Doctor-tamer Joe Califano recently told a medical audience that when the proctologic part of his latest physical examination was completed, a physician stepped forward and asked the HEW secretary, "Mr. Califano, would you like to have a second opinion?"

The doubtful authenticity of this examining-room yarn need not concern us. But in looking for the sources of the animosity that has developed between medicine and government, a good deal of it can be found in Washington's encouragement of a kind of second-opinion process aimed at the standard methodologies of modern medicine. This has nothing to do with another doctor taking a look at the patient; rather, it involves systematic examination of the ways doctors respond to given medical problems. And, what has been found, in matters big and small, is that modern, supposedly scientific, medicine often has no justification for many of its methods, apart from custom or what amounts to little more than a seat-of-the-pants sense that that's the way to do it.

Take, for example, something as hallowed as the elaborate surgical scrub that precedes action in the operating room, both on and off the TV screen. Surely there must be otherwise unobtainable germ-ridding value in that 10-minute ritual (think of it: that's a long time to be washing your hands) if all that high-priced talent goes about it so diligently. Well, at last it was decided to examine the matter carefully. The results, according to a report in the journal Surgery, Gynecology and Obstetrics: A three-minute brushless scrub with a bland soap and standard antiseptic is satisfactory for reducing bacterial counts -- especially since, whether the scrub is long or short, after an hour in the surgical gloves, bacteria drop to near zero.

Then consider coronary-care units (CCUs), those electronics-packed, $500-a-day workshops of super-modern medicine where, presumably, miracles can be wrought for victims of heart attacks. But some studies have found that for patients with similar conditions, the survival rate is actually higher among those treated at home. A speculation offered in explanation of this finding is that a coronary-care unit is quite a stressful place, and that, in comparison, a patient's own home is more likely to be conducive to recovery. In any case, while most of the public perceives coronary-care units as a triumph of medicine, as does, of course, a major segment of the medical profession, the second-opinion process continues to raise doubts about the role of CCUs in medical care. In the opinion of the leader of a Johns Hopkins University team that reviewed various studies of their efficacy, "the better the study, the less the benefit that has been shown form CCUs."

Even something so well established in medical practice as the appendectomy has been attracting reconsideration. According to a recent study by the congressional Office of Technology Assessment (OTA), surgical treatment of appendicitis seems to bear a curious relationship to the availability of surgical insurance. Thus, it was found that in a cost-conscious, prepaid plan for federal employees, the appendectomy rate was 110 per 100,000; for a similar group enrolled in a Blue Shield reimbursement plan, the rate was 210 per 100,000. Noting that appendectomies annually take an operating-table toll of at least 35 lives and cost more than $350 million, the OTA report observes that "there is strong evidence suggesting that appendicitis may be treated with substantially fewer appendectomies without increased loss of life."

Though doctors sincerely insist that they are best qualified to decide what symptoms should be regarded with concern, the New England Journal of Medicine recently reported a study that "suggests a tendency of physicians to over-recommend (or overestimate) utilization of medical services hased upon symptoms.... Furthermore, studies of unattended common illnesses... seem to show that many patients with symptoms that might be of concern to physicians receive no care at all, and subsequently appear to be none the worse for avoiding the encounter."

While that finding does not provide justification for shunning, or failing to provide, medical treatment, it does raise questions about the therapeutic value of a lot of doctor-patient transactions.

Finally, there's the controversy over what happened several years ago when doctors in Los Angeles went on a five-week slowdown in protest against rising malpractice insurance premiums. By some accounts, the reduction in elective surgery was accompanied by a drop in the death rate -- by as much as 1.4 to 5.8 percent. Critics of modern medical practice grasp those numbers with glee, while practitioners in the mainstream of medicine contend that it is absurd to link the medical slowdown to variations in the death rate.

The basic point, however, is that doctors don't like to be charged with withc-doctoring, and that, in effect, is what they're being accused of wnen the established methods and techniques of their profession are systematically examined and found lacking.

The burden that medicine has to bear is that is has evolved pragmatically and is more craft than science -- though the proportion of the latter is increasing. However, its inability to provide scientific rationables for its ways of doing things is red meat for Mr. Califano and his cost cutters. Washington is telling the doctors that, to a large extent, they really don't know what they're doing. And, understandably, they resent that message.