In it he extended to physical science the philosophical principles which Immanuel Kant (1724–1804) had applied to epistemology and morality. Oken had been preceded in this by Gottlieb Fichte (1762–1814), who, acknowledging that Kant had discovered the materials for a universal science, declared that all that was needed was a systematic coordination of these materials. Fichte undertook this task in his "Doctrine of Science" (Wissenschaftslehre), whose aim was to construct all knowledge by a priori means. This attempt, which was merely sketched out by Fichte, was further elaborated by the philosopher Friedrich Schelling (1775–1854). Oken built on Schelling's work, producing a synthesis of what he held Schelling to have achieved.
Oken produced the seven-volume series Allgemeine Naturgeschichte für alle Stände, with engravings by Johann Susemihl (1767–1847), and published in Stuttgart by Hoffman between 1839 and 1841.
In the Grundriss der Naturphilosophie of 1802 Oken sketched the outlines of the scheme he afterwards devoted himself to perfecting. The position advanced in that work, to which he continued to adhere, is that "the animal classes are virtually nothing else than a representation of the sense-organs, and that they must be arranged in accordance with them." Consequently, Oken contended that there are only five animal classes:
In 1805 Oken made a further advance in the application of the a priori principle in a book on generation (Die Zeugung), in which he maintained that "all organic beings originate from and consist of vesicles or cells. These vesicles, when singly detached and regarded in their original process of production, are the infusorial mass or protoplasma (Urschleim) whence all larger organisms fashion themselves or are evolved. Their production is therefore nothing else than a regular agglomeration of Infusoria—not, of course, of species already elaborated or perfect, but of mucous vesicles or points in general, which first form themselves by their union or combination into particular species."
A year after the production of this treatise, Oken developed his system one stage further, and in a volume published in 1806, written with the assistance of Dietrich von Kieser (1779–1862), entitled Beiträge zur vergleichenden Zoologie, Anatomie, und Physiologie, he demonstrated that the intestines originate from the umbilical vesicle, and that this corresponds to the vitelius or yolk-bag. Caspar Wolff (1735–1794) had previously claimed to demonstrate this fact in the chick (Theoria Generationis, 1774), but he did not see its application as evidence of a general law. Oken showed the importance of the discovery as an illustration of his system. In the same work Oken described and recalled attention to the corpora Wolffiana, or "primordial kidneys."