How the immune system works: Contrasting perspectives from science and alternative medicine

One of the biggest issues I’ve seen again and again in the comments sections of every vaccination article is a fundamental lack of understanding of how the immune system works. Many people talk vaguely of “toxins”, “pathogens” and “immunity”, but it’s clear that they have no idea exactly how this works. So I thought that I’d invite a regular commenter, Dr. Scott Nelson, to write an explanation. I think that Dr. Nelson, who teaches this subject in university courses, has done an excellent job of making a complex topic accessible to people who are not scientists or physicians.  (Note that we have provided hyperlinked definitions of many of these terms from Wikipedia for convenience. Dr. Nelson and I have both reviewed them and agree that they’re accurate. If you would like additional information beyond what is provided here, we recommend consulting any basic major textbook).

If you are “doing your own research” on vaccines, I urge you to read all the way through the end, and then watch the video, which shows an animation of the processes that Dr. Nelson describes.  Finally, because I think it’s important to illustrate the vast differences between the scientific explanation of how the immune system works, and the “alternative medical” explanation, I’ve included the homeopathic version at the end of the post. I encourage you to share your thoughts on which you find most compelling, and why. My comments following Dr. Nelson’s are in bold


A common thread through many anti-vaccine posts is fear about “all the stuff that you are jabbing into a kid”. I would like all the people who think this to perform a simple experiment. Take a piece of meat-any meat-make sure it’s fresh and smells good. Put it on the counter in a nice warm place-about body temperature-cover with a screen if you like. Let it be for three days and then look at it carefully, note all the different shapes and colors. If you know somebody with a microscope, scrape a bit of stuff off and look at it under a microscope. How many different things do you see now? Each spot, each color, each bug you see under a microscope represents something that the immune system is dealing with every second of everyday. After all-wasn’t it exposed to the exact same air that you’re breathing right now? Your body is that piece of meat-your immune system is what keeps it from rotting. Right now, our best estimates are that there are 10 microorganisms for every cell in your body. Your immune system “knows” them all and has responded in various ways, which science is currently exploring.

The immune system has a tough job. It must recognize a vast variety of pathogens (things that could hurt or kill you) and eliminate them, while at the same time recognizing a very large number of antigens (anything the immune system can recognize) that are part of the body, and not react to them. To make the problem even harder, the immune system doesn’t “know” what the foreign pathogens are or what they look like. To do this, the immune system has developed two separate arms-the innate and the adaptive immune system. I’ll talk primarily about the adaptive side of the system in this blog-but bear in mind that the innate system also exists and interacts with the adaptive side.

The adaptive side has two arms: the T-cell side (these are cells that were derived from the thymus- a immune organ that sits right above the heart. They have a number of markers that we can identify them with) and the B-cell side. B-cells generate antibodies that recognize antigens in that are floating around in the body; they don’t necessarily have to be interacting with proteins from the body. T-cells, on the other hand, recognize antigens in the context of specialized proteins called the Major Histocompatibility Complex (MHC).

Antibodies bind antigens (From:
Antibodies bind antigens (From:


There are two major types of T-cells–CD4+ and CD8+-which we’ll come back to in a minute. The MHC proteins are fairly divergent-there are lots of different types of them.   You may also know them as the “transplant” antigens, because they govern who can be an organ donor and who can be a recipient. For example, identical twins have identical MHC’s and can give organs back and forth with no problem. A child will have MHC antigens, half from the mother, half from the father. If the MHC’s of the parents aren’t too different, they may be able to donate to the child-but another child from the same parents has about a 1:4 chance of matching well with the siblings.

To make matters more confusing, there exists within the MHC, two separate classes- named Class I and Class II.   MHC class I is found on almost every cell in the body, MHC class II is found mostly on cells called Antigen Presenting Cells, however their function is basically the same: they present peptides (small protein fragments) from the inside of the cell to their respective T cell. MHC class I presents to CD8+ cells, MHC class II to CD4+ T cells. The MHC class II primarily presents peptides that the cell has internalized from the outside of the cell (think bacteria and viral fragments), while the class I presents peptides from the inside of the cell (think proteins from viruses replicating inside the cell), as well as “normal” proteins that are being turned over in the cell all the time.   T cells recognize the complex of MHC molecule plus the peptide.

From: Immunity, Vol. 7, 473–481, October, 1997 (Andre´ a Dessen, C. Martin Lawrence, Susan Cupo, Dennis M. Zaller, and Don C. Wiley).
X-Ray Crystal Structure of HLA-DR4 (DRA*0101, DRB1*0401) Complexed with a Peptide from Human Collagen II


Here we have to stop for a moment. How does the T-cell or B-cell “know” how to recognize the antigen? It takes roughly 2000 bases of DNA to code for a single T-cell or B-cell receptor (a protein that responds to a signal). There are about 3 billion bases in a human genome, so if every single base of the genome were dedicated to B-cell and T-cell receptors, we could encode about 1,500,000 receptors-which sounds like a big number, but now we are left with nothing to encode the rest of the body. In fact, we have sequenced the entire human genome, and it turns out that it only encodes about 20,000 different genes. Obviously, we have a problem here. We know that there are far more than 2000 antigens, if we dedicated 10% of the coding sequences to specific antigens. The other problem is that if there were only 2000 antibodies available, pathogens could quickly “learn” to avoid those sequences, and the immune system would be quickly overrun-and you would die. This doesn’t happen, so how do we avoid this problem? It turns out that the immune system uses chance to generate diversity. There exists within the genome a series of gene fragments that are recombined to generate a multitude of different specificities. It then sticks these antibodies on the surface of the cell.

How does the body “know” which one to use? It doesn’t. The body eliminates some of the antibodies that react with the body (a process we are still figuring out), the rest are waiting around, waiting for an antigen they recognize to float by. This is not as random a process as you might think. Your body has a secondary circulatory system called the lymphatic system. Fluid that is squeezed out of the blood vessels comes back to the heart via the lymphatics, where it is filtered through the lymph nodes-where the B-cells reside, so anything that is out in the periphery of the body is brought to the B-cells. If a B-cell binds an antigen, even at a low affinity, a remarkable thing happens. The B-cell activates, becoming a plasma cell, cranking out large amounts of the antibody. At the same time, it starts to mutate the genes that make up the antibody. A lot of the mutations reduce the affinity and those cells are no longer stimulated-but some of them increase the affinity for the antigen, and those cells are stimulated even more. As the antigen disappears, the cells are less stimulated, and some die off, but others just go quiet. They are now “memory cells”. The next time the antigen comes around, they are there with a high affinity antibody, ready to be made within a few hours-instead of the several days to weeks that it takes the first time it sees the antigen.

T-cells go through a similar recombination process, but then go through the thymus, where cells that can’t recognize the MHC in the body are eliminated, as well as those that recognize it too well. What we are left with is cells that recognize the MHC with an intermediate affinity. When the appropriate peptide is bound to the MHC, that increases the affinity, allowing the T-cell to “activate”. When CD8+ cells are activated, they release signals that cause the target cells to die, either by their own hand (apoptosis) or by the actions of the T-cell.

This is the mechanism by which we clear most of viruses that infect us that are replicating. What about the CD4+ cells? They are out scouting around, checking the cells of the innate system, as well as the B-cells. When they recognize their peptide antigen, they stimulate the cell that is presenting it to grow and proliferate, as well as stimulating themselves to grow. These cells are at the heart of the immune system. A recent search of Pubmed for CD4 T-cell only returned 86,445 papers on these cells, so it is hard to summarize all that is known about these cells. There are multiple subtypes of these cells, and they are at the heart of the immune system. If anybody remembers when AIDS was first reported, back in the early 1980s, you have a perfect example of what the CD4+ cell does. Without them, (since HIV actually binds to the CD4 molecule and slowly eliminates these cells) you slowly succumb to a variety of nasty infections and tumors that the normal healthy person brushes off without a second thought.

A scanning electron microscope image of a healthy human T cell. (From
A scanning electron microscope image of a healthy human T cell. (From


Where do vaccines fit into all of this? The best analogy that I’ve heard is from Dr. Lauren Sompayrac. Think of vaccines as of them as war games. You show the immune system what the enemy looks like, get the troops ready for battle, generate all the weapons you need to combat the enemy, but you hurt your own troops as little as possible by giving them a weakened enemy (like the Sabin vaccine), a dead enemy (the Salk vaccine), a disabled enemy (tetanus toxoid) or, more recently, just a portion of the enemy (Gardasil, acellular pertussis). That way, should they ever encounter the enemy, they don’t have figure out how to fight the enemy and how to make the tools, they just have to pull them out of storage.

Here is another place where you can read more about how the immune response works, and here is an excellent animation of these processes:

One caveat at the end here: Reading this does NOT mean you now know everything about immunology. I’ve painted with a very broad brush here to give a general overview. However, if you really want to know what is going on in the immune system, you’re going to need and undergraduate degree in the biological sciences and several years of post-graduate training-to come up to speed. The field is extremely dynamic, and the points presented here have stood the test of time, but there are many, many details that have been omitted.

–Dr. Scott Nelson


I think that it’s interesting to show the contrast between the evidence-based explanation of the immune system, and an alternative medicine practitioner’s description of how it works.

“Just as the regulating forces in nature keep the plants alive, homeopaths believe that human beings have an energy, known as the ‘vital force’. This ‘vital force’ keeps us alive. Homeopaths believe that if our vital force is out of balance, then our bodies and minds produce symptoms of illness as an outward expression of the imbalance. Homeopaths prescribe remedies to stimulate the energy of our vital force, and create balance.”

I think this difference makes it clear why physicians heal and homeopaths just provide expensive placebos.

A question for the comments: Why are the scientists who are experts in this process less credible when they explain the effects of vaccination?


53 thoughts on “How the immune system works: Contrasting perspectives from science and alternative medicine

  1. keithnoback April 20, 2014 / 12:38 pm

    To answer your question: Jim-Bob’s razor, i.e. “I have been baffled by bullshit, therefore, everything baffling is bullshit.”

  2. David Colquhoun April 20, 2014 / 2:37 pm

    It’s good to see you taking a swipe at quackery. Just about every quack (not only homeopaths) repeats endlessly the mantra that their on brand of magic “boosts the immune system”. The immunologists whom I’ve asked about it say that there is no such phenomenon. I’d welcome an extended account of what’s known about that question.

  3. Nick April 20, 2014 / 3:15 pm

    The alt-med model of the immune system is a computer that is thrashing (a real computer memory technical term, although appropriately one that is not quite valid in this context) with inadequate memory. Boosting it means adding more RAM chips. This is bullshit, but it has the merit of not being more complicated than a computer problem, which a few alt-med consumers might like to vaguely imagine that they understand (even though they probably have to map that onto a simpler analogy such as a car with a small engine pulling a trailer up a hill).

    • Colin April 20, 2014 / 4:02 pm

      I think it’s even simpler than that. The immune system is normally described as how we “fight off” illness. “Boosting” the immune system or making it “stronger” is just a natural extension of the same analogy; if your immune system is stronger you can fight off more disease, just like if you’re stronger you can lift heavier rocks. If your understanding of biology is limited to the analogy, it makes perfect sense.

      • Alison Marie June 5, 2014 / 9:02 am

        Anti-vacc people have hijacked that analogy. For example: Some see vaccines as boot camp and doctors are over doing it. Too much training will lead to weakness and injury, especially in babies because they are fragile and weak. That’s why some of them agree to spread out the schedule, which can be really dangerous as some diseases target very young babies during that vulnerable window after the mother’s immunity wears off. Also anti-vacc people are generally educated enough to want to know more but not educated enough to understand that thought experiments supported by comments on forums are NOT equivalent to peer-reviewed journals.

  4. Matt Fluger April 21, 2014 / 9:56 pm

    For years I bought into the myths of products that promised to boost my immune system. I eventually realized there is no substitute for well-balanced living.

  5. jesirose April 22, 2014 / 12:07 am

    I’m really glad you are working on conveying this info to people. I was very skeptical of vaccines (having worked for a veterinary homeopath) but when I began to study immunology at university I realized how ignorant I’d been and have changed my stance completely. It took a huge amount of work to understand what I learned in my immunology class, and I drew a lot on things I’d learned previously about cell biology, genetics, and organic chemistry. Without that background, I would have been mostly lost when reading Dr. Nelson’s explanation above. I think experts forget how often they use jargon that people like my mom, who has a high school education, have never heard before. People like my mom also don’t automatically look to Google or Wikipedia to clarify things they’re unfamiliar with. There are ways to simplify scientific ideas so they are understood by ordinary people without being condescending. Diagrams, animations, and analogies are all tools that I think work better than a long block of scary text full of strange words that can make people feel lost enough to give up.
    Maybe I’m giving the average person less credit than he/she deserves, but I think the more accessible this information the better off we all are. The ideas are such that a fifth-grader can understand, if only they are communicated in a way that makes sense.

    • Scott Nelson April 22, 2014 / 4:21 am

      Jesirose, thanks for your thoughts. If you have any ideas on how to make the concepts easier to understand, I’d be delighted to incorporate them. Your concerns are precisely my concerns in writing this, and I did my best to try and clarify things, without writing a textbook. Being one person, I’m stuck with seeing things through the lens of my own experiences, and anything I can do to make the concepts easier to understand I’d appreciate. I thought the video might have helped, but I’m always open to learning

      • Gary April 22, 2014 / 8:40 pm

        Great article and explanation Scott. Only suggestion I have, as an MD who writes for all different audiences, is to simplify it even further. Though we know exactly what “peptides” are and think of them as the most basic of concepts, those in the lay audience may feel stymied if they read too many words with which they are unfamiliar. Still, excellent job overall. Unfortunately, not even the simplest of explanations will convince those who have blindly accepted some ignorant fool’s word on the matter. But c’est la vie. Thanks for writing the article.

  6. Joel Shearer April 22, 2014 / 4:38 am

    Thanks so much for this, but I’m afraid what looks to me to be an immaterial slip has appeared in the text. Dog knows what anti-vaccers will try to make out of it. In describing vaccines, Dr. Nelson refers to “a weakened enemy (like the Salk vaccine), a dead enemy (the Sabin vaccine).” Is not that backwards?

    Thanks again. I am grateful to have found this blog, for the chance to learn; both from your defense of science-based medicine and championing of science against superstition, and from your discussion of your own fascinating field.

    • Jennifer Raff April 22, 2014 / 8:23 am

      We’ve corrected it–thanks for pointing it out!

  7. Roman (@Roman100) April 25, 2014 / 9:07 am

    The information is fascinating and essential but I would second Gary’s suggestion: make it even simpler (if such a thing were possible). Thank you kindly!

  8. Scott Nelson April 25, 2014 / 9:40 am

    All who read here-
    I would love to make this even simpler. Could you please comment and tell me what is difficult to understand, what terms befuddle you. I would love to simplify even more, but I am too far inside-I NEED the outsiders perspective.

    • Tony Goodfellow April 25, 2014 / 11:56 pm

      Thanks for the article Scott, good work. An excellent summary that shows the complexity of the process.

  9. tom April 26, 2014 / 3:27 am

    Hi jen & Scott,
    Firstly, thank you for writing & publishing this, it’s excellent.
    Secondly, Scott, you wanted suggestions to make it simpler. I think you could scrap pretty much the whole digression about MHC I & II (the paragraphs between the first two images) without losing anything important for a lay reader. You don’t refer to the different types later, and it would make it more linear & thus easier to understand.
    Maybe keep it as a footnote if you wsnt , because it is interesting, just notneeded for a lay blog article.

  10. Roman (@Roman100) April 26, 2014 / 6:58 pm

    On further thought, while simplification is very nice, it can only go so far. The interested lay reader ought to do some homework too. What comes to mind here is Dr. Raff’s excellent helpful article, “How to read and understand a scientific paper: a guide for non-scientists”

    As she writes: take notes, read it multiple times, and probably go look up other papers for some of the details. Take note of unfamiliar words, terms and concepts, and look them up. That ought to go a long way towards achieving a state of understanding.

  11. Mouse May 1, 2014 / 11:25 am

    “Why are the scientists who are experts in this process less credible when they explain the effects of vaccination?” I don’t have an answer, but this reminds me of when I was studying relativity and was enthusiastically explaining it to a non-science student who simply refused to believe me. “There’s no way that can possibly true, it just doesn’t make sense,” he told me. And then he proceeded to try to disprove the theory of relativity.

    Having said that, I have taken 5 college-level courses in physics and 4 in chemistry, but I haven’t taken biology since high school and I had a very hard time understanding Dr. Nelson’s explanation. I felt bogged down by terminology I was unfamiliar with. I had no problem with the first two paragraphs, but after that, I got lost. Now granted, I’m reading this on my lunch break and didn’t re-read it and dissect it the way I probably should.

    Since Dr. Nelson has asked for feedback, what would help me is less terminology. Since I have no background, the terminology is like a foreign language and I have nothing to relate it to. If certain terms must be used, perhaps you could compare them to other terms that most people are familiar with?

  12. John Scudamore June 1, 2014 / 3:10 pm

    “I think this difference makes it clear why physicians heal and homeopaths just provide expensive placebos”

    Fact, physicians, allopathic ‘science’ physicians kill 780,000 every year in the USA alone. PLUS the hundreds of thousands they kill with chemotherapy every year.

    Fact, homeopaths don’t kill anyone with their medicine, so are a million or so cures ahead af the Allopaths BEFORE THEY HAVE EVEN STARTED. Chew on that.

    And Nutritional medicine, REAL science has the proven cure for infections for 70 years or so as PROVEN by 1,200 citations from research and clinical practice. So that would make vaccination unnecessary, and so they are ahead on the millions of vaccine damaged, BEFORE THEY HAVE EVEN STARTED.

    As to your science babble on the immune system, you only have a basic understanding of the human newborn immune system, so on that fact alone vaccination is just an EXPERIMENT.

    “I would challenge any colleague, clinician or research scientist to claim that we have a basic understanding of the human newborn immune system. It is well established in studies in animal models that the newborn immune system is very distinct from the adolescent or adult. In fact, the immune system of newborns in animal models can easily be perturbed to ensure that it cannot respond properly later in life.” ——This testimony was given verbally to the United States Senate on May 12, 1999 by Dr Bonnie Dunbar, Professor of Immunobiology with specialise work in vaccine development and autoimmunity for over 25 years, the past 17 at Baylor College of Medicine in Houston.

    And if you think the energy body doesn’t exists by using this quote, then you need to do some research, start with acupunture, yoga, psychedelics etc, and we have PROVEN it exists through clinical experience and by machines that can detect it. See the assemblage point book on the subject

    You act like a scribe for the vaccine houses.

    “Just as the regulating forces in nature keep the plants alive, homeopaths believe that human beings have an energy, known as the ‘vital force’. This ‘vital force’ keeps us alive. Homeopaths believe that if our vital force is out of balance, then our bodies and minds produce symptoms of illness as an outward expression of the imbalance. Homeopaths prescribe remedies to stimulate the energy of our vital force, and create balance.”

    • userdude100 June 3, 2014 / 10:24 pm

      Scientific medicine constantly criticizes itself and publishes the critiques for all to see. There is NOTHING comparable in the world of alternative medicine, and even less so in the domain of the woo called homeopathy.

      Here are some pertinent thoughts as to this last, by the eminent physician Dr. Mark Crislip, MD:

    • userdude100 March 31, 2015 / 3:14 pm

      @John Scudamore

      “Fact, physicians, allopathic ‘science’ physicians kill 780,000 every year in the USA alone. PLUS the hundreds of thousands they kill with chemotherapy every year.”

      If this is “fact” then it must be supported by evidence. Citation?

      Your hypocrisy is in complaining about the risks of real medicine without acknowledging that real medicine actually has benefits to offset those risks (unlike quackery).

      As a layman I would suggest that, even if true, the number you bandy about would be very much higher if there were no hospitals and conventional doctors.

  13. Nikhil Autar June 5, 2014 / 8:52 am

    Great post – but I don’t think a layman would be able to understand a lot of it, though it is definitely a great intro into the adaptive immune system!
    To make it simpler – put a few foot notes or hyperlinks to a “further explanation” thing down the page (reply/email/somehow contact me below if you wanna know how to do that) and just put a brief outline of different parts. Linking bits of wikipedia, which is also pretty hard to understand without clicking 50 different links at times, is a little hard.
    I know the pain of doing this myself lol – I write a blog where half my regular reader-base is of a medical background, while the other half are not (I think it’s like that sort of ratio at least).
    This was a post I did on the fraud behind the whole “vaccination causes autism” idea. The other posts – they’re all about my journey through cancer and how I adapted. Have a look if you’d like – I’m definitely reading a few more of yours!

    • Scott Nelson June 5, 2014 / 9:43 am

      Nikhil-great suggestion, but my problem is to figure out what parts need simplification without making this an introductory textbook on immunology or biochemistry. What, in your experience, are the terms that need simplification and how did you do it?

      • Nikhil Autar June 5, 2014 / 6:36 pm

        Hey Scott,

        The bits on the MHC class 1 and 2 and the differences between CD4+ and CD8+ can be footnoted (put jump links in between, as I said, to allow the reader to click there for more into rather than get a sometimes even more complicated wiki page or other external link for it), your explanation of VDJ recombination could be made a little more clear I believe and otherwise just reduce the overuse of terms such as “recombination” and substitute them for easier terms, or at least, expalin that better. In terms of the VDJ recombination just say something along the lines of “to maximise the amount of antigens that can be recognised by the immune system, considering we only have a limited amount of genes available to code for the body, we code separate parts of the antigen recognising receptors and combine them in different ways to confer the most immunity out of the limited number of coding genes we have” sort of thing. I think the whole MHC –> VDJ recombination –> thymus part was a chunk of text that would leave most biology students confused, yet alone a layman, so just subtle changes there would be great.

        As it stands, it’s a great intro into the adaptive immune system actually. The way in which you conveyed it throughout, in a conversational tone, almost as if you were teaching them personally, was beautifully maintained, and would keep people interested! It’s something I always try and maintain in my blog posts and I always get feedback that it’s helped people understand some things they’d never gotten before (though admittedly I don’t get as much feedback as you have on this except on my most popular posts) I know it’s harder on you, because you don’t wanna oversimplify things, but just taking out the jargon at times, or explaining it, and rephrasing how you say some of the more complicated bits can help a bit =]

  14. Paracelsus June 15, 2014 / 11:13 am

    Since the immune system is so complex, and the preceding is an excellent presentation of that complexity, it would be amiss to not include in the discussioin autoimmune disease and how it relates to the vaccine theory. Kind of like not seeing the forest for the trees.

    • Chris June 15, 2014 / 12:55 pm

      ” not include in the discussioin autoimmune disease and how it relates to the vaccine theory.”

      Citation needed.

      • Paracelsus June 16, 2014 / 8:58 am

        I guess to keep it simple one could just discuss Guillain–Barré. The distraction of course would be the debate on the extrapolation to other auto-immune conditions, which certainly could be triggered by the same mechanisms.

        • Chris June 16, 2014 / 10:13 am

          Which happens more with actually getting influenza.

          • Paracelsus June 16, 2014 / 10:19 am

            Would that be influenza or influenza like illness? Since you seem so read on the topic, feel free to answer the original question rather than the the soft shoe.

          • Chris June 16, 2014 / 10:44 am

            I am not well read on it, which is why I asked for citations. I have just read in reliable medical sites that it happens with many infections, “The exact cause of Guillain-Barre syndrome is unknown. But it is often preceded by an infectious illness such as a respiratory infection or the stomach flu..” If you have a citation that it occurs more often due to a vaccine, then please present it.

            By searching PubMed I did find a recent review, An Update in Guillain-Barré Syndrome, which says (emphasis added):

            Three quarters of patients give a history of a preceding illness usually respiratory or gastrointestinal which may be so mild as to be completely asymptomatic. The neuropathy typically begins 7–10 days after any triggering infection. Numerous other antecedent events are described including surgery and immunisation. Most recent epidemiological surveys show the risk of immunisation triggering GBS to be very low [11]. It is estimated that the risk of contracting GBS from current influenza vaccines is significantly lower than the risk of getting GBS from influenza itself. Serological studies have shown that Campylobacter jejuni, Epstein Bar virus, and Cytomegalovirus are the most frequent antecedent infections. Patients sometimes continue to secrete C. jejuni in their stool for up to 3 months following the onset of GBS [12]. Persistent infection with CMV or EBV is very rare. A number of reports associate GBS with mycoplasma pneumonia, influenza, and varicella [13].

            I am always curious to know how a vaccine can cause a greater impact on the immune system than a disease. That seems contradictory.

          • Paracelsus June 16, 2014 / 2:49 pm

            Diseases don’t typically find it necessary to team up with adjuvants. Vaccine makers find the addition of adjuvants necessary to their model. In the future genetic makeup will be shown to determine “most likely” to have a reaction to these adjuvants. Then when an individual is found to have genetic propensity to over-react to adjuvants do you still force them for the sake of the “herd”. That’s akin to discrimination. (Never mind the flimsy argument of “herd effect” anyway.) Cytokine activation in relationship to adjuvants isn’t contradictory, it makes total sense. However small the number of GBS you relate to vaccines, the mechanism is still important. The mechanism is auto-immune. While the demylenating auto-immune reaction handily makes it self apparent do to respiratory failure, lessor obvious type auto-immune reactions can occur but can easily be discounted because they aren’t as dramatic. The mechanism no less exists.

            • Scott Nelson June 23, 2014 / 3:13 pm

              Sorry, I was off on a vacation for a week.

              Actually, bacteria viruses serve quite well as adjuvants. Components of the bacterial membrane, such as lipopolysaccharide, as well as DNA from both bacteria and viruses, strongly stimulate the innate side of the immune system. I deliberately glossed over this phenomena, as trying to explain the interaction of the innate and adaptive system would quite literally require the writing of a text book-a couple of inches thick, as well as a strong understanding of cell biology and biochemistry, and I thought it far beyond the scope of this blog. I can recommend a couple of textbooks should anyone be up for the challenge.

          • Chris June 16, 2014 / 2:59 pm

            Please support your assertions with actual scientific citations. Explain how infuenza vaccines impact the immune system more than the actual disease. Especially since seasonal influenza vaccines in the USA do not have adjuvants: “Seasonal influenza vaccines used in the United States do not contain adjuvants.”

            And in addition some more data: “Pandemrix was not licensed for use in the United States. In fact, no adjuvanted influenza vaccines are licensed in the United States, and no adjuvanted influenza vaccines were used in the United States during the influenza pandemic or in any other influenza season.”

            So please explain, with citations, how an influenza vaccine can impact the immune system more than the actual disease without mentioning adjuvants.

            Notice that I included a URL inside some blue text. That is to show that I am not just making stuff up. I have asked you several times to provide citations for your statements, and you have not provided any.

            • Paracelsus June 18, 2014 / 9:03 am

              Hey Chris…..Look…..a squirrel ! How this morphed into a discussion of flu vaccine is beyond me. The original request was for a comment on proposed auto-immune mechanisms and how that might somehow related to vaccine theory. Since you were so inclined to mention Pandemrix, why don’t you comment on why it wasn’t approved for use in the United States. A brief discussion about Europe’s experience with it, more specifically the children, and European scientists theories on its relationship to the narcolepsy it induced. Then lets get back to the US vaccine schedule, that has plenty of adjuvants, ooopps, there is that nasty word. Their ability to stimulate an auto-immune mechanism is quite relevant. When you’re done scratching the surface go back to your day job.

              • Chris June 18, 2014 / 10:38 am

                “How this morphed into a discussion of flu vaccine is beyond me”

                Let me remind you, after I responded that Guillain–Barré happens more by actually getting influenza you said: “Would that be influenza or influenza like illness?”

                “Since you were so inclined to mention Pandemrix, why don’t you comment on why it wasn’t approved for use in the United States.”

                It uses an adjuvant that has not been approved for use in the USA. There are eight other approved influenza vaccines, none of them with adjuvants, so there is no reason to go through a lengthy approval process. Try reading the pages the links go to instead of just what I quote.

                Now about that reference: “Self-Organized Criticality Theory of Autoimmunity”

                It is in mice. The “immunization” is not a vaccine but with a real pathogen, staphylococcus enterotoxin B (SEB). In other words the full blown unaltered bacteria not a vaccine. The paper has nothing to do with any real vaccine, nor with any adjuvant. It essentially proved that rodents get autoimmune responses with repeated staph infections. They even say “The method we have chosen was to stimulate the system maximally by antigen to the levels <b<far beyond its steady-state just like testing the capability of automobile.”

                It in no way shows a vaccine has a greater impact on the immune system than the actual disease.

                Now, again, please post the citation that shows a vaccine causes greater autoimmunity problems than the disease. You have made a claim, and it is up to you to provide the verifiable evidence for that claim.

                Just chose one vaccine and one disease. For example explain how the DTaP causes greater harm to the immune system than pertussis. Make sure the studies you post actually support your statements (try reading them). You can probably start by using these two lists of papers:

                Vaccine Safety: Examine the Evidence

                Vaccine Safety Datalink Project Publications

                “When you’re done scratching the surface go back to your day job.”

                The only head scratching is wondering why someone would make outlandish statements about “autoimmune disease and how it relates to the vaccine theory”, but not provide one shred of scientific evidence to support those claims, plus not even read the citation that is finally presented.

  15. Paracelsus June 15, 2014 / 11:17 am

    Would be interesting to hear about the immune systems relationship to inflammatory cytokines and the modulation safeguards that act to regulate the “volume” control on the subsequent immune pathway activations. Kind of another forest and tree thing.

    • Scott Nelson June 23, 2014 / 3:27 pm

      Regulation of the the immune system is a area of intensive research, and to say that we totally understand it would be a dramatic overstatement. I wish I could say that there is an easy answer, but the truth is that we are at a point where we have a jigsaw puzzle with hundreds of pieces and we’ve started to put a few pieces together, but we really don’t have a handle on what the picture looks like. To get an idea of the pieces, here’s a link to a company’s website that shows some of the pathways involved. how all these pathways interact, and add in the fact that the cells move around and the timing of the stimulation(s) varies the effects, and you’ll start to get an idea of the scope of the problem.

  16. Paracelsus June 15, 2014 / 11:23 am

    Was curious about your thoughts on the DTaP failure rate (est. 25%) in relation to the old DTP ? Why the new DTap and not the old version ? Any insight on the roll AC Toxin antigen plays out in this would be welcomed.

    • Paracelsus June 21, 2014 / 7:41 pm

      That’s what I thought

  17. Anna July 15, 2014 / 10:31 pm

    I think this is really great post and important issue. The lack of understanding how our body works can lead to misinterpretation of scientific information, especially in regards to vaccination. People have to understand how immunity is build and why vaccines prevent the disease. It is also important because many people think that if some vaccines are not 100% effective they should not be used. The deep knowledge about immune system and vaccine design could help people to appreciate how hard it is to make effective vaccine and understand that even though some vaccines are not 100% effective they greatly reduce the disease burden and help save lives.

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