Awesome! Thank you for posting this as it makes for worthwhile reading.
It usually takes an external perspective to see and understand the disease process in a non-dogmatic matter. The medical establishment is ripe with age-old dogma that is not only false, but harmful to the general public - some glaring examples of this include the lipid hypothesis and the current suppression model of disease treatment. As a physicist, you offer a unique and outside the box perspective to a medical paradigm that can more or less be considered a failure, if you adequately look at the statistics in the war on cancer and autoimmune diseases.
The growing research in the realm of microbiotica suggests that our gut bacteria are very much responsible for disease expression. The way we reinforce them (or not) is absolutely crucial for our survival in the future. I've posted studies on c-section and antibiotic babies have poorer health trajectories vs their regular counterparts. Those who live in cleaner environments (and take more antibiotics) generally also have worse health outcomes. The hygiene hypothesis is not just turning out to be true, but it offers a way to prevent and treat diseases in the future.
I glanced through the paper and there a couple things that I'd like to add-
1) My gripe with the SCD and paleo diet is the same as yours, to the extent that they don't adequately address the microbiotica aspect of it. Even in the paleolithic age, our ancestors ate "dirty" vegetables full of microorganisms and interacted with soil by virtue of just living outside and running barefoot. We aren't doing any of that sort, so it's difficult to coalesce with the microorganisms that more or less defined our immune system. I think adding in SBOs like prescript
assist is a wonderful start, but more than that we must interact with the soil in some way - whether through walks or having pets who roam around in the dirt.
There is, however, a remarkable paradigm shift with the advent of resistant starches as you mentioned. Mark Sisson has considerably changed his prior stance, and I think it's hard to classify paleo as a one size fits all diet now - people are adding in raw dairy, tubers, psueograins like quinoa, buckwheat, etc and still having great success in conquering disease. It is also worth noting that, pound for pound, the single greatest dietary source of butyrate is butter
, if you aren't including precursors like RS.
Have you considered doing an American Gut
analysis before you begin your journey? Should you succeed in your journey, you could do a sample afterwards and do a side by side comparison of the bacteria. For more on this, check out freetheanimal.com since it is rife with topics on gut bacteria, RS and probiotics.
2) UC is just as much of a mitochondrial disorder as it is bacterial, which is why some percentage of UC patients also have chronic fatigue, fibro and other autoimmune problems. Antibiotics not only destroy the microbial balance, but they wreck the mitochondria too (google "dodging antibiotic side effects" for the harvard study). Just as important as repairing the lining of the cell as SCFA/butyrate is the presence of cholesterol (coq10, vit D precursor) and proteins like proline, glycine and cysteine (glutathione precursors). I think addressing the microbial aspect with the mitochondrial aspect will yield a greater chance of success in your journey. This where eggs, organ meats and broths come into the picture. There isn't a vegetable counterpart that has higher coq10 than salmon or liver.
"An expert is a man who has made all the mistakes which can be made, in a narrow field." - Niels Bohr