Friendly Fire: How does an Auto-Immune Illness Happen?

I’ve written a lot now about my health journey this year, where a rare auto-immune disease almost killed me, crippled me, put my family through hell, and how I’ve spent over a year trying to get my life back together. This has been a frightening but motivating journey for me.

A picture of me in the ICU, February 2019

Many questions have hounded me over these long, trying months: What happened? How did it happen? Why did it happen to me? How do I prevent it from happening again? How can I help my friends and family avoid similarly debilitating illnesses?

I refuse to believe some diagnoses that I was just unlucky. There must be more than that. So I’ve been engrossing self at my medical records, medical textbooks, journals, studies, research, and expert opinion. So I’ve put together this post about what I think happened to me, and guidance to help you and your loved ones from suffering as I did.

I certainly Do NOT claim to be an expert on this topic, nor any sort of authority, so please do not take my interpretation as gospel. 


What happened to me? Months after I was discharged from hospital, my neurologist went through all my test and scans thoroughly and found the name for what fell me: Transverse Myelitis (TM). It’s a very rare auto-immune neurological illness where my own immune system mistakenly attacked the myelin sheath around the spinal cord and brain stem causing a loss of nerve signal control. It’s very similar to the slightly less-rare Guillain-Barré syndrome (GBS). Another report called it meningococcal encephalitis. One of my doctors said it didn’t really matter what you call it; I had a rare auto-immune neurological illness and the treatments were pretty much the same.

Illustration of the how lesions that form in the spine cause transverse myelitis

But let’s go back a little bit: What is an auto-immune illness? It’s not HIV or AIDS; that’s where the immune system is suppressed or destroyed. It’s almost the opposite. The wonderfully advanced, complicated, sophisticated, automatic system that protects us from pathogens, harmful bacteria, and infections, somehow starts attacking the healthy tissues of the human body. It attacks the very body that it is meant to protect.

Components of blood: Blood is made up of red blood cells, platelets, and different kinds of white blood cells. These cells are all suspended in liquid plasma. (image source)

One of the books I’ve read recently is “The Autoimmune Epidemic” by Donna Jackson Nakazawa. Her book, like several others I’ve read, collect evidence about the growing auto-immune disease problem, the potential causes, and reason why western medicine has been slow to catch up. She suggests that for most of the 20th century, modern medicine did not believe that the immune system could harm its host. In the early 1900’s, immunologist and Nobel laureate Paul Ehrlich published the theory of “horror autotoxicus” when put into medical dogma that it was impossible for the immune system to harm the body. It is becoming increasingly clear that this is not true.

Norman immune response vs. autoimmune disease (Illustration by Emily Roberts, Verywell)

I had/have transverse myelitis (TM), which is very rare, but there are many, many other auto-immune illnesses, and if they do have a similar cause, represent a significant portion of ALL illnesses plaguing humanity. Here is an incomplete list of some autoimmune illnesses:

  • Neurological: Guillain-Barré Syndrome (GBS), encephalitis, myosititis, myasthenia gravis, and multiple sclerosis (MS).
  • Thyroid: Hashimoto’s disease, thyroiditis, and Graves’s disease
  • Digestive: Crohn’s disease, ulcerative colitis, celiac, inflammatory bowel disease, and type-1 diabetes
  • Muscles: Rheumatoid arthritis, polymyalgia rheumatica
  • Resperatory: Fibromyalgia,  wegener’s granulomatosis
  • Skin: psoriasis, scleroderma
  • Blood: Leukemia, lupus

There’s even talk that COVID-19 is triggering auto-immune illnesses. In fact, Grammy-winning artist Christopher Cross recently acquired GBS because of COVID-19!

Not all are auto-immune illnesses are immediately fatal, but certainly debilitating, and unfortunately not yet well understood. Data collection from the John Hopkins Hospital assert autoimmune disease affects 23.5 million Americans. That makes it more common than cancer and just a little less common that heart disease.

Some of the many autoimmune disorders (image source)


Before I start talking how the immune system goes awry, I’ll briefly describe how it should work, in a very simplified way. I’m going to put some term in “quotes” because I am going to grossly oversimplify, and broadly categorize some of these very complicated functions.

Illustration of an infection (in this case strep bacteria) “hiding” in the body. Then they identified and dealt with by the immune system (image credit)

The immune system is probably the most complicated system in the human body. It automatically “detects” and “reacts” to harmful pathogens, harmful bacteria, and/or other infections. It consists of over a hundred different kinds of cells, dozens of enzymes and other chemicals, and also relies on millions of beneficial bacteria that live in our digestive system and bloodstream.

The immune organs and immune systems with three lines of defense in the body (image source)

One of the immune systems responses to an infection is called inflammation. This is actually a collection of responses where the local blood vessels and capillaries dilate, temperature increases, and all sorts of chemicals and “infection-fighting” cells make their way to the infection site. And “signals” are sent for “reinforcements” so the body makes more cells and chemical to keep fighting the infection.  Eventually, a “message” is sent by “regulatory” elements that the fight is over. Then the body “remembers” what worked so that it can use the same techniques again. So, inflammation usually helpful albeit uncomfortable, unless the “target” isn’t actually sick. 

Illustration of the inflammation response (image source)

Imagine a fire truck hosing water on a house that is on fire: The process is destructive and damaging, but preferable to letting the fire spread. But, imagine the horror if a perfectly fine house was being deluged by a fire hose! That situation is analogous to an unwelcome auto-immune response.

Imagine a fire truck dousing water on a perfectly fine house. That is analogous to inflammation in health tissues caused by an autoimmune illness.
Illustration of a healthy immune response (left) and autoimmune disease response (right)

So, what causes the immune system to cause an auto-immune response? It’s a LONG story and not well understood yet. The body reacts to an infection or mock infection like vaccine. Then somehow the immune system gets “confused.”  The confused immune system then starts attacking something else.

So, here’s another grossly oversimplified analogy: Imagine the immune system is like a security team. Someone on the team spots suspicious characters wearing a green vests and calls the rest of the team to help stop them. However, imagine the security team just finished a double shift, their coffee has run out, or for some other reason they aren’t at 100%. The security team might miss these intruders in the green vests. Or, worse, in their confusion, start apprehending anyone and everyone wearing green! This is where the immune system is mistakenly targeting the wrong, “innocent” cells.

A gross analogy of an autoimmune response. A target in a green vest is identified as suspicious and the rest of the immune system is alerted. But instead, for some reason the immune system targets others wearing green.

There are “regulatory” cells that should keep this from happening. Imagine the shift supervisor of the security team that notices that innocent people wearing green are being targeted. This supervisor would “straighten thing out”. Or, when the suspicious fellows in the green vests are gone, the supervisor could tell the team they don’t need to search for them anymore. If these “regulatory” cells where they aren’t working properly or aren’t there at all, the risk if an auto-immune illness increases significantly.

But what causes the immune system to get confused? That part is really complicated and not well understood. From this point forward, the information I’m going to present is much more speculative, theoretical and hypothetical.

Genetics plays a role. And the existing state of your immune system and its “history” is part of the story too. But since we don’t choose our genes or all of our infections over our lifetime, it’s hard to know how that contributes.

A carcinogen is the catch-all term for something that can contribute to the risk of cancer. In Donna Jackson Nakazawa’s book “The Autoimmune Epidemic” she coins the term “autogen” to categorize factors that can contribute to an auto-immune illness. There are a lot of potential autogens, but few, if any have been definitively confirmed.

Image source

Dr. Amy Myers’ book, “The Autoimmune Solution” categorizes the underlying causes of auto-immune illness as follows:

  • Leaky Gut
  • Gluten
  • Toxins
  • Infections
  • Stress

Dr. Myers’ book also goes on to explain ways to reverse autoimmune disease:

  • Heal your gut
  • Remove gluten, grain, and legumes from your diet
  • Test for heavy metals and mycotoxins
  • Find and treat infections
  • Manage your stress

Each of the above could be a long and detailed post, and if there is interest I can publish more about them and my interpretations of them.

I highly recommend anyone interested to read Dr. Amy Myers’ “The Autoimmune Solution” as a guide to treating and preventing auto-immune illnesses. Where Nazakawa’s “The Autoimmune Epidemic” reads like punchy, depressing headline news, Myers’ “The Autoimmune Solution” is like an uplifting infomercial. I can almost hear the “but wait, there’s more!” It even has meal plans, supplement guides, and recipes!


So, could a flu shot or other vaccine trigger an auto-immune illness? Yes, the CDC confirms it. In fact, the detailed product monograph for a common brand of flu shot explicitly lists Guillain-Barre Syndrome and other “immune system disorders” as possible side effects.

Excerpt from page 14 of the product monograph for Flulaval Tetra, a common flu shot. Guillain-Barre Syndrome is listed as a “Post-Market Adverse Drug Reaction”

But, a stomach bug can also cause an auto-immune illness. So could a bacteria on a fruit or vegetable that wasn’t washed thoroughly. And so could someone sneezing on you. Or mould in that old office or house. Or a pathogen in the water. In fact, there are so many potential triggers for an auto-immune illness that it seems like the risk from a vaccine is rather small. And considering that the flu causes significantly more deaths per year than autoimmune disease, avoiding flu shots for this reason isn’t very convincing.


One of my many doctors was an infectious diseases specialist. I told him how I had two stomach flu’s in the month before my auto-immune illness. In his follow-up, he said that he has colloquially noted a large correlation between stomach bugs preceding auto-immune neurological disorders. I did a little internet digging and I don’t think it’s just a coincidence.

I had a test done on my own digestive system, and found at least two undesirable bacteria in my GI tract: The most interesting bacteria of note were prevotella spp and fusobacterium spp. There is quite a lot of recent literature linking these two microbial communities to inflammatory and auto-immune illnesses. And more research continuing. I’m not even going to begin trying to explain these articles, but there are a lot of them, and they are peer reviewed and highly cited.

Prevotella copri bacteria, computer illustration. Prevotella are Gram-negative, anaerobic, rod to coccobacillus shaped, prokaryote (bacterium). Prevotella spp are generally found in the oral cavity, vagina, intestine, it can cause opportunistic infections. Prevotella copri is thought to have immune relevance in pathogenesis of rheumatoid arthritis. (Image source)

How did these bacterial get there? I don’t know. They might have been there in minute quantities all my life. Or from something I ate or drank at some point. They may have lay dormant for years. Then, when my immune system was suppressed from stress, or poor diet, or toxins, perhaps they had a chance to multiply and cause havoc. My immune system did its job and responded to this or some other infection. Regrettably, it seems my immune system got confused and also attacked something else: My brain stem.

This is the working theory I’ve come to. It’s pretty shaky and makes quite a few leaps of fuzzy logic. Maybe in 20, 30… 50 years, this will be as well-understood as cancer. But for now, this is my working theory. And at least I have some direction of how to try to prevent it from happening to me again.


So, why aren’t auto-immune diseases headline news? They are widespread, and quickly getting worse! I think there are a couple of reasons:

The first is that there isn’t really a dedicated field or “-ology” for auto-immune diseases. Until recently, the auto-immune diseases were treated by their respective specialties, for example Neurologists for GBS, and rheumatologist for lupus. Infectious disease specialists are starting to have specialized fields to study autoimmunity, but they are years behind what oncologists have done for cancer.

Another reason I suspect autoimmune diseases aren’t well know is that there haven’t been many lawsuits. We live in a litigious society, and business owners, chemical producers, and manufacturers are busy and don’t usually think about the their actions unless there are consequences. Lawsuits have made companies VERY aware of the consequences of carcinogenic products. WHMIS and GMS labels for potentially cancer-causing substances are rather ubiquitous. But, because the mechanisms of auto-immune illness are not well understood, and may involve many compounding factors, it’s hard for a suit to seek damages on a particular chemical or process.

I hope this post has raised awareness of auto-immune illnesses, and made you think about what you can do protect yourself and those you love. Years from now, we may have a much better understanding of this. But, at this point, this is what I know, and wanted to pass it on to all of you.

Home Made Bone Broth

My naturopath got me into bone broth last winter. It’s a drink or soup that contains the results of boiling bones and veggies.

It contains collagen, which seems to be in a lot of highly marketed supplements and skin-care products. It can help reduce joint pain, help fight infections and inflammation, help with digestion, and help with sleep [source]. And, I think it tastes pretty good; like all the best parts of chicken soup.

Image Source:

There are bone broths you can buy in cartons and bottles. I’ve found them to be hit and miss, and a lot of them are filled with added salt and preservatives. The most cost-effective source of bone broth we have found is a Korean superstore, P.A.T. Supermarket on Dundas Street in Mississauga.

I often use it as a base for chilly or stews. But you can also just drink it straight to accompany a meal, or as a filling snack.

I had bought some chicken thighs last week and I didn’t buy the ones that had already been de-boned. Rather than cook them with “bone in”, I decided to butcher them myself to remove the bones. To be fair, I butchered them rather amateurly and left a lot of meat on the bones. I was about to throw the bones in the compost, then thought I’d try cooking my own bone broth! And I’d like to share the experience with all of you!

I based my recipe on this one from Platings + Pairings, but the Amy Myers cookbook has a similar, really good recipe too. I used the ubiquitous Insta Pot but I imagine any pressure cooker will work.


  • 1 pound chicken bones
  • 2 carrots (chopped roughly)
  • 2 celery stocks (chopped roughly)
  • 1 shallot onion(chopped finely)
  • 2 tablespoons minced garlic
  • 1 teaspoon black pepper
  • 1 teaspoon sea salt
  • 1 teaspoon red wine vinegar (the recipe called for apply cider vinegar, which I didn’t have)
  • 10 cups of water
The raw ingredients. Not pictured, garlic, salt, and red wine vinegar

After giving a wash to your carrots and celery, chop them and add them with everything else into the pot.

Ingredients assembled! Just need to add water.

After adding the water, put it in your pressure cooker on “manual” for 2 hours at high pressure. My version of the Insta Pot doesn’t have a “manual” button, so I pushed “pressure cook”.

Set to 2:00 in the pressure cooker

After that time expires, let the pressure release “naturally.” The recipe says it takes 15-30 minutes. I was busy doing something else so 60 minutes had elapsed by the time I came back to it and the pressure had released.

Then, strain the broth through a colander (strainer).

The “solid” ingredients are separated during straining.

That left me with a bowl of fresh bone broth. Note the suspended fat in the still-warm broth. The fat had to come from somewhere, and it wasn’t the veggies! Fat got a really bad rap with the “low fat” and “fat free” craze, but getting “good fats” is really important. I’d like to think that this is a source of good fats.

Fresh, strained bone broth

Then I transferred the broth to smaller containers. I think I got about 2.5 litres out of this batch.

Bone broth sectioned off into containers. Ironically, these were containers for bone broth we had previously bought at P.A.T.

I drank the one on the left shortly after cooking. It was yummy. In retrospect, the flavour is a little thin. It could have used a bit more bones, or maybe more pepper. My wife says she likes this better than the beef bone broth we get from P.A.T.

Yummy, fresh bone broth

I left them in the fridge, and some of the fats accumulate on the top. That’s not good to eat, and worth scraping out with a spoon. The cooled bone broth is actually almost gelatinous, but can be “liquefied” again by warming it up on a small pot on the stove.

In the end, it’s a lot of time and a bit of mess to make your own bone broth, but most of it is waiting, so it’s not so bad. Will I do it again? If I have leftover bones, indeed!

COVID-19 June 2020 Update

This is my 3rd monthly post about life during the pandemic. I am surprised that the pandemic is lasting so long! I guess I naively thought that after two weeks of lockdown it would be contained. Almost two months later and many, many restrictions remain.

Below is a neat graphic about how COVID has eclipsed the bottom 7% of causes of death.

300,000+ deaths in 6 months is pretty daunting, but in context, it still is not quite in the top 10 global causes of death:

I’m not entirely sure this should have been labelled a pandemic. COVID-19 is in many countries and causing a lot of deaths, but it isn’t really affecting a high proportion of the population. It isn’t the apocalypse plague that the media portrayed it as. And, thank goodness it isn’t because this has shown how unprepared we are as a society:

  • There weren’t good stockpiles of medical supplies
  • Procedures were spotty and haphazard
  • Lots of people weren’t listening to authorities and spreading the disease needlessly!

Maybe this is the warning we needed for if (or when) something worse strikes!

It has been nice that that some restrictions caused by this pandemic are relaxing. I worry a bit that some people are getting a little ahead of themselves: They’ve been given an inch, they take a mile!

Comparing Curbside Pickup Services

Mind you, many places are limiting the number of customers, so there are lineups to get into some stores. In some ways, curbside pickup seems like a more convenient, safer, and faster. We noticed some big differences in the quality of the curbside pickup experience.

At the Home Depot, we had an exemplary experience: After ordering online, we got the notification that the product was ready for pickup. We parked in the marked spot, and there were instructions on a sign with a number to text. What followed was an automated text asking for the order number, parking spot number, then type of car. Within 5 minutes, someone came out with the product.

We had an opposite quality experience at Lowes. We parked in the marked spot, where a sign gave us a number to call. We called that number and they told us to flag down someone with a clipboard in the parking lot. Then the clipboard person took our info and went back into the store. 30 minutes later someone finally brought our product. Not impressed!

Life Updates – Full Time Dad Duty

And I’m not back at work yet, and it may yet be some time until I get there. I heard back from the Long-term disability (LTD) insurance company this month. Based on the info from my doctors, there would need to be some accommodations for my return to work. My employer is not willing to accept any of these accommodations. Not getting cleared for work does make me feel a little broken. But, I get to spend more time with my family and I don’t have to commute through the pandemic. In many ways I’m really very lucky. I know I have to go back to work sooner or later, but it could be several more months before I can actually return to work.

Completed Strava’s May walking challenge!

I have been continuing to try to get better and I have been walking a lot. I got in a pretty respectable 56km in the month of May! I’m walking about 3km per time, usually pushing my daughter in her stroller. I also got into Pokemon GO in a big way, and the stroller makes a great holder for my phone. I usually route the walks to hit many Pokestops in the neighbourhood. And when I let my daughter out of the stroller in the abandoned parks, I usually catch a couple of virtual Pokemon.

Does anyone else still play Pokemon GO? Let’s share friend codes!!

I was getting a little worried that it was getting harder and harder to wake up each morning. I had a suspicion of what it was, so I went to bed wearing my Garmin watch to measure my heart rate. Turns out my resting heart rate is a pretty respectable 52 beats per minute. Looks like the exercise is starting to show. It was closer to 100 bpm when I was in the hospital! I remember at my peak of fitness my resting heart rate was under 40 BPM, and it would freak out doctors or anyone who checked me. This low heart rate is good for me in general, but means I need some will power to get the old ticker going in the morning.

Wore my Garmin watch overnight to use the heart rate tracker. Pleasantly surprised that my resting heart rate is improving.

My wife and I are also continuing to dominate Overcooked 2. I think we’ve finished all of the levels and expansion levels. We’re working our way through beating our old high scores.

My wife’s maternity leave ended last month, but her back-to-work is virtual. It’s nice that she doesn’t have to commute or be at risk seeing anyone face-to-face. But, this puts a little more pressure on stay-at-home-daddy. I don’t think I’d call it work though.

As in previous months, I’ve been cooking up a storm. I like to think I’m getting even better at this. The unseasonably warm weather even got me out at the BBQ a few times.

In March when the lockdown started, I began a greenhouse with herbs and tomato seedlings. Unfortunately, it seems there was some mold with the tomato seeds which spread and killed everything. So, I restarted! I tried some new tomato seedlings, but I fear they are too late to yield any fruit this year. I also planted some sunflower seeds, and they are growing like crazy! In 4 days some of them are 3″ tall already!

Greenhouse, round 2! The sunflower seeds on the left are growing like mad! The tomatoes on the right are going too. I hope they survive transplanting.

Studying Blues

I’ve been spending some time each night doing my self-study course in preparation for the Masters Electrician Exam. I really wish there was an in-class option because I feel very unsupported in this way. There is usually an in-class portion that lasts about 63 hours, but that won’t happen while COVID is still around. So, I was sent a 2000 page workbook and 2000 pages of provincial regulations, I ordered the 3000 page Ontario Electrical Safety Code book, and we have an answer key online. That’s it! Lots of really boring reading.

It was hard to get back into a studying mode. I’m a long way out of University now. I did a serious (100+ hours) study binge before my Project Management Professional (PMP) exam in 2014, but at least there was an in-class session before that. This feels rather unguided and endless.

From a professional point of view, I’m frustrated and disappointed I was never taught about the Electrical Code properly. My first manager didn’t use the code, and when I got into situations where I needed it, I would dive into the specific sections I needed. As a more experienced engineer now, I found myself teaching and mentoring younger engineers in detail how to use the Code. That’s an experience I wish I had.

And now, I need to get intimately familiar with the entirety of the Code and related regulations, without any guidance except for a glib answer key. Not a very fun way to spend 2 hours per night for 3 months.

Hope you are all staying safe during this lockdown. See you all soon!