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Germ theory is the theory that microscopic organisms (bacteria, viruses, or certain protozoa, as well as a few very weird things like free-living prions and cancer cells) cause infectious diseases. Confirmed in the 19th century by French biologist Louis Pasteur, germ theory is one of the most well-established principles in medicine and epidemiology, as well as a cornerstone for public sanitation policy. Incredibly, despite a mountain of evidence that would make evolution look like a statistical glitch, it still has its deniers, many of whom portray Pasteur as a shill for the French wine industry or an outright fraud. Such people, curiously, will seldom offer to take an injection of HIV or a shot glass of salmonella to prove their thesis.
Germ theory states that microorganisms can and often do cause disease. The often referred-to Koch's postulates are one method that demonstrates the relationship between a microorganism and a disease, but they are not always dispositive.
Humans have explored the causes of disease transmission since written records existed. Herodotus discussed the origins of smallpox, Hippocrates studied many infectious diseases, and described them quite accurately.
Early theories focused on miasmas (some force that apparently could only be observed by its effects on people, thought to be carried invisibly in air), humoral imbalance (the assumption that four vital substances existed in the body and an imbalance of them caused disease), and other speculative ideas. Do note that despite these ideas appearing quaint or preposterous in our more enlightened times, these concepts were based on real observation and taken very seriously. Even if flawed, these concepts are the precursor to modern science in that they were honest attempts to learn and build a foundation for saving lives. Still, actual progress in germ theory wouldn't take place until the 18th and 19th centuries.
In the 19th century Ignaz Semmelweis made seminal observations on childbed fever (puerperal fever), noting that in situations where doctors washed their hands between procedures, the incidence of sepsis among delivering mothers dropped off drastically. Other researchers, such as Theodor Billroth (discovery of streptococci in pus), Pasteur (discovery of strep in the blood of a septic woman), and Joseph Lister (pioneer of antisepsis in surgery) cemented the germ theory of disease as one of the foundations of modern science.
The strongest opposition to germ theory (more specifically, microscopic life giving rise to macroscopic life and disease) was "spontaneous generation" or abiogenesis, the concept that life needed no precursor and literally spawned from nothing or from inert material. Actual microbial life was very certain and undeniable at this time by all but the most stubborn researchers. Abiogenesis suggested a great obstacle to transmission of disease (though never truly made clear as to how) from person to person. Disproving abiogenesis took many people and experiments but it is Robert Koch who is generally regarded as disproving abiogenesis by forming postulates and testing them by isolating Bacillus anthracis. The postulates are as follow.
- The organism should be in abundance in the infected host, but not in a healthy organism.
- The organism must be isolated and grown into a pure culture.
- The organism should cause disease in a healthy host.
- The organism must be isolated again from the newly diseased host and found to be the same organism.
Though this was massive evidence for germ theory, there are now some obvious limitations. Viruses had not yet been discovered and can not be cultured independently, some things may be more affected than others or some not at all by a pathogen, and some hosts can't be infected.
 Modern Era
Before the onset of the AIDS epidemic, it was thought that infectious diseases were on their way to being wiped out, penicillin was paraded as a miracle drug (and it certainly was) and a step shy of complete success. Still, today reemerging pathogens such as Staphylococcus aureus become resistant to old defenses and infect again. Many pathogens mutate, combine with the DNA of other, dead bacteria or sexually transfer ribosomal information between one another. Even unaltered pathogens that have been long-conquered pose an incredible risk to a population with misconceptions and wariness of vaccines (and so avoids them).
Members that choose for themselves or their children to remain unvaccinated can pose a danger or inconvenience to vaccinated members of the population. Costs of treating preventable disease later in life can be monetary, loss of time (and time is money), and should a person who chose to remain unvaccinated die after attempts to treat them (wasting the resources) the population will suffer the loss with emotional grief and resources and money lost with disposing of the body. Vaccination is relatively inexpensive and vastly more responsible if that vaccination has been properly tested for risk.
 Germ theory denialism
The new, modern area of pathology has continued to grow in success and sophistication, especially with the study of genetics and genomics and just plain statistics. Despite this, a fringe denialist movement has cropped up in recent years, and many forms of alternative medicine either ignore or outright deny germ theory. This will likely be to their own undoing and make them responsible for any harm to their children or others'.