In deciphering Yin-Yang and Five Elements (Five Phases) thinking, #Kaptchuk (1983) has a footnote and then an appendix that clarifies the way forward for appreciating foundations of Chinese medicine favouring the former. For philosophical correctness, Keekok Lee (2017) would frame the Chinese implicit logic as dyadic, rather than as a Western explicit logic of dialectic.
Yin (陰) and Yang (陽) Theory
The logic underlying Chinese medical theory — a logic which assumes that apart can be understood only in relation to the whole — can also be called synthetic or dialectical. In Chinese early naturalist and Taoist thought, this dialectical logic that explains relationships, pattern and change is called Yin-Yang theory. [†† ]Kaptchuk (1983), p. 7
- [††] Although the Chinese identify the relationships between phenomena primarily by the patterns of Yin and Yang, another system of categorization, known as the Five Phases, was also in use in early China. In this system, Wood, Fire, Earth, Metal and Water were seen as a set of emblems by which all things and events in the universe could be organized. Although the Five Phases categories permeate virtually every aspect of the traditional thought, leaving a significant impression on Chinese medical theory, this influence is for the most part formal and linguistic in nature. The Five Phases proved too mechanical, while Yin-Yang theory, because of its greater flexibility, was much for practical for the Chinese physician. It accommodated clinical changes and theoretical development that the tradition required in order to grow. (For a detailed discussion of the Five Phases in Chinese medicine, see Appendix H).
This important footnote seems to NOT show up the eBook versions for later editions that I’ve seen on the web (or maybe the previews are just incomplete).
Let’s jump down to Appendix H: The Five Phases (Wu Xing), with the note: This appendix was written in collaboration with Dan Bensky and the assistance of Kiiko Matsumoto. (We’ll skip over the preliminary Five Phases description, to get to discrepancies with Yin-Yang Theory).
The number five was important in the numerology of the period, particularly in for classifications of Earthly things. Various other numbers, such as six, four, and three, turn up in early classification schemes for things pertaining to Heaven. It is difficult to determine whether the importance of the number five led to Five Phases theory or the popularity of the Five Phases theory led to things being classified in fives.Kaptchuk (1983), p. 346
-  Jia De-dao, Concise History, pp. 29-30. For example, Lu’s Spring and Autumn Annals (246-237 B.C.E.) mentions Four Phases, omitting Earth.
During the third and fourth centuries B.C.E., the Five Phases theory and the Yin-Yang theory existed simultaneously and independently of each other. For example, Lao Tzu and Chuang Tzu refer extensively to Yin and Yang but do not mention the Five Phases. Unlike other traditional cultures with systems of elemental correspondences (e.g. the Greek Four Elements or the Hindu Three Doshas), the Chinese thus had two systems of referents. It was not until the Han dynasty, a period of great eclecticism and synthesis, that the two systems began in merge in Chinese medicine. “The five elements [Phases][which] had not been part of the most ancient Chinese medical speculations” were incorporated into the clinical tradition that culminated in the Nei Jing. Certain parts of the Nei Jing refer to the Five Phases, whlle others do not. Yet other texts, such as the Discussion of Cold-Induced Disorders and the biography of Bian Que in the Shi Ji or Historical Records, make no mention whatsoever of Five Phases theory. The Five Phases theory continued to undergo changes even after its incorporation into Chinese medicine. It is not until the Song dynasty (96-1279 C.E.) that the relationships between the Phases were commonly used to explain the etiology and processes of illness.Kaptchuk (1983), p. 346
-  Fung Yu-lan, History of Chinese Philosophy, vol 1, p. 8; Chan, Chinese Philosophy, p. 224; Hans Agren, “Patterns of Traditional and Modernization in Contemporary Chinese Medicine,” in Medicine in Chinese Cultures: Comparative Studies of Health Care in Chinese and other Societies, ed. by Arthur Kleinman, et al. (Washington, D.C.: John E. Fogarty International Center, U.s. Dept. of HEW, NIH, 1975), p. 38
-  Lu Gwei-djen and Joseph Needham, “Records of Diseases in Ancient China,” American Journal of Chinese Medicine 4, no. 1 (1976): 12.
-  Dan Bensky, “The Biography of Bian Que in the Shi Ji,” unpublished manuscript, University of Michigan, 1978, p. 2.
-  Recent archeological discoveries of pre-Nei Jing texts confirm the impression that Yin-Yang was originally a much more important port of Chinese medicine than the Five Phases theory. See “A Simple Introduction to Four Ancient Lost Medical Texts Found at the Tomb of Ma-wang,” Medical History Text Research Group of the Academy of Traditional Medicine, Wen Wu, no. 6 (1975), pp. 16-19. The Five Phases are not mentioned in these ancient medical writings. See Chapter 4, Note 3.
-  Jia De-dao, Concise History, pp. 165-166.
Many attempts were made to fit the Five Phases neatly into the Yin-Yang structure. For example, Wood and Fire were considered the Yang Phases, being active in character, while Metal and Water, associated with quiescent functions, were the Yin Phases. Earth was the balance point between Yin and Yang, despite this apparently successful marriage between Five Phases and Ying-Yang theory, the two systems of correspondence frequently yielded different interpretations of health and disease 
For example, Five Phases theory might emphasize the following correspondences stated in the Nei Jing: The Liver opens into the eyes; the Kidney opens into the ears; the Heart opens into the tongue. Disorder in a particular orifice would necessarily be linked into is corresponding Organ.
Yin-Yang theory, on the other hand, might emphasize the the following quite different assertions of the Nei Jing: The pure Qi of all Organs is reflected in the eyes; all the Meridians meet in the ears; the tongue is connected to most of the Meridians. Yin-Yang theory would not necessarily see a link between a part and a part. Rather, all disharmonies of the eyes, ears or tongue would be interpreted in terms of patterns. Thus, an eye disorder could be part of a Liver disharmony or perhaps a Lung or Spleen disharmony, depending on the configuration of other signs.
The differences between these medical interpretations stem from the fact that Five Phases theory emphasizes one-to-one correspondences, while Yin-Yang theory emphasizes the need to understand the overall configuration upon which the part depends. And so, although Five Phases theory is ideologically more dynamic than, for instance, the Greek or Hindu systems, and is actually being applied creatively to medical practice, it became a rigid system. Yin-Yang theory, on the other hand, with its emphasis on change and view of the importance of the whole, allowed for a great deal of flexibility. It was therefore easier to adapt to the needs of clinical practice.Kaptchuk (1983), p. 346-347, editoral paragraphing added.
-  Porket, Theoretical Foundations, p. 118. “Traditional Chinese thought has a general tendency to reconcile and harmonize different or even mutually exclusive ideas in an arbitrary syncretism. Contrary doctrines — for instance, Nakamura’s discussion of this Chinese characteristic states: “What stand out in this sort of reasoning is a certain sort of utilitarianism and early compromise with cold logical considerations completely abandoned.” Hajime Nakamura, Ways of Thinking of Eastern Peoples (Honolulu, East-West Center Press, 1968), p. 291.
In that last paragraph, “Yin-Yang theory emphasizes the need to understand the overall configuration upon which the part depends” could be interpreted either as a systems approach, or as a context for the dyadic. Five Phases theory appreciates part-part interactions, but may miss the whole (that is foundational to systems thinking).
Chinese medicine has had to take many liberties with the Five Phases theory to fit it to actual medical experience. The physiology that grew out of Five Phases theory, for example, is not identical with traditional Chinese physiology. The tradition is based on empirical observation and is ultimately connected to Yin-Yang theory, concentrating on the functions of the Organs and extrapolating their interrelationships from their functions. The Organs are thus the key to the system. Five Phases theory does not always agree with this understanding, and in that case, it is simply ignored. For example, in Five Phases physiology, the Heart corresponds to Fire. Traditional texts, however, consider the Kidneys (Life Gate Fire) to be the physiological basis for the Fire (Yang) of the other Organs. And so, the Five theory’s formal correspondence would be conveniently forgotten.Kaptchuk (1983), p. 347
-  Qin Bo-wei, Medical Lecture Notes , pp. 15-22.
We’ll skip over the “Use of the Five Phases in Medicine” (pp. 347-351), towards favouring Yin-Yang theory.
Criticism of Five Phases Theory
The Five Phases theory has been the subject of criticism ever since its invention. The challenges to its veracity and practicality date as far back as Mohist contemporaries of Zou Yen (fourth century B.C.E.). For example, one comment on the Mutual Control order reads: “Quite apart (from any cycle) Fire melts Metal, if there is enough Fire. Or Metal may pulverize a burning fire, if there is enough Metal. Metal will store Water (but does not produce it). Fire attaches itself to Wood (but is not produced from it).”Kaptchuk (1983), p. 351
-  Quoted in Needham, Science and Civilization, vol. 2, pp. 259-260.
A few hundred years later, the great Han dynasty scientist and skeptic Wang Cong satirized the results of literal application of the Five Phases theory. Here are two short excerpts from his work:Kaptchuk (1983), p. 351
The body of a man harbors the Qi of the Five Phases, and therefore (so it is said) he practices the Five Virtues, which are the Tao (Way) of the Phases. So long as he has the five inner Organs within his body, the Qi of the Five Phases are in order. Yet according to the theory, animals prey upon and destroy one another because they embody the several Qi of the Five Phases; therefore the body of a man with the five inner Organs within it ought to be the scene of internecine strife, and the heart of a man living a righteous life be lacerated with discord. But where is there any proof that the Phases do fight and harm each other, or that animals overcome one another in accordance with this?
The horse is connected with the sign wu (Fire); the rat with sign zi (Water). If Water really controls Fire, (it would be more convincing if) rats normally attacked horses and drove them away.Wang Cong, cited in Kaptchuk (1983), p. 352
-  Ibid., pp. 265-266. Translation altered by author.
Despite such early criticism, the Five Phases theory became entrenced in Chinese medicine. One reason for this is that Chinese investigative study tends to be inductive only to a point and then proceeds with deductions based on classics. The Five Phases theory thus served as an orthodox reference for numerous speculative deductions.. Most modern Chinese critics describe Five Phases theory as a rigid metaphysical overlay on the practical and and flexible observations of Chinese medicine.Kaptchuk (1983), p. 352
-  Nakamura, Ways of Thinking of Eastern Peoples, p. 190.
Another major criticism, and a primary difﬁcu!ty in the application of the Five Phases theory to medicine, is its lack of consistency. To fit the theory to reality, the referents of the Phases and the relationships between them haye continually been changed and corrupted. The results of such corruption cap be seen in Tables 74 and 75 on the clinical use of the Five Phases.
Such a problem exists in all traditional systems of elemental correspondence. The original classical Greek formulation by Empedocles of Agrigentum (c. 504-433 B.C.E.) is a system in which the basic elements of fire, earth, water, and air were considered the ultimate constituents of matter and were associated with various other categories of four such as the four fundamental qualities and the four humors. All varieties and changes in the world were associated with different mixtures of the four elements. [….]Kaptchuk (1983), p. 352
-  To get a sense of the cultural, physiological, scientific, ideological, religious, and intellectual factors that are involved in a correspondence system, it is worth examining the transition from the Aristotelian system of Four Elements to the Paracelsian Three Elements (tria prima: salt, sulphur and mercury) in sixteenth-century Europe. an interesting discussion appears in Allen G. Dobus, “The Medico-Chemical World of the Paracelsians,”, in Changing Perspectives in the History of Science, ed. by Mikaluas Teich and Robert Young (Dordrecht, Holland, and Boston: D. Reidel Pub. Co., 1973), pp. 88-92
Western practitioners of acupuncture and Chinese medicine have special problems dealing with the Five Phases theory. The major difficulty is that much of the literature available in English describes diagnosis and treatment exclusively in terms of Five Phases theory. Writings that refer to the theory as the “Law of the Five Elements” betray a misunderstanding of Chinese science—natural laws such as those promulgated by Aristotle and Newton simply were not developed in traditional China. These writings also put undue emphasis on the importance of the Five Phases to the Chinese medical tradition; even respected defenders of the Five Phases theory readily admit sometimnes it is useful and sometimes it is not. Even so, it is unfortunate many practitioners simply consider Five Phases theory unscientific gibberish, and do not try to understand it. It is actually an important secondary emblem system used to assess and discuss clinical reality.
-  An example is Denis and Joyce Lawson-wood, The Five Elements of Chinese Acupuncture and Massage (Rustington, England: Health Science Press, 1965). The English overemphasis on the Five Phases is not derived from the Chinese tradition. Instead, the fascination of European acupuncturists with this method is due to the influence of the “Nan Jing traditional acupuncture movement” and to to somem of the Kei Raku Khi-Riyo (Meridian Treatment) schools, both of which developed around the turn of the twentieth century, in Japan. The European adoption of this method stems partly from a desire for an exotic schema and partly from lack of adequate information.
-  See Needham’s discussion of Chinese thought and “law” in Grand Titration, pp. 299-330.
-  Qin Bo-wei, Medical Lecture Notes, p. 22.
-  An example is Frank Z. Warren, Handbook of Medical Acupuncture (New York: Van Nostrand Reinhold Co., 1976).
Kaptchuk, Ted J. 1983. The Web That Has No Weaver: Understanding Chinese Medicine. Chicago: Congdon & Weed.