The theories before Pasteur’s experiments on fermentation and pasteurization were weak. There was the demonic theory of disease that demons caused disease or the angry gods caused disease. There were some that related diseases to the atmospheric conditions. The miasma theory held that insanitary conditions were the cause of disease and they had a little evidence because they would clean the areas and disease probability would decrease. These theories were all weak and didn’t explain how disease was caused.
The anomaly that Pasteur picked out at first was that a chemical process like fermentation could not give rise to bacteria. He looked in for more details to see that fermentation and purification did not cause microbes but microbes were the cause of fermentation and purification. A little bit of clearer observation and repeating of an experiment made him derive this. Then, Lister, the surgeon, would use antiseptics to keep his patient’s wounds from being infected. This could not be explained at first but with Pasteur’s idea of germ’s causing certain processes, it could. Louis Pasteur’s experiment is a simple case of causal inference and other factors help to make the inference stronger. For example, the vaccination method, using dead microbes or pus samples could help people develop immunity against the disease. And the pasteurization of any liquid that resulted in purifying it from microbes was helpful in determining the cause of a disease is a germ. Then, the different microbes that were leading to different diseases and their mode of action could be supported with evidence at times and coupled with a little bit of prediction could explain how germs were causing diseases.
Many ancient theories of medicine and disease referred to a disease as an imbalance in the natural state of the organism or the universe. For example, around 400 B.C. Hippocrates came up with the humoral theory of disease in Europe. This theory stated that there are four humours in a body; yellow bile, black bile, blood and phlegm; and the imbalance of these can cause disease. Similarly, the older Chinese theory of disease held the same yin and yang belief that everything in the universe is in a balance and if the balance is disturbed, good becomes bad. Indian medicine held a similar view and believed in the Ayurveda health, which is a state of balance between the consciousness, body and mind. In 1860s and 1870s came the germ theory of disease stating that germs are the cause of disease. This theory came up with the particulars like Vibrio cholerea as the cause of cholera, HIV as the cause of AIDS, Mycobacterium tuberculosis as the cause of tuberculosis, prions cause mad cow disease, etc.
Of the different views to a particular theory that philosophy of science has, my study illustrates that the best view to the germ theory of disease. In 1965, the logical positivists thought that universal generalisation in formal language were enough to represent theories. However, this fails to fit the germ theory because it looks like many other things are accountable and the cause and effect in this case does not give us a hundred per cent ratio. Every person injected with a particular pathogen, say, plasmodium will not come up with malaria. Hence, syntactic view that uses universal generalisation in language cannot sum up the germ theory.
Next is the idea of a paradigm from Kuhn in 1962. For the germ theory to be a paradigm, it has to be a world view which the most general of theory is not. Germ theory of disease is still not the world view so it cannot be a paradigm. Following this was Karl Popper (1959) with an idea similar to the logical positivists. He believe that apart from the first world of physical things and the second world of mental things, there is a separate world for theories. He says that the third world is ‘‘the world of possible objects of thought; the world of theories in themselves, and their logical relations; of arguments in themselves; of problem situations in themselves.’’ Evaluations, discover, causal relations and all similar subjects cannot be explained through Karl Popper’s third world.
The most plausible way to look at germ theory as a theory is to use the cognitive conception method. Here, discovery, explanation and evaluations can all be accounted. A medical explanation for a disease is done by linking the relative disease to the cause and those representations can be put in a building block manner to look at the discovery of the theory. Evaluation of the theories available is also a mathematical process by which one can compute which theory gives the best explanation of all evidence. Hence, the germ theory can be explained in terms of mental representations of the cause of disease. For instance, take an illness like influenza and its symptoms which are runny nose, fever, chest infection, etc. Now mental representation of the symptoms can be done using senses. We can examine the runny nose, it can be seen, heard at times, similarly fever can be felt and seen on a thermometer. The influenza virus can be caught and viewed under an electron microscope; so it is possible to gather enough auditory, visual and perceptual representation of the cause. The mind interception of the cause can also be explained in ways that Kant has, there is no denial here that even children know when one event will lead to another.
Another way to look at it is to consider the branch theory reductionism. Most high-level abstract theories in the biomedical sciences can be reduced as a branch to derive the theory. In our case, the reductionism we are dealing with is the one in which the demonic theory of disease has reduced to the germ theory of disease. Reductionism in theories has proved advantageous since Galileo and in all forms of natural sciences. Reduction is based on the study of history of science and our progress in understanding the natural phenomenon. Reductionism causes a more descriptive and clearer view of the phenomenon and allows a better control on the environment. A demonic theory of germ or the miasma theory of disease was not able to help controlling the environment as much as the germ theory of disease. 
Rosenberg believes that biological explanations are almost always teleological and he puts it this way:
Ask a molecular biologist why the DNA molecule contains thymine whereas the RNA molecule transcribed from the same DNA molecule contains uracil (even though both would appear to perform nearly the same function). The answer is teleological: Although the two molecules are otherwise the same in nucleotide composition, DNA is made of thymine in order to minimize mutation (in particular, what are called point mutations arising from deamination), whereas RNA contains uracil in order to minimize the costs of protein synthesis.
The trouble is that future events can never bring about past effects, which means that a teleological explanation is not able to explain a biological theory, making biology either physics or chemistry.  Consider, Koch’s postulate that helped determining the cause of disease and they were as follows:
This method of using the effect to find the cause means to look at biology in the teleological way. Rosenberg uses natural selection phenomenon to make teleology safe for science. He believes everything related to biology is routed to natural selection. And if a giraffe has a long neck it is because he has to eat leaves from trees; this is a teleological point of view. One can also look at the problem as the adaption of a giraffe is for its survival. There was once a time when giraffes had all types of necks but the long necked survived better. When it comes to a disease caused by a germ, we need to look at the circumstances in which germs cause this disease. They may not always but they do for their survival. In natural selection, teleology is safe. 
“Cause of a disease event is an event, condition or characteristic that preceded the disease event and without which the disease event either would not have occurred at all or would not have occurred until some other time.” The next question is what a causal effect is? To determine a causal effect, we always need to set up a causal contrast against some reference ideal, that is, a “causal contrast” between exposed and unexposed organism. “A causal contrast compares disease under two exposure distributions, but during one etiologic time period.” If the ideal causal contrast is met, the observed effect is the “causal effect.” This being met through Koch’s postulate helped in determining that the particular germ caused the particular disease.
The germ theory of disease can be justified in the world of philosophy of science by the help of a cognitive conception method. The explanations, evaluations and discovery are all justified and can be explained using the senses. More than one experiment and different approaches can be led to conclude that germs are the cause of disease. It may be a teleological deduction but it can be legal in science in ways Alexander talks about them.
Bunge, Mario. Philosophy of science: From problem to theory. New Brunswick: Transaction, 1998.
Dahnke, Michael D., and Heyward Michael Dreher. Philosophy of science for nursing practice: concepts and application. New York: Springer Pub., 2011.
Herbst, Judith. Germ theory. Minneapolis, MN: Twenty-First Century Books, 2008.
Lambert, James. The germ theory of disease. London: Bailliere, Tindall, & Cox, 1883.
Logue, Jeanne. Beyond the germ theory the story of Dr. Cooper Curtice. College Station: Texas A & M University Press, 1995.
Maslow, Abraham H.. The psychology of science; a reconnaissance,. [1st ed. New York: Harper & Row, 1966.
Rosenberg, Alex, and Daniel McShea. Philosophy of Biology A Contemporary Introduction.. Chicago: Taylor & Francis, 2006.
Rosenberg, Alexander. The structure of biological science. Cambridge [Cambridgeshire: Cambridge University Press, 1985.
Rosenberg, Alexander. Philosophy of science: a contemporary introduction. London: Routledge, 2000.
Rothman, Kenneth J. and Sander Greenland. Causation and Causal Inference in Epidemiology. University of California, Los Angeles: 1989). p.14.
Salmon, Merilee H. (et al.). Introduction to the philosophy of science. Reprinted. ed. Indianopolis: Hackett publishing company, 1992.
Tomes, Nancy. The gospel of germs: men, women, and the microbe in American life. Cambridge, Mass.: Harvard University Press, 1998.
 James Lambert. The germ theory of disease. (London: Bailliere, Tindall, & Cox: 1883). p.47.
 Judith Herbst. Germ theory. (Minneapolis, MN: Twenty-First Century Books: 2008).p.178.
 Judith Herbst. Germ theory. (Minneapolis, MN: Twenty-First Century Books: 2008).p.180.
 Merilee H. Salmon (et al.). Introduction to the philosophy of science. (Indianopolis: Hackett publishing company, 1992). p.310.
 Mario Bunge. Philosophy of science: From problem to theory. (New Brunswick: Transaction, 1998). p.290)
 Alexander Rosenberg. The structure of biological science. (Cambridge Cambridgeshire: Cambridge University Press, 1985). p.69.
 Merilee H. Salmon (et al.). Introduction to the philosophy of science. (Indianopolis: Hackett publishing company, 1992). p.312.
 Alex Rosenberg, and Daniel McShea. Philosophy of Biology A Contemporary Introduction. (Chicago: Taylor & Francis, 2006). p.14.
 Alex Rosenberg, and Daniel McShea. Philosophy of Biology A Contemporary Introduction. (Chicago: Taylor & Francis, 2006). p.16.
 Kenneth J. Rothman and Sander Greenland. Causation and Causal Inference in Epidemiology. University of California, Los Angeles: 1989). p.14.