Squibb spent four years as a medical officer aboard the Perry, the Erie, and the Cumberland in Mexican and South American waters and the Mediterranean. During his time at sea Squibb was dismayed that the navy used poor quality drugs. In fact, he often took drastic measures to improve the quality of care he gave. For example, in Doctor Squibb: The Life and Times of a Rugged Idealist, Lawrence G. Blochman wrote that "In overhauling the Cumberland's dispensary, Dr. Squibb threw overboard great quantities of medicines he considered unfit for human consumption." Upon finishing his last voyage, Squibb compiled a report of his complaints regarding the hygiene and medical conditions he witnessed and supported his claims with detailed health records that he had kept throughout his assignment. Squibb sent his report to the American Journal of the Medical Sciences. It was published in January 1852, to ensure that the medical community was aware of the problems.
After a brief leave from sea, which Squibb spent brushing up on the latest medical advances at Jefferson Medical College, Squibb was ordered to return to sea aboard the steamship Fulton. He was unhappy about returning to sea under the poor medical conditions of the navy and managed to get reassigned to the Brooklyn Naval Hospital.
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