John Duke was included in the Navy List of Medical Officers in 1814  He was employed as Surgeon Superintendent to the convict ship Atlas in 1819. It was his only voyage on a convict ship.
Convict Ship Atlas
John Duke joined the Atlas on 12 May 1819. His Medical Journal began on that day. He provided a day by day entry describing weather conditions, punishments and illnesses.
The following entry in the surgeon's journal reveals that the prisoners were defrauded of their allowances for a part of the voyage: July 30th - Prisons scraped, cleaned and ventilated. The usual number of prisoners on deck throughout the day. Windsails at each hatchway. It was this morning discovered that Evan Griffiths a man who had been engaged to serve out the provisions to the Guard and Prisoners during the voyage has been in the habit of adulterating the wine before it was issued to the prisoners. It was proved that he first measured out four gallons of wine which he divided into two buckets but as each prisoner was allowed one gill of wine twice a week it required five gallons each issuing day to give this allowance; therefore instead of measuring off five gallons he measured off only four and to make up the deficiency he added half a gallon of water to the quantity of wine in each bucket. Have also proved that he was in the habit of adulterating the rum allowance for the guard and the manner in which he managed this discovered no less ingenuity than cunning and duplicity. As the Sergeant of the Guard attended daily and saw the proper allowance pumped from the cask it was impossible that he could openly adulterate it but he uniformly contrived to introduce the pump into the cask previously filled with water and when so fitted he pumped off the soldier's allowance. It appeared that he had been in the habit of abstracting butter, wine and rum from the casks and converting them to his own purposes. He had the dexterity to carry on these nefarious practices for a considerable time notwithstanding a certain number of the prisoners daily attended to see that they weighed their just and proper allowance. I am sorry to add that Mr. Watson the Chief Mate was implicated in these disgraceful proceedings. Griffiths was immediately dismissed from his situation and put in irons; and the Chief Mate was suspended from his duty.
John Duke departed Sydney on the Atlas on 10th January and Hobart on 2nd February 1820 bound for Madras arriving there on 3rd April -
He was probably on board when the Atlas was wrecked on 9th May 1820 .
On the forenoon of May the 9th, 1820, the ship riding heavy, and the sea breaking with great force over her, hove gears overboard ; she then parted from her small bower cable . and being observed to be drifting fast on shore, owing to the breakers, slipt her chain cable, and put to sea under the storm stay sails, which were instantly blown to pieces ; the ship at the same time falling upon her beam ends. It was then found necessary to cut away the mizen-mast in hopes of her righting, which carried away both her quarter-boat wheels, binnacle, and nearly one third of the round-house. At half-past 3 p. m. the main mast went with a heavy crash, close by the board; the ship still righted, but would not wear ; the main-mast, in falling, disabled the lee pumps, and tore away the planks in the wake of the channel bolts, which occasioned her to leak considerably. It now blew a hurricane ; the ship, being entirely upon her beam ends, was quite unmanageable. At 5 P. M. experienced a sudden shift of wind to the S. W. and found the ship drifting fast towards Ponlieat Shoal. At half-past 11 P. M. the ship struck, with a heavy crash, amongst the breakers on Poulicat Sands; immediately cut way the foremast, she being inclined to swing broadside on the water, which, at that time, was rising as high as her main deck beams.
At 1 A. M. the ship, being struck with a heavy sea, parted in two, in the wake of the mizen chains ; the crew endeavouring to save themselves, upon the quarter deck ; which at about two A. M. separated from her lower works and was drove by the breakers towards the shore; the crew closely clinging to it, as their only resource At about half past 3 it struck the beach ; and, upon mustering the crew found five deficient ; viz. two men and one boy (European), and two natives.
The Commander, Officers, and crew, return their most sincere thanks to Dr. Bronnickam, resident at Poulicat, for his attention towards them in their then helpless state ; and take this opportunity of paying the public tribute of gratitude, which they consider so justly due to his humanity, and the hospitable manner in which they were received and treated by that Gentleman - 
John Duke was appointed surgeon to the Superb in 1822.
John Duke and Patrick Coleman were appointed surgeons to the Ocean in 1824. 
John Duke was on the List of Surgeons of the Royal Navy who were fit for service in 1841
Notes and Links
National Archives. Reference: ADM 101/6/2 Description: Diary of occurrences on board the Atlas convict ship between 12 May and 7 November 1819, during which time the said ship was employed in transporting convicts from England to New South Wales by John Duke, Surgeon. (Sea victualling between 22 May and 30 October 1819). The bulk of the journal is in diary form, recording daily rotation of prisoners on deck, cleaning of prison, numbers on the sick list and casks of provisions opened, as well as other observations such as the weather and ship's position.