Vaccines don’t “bypass the immune system”

I frequently encounter anti-vaccers who argue that vaccines are bad because they are “unnatural” and “bypass the natural immune system.” This argument is nothing more than an appeal to nature fallacy. Whether or not something is natural has no bearing on whether or not it is safe and beneficial, so I could stop right here, but let’s look at this argument further, because the core premise of this argument is not even true. Vaccines don’t “bypass” the immune system, if they did, they wouldn’t work. Rather, vaccines train your immune system to recognize deadly pathogens before you are exposed to them.

Before I can explain how vaccines train your immune system, you need to understand the basic concepts of how your immune system works. It can be broken into two broad categories: the innate immune system and adaptive immune system. Your innate immune system is, well, innate. It’s always there acting as your first line of defense. It includes things like your skin (which acts as a barrier to pathogens), mucosal surfaces, and non-specific immune cells like phagocytes and macrophages. That last qualifier is particularly important: the innate immune system is non-specific. It targets anything that does not belong in your body, but it is not specialized for particular pathogens. Think of it like your basic infantry. It’s a vital part of the military, but for particularly dangerous threats, you often need more specialized troops and weapons. This is where the adaptive immune system comes into play.

The adaptive immune system (aka acquired immune system) provides a targeted response that is specific for a given pathogen. You see, your immune system uses tiny molecules on the surfaces of cells to recognize friend (your body’s cells) from foe (foreign pathogens). These molecules, known as antigens, are specific for each type of cell, and your body can use them to engineer specialized cells that are specifically intended to fight a particular pathogen. Thus, when your body detects the presence of a novel pathogen (via its antigens), it triggers the adaptive immune system and begins producing B and T cells that are specific for that pathogen. Think of them like your special ops, snipers, stealth bombers, etc.

The catch is that because the adaptive immune system produces cells that are specific for a given threat, it can’t start producing those cells until your body has encountered the threat, and by that point, your body has already been invaded. In other words, it takes time for your body to mount an adaptive immune response, learn to recognize and target the invading pathogen, and produce sufficient numbers of the specialized cells. Meanwhile, despite the best efforts of your innate immune system, the enemy pathogens are replicating, spreading, and amassing a formidable army. Thus, for highly pathogenic diseases, by the time that your adaptive immune system is ready to go, the invaders have already claimed territories and your immune system is going to war, resulting in you being sick and potentially dying.

If you win the war and survive, your body will remember the disease and keep low levels of specialized troops circulating (via memory B and T cells). That way, a specialized force is ready to go if you are ever re-invaded by that pathogen in the future. This is what we know as “natural immunity.” It’s not perfect, and it can wear off overtime if your body stops producing and maintaining those specialized cells, but, combined with your innate immune system, it does a pretty good job of protecting you.

So, now that you understand the broad strokes of how your immune system works (it’s obviously far more detailed than what I explained), let’s talk about how vaccines fit into this. Vaccines present your body with the antigens of a given pathogen (usually via a dead or weakened form of the pathogen [see note about COVID mRNA vaccines]), along with an adjuvant to stimulate your immune system. This causes your adaptive immune system to mount a response even though you aren’t actually under attack. Thus, your body produces the specialized cells for fighting a given disease even though you don’t have the disease. Think of vaccines like scouting reports from spies that inform generals about the enemy’s plans and movements before the enemy attacks, thus allowing them to plan an appropriate defense. That is fundamentally what a vaccine does. It trains your adaptive immune system to be ready to fight a disease before you actually encounter the disease.

Further, following a vaccination, your body will continue to maintain a reserve of the specialized troops, just like it does after an actual infection. This is what actually protects you from diseases. It’s not the vaccine itself that protects you. Rather, it is the immune cells that the vaccine stimulates your body to produce (along with the antibodies some of those cells produce). Like natural immunity, the immunity from vaccines can wear off overtime, but a simple booster shot will remind your body that this pathogen is important and cause it to continue to maintain adaptive immune cells that are ready to rapidly divide and fight the pathogen as soon as it enters your body.

Thus, as you can hopefully now see, vaccines don’t “bypass your natural immune system.” Rather, they stimulate your immune system and train it to recognize and fight pathogens before you are exposed to them. Indeed, they work exactly like “natural immunity” with only one important difference: natural immunity requires you to get the disease, whereas vaccines train your immune system without you getting the disease.

Update regarding mRNA COVID vaccines: This is an old article that was written pre-COVID, and the mRNA COVID vaccines are slightly different, so it is worth briefly mentioning them. mRNA vaccines don’t use a traditional antigen. Rather, they use a fragment of mRNA for a viral protein, which causes the body to produce that protein (note: producing a single protein is very different from producing a functioning virus and does not carry any risk of infecting you with COVID; also mRNA cannot replicate itself; it only instructs cells to produce a protein). Thus, these vaccines make your body produce the antigen (for a short time), rather than the vaccine directly injecting you with the antigen. Once your body produces the antigen, the immune system follows the steps described for conventional vaccines (so, again, no part of the immune system has been “bypassed”). This approach is very advantageous, because it cuts out many of the time-consuming, difficult steps in vaccine design and manufacturing by having your body produce the protein, rather than the protein being made beforehand.

Suggested further viewing

If you want an excellent and much more detailed overview of the immune system, Hank Green’s three part Crash Course video series is about the best 30-minute introduction you could ever hope for (note: I didn’t watch these videos until after writing the post [I was looking for good videos to recommend to my readers], but he amusingly uses more or less the same military analogy that I used).
Part 1: Innate immunity
Part 2: Adaptive immunity (B cells)
Part 3: Adaptive immunity (T cells)

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11 Responses to Vaccines don’t “bypass the immune system”

  1. In the NCPD Autistic (Advocacy) Council of Ireland we have many groups- because so many autistics are attacked, bullied and harrased by Anti-Vaxxers, many do not allow such discussions or topics, as we can easily get a few thousand people quitting and complaining as a result of such a discussion. Instead we have opened up discussions of hundreds of Autism causes Vaccine discussions from the researchj set up to attempt to find such links as they use, from the reasons such research is conducted. The results have always come back proving the opposite. The responses come back with results like 0.6% less likely to be diagnosed after getting vaccine,m due to higher socialisation, and that autistic genetic and neurological history proceeded vaccination …. and traits they claim are vaccine injury occcur in those who are not vaccinated, and so does autism and related co-morbidities preceed vaccine. One group where we allow discussion and provide science to combat anti-science and flawed suggestion as if it is proof is in

    Damon Matthew Wise Âû, National Secretary/CEO (unpaid Voluntary) NCPD Group incl. members and charitable CLG,a and co-ordinator/advocate, NCPD Autistic (Advocacy) Council of Ireland


  2. Indeed, so far from being unnatural, vaccination might be compared to organic farming. You are getting the desired result (desired plant growth, or desired immune system growth) by using natural organic material treated so as to make it most effective (composted manure, or inactive virus)

    But I fear of the roots of antivaxx are as difficult to root out as those of ground is difficult to accept that a dramatic, indeed disastrous, outcome is not the result of a clear, traceable, and preventable cause. It must also be paradoxically tempting for parents to blame themselves for having caused the condition, so that they can atone by activism.

    Disclosure: a very close family member was diagnosed as autistic. He received excellent training in language and personal skills through the UK’s NHS (I don’t know whether this would still be available), and is now a happy parent, well befriended, and doing very well in an extremely responsible position

    Liked by 1 person

  3. KennyS says:

    Are there any studies comparing Autism diagnoses in vaccinated vs unvaccinated populations?

    Liked by 1 person

    • Yes, most of the studies done funded by Autism $peaks looked at autism before and after vaccine and recorded where not vaccinated. I was thought to be classically autistic until I started walking and talking about 5 years old. Had annual Psycchological Medical and Social Centre tests groing up in Belgium, and many atypical reactions (later known as Co-morbidities detected); I was pushed into cpontact with family friends and kids with all childhood diseases, and kept on getting extreme and relapses. My parents were concerned I may have been sterily. I was diagnosed with Asperger officially in 1991, after 18 issues and traits, any 3 or which or more would now be indication of an ASD,. My first vaccines were in 1987, when 17 and a few months old. Genetic and Neurological tests and studies from of the 3.5 million in the studies of the AGP, and such record vaccination age, or not for background information, and in stats we regularly report. First study in genetic and family history I did as part of my thesis “Living With Aspies: Education and Autism” which recorded AD(H)D, OCD, Dyslexia, anxiety and depression and other very common family traits, previously reported as “nothibng to do with aurism” and “mrerely anecdotal”, but we knew these were extremely common and connected with autistic traits in our family members diagnosed and wanted to see if others had multiple families and traits, which the Psychs debunked. This research formed part of my in 1999/2000 Thesis report and statistics.
      Recently A$ apologised for suggesting there was a link, after funding so much research on link all proved opposite and vaccinated and non-vaccinated populations both showed autism.


    • Fallacy Man says:

      Yes, this has been looked at many times in many different ways (often by independent scientists with no ties to pharmaceutical companies), and the result has always been that there is no association between vaccines and autism. The largest study to date was a meta-analysis involving over 1.2 million children.

      I talked about these studies at length here


  4. Michael Smith says:

    Fourth sentence in the second graf is a bit confusing and seems to say the skin is a barrier to mucosal surfaces etc. You might want to recast it: “It includes things like your skin (which acts as a barrier to pathogens), mucosal surfaces, and non-specific immune cells like phagocytes and macrophages.”

    Good post. Interesting that two of the first three responses focus on autism, even though you did not mention that particular bit of Internet-mediated nonsense, and the third mentions the topic in passing.

    And yes, KennyS, there are such many studies, See this one ( as an example.

    Liked by 1 person

  5. Dorit Rubinstein Reiss says:

    Great post. Would you consider following up with a post looking at autoimmune diseases and explaining why the claim that vaccines “hyperstimulate” the immune system and cause autoimmune diseases is ill founded?


    • Fallacy Man says:

      Perhaps I will at some point, but I’m not sure that it really requires it’s own post because it was indirectly covered here. Since all that the vaccine is doing is training your body for one more disease, claims or hyperstimulation are clearly incorrect. I suppose that given how the internet works, however, it probably isn’t a bad idea to highlight that separately. Thanks for the suggestion.


      • This is a tricky one. The problem with refuting a claim is that thereby, inevitably, you spread it. So unless this weird claim is already rampant, it may be wiser to remain silent. Your decision, and not an easy one


  6. Bitty says:

    I genuinely thought the analogies you used here were fantastic and really put vaccines into a new and understandable light.


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