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 Rh 1720 was able to begin his botanical lectures in the Garden, followed in November by a course on Materia Medica. These courses he carried on until 1739 when he was given the University Chair of Botany and Materia Medica, and the two Botany Schools were thus merged in one. Alston was now colleague of Munro, Rutherford, Sinclair, and other famous men who at this time were increasing the reputation of the University as a Medical School, and he continued to teach Botany and Materia Medica until his death in 1760.

Alston's teaching was mainly directed to the Materia Medica. His full course of lectures on the subject prepared for publication by himself appeared only as a posthumous work edited by his successor Dr Hope, and they reflect the best knowledge of the time, showing rational scepticism of the efficacy of many simples which experiment had not tested. Essays "On Opium," and "On tin as anthelmintic," and an "Index of Simples" published by him tell of his pharmacological investigations, to which his correspondence with Fothergill and others is also witness. The subject in this line to which he gave most attention and on which he wrote three dissertations based on experiments is that of Quicklime and Water—its efficacy in Calculus and also as an agent for keeping water sweet. From Alston, Stephen Hales, then in touch with the Admiralty upon questions of ventilation and other matters of sanitation, obtained early suggestions, and a long correspondence followed.

Alston, who had to earn his livelihood by medical practice, gave much time to the administration of the Botanic Gardens under his charge, and the elaborate lists which he prepared showing the disposition of plants in the Gardens, witness to his interest in their cultivation. His predilection in systematic arrangement was Tournefortian, and on the promulgation by Linnaeus of his "sexual system" in 1736, no writer was more trenchant than Alston in opposition to it, and by this he became widely known. His criticism was directed against it, not as a method of arranging plants by readily recognised characters, but from the standpoint of denial of the existence of sex. By various experiments as well as by argument, Alston endeavoured to disprove the necessity of the stamens