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).
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.
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.
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 Salk vaccine), a dead enemy (the Sabin 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?