In Cologne his religious instructor Wilhelm Smets [de], a priest and novelist, emphasized the individuality of the human soul and the importance of free will.

[3] Müller is considered to have founded scientific medicine in Germany, publishing his Handbuch der Physiologie des Menschen für Vorlesungen in 1837–1840.

To carry it out, he designed and built an apparatus that enabled him to pump the gases oxygen and hydrogen out of the incubation chamber at specific times.

[11] Schwann carried out a series of microscopic and physiological experiments focused on studying the structure and function of nerves, muscles and blood vessels.

[9]: 85–86  Instead, in 1839, Schwann accepted the chair of anatomy at the Université Catholique de Louvain in Leuven, Belgium, another Catholic city.

[12]: 87 [13] In examining processes such as muscle contraction, fermentation, digestion, and putrefaction, Schwann sought to show that living phenomena were the result of physical causes rather than "some immaterial vital force".

"[8]: 645  Some writers have suggested that Schwann's move in 1838, and his decreased scientific productivity after that, reflect religious concerns and perhaps even a crisis relating to the theoretical implications of his work on cell theory.

[13][9]: 85–86  However, other authors regard this as misrepresenting his thinking, and reject the idea that Schwann went through an existential crisis or a mystical phase.

[9]: 85–86  Ohad Parnes uses Schwann's laboratory notebooks and other unpublished sources along with his publications to reconstruct his research as a unified progression.

[15]: 126  Florence Vienne draws on unpublished writings to discuss the ways in which cell theory, as a "unifying principle of organic development", related to the philosophical, religious, and political ideas of various proponents including Schwann.

[11] At Liège, Schwann continued to follow the latest advances in anatomy and physiology but did not himself make major new discoveries.

One of his projects was a portable respirator, designed as a closed system to support human life in environments where the surroundings cannot be breathed.

[17] When viewed in the context of his unpublished writings and laboratory notes, Schwann's research can be seen as "a coherent and systematic research programme" in which biological processes are described in terms of material objects or "agents", and the causal dependencies between the forces that they exert, and their measurable effects.

Schwann's idea of the cell as a fundamental, active unit then can be seen as foundational to the development of microbiology as "a rigorously lawful science".

[15]: 121–122 Some of Schwann's earliest work in 1835 involved muscle contraction, which he saw as a starting point for "the introduction of calculation to physiology".

[15]: 122  He developed and described an experimental method to calculate the contraction force of the muscle, by controlling and measuring the other variables involved.

He conceptualized digestion as the action of a physiological agent, which, though not immediately visible or measurable, could be characterized experimentally as a "peculiar specific substance".

[17][22] Even more importantly, Schwann wrote, by carrying through such analyses one could eventually "explain the whole developmental process of life in all organized bodies.

[6] Powerful microscopes made it possible for him to observe yeast cells in detail and recognize that they were tiny organisms whose structures resembled those of plants.

Schwann used the microscope to carry out a carefully planned series of experiments that contraindicated two popular theories of fermentation in yeast.

This was strong evidence against the theory of spontaneous generation, the idea that living organisms could develop out of nonliving matter.

[28] He concluded that sugar was converted to alcohol as part of an organic biological process based on the action of a living substance, the yeast.

[6] They were strongly opposed by Justus von Liebig and Friedrich Wöhler, both of whom saw his emphasis on the importance of a living organism as supporting vitalism.

Schwann remembered seeing similar structures in the cells of the notochord (as had been shown by Müller) and instantly realized the importance of connecting the two phenomena.

The first two were correct: By the 1860s, these tenets were the accepted basis of cell theory, used to describe the elementary anatomical composition of plants and animals.

Biologists would eventually accept the view of pathologist Rudolf Virchow, who popularized the maxim Omnis cellula e cellula—that every cell arises from another cell—in 1857.

[17] How the fatty myelin sheaths of peripheral nerves were formed was a matter of debate that could not be answered until the electron microscope was invented.

[17] He speculated that the muscular nature of the esophagus enabled it to act as a pipe, moving food between the mouth and the stomach.

[17][41] In his Microscopical researches, Schwann introduced the term "metabolism", which he first used in the German adjectival form "metabolische" to describe the chemical action of cells.