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Medicine
Stahl mainly focused on the distinction between the living and nonliving. Although he did not support the views of iatro-mechanists, he believed that all non- living creatures are mechanical and so are living things to a certain degree. His views were that nonliving things were stable throughout time and did not rapidly change. On the other hand, living things are subject to change and have a tendency to decompose.

His main argument on living things was that there is an agent responsible for delaying this decomposition of living things and that agent is the anima or soul of the living organism. Anima controls all of the physical processes that happens in the body. It not only just controls the mechanical aspects of it but the direction and goals of them too. How anima controls these processes is through motion. He believed that the three important motions in the body is the circulation of blood, excretion and secretion.

These beliefs were reflected on his views in medicine. He thought that medicine should deal with the body as a whole and its anima rather than the specific parts of a body. Having specific knowledge in the specific mechanical parts of the body is not very useful.

Chemistry
The best of Stahl’s work in chemistry was done while he was a professor at Halle. Just like medicine, he believed that chemistry could not be reduced to mechanistic views. Although he believed in atoms, he did not believe that atomic theories were enough to describe the chemical processes that go on. He believed that atoms could not be isolated individually and that they join together to form elements. He took an empirical approach on his descriptions for chemistry.

Stahl used the works of J.J Becker to help him come up with explanations of chemical phenomena. The main theory that Stahl got from J.J Becker was the theory of phlogiston. This theory did not have any experimental back up until Stahl worked on it. Stahl was able to make this theory applicable to chemistry. This theory was later replaced by Antoine-Laurent Lavoisier’s theory of oxidation. Although his theory was replaced, Stahl's theory of phlogiston is seen to be the transition between alchemy and chemistry.