One of the most substantial collections of early printed books left to the Library was given by Thomas Baker, nonjuring clergyman and antiquary, who gained his BA from John's in 1678, MA in 1681, and became Ashton Fellow in 1680. From the age of seventeen he lived most of his life in the College, except for a brief period as rector of Long Newton in the diocese of Durham, which living he had to relinquish in 1690 when he refused to swear the oaths of loyalty required by the recently installed William III. Baker returned to St John's disappointed at the disruption to his career, but embarked upon the production of a work on knowledge entitled Reflections upon Learning, before devoting himself to his antiquarian studies and the collecting of books and manuscripts. Later in life he was to experience further disappointment when he was removed from his fellowship for refusing to take an oath of abjuration in 1717. He looked upon this as a disgrace and even considered leaving St John's and Cambridge. He stayed however and died of a stroke at the age of 83. The bulk of his collections were left to his College Library despite his disillusionment, the total number being so great that the dwarf cases in the Upper Library had to be raised to accommodate them.
Baker collected a great many valuable early printed books, particularly relating to the history of church and state during the 16th and 17th centuries. Among some of the more notable items are:
For a full description of Baker's library see Frans Korsten's A catalogue of the library of Thomas Baker (Cambridge, 1990).
Many, although by no means all, of Baker's books contain a book label detailing his bequest. Translated it reads:
From the gift of the Reverend Thomas Baker BD who was once a Fellow of this College: afterwards in truth, having been expelled by decree of the Senate, he grew old as a guest in this house; of blameless life and celebrated reputation, which followed from his study of antiquity.
Because of his modest income many of the books he collected were imperfect and he applied himself to their repair, often transcribing missing sections. These transcriptions and the sometimes copious notes he left in his distinctive hand often mark out his volumes. Another mark of his ownership is the note "Thomas Baker Collegii Johannis Socius Ejectus" which he placed in all his books showing his distress at the removal of his fellowship.