Updated on March 12, 2015

There is a lot of variability when stepping through Dr. Shoemaker’s protocol in terms of symptom relief. Don’t expect to feel better after a month of cholestyramine (CSM) – a nasty nasal infection called MARCoNS can hamper improvement. Likewise, don’t expect to feel better after knocking out MARCoNS. Even though VCS visual testing should be improving after getting away from mold, continuing on CSM, and clearing MARCoNS, other factors like high TGF-beta 1, high C4a, low MSH, low VEGF and the like can easily keep you very symptomatic – especially 4-3-53 and 11-3-52B haplotypes. In fact, that’s why Dr. Shoemaker introduced VIP at the end of the protocol. In other words, and this is a very important point, if you rely on symptom relief to gauge the efficacy of Dr. Shoemaker’s protocol, it is very likely you’ll mistakenly conclude it’s not helping; when in fact, it is.

That’s why he took lots of labs all through out treatment. He learned early on that this was an illness with lots of symptoms that bounced up and down dramatically. Using symptoms to gauge efficacy of treatment was like playing “Whac-A-Mole” at the fair. Whac-A-Mole is when you use a rubber mallet to hit mole figurines on the head when they leep up from one of many holes in a large wooden board. Just as you bop one mole on the head driving it back into the board, another one immediately pops up somewhere else. You can not rely on symptoms to gauge improvement!

Furthermore, completion of previous steps is required in order for following steps to be successful. For example, the next two steps after clearing MARCoNS is a gluten-free diet for those with anti-gliaden antibodies (AGA) and a no-amylose diet along with taking 2.4 g EPA and 1.8g DHA omega-3 fatty acids for those with high MMP9 or high TGF-beta1 (unless MMP9 is under 900 wherein you may elect to skip treating MMP9). The point is that it would not surprise me one bit if people that didn’t treat MARCoNS first, and instead jumped right to trying to bring down MMP9, were unsuccessful. The success of many of the steps relies on completing all the previous ones. If you’re the type that is considering playing “leap-frog”, jumping from here to there willy-nilly through the protocol, I can spare you the hassle of finding out for yourself how this type of experimentation will work out; it won’t.

Depending on your genotype, you may have to progress quite a ways through the protocol before seeing improvement, and even then it will be incremental. For me, it took at least six months into treatment. One day I was taking a boat ride with a friend and remarked how I just realized that my mental status had markedly shifted. It wasn’t completely claustrophobic and the peace I knew so well through decades of meditation was starting to reappear. The damage that is done to areas in the brain alone (like atrophy of the caudate) is dramatic and can take months to years to heal. All too often I hear about people saying they tried some part of Dr. Shoemaker’s protocol and because they didn’t realize any symptom relief, they incorrectly conclude his protocol doesn’t work. Without a foundational understanding of Dr. Shoemaker’s protocol, people that could benefit greatly give up!

For individuals, I can see how they may make this mistake – Dr. Shoemaker’s protocol is long and complex. Except for Dr. Shoemaker, no one takes the time to explain the importance of going step-by-step through the protocol and what to expect. On the other hand, there are doctors that are clearly missing this foundational understanding too. These doctors draw the wrong conclusions and then give poor advice after haphazardly trying one part or another of Dr. Shoemaker’s protocol. Not surprisingly, these ill-informed doctors go on to dabble in various unproven therapies (often without following labs) as if they were on the same scientific footing as Dr. Shoemaker’s work. I wish I had a big stick that could make these ill-informed doctors stop. All they are doing is confusing people with unsubstantiated claims and consequently keeping those with CIRS from having the best chance possible at getting better.

Does this mean Dr. Shoemaker’s protocol is a magic bullet that works perfectly for everyone? The answer is absolutely not. I’ll say that again, absolutely not. Nonetheless, it is the best those with Chronic Inflammatory Response Syndrome (CIRS) have. Really, I’d love it if some other doctors treating CIRS would provide meticulous and scientifically collected data showing alternatives to Dr. Shoemaker’s approach. Unfortunately, so far all I’ve seen is a lot of loosely substantiated conjecture. Given the uncertainty in alternative approaches, my advice is to do everything you can to follow Dr. Shoemaker’s protocol. If you get stuck at a step, then you may have to tack on adjunct therapies that allow you to complete that step. Who knows, maybe the alternative therapy will accomplish the same effect – confirmed by labs. In other words, my strong advise is to make Dr. Shoemaker’s protocol the core of your treatment plan and then add on whatever other therapies that you find helpful – so long as they don’t get in the way of his core protocol.