As best I can tell from a non-exhaustive survey of their NIH alternative medicine website they are attempting to use the basic scientific methods to investigate certain treatments - typically herbs and the like-using more or less what we generally do to see if a given treatment works.That seems to be basically what their mission statement claims. Much of alternative medicine is simply not the subject matter for scientific investigation. For example, how do you scientifically investigate the statement that one's illness occurs when the person is "out of balance with nature".
Jacob Bronowski in his "The Origins of Knowledge and Imagination" talks about a major difference between eastern holistic thought and western scientific thinking. Speaking of the scientific method he says, "It is, therefore,an essential part of the methodology of science to divide the world for any experiment into what we regard as relevant and what we regard, for purposes of that experiment,as irrelevant. He talks about putting a fence around the law of nature we are trying to tease out. The best we can get out of this is to put together an approximation of what goes on inside the fence and possibly makes some speculations about the world outside this conceptual fence. As we earn more and make conceptual advance we may be able to enlarge the area surrounded by the fence. We cannot determine if herb x will rebalance someone with nature, but we know to go about finding out if herb x lowers blood pressure or cholesterol using among other things the methods of randomized clinical trials. I don't believe we are really integrating anything in this way. We are just finding particular therapies and investigating to see if they work or cause harm. We seem to be trying to find a few very small islands of medical usefulness in a ocean of mumbo-jumbo.Something works or it does not. Arnold Relman had something to say about that in his 1998 essay about Andrew Weil and is republished on quackwatch. Relman says " There are not two kinds of medicine, one conventional and the other unconventional, that can be practiced jointly in a new kind of 'integrative medicine'. Nor, as Andrew Weil and his friends also would have us believe, are there two kinds of thinking, or two ways to find out which treatments work and which do not. In the best kind of medical practice, all proposed treatments must be tested objectively. In the end, there will only be treatments that pass that tests and those that do not, those that are proven worthwhile and those that are not. can there be any reasonable 'alternative'? "