In 1945 he continued his work for the pharmaceuticals industry in the Institute of Biology and Serum Therapy (IBYS) in Madrid, which specialised in serums and vaccinations.
His experimentation in immunity led him to induce that the initial event in any immunization process is the multiplication of the antigen (the external immunizing protein) within specific cells of the immunized animal.
Whereas current immunology considered that the main effect of all immunizations is the multiplication of the antibody (a protein of the immunized animal that, when released, renders the foreign antigen inactive), Cordón considered this effect to be a secondary response to the first intracellular multiplication of the antigen (the immunized foreign protein), or of one of its structures, in a type of animal cells that have a very similar protein.
Shortly after drawing up this new hypothesis, he read the Treatise on Immunology by R. Doerr (Die Immunitätsforschung), published in eight volumes, which he studied and translated. This work allowed him to contrast his views with the commonly accepted ones, and showed him that all the events observed by immunology were compatible with his interpretation and that the poorly interpreted or uninterpreted facts in the current theoretical model fitted well in his theoretical model. For all these reasons he stuck to his hypothesis that foreign proteins multiply in certain specific cells of animals, causing processes of immunity in them.
To compare the current interpretation of the phenomena of immunity with his own, he performed an experiment in which he measured the immunological determinants of the tetanus toxin (an antigen), which he injected into the brain of guinea pigs. He demonstrated that the inoculated animals multiplied the immunological determinants of tetanus in their brains until they greatly exceeded the inoculated toxin. He was able to measure them due to their ability to neutralize anti-tetanus serum. In 1954 he presented his interpretation of immunity in the book Inmunidad y automultiplicación proteica. (Spanish).
His research into immunity gradually convinced him that the globular protein is not reducible to a simple macromolecule, nor can its behaviour be explained exclusively by the laws of chemistry. His observations pointed to the existence of an intermediate organisation between the cell and the molecule, with a characteristic behaviour that differentiated it from them. He postulated the existence of a living being that was proteinaceous, directly subcellular and supramolecular, which he confusedly called the protoplasmic individual.
“Of course, initially I was reluctant to accept the idea that there was a focus of action, experience and awareness at a level lower than the cell—it went against my prejudices. For a hundred years the cell had been considered as the primordial unit of life, though it was true that previously the cell had been conceived as a kind of box in which living material operated. My discovery went back to this classical way of thinking”.
His works on immunity led him to begin to adopt a critical attitude towards current biology. Whereas current immunology, like biology in general, attempts to explain living beings by studying the behaviour of their molecules (it vainly seeks to explain biological events through the laws of chemistry), Cordón's experiments on immunity led him to change from a chemist to a biologist due to his conviction that the phenomena of immunity cannot be studied without understanding the living beings that cause them.
At this time, though Cordón was already convinced of the existence of a proteinaceous level between the molecule and the cell, he did not yet have a clear understanding of the nature of the protein (he was later to make a full study), so he set out to understand what he called the proteinaceous or protoplasmic level. He began by comparing the behaviour of proteins with that of molecules and by considering the process of emergence of proteins from complex molecules. In other words, he considered the origin of living being from organic matter on the earth's surface.
Meeting with his assistants at the Institute of Biology and Serotherapy (IBYS). Madrid, 1958
For biologists, the origin of life is a synonym of the emergence of the cell from the molecule, because they consider the cell to be the simplest living being. Furthermore, the dominant interpretation of the origin of the cell is that it was organised from nucleic acids, after which random mutation of the nucleic acids in the cell was the driving force of biological evolution.
Cordón considered that this assumption gave nucleic acids abilities that are incongruent with the molecular level, and ones that no chemist has observed in any molecule. F. Cordón stated that by assuming 1) that nucleic acids can induce their own reproduction and produce other molecules of a very different composition to them—proteins—without consuming themselves, and 2) that proteins are molecules capable of recognising themselves spatially and coordinating themselves to establish the incessant dynamics of the interior of the cell, one is attributing to nucleic acids and proteins properties that go beyond the behaviour of all types of molecules.
The later discovery in biology (contradicting the initial interpretation of nucleic acids) that nucleic acids and proteins are produced within the cell through processes caused by the activity of coordinated proteins rather than by nucleic acids failed to question the notion that molecules of nucleic acids have the mysterious substantive abilities that are attributed to them. Cordón argued that the fact that these incongruities are maintained in the interpretation of the abilities of nucleic acids is due, once again, to the importance of the development of chemistry over biology, i.e. the reduction of biology to a molecular level. The consideration that living beings are molecular systems of varying complexity forces the biologist to neglect his goal: to understand living beings in their essential condition as agents. An introduction to the reproduction and heredity of integrative units.
“...Since, in my forties, I perceived the fragility of some principles of accepted science (i.e. I demystified science and saw it as it is: not a completed edifice but a work in progress), my thinking took on a new quality: ...I have had the tendency, not to deny my own convictions, but to try to find support for them in generally accepted thinking. I have always tried to make a constructive criticism that sought fully to grasp not the shortcomings and weaknesses of what I read (which is in general easy), but the basis of truth that is revealed in it…”
At that time his response to the origin of living beings from the molecule was limited to arguing that the proposal of the existence of a proteinaceous level between the molecular and cellular levels made it necessary to interpret the process of evolution from the molecule to the first cell in two large successive stages: 1/ the stage of evolution of the molecule, from which the first protein emerged, and 2/ the stage of evolution of the protein, which culminated in the origin of the first cell. His fundamental conclusion at that time was that it is not possible to understand the origin and evolution of living beings without a correct interpretation of their nature.
At this time Cordón was already firmly convinced that, based on the experimental data, it was necessary to define the biological concepts to form the foundations of a biology that was not dissociated from the process of evolution. He thought that this involved interpreting it on the basis of the successive appearance of living beings of different levels of complexity, because the hierarchy of their composition suggested implicitly that they did not emerge simultaneously but rather sequentially in stages of biological evolution.
In 1958 he brought together a series of lectures on his more general ideas of the time in a book entitled Introducción al origen y evolución de la vida.(Spanish).
Furthermore, during this period he made the first translations into Spanish of key books in the biology of the time, such as Genetics and the origin of species, by T. Dobzhansky and Animal Species and Evolution by E. Mayr, which allowed him to intuit the implications of his incipient concepts in the field of biology.
His experimental work on immunity gave rise to the original nucleus of his theory on living beings. He began to wonder what a living being is, how a living being emerges from living beings of the immediately lower level and how many levels of living beings there are.