knighthood on his return) was appointed director of the Challenger expedition commission to superintend the arrangement of the collections and the publication of the results at the public expense. He also resumed his university duties, delivered the Rede lecture at Cambridge in 1877, and in the following year presided over the geographical section at the meeting of the British Association in Dublin. But he had undertaken more than his constitution could bear. He was struck down by an illness in the summer of 1879, which prevented him from resuming his lectures, and he died at his house, Bonsyde, near Linlithgow, on 10 March 1882. He married, in 1853, Jane Ramage, eldest daughter of Adam Dawson, of Bonnytown, Linlithgowshire, who survived him. Their only son, Frank Wyville Thomson, became surgeon-captain in the 3rd Bengal cavalry.

Thomson received the following honorary degrees: LL.D. of Aberdeen, 1853, LL.D. 1860, and D.Sc. 1871, of the Queen's University, Ireland; LL.D. Dublin, 1878, and Ph.D. Jena. He was elected F.R.S.E. 1855, M.R.I.A. 1861, F.R.S. 1869, and was a fellow of the Linnean, Geological, Zoological, and other societies, besides receiving the honorary membership of various scientific bodies, colonial and foreign. He was awarded a royal medal in 1876, and in 1877 was created a knight of the Polar Star when a delegate from the university of Edinburgh to that of Upsala, on the occasion of their quater-centenary.

Thomson's more important papers, including official reports, are about forty-five in number. They deal with varied subjects, but the majority treat of echinids, crinoids, or other echinoderms, for he made this class his special study. Besides these he wrote two books, ‘The Depths of the Sea,’ already mentioned, and ‘The Voyage of the Challenger in the Atlantic,’ 2 vols. 1877. The latter gave a general account of the results of the exploration of the Atlantic. His illness prevented him from continuing the publication of the results of the expedition, and the heavy task was undertaken in the beginning of 1881 by Dr. John Murray, a member of the civilian staff. The series of volumes was completed in about thirteen years.

A marble bust of Wyville Thomson is in the university of Edinburgh, and a memorial window was erected to his memory in the cathedral of Linlithgow.

[Proceedings of the Linnean Soc. 1881–2, p. 67; Transactions of the Edinburgh Botan. Soc. xiv. 278; Quarterly Journ. Geol. Soc. 1882, Proc. p. 40; Reports of Challenger, Zoology, vol. iv. (1882); information from Dr. John Murray.]  THOMSON, DAVID (1817–1880), professor of natural philosophy at Aberdeen, eldest son of David Thomson, merchant of Leghorn, was born at Leghorn on 17 Nov. 1817. Receiving his school education in Italy and Switzerland, he entered the university of Glasgow in 1832 and Trinity College, Cambridge, in 1836, graduating