After his degree Hutton returned to London, then in mid-1750 went back to Edinburgh and resumed chemical experiments with close friend, James Davie. Their work on production of sal ammoniac from soot led to their partnership in a profitable chemical works, manufacturing the crystalline salt which was used for dyeing, metalworking and as smelling salts and previously was available only from natural sources and had to be imported from Egypt. Hutton owned and rented out properties in Edinburgh, employing a factor to manage this business.
This developed his interest in meteorology and geology, and by 1753 he had "become very fond of studying the surface of the earth, and was looking with anxious curiosity into every pit or ditch or bed of a river that fell in his way”. Work in clearing and draining his farm provided ample opportunities, and he noticed that “a vast proportion of the present rocks are composed of materials afforded by the destruction of bodies, animal, vegetable and mineral, of more ancient formation”. His theoretical ideas began to come together in 1760, and while his farming activities continued, in 1764 he went on a geological tour of the north of Scotland with George Maxwell-Clerk.
He had a house built in 1770 at St John’s Hill, Edinburgh, overlooking Salisbury Crags. He was one of the most influential participants in the Scottish Enlightenment, and fell in with numerous first-class minds in the sciences including John Playfair, philosopher David Hume and economist Adam Smith. He was a particularly close friend of Joseph Black, and the two of them together with Adam Smith founded the Oyster Club for weekly meetings, with Hutton and Black finding a venue which turned out to have rather disreputable associations.
Between 1767 and 1774 Hutton had considerable close involvement with the construction of the Forth and Clyde canal, making full use of his geological knowledge, both as a shareholder and as a member of the committee of management, and attended meetings including extended site inspections of all the works. In 1777 he published a pamphlet on Considerations on the Nature, Quality and Distinctions of Coal and Culm which successfully helped to obtain relief from excise duty on carrying small coal.
At Glen Tilt in the Cairngorm mountains in the Scottish Highlands, Hutton found granite penetrating metamorphic schists, in a way which indicated that the granite had been molten at the time. This showed to him that granite formed from cooling of molten rock, not precipitation out of water as others at the time believed, and that the granite must be younger than the schists.
He went on to find a similar penetration of volcanic rock through sedimentary rock near the centre of Edinburgh, at Salisbury Crags, adjoining Arthur's Seat: this is now known as Hutton's Section. He found other examples in Galloway in 1786, and on the Isle of Arran in 1787.
The existence of angular unconformities had been noted by Nicolas Steno and by French geologists including Horace-Bénédict de Saussure, who interpreted them in terms of Neptunism as "primary formations". Hutton wanted to examine such formations himself to see “particular marks” of the relationship between the rock layers. On the trip to Arran he found his first example of Hutton's Unconformity, but the limited view meant that the condition of the underlying strata was not clear enough for him.
Later in 1787 Hutton noted what is now known as the Hutton Unconformity at Inchbonny, Jedburgh, in layers of sedimentary rock. As shown in the illustrations to the right, layers of greywacke in the lower layers of the cliff face are tilted almost vertically, and above an intervening layer of conglomerate lie horizontal layers of red sandstone. He later wrote of how he "rejoiced at my good fortune in stumbling upon an object so interesting in the natural history of the earth, and which I had been long looking for in vain." That year, he found the same sequence in Teviotdale.
In the Spring of 1788 he set off with John Playfair to the Berwickshire coast and found more examples of this sequence in the valleys of the Tour and Pease Burns near Cockburnspath. They then took a boat trip from Dunglass Burn east along the coast with the geologist Sir James Hall of Dunglass. They found the sequence in the cliff below St. Helens, then just to the east at Siccar Point found what Hutton called "a beautiful picture of this junction washed bare by the sea". Playfair later commented about the experience, "the mind seemed to grow giddy by looking so far into the abyss of time". Continuing along the coast, they made more discoveries including sections of the vertical beds showing strong ripple marks which gave Hutton "great satisfaction" as a confirmation of his supposition that these beds had been laid horizontally in water. He also found conglomerate at altitudes that demonstrated the extent of erosion of the strata, and said of this that "we never should have dreamed of meeting with what we now perceived”.
Hutton reasoned that there must have been several cycles, each involving deposition on the seabed, uplift with tilting and erosion then undersea again for further layers to be deposited, and there could have been many cycles before over an extremely long history. In a 1788 paper he presented at the Royal Society of Edinburgh, Hutton remarked, "we find no vestige of a beginning, no prospect of an end." (This memorable line was quoted in the 1989 song “No Control” by songwriter and professor Greg Graffin.)
Following criticism, especially Richard Kirwan's, who thought him atheist and not logical, among other things, Hutton published a two volume version of his theory in 1795, consisting of the 1788 version of his theory (with slight additions) along with a lot of material drawn from shorter papers Hutton already had to hand on various subjects such as the origin of granite. It included a review of alternative theories, such as those of Thomas Burnet and Georges-Louis Leclerc, Comte de Buffon.
The whole was entitled An Investigation of the Principles of Knowledge and of the Progress of Reason, from Sense to Science and Philosophy when the third volume was completed in 1794. Its 2,138 pages prompted Playfair to remark that “The great size of the book, and the obscurity which may justly be objected to many parts of it, have probably prevented it from being received as it deserves.”
As well as combating the Neptunists, he also opened up the concept of deep time for scientific purposes, in opposition to Catastrophism. Rather than accepting that the earth was no more than a few thousand years old, he maintained that the Earth must be much older, with a history extending indefinitely into the distant past. His main line of argument was that the tremendous displacements and changes he was seeing did not happen in a short period of time by means of catastrophe, but that processes still happening on the Earth in the present day had caused them. As these processes were very gradual, the Earth needed to be ancient, in order to allow time for the changes. Before long, scientific inquiries provoked by his claims had pushed back the age of the earth into the millions of years still too short when compared with what is known in the 21st century, but a distinct improvement.
Hutton gave the example that where dogs survived through "swiftness of foot and quickness of sight... the most defective in respect of those necessary qualities, would be the most subject to perish, and that those who employed them in greatest perfection... would be those who would remain, to preserve themselves, and to continue the race". Equally, if an acute sense of smell was "more necessary to the sustenance of the animal... the same principle [would] change the qualities of the animal, and.. produce a race of well scented hounds, instead of those who catch their prey by swiftness". The same "principle of variation" would influence "every species of plant, whether growing in a forest or a meadow".
He came to his ideas as the result of experiments in plant and animal breeding, some of which he outlined in an unpublished manuscript, the Elements of Agriculture. He distinguished between heritable variation as the result of breeding, and non-heritable variations caused by environmental differences such as soil and climate.
Hutton saw his "principle of variation" as explaining the development of varieties, but rejected the idea of evolution originating species as a "romantic fantasy". As a deist, to him this mechanism allowed species to form varieties better adapted to particular conditions and was evidence of benevolent design in nature. Hutton's ideas on geology were clarified in Charles Lyell's books, which Charles Darwin read with enthusiasm during his voyage on the Beagle, and it remained to Darwin independently to develop the idea of natural selection to explain The Origin of Species and bring it to the forefront of public consciousness at the same time as providing the voluminous evidence necessary to win over the scientific community to the theory.