The Curse of the Scientific Method in Medicine

Appeared on Substack on February 18, 2026.

https://anandanandalingam649613.substack.com/p/the-curse-of-the-scientific-method?r=o7w77

Recently there has been controversy about the new U.S. government advice on childhood vaccines which has reverberated globally. On January 4th, federal health officials that the slate of routine vaccines recommended for American children would be reduced from 17 to 11. The vaccines dropped were for Hepatitis B (for newborns and infants), Rotavirus (at 2 and 4 months), HPV and Meningococcal (for 11- and 16-year-olds), and annual flu and COVID-19. There is of course a hue and cry from pediatricians all over the United States and the mainstream media. Some pediatric practices have said that they would follow the old recommendations, and if patients balked that they would be advised to find another doctor and/or practice.

On the one side there is Robert F Kennedy Jr. who has some fringe views on many things related to health and thus very little credibility with the educated elite of the country. Most of the latter are concerned that the new vaccine regime is the outcome of a group of people selected by Kennedy to push unscientific viewpoints into public health. On the other side are most physicians in the United States who have been trained in western medicine that truly believe in the procedures and protocols that come out of the research in academic institutions and pharmaceutical companies that purport to follow the scientific method.

What exactly is the “scientific method”?

What most people may not appreciate is the fact that the way science is practiced in many fields, and especially in medicine is based on statistical analysis. There is no guarantee that a vaccine taken will definitely prevent a disease. All that can be guaranteed is that the chances, i.e. the probability, of being affected by the disease becomes very small if a vaccine is taken. All the research done by pharmaceutical companies, sometimes with the help of prestigious university medical schools like Harvard, John Hopkins and Stanford, mostly attests to the fact that vaccines administered can reduce the advent of the diseases that they target by close to one hundred percent. It is very rare to have exactly 100% efficacy and so the question is at what percentage does one move ahead with recommending the vaccine. In much of quantitative scientific research, even in fields as disparate as economics and sociology, a “confidence level” of 95% is considered satisfactory. That may not be sufficient in medicine.

In medicine one needs to content with three important questions: What happens to the 5% for who the medicine including the vaccine does not work, what is the trade-off between giving the medicine/vaccine and not giving the medicine/vaccine, and, very importantly, what are the side effects of giving the medicine/vaccine.

Take one of the vaccines that was dropped by Robert Kennedy Jr’s health department: Hepatitis B. The medical community and the pharmaceutical industry are single-minded that the hepatitis-B vaccine needs to be administered to newborns with a day of birth. It is based on the fact that newborns can easily contract the disease because their immune system is very weak at birth, and if they contract the disease, while it can be treated easily, the virus could stay in the system like the chicken pox virus and increase the chances of getting liver cancer in the distant future. Really dire! The medical/pharmaceutical community will not engage you about what happens if the newborn does not get the vaccine because the positive impact of not getting Hep-B is apparently so significant that nothing else needs discussion. The potential short-term side effects are very minor, pain and redness in the injection site, and in some cases abdominal cramps and diarrhea. There is no research, as yet, on possible long-term negative health effects because administering hepatitis-B vaccines to infants only started in recent years.

How does a newborn get hepatitis-B? Turns out, being born to a mother who has hepatitis-B is the most likely pathway, in fact close to 100%. If the mother does not have hepatitis B, the probability of the newborn getting hepatitis-B is almost zero. Hepatitis B is not inherited genetically and is rarely transmitted in the absence of maternal infection. The average population-level risk of a newborn contacting hepatitis-B is low (less than 0.1%) in the U.S. and Western Europe, and around 0.2-1.0% in intermediate-prevalence countries (including India) almost entirely from undiagnosed maternal infection. In some parts of Sub-Saharan Africa and East Asia, it is 1–5%.

Of course, the potential of those who get hepatitis-B getting liver cancer in one’s lifetime is quite scary. However, the numbers are not too bad. About 42,000 new liver cancer cases are expected in the U.S. in 2025 out of a population of 360 million; the “age-adjusted” incidence rate is roughly 8.4 cases per 100,000 people per year which comes to only about 30,000. These are very small numbers compared to several other diseases. Chronic hepatitis B carriers have a significantly higher lifetime risk of liver cancer, 10–25% without treatment. It is of course easy to treat hepatitis-B. For most people, the effect of the virus just goes away with time. For most patients it is moderately easy to control with Oral antiviral pills such as tenofovir and entecavir. These suppress viral replication by >95–99% and dramatically reduce liver inflammation, progression to cirrhosis and the risk of liver cancer. However, the virus never really goes away.

One really needs to deal with the trade-off between the long-term effects, both positive and negative, of the hepatitis-B vaccine. Given the most highly likely pathway for newborns to get the disease, why not simply test pregnant women for hepatitis-B just before they give birth, especially in advanced industrial countries rather than subject the newborns to yet another vaccine?

The truth of the matter is that there is insufficient evidence regarding the long-term negative effects of this vaccine. While the vaccine will certainly boost the newborns immune system to fight against hepatitis-B, will it linger as long as hepatitis-B in the system? The recommendation that the hep-B vaccine be given within 24 hours of birth has only been in the guidance of the Advisory Committee on Immunization Practices (ACIP) since 2018. In 1991, ACIP recommended all infants be vaccinated against hepatitis-B as part of the routine childhood immunization schedule. The recommendation became a “preference” in 2002. It is unclear whether the CDC or ACIP followed up with infants getting the vaccine versus not getting the vaccine to see if there was a difference in the incidence of Hep-B. I would be quite surprised if such a study exists because, for one, the incidence of liver cancer and cirrhosis is extremely low, and the cost of following the immunized children as they moved into adulthood would be very large especially in a vast and mobile country like the United States. Of course, the medical community could ask those who get liver cancer or cirrhosis whether they received the Hep-B vaccine. Very few of us remember what vaccines we received as infants, and there are many different causes of the disease like excessive consumption of alcohol that the information may not be scientific enough.

The point is that what is portrayed as “science” in medicine is fraught with judgment calls based on the probability of this happening or that. The causality is not a clear straight line. However, the medical community, perhaps boosted by its inevitable closeness to the pharmaceutical industry, perhaps wanting to err on the side of known facts and caution, make pronouncements about medications that are cut and dry. There is also the tendency among a vast majority of doctors to not prevaricate lest they appear too mortal in the eyes of their patients. The educated elite, throw “science” at every juncture of disagreement by the public even though we only know things up to a certain level of probability and statistical confidence. Without being true to the authentic scientific method which is based on probability and statistics especially in medicine, the elite in the U.S. and even across the globe, use “science” as a way to show their superiority and contempt for those who do not follow the advice of “professionals”.

There is another issue at stake here: private versus public impact of health effects. There are many diseases that children could get without vaccines like measles, mumps, rubella that are very infectious. It is important to protect the population at large, and especially children from these deadly infectious diseases. Conversely, some diseases like Hepatitis-B can only be transmitted by skin puncture or mucosal contact with the blood or body fluids of an infected person. For example, semen, saliva, sharing needles or syringes, and contact with open sores of an infected person can all facilitate person-to-person spread. Fortunately, HBV is not spread through food or beverages, casual contact like hugging or handholding, or sneezing (as long as no blood from an infected person accompanies these activities). Perhaps rather than mandating vaccines for something that only affects private individuals, the medical community could consider making it a recommendation instead.

Given some anecdotal evidence of who got COVID and who didn’t and who succumbed to COVID and who didn’t during the recent virus crisis, there is now the danger that the public have lost their trust in the medical establishment which insisted on only one way of recourse to fight the potential disease. Here comes along someone like RFK Jr. who plays into the hands of this mistrust, and the whole world of medicine has gotten into the danger of upheaval. What is needed is an honest conversation about the pros and cons of medical interventions including giving the public some choices and advice in cases, like the Hepatitis B vaccine, rather than mandates. It is important for the medical community and the educated elite to be honest about the scientific method, explain about how one should deal with statistical confidence levels and thus, make it the most powerful tool we have in order to deal with a world of uncertainty and change. Pretending that the “science” of medicine, especially in the case of drug intervention, is infallible and that mandates are essential will only make matters worse with the public.