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Thomson became scientific adviser to a team with Whitehouse as chief electrician and Sir Charles Tilston Bright as chief engineer but Whitehouse had his way with the specification, supported by Faraday and Samuel F. B. Morse.

Thomson sailed on board the cable-laying ship HMS Agamemnon in August 1857, with Whitehouse confined to land owing to illness, but the voyage ended after just 380 miles when the cable parted. Thomson contributed to the effort by publishing in the Engineer the whole theory of the stresses involved in the laying of a submarine cable, and showed that when the line is running out of the ship, at a constant speed, in a uniform depth of water, it sinks in a slant or straight incline from the point where it enters the water to that where it touches the bottom.[22]

Thomson developed a complete system for operating a submarine telegraph that was capable of sending a character every 3.5 seconds. He patented the key elements of his system, the mirror galvanometer and the siphon recorder, in 1858.

However, Whitehouse still felt able to ignore Thomson's many suggestions and proposals. It was not until Thomson convinced the board that using a purer copper for replacing the lost section of cable would improve data capacity, that he first made a difference to the execution of the project.[23]

The board insisted that Thomson join the 1858 cable-laying expedition, without any financial compensation, and take an active part in the project. In return, Thomson secured a trial for his mirror galvanometer, about which the board had been unenthusiastic, alongside Whitehouse's equipment. However, Thomson found the access he was given unsatisfactory and the Agamemnon had to return home following the disastrous storm of June 1858. Back in London, the board was on the point of abandoning the project and mitigating their losses by selling the cable. Thomson, Cyrus West Field and Curtis M. Lampson argued for another attempt and prevailed, Thomson insisting that the technical problems were tractable. Though employed in an advisory capacity, Thomson had, during the voyages, developed real engineer's instincts and skill at practical problem-solving under pressure, often taking the lead in dealing with emergencies and being unafraid to lend a hand in manual work. A cable was finally completed on 5 August.

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