Lab Snob

Kenya Medical Research Institute (KEMRI)


People warned me about the lab facilities in Kenya. Everyone expressed some variation of  “You know it’s not the same as in the US, right?” And every time I looked at them like they were crazy, but not because I was surprised. I am not some naive, sheltered PhD student who thinks everyone gets an LSR-II and precast gels. Nor am I a lab snob- at least I try not to be. I have worked in low budget labs, low access labs, unsanitary labs, you name it. I have also worked in a lab abroad before so I’m not exactly a noob. Whatever my situation was, I made it work.

So you don’t think I’m full of shit, here’s a brief example. A few summers ago I worked in a lab in China- a land of duality with old and new co-existing everywhere you look. The lab was no different. We had a NanoDrop but were still developing Western Blots on film in a dark room (which smelled like a rotting vivarium fyi). It was a weird place to do science. At one point, the air conditioning broke in the main lab room and, because of nonsense bureaucracy, it didn’t get fixed for a couple of weeks. Beijing in the summer is easily 90 degrees Fahrenheit and humid. If I wore my gloves for more than 20 minutes, sweat would start to pool in the fingertips causing my fingers to prune. Super cute, I know. We had to do all our experiments on ice just in case. But we did it and we got beautiful data for the grad student we were assisting! Long story short, science doesn’t care about your comfort.

So when people warned me about Kenya, I looked at them like they were crazy because duh. Literally duh. Of course it’s not the same. I would never expect to have the same luxuries that I have at Emory, but it’s not like that would ever deter me from the experience. Regardless, I heeded the warning and steeled myself up for terrible lab conditions. Now that I have spent three weeks here I can safely say that everyone is a Big. Fat. Baby. The TB lab at KEMRI is SO NICE. Now maybe my opinion is biased because I was expecting a shit hole, but really the facilities are pretty awesome.

Like this is the avenue you drive down to get to the lab (after driving through two guard posts mind you). Not a bad place to spend 3 weeks.


My first day in the lab, I got three separate tours. Everyone wanted to make sure I could orient myself and show me what kinds of projects they had going on at the site. Each one of my tour guides kept saying things like “I know it’s not much” and “It’s not like at Yerkes/Emory/The US.” And I was just staring at them blankly because in a lot of ways it is EXACTLY like the US. They have all the standard immunology stuff- hoods, incubators, centrifuges, autoclave, ELISA readers. There were even a few crazy, high tech pieces of equipment that I did not recognize. I really didn’t understand everybody’s sheepishness.

IMG_5792 (1)I later discovered that the building the TB lab is in is in fact one of the nicer ones on campus. On day two I shadowed one of the scientists doing helminth diagnostics. We went to a Neglected Tropical Disease (NTD) room in another building and it was pretty dated. But then again, so are the methods used to diagnose NTDs so I wasn’t that surprised. The only things you need for helminth diagnostics are stains, slides and a simple light microscope. Plus NTD diagnostics usually involve poo so who wants to waste a fancy clean room on that. The point is that it doesn’t really matter how nice the facility is as long as you can do your work. Does the campus here have all the hoity-toity cores that we have at Emory? No, of course not. I’m not even sure there is a vivarium. But for standard immunology and microbiology assays, they are pretty set.

I feel like it is important to disseminate this information so that other scientists think to partner with KEMRI or even come here to do their own work. I certainly didn’t have a good grasp on the lab facilities prior to working here and I cannot be the only one. Plus back home people have this misconception that if a lab isn’t state of the art, that the science conducted is sub-par. But fancy equipment isn’t as important as good scientific questions and experimental design. Eight color flow cytometry can answer A LOT of questions if you design your panel well and have the right samples. And boy does KEMRI have all the right samples for scientists like me.


As stated in my last post, it is beyond weird that we just take these samples and run back to the US to study them. Why do we do that? Or I guess the better question is why don’t we study them here? Why not conduct science in a place where the results actually matter? Why not bridge the gap between the patient population and the bench work? I fully admit that I’m being a huge hypocrite in saying this because in fact I could not do my 13-color flow assay here, but there are a lot of things I CAN do for my project. During this trip I ran 18 ELISA plates to quantify antibodies against the worm I study. There was a moment when I was prepping plasma for a plate and a new sample came in from a study participant pertinent to my assay. The lab techs aliquoted off some plasma for me right then and there and continued on with their day. Easy as that. No freezing. No waiting for enough samples to batch in a shipment. Furthermore, while the results of this assay will be a blip in a paper when I graduate, they matter tremendously to the scientists and community here. I briefly presented my results regarding discordant diagnostic results during seminar last week and it stirred up quite a discussion between the various teams here.

I get that there are challenges in conducting certain experiments here, especially since there are issues with the supply chain and government corruption (more on that later). I concede that not everything can be done on site, but there is always a happy medium. My boss has done a great job at finding that medium. While she has a majority of samples shipped back to the states, she leaves what she can here in Kisumu for the Kenyan scientists to conduct their own experiments. She makes a point to leave at least two vials of cells from every participant here, even if there are only two to begin with. She also works with the students here to help them develop and execute masters and PhD thesis projects. This way some of the work and expertise always stays local.

This is so important because it builds capacity at places like KEMRI. By physically basing science here, it empowers local scientists here to take agency over their work. It trains these scientists in new techniques which can then be passed on to the next generation further building the scientific community. Increasing capacity in turn entices more people to base their studies here, bringing in money, supplies and expertise from around the world. And so the cycle repeats.

We shouldn’t treat KEMRI like it’s a post office. It’s not. It’s a fully functional scientific campus. And more importantly it is full of people ready and willing to work towards the same goal we (presumably) all have- to improve human health and eradicate nonsense like TB.


When I was little, I was pretty much a bubble child. I was allergic to grass, most pollen and the bougainvillea growing on the side of my house. I was also lactose intolerant, had chronic migraines, was horribly motion sick and got croup on the reg. Needless to say, I stayed indoors a lot. It sounds like a pretty depressing childhood but I’m not mad about it. I read like crazy and got to watch a lot of movies with my mom. We had a particular fondness for disaster films. I’m talking Dante’s peak, The Core, Airplane, the entire Resident Evil franchise. We did not discriminate. But the one that stood out was (I’m sure you can guess) Outbreak!

I freaking LOVED that movie as a child.  I wanted a monkey and a hazmat suit like it was nobodies business. Looking back, perhaps I didn’t quite understand the role of the monkey in that movie very clearly, but hey I was young. And the quote that opened the movie:

“The single biggest threat to man’s continued dominance on this planet is the virus” – Dr. Joshua Lederberg biologist and Nobel Laureate

Chilling to this day.

So of course when it came time to write my graduate school applications to immunology and microbiology PhD programs across the country, it also served as the opening line of the personal statement. I’m not even kidding. This was the first paragraph of my Emory statement

“I still remember the opening quote from Outbreak: “The single biggest threat to man’s continued dominance on the planet is the virus. − Dr. Joshua Lederberg, biologist and Nobel laureate.” The idea that something like the flu could wipe out mankind was powerful and something about it struck my eight-year-old psyche. Growing up in a household full of books and movies, I remember reading Ill Wind, and watching Outbreak and being fascinated by microbes and disease. I didn’t know exactly what I wanted to do, or even what I could do, but I knew that I wanted a HAZMAT suit. Now, having the same conviction I had at twelve, I have gained a much better understanding of the biomedical field and have two fundamental objectives for my scientific career, both of which necessitate my continued education.”

I saw it fitting, therefore, to have half of my sign in the March for Science be dedicated to the concept that first inspired my love of science.


The idea that a tiny little organism can bring about the destruction of a supposedly superior species is insane. But what is vastly important to understand about a microbe bringing down the human race is that a microbe causes destruction with no ill will and often for no personal gain. 

The objective of a microbe is to survive, replicate and transmit itself to another host in perpetuity. So when a microbe causes intense destruction in a host, it is often to the detriment of the microbe itself. Something like the Ebola Virus is so destructive to the human body that it burns through a population. Historically, this happens so fast that outbreaks can often be self contained and are therefore, counterproductive to the goal of the microbe, to spread indefinitely. A perfect pathogen is one that completes it’s “life cycle” with little or no damage to a host. (Like TB, just saying.)

A microbe doesn’t have a brain. It doesn’t have emotions. It has no desire to kill you. It has no master plan to dominate the earth. It can’t listen to reason and choose amongst a set of alternatives. I call microbes smart and sneaky because I revere them, but not because they have consciousness or choice.

Humans, however, do.

We have reason, logic, and rational thinking. We have love, empathy and altruism. And still we continue to make choices that sow the seeds of our destruction.

More than ever, I feel as if we will be the own cause of our decline on this planet. And so I edited my sign for the march.

“The single biggest threat to man’s continued dominance on this planet is the virus OURSELVES” – paranoid grad student fretting about the future of science

As I have watched the relationship to truth, data, and reason deteriorate, I wanted to use my voice in the March for Science to remind people that by choosing to ignore science, we are ensuring our own demise. It will be no ones fault but our own if we are no longer sustained, if we are no longer safe, if we are no longer dominant on this planet. It will not be Ebola or Zika or Measles that will doom us. It will be us, and our greed and our fear and our stubbornness.

After all, every disaster film starts with a scientist being ignored.

We are all doomed. Everything is toxic.

We are an extremist society. We diet. We binge. We fear vaccines. We love viagra. We won’t touch gluten. We pop antibiotics like candy. At some point we decided that we know better than trained professionals. So we self diagnose. We self medicate. We classify any substance we don’t know as “toxic” without evidence and sometimes in spite of overwhelming evidence to the contrary (seriously Vani Hari, go away).

To be clear, “toxic” is an adjective that encompasses not only the substance itself but also the dose and route of exposure. If you want to call something “toxic,” you have to be specific about all three factors. I mean, water can be toxic if you consume too much of it! I know that sounds like bullshit, but it’s totally real (1). So be careful before you casually toss out the word “toxic.”

As an advocate for science literacy, I fully support people’s efforts to be aware of and understand the items they put in their bodies. Unfortunately, many people only take the time and effort to do the first part. They scrutinize ingredients in food and medicine, but don’t actually know what those ingredients are or what they do when they enter your body. They google thoughtlessly and reverently, sifting through thousands of hits trying to find answers. But when you treat Google like God, sometimes you end up with bad answers.

Imagine this scenario: You’re at your crunchy neighborhood grocery store looking for a sweet fix. You read the ingredients on the back of an ice cream container and see polysorbate 80. Wait, WHAT? What is that?? It could be toxic! You quickly google it and someone, somewhere has decided it’s bad for you. So you stop eating ice cream forever.

How tragic would that be!? No more ice cream? Ever? No thank you. I’ll just be over here enjoying my toxic ice cream!

But that’s because I know what polysorbate 80 is and that it isn’t toxic… Actually, if I’m being honest I totally didn’t know what it was prior to writing this article. BUT I knew what to google and where to look for pertinent information. Now I usually go straight to PubMed (basically google for scientific papers) for my information because I am a masochist and like to read primary scientific papers with data and methods and stuff. For an easier to read, yet trustworthy source for vaccine information, I recommend sites that are affiliated with pediatric hospitals and organizations. The Vaccine Education Center  (part of the Children’s Hospital of Philadelphia) is one of my favorites. I also love the journal the American Academy of Pediatrics puts out.

So yes PLEASE ask questions. Be skeptical. It’s your body after all! But perhaps consider the answers and sources a bit more critically before crying “toxin.” And since the chemicals in vaccines get called toxins on a daily basis, I figure why not start there. [Note: I will only be discussing the acute toxicity of the components. Come back for the long term stuff.]

Artwork by Maddie McCormick

If you are really curious, you can get the full list of ingredients and processing specifications for every vaccine from this website. But each insert is pretty hefty and I’m sure most people really don’t want to read them because most people are not super nerds. So for all the normal people in the world, here is a more simplified list of ingredients utilized in vaccines.

Interestingly enough, if you go onto some of the anti-vax websites (here is one for kicks) and look at their discussion of vaccine ingredients, they will often pull that second document up as if it’s proof of something shady. They then go through all the nebulous items (amorphous aluminum hydroxyphosphate sulfate, anyone?) and try to convince readers of how dangerous each one is. To be fair, some of the references are legitimate scientific papers. Some of the information is even true! If they weren’t so extremist and fear mongering, I’d actually give them a gold star for effort. But when dissecting their arguments, it’s clear that some of the writers have no idea how basic chemistry works. So I’m going to go through the ingredients in childhood vaccinations based on what purpose they serve and address the controversial items along the way. [Note: I will not discuss the flu vaccine ingredients since the vaccine changes every year]

All the chemicals and stuff in vaccines can be divided into two categories:

  1. Items used during the creation of the vaccine backbone.
  2. Items added to the final vaccine product

Items used during the creation of the vaccine backbone.

I’ve already discussed all the different types of vaccine backbones. As you may guess, each one is created with a slightly different method. Despite these differences, every vaccine goes through a purification step that removes everything but the actual vaccine itself. This means that most reagents used in the production of the vaccine backbone never make it into the final product (2)! Yes, I’ve just said the same thing twice. It’s that important. It’s quite possibly the most important thing to take away from this whole article. Such ingredients are mentioned for full disclosure in case a bit slips through all the processing steps. But if they are present, it’s in tiny undetectable “trace amounts” that produce no effect biologically (34). These ingredients serve three main purposes: to grow the microbe, to wreck the microbe and to purify the microbe.

  1. Grow the Microbe

Food for the bug (Any item that has the word media, cell, yeast, or egg in it). Every vaccine starts with some sort of living entity. Viruses are grown in mammalian cells or, in the case of flu, chicken eggs. Proteins are made by cells (often yeast, although HPV is done in insect cells which is weird). And of course bacteria are bacteria. In order to keep something alive, you need to feed it. Food for cells is always some sort of “media” (sciencey word for a liquid full of nutrients- vitamins, carbohydrates, etc 5). Occasionally this media is supplemented with some sort of animal blood serum (Not as gross as it sounds, it’s just more proteins and what not). All of these things are completely natural biological products. Often times they are human derived products. If you think about it, microbes infect animals so that’s where they want to live. If you want to keep a microbe alive while you are making a vaccine, you need to use animal products to do so. You need to mimic the microbe’s natural environment.

Now, some people have moral objections to the use of human generated cell lines and cultures. I don’t understand it, but I respect ethical stances when they are consistently held. If you are one of these people, then you do you dude. But you should probably avoid all other medical treatments, particularly ones for cancer because they too were produced and tested on human cells.

Another concern I’ve seen in response to the use of mammalian cells and products is the fear that without blood typing, a child could develop symptoms similar to serum sickness or a transfusion reaction (claimed here). This happens when your immune system attacks a mismatch in your blood stream because it looks foreign (6). There are two main reasons why this fear is silly. One- All this stuff is removed. If anything remains, it’s usually only protein and it’s not enough to cause a reaction. Two- vaccines are not administered intravenously (more on that later) so they won’t be in your bloodstream to cause a reaction in the first place (7).

Antibiotics are used to reduce contamination from outside sources. You only want your favorite microbe in the mix at the end. Anything else could compromise the vaccine. Since bacteria and fungi are present in the air, creating a sterile environment is too challenging. Thus antibiotics are used to prevent the unintentional inclusion of extra microbes. They are a bit harder to purify out at the end of this phase so you’ll see antibiotics in the inserts quite a bit actually. Only drugs that have been approved for use in humans are used though, so the only concerns should be allergies to medications and even these are unlikely (8).

Salts are used to regulate the pH of the growing environment. Biological systems require a very precise pH (usually 7ish which is neutral) in order to stay alive. Too acidic, things die. Too basic, things die. God forbid, you accidentally kill your microbe before the appropriate time. And since salts are quickly modified by the growing environment to become harmless elements (much like table salt dissolves in water) they are non-toxic.

  1. Wreck the Bug

Chemicals such as glutaraldehyde and formaldehyde allow you to kill microbes for inactivated and toxoid vaccines.

These chemicals get discussed amongst the vaccine hesitant allllll the time. I’m like 90% sure this is an ick factor thing. Yes, formaldehyde is used in the processing of dead bodies in mortuaries, but really it isn’t as gross as you are probably thinking. Formaldehyde is used in A TON of products from shampoos to mouthwash as a sterilizing agent. In other words it’s used to clean things and make sure there are no live organisms in it. Duh that’s why people use it to kill microbes for vaccines (9).

Of course aside from the ick factor, there is also a great deal of concern about the safety of using formaldehyde. This is partially because the International Agency for Research on Cancer has deemed it a suspected carcinogen (10) and partially because of the side effects listed on the material safety data sheet (MSDS).

Please for the love of science and all things beautiful in the world, DO NOT use MSDS sheets to get your information about chemicals. They will just scare you. MSDS sheets go through all the physical data including molecular weight and specific heat, as well as all the health cautions for every chemical ever. They prepare scientists for every possible exposure to a chemical they could possibly have. They are meant for people like me in moments when we accidentally dump formaldehyde on our faces. They are not meant for the general public to scrutinize the tiny amounts present in their food, cleaning supplies, toiletries and medicine. Just to emphasize this point, here are the MSDS sheets for formaldehyde and acetic acid (commonly known as vinegar). Notice that they receive the same number for their overall health risk. They even have a lot of overlap in possible acute health hazards. Don’t even try looking at the one for alcohol. The possible chronic health effects are enough to keep anyone sober. But again these are the warnings for people in laboratories!

Now I’m not going to sit here and tell you that these chemicals can’t be dangerous, because they can. However it’s dependent on the dose and the way you were exposed.

For example, I work with a version of formaldehyde in lab and we have to be in a special hood that filters the air to prepare the diluted solutions we use. This is because A. I’m working with large quantities (I’m talking grams (plural) of the pure form and liters of a 10% or 4% solution) and B. inhalation is the route of exposure that will most likely result in adverse effects, such as cancer (11).

In contrast, vaccines contain less than .5 mg (DTaP) or .02% (Polio) formaldehyde and it goes nowhere near your airways. I’m sure that still seems like a shit ton to put in your body, especially a baby body, but you produce about .2 mg/mL (a normal infant has about 1.1 mg circulating) in your own body at any given time (12). I mean you could potentially be exposed to more formaldehyde from your mouthwash, makeup, or ambient air than from a vaccine (13).

Detergents allow you to break apart cells that were growing your virus or proteins. These are particularly necessary in subunit and conjugate vaccines. The detergents scientists use are a bit stronger than those used in your laundry or dishwasher but they are still completely safe.

  1. Purify the Bug

First you remove your vaccine backbone from the environment you grew it in (aka everything we’ve talked about thus far). That’s easy for things like cells and debris (from breaking open a subunit vaccine for example) since they are so much larger than the vaccine itself. You can use a physical filter to remove them.

For the smaller stuff you can use chemicals to remove other chemicals. I know that’s a super weird concept to wrap your head around and I’m seriously banking on people either remembering high school chem lab or being heavy drinkers with this one. If anyone has done a Cement Mixer shot, you might know what I’m talking about. When you add lemon juice to Bailey’s, the cream in the Bailey’s starts to curdle. The shot gets chunky and nasty within like a minute. That’s because the acid (a chemical) causes the casein (a protein/chemical) to aggregate into chunks. Yum. Anyways, biologists use chemicals like alcohols and ammonium sulfate to clump things in the vaccine mix which can then be filtered out just like the bigger stuff.

Items added to the final vaccine product.

In other words, anything that is intentionally included in the liquid that you get shot in the arm with. These compounds ARE in the vaccine in defined concentrations and play a variety of roles as listed below.

Adjuvants are added as a way to alert your immune system to the presence of danger (the thugs and fire in my car analogy). If you see any compound with “aluminum” in it, it’s an adjuvant.

Because adjuvants are present in many vaccines, a great deal of concern has been raised about aluminum toxicity. And if you read any anti-vax website, upon first glance, you can see why. They do a lot of impressive (wrong, but impressive) math about weight and tolerance and the amount of aluminum in a vaccine, and come out at the end with this crazy number suggesting that the Hep B vaccine doses your baby with 14 times the allowable amount of aluminum. Now that is a scary number! It’s also completely irrelevant when you consider that the FDA guidelines they reference for their calculations are for IV aluminum toxicity (14). That means that every single anti-vax website I’ve looked at is operating under the impression that vaccines are delivered into the bloodstream, when in fact they are delivered intramuscularly (15). I completely understand how someone not well versed in science or medicine could confuse this. A needle is in fact jabbed into your arm and a liquid is squirted into your body. I bet if I took a bunch of random people off the street, at least a few of them would have never even contemplated the difference. If, however, you are claiming to understand the science of vaccination then you should at least understand the route of administration.

Ironically, the dose of aluminum present in vaccines is not acutely toxic because of the route of injection. Slow release from the site assures that the level of aluminum in the bloodstream stays well below the allowable level in infants. (1617). Furthermore, just as with formaldehyde, vaccines are a negligible source of aluminum in the grand scheme of the world. There is more aluminum in baby formula than in vaccines, even when you consider multiple shots in one sitting. As far as long term side-effects, well that’s a topic for another day.

There is also a lot of buzz about adjuvants causing “unnecessary” side effects. For example this anti-vax website has quotes from doctors stating their concerns about certain vaccine ingredients. With regards to squalene (an adjuvant) one doctor’s concern is that “the body identifies [squalene] as a threat and creates antibodies to attack it.” Well, yes. That’s the point you idiot. Since the purpose of adding an adjuvant is to stimulate the immune system, stimulating the immune system is also a side effect of the adjuvant (18). Often, people will notice swelling at the injection site (especially with a tetanus shot). This inflammation is a hallmark of local immune activation and is actually a good sign (19). Similarly, others will develop a fever or symptoms similar to allergies as a result of immune activation from adjuvants. I think a lot of people don’t understand why adjuvants are necessary and so they consider them a superfluous danger. Really they are more of a necessary annoyance.

Emulsifiers  like polysorbate 80 and polysorbate 20 keep things mixed. Just like oil and vinegar separate in salad dressing, vaccines have components that separate over time. And just like salad dressing needs to be shaken, vaccine manufacturers use emulsifiers to keep vaccines mixed. This is absolutely critical so that each vaccine dose has the correct proportions of each item. They are also totally safe (20). So safe that they are somewhat ubiquitous in household items, like the ice cream I mentioned in the very beginning. In fact they are in much higher doses in ice cream than they are in vaccines. So cheers to ice cream and remaining HPV free.

Preservatives/Stabilizers maintain the shelf life of vaccines. Vaccines are much more complex than let’s say, ibuprofen, which is just a chemical. Ibuprofen can sit on your shelf for ages without degrading into something else. Vaccines on the other hand contain biological components as well as chemical components. Think of it like soup. If you made a pot of soup and then left it on the counter, eventually it would no longer be edible. It might grow mold or the carrots would disintegrate or the broth would evaporate. You could put the soup in the fridge and that would make it last a little longer. OR you could can the soup and put a bunch of chemicals and preservatives in it and then it could remain soup through a nuclear fallout. Preservatives and stabilizers keep the vaccine in the exact form it was manufactured in throughout processing, packaging and use. The two biggest issues people have with these ingredients are the use of amino acids (which is bizarre) and the use of thimerosal (which is complicated).

The idea that the amino acids in vaccines will make your baby develop an autoimmune disorder is a fascinating myth (claimed here). The two thoughts that form the foundation of the argument are actually true individually. The first is that our bodies don’t make all 20 amino acids (building blocks of protein) so we have to get some of them (essential amino acids) from food (21). The second is that if proteins enter our bloodstream before we eat them our body will recognize them as bad and will mount an immune response (this is actually only kind of true and I’ll probably write an entire article on it because it’s rad). However when you put the two together it doesn’t support the argument that vaccines cause autoimmunity against essential amino acids. Babies receive all 20 amino acids within the first days of life from breast milk or formula (22). Like seriously, oh my god, what are you doing to your child that they have not digested all 20 amino acids before they get vaccinated? Also, as discussed before, vaccines aren’t delivered into your bloodstream (15). So it’s a moot point. Or a moo point if you are a Friends fan.

And then of course there is the dreaded thimerosal. Okay first off, everyone needs to calm down because thimerosal is only present in a hand full of flu shots, one brand of mening shot, and one brand of DT shot. If you don’t want to deal with thimerosal, you can easily avoid it. Second, thimerosal isn’t the same thing as mercury; it is a mercury containing compound. Third, there are a lot of different kinds of mercury and they are not created equally. Fourth…. actually I’m just going to stop. I will talk about thimerosal on another day when I discuss the Andrew Wakefield/Autism controversy.

As you can see, there’s a lot to consider when you break down each vaccine into its components. What’s necessary? What’s a risk? What and who do you trust?

It’s important to keep in mind that anti-vaxxers are not the first people to question the ingredients and safety of vaccines. Every drug that you can get your hands on (legally) in the United States has been rigorously tested by multiple organizations for safety. This isn’t the old days where I could just borrow the neighbor’s kid and shoot him up with smallpox. So when someone claims that they know more than the thousands of scientists, manufacturers, doctors, nurses and government employees who work together to produce and approve vaccines, it’s because they have an inflated ego and an overzealous googling habit.

And when I say I trust vaccines, it’s because I trust the data behind their creation. Are they perfect? No. Can they be improved? Duh. Is it worth it? To me it depends on the shot. I personally don’t get the flu shot (mostly because I’m lazy), but you can be damn sure that I’d take the rabies shot in a heartbeat if necessary.

And I think that’s where I most differ from the anti-vax community. It’s not because we have different opinions about vaccines. It’s because I am not an extremist. I do not claim that everything in vaccines is 100% safe for 100% of people. Every human body is different. It is wildly irresponsible to make claims like that. You should ALWAYS ask questions before taking ANY kind of medication.

So if you want the truth… Everything in vaccines can cause adverse effects. Formaldehyde can cause cancer. Aluminum can cause inflammation. Egg proteins and Antibiotics can cause an allergic reaction. Acids can melt your skin. Ethanol can cause liver failure. Sucrose can cause obesity. Salt can cause dehydration.

But at least we won’t die from Tetanus.

Kill It. Maim It. Mimic It.

Artwork by Maddie McCormick
Artwork by Maddie McCormick

In my field, stories of famous scientific discoveries are like childhood fairy tales. Ask any immunologist and they can tell you the one about Jenner, the milkmaids, and the neighbor boy (wow, that almost sounded dirty).

Jenner notices that local milkmaids who had had cowpox never seemed to get smallpox. He reasons that cowpox is just a less dangerous version of smallpox and that maybe your body learns to recognize the pox-causing agent by being exposed to cowpox. So he takes some gunk (that’s the technical term) from a cowpox pustule and jabs the neighbor boy with it. He then exposes the neighbor boy to smallpox and lo and behold the boy doesn’t get sick.

And there you have it, the beginning of modern vaccination. These days, vaccination has a bit more finesse to it. However the same basic principle still applies. You take a dangerous microbe, find or create a less dangerous version of it, and give that version to someone. In this way you can teach the immune system to recognize the dangerous microbe.  More specifically, you are teaching your immune system to recognize parts of the dangerous microbe called antigens.This recognition is called immunological memory and it allows your body to fight infection quicker and smarter (1). It’s the reason you only get chicken pox once (well, if you are lucky).

To be successful, a vaccine must strike a very delicate balance in the human body. On the one hand you want your vaccine to really trigger the immune system. Your body is constantly interacting with microbes. Most of these are completely harmless and your immune system has a way of realizing this and giving those microbes a free pass. The technical term is called “tolerance.” If you make your vaccine super wimpy then your immune system will think that it, and anything that looks like it, are benign and learn to tolerate them. If this happens, you will be totally screwed if you get the scary, dangerous version later because your immune system won’t care (2).

On the other hand, you don’t want to risk actually getting sick from the vaccine. If the microbe isn’t wimpy enough, then you run the risk of actually developing symptoms from the vaccine itself, and that’s no good either!

With the progress we have made in modern medicine, this balance can be achieved in a variety of ways. All vaccine types, however, utilize three general strategies to make the microbe wimpy. You can kill it, maim it, or mimic it; each has its merits and its drawbacks.

To illustrate this, I’ve decided to get fancy and use an extended metaphor of a car accident…

Sometimes cars (microbes) cause car accidents (disease). Not all cars do, but sometimes a car is just too fast or powerful (a pathogen) and thus wreaks havoc on the road. In order to prevent car accidents, we are training the police (your immune system) to recognize the overly aggressive cars. To do this, we are presenting the police with a broken down version of the super aggressive cars (vaccine). The only catch is, we aren’t telling the police we are doing this (3).

Kill It (Inactivated or Toxoid Vaccines)

Artwork by Maddie McCormick
Artwork by Maddie McCormick

1. Inactivated Vaccines consist of a whole microbe that has been killed with chemicals, heat, or radiation. 2. Toxoid Vaccines are similar, except that instead of a whole microbe, only the toxin from the microbe is being destroyed. This is always achieved with chemicals (4).

Pros: Aside from the chemicals used, this vaccine platform is really safe. It cannot cause the disease that the original microbe can cause because it’s dead.

Cons: It’s pretty wimpy so you must often combine the vaccine with immuno-stimulatory components known as adjuvants (5) so you don’t develop tolerance. The adjuvant tells your immune system that something foreign and bad is present. Thus when your immune system finally “sees” the vaccine with the adjuvant, it just assumes that they are both bad.

I equate this first strategy to taking a car and then removing the entire engine. It cannot move; therefore, it cannot cause accidents so it is safe to put on the street. It also clearly still looks like a car, so the police will recognize it if they ever see it again. The only problem is that since we took the motor out, upon first glance the police will have no idea the car is bad. It’s not doing anything crazy, so how will they know that they are supposed to remember it? The solution is that we put Lord Voldemort next to it (an adjuvant) who lights some nearby storefronts on fire to capture the police’s attention.

Maim it (Subunit, Conjugate or Live Attenuated Vaccines)

Maim It.
Artwork by Maddie McCormick

3. Subunit Vaccines literally just consist of antigens (usually proteins) that are normally produced by the microbe but are no longer attached to a living or dead microbe. You can do this in one of two ways. You can grow a lot of the microbe and then cut it up into tiny pieces and purify out the proteins you want. Alternatively, you can teach other cells to grow the protein for you and make mass quantities of it (4).

Pros: They can direct your immune system to an exact part of a microbe. For example, you can make sure that your immune system really efficiently recognizes the outside of the microbe or another feature of the microbe that doesn’t change over time. It’s also ridiculously safe because the proteins are no longer attached to a microbe.

Cons: Proteins are just proteins. You have to toss an adjuvant in with this kind as well, to get the immune system revved up. This is where a special subset of subunit vaccines called 4. Conjugate Vaccines comes into play. Conjugate vaccines link the aforementioned subunits to something the immune system already knows is bad, like a toxoid (4).

This kind of vaccine would be the equivalent of taking a dangerous car and cutting it up into pieces. Then you would take the really distinctive and really important pieces, like the hood and the engine respectively, and spread them all over the side of the freeway. Not as subtle as the silent whole car, but still a little too subtle to catch the attention of the police. So then you set it on fire and it becomes a conjugate vaccine.

5. Live-attenuated vaccines are made from microbes that are, as the name suggests, alive but weakened to the point where they cannot cause disease. There are many ways to do this but the general idea is to remove or mutate genes that make the microbe dangerous. The only issue is that when you are mutating genes, sometimes you have no idea whether or not you are actually creating a legitimately safe microbe (4).

Pros: It creates the absolute best immune memory. Because it is still alive, it triggers the immune system in a very natural and robust way. Because the immune response is so good, sometimes you can get lifelong immunity to microbes with just one dose.

Cons: To quote Jurassic Park… “Life finds a way.” You always run the risk (it’s a tiny risk, but it’s there) with live-attenuated vaccines that somehow they will mutate back to their disease-causing state before your immune system clears them. For healthy adults this is highly unlikely. Children, the elderly, the immunosuppressed, etc. however, take longer to clear vaccine from their bodies. This gives the microbe a longer window to “find a way.”

This one is a little bit harder to compare to a car, but I will try. Imagine you throw a wrench into the car. Your car can’t cause a car crash if there is a wrench in the engine because it can’t really move. Yet somehow you are still able to turn it on, flash the headlights and putt putt down the street in neutral with the engine smoking. This is definitely going to catch the attention of the police so they will for sure remember the car. There is also, however, the chance that the wrench will wiggle its way loose while rolling down the street and then the car will be able to go off and cause an accident. This chance is slim, but real. So you toss a few extra wrenches in the engine just to be sure.

Mimic it (Recombinant Vector Vaccines)

Mimic It.
Artwork by Maddie McCormick

6. Recombinant Vaccines make a living, wimpy microbe (that’s the vector) look like it’s a bad microbe. To do this, you mess with the wimpy microbe’s DNA so that the outside of it resembles a dangerous microbe. The important part is not to mess with it too much, so that you don’t turn the wimpy microbe into a dangerous microbe (4).

Pros: The microbe used is in fact alive so it does stimulate a natural and robust immune response. But since it has no way of truly becoming the full-fledged, dangerous microbe that it’s pretending to be, it’s way safer than a live-attenuated vaccine.

Cons: This type of vaccine can be somewhat confusing to the immune system because you have both wimpy parts and dangerous parts. Your immune system may not know what to remember. Additionally, your immune system could recognize it for what it is (wimpy), clear it, and not remember it at all. Scientists are still trying to sort that issue out which is why these are mostly still experimental.

This is like taking an old station wagon and dressing it up to look like a race car and then having it drive down the freeway slightly above the speed limit. Underneath it all, it’s still a station wagon and isn’t going to terrorize the streets. But it looks big and bad and so the police think it’s big and bad and make note of it for later.

So where do all these vaccine backbones rank in terms of safety? I wish there was a simple answer to that. The biggest safety concern in vaccination is that a patient will develop the disease that the vaccine is supposed to protect them from. This can happen for one of two reasons: either the vaccine wasn’t potent enough or the vaccine itself caused the disease. The first is more of an issue of efficacy, while the second is more an issue of risk. Since these two reasons are very much dependent on the starting microbe, it’s hard to discuss the efficacy/risk balance of the different platforms as a whole. You almost need to do it vaccine by vaccine.

For example, within the most controversial type of platform (live-attenuated) you have a range of vaccine safety. The live-attenuated vaccine for yellow fever is considered the gold star among vaccines. It is highly effective but without the risk of developing yellow fever itself. And to be perfectly honest, biologists are still not certain why it is so amazing (6). In contrast, while the live-attenuated poliovirus vaccine is equally as effective (with just one dose, you can get full protection from poliovirus disease) there are cases of people developing polio-like disease from the vaccine itself (7). These cases are rare and far outnumbered by those who are protected, but they are real. Thus, live attenuated vaccines are highly effective but can have variable levels of risk.

What it really comes down to, as both the creator and the consumer, is what level of risk you are willing to take to get protection. Just know that, as the consumer, there are so many organizations that have pondered that question before you (8). Because of this the risks of vaccination are dramatically, comically low compared to the benefits of protection.

Vaccine Platform Chart
In bold are the recommended childhood vaccinations. [Note: some of the subunit vaccines will have “recombinant” in the name but it has a different meaning in that context. HPV can be considered a subunit or a recombinant vaccine depending on your definition of vector]

TB or not TB? That is the question.

11041415_10152771060904072_1424566537_nMy mom checked into the hospital towards the end of February for a somewhat routine procedure to remove a mass from her lung. At least that’s what we all thought. The two weeks that followed, however, might as well have been pulled from the script of a prime time medical drama (think House not Grey’s Anatomy). For the sake of science I will only recount one of the storylines I found myself a part of. I give you the very real human drama of TB quarantine

The Prelude

By the time this story starts, my mom had had “pneumonia” off and on for about 8 months with no help from antibiotics.

Now here is the first bit of science… “Pneumonia” is really just a vague medical term for crap in your lungs. You can get “pneumonia ” from bacteria, viruses, or even fungi (1). So trying to diagnose what might be the cause of the pneumonia can be pretty difficult, especially when broad-spectrum antibiotics (which should kill most of the causative agents of pneumonia) don’t work (2).

Since her primary care physician could not figure out why my mom hadn’t been able to shake the cough and relapsing pneumonia, she ordered a chest x-ray. The chest x-ray showed a non-trivial mass in my mom’s lower right lobe. At this point in time, we were all nervous (read: in a fucking panic) about what the mass could be so I joked that she probably just had a hunk of bacteria in there. I actually said the words “It’s probably just TB (tuberculosis 3), don’t worry” in an offhand, tongue-in-cheek way. Following the X-ray, my mom was referred to a thoracic specialist. He offered to do a biopsy of the thing so she could make an informed decision. My mom responded she didn’t care what it was and promptly demanded that the thing be removed. So typical. I love her for being that bold.

Fast forward about a month.

Act 1: Denial

My dad checks my mom into the hospital for surgery. Everything goes well and the chunk of lung goes off for a biopsy. Three days later shit hits the fan in really, a quite spectacular fashion. The biopsy comes back and along with the original tumor, it contains traces of acid-fast bacilli and granulomatous tissue (don’t worry I’ll explain later). Given my background in microbiology I know immediately what that means… TB. Dammit! Lesson learned: never joke about TB.

The Infectious Disease (ID) doctor comes to see my mom and asks her a series of questions about her travels and upbringing, the progression of her illness, and her most recent TB test (which had been within the year). He then declares that she probably doesn’t have TB but that until they can positively confirm or deny this, the hospital will likely mandate respiratory isolation. He then bounces out of the room.

Seeing as I am the only microbiologist in my family, and I’m pretty sure everyone blacked out the minute TB was mentioned, I start explaining all the terminology to my family. It helps that I currently work in a TB lab.

Bacilli just means rod shaped bacteria (4).

Acid Fast refers to a stain used to identify bacterial species. When you first get something like a biopsy and you are trying to determine what’s in the tissue, you often do a series of stains to identify certain cell types or organisms. Acid Fast is one of these staining methods and it is used to identify microbes in the genus of bacteria called mycobacterium (5).

The mycobacterium genus contains a lot of different kinds of bacteria, including the species that causes tuberculosis (mycobacterium tuberculosis) but the acid fast test can’t tell you which one it is (6).

Granulomatous tissue means that the bacteria were found within a granuloma which is a structure formed by immune cells. If your immune system is fighting a losing battle with some sort of pathogen, sometimes it will just form a wall around the pathogen blocking it off from the rest of your body. This is a hallmark of a TB infection (7).

nri3211-f1Not ten minutes later, nurses come in wearing gowns and masks to whisk my mom away to her isolation unit. We hear the ID doctor stamping around the ER telling everyone that putting her in isolation is ridiculous, that she doesn’t have TB, and that when the tests come back they will prove him right. I love him for his confidence because I agree. There is no way it’s TB! But no one listens to him and obviously I have zero clout in this place, so off she goes. I can’t believe it… my mom is under quarantine! I thought that kind of thing only happened in movies! My whole family has to wear masks and go through an anti-chamber to even get to her special air-locked room. They are not messing around. I don’t even go through this much prep before handling samples in lab!

By the time we are allowed to see her, my mom is in a tizzy! She is dead certain she has TB because everyone around her is treating her like a leper (ah, the irony). Now given all the evidence pointing to TB why doesn’t the ID doctor think (and obviously more importantly why don’t I think) it’s TB? It’s kind of a consecutive series of reasons which I start explaining to my family…

You can only get TB from another person with active TB disease (8). Now this is a very important distinction. About a third of the world has some sort of TB infection (9). Most of these people, however, have a latent infection. A latent infection occurs when the immune system and the bacteria reach a stalemate and the person is asymptomatic. Someone with a latent TB infection cannot spread TB (10).

For everyone’s benefit, I compare it to the whole Ebola debacle. Unless someone with a raging Ebola infection spews liquid on you, you aren’t going to contract Ebola. I get some dirty looks from some of the people nearby for being so. Apparently it’s still too soon to joke about Ebola.

My mom then wonders if maybe she had been in contact with someone with active TB. I tell her it’s highly unlikely and remind her that the doctor had asked about her travel history.

Despite the high prevalence of TB in the world at large, TB is super uncommon in the US (11). My mom has done a fair amount of traveling but never to regions like India, Southeast Asia, or Subsaharan Africa where TB is endemic (regularly detected in people 12).

So it’s like where the fuck would she have gotten TB?

UntitledShe says that a lot of the people she works with have traveled to those regions and that maybe one of them had it and gave it to her. I remind her that the person would have had to have an active infection. She asks what a person with active TB disease looks like.

Horrible. It looks horrible. Does anyone remember that old-timey disease “Consumption” that killed Val Kilmer in Tombstone and Nicole Kidman in Moulin Rouge. Well that’s TB! You lose a bunch of weight. You look pasty and sweaty all the time. You feel fatigued and sometimes faint unexpectedly. You have a raging fever and cough and when you cough, it usually contains blood. Yikes. (13)

Now my mom works for a prep school in the area so I’m pretty sure someone would have noticed a teenager falling over in PE and hacking up blood in Algebra II. If nothing else, one of their overbearing parents would have definitely realized something was wrong.

My family starts to relax a bit and trust me when I say it’s not TB. So much so that when the night nurse comes in wearing a full blown gas mask and trying to convince my mom she has TB, she is ballsy enough to tell him to go check the chart again. Atta girl!

The following morning my mom goes in for a second surgery to have the rest of the lobe removed. Better safe than sorry, I guess.

Act 2: Despair

The next few days pass in a series of nurses and tests. The main focus is clearly recovery from the second surgery but I know that TB is hovering in the back of everyone’s minds. The isolation unit is enough to remind us every time we go to visit her.

The nurses change shift every eight hours and you can tell when they happen without even looking at a clock. All of a sudden, strangers are coming by and sticking their faces in the window of the air-locked door. I feel bad that my mom has to deal with all this negative attention. Some nurses are totally cool, and get that it’s just a precaution. Others act like they are afraid of her. Some ignore her entirely. Maybe I’m just bitter but I figure they just think it’s too much of a hassle to suit up in order to treat my mom like a person. I notice her mood go up and down depending on how the nursing staff is treating her. My dad’s patience and my attitude do the same thing. It’s crazy what a big difference a nurse can make!

IMG_9366We try to keep my mom’s spirits up by having a rotating onslaught of visitors to distract her. My sister even flies back from New Zealand to surprise her! I never realized how hard it is to cheer someone up when they can’t see your face. Pretty much all our facial expressions are blocked by the stupid masks we have to wear so she can’t see us smile or laugh. My sister and I come up with the idea to sharpie funny faces on them to make it a little bit better and that does cheer her up a bit. It can only do so much though. I can only imagine what it’s like to be stuck in a dark lonely room when you are really really sick. It breaks all our hearts a little bit.

In contrast to the overly wary nurses, the doctors cannot be bothered with the precautions the hospital has demanded we take to protect everyone from my mom. The ID doctor doesn’t put on a mask when he comes to visit and the surgeon straight up opens the air locked door to come debrief her after the surgery. I love them for giving no fucks. They know it’s bullshit, just like I do. My mom actually perks up a little bit every time they visit. I feel like they give her hope!

Act 3: Anger

After those few days, my mom recovers enough to be moved out of the ICU to another wing of the hospital. Unfortunately though, she’s still being quarantined because they still have no idea whether or not it’s TB. All of us get cranky and obstinate. Why is it taking so long???

One day, I lose my mind and start stomping around the isolation unit complaining about the fact that it’s been three days since the second surgery and they still don’t know what it is. I start rattling off facts about TB’s doubling time (24 hours) and all the tests I could have done if they had only given me the sample to run in my lab. I actually uttered the words “I could PCR that shit and give you an answer quicker than this!”

My mom asks why they don’t just do the TB test that they do at her school every other year and I have to explain that that can’t differentiate between an active and latent infection. In fact the test can’t even tell you if you have a current infection at all.

The TB tests that some people get for work (like my mom because she works with kids or me because I work in a laboratory) cannot actually test for the current existence of bacteria. It makes sense, if you think about it. The test is administered on your arm and the bacteria would be in your lung. Instead, it tests your body’s immune response to the bacteria by sticking a little bit of crushed up TB protein just under your skin. If your body has ever encountered TB, it will remember that and you will have a reaction to the test. This can therefore tell you if you have ever been exposed to the bacteria but cannot tell you if you have a current infection (14).

The ID doctor comes in every day to check on my mom. He tells us that they had been trying to identify it by culturing (growing) the bacteria. This is a pretty standard way to identify something in a hospital setting. It’s inexpensive and can give you a definite identification. But it can also take weeks to get answers, especially with TB. Needless to say I’m a bit peeved. You’d think that when someone is under quarantine, everyone would want an answer just a tad bit quicker than normal! I digress…

Anyways, the ID doctor informs us that they did not recover enough bacteria in the tissue from the second surgery to do a culture. Since there wasn’t enough bacteria in the ENTIRE LOBE to culture he reasons that the infection has essentially been surgically removed. Despite this, hospital policy still requires that he disprove the existence of TB in the first place before my mom can be moved out of quarantine. To expedite the process, he sends what little material they do have to labs at Stanford to basically get a yay or nay on TB. He says he doesn’t care what mycobacterium species it is as long as it’s not TB.

The mycobacterium genus contains a lot of fun microbes. One is found in smegma (mycobacterium smegmatis)- gross I know. One is the causative agent of leprosy (mycobacterium leprae 15). Most of them, however, are harmless soil bacteria. Of these, a few cause minor disease when they get in your lungs, but most are usually cleared by your immune system (16). Doctors don’t normally treat for these species because the drug regimen to treat mycobacterium is insane. It’s 6 months of 4 different kinds of antibiotics (17). This is not only toxic to your liver (18) but can also really mess up the balance of microorganisms in the rest of your body. So if TB isn’t the reason she is sick, then no doctor would subject her to that kind of drug treatment.

So that’s good news and bad news. But mostly, it’s more waiting. And on top of all the waiting, the staff in this new wing is treating us like we are morons. With the exception of like one or two nurses, every new face is like….

“Do you know why you’re in this room?” (No. We just submit to the will of authority without thinking critically or asking why our freedom is being taken away)


“Do you know why you have to wear the mask and gown?” (Oh! Is that required? I just thought it looked cool!)

It gets to the point where all of us are so annoyed that even the sweet well-intentioned physical therapist trying to comfort my mom by telling about how she had to go to the TB sanatorium as a child bugs me.

I get so annoyed, I stop wearing my gown and then stop wearing my mask as a f@$k you to “the man”. Of course, I put them on really quickly anytime I hear someone coming, so it’s not that bold of a f@$k you, but it makes me feel better.

Act 4: The Resolution

The morning of my departure back to Atlanta, the surgeon and the ID doctor agree that she can be released. We start packing her up only to have some lady from the health department come in and tell us she can’t leave. Apparently only two of the tests for TB came back negative in the 8 days she’s been in the hospital and that’s not good enough for The State. Nevermind that the guy who studies this for a living and the surgeon who took the hunk of bacteria out of her both agree that she doesn’t have TB, this rando who just showed up gets the final say so.

My mom is so disappointed, I can feel her withdraw from all of us. We make jokes about preparing an escape and try to get her to laugh at the image of her (she’s a tiny little Filipino women with a palm tree of a pony tail at this point) running down the hall in her bright yellow non-slip socks and gown carrying an IV of drugs. Nothing works though. I can tell she thinks she’ll be stuck in this hospital forever.

I hesitate when packing and almost change my flight but in a weird way I actually feel okay leaving. She’s recovering from the surgery and my whole family is there for support so really the final hurdle is the whole pesky TB thing. Her doctors, however, have made it their mission to get her released and I trust them. They have been such badasses this whole time, I can’t help it.

I get the call two days later from my sister saying that the surgeon and the ID doctor won the pissing match with the representatives of the state! My sister overheard part of the phone call and tells me that the two doctors had an excellent, performance rational, calm discussion. Against the wishes of the health department, the hospital releases my mom to go home. She then quarantines herself. You know, just in case.

A week later we finally get the results back from Stanford. Not TB. Duh.

The Epilogue

I can joke about this now because my mom in fact did not (and still doesn’t) have TB. I can look back on the situation somewhat objectively and think about how every moment in those 13 days affected me. I can reflect on every moment of frustration, insecurity, confusion, anger, sadness, worry, etc. that every member of my family experienced. And we were lucky.

With all the health issues my mom was facing, TB was the least of our worries during those two weeks, because we were educated. I knew so much about TB from my professors, my lab mates, and my mentor at Emory. I had lecture slides I could show my mom and papers I had read to answer any question anyone had. When moments of doubt or concern rolled in, we had the resources to quiet the unsettled feeling in our chests. Those two weeks were hell and would have been infinitely worse without that knowledge.

Yes both my mom’s doctors were fantastic, but doctors can’t be there for you when you are lying in bed at night and the fear starts creeping in. They can’t follow you around to answer that one question that is gnawing at the back of your mind, distracting you from everything around you. The only resources you have in those moments are yourself and your loved ones.

People think that they don’t need to worry (and therefore don’t need to learn) about TB or measles or Ebola, because that will never happen to them. The truth is, it could. However unlikely it was, my mom could, in fact, have had TB. The bottom line is that every person needs to take an active role in their health, and part of that is staying educated. You don’t want to be learning about a disease after being hospitalized for it. Trust me.

Devil’s Advocate

I just want to preface this article by saying that I did not start this blog as a platform for science propaganda. It is meant to be a place to share information and ask questions in a casual way. That being said, with all this measles nonsense taking over my newsfeed, I did for a moment feel the need to get on my soapbox and tell everyone to get vaccinated. Your untimely death won’t count for a Darwin Award (1) if you take out a good chunk of the population with you. Fortunately though, that’s not what this post has turned into. It’s two parts tonight guys.

The 10th Man Rule

I can’t have been the only one to notice that social media has become a battleground for the vaccine debate. I have friends who tell me stories of old high school acquaintances posting absurd articles to Facebook (absurd because they aren’t well researched/written, not because of the topic itself) about vaccines and measles and the right to choose and what not. I laugh at their frustration and sit back to observe the fall-out when a full-blown war starts in the Comments section. In a recent skirmish, one girl actually said, “I’m not looking to change anyone’s opinion, and I have no intention of changing mine. I am looking for a discussion.” What kind of bizarre discussion is that? And of course that kind of response gets everyone’s blood boiling and it turns into a frenzy. Tip: Don’t mess with immunologists when it comes to vaccines. We feed off each other’s disdain and use far too many infographics.

Personally, I think fighting on Facebook is ridiculous and ineffective. No one ever cites a Facebook post as the reason they changed their minds about something this contentious. And so I don’t (read: try not to) engage in these comment wars. But there’s another less noble reason I don’t participate… I just don’t really have Facebook friends who disagree with me on this particular issue. Other issues, sure, but not vaccines. I only ever see people posting either articles about why you should vaccinate, or satirical pieces about anti-vaxxers (23) . And the truth is that this isn’t entirely a coincidence. It’s because I tend to purge my Facebook of posts and people inclined to scientific beliefs that I find outlandish. As a girl in my program said, “Posting a status about vaccines is a great way to clean out your friends list.” And as satisfying as it is, maybe I shouldn’t be deleting people from my life so easily. Then at least someone would be disagreeing with me.

Being in grad school, I am perpetually surrounded by highly intelligent people who for the most part have the same views as me, at least with regards to things like antibiotics, vaccines, Ebola, and the like. This is VERY dangerous for me. Nothing is more dangerous intellectually than being surrounded by people who agree with you.

In situations like this I am reminded of the movie World War Z. There’s this dude in Jerusalem who predicted the whole zombie apocalypse thing and prepared for it by building these gnarly walls to keep the zombies out. When Brad Pitt’s character asks him how he possibly could have believed in zombies, he tells him of the “10th Man” rule. The basic idea is that if everyone agrees on a current issue, one person is obligated to act under the premise that they are all wrong. Just in case. Moral of the story- if everyone always agrees all the time you get killed by zombies. Or in my case, you close yourself off to new information that could possibly change your mind.

Which is why I owe a debt of gratitude towards my closest friend who always plays Devil’s Advocate with me. He’s the person that sends me lists of articles from legitimate sources analyzing the dangers of vaccines (even when it pisses me off), just to make sure I know the opposition. He’s the person that believes nothing unless you put documents of data in front of him. He’s the person who will learn how to do something himself just to make sure he can appropriately assess other people’s claims. So when I talk about wanting to write an article about how everyone who doesn’t want to vaccinate should be moved to Molokai with the lepers (4) and see how long they last, he points out MY bias. Because of course I’m biased! Everyone’s a little bit biased. Okay, a lot biased in my case. I can’t help it. My hopes and dreams in the world are built on vaccines.

Notice the label across the first person’s forehead… Prejudice and bias are dangerous from both sides of the debate.

There’s a quote that I love from Sam Harris that I always use to write off the anti-vax community. He says “If someone doesn’t value evidence, what evidence are you going to provide to prove that they should value it? If someone doesn’t value logic, what logical argument could you provide to show the importance of logic?”

I remind myself of this quote when I encounter people like the girl I mentioned earlier who flat out admitted she wasn’t going to change her mind. She was just looking for an argument. She didn’t care how much data you put in front of her face. She had her beliefs and that was that. I tell myself that there’s nothing I can do about “them” because they don’t value evidence the same way I do. But even with the reverence I have for data, I disregard data that doesn’t support my currently held beliefs about vaccines. So I’m just as bad. Yes, my bias is probably better informed because I at least read articles and have the bio background. But it’s a bias nonetheless. And that brings me to this post.

I’ve decided for everyone else’s benefit, to go behind enemy lines. I am going to very earnestly research the anti-vax positions. And I promise to try to keep an open mind as I sift through their data. I will report back everything I find and my responses. I will also write up whether or not this new information has changed my mind in any way. It is taking every fiber of my being to refrain from adding a haughty line about how “I doubt it.” I am only human after all. But in this case, I need to be better than that.

Since promising a future article is a total cop-out, here’s something a little bit scientific to introduce the vaccine debate.

Jonas Salk is a Boss


Whatever your beliefs about the danger of vaccines, I think it’s pretty clear that vaccines do work. Not 100% of the time, of course, but they confer at least some protection to future infections. And just to open up this discussion, let’s take a look at the development of the polio vaccine as a model.

Jonas Salk, lovely man, is the scientist credited for creation of the vaccine against poliomyelitis virus, the causative agent of the disease polio (5). In 1955 he published a paper entitled “Considerations in the Preparation and Use of the Poliomyelitis Virus Vaccine” which details his study (6). In it he discusses everything from how they created the vaccine to how they monitored and assessed protection in children who received the vaccine. Here’s a VERY simple synopsis… They selected a highly antigenic (stimulates your immune system to “remember” it) strain of the virus with low pathogenicity (how badly ill it makes you). They then “killed” the virus and used the killed virus to vaccinate children with no prior exposure to any strain of the virus. They then looked at the immune response immediately following vaccination, as well as two and a half years later. They assessed immune function by looking at antibody levels as this had previously been shown to be a measure of protection against poliomyelitis virus (7).

The bottom line is that when prepared properly, a safe vaccine from killed poliomyelitis virus induced antibody levels equivalent to those seen in a natural infection. Even being an old paper, it is incredibly convincing and thorough. He had created a lot of different variations of the vaccine preparation and had good controls for each stage of preparation. He also had a huge sample size. In his individual study alone, he looked at 15,000 children. He also had the foresight to follow a subset of these patients over time to make sure the initial response persisted.

What I admire most about the paper though is how careful he is. He is careful to make sure the preparation is safe. He is careful to make sure that the same exact preparation can be made in large quantities and in other laboratories. He is careful to make sure he doesn’t overstep his research with claims he can’t support. He poses this question in his introduction

“Can durable immunity be induced by a noninfectious poliomyelitis vaccine?”

And then proceeds to fully admit that “since the ultimate answer to this question cannot be obtained until time has passed, we must content ourselves only with an examination of facts now known.”

Well time has now passed, and I think we can safely say that durable immunity can be induced. Proof of this can be seen in the dramatic decrease in polio case rates after the introduction of the vaccine. Prior to the vaccine, the US alone saw about 15,000-20,000 cases of polio each year. And while the death rates had decreased prior to the introduction of the vaccine (Probably due to the use of the Iron Lung 8), the number of infections and paralytic cases had not been markedly reduced. After the introduction of Salk’s vaccine in 1955, however, this number dropped dramatically to 2,525 in 1960 and just 61 in 1965 (9). The last true Polio outbreak that originated in the US was in 1979.


The same trend can be seen globally. After the foundation of the Global Polio Eradication Initiative in 1988, 2.5 billion children have been immunized against Polio. Prior to this endeavor 1000 children were newly infected with poliomyelitis virus every day world wide (10). As of 2013, this number has dropped to 482 new infections in the entire year (11).

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Now one could still argue that other factors (such as sanitation) have caused the significant decrease in polio incidences over the last 60 years because, after all, these global statistics only assert a correlation. When combined with the clinical science conducted by Salk and the bench work conducted by his predecessors, however, a clear causation is demonstrated.

Vaccination induces long term antibodies against poliomyelitis virus. Antibodies protect against poliomyelitis virus. Vaccination with poliomyelitis virus must then confer protection. Furthermore, when nations started mass immunizing with the poliomyelitis virus vaccine, the number of polio cases each year dwindled down to nothing. That’s a pretty strong case in my opinion.