True facts about Helicobacter pylori

Helicobacter pylori is a bacteria found only in the gastrointestinal tracts of humans and closely related primates.  When I say in the stomach, I mean in the stomach.   H. pylori burrows into the mucous coating your stomach and touches the epithelial cells.

Image Credit: Zina Deretsky, National Science Foundation, under US Government Works license
Image Credit: Zina Deretsky, National Science Foundation, under US Government Works license

Fun fact: in the presence of acid, the gastic mucous hardens in an almost solid shell, which H. pylori cannot penetrate.  It works around this by preferentially seeking out high pH areas within the stomach, and by releasing ammonia to neutralize the acid.  So H. pylori can be both a cause and consequence of low gastic acid.  This fits in with my general view on physical processes and life in general:  everything either stops on its own or is part of a self-reinforcing loop.

H. pylori is most famous for causing gastric ulcers.  This was especially important because it was a beautiful example of something previously considered a “lifestyle” disease having a distinct, exogenous cause.  I use it as a go-to example of medical science not respecting its limitations.  Alas, my example was itself oversimplified not respecting its limitations: only 60% of ulcers are caused by H. pylori.  Half the remainder (20% of the total) are caused by NSAIDs, and other half are caused by “Other”.    I do wonder how they’re determining presence.  I had two different H. pylori tests done (both on a stool sample), and only one cam back positive.   Putting this on the list to investigate further.

The coolest cause I found was Zollinger-Ellison syndrome,  in which tumors made of gastrin-secreting cells cause an overproduction of gastrin.  This is how I learned they can test for gastrin levels directly, which I am curious about given its likely contribution to my digestive issues.

H. pylori also raises your lifetime risk of stomach cancer, but only by 0.6 percentage points.

Despite that scary sounding list,  80-85% of infected people  show no symptoms.  That may be due to genetic differences in the bacteria infecting them.  There is also research suggests that H. pylori is, or at least was, mutualistic with humans, and that lack of it increases a person’s risk for gastrointestinal issues.  If that is true, the question becomes:  is this pathogenicity -causing-strain new, or has it always been present, and only recently became dangerous?

H. pylori treatment protocols commonly include proton pump inhibitors , which make the stomach less acidic.  This struck me as a rather interesting choice for fighting a pathogen that prefers high-pH environments: apparently the goal is to coax the bacteria into areas more easily reached by antibiotics.

Confession: I thought that the stomach had a thriving bacterial ecosystem, of which H. pylori was an unwanted guest.  It turns out I was thinking of the large intestine.  Almost nothing survives in the stomach, and of the things that do, it’s unclear that establish permanent residence, much less are mutually beneficial.

Adventures in amateur research: implausible mechanisms

I’ve referred to the scientifically questionable book my scientifically questionable sensory integration therapist gave me before.  It’s name is  The Fabric of Autism.  Let me walk you through its loss of credibility.

As I mentioned before, TFoA refers to the hypothesis that thiomersal causes autism as accepted fact.  That is a very big strike against it.  But all the best theories were once fringe hypotheses, and people who believe one fringe hypothesis will often believe another, so I kept reading.

Then TFoA referred to information the author received from patients using Facilitated Communication, accepted as naturally as if the patient spoke.  I vaguely remember FC from a psych 101 class I took in 2004: FC was a breakthrough that allowed autistic people to write out their thoughts, thoughts mainstream practioners had denied they even had.  People thought to be entirely nonverbal were writing novels.  It was a miracle.

Only FC was being used by people who had never learned to read or write.  You can pick up verbal language without explicit instruction, but not written.  And even if you could, autists were writing full sentences without looking at the letters- and the FC hunt-and-peck method is simply impossible to touch type with.  FC went on to fail every double blind trial thrown at it.  In the time between introduction and discrediting, several people were sent to jail for sexual abuse, where the only evidence was FC-expressed accusations.

I checked wikipedia, and my recollection was more or less correct.  They present it as more controversial and less laughably terrible than my class, and it’s always possible new research was done or the technique has changed since I took my class.  Or maybe it just happened to work for these individuals. But given how horribly misused faciliated communication was in the past, I believe the author should note that history and what makes this FC different from the bad old days.  Failure to do so is strike two.

Then the book had a good stretch.  It posited some plausible mechanisms for how sensory and inner ear problems could hurt the digestive system.  Then it tried to do the reverse.  I’m well disposed to this sort of thing.  Anything that isn’t self-reinforcing will stop.  But the mechanism proposed was that poor digestion leads to bad posture, and that causes the endolymphatic sac in the ear to underinflate (this is what we spent so much time on Wednesday).

I can’t prove that doesn’t happen.  But I am very, very certain that bad posture would have a lot of other, more noticeable effects, some of which would themselves affect the ear.  A mechanism that broad should be accompanied by a list of other expected symptoms- something the user can compare their own symptoms to and see if this offers a parsimonious explanation.  TFoA does none of that.  It offers no checkpoint for a user to say “oh, this isn’t me” and walk away.

I didn’t consciously decide that that was the last straw, but I haven’t picked up the book since.  And while I kept up with my old exercises, I didn’t work on incorporating new ones.  This is to my detriment, since the exercises really do seem to help no matter how terrible the science they’re based on is.  I have some hypotheses as to why that is, but I can’t share them without committing all the sins I just accused the book of, so they will need to wait for more research.

Digestion, hormones, acid, and bacteria.

When I was first diagnosed with low gastric acid, I assumed that the acid was needed to physically break down the food, which never quite made sense because protein itself is mildly acidic.  It turns out that I was wrong, and that the primary effects of gastric acid are to denature protein (which a protein loses its shape without losing any of the covalent bonds between amino acids) and to activate digestive enzymes.

[Backing up a step: enzymes are biological catalysts.  Given the right materials, they make chemical reactions happen faster.   But enzymes are not perfectly specific, and can do a lot of damage in the wrong environment.  For example, food enzymes digesting your food is good.  Food enzymes digesting your stomach is bad.  One way to maximize positive effects and minimize negative effects, or simply waste, is to produce the enzyme in an inactive form (known as a  zymogen) that can be activated once the enzyme has moved to the correct environment or the correct raw materials are available.]

There are many digestive enzymes, but the one of interest to me right now is pepsin. Pepsin is one of three primary enzymes that digest protein, and the only one produced in the stomach.  Or rather, the stomach produces it’s zymogen, pepsinogen.  Pepsinogen is useless until it’s turned into pepsin by gastric acid, which is also produced in the stomach (but in a different cell type).  Pepsin can also be inactivated by high concentrations of the products of the reactions it’s catalyzes, a common pattern called a negative feedback loop.

So high gastric pH/low gastric acid inhibits protein digestion by keeping pepsin in its inactive form.  It’s possible that what I have is not low gastric acid but low pepsin levels. All HCl supplements contain significant amounts of pepsin, so that could be why they help.  Digestive enzymes didn’t do me any good until I started HCl, so I don’t think that’s the explanation, but I can’t rule it out with the current data.

Gastric acid production is stimulated by the hormone gastrin (note that this is far from the only effect of gastrin release), which is itself stimulated to production by gastrin-release peptide.  GRP is stimulated to production by “the vagus nerve”, which is technically true but not informative, because nerves are mere messengers, and the real question is who is sending the message.  There is the research pointing to a link between  sensory input and digestive chemicals.  Other research pointing to a link between gastric flora and gastrin (more).  But  the honest answer is that we don’t know.

Which puts the question in good company.  This post barely scratches the surface of  what we know about the chemistry of digestion, and there’s a lot of we don’t know, and that we don’t know we don’t know.

My medical issues: digestion

In March 2013 (age 28), I was diagnosed with low gastric acid.  This turns out to be really important for things like “digesting food.”  I could manage macaroni and cheese and candy and other things that aren’t really food, but protein and fiber made me feel ill.    My doctor prescribed me HCl Supplements as both diagnostic test and treatment, and suddenly I was able to eat both.

In hindsight, this went back a very long time.  When I was in pre-school or early elementary, the family joke was that I must photosynthesize, because I never ate anything.  I distinctly remember my mom telling me I would never make it as a cave man because all the plant life was too tough for me to chew, and meat was just out of the question.  My best friend from 3rd grade still remembers how I ate nothing but bagels when I slept at her house.

So from age 0 to 28, I survived on spaghetti with tomato sauce.   This transforms the question from “why do I have so many chronic problems (constantly sick, anxious, musculoskeletal pain, terrible oral health, adrenal-fatigue-no-hypothyroidism-no-adrenal-fatigue-again)?” to “how are my chronic issues so minor?   Were we on to something with the photosynthesis thing?  My hometown is the #2 most overcast city in the country, and my current home is #1.  What super powers would I develop if I moved to Phoenix?”

Now that I have the HCl supplements and can actually digest food, I’m feeling a lot better.  I have more energy and more cope.  I get sick less and recover faster. My dentist commented that my (previously miserable) oral health was looking a lot better, without being told anything had changed.  Friends commented on how much better my skin looked. I gained muscle mass. And oh yeah, I don’t constantly feel ill for no reason.  Pretty much everything you would expect for someone suddenly gaining the ability to digest food.

Coming up: My experience with hypochlorhydria and its treatment and the science of the stomach.

Why “Aceso Under Glass”?

You may be familiar with the rod of Cauceus as a symbol of medicine

Caduceus symbol by Rama and Eliot Lash (public domain)
Caduceus symbol by Rama and Eliot Lash (public domain)

I hesitate to call this usage wrong, because it’s been used as such for 150 years and people will reliably interpret it as medical, but it is based on bad mythology.  The caduceus staff was associated with Hermes, who had nothing to do with medicine.  It was used out of confusion with the  Rod of Asclepius.

Rod of Asclepius, author: Rama, public domain.
Rod of Asclepius, by Rama (public domain)

Ascelpius was a god or demi-god of healing.  He had six daughters.  Hygieia and Panacea did pretty well for themselves, to the point that I don’t need to tell you what they’re the goddesses of,  and both have lavish wikipedia entries.   Two others (Meditrina and Aglaea) have little to do with health and appear to be engaged in some horizontal myth transfer, since there are characters with similar names and related areas of focus but very different  parentage in Greek mythology.    The remaining two are Iaso (Recuperation) and Aceso (Healing and Curing).  They have short wikipedia entries, but at least everyone agrees on who they are.

Recuperation is a good thing, but doesn’t captivate me.  Healing and curing interests me a great deal.  I’m interested in how they work, how they’re blocked, how you know they’ve worked, the distinction between the two, why something heals one person and hurts another, and… well, this list gets very long very fast.  So that’s why I chose “Aceso.”

The “under glass” part represents a few things.  One is that I’m very literally studying the healing process.  But I’m also studying how we study the healing process.  Right now we have the choice between relying on traditional large peer reviewed studies, and qualitative provider accounts.  Both of these have serious limits, and I want to explore what those are.

So that’s how I arrived at “Aceso Under Glass”.