The return from his three years on the Continent may be said to mark the close of Ray's apprenticeship to his work in science. The tour had given him a great range of material, larger perhaps than that of any previous botanist except De l'Ecluse, and including a knowledge of animals, birds, reptiles, and fishes such as no other Englishman had ever acquired. In addition it had given him status in the world of learning and a measure of confidence in his own capacity. The shy student who in 1660 had hesitated to send a copy of his Cambridge Catalogue to Hartlib was now the friend of Hoffmann and Corneli and Marchetti, of Steno and Magnol and Marchand; and could thenceforth exchange opinions with the leaders of contemporary research on level terms. In some sense the rest of his life was the examination and exposition of the data thus obtained. Though he did in fact undertake a large amount of further field-work and never gave up the desire for it, this, except in insects and to a less extent in cryptogams, was only supplementary.

It was, as we have seen, on 18 April 1684 and after the completion of the Historia Piscium that Tancred Robinson, writing from Geneva, revived Willughby's project for a General History of Nature. The proposal in its main outline was clear—that he should produce a series of hand-books or Synopses surveying the whole order of Nature, and anticipating the work carried out in the next century by Linnaeus. According to the classification then in vogue this would have meant surveys of Animals, Reptiles, Birds, and Fishes; Exanguia, that is Cephalopods, Crustaceans, Shell-fish, and Insects; Plants; and Fossils—these including Minerals as well as ‘formed stones’. Ray had got the material for some of these: to condense the Ornithology and the Ichthyology and even the Plants would not be a very serious business. But to deal with Animals and Reptiles was to break new ground; and the rest, except for some small notes of Insects, were wholly untouched. We have seen that he very rapidly put together the Synopsis Stirpium Britannicarum and followed it up with the Sylloge Europeanarum.

‘A good book needs no preface; a bad book deserves none.’ That is no doubt true. But when a student of theology turns aside (as it would seem) from his proper concern, when a normally active citizen in the middle of a great war fills much of his time with the life and work of a naturalist of the seventeenth century, it is reasonable that he should give some account of his eccentricity. Hence this personal explanation.

The history of science, with every respect for Mr Crowther and even Dr Hogben, has not yet been written. Nor in these days, when the use and abuse of scientific achievements are so significant, can the subject be regarded as unimportant. But my concern is not with the general record of man's discovery of the scientific method or of his application of it to the service of his needs and ambitions, so much as with one consequence of those events. As a theologian my primary task long ago convinced me of the importance of the change in man's aesthetic, moral and religious outlook which had accompanied and in large measure inspired the scientific movement. It was plain to me as a parson that the mixed folk whom I met as an entomologist and a bird-watcher had found an interest in nature which was singularly rich in educative and recreational value.

The move from Middleton, though it released Ray from other ties and on his mother's death enabled him to devote twenty-five years to study and writing, had one serious effect. It cut him off from the collections and notes gathered during his continental tour, from books and other aids to his work. In the same letter to Aubrey he had written: ‘Mr Willughby's library remains at his house at Middleton for the use of his son and heir’, and when he was publishing the History of Fishes he complained that it was now impossible for him to get at the records or material. Later on Sloane was very good in sending him literature: the Braintree carrier was constantly taking parcels to and fro into which the kindly Irishman would put a present of sugar for the family. But the want of access to other books tended to confine Ray to botany, where he had a library of his own which he had refused even in the years of his homelessness to part with.

As soon as the Ornithology was off his hands Ray turned to his second task, and in December 1674 wrote to Lister:

In these days when we all realise the importance of heredity and early environment in determining and in interpreting character, the student or John Ray will deplore more strongly than did any of his biographers our almost total ignorance of his parents and childhood. To Derham or to Dale the fact that he was the son of a village blacksmith had to be stated but should then be forgotten. It was unconventional if not indecent. They knew it; but neither they nor their successors thought it necessary to amplify it. For more than a century the year of his birth, though correctly given in at least one of his books, was wrongly stated as 1628; until 1847 no one had taken the trouble to search the parish register, and even then he was sometimes identified with the wrong John Ray. W.H. Mullens, who discovered that he had been baptised twelve months before the traditional time, did not prosecute his researches further or spend the few hours needed to run through the long vellum pages that form the scanty annals of Black Notley in the first half of the seventeenth century.