In 1958 he created the Research Department of IBYS, which he directed until 1966. This work forced him to de-specialize and to shift his attention from immunity to other problems of biology. In this period he dealt with a great diversity of subjects and techniques, such as purifications of settled antitoxins and toxoids, preparations related to blood coagulation, hepatic protectors, prevention and treatment of atheromatosis, replacement of digestive enzymes, replacement of the intestinal flora, diuretics, remedies against gastroduodenal ulcers, and the study of an antacid.
Whilst experimenting with a preparation that balanced the effect of gastric secretion, Cordón undertook first a study of the gastric function and later a study of the animal.
The animal is the type of living being to which we belong, with which we are most familiar and on which we have by far the deepest knowledge (taxonomy, anatomy, physiology, zoological embryology, the theory of natural selection, studies of the animal and human behaviour, etc.). He began his work on the animal by attempting to understand the laws of its evolution, based on a systematic review of Darwin's work. The conclusions of his reflection corresponding to this stage were summarized in the book La evolución conjunta de los animales y su medio. (Spanish).
"...(experimental biologists) have applied a variety of techniques to elucidate phenomena and processes from very different points of view, mostly concerning the internal aspects of living beings, which has led them to specialize in the development of bodies of experimental knowledge (animal physiology, vegetable physiology, cytology, biochemistry, immunology, etc.) that are highly disconnected from each other and tend to lack a general theoretical system of their own. I think that the current task of evolutionist biology must be not only to study the very rich stock of experimental data in order to further unravel the process of biological evolution. Complementarily (as Darwinism did with the empirical biological sciences that preceded it), it must achieve a general theoretical interpretation for the experimental biological sciences as a whole and for each one individually, because all manifestations of all living beings and their associations must have originated within the general process of biological evolution.
In the last paragraph of the Origin of the Species, Darwin's concept of the proliferation of animal species over the ages through distanced processes of bifurcation of one species into two led him to formulate his powerful induction that all species may stem from a very small number of remote original species, perhaps -he says- from a single one.
Despite this statement, he was unable to enunciate the problem of how the first animal emerged, which may today seem obvious to us. It is understandable that for his objective and rational mind the emergence of the first animal was not a meaningful topic of study. Before the exploration of the cell and the complex intracellular events, he could only have imagined that such highly complex animate beings were produced directly from inorganic matter, which was obviously senseless. In our time, however, we must consider a different order of evolutionist problems to those of Darwin's time. The progress of experimental sciences has accumulated a great stock of knowledge that allows us to consider questions of a new type such as how the first cell was produced on the basis of the evolution of the living beings of the directly supramolecular and infracellular level, and what the cellular unit is in terms of its process of origin.”
The study of Darwin's work led Cordón to wonder about the origin and the nature of the animal, and the experimental work that he was carrying out on gastric secretion suggested possible answers, some of which are recorded in his prologue (Spanish) to the book by Antonio Colodrón, La medicina corticovisceral. Sus fundamentos fisiológicos (pp. 7-83) and in Conversaciones con Faustino Cordón sobre biología evolucionista by Antonio Núñez, (pp. 199-240). (Spanish).
At this time he proposed a preliminary hypothesis on the origin of the animal through an association of phagocytes that, by specific selective advantages, gradually formed a digestive system that would coordinate the protomuscular and protonervous cells with increasing efficacy until it culminated in the first nervous system and therefore the first animal. For the first time in evolution, the particular mechanical action of the animal allowed it to take up solid nutrient that, after being degraded by its digestive cells, was distributed to all the cells of the animal soma and incorporated by them to replace what had been used. An introduction to the origin of an integrative unit in phylogeny. FIBE, 2005.
At the Institute of Biology and Serotherapy (IBYS). Madrid, 1959
His reflection on the nature of the animal allowed Cordón to further progress in his attempt to understand the living being more objectively than through a description (i.e. through the data on its composition and its structure). It was at this time that he expressed his first definition of the living being, in which he highlighted the properties that he considered to be consubstantial with it, and that current biology failed to take into account. He defined all living beings as agents that perform actions on their environment and note their useful or harmful effects in order to correct them to their own benefit, as units capable of action and experience.
Cordón's early definition of the living being as a unit with action and experience led him to claim that the only living beings that exist are the protein, the cell and the animal, because they are the only biological agents that are able to perform a unitary action on their environment and to perceive its effect in order to decide on the following action. All other biological phenomena (organelles, tissues, organs, organ systems, plants, ecosystems, etc.) are consequences of the actions of living beings of these three levels.
Furthermore, Cordón considered the nature of the action of the living beings of these three levels to be qualitatively different:
1) The globular protein (which he also called the basibion, the basic living being) manipulates molecules one by one in still water to replenish its needs; its evolution gives rise to the emergence of the first cell. A. Núñez. Conversaciones con Faustino Cordón sobre biología evolucionista (p. 1-113) (Spanish). An introduction to the protein as an integrative unit of the first biological level..
2) The cell governs the associative activity of its proteins with the effect of moving masses of water that provide its proteins with dissolved molecules; its evolution gives rise to the birth of the first animal. A. Núñez, Conversaciones con Faustino Cordón sobre biología evolucionista (p. 113-188) (Spanish).
3) The animal governs the coordinated activity of its cells, with the result that it performs a mechanical movement that allows it to act on solids to ensure that its cells receive nutrient. A. Núñez, Conversaciones con Faustino Cordón sobre biología evolucionista (p. 197-343, Spanish).