Biology is stemmed from two traditional researches.
The first is the traditional anatomy-physiology research of functional biology.
The second is the traditional natural history-taxonomy research on diversified biology.
Physiology is a typical research focusing on internalities of organisms and extending inwardly, and taxonomy is a representative study focusing on the externals of organisms and extending outwardly. They were two major directions along which biology was going when it was formally initiated.
Among them, there was connotation meaning structure research, which originated when taxonomic research carried out and moved forward.
Traditional research of diversity biology has a long history as knowledge about animals, plants, and newly-found microorganisms continually accumulates during the long-term life practice of human beings. This formed the basis for the emergence of the early diversity biology. Systematic taxonomy was the first step to theorize knowledge about biodiversity. It attempted to set up a necessary classification order for the phenomenon of biodiversity, and consequently facilitated interspecific comparative study of traits and structural similarities. On the contrary, similarities of traits among organisms became the foundation for building this taxonomic principle.
Primarily, natural philosophers added so much individual preferences on the classification that an arbitrary taxonomic order was arranged for the given organisms. For example, plants were classified according to their effects on diseases treatment, and organisms were classified based on their benefits and relations to human being. During this period, man had shallow knowledge about taxonomic order.
Later, more knowledge about biodiversity was absorbed into taxonomy, and taxonomists increasingly realized that intrinsic natural structures existed in living systems. They began to see how complex the issue really was. Thus, they gradually moved away from individual tastes in their classification work and turned to find a method and standard system which could fit the systematic relations of organisms themselves. Therefore, they would pay more and more attention to compare similarities and disparities of biotic traits and structures. At that time, man's knowledge about taxonomic order began to reach a relatively in-depth level.
During this period, taxonomists gradually found that comparison of one or several major traits was unable to meet the actual needs of classification. This led them to enlarge the range of common configuration comparison to include more broad traits such as behavior characteristics and physiological and ecological traits. They took as much as possible the relevant knowledge in all disciplines into the comparative studies of taxonomy.
Therefore, taxonomy gradually shifted its attention to the systematic research on the biosphere system, when it had been used simply for classification purposes at the beginning. Viewing the biosphere as a systemic object characterized the taxonomic research as a different matter from simple classification of different species. Now taxonomy has involved such major aspects as physiological functions, development and life history, biogeography, and ecological environment in the exploration of the essence of natural systems (said by Carl Linnaeus).
Taxonomy has not made any theoretical breakthroughs as significant as what its contemporary physiology has, and the major reason for that is systematic research of the biosphere system is far more difficult than physiology, and biodiversity is much more complex than biological process. Consequently, although theoretical research of taxonomy continuously progressed toward the essence of the issue, the most essential area has not been reached. Therefore, for a long time, systematic taxonomy was involved in a debate on methods and principles. This debate is still ongoing, and the taxonomic system we use is a temporary compromise resulting from many discussions. Once we scrutinize the system, a series of thorny issues might emerge. On the contrary, this demonstrates that a successful systematic taxonomy should be built on a basis of a theoretical system that can satisfy the needs to represent biodiversity and historical evolution.
Taxonomy has experienced evolution for hundreds of years and its history shows that classification is far more complex than previously predicted. On the surface, it seems that classification could be done by identifying similar and distinctive traits between different organisms. But in fact, these similarities and disparities are deeply related to the internal organic structures and the essence of functional relations, and each trait represents a certain profile of the system, so it is necessary for classification to study the systemic structure and functions of organism. From a deeper perspective, the systemic structures and functions of different organisms have been developed historically in the evolution. Therefore, it is essential to track down the whole historical process of biotic structures.
The diversity biology is essentially different from functional biology. The history of diversity biology shows that, in its long-term developmental course, it always tends to seek a lasting tentative ideal which believes that a deep-seated systematic order underlies the extrinsic diversified appearances of organisms. This order is beyond the scope of individual organism and invasive in the internality of the individual at the same time. It permeates both intrinsic and extrinsic parts of an individual and exists at all levels, but it is not elusive and invisible. We can reveal its true features through comparative study and classification. All taxonomists believe in this ideal in a way. This ideal is entirely different from the traditional goal of functional biology. Although biology has experienced many changes, this ideal holds on and keeps on its independent course.
Today, as both types of biological researches have reached in-depth levels and knowledge has greatly increased, the relationship between biotic deep systematic order and the functional structure manifests itself more and more clearly, making the ancient ideal assumption more realistic and reliable. Aren't you amazed at the fact that modern science is the continuation of the ancient pre-scientific principles, and that they come down in one continuous line?
Deep-structure of life is a new concept and a novel research field which modern scientific research will inevitably touch on, and it is a resurgence and heir of the ancient biological ideal. If the so-called "natural systems" (Linnaeus' words) were able to position all living organisms accurately and rationally, then it should be able to find an order of the meaning system which can reflect the relationship among all living organisms. In other words, natural system theory underlies the ideal of connotation meaning structure. Believing in the existence of natural systems is equivalent to accepting the existence of a connotation meaning structure.
Connotation meaning structure theory came into being in the first half of the nineteenth century. George Cuvier's comparative physiology and comparative embryology brought along a revolution in the biological concepts, and this changed the previous separated research on isolated characters into the comparative studies of organism's systemic structure and physiological functions, and all the traits need to be taken as references in the comparative studies of the whole system. The core idea is that all the specific internal characteristics of an organism are mutually related and work together. Because they are closely tied to other parts, each trait cannot change singly on its own.
Comparative physiology and comparative embryology underlie the comparative means for taxonomic study. This makes sense because comparative physiology is the bridge of knowledge between biophysiology and biodiversity research and integrates the two major branches of biology. Later, in 1869, based on the cross-layer bridge established by Cuvier, Darwin successfully made the first theoretical cross-layer synthesis. Although Darwin did not put forward the concept connotation meaning structure, if we scrutinized the analytic system of evolution from the perspective of scientific reductionism, we would find that a two-tiered reductionistic connotation meaning structure has actually been built. Therefore, strictly speaking, Darwin was the first person who successfully studied connotation meaning structure from a perspective of substantialism, and evolutionism opened up a path for the development of connotation meaning structure theory.