Claim: No studies have been done that compare vaccinated vs unvaccinated children.
Claim: There are no (long-term) studies on the efficacy of vaccines/vaccination.
Not only are efficacy studies done for vaccines, many use varying primary endpoints. For example, some studies use seroconversion (i.e. antibody formation) as a marker of efficacy. In the HPV trial above, statistically significant risk reduction was the primary endpoint and showed decreased risk of CIN cervical/vaginal/genital lesions as well as decreased risk of genital warts. Thus, it’s clear that tangible effects are created as a result of vaccination (e.g. decreased rates of cervical cancer or CIN )
Claim: Vaccines cause the disease they claim to be protecting against.
Conclusion: Partly true
This claim is only true in a single circumstance. That is Vaccine-Associated Paralytic Poliomyelitis (VAPP). This is a rare, albeit extremely serious, adverse event of the Oral Polio Vaccine (OPV). The OPV uses a weakened polio virus that replicates well in the GI tract (where primary infection often takes place – thus creating good mucosal immunity) The virus, however, has been shown to mutate and become virulent, creating a subpopulation known as circulating vaccine-derived poliovirus (cVDPV). It’s important to recognize that VAPP is an extremely rare event, with fewer than 760 cases since 2000, while natural polio infection has dropped by nearly 99% and an estimated 13 million cases of polio prevented!  Inactivated Polio Vaccine is now used instead . Moreover, vaccines can be made using various methods. For instance, the Hep B vaccine is a subunit vaccine – that is, it only contains antigens – thus it has a zero percent chance of reversion.
Claim: Vaccines cause many chronic diseases/conditions, including but not limited to: MS, atopy, arthritis, asthma, diabetes, chronic fatigue syndrome, autism, epilepsy, hypotonic hyporespontsive episodes, etc.
Conclusion: Mainly False!
The general consensus is that vaccines DO NOT cause any serious, chronic conditions. Someone mentioned a good point to me when I brought up data that supported, for instance, an association between vaccines and macrophages myofasciitis . This commentator gave me some insight. Some studies have been funded by large, anti-vax organizations, such as the Dwoskin Family Foundation.  Thus, it’s apparent that conflicts of interests exist on both sides of the debate but the overwhelming majority of evidence supports the safety and efficacy of vaccines. However, its important to recognize vaccines DO carry some risks, a majority are relatively minor (i.e. injection site soreness) but some adverse events are more serious, albeit exceedingly rare. For example, a casual relationship between hypotonic hyporespontsive episodes (HHE) & DTP vaccination has been shown. Recent data suggests, however, full-recovery post HHE with no long term sequelae – in addition a decrease in overall incidence has been seen with the switch to acellular pertussis vaccines aka “DTaP” . The flu vaccine and Gillian-Barre Syndrome (GBS) also share a casual relationship. Changes in manufacturing have led to a reduction in GBS with all vaccines. For example, the old rabies vaccine was produced using mammalian tissue and had a strong association with GBS, with a switch to chicken embryo cultures a dramatic decrease in GBS associated with rabies vaccines was seen. 
As i postulate in some of my posts, i think it’s important to continue the study of diseases and all possible etiologies (including vaccines). Only when we are honest with our intentions, try our best to overcome bias, can we really scrutinize data to understand a complete picture. Legitimate inquiry needs to continue in this debate. Although i consider myself a vaccination supporter, i do understand the sentiment of many concerned parents and citizens alike. We are often lied to by the government (MK ultra, tuskegee experiments, etc.) and by corporations (panama papers). So it is understandable that some are skeptical about real and perceived conflicts of interests. This goes both ways, however. Ultimately, this debate is inflammatory because vaccination has implications further reaching than just the individual, Herd immunity is the ideal of why everyone should get vaccinated. Rightly so, for those that are unable to get vaccinated, herd immunity protects everyone, unvaccinated included. This is an ethical dilemma, for the time being, we must respect the law and allow individuals to opt out of vaccinations but work together to seek alternatives that are amenable to both sides (perhaps more research on different adjuvants, instead of a decades old invention. Or using cell-lines/cultures that aren’t “tumorigenic” in vaccines – to be my next topic) 😮
 Epoke, J., F. Eko, and Cl Mboto. “Vaccinated versus Unvaccinated Children: How They Fare in First Five Years of Life.” National Center for Biotechnology Information. U.S. National Library of Medicine, 1 Apr. 1990. Web. 04 Nov. 2016.
 Schmitz, Roma, Christina Poethko-Müller, Sabine Reiter, and Martin Schlaud. “Vaccination Status and Health in Children and Adolescents: Findings of the German Health Interview and Examination Survey for Children and Adolescents (KiGGS).” Deutsches Ärzteblatt International. Deutscher Arzte Verlag, 1 Feb. 2011. Web. 04 Nov. 2016.
 Basu, Partha, Dipanwita Banerjee, Priyanka Singh, Chandrani Bhattacharya, and Jaydip Biswas. “Efficacy and Safety of Human Papillomavirus Vaccine for Primary Prevention of Cervical Cancer: A Review of Evidence from Phase III Trials and National Programs.” South Asian Journal of Cancer. Medknow Publications & Media Pvt Ltd, Oct.-Nov. 2013. Web. 04 Nov. 2016.
 Grabenhenrich, Linus B., and Et Al. “Early Determinants of Asthma from Birth to Age 20 Years: A German Birth Cohort Study.” The Journal of Allergy and Clinical Immunology. The Journal of Allergy and Clinical Immunology, 1 Apr. 2014. Web. 4 Nov. 2016.
 Haber, P., and Et Al. “Vaccines and Guillain-Barré Syndrome.” National Center for Biotechnology Information. U.S. National Library of Medicine, 2 Jan. 2009. Web. 04 Nov. 2016.
 Gherardi, RK, and Et Al. “Macrophagic Myofasciitis Lesions Assess Long-term Persistence of Vaccine-derived Aluminium Hydroxide in Muscle.” National Center for Biotechnology Information. U.S. National Library of Medicine, 1 Sept. 2001. Web. 06 Nov. 2016. <https://www.ncbi.nlm.nih.gov/pubmed/11522584>.
 Kullmann, Dimitri, and Et Al. “Central Nervous System Disease in Patients with Macrophagic Myofasciitis.” Oxford Journal. Brain – A Journal of Neurology, 1 May 2001. Web. 06 Nov. 2016. <http://brain.oxfordjournals.org/content/124/5/974.long>.
 Gold, MS. “Hypotonic-hyporesponsive Episodes following Pertussis Vaccination: A Cause for Concern?” National Center for Biotechnology Information. U.S. National Library of Medicine, 2002. Web. 05 Nov. 2016
 WHO. “Information Sheet: Observed Rate of Vaccine Reactions Diphtheria, Pertussis, Tetanus Vaccines.” WHO – Global Vaccine Safety (2014): n. pag. WHO. WHO – Global Vaccine Safety: Essential Medicine and Health Product, 1 May 2014. Web. 4 Nov. 2016. <http://www.who.int/vaccine_safety/initiative/tools/DTP_vaccine_rates_information_sheet.pdf>.
 Ares-Reye, L. “Efficacy and Safety of Human Papilloma Virus Vaccine in Cervical Cancer Prevention: Systematic Review and Meta-analysis.” National Center for Biotechnology Information. U.S. National Library of Medicine, 1 Dec. 2012. Web. 05 Nov. 2016. <https://www.ncbi.nlm.nih.gov/pubmed/23224305>.
 Vincenzo, Rosa De, Carmine Conte, Caterina Ricci, Giovanni Scambia, and Giovanni Capelli. “Long-term Efficacy and Safety of Human Papillomavirus Vaccination.” International Journal of Women’s Health. Dove Medical Press, 3 Dec. 2014. Web. 05 Nov. 2016. <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4262378/>.
Vincenzo, Rosa De, Carmine Conte, Caterina Ricci, Giovanni Scambia, and Giovanni Capelli. “Long-term Efficacy and Safety of Human Papillomavirus Vaccination.” International Journal of Women’s Health. Dove Medical Press, 3 Dec. 2014. Web. 05 Nov. 2016. <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4262378/>.
 Hartfield, J., and Et Al. “Efficacy of Measles Vaccinee.” NCBI (n.d.): n. pag. NCBI. Child Health Research Unit of the West African Council for Medical Research, 1 Jan. 1963. Web. 5 Nov. 2016. <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2134550/pdf/jhyg00119-0147.pdf>.