Parkinson's interest gradually turned from medicine to nature, specifically the relatively new field of geology, and paleontology. He began collecting specimens and drawings of fossils in the latter part of the eighteenth century. He took his children and friends on excursions to collect and observe fossil plants and animals. His attempts to learn more about fossil identification and interpretation were frustrated by a lack of available literature in English, and so he took the decision to improve matters by writing his own introduction to the study of fossils.
In 1804 the first volume of his Organic Remains of a Former World was published. Gideon Mantell praised it as "the first attempt to give a familiar and scientific account of fossils". A second volume was published in 1808, and a third in 1811. Parkinson illustrated each volume and his daughter Emma coloured some of the plates. The plates were later re-used by Gideon Mantell. In 1822 Parkinson published the shorter "Elements of Oryctology: an Introduction to the Study of Fossil Organic Remains, especially of those found in British Strata".
Parkinson also contributed several papers to William Nicholson’s "A Journal of Natural Philosophy, Chemistry and the Arts", and in the first, second, and fifth volumes of the "Geological Society’s Transactions".
On 13 November 1807, Parkinson and a number of other distinguished gentlemen met at the Freemasons' Tavern in London. The gathering included such great names as Sir Humphry Davy, Arthur Aikin and George Bellas Greenough. This was to be the first meeting of the Geological Society of London.
Parkinson belonged to a school of thought, Catastrophism, that concerned itself with the belief that the Earth's geology and biosphere were shaped by recent large-scale cataclysms. He cited the Noachian deluge of Genesis as an example, and he firmly believed that creation and extinction were processes guided by the hand of God. His view on Creation was that each 'day' was actually a much longer period, that lasted perhaps tens of thousands of years in length.
He died on 21 December 1824 after a severe stroke, bequeathing his houses in Langthorne to his sons and wife and his apothecary's shop to his son, John. His collection of organic remains was given to his wife and much of it went on to be sold in 1827, a catalogue of the sale has never been found. He was buried in St. Leonard's Church, Shoreditch.
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