I'm a chemical biologist/biochemist, and history & philosophy of science has been a longtime interest of mine, so I think I’m qualified to comment - I skimmed the comment quick. I’ll cover the main point, but I don't really have the time or inclination to research every specific instance cited and respond to it. I will go over a couple things that overlap my field, and I have at-hand knowledge on as we go.

In a general sense, this comment is misguided at best. The main fallacy of this comment is the insinuation that the best practices of the 18th, 19th, and early 20th century are still today’s gold standard, and assuming that the imperfections of those old practices reflect incompetence by the practicioners. It is analagous to discounting the performance specifications that BMW gives for their vehicles based on the performance of a Ford Model T, while simultaneously discrediting the engineers on the Model T because it fails to match a modern BMW.

A quick terminology primer before we go further. Variolation is the practice of penetrating the skin with the dried scabs/pus of a human smallpox sufferer. The idea is that you are able to expose someone to the disease in a more-or-less controlled fashion. The immune system would then have “memory” of the disease, and could fight it off in the future. The word itself comes from the virus’ family “variola” which includes both human variants, as well as cowpox. Vaccination, in its original sense, is deliberate infection with cowpox, which is similar enough on a molecular level to create the required “memory” of the disease, and the immune system would easily handle future challenges from smallpox.

Most of the points in the comment can be boiled down to “many, many people got sick despite being vaccinated.” This is a history sub, and you need to put that in context. We have nothing like smallpox today, nothing comes close. In the 18th century, 2-3% of people who were variolated died. Those are, and were at the time, reported numbers - there were no illusions about the safety of the practice either in the medical community or in the public. Imagine a disease so contagious, and so deadly, that a direct mortality rate of 2-3% was an acceptable alternative. Additionally, the practice of variolation usually resulted in significant illness, and nearly always some amount of localized scarring (one other raison d’être of the procedure is that these scars, though fairly visible, would be somewhere discreet, rather than on the face). Here’s a quote to demonstrate why people would choose this - “The case-fatality rate varied from 20% to 60% and left most survivors with disfiguring scars. The case-fatality rate in infants was even higher, approaching 80% in London and 98% in Berlin during the late 1800s.”

Many people died because they were variolated. Some epidemics started because of the practice, and the hazards and mortality of this practice inform many of the argument agains vaccination in the comment you cited. This is not a good comparison, as it was merely a first step in the science of protection against smallpox. And despite the huge dangers, it was considered less dangerous than the exposure to smallpox that would be expected by chance.

Vaccination in its original form (the vacci in the word comes from the late word for “cow”) was far less hazardous than the practice of variolation which it replaced, though still not harmless, and though very good, still imperfect at protecting against smallpox. It is worth pointing out that the relationship between contracting cowpox and subsequent immunity to smallpox was not unknown before Edward Jenner, and was imperfectly understood, but he was the first evangelist of the practice. and with his boosting, the practice became widespread.

Quick science note before we get into Leicester - vaccines (in the general sense of the word here) are never perfect, and especially in the case of person-person transmitted diseases, they do not have to be. Viruses are capable of changing sufficiently to evade a vaccine, and individual humans have individual responses to a vaccine. That is to say - a hypothetical vaccine may be imperfect because it protects against only 90% of the viruses that one may encounter, or it may be imperfect in that it only protects 90% of the people who get it. This hypothetical vaccine will still be able to stop most any contagious illness from spreading widely, even though there may be isolated cases (this is the mathematical understanding of “herd immunity”). This covers many other arguments in that comment you cited, which seem to equate imperfection with failure. Obviously, perfect protection is desirable, but not necessary for a vaccine to do its job extraordinarily well.

Subsequent to Jenner’s dissemination of cowpox vaccination a series of laws known as “Vaccination acts” were passed in England to make vaccination mandatory - the first law was in 1840, the most important amendment was in 1871 to make failure to punish non-compliance punishable (weird sentence, I know). It is also worth noting that smallpox vaccinations are still pretty miserable, and result in an unpleasant skin irritation. I know some elderly people who have scars from their vaccinations in the 1940s. So to set the stage in Leicester you have the government forcing its way into the business of children’s health, and though (in my opinion) this was justifiable, smallpox vaccines are not exactly benign. Worth noting is that this uncomfortable government intrusion into private lives, and not primary health outcomes, is the most cited reason for the anti-vaccination movement in Leicester.

In addition there were still low levels of smallpox present. Thanks to widespread vaccination, there were only 6 smallpox deaths between 1859 and 1861, but between 1864 and 1868 120 people died of smallpox (as an aside, the Medical Officer of Health in Leicester maintained that this was far lower than an unvaccinated population would have experienced. He is unequivocally correct). Not coincidentally, this uptick (which occurred throughout England, not just in Leicester), corresponds to the more draconian 1871 Act, and the subsequent protests to government intrusion. There are many things that could have caused this uptick - vaccination rates of children had declined, since smallpox itself had, and maybe the “herd immunity” effect vanished; the concept of “booster shots” was not understood at that time so maybe there were enough people who were not longer immune, but none of these things would have been well understood at the time. Some perception of the ineffectiveness of vaccination is also bound to creep into people’s psyches at that point as well.

The obvious suffering that vaccination caused to children, the fact that this suffering was government mandated, and the growing perception that it was all for nothing, were the primary motivations behind this anti-vaccination movement. Other reasons included the ~50 people/year who died from vaccination in England, or religious objections that the cow derived vaccine was “unclean” having come from an animal. The anti-compulsory vaccination movement was present throughout England, but especially in Leicester. In any case, after a demonstration of ~20,000 people in Leicester, the city moved toward a policy of quarantine as a means of smallpox control.

This “Leicester Method” consisted of very sound epidemiological methods such as mandatory early reporting of disease, strict quarantine, full doctor supervision (and doctor go-ahead for ending isolation), full disinfection of sick chambers, and burning bedding and clothing associated with recovered sufferers. I am not going to argue that this was not effective: it was and is very good practice for dealing with contagion, and with its help, Leicester had very low levels of smallpox despite declining (note, not 0) vaccination of infants. I will also point out that this method is particularly well-suited to smallpox, which can’t really be mistaken for any other disease (unlike early-stage mumps or pertussis, for instance). But be very clear, Leicester’s experience is not a “placebo controlled study to debunk the Savior Myth of vaccination” as the comment you linked seems to think. For one thing, adults in Leicester had, largely, been vaccinated, and anyone traveling to or from Leicester did so from areas that were nearly universally vaccinated.

As a coda. The history of the anti-anti-vaccination movement has not always been pleasant. Vaccines are not always fun, the science behind them is fairly opaque for most people, and the principal people directly interacting with them are infants or children. In Richard Preston’s excellent book about smallpox, The Demon in the Freezer, he interviews WHO officials who went to villages in India with UN soldiers, and physically held people down against their protest to vaccinate them. This is a clear violation of human rights, and I am not one to hold as a truism that the ends justify the means. But in the 1600s, millions of people died every year from smallpox (and that with a much, much smaller human population) - nobody has contracted this horrible disease since the 1970s.

Hi, while you may get answers here, it's probably worth x-posting this one to /r/AskScience, since it's recent medical history