Moyle made putting the surgical supplies aboard and setting up sound nice and neat - just find a place on the ship where it's dry and secure everything. The surgeon's mate dwelled within the bowels of the ship, in a six-foot-square canvas enclosure in the cockpit on the orlop deck, directly above the hold in the front of the vessel, where the rocking was greatest, the air foulest, and the natural light faintest.
Lighting would be a significant challenge for a ship's surgeon dwelling in the bowels of ship during delicate operations. Atkins' comment above also notes that candlesticks will be less disturbed 'by the Motions of the Ship.' A ship at sea almost constantly rocks - the larger the waves, the more the ships moves. The quality of the air that Bown mentioned may seem like a curious issue, but it must be remembered that the men often had their sleeping quarters on the orlop deck and bathing was not quite as prevalent as it is today. Speaking of water, although Bown does not mention it specifically, a ship was a very damp place to be. While regular maintenance of wooden vessels called for caulking them with cotton and oakum (hemp fiber soaked in pine tar), she may still not stay dry as Hamilton suggests. The last thing Bown mentions are the quarters, which we have already noted would be very cramped. On top of everything else, the orlop deck could be particularly noisy especially during a storm. I should note that representing every ship's orlop deck exclusively in these terms would be most unfair.
In sum, there was much that the surgeon might be required to deal with during any long voyage, such as those to and from the Caribbean. Pirate ships would be particularly susceptible to problems associated with their vices - those of drunkenness and indiscreet behavior while on land.

Of course, like the would-be truant school boy, a man couldn't just claim to be sick in order to avoid work and be allowed to lie around in bed. Those requiring treatment of health issues which did not require them to be relieved of duty were to meet with the surgeon or his mates or assistants at a scheduled time to be treated. Of course, before going to the mast, the surgeon or his mates had to prepare everything that they might need for treatments.
John Woodall gives a little more detail to the needed preparations when he explained to the surgeon's mate what was required to be in his plaster box.
Price Realized is hammer price plus buyer’s premium and does not reflect costs, financing fees or application of buyer’s or seller’s credits. Prospective purchasers are advised that several countries prohibit the importation of property containing materials from endangered species, including but not limited to coral, ivory and tortoiseshell. Works of Art from the Royal House of Hanover, Sotheby's, Schloss Marienburg, Hannover, Germany, 5-15 October 2005, probably lot 5658 (part).
Being at or below the waterline meant there would be no openings in the side of the ship to let in ambient light. As waves washed over her deck, the water would make its way downward, going in open hatches and between deck boards in ships that were not well sealed. When not in use on a small ship (such as the pirates would have used), the surgical equipment would have to be stowed out of the way as Moyle suggested. Bown, Scurvy: How a Surgeon, a Mariner, and a Gentleman Solved the Greatest Medieval Mystery of the Age of Sail, p.
Even pirates, as a general rule, preferred to rely on their reputations to convince their prey to strike their colors and surrender if they could avoid a fight.

There were the hazards of falling from the rigging onto the deck or down the steep ladders resulting in bruises and fractures.
Each required a full complement of men; the naval captain because he had to have an adequate number of soldiers should they be needed for an attack, the merchant because he was usually lightly manned and the pirate because he needed to be able to put on a good show of force when trying to convince his prey to surrender without a fight, or to join the fray if such were required to take the prey ship.
Moyle details the preparation of the plaster box, ordering the surgeon to "see that your dressing box is furnished.
Accordingly, prospective purchasers should familiarize themselves with relevant customs regulations prior to bidding if they intend to import this lot into another country. We have already discussed the use of the canvas enclosure and why pirates would probably not have them set up for the surgeon.
While we can't say with certainty that pirates were more lax about cleaning their ship than naval seamen, it does not seem like a stretch to suggest this. So the majority of a surgeon's work involved the day-to-day health problems that sailors encountered.
Fingers could be pinched in pulleys and under cannon and cargo, skin could be burned while running rope through it and opportunities for cuts and minor contusions abounded. Even so, the cockpit and its close neighbor the cable tier would have been pretty challenging places for a ship's surgeon to work on a naval ship, let alone a pirate vessel.
There were problems associated with diet including upset stomachs, diarrhea, and decaying teeth.

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