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Medical men were still divided into dogmatic schools of thought, according to the theoretical basis on which they practiced. The dominant school, the allopaths, depended upon the administration of powerful dosages of drugs to combat the suppositious causes of sickness or to neutralize its effects; the homeopaths believed in small doses of medicine, operating on the theory that "like cures like." The nature of the curative agents largely relied upon by the medical profession led Dr. Oliver Wendell Holmes to observe, in an address before the Massachusetts Medical Society in May 1860, that "if the whole materia medica, as now used, could sink to the bottom of the sea, it would be all the better for mankind—and all the worse for the fishes."

Dr. Holmes granted that there were exceptions to his sweeping condemnation, but his opinion as to the efficacy of much of the orthodox treatment of disease was warranted by the fact that methods of treatment were derived more from speculation and theory than from directed and controlled experimentation.

Even if there had been a more general recognition of the importance of experiment and scientific observation, there was, in America in the early 1860's, little of the apparatus or equipment for observation of even simple symptoms. Even such familiar tools of the physician as the clinical thermometer and the stethoscope were all but unknown and little used, and it was not until the war was half over that the headquarters of the Medical Department of the Army enjoyed the possession of an achromatic microscope, the basic working tool of the pathologist.

Not because of these lacks—for at the time they were not recognized as such—but because of the almost total lack of organized readiness for the removal and treatment of the wounded, the Medical Department of the Army came under criticism and condemnation. To many, the suffering of the sick, and especially of the wounded, seemed unnecessarily severe because of the failure of the Department to foresee the mounting needs of war and to organize to meet them. The charge against the Department was "stiff adherence to antiquated forms and modes of action outworn even for peace conditions."

Whether the deficiencies of the Medical Department were greater than those of other staff departments of the Army may be questioned, and certainly the framework of the governing law, under which the Medical Department was compelled to rely on the quartermaster for transportation and hospital construction and upon the Commissary Department for subsistence, was faulty.