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Basic vaccine chemistry for anti-vaxxers

One of the problems, among many, with anti-vaccine activists, is a complete misunderstanding of the basics of vaccine chemistry. People get scared of long chemical names, or chemicals themselves, and wonder if a vaccine might be dangerous.

Setting aside the fact that vaccines undergo substantial and robust preclinical and clinical testing which has shown that the safety and effectiveness of vaccines are settled science, most of the chemicals in vaccines are not dangerous, especially from the aspect of toxicity.

The website, The Logic of Science, published an article about five simple chemistry facts. It’s a valuable article, so I wanted to utilize their list and apply it to an article about basic vaccine chemistry.

I know that this will oversimplify vaccine chemistry. But I think most of us, who focus on the overwhelming evidence that vaccines are safe and effective, know that the fundamental principles of chemistry are the basis of biomedical science which is the foundation of vaccines.

Without further ado, let’s look at basic vaccine chemistry.

colorful liquids in laboratory glasswares vaccine chemistry
Photo by Kindel Media on

What is chemistry

Simply put, chemistry is a physical science, the branch of natural sciences that deals with non-living systems. A chemist studies the composition, structure, properties, and changes of matter.

Chemistry includes the study of the properties of individual atoms, how atoms form chemical bonds to create compounds and molecules, the interactions of these substances through intermolecular forces, the general properties of matter, and the interactions between substances through chemical reactions.

I thought it would be prudent to explain what a chemical is because that’s a critical point for vaccine chemistry. A chemical is a form of matter (any matter) that has a constant composition along with characteristic properties.

A chemical cannot be separated into its basic components by physical separation methods. For example, you cannot break table salt into sodium and chlorine through crushing or shaking. It requires a chemical reaction to break its chemical bonds, which is fairly easily done with water.

Chemicals can be elements, compounds, molecules, ions, or alloys.

Chemistry is considered a bridge between all of the other natural sciences, such as physics, geology, and biology. Biochemistry, a branch of biological sciences, studies chemical processes in living systems.

One needs to have at least two years of chemistry (basic and organic) to receive a university-level biology degree. And if you want to get an advanced degree in the biological sciences, such as a Ph.D., a candidate would have probably 3-4 years of chemistry.

Before I received my bachelor’s degree in biology, I had taken 4 years of chemistry – basic inorganic, organic, physical, and biological. At my university, the biology and chemistry buildings were right next to each other, and I might spend days without leaving that small area of the planet.

With that basic information, let’s take a look at vaccine chemistry in detail.

woman holding an erlenmeyer flask with red liquid
Photo by Kindel Media on

1. Everything is a chemical

There’s no magic to this fundamental point about everything you touch, consume, breathe, see, or smell. Everything in the universe is a chemical (with the important exception of subatomic particles).

Water is a chemical. Air is a chemical. Your own body is a complex mix of over 1014 molecules. That’s a 1 followed by 14 0’s. If that has a name, I don’t know what it is.

If you’re going to criticize the chemicals consumed in your food or injected into your arm, it would be nonsense. Every single system in your body is dependent upon chemicals, from the water in your blood to the fatty acids that form each cell’s walls, to the DNA and RNA required to replicate your cells, and to the almost infinite number of molecules forming everything in your body.

You cannot survive more than a few seconds without chemicals. The air you breathe includes oxygen (actually O2) and nitrogen. You need oxygen for all of your cells to react with glucose (another chemical) to create energy. And nitrogen in the air is used by plants to create proteins.

There’s an old trope from the chemistry deniers that if a third-grader cannot pronounce the name of a chemical, then don’t eat it or inject it.

Hey, let’s look at table sugar or sucrose. It is officially known as (2R,3R,4S,5S,6R)-2-[(2S,3S,4S,5R)-3,4-dihydroxy-2,5-bis(hydroxymethyl)oxolan-2-yl]oxy-6-(hydroxymethyl)oxane-3,4,5-triol.

That word is complicated and long. But if you’re a biochemist, it only means a disaccharide (two sugars), glucose and fructose, connected by a chemical bond. It isn’t that scary. Besides, no biochemist I know would remember the chemical name of sucrose, and no professor ever required me to remember it either.

Vitamin D is cholecalciferol. Vitamin D sounds like it’s important to your health. Cholecalciferol sounds like a space alien.

I do not claim that all chemicals are safe. That’s simply not true. However, just because it has a long, scary, unpronounceable name does not mean it’s bad. And your world is filled with chemicals. And your body is filled with chemicals.

Relax. They’re not out to get you.

Aureolus Theophrastus Bombastus von Hohenheim [Paracelsus]. Credit: Wellcome Library, London. Wellcome Images Aureolus

2. The dose makes the poison

Paracelsus, a 16th-century Swiss-German physician, alchemist, and astrologer, is traditionally thought to have founded the discipline of toxicology, an important branch of medicine, physiology, and pharmacology. Paracelsus wrote one of the most important principles of toxicology:

All things are poisons, for there is nothing without poisonous qualities. It is only the dose which makes a thing poison.

This is one of the basic tenets of toxicology. Everything can be poisonous or non-poisonous depending on the dose. This is simple math.

Water might appear to be an innocuous, extremely safe chemical, dihydrogen monoxide. Yes, water is a chemical.

However, one could easily consume enough water to cause death. Water intoxication is an actual medical condition caused by the overconsumption of water – excess water causes an electrolyte imbalance. This leads to a fatal disturbance in brain functions. This leads to death.

And we’re not talking about a lot of water to do this. Consuming 5-10 liters of water in a short period of time can be deadly.

With respect to vaccines, the formaldehyde “contamination” of vaccines is a basic trope of vaccine deniers. Formaldehyde is a fairly simple biochemical that is used in the purification of the vaccine. The process removes bacteria and viruses which may be harmful if injected. And, over 99.9% of the formaldehyde is removed during the final steps of manufacturing.

The package labeling of a typical vaccine does not include the amount of formaldehyde. Why? Because it is so tiny, so minuscule, that the amount actually cannot be measured.

Plausibly, there may not be any formaldehyde in the vaccine solution. In fact, the level of formaldehyde is so low it cannot be detected by normal methods. However, there may be a few molecules of formaldehyde remaining in the vaccine. If we recall that dose makes the poison, then the dose of formaldehyde in the vaccine is far below what could be considered toxic.

Let’s look at the simple math:

  1. The normal blood level of formaldehyde is 2.74 +/- 0.14 mg/L. Yes, formaldehyde, which is a byproduct of natural biochemical reactions in cells, floats in your blood at all times. A normal, healthy child has a blood volume of 2-3 L, so that child has 5-9 mg of formaldehyde naturally floating in their blood. Again, it’s natural, nothing but the normal metabolic and biochemical processes in the body causes it.
  2. On the other hand, vaccines contain somewhere between 0.5 and 100 µg (or 1/1000 mg) per dose.
  3. It would take up to 10-20 thousand doses of vaccines to just match the formaldehyde level in your child.

Moreover, many foods have formaldehyde concentrations that are far above vaccines. For example, a single apple contains between 428.4 – 1,516.4μg of formaldehyde, which works out to be 4X to 3000X higher in formaldehyde than found in a vaccine.

When it comes to the toxicity of a chemical, a real scientist asks two questions:

  1. What dose of the chemical is toxic?
  2. What is the dose of a particular product?

Without answers to either of those questions, it’s a fallacy to invent some sort of claim that a chemical is poisonous.

close up photo of sugar cubes in glass jar vaccine chemistry
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3. Natural and synthetic chemicals are equal

I write a lot about high fructose corn syrup (HFCS), which is simply an aqueous (water) solution of glucose and fructose. In other words, you could throw a spoonful of sucrose (table sugar) into a cup of water and create something close to HFCS.

Of course, this leads to the second argument about chemicals. HFCS is created through a manufacturing process from corn, so the argument is that it must be different than “natural” sucrose.

However, I want to make this clear. There is simply no difference between the fructose and glucose molecules in HFCS and the fructose and glucose molecules in sucrose. The chemical formulas are exactly the same. It’s the exact same carbons, the exact same hydrogens, and the exact same oxygens. No difference.

Moreover, the formaldehyde in vaccines is the same as the formaldehyde in apples. There are no differences.

Unfortunately, there are people who buy into the Appeal to Nature logical fallacy. They think that only “natural” is good, so the ingredients in a vaccine, whether derived from a natural source, like a virus or created through a manufacturing process, are all unnatural.

photo of stream during daytime
Nature. Photo by Michael Block on

4. “Natural” chemicals are not always good

Or, on the other hand, not all artificial chemicals (whatever that is) are inherently bad.

This issue is related to point 3. However, it embraces the Appeal to Nature fallacy even more.

There is a belief, among many, that natural chemicals (if they buy into the fact that nature produces chemicals) are always good for us. Well, I could spend a lifetime listing “natural” compounds which are dangerous. Arsenic, uranium, snake venom, viruses, cyanide, and many poisons are “natural.”

The list of food plants that are toxic to humans is huge. Potatoes, tomatoes, cherries, apples, and many other agricultural products have parts that are very toxic to humans (and, in some cases, to pets). “Nature” gave the planet these toxic plants — well actually, it’s natural selection, since these poisonous plants gave an evolutionary advantage to survive and reproduce.

This argument extends to vaccines in the most laughable ways. One of the arguments against vaccines is that “natural” infections from viruses and bacteria (both made up of complex chemicals) are better than vaccines, which are unnatural.

But this argument fails on so many levels. The “natural” infection has an important side effect – the pathogen can cause serious side effects and death. The “unnatural” vaccine uses chemistry to isolate the key antigens which induce the immunologic effect to prevent a “natural” virus from causing an infection.

I think people also impart certain magical properties to “nature.” There is no supreme being controlling nature. Everything that is “natural” arose from random, stochastic processes controlled by nothing but chance. That’s evolution.

The earth arose from a random accretion of material over billions of years. And, it randomly developed into the right size and right orbit around the sun to allow life to arise randomly.

The poisonous plants arose through the process of natural selection in response to the evolution of herbivores or pests who consumed the plants. Tomatoes are not poisonous because “nature” made some decisions to do so. The poisonous parts arose over time as random mutations accumulated that provided some resistance to pests.

We now grow tomatoes that aren’t toxic, by manipulating the genome through artificial selection.

Chemicals, whether created by random processes called “nature” or by humans, are all inherently the same. They obey the same laws of chemistry and physics. They all form according to well-understood and studied processes. And they all must obey the physical laws of chemistry.

Human beings are not special creatures that all of nature arose to support. Therefore, not all chemicals created on this planet, whether from natural or artificial sources, have an effect on humans. And whether that effect is “good” or “bad” has nothing to do with the source, it has everything to do with how that chemical interacts with the chemicals in a human. Generally, we can predict that interaction. And it has nothing to do with nature.

people woman technology health
Photo by Karolina Grabowska on

5. The whole is greater than the sum

Chemistry is a fascinating field of science because when elements or compounds are bound together, they form whole new molecules that have special properties.

Let’s look at table salt, sodium chloride, or NaCl. It’s actually quite a simple molecule, made up of sodium metal and chlorine gas. Pure sodium is a fun element. It is so reactive that when it contacts water, it literally explodes. There are many anecdotes where chemistry students at my university flushed sodium down the toilets causing massive explosions. I do not recommend this, but they do make great stories.

Chlorine, on the other hand, is a poisonous gas. Once again, the dose makes the poison. In small doses, it can purify water. In high doses, it can be used as a weapon, as it was during World War I.

When sodium and chlorine are combined into table salt, it no longer has the properties of either sodium or chlorine. It is neither explosive nor poisonous (although it can be deadly if you eat a lot of salt, again dose makes the poison). When you consume NaCl, water breaks the bonds of the two elements, but they do not revert to explosive sodium or poisonous chlorine. They form ions that bind to other ionic compounds. Chemistry is cool.

Let’s talk about one of the most vilified vaccine chemicals, thiomersal (or thimerosal for Americans). Thiomersal is ethyl mercury, a molecule that is used as a preservative in many medical products, including vaccines. Although there is absolutely no evidence that thiomersal causes any harm at the levels found in vaccines, anti-vaxxers always want to claim that there is mercury in the vaccine, harming children.

But like table salt, it’s not the individual parts that matter but it’s the whole molecule. Thiomersal is not elemental mercury, which is, admittedly, a fairly dangerous neurotoxin. Clearly, the vaccine does not contain elemental mercury (which can’t go into an aqueous solution, because it’s a metal), it contains the compound, thiomersal.

Thiomersal is not the same as mercury. In this case, the metal, mercury is bound to an ethyl group, written as HgCH2CH3, known as “ethylmercury.”

The mercury that is commonly found in “nature” is methylmercury or HgCH3. That additional CH3 in thiomersal makes all the difference, even though it’s small. Methylmercury is, in fact, quite dangerous and consumption should be limited. Methylmercury contaminates our food chain (much of it from “natural” sources, so there’s that issue of natural vs artificial), and accumulates in some apex predators.

Unlike NaCl, which does dissociate into ions (though not the elements themselves), ethyl mercury does not disassociate. Ethylmercury remains one molecule until it is cleared by the kidneys into the urine.

If you’re going to claim that ethylmercury, or thiomersal, is dangerous, then you’re asking us to set aside all of the chemistry we know to invent something that doesn’t exist. Thiomersal is safe because it isn’t mercury. It isn’t methylmercury. It’s a different chemical, a different molecule, that has completely different properties.

This is an important point. Small changes in molecules can create massive changes in their biological effect. Just because ethylmercury has just one carbon and three hydrogens more than methylmercury doesn’t mean it’s biologically similar. They aren’t.

Basic vaccine chemistry

Let’s simplify this story into five essential points:

  1. Everything in the universe, and by extension, this planet, is a chemical.
  2. The dose makes the poison. A chemical becomes a poison, once a particular dose is exceeded.
  3. A naturally occurring chemical is identical to a synthetic chemical. There are no special atoms or bonds in nature that make it different.
  4. Natural chemicals are not inherently good or evil, and manmade chemicals are not inherently evil or good. There is no dichotomy between the two, a chemical is just a chemical.
  5. The whole chemical is different than the sum of the parts it’s made of. You cannot say “table salt” has explosive sodium, so it will explode in your body. No, it doesn’t do that. And you cannot make thiomersal equivalent to mercury.

Inventing fake vaccine chemistry just to create a narrative about vaccines is just not science. It’s pseudoscience.

Michael Simpson

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