A: Most of the decline in disease occurred before the vaccines were introduced, thus there is no reason to believe that the decline after introduction of the vaccines is due to the vaccines. In addition many comparable diseases for which no vaccine was developed showed a similar decline in incidence. The decline in many of these diseases should actually be attributed primarily to increased hygiene and improved nutrition, with an additional minor role for genetic change.

Chicken, you are presuming several incorrect things.

First, it is understood that diseases naturally vary in incidence over time. When I study dengue virus incidence with regressions, for example, I look for trends over time before and after the intervention period, and never is a single covariate (in this case vaccination) given all the credit. For example, in dengue, we consider rainfall and temperature, both of which increase the numbers of mosquitoes in the area. Only then do we consider whether interventions are working.

Second, you are misunderstanding the flow of inference. We begin with small cohort studies, in which two populations are carefully characterized. We confirm that in those small cohorts, vaccination leads to lower rates of incidence. And yes, we do attempt to control for hygiene and nutrition. We also use race and family ties as proxies for genetic variation.

Only then, when we view a decline in a larger population, there is at least a little reason to believe that the results from the small population have generalized. You paint yourself in a corner when you say that there's NO reason. There certainly is: small cohort studies in which things like hygiene and nutrition and genetics were more carefully considered.

As an example, an increase in vitamin A intake in a population has the effect of significantly reducing measles mortality.

Just because you can give an alternate pathway to decreased mortality does not imply that other pathways have no influence. When you say there is "no reason," you have gone entirely too far in black-or-white thinking, because no reasonable person should say that the decrease in incidence is entirely due to vaccination.

There's a correlation between the number of vaccines administered in a country and the infant mortality rate. The United States has the highest number of vaccines administered in the world, and yet 33 nations have a lower infant mortality rate. The correlation between number of vaccines received and infant mortality is extremely high.

I believe you're again engaging in black-or-white thinking. From the paper:

It is instructive to note that many developing nations require their infants to receive multiple vaccine doses and have national vaccine coverage rates (a percentage of the target population that has been vaccinated) of 90% or better, yet their IMRs are poor. <...> These examples appear to confirm that IMRs will remain high in nations that cannot provide clean water, proper nutrition, improved sanitation, and better access to health care.

Are you familiar with Simpson's paradox? Of course a country with poor sanitation has a higher need for more vaccination than a country with good sanitation, which itself would lower the incidence of, say, diphtheria. Of course a country with poor sanitation is going to have higher IMR.

You cannot seriously make A and B arguments simultaneously. In B, you're not considering the sorts of confounding factors that you're basing your argument in A on. There is no proxy for hygiene in B, for example, but that's part of your argument in A!

This analysis did not adjust for vaccine composition, national vaccine coverage rates, variations in the infant mortality rates among minority races, preterm births, differences in how some nations report live births, or the potential for ecological bias.

Do you understand the irony of quoting B as evidence, given your argument in A? Essentially: if incidence decline after vaccination begins, then it's because of confounding factors. Next: countries with more vaccinations have higher IMR, confounding factors be damned.

Edit: I would also like to add that genetic variation is sometimes explicitly studied in the context of vaccination. In this study of measles vaccine for example, SNPs associated with cytokine (cell signaling proteins) production or reception are associated with different responses to vaccines. This is an example of where chicken has inference backwards. We begin with a small population, characterizing them down to the level of individual DNA molecules, and only then conclude what might occur in larger populations.