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With the exception of these entomological researches, and a small devotional work, ‘A Persuasive to a Holy Life,’ published in 1700, the chief labour of the last years of Ray's life seems to have been the third volume of the ‘Historia Plantarum.’ This embodied Sloane's Jamaica collections, those of Father Camel in the Philippines, and others, 11,700 species in all. It was published in 1704. It is upon the completeness and critical value of this work that Ray's fame as a systematic botanist mostly depends. Pulteney, summarising his work as a zoologist and botanist, says that he became, ‘without the patronage of an Alexander, the Aristotle of England and the Linnæus of his age.’

Ray died at the Dewlands, 17 Jan. 1705, his last letter to Sloane, dated ten days before, in the middle of which his strength failed him, being printed by Derham in the ‘Philosophical Letters’ (1718). He was buried in the churchyard at Black Notley, a monument being erected at the expense of Bishop Compton and others, with a long Latin inscription by the Rev. William Coyte. This monument was removed into the church in 1737, an inscription being added describing it as a cenotaph; but it was replaced, probably by Sir Thomas Gery Cullum, who added a third inscription, in 1782.

By his wife, Margaret Oakeley, who survived him, Ray had four daughters—twins born in 1684, one of whom, Mary, died in 1697, and two others. Jane, the youngest, married Joshua Blower, vicar of Bradwell, near Braintree. Two letters from her to Sloane, dated 1727, are printed in the ‘Proceedings of the Essex Field Club’ (vol. iv. pp. clxii–clxiii).

Ray's collections passed into the possession of Dale, who was with him shortly before his death, and his herbarium thus came subsequently into the possession of the Society of Apothecaries, and in 1862 was transferred to the botanical department of the British Museum. His library of fifteen hundred volumes was sold by auction in 1707, and the catalogue, ‘Bibliotheca Rayana,’ is in the British Museum (Ellis, Letters of Eminent Persons, Camden Soc.) Many letters from him to Sloane and Petiver are in the Sloane MSS., and were published by Dr. Lankester in his edition of the ‘Correspondence’ (1848); but others by him and his correspondents passed with his unfinished work on insects into the hands of his friend, Dr. William Derham (1657–1735) [q. v.], rector of Upminster. Derham published the letters, omitting all merely personal matters, in 1718, and after his death, in 1735, all the manuscripts came into the possession of his wife's nephew, George Scott of Woolston Hall, Essex, who in 1760 published the ‘Select Remains of John Ray,’ including the itineraries of three of his botanical tours, and an unfinished sketch of his life by Derham. These manuscripts are all now in the botanical department of the British Museum.

Ray's ‘varied and useful labours have justly caused him to be regarded as the father of natural history in this country’ (Duncan, Life). Though in this connection it is undoubtedly his employment of system which has attracted most attention, an antecedent merit lies, perhaps, in the precision of his terminology. Gilbert White, in the ‘Natural History of Selborne,’ says of him (Letter xiv): ‘Our countryman, the excellent Mr. Ray, is the only describer that conveys some precise idea in every term or word, maintaining his superiority over his followers and imitators, in spite of the advantage of fresh discoveries.’ This precision, and the strong bent of his mind towards the study of system as exhibiting the natural affinities of plants or animals, Ray probably owed in a considerable degree to his early association with Wilkins. It is especially in his zoological works that he shows himself to be no mere species-monger, but a philosophical naturalist. Of his ‘Synopsis Methodica Animalium’ (1693), Hallam says (Literary History, iii. 583): ‘This work marks an epoch in zoology, not for the additions of new species it contains, since there are few wholly such, but as the first classification of animals that can be reckoned both general and grounded in nature.’ With the exception of the merely descriptive work of Gesner, zoology had been, in fact, at a standstill since the time of Aristotle, and Ray was, as Cuvier said, ‘the first true systematist of the animal kingdom.’ Hallam calls attention to his method, Cuvier to its results. He was, says the former, ‘the first zoologist who made use of comparative anatomy. He inserts at length every account of dissections that he could find. … He does not appear to be very anxious about describing every species.’ ‘The particular distinction of his labours,’ writes Cuvier, ‘consists in an arrangement more clear and determinate than those of any of his predecessors, and applied with more consistency and precision. His distribution of the classes of quadrupeds and birds has been followed by English naturalists almost to our own days, and we find manifest traces of that he has adopted as to the latter class in Linnæus, in Brisson, in Buffon, and in all other ornithologists.’