The extraordinary scope of Cooper's operative experience is readily apparent from a scanning of his bibliography. He was capable of performing the most advanced procedures then being undertaken in the fields of ophthalmic; head and neck; thoracic; abdominal; orthopedic; and vascular surgery. Since his bibliography refers specifically to many of these operations and we have already described certain of them, we shall limit our further consideration of this subject to pointing out that Cooper performed, on two occasions in each, the most difficult and controversial operations in the surgical armamentarium at mid-century. These procedures were caesarean section and ligation of the innominate artery. We have already reported amply on Cooper's two caesarean sections and their outcome.
Ligation of the Innominate Artery
We have not, however, previously mentioned that he twice ligated the innominate artery. This artery, the first and largest branch of the aortic arch, ascends to the thoracic inlet where it divides behind the upper sternum into the right common carotid and subclavian arteries. These vessels are the main blood supply to the right side of the head and the right upper extremity. Aneurysm (i. e., circumscribed dilatation) of the innominate, carotid and/or subclavian arteries may occur at the bifurcation of the innominate, usually as the result of trauma or arteriosclerosis. Unless successfully treated, death from spontaneous rupture of aneurysm in this location is a near certainty.
At present, such aneurysms may be removed and replaced by synthetic vessels without undue risk. However, when Cooper practiced, the treatment consisted of ligating the innominate artery, a procedure considered the most formidable operation of that day. Valentine Mott (1785-1865), Professor of Surgery at Columbia College of Physicians and Surgeons in New York, was the first surgeon, world-wide, to ligate this vessel for aneurysm with survival of the patient. He performed the procedure on a fifty-seven year old sailor at New York Hospital on 11 May 1818. The only "anesthesia" administered was a drink containing seventy drops of tincture of opium. The operation occupied about one hour. Although the patient died of secondary hemorrhage on the twenty-fifth postoperative day, the case established the practicability of the operation. For that reason it was acclaimed throughout medical circles in Europe and America. In consequence of this operation, Professor Mott attained an international reputation by the thirty-fourth year of his age. As predicated by John Bell's postulate, Professor Mott is best remembered to this day for the great operations he performed, particularly his ligation of the innominate.  
During the forty-year period from 1818 to 1858, eleven surgeons from around the world, including Professor Mott, succeeded in ligating the innominate artery. The outcome was the same in every case - the patient died. 
The following data were derived from p. 1487 and pp. 1502-1517: The first fourteen surgeons to ligate the innominate artery were: Mott (1818), Graefe (1822), Norman (1824), Arendt (1827), Bland (1832), Bujalesky (1833), Unknown Surgeon reported by Dupuytren (1834), Lizar (1837), Hutin (1841), Pirogoff (1852), Gore (1856), Cooper (1859), Cooper (1860) and Smyth (1864).
In March 1859, Cooper was consulted by a man with a combined aneurysm of the right common carotid and subclavian arteries. Ligation of the innominate artery was the only known treatment for his condition. Undeterred by the knowledge that all eleven of the previous operations had been followed by death of the patient, Cooper decided to operate. He had the advantage of general anesthesia which had not yet been discovered when nine of the previous cases were done. During the operation, Cooper removed the medial end of the clavicle and a portion of the upper end of the sternum to improve the exposure, this being the first time this valuable maneuver was employed during ligation of the innominate.
The procedure went well and the vessel was tied off with minimal blood loss. Postoperatively, the patient was comparatively comfortable for five days. After that time he became restless, short of breath, and unable to void. He gradually sank until the ninth day when he died. An autopsy was done and failed to reveal the cause for the patient's rapid decline after an initial period of satisfactory progress. The major causes of death after ligation of the innominate in past cases had been severe wound infection and exsanguinating hemorrhage. Neither of these conditions were present in Cooper's patient. Since the patient had developed anuria postoperatively, Cooper believed renal failure to have been the cause of death rather than anything directly related to the operation. It was a tantalizing thought that, except for this unforeseen and unrelated circumstance, success would have crowned his efforts and the acclaim for a truly "great operation" would have been his.
Cooper's disappointment in the outcome was reflected in the brevity of his report on the operation which he mailed to the editor of the American Journal of Medical Sciences on 20 March 1859. His perfunctory description of the case, only a page and a half in length and lacking many relevant details, was published in the October 1859 issue of the American Journal. 
Cooper thought that he had done his duty by simply reporting the failure of the ligation, and that the case was closed. He was therefore quite unprepared for the harsh rebuke he was soon to receive from his former colleague and friend, Professor Daniel Brainard of Rush. As editor-in-chief of the Chicago Medical Journal, Brainard utilized the pages of the December 1869 issue of the Journal to attack Cooper for his temerity in undertaking the ligation, and for reporting the case so incompletely. Professor Brainard was quite stern: 
The October number of the American Journal contains a report of a (ligation of the innominate), if report it may be called, which omits nearly every important fact connected with the history of the case, the seat and extent of the disease, its effects, etc. . .
We notice this operation, to say that it is one which cannot receive the approbation of any judicious surgeon. Ligature of the arteria innominata had been performed (eleven) times (previously). In all the result was fatal. . .
Cases of this kind, published without comment, and thus partly endorsed by journalists, have given rise to the term "audace Americaine," used by Trouseau. If editors, in giving currency to this and similar reports, would express their opinions of the propriety of such operations, it is likely that fewer would be done, and the responsibility be thrown upon the individuals who, without any prospect of benefit to their patients, think fit to resort to them.
We know of Cooper's high regard for Professor Brainard who had been his mentor and paragon in times past, but the Professor's public attack on his competence, judgement and integrity was intolerable. Soon after he acquired his own editorial voice in the San Francisco Medical Press, Cooper responded to Brainard with a Commentary in the July 1860 issue of the Press: 
Nothing we commend more than just criticism even when touching the faults of our own performances, and such critique would have to be very severe indeed if we did not take it in good part with the writer.
Our report, as published, of the operation (mentioned in your editorial), was justly obnoxious to severe criticism, partly owing to our own carelessness and partly that of our Amanuensis; so much so that we were really chagrined on seeing it in print with so many imperfections. . . But a critique above all other productions is expected to be free from faults. (Your editorial), however, is not one of that kind. In addition to special pleading against the operation of ligating the arteria innominata under any circumstances, based solely upon assertion and individual authority, there are forced conclusions which show much more of a disposition to criticize, than industry in preparing for the same. . .
For the editor of the (Chicago Medical Journal) to say that no judicious surgeon would perform that operation, without giving any reasons for the statement, when Mott (and ten other) eminent (surgeons) thought proper to operate, is arraying individual opinion against an amount of authority which we conceive to be very bad taste to say the least. Why should not a judicious surgeon operate? Is it because patients demanding it (as is conceived) could ever recover without? No; every one would die at no distant period
We can readily imagine a case in which it would be very injudicious to operate. Take for instance a small aneurysm growing very slowly, especially in an old person. But such has not been the case with those upon whom the operation has been performed.
Surgeons will differ in opinion in regard to the propriety of hazardous operations in hopeless cases. Occasionally the wishes of a patient might rightfully have much to do with deciding whether to operate or not. . .
Again, the idea that a French surgeon would apply to American surgery the term "Audace Americaine," is or ought to be regarded as simply ridiculous by one who has ever witnessed much practical surgery in the Parisian hospitals. Everybody knows who knows anything of the matter, that no surgeons in the world operate upon more hopeless cases than those of the French Hospitals.
In his caustic response to Brainard's reproach, Cooper made it clear that he believed ligation of the innominate to be a justifiable operation under proper circumstances. Within a few months he had an opportunity to act on this conviction.
On 23 September 1860 a 31 year-old man, otherwise in excellent health, was admitted to the Pacific Clinical Infirmary with a large aneurysm of the right subclavian artery filling the entire supraclavicular triangle. On September 30th Cooper operated and for the second time ligated the innominate artery. As in his previous case he resected the medial end of the clavicle and a portion of the upper end of the sternum to gain the necessary exposure.
The operation was at once the subject of intense interest to the American profession. Cooper received a barrage of letters and made the following progress report to the editor of the American Medical Gazette (New York) on 30 October 1860: 
Today is the 30th day (since I ligated the arteria innominata), and the patient has every prospect of recovering, so far as could be judged by any other evidence than that based upon the results of past experience of other surgeons. . .
On the 20th day after the operation a most violent hemorrhage began, but was arrested at once by the promptitude of a medical student. . . I do not permit myself to hope that the case will terminate favorably; but still the patient is vigorous, cheerful, has a good appetite, sleeps well, laughs and talks to his friends, and declares that he will live, notwithstanding he has been informed that no other ever survived this operation.
Cooper's next, and last, progress note on this patient was published in the January 1861 issue of the San Francisco Medical Press: 
To the inquiries of several medical friends, in regard to the recent ligating of the Arteria Innominata, we would state, without further answer, that the patient died on the forty-first day. A slight hemorrhage occurred on the (20th), but not again until the 39th day. The bleeding (on this last occasion) stopped without any interference. On the next day, it began with considerable violence being difficult to arrest. The day succeeding, it was found impossible to prevent bleeding although we had invented an apparatus which pressed with much force directly upon the bleeding surface, and controlled the hemorrhage far better than any compress and bandage.
At three P. M. of that day, the patient was informed that all hope of recovery was lost, but that he had remaining a sufficient length of time to arrange his earthly matters. He expressed no wish to use the time in that way, and, as soon as he was alone, forcibly removed the apparatus, and bled to death at once.
From his vantage point as editor of the Pacific Medical and Surgical Journal, Wooster had kept a watchful eye on Cooper's every move, and saw in this case an opportunity to revile him: 
California is not behind any portion of the world in the art of crime. She is equal to other portions of the world in arts and science and experiment, quoad the ability. She merely lacks the development.
The arteria innominata has been tied in this city and the case is dead, and the autopsy has been made. Result: he died from the effects of the operation. Any surgeon who ties the innominata is either insane, a knave, or ignorant of hydrodynamics. This operation is necessarily fatal, as any physicist can demonstrate, without recourse to physiology. The ligation external to the tumor is rational, and should be sometimes successful.
Cooper's definitive report on his second operation finally appeared in the August 1861 issue of the Cincinnati Lancet and Observer. He gave details of the operation, postoperative course and autopsy. In this case, and presumably also in the first, the innominate artery was tied with "four strands of saddler's silk." In accordance with standard practice at the time, the ends of the silk at the knot were left long and brought out through the wound. Due to the inevitable wound infection, the tie around the artery gradually eroded entirely through the vessel and was then drawn out of the wound by traction on the long ends. In this second case the detachment of the ligature occurred on the eighteenth day. As might be expected, hemorrhages began shortly thereafter for the ligature had completely divided the artery and the force of the blood pressure expelled the clot that temporarily occluded its lumen.
The failure of early operations for ligation of the innominate was generally the result of ligatures cutting through the artery because of infection. For that reason, frequent success of the operation was not achieved until well into the aseptic era. Only then did it become possible, because of the sterile operating field and primary wound healing, to ligate the innominate with ligatures that remained permanently in place and did not slip off or cut through the vessel.
Cooper was devastated by the terrifying hemorrhages and fatal outcome of his second case. The patient's robust physical condition, the technical precision of the operation, and the prolonged postoperative survival had filled him with hope His report concludes with the following disconsolate thoughts: 
This case, more than any other that has yet occurred in my practice, made the strongest impression on my mind. Never before have I felt so humiliated by the inefficiency of the surgical art in rescuing patients from death. What are we to do with such cases? Is there no new process for treating these aneurysms more available than any yet established, and can the skill of the whole surgical world avail nothing? Time will prove. . .
I write for those who are inexperienced, because having had two cases terminating in the same way, I never expect to have more experience upon the subject, and would fain benefit those who are disposed to, but have not yet tried, this most hazardous of all operations upon the arteries.
The first surgeon, ever, to report long-term survival after ligation of the innominate artery was Andrew Woods Smyth at the Charity Hospital in New Orleans. On 15 May 1864, just four years after Cooper's second case, Dr. Smyth ligated the right common carotid and the innominate for an aneurysm of the right subclavian artery in a 32 year-old mulatto man. Thirteen days after operation the carotid ligature came away and on the fourteenth the first of several self-limiting hemorrhages occurred. On the sixteenth day the innominate ligature came away and at about this time hemorrhage recurred. Dr. Smythe happened to be in the hospital at the time of the bleeding and was about to go hunting. He promptly opened the wound and poured the contents of his bag of bird-shot into it and put on a compress. Miraculously this procedure, plus ligating the vertebral artery, controlled the hemorrhage. The patient survived for eleven years, and then died by hemorrhage from a recurrence of his subclavian aneurysm.  
Following Dr. Smyth's case, the next twelve ligations of the innominate ended in death.
It was not until 1889, after the beginning of the aseptic era, that a second patient had a long-term survival following ligature of the innominate. The operation was performed by J. Lewtas while in the British service in India. The patient was a twenty year-old man, an Indian national, who had a traumatic aneurism of the right subclavian artery secondary to a gunshot wound. The carotid and innominate arteries were ligated. No infection occurred, the wound healed by primary union, and the patient recovered. Mr. Lewtas remarked in his report that he probably wouldn't have undertaken the procedure if he had known how dangerous it was. Thereafter, only four successful ligations were reported until after the turn of the century when they became increasingly frequent. 
From Mott's operation in 1818 to the end of the century, only Cooper reported having twice ligated the arteria innominata. 
We have already mentioned Cooper's one lasting contribution to the procedure for ligating the innominate. He was the first to remove the sternal end of the clavicle and a portion of the summit of the sternum to gain adequate exposure for the removal of large and complicated aneurysms. He wished to be remembered for this significant innovation and made special mention of it in his summation of each operation. In 1922 Dr. Emile Holman was the 88th surgeon to ligate the innominate. The lesion was a very complicated post-traumatic aneurism of the subclavian artery. He was ultimately successful in extirpating the aneurism by gaining the necessary exposure through the approach pioneered by Cooper sixty-three earlier. When Dr. Holman performed this operation in 1922 he was a Resident Surgeon at Johns Hopkins Hospital. When he later became Professor and Executive Head of the Department of Surgery at Stanford Medical School in San Francisco from 1926 to 1955, he was, in effect, the linear successor of Professor Cooper. 
Cooper still lives in the annals of those who have performed truly "great operations." But we have seen that these cases brought him little acclaim and much criticism.