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Immunity? Easy Peasy…. Lemon Squeezie

Kylie over at the Token Skeptic is poking fun at the Anti-Vax. Her literature is cool but I know something that is lacking in skeptic land.

One of the major problems with the vaccination movement is that most people cannot understand how vaccines are meant to work. Many anti-vaccine advocates simply think that injecting someone with a disease is a good way to make someone sick rather than make someone immune to a disease.

There is an absolute hand grenade of question that I have found turns the vaccination debate into an utter rout. How does the Immune System Function?

This simple question (I learnt it in high school) when used turns even the most stalwart of anti-vax into a blithering mess. I have heard everything from a near perfect explanation of human immune systems (they stopped at explaining the specific immune system) to the retort that “The Immune system has nothing to do with vaccinations”. I have even heard such ridiculous claims as “I prefer the non-specific immune system to be boosted as that is more important” which doesn’t explain why HIV positive patients get sick so much more easily (Their specific immune system is shot. Their non-specific is still normal.). A lot of parents simply don’t know. They have been buying into the silliness of anti-vax because there is no equal on our side. There is no “idiot’s guide” to immunity.

With that in mind, I have produced this primer on immunity and how vaccination works. There are pretty pictures and analogies.

An immune system in a human being is a series of defences designed to deal with an infection by a foreign organism. It is a multi layered defence system which reduces infection as well as actively combats germs and parasites. Like onions, ogres and parfait.

It’s both a physical and a biological entity and it’s responsible for a lot of medicine, from vaccinations to blood transfusions and organ transplantation. It’s also involved in diseases such as auto immune disorders which are increasingly common.

Basically, immunity is this amazing system that keeps most of us healthy. It can be summarised as

Parts of the Immune System 

Innate – 

This is the cell’s innate ability to detect foreign material and eliminate them without the bodies own specific response. It is a generic quick response to disease causing organisms  (Pathogens) which invade our body to either prevent an infection or slow it doen sufficiently for the slower but more effective and selective Adaptive Immune system to activate. It consists of

Anatomical barriers -

These consist of physical barriers. The skin itself is impermeable to pathogens providing defences like a solid wall. Our nasal passage is lined with mucous that is constantly moved into the stomach catching pathogens and killing them. Our eyes are covered in caustic tears and our mouths in saliva which contains a variety of enzymes. These ensure that the vast majority of pathogens are killed before they can even enter an area where they can cause harm.

Inflammation -

This is not a bad thing but the symptoms we associate with inflammation are due to the localised response to the presence of a foreign body or pathogen. It’s main purpose is to provide a physical barrier to control the spread of infection and to heal damaged tissue in the region.

Damaged cells give out a bunch of chemical factors which cause pain and blood vessels to become more permeable. This attracts phagocytes and alerts you to the injury allowing you to cover it to prevent further infections. Phagocytes are “cells that eat”, they recognise foreign or dead tissue and physically consume it and digest it.

The inflammation is simply noted by the moniker of rubor, calor, tumor et dolor (red, hot, swollen and painful). Normally inflammation is a good thing (it’s what makes insect bites itch) but its bad in auto immune diseases such as arthritis.

Complement System -

This is a biochemical cascade that once activated causes the influx of phagocytic cells from blood into the tissue. The thing to remember is that our blood vessels are actually permeable and the phagocytes can actively squeeze through to get into the tissue area.

It is via this system foreign cells are recognised and either “eaten and digested” by the White Blood Cells or are lysed by general antibodies. The complement pathway has a long evolutionary history with parts of it even seen in plants.

Cells Involved -
The white blood cells (WBC) involved are

Mast Cells – A cell associated with allergy and anaphylaxis. A mediator of inflammation response.

Mast cells, the pink dots
are histamine which causes hayfever.

Phagocytes –  Large cells that move like amoeba. They “eat” other cells by surrounding them with their plasma membranes producing “bubbles” in which they can release enzymes safely without damaging other cells. They have a role in normal development as our normal cells do “commit suicide” in specific ways to produce our shape. These help with clean up.

Macrophages – Large Phagocytic cells that efficiently consume multiple pathogens. Heavily motile and actively cross from the blood stream into tissue to hunt down pathogens. They kill by the use of free radical oxygen.

Macrophage “om nom noming”
on pathogens

Neutr/Eosin/Basophils -  A series of similar cells that target a variety of different pathogens non specifically. Have “granules” similar to ground coffee that have specific actions.

The big pink cell with all the weird
purple nucleus is a eosinophil

Natural Killer Cells – These are interesting, they don’t target pathogens but cells infected by viruses or cancerous cells. They recognise these and induce controlled cell death halting the spread of cancerous tissue or viruses. Yes. We do have a mechanism that kills cancer cells. We are looking into cancer and cell signalling to figure out a way to use this mechanism to specifically destroy cancer cells allowing us to effectively eliminate cancerous cells.

Dendritic Cells and Gamma/Delta T Cells – These are the bridge between the innate and adaptive systems and their main role is antigen presentation. They harvest proteins from damaged pathogens and present them to T-Cells.

Adaptive -

The dendritic cells activate our adaptive immune system. It’s a series of specialised cells that produce antibodies which “mark” out pathogens for destruction with greater specificity. It basically any cell marked with an antibody gets destroyed. Evolutionarily speaking it’s quite elegant utilising mutations (somatic hypermutation) to produce endless varieties of “antigen receptors”. When an antigen matches a receptor, antibodies are produced specific to that antigen.

The antibodies are the main weapon of our body to fight disease. It is a larger response than innate immunity and once sensitised the adaptive immune system often fights of diseases even before we can manifest the signs of disease.

Cells involved -
These are called Lymphocytes mainly as they are found circulating in lymph more than in blood, their role is determined by the cell itself.

T – Lymphocytes – The main role of the cell is to recognise cells infected by viruses and trigger the apoptotic pathway destroying the cell and its viral load. Since viruses only replicate inside cells this kills them enmasse as phagocytes consume the destroyed cell debris and digest the contents. The antigen of the viral cell is recognised by surface antibodies on the T-Lymphocyte. There are also helper T-Lymphocytes whose role is control and organisation of the response.

B – Lymphocytes - The main role of these is to produce humoral (free floating) antibodies that recognise pathogens and mark them for destruction by activating the complement system and by causing the pathogen to become “sticky” but only with other pathogens. This causes them to clump together and make them easier to kill.

Memory Cells - After the infection has passed, most of these cells die. However a few are maintained in circulation as “memory cells”. In future infections these are rapidly activated to produce a humoral response which quickly destroys any new infections even before they produce any symptoms.

Lymphocytes are like Wizards. They Show Up Late to Save the Day with the Estranged Son of the Possessed Horse Lords. This Analogy May Have Gotten Away From Me.

In Infants, there is a version of this system called passive immunity. Certain classes of antibodies can cross the placental barrier and can be absorbed through milk particularly the colostrum (first milk). These give the new born baby the same range of protection as the mother. We can also produce artificial antibodies for this purpose in some disorders or for commercial use. We use clonal cells for this (Cells that are copies of each other to ensure the same antibody is produced) to produce these monoclonal antibodies which have a variety of uses. The home pregnancy test kit actually functions using these antibodies to detect Human Chorionic Gonadotropin in human urine.

Incidentally? The pregnancy test kit can also detect some forms of testicular cancer which produces HCG. A man with a positive pregnancy test can indicate a tumour.

This is how our natural system works. It doesn’t recognise our own cells as self recognising antibodies are actively destroyed. However in cases of organ transplant, blood donation or foetal blood incompatibility the body can target itself. In autoimmune diseases we can see a pathological breakdown of this system targeting the self rather than pathogens.


Hacking the System -

All of this sounds pretty damn awesome, but it’s not infallible. Remember the pathogens themselves have their own tricks to avoid being caught and killed while remaining long enough to survive and spread. They also have very short generation times and so can evolve out of our bag of tricks. The adaptive nature of our immune system is actually a very smart way of keeping track with these evolutions.

The range of tricks is colossal from lysogeny (the ability of a virus to integrate it’s DNA into ours. Herpes does this! The cold sore is a form of this ability) to shuffling antigens (the common cold does this.). Some bacteria produce incredibly virulent toxins that causes massive diarrhoea or vomiting in order to spread before the antigen response occurs. Some bacteria such as the Clostridia produces incredible toxins that plain murder everything in sight stopping the immune system coming even close to the bacteria.

So what we need is a way of beating diseases at their own game. A way of acquiring immunity to diseases without the disease itself.

That way is vaccination. The idea is simple, you take known antigens and inject them into the body. The body’s cells recognise these “bits and pieces” and produce an immune response as if there were a real threat maintaining a population of “memory cells” to deal with subsequent infections. Every infection you stop actually increases your immune response. So there are a variety of different responses. The response to just an antigen mix is less than a dead/killed cell which is less than a severely weakened cell. These are a training simulator except the body doesn’t know that and responds as if the infection were 100% real. The body responds to the next infection like a badass expert rather than some green recruit. You don’t even notice it.

Some diseases don’t produce antigens that last forever. It’s very finicky biology but it has to do with core structures and the like. However as long as we are under a vaccinated period we should be able to fight off an infection and we can simply top up when needed. Vaccination isn’t 100% fool proof but it means that the vast majority of people are immune to a particular disease preventing it’s spread in general. The more people who are vaccinated the stronger the vaccine’s effects because it cuts out lines of transmission. It protects those who cannot take the vaccine or haven’t been vaccinated yet. This is the reason the anti-vax are so “healthy”. Eventually if their numbers rise they will be sources of infection and these may be self sustaining till we vaccinate again.

Vaccination is merely a trick, to trick our bodies into thinking that it has fought of a disease when it has not. At worst you save time and money that would have been wasted in treating the sick and at best you save lives out of it.


  1. says

    Definitely bookmarked.

    I’m on the Community Advisory Board for the Seattle HIV Vaccine Trials Unit. A common question we get is from new CAB members and study participants is “How do vaccines work?” You gave a really good introduction.

  2. says

    You are welcome to take a printout for them or send them over to the link.

    And everyone knows the correct answer to “How do vaccines work?” is “Fucking Magnets!”

    What can I say? I am really really up to date with my memes.

  3. Chuck says

    Lymphocytes are like Wizards. They Show Up Late to Save the Day with the Estranged Son of the Possessed Horse Lords.

    A wizard is never late, Frodo Baggins. Nor is he early. He arrives precisely when he means to.

  4. Bex says

    Wondering if you could stick a few extra definitions in for us dummies? I’m an engineer-physicist, but am about as good at biology as most lumps of wood. Probably worse. And I can’t Wikipedia fast enough to keep up with all the terms in this I don’t recognise ie “apoptotic pathway”. I know a few wavering vaccies, and would like to educate them, but if this is (mostly) hard going for me it’ll be a three-line sinker for them. The summation is very good but you’ve gone from the extremely specific to the general without joining the dots for the mid-level reasoners in between. Maybe I’ll go back and read it again until I get it. Or ask a med student, they’re great at explaining things to me (wrong), then telling stories about what people stick up their bums.
    Thanks for your writing and your work to keep Pasteur’s dream alive,

  5. says

    @Lance – If you are talking about mine, go right ahead. The whole thing took me a little more than an hour to go through when I gave it, skipping the slides about where HIV came from. If you want to include those, check for spelling: I didn’t proof those as well as I should have. I had meant to create a table of references to go with it but didn’t have the time; the other links on the page, though, should give most of that information.

  6. carlosribeiro da fonseca says

    Am I the only one that upon reading this “The thing to remember is that our blood vessels are actually permeable and the phagocytes can actively squeeze through to get into the tissue area.” immediately remembers this: and the cute little white policemen squeezing themselves through the blood vessels to attack the bad guys?

    The series “Il etait un fois… La vie” (Once upon a time… Life) was a great french animation series that described how the human body works. It probably wasn’t 100% scientifically correct, but it was aimed at kids, I was about 10 when I saw it :)

    In the 3rd episode, the viruses manage to get in and the immune systems has to defeat them: the first defense comes from the little policemen (the phagocytes — notice that the policeman is eating a bug) while Pedrito and Psi (the Lymphocytes), with the help of Mestre, scrambled to find a better way to kill the viruses. When they finally do, they “bomb” the viruses with little Metros :)

    The great thing was, we saw how it all fit in the bigger picture, if I recall correctly, it was the story of a kid getting a cold, so we saw how a lot of viruses where expelled in the nasal mucus, how is temperature went up as the battle between the viruses and the policemen raged, and finally how it went back down as Pedrito, Psi and the little Metros knocked out the viruses.

  7. F says

    Many anti-vaccine advocates simply think that injecting someone with a disease is a good way to make someone sick rather than make someone immune to a disease.

    Since one is not being “injected with a disease“, they are already off to a bad start. A disease isn’t even a thing, it’s a condition. Hell, break it down now: dis-ease. But one is injected with something which presents antigens: Bits of virus coating, defunct or weakened virii, occasionally bacteria.

    Hand grenade (of stupid), indeed.

    Macrophage “om nom noming” on pathogens

    I can’t even begin to speculate how many internets you win for this alone, never mind the entirety of the posted content.

  8. nermd says


    yes yes yes i saw this, it was all over Austrian television (which consisted of two channels *lol*) in my childhood. I loved the series and was fascinated. It really kind of influenced me :).
    After checking wikipedia it seems that the series never run in the US … to be honest i think its because – oh gush, gowd help us – it shows naked people creating new life in the opening sequence already (

  9. left0ver1under says

    One would think that even the anti-vax simpletons could understand why you can’t catch the same cold or flu twice. But apparently, they can’t.

  10. Chris from Germany says

    Thanks for this great article! Since you are well-versed in this subject, you might answer a question I had that confused me a bit – from what I heard, dengue fever is actually worse if you get it the second time (much more likely to be lethal), so I never quite understood how that fits in with the way the immune system works. Perhaps you could shed some light onto this? Or is it simply a misinformation that dengue fever is worse the second time around?

  11. R.T. says

    One, I love this article and am saving it for later use.

    Two, you’ve rather consistently reversed “it’s” and “its.” That’s not a content critique but it gives me a twitch when reading and I’m worried that someone who needs to read it will dismiss your points because of the issue.

    Feel free to delete this comment, there just wasn’t an easy email way to contact you.

  12. slothy says

    Excellent summary. The main problem with this type of stuff is it requires some effort on the part of the reader to engage some thinking and learning. I think most anti-vaxxers don’t want to input that effort especially when they are so entrenched in their views.

    @bex The apoptotic pathway is one of the ways cells of the immune system (and cells themselves) trigger cell death in infected cells. Viruses and bacteria can cause damage by causing cells to lyse (basically break open in an uncontrolled manner). The lysing of cells is bad news as certain things you want to keep in the cell spill out and can cause damage to neighbouring cells (including in the case of infection replicating viruses or bacteria). Apoptosis is the opposite of this, it is the breaking down of the cell in a controlled and preprogrammed manner so damage to neighbour and release of infecting virus or bacteria is limited. Essentially as much as possible is broken down inside cell as possible and the membrane undergoes a process known as ‘blebbing’ to create small apoptotic bodies that can be ingested by phagocytes. This explanation has probably lead to more questions than answers, sorry!

    OH if anyone wants to read why vaccination rates also matter I wrote this once:

  13. says

    @Chris #15 – It is not getting it a second time that is the problem, it is getting a seconary infection with a different strain of the virus.

    If I recall, the immune system pretty much goes into overdrive trying to fight the double infection, and starts destroying everything in sight. The body responds by, among other things, making capillaries less permiable, which leads to necrosis as cells are starved, asphyxiated and drowned in their own waste. As the infections receed, damaged capillaries and other tissue become leaky, leading to the hemorrhagic of severe dengue infection. This, more than the virus itself, is what makes dengue so dangerous.

  14. Kazim says

    Hi Avicenna, great article. I’d just like to ask a question because this is definitely an area where I could stand to bone up on my technique.

    “There is an absolute hand grenade of question that I have found turns the vaccination debate into an utter rout. How does the Immune System Function?”

    Would you mind gaming this conversation out for me a little, either in comments or in a new posts? Let’s say the antivaxxer says either “How the hell should I know?” or gives an entirely wrong answer. Then what? Do you give this entire lecture about how it really works? Or is there a key point that will drive the point home, some major bit of information that you can use to make their ignorance really obvious?

    Maybe you could provide a short Socratic dialogue of how you’ve seen this conversation go from there after you’ve tossed the grenade, or link to a forum thread or something?

  15. nermd says

    their is more than one “type” or strain of dengue virus and if you got one, you are only immune to that strain. That fact that certain type of strain combination in subsequent infections ( lead to a more severe form of the disease has been seen through epidemiological studies. I found a paper on pubmed ( that explains this through a mechanism called “Antibody-dependent enhancement” (their is also a source in the nature paper that says this). Now it gets complicated and to be honest my scientific english is probably not good enough to explain it in a way that wouldn’t be totally confusing :). Its kind of a complicated interactions between the antibody against certain antigens from the strain of a previous infection and the new virus that – paradoxically – interferes with immune-response to the new virus. Hope this helps a little bit …

  16. Kylie Sturgess says

    I’m not poking fun at anti-vaccinationists, btw. I’m confused as to how you came to that conclusion through the very little personal input I made with my blogpost.

    In the blogpost you reference, I’m pointing out a useful new resource and a well-known scientist (who is very highly regarded in this country) who supports the resource.

    As for my views on anti-vaccination claims and the range of people who hold them and why, I’d highly recommend this forthcoming documentary “Jabbed”; I interviewed the director for the podcast and there’s a partial transcript here where she talks about approaches:

    “…I am hoping that Jabbed will do that. I am really grateful to the families, who have offered their stories. Because the families come from those who have experienced the diseases that the vaccines could have prevented, but for various reasons didn’t. The stories also come from those very rare individuals, who have genuine vaccine injuries and vaccine reactions. I personally make a distinction between those two.

    I am hoping that, for those that just don’t know which way is up, it might help a little.”

  17. Tsu Dho Nimh says

    These give the new born baby the same range of protection as the mother.

    It’s important to point out that this immunity is not permanent – it lasts a few months.

  18. texasaggie says

    A couple minor quibbles:

    1. In the first sentence, last paragraph, I think you mean that some diseases don’t produce ANTIBODIES that last forever.

    2. Under innate immunity you could also include the inability of certain organisms, particularly viruses, to attach to human cell receptors and thus they can’t invade human cells. Some people lack the receptor that HIV uses to enter T cells so they never are really infected. Your dog may get parvovirus, but you won’t because the virus can’t enter your cells.

    The article is an excellent presentation of basic immunity and deserves time in the classroom.

  19. Paul Jones says

    Nice introduction – i have often thought a simple explanation of the immune system would help. However, here in Australia, we have an antivaccination group called the Australian Vaccination Network. Several of the members have expressed views that germ theory is wrong, and that germs do not cause disease. How do you argue with people like that?? They actively lobby against vaccination, and were openly celebrating a drop in vacc levels that have led to outbreaks of pertussis. Their solution to the outbreaks? Cease vaccination altogether, and the outbreaks will go away!
    Oh my head…

  20. texasaggie says

    This is a good explanation of how the hemorrhagic syndrome comes about. It is basically an out of control inflammation reaction when a second infection with a different strain cross reacts with the immune cells stimulated by the previous infection causing them to release all sorts of cytokines and other substances that cause inflammation with leaky capillaries.

    With certain whole cell bacterins against Mannheimia hemolytica in cattle, you get a similar situation. Vaccination primes the immune system and a real infection causes worse pulmonary inflammation than infection in a naive animal would. This is a good reason for not using killed bacterins in that particular situation because attenuated vaccines or toxoids against the alpha lysin (I think is what it’s called) don’t cause that reaction.

  21. says

    Kylie – Pretty much pointing out anything real at the anti-vax brigade is poking fun at them. Also it was an excuse to update an old post with new material.

  22. says


    @bex and @slothy;
    Perhaps a simplistic analogy for lysing/aptoptosis, for the non-biology types, is the difference between shutting down the computer by removing the power source vs. doing it the slow way, letting the software shut down open programs, etc. first.

  23. says

    Thanks for this. I wish it had been written a couple years ago, when I had a months-long discussion with a friend of mine who, to my great surprise, turned out to be passionately anti-vaccination.

    I engaged with him openly and honestly, trying to understand where he was coming from. I am not a scientist, never mind a biologist or immunologist, and perhaps he knew something I didn’t.

    Ultimately, he sent me a book called Vaccine Safety Manual. It purports to be a summary of relevant scientific literature targeted to the intelligent layperson. It argues that vaccines are dangerous, ineffective, and often actively harmful.

    I read selected chapters of the book, and wrote a review that might be of interest to you. Vaccine Safety Manual is filled with misdirection, logical fallacies, and intellectual high crimes and misdemeanors.

    For those interested in an analysis of anti-vaccination claims taken from a logical perspective without gettting into the (essential!) details of biological systems, I recommend taking a look.

    Let me know what you think.

  24. redpanda says

    I know a few anti-vaxxers who are otherwise intelligent people with what seem to be well-developed critical thinking skills, and I struggle to understand how they don’t realize how much they’re cherry picking. These are people who understand what cherry picking is and can readily recognize when someone else is doing it, but fail to apply those same standards to certain beliefs that they are personally emotionally invested in (vaccines, religion, etc.).

    I was talking to my sister a few months ago about the rubella vaccine, and she argued that the worst part of rubella is its potential to cause congenital rubella syndrome. Given that, she asserted that vaccination actually increases the incidence of CRS because when you give the MMR to children they are only immune for a couple decades at best and are less likely to get their boosters. So you have all of these young adults who are pregnant and no longer immune to rubella because they had a childhood vaccine instead of a childhood disease. Hmm.

    So I spent fifteen minutes on my university library website and found a meta-analysis that analyzes rubella vaccination strategies around the world and draws conclusions. Surprise surprise, my sister’s argument is exactly why we don’t advocate a childhood-only vaccination schedule. Effective strategies (you know, the ones practiced in countries that have experienced dramatic drops in both rubella and CRS incidence since starting the programs) involve things like giving the MMR to children AND targeting high-school and college-aged girls.

    So here we have an intelligent, educated person who uses an argument that is theoretically sound but completely unsupported by actual real-world research. I pointed this out to her in a follow-up e-mail and she never responded. If I keep doing this, perhaps some day she’ll change her opinion.

  25. Peter Ozzie Jones says

    A complex topic, nicely introduced, ta.

    Small typo in Adaptive section:
    “the adaptive immune system often fights of . . .”
    fights off

  26. says


    Since one is not being “injected with a disease“, they are already off to a bad start. A disease isn’t even a thing, it’s a condition.

    I wonder how much anti-vaccination thinking overlaps with essentialism (eg, Platonic forms) as applied to the concept of “disease”. Under this thinking, a disease can’t merely equal some arrangement of molecules; it is an essence unto itself. Ergo, either vaccines are entirely useless (the immune system is merely exposed to particles that “look like” the disease, not to the “real” disease itself) or they are actively harmful (if a disease really does consist of particles, then by definition, if you are injected with those particles you will become sick).

    Explaining the truth can be tricky; even a lot of advocates think that vaccines necessarily involve exposure to “the disease” and thus that all inoculation carries a tiny risk of infection. The truth, if I’m not mistaken, is that only some vaccines, the “attenuated” or “live” ones, carry that risk. A jab of a properly-prepared inactivated virus can’t get you infected at all (it won’t “come back to life”), although there is still the risk of an immune overreaction.

    Anyone who happens to see this zombie post, feel free to correct any mistakes.

  27. Dr Jeff says

    Your explanation is not entirely correct. It is also loaded with errors and missing information. Try researching into compartmentalization of immune systems. Hint: You can not give a shot in the arm and expect it to produce immunity in the oral mucosa. It doesn’t work like that.

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  1. [...] Word for Word. They didn’t even check who wrote the article. The people who want you to not vaccinate have no grasp of human biology and either are speaking as mothers (an euphemism for saying things with the notion that possession of a child gives you the innate ability to understand your child’s biology), speaking from positions of ignorance or worse. [...]

  2. [...] No so called “Doctor” who is anti-vaccine has been able to answer my simple question correctly. Well one has and he did so by quoting everyone’s most adorable medic. AKA Me. How does the human immune system function? For bonus points explain why blood typing, pregnancy tests, anti-venom, IMVIG and ELISA work but Vaccines do not. The only man to answer that didn’t know what he was posting. [...]

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