Curing Crohn’s Disease

When I was nineteen I was diagnosed with ulcerative proctitis, a diagnosis soon changed to ulcerative colitis because, I suppose, my gastroenterologist felt my disease’s chronic nature and severity warranted this more serious diagnosis. At that point I felt pretty dejected. I’d always prided myself on being a good athlete, and now that I was grown I wanted to take my fitness further, but I would frequently go through periods of unavoidable weight loss, and the fact I had a stomach ache at least once almost every day, and almost never went two days without a stomach ache, gas, and bloating following a meal, checked my love of food and often left me not wanting to eat again till I was really hungry. Then there were the sporadic “flare-ups” of the disease. I won’t go into the details of those painful periods; suffice it to say I was so stubborn and distraught with the idea that one of these flare-ups would kill me without intervention with steroids and anti-inflammatories, that once, when I had run out of meds., I didn’t eat for more than four days to try to naturally wrest myself from the episode. It didn’t work though. In the end only steroids worked.

All this for a nineteen year old who’d always been in the peak of health, and my doctor said it would be this way for the rest of my life, if I was lucky and it didn’t get worse – that there was no cure and that people didn’t recover from colitis once it became chronic. So I was pretty dejected. I asked him repeatedly if there was anything I could do about my diet, or if quitting drinking would help. He said there was no evidence that was the case, except of course that I should, like anyone, only drink in moderation. My medical records from this time all said I was asthenic but seemingly in excellent health otherwise. I felt that this was how I looked in the mirror, but that something very wrong was going on inside me. But I figured there was little I could do, so for about six years things went on like this.

Both Ulcerative Colitis and Crohn’s Disease are characterized by causing ulcers and general inflammation in the digestive tract. But whereas Ulcerative Colitis, as its name suggests, is confined to the colon, Crohn’s Disease can manifest as inflammation anywhere from the esophagus to the colon and rectum, yet almost always includes inflammation and ulcers in the small intestine (that’s really how they diagnose it). The presence of severe inflammation and ulcers in the small intestine generally makes Crohn’s Disease the bleaker prognosis to get, because while both are considered incurable, the small intestine is where the vast majority of nutrient absorption occurs, and while ulcers in the relatively thicker, more muscular large intestine (colon) usually remain superficial, ulcers in the small intestine can at times eat right through the intestinal wall. And that’s not good. For this reason about fifty percent of Crohn’s patients have to get part(s) of their small intestine removed at some point in their lives.

During my initial six years with Ulcerative Colitis, I did at least find solace in the fact that my disease, while it seemed to be slowly getting worse, was chiefly a disease of (sometimes terrible) discomfort, and not one of lasting internal damage, except that I had a much greater chance of getting colon cancer than most people. Then, two and a half years ago, while on a trip to my friend’s farm in Tennessee, I got really sick. My medication didn’t work and I ended up in the emergency room twice and was laid up for several days. They gave me a different anti-inflammatory. It worked. And when I got home I received a colonoscopy. Severe inflammation and ulcers were found in my large and small intestines, and I was diagnosed in short order with probable Ileocolic Crohn’s disease. You see, when I was nineteen I’d only had a sigmoidoscopy, which doesn’t look at the small intestine. A cheaper option because it’s a quicker ‘periscope up yours’ maneuver and they don’t need to put you to sleep or use anesthetics for it. Lucky me. So who knows if my disease was already manifesting as Crohn’s back then. It’s likely I’d had Crohn’s for six years without knowing it.

So I asked my new gastroenterologist if there was anything I could do. – Diet? Drinking? And got the same answer: “I know how it is to be young, but if you drink, only drink in moderation. As for Crohn’s though, there’s no conclusive evidence diet or alcohol play a role.” One thing I simply had to do though was take a new medication four times a day, because Crohn’s was a serious diagnosis, but if I stayed on top of my treatment there was a good chance I’d never have to move to stronger, more side-effect prone anti-inflammatories, or more serious interventions (i.e. surgery). So again, dejection. I took the pills. They helped the symptoms. But I’d been considering leaving my job of three years, and when I asked how much my single medication would be without my employer-provided insurance, the pharmacist said $725 per month. To put that in perspective, now I’m paying $350 per month, for rent. So I demurred. But after several months of this, I said, “Fuck this. I’m not living my life this way, unable to digest food properly, stuck at a dead-end job or saving to move to another one, and just waiting for the other shoe to drop with this disease.” Most everyone I’d spoken to who either had Crohn’s or knew somebody with Crohn’s said they were in terrible shape. If that was going to happen to me, I was damned sure going to go down in flames trying to make myself better, so I started looking for a cure.

Everything I read about intestinal candida overgrowth resonated with how I remembered having felt in the six months previous to my first ulcerative proctitis diagnosis, so I decided to start there. I found what seemed to be a really good anti-fungal diet book and started it. After a bit I knew I had to quit my medication because it was masking my symptoms, so I quit cold turkey and—my colon stopped working. After less than six months on this drug, the least side-effect prone/detrimental drug of its kind, quitting it was like turning off my plumbing, so I had to go back on it and slowly wean myself from it over the course of a month.

After doing so I felt somewhat better some of the time, but still something wasn’t right. I felt bloated and still had stomach aches, though maybe not as frequently. Part of me wanted to give it more time, but part of me believed that if this was the answer I’d be feeling more linear progress, and more quickly, so I continued to look for answers.

I seriously considered going vegan, and began to move in that direction, after reading Self Healing Colitis and Crohns by David Klein. I wasn’t very convinced by the author’s arguments as they pertained to me, yet I’d much rather have tried veganism than go back to the pills. Then I found a book online called “Breaking the Viscous Cycle” by Elaine Gottschall via “Crohn’s Boy’s” site (Praise be to Crohn’s boy!) which has become the first step toward my new, healthy life. Gottschall got a M.S. in microbiology studying digestive processes and bacteria of the digestive tract, and her interpretation of the cause of Crohn’s, colitis, and several other diseases is brilliant.

Briefly put, people with diseases like mine (of similar origin but perhaps involving different, pernicious bacterial and fungal species at different loci of interaction with our digestive tracts) get an infection. In response to the infection, our bodies mount an inflammatory response. The inflammatory response is not fully effective in purging the system of bad bacteria, and the assault from the bacteria, the inflammatory response, and the mucosal discharge that’s a part of it, all combine to disable the tips of little microscopic protuberances (a bit like taste buds) called villi, which line our small intestine. This is significant because it’s at the tips of these villi that our bodies break down complex carbohydrates into simple carbohydrates so they can be absorbed, so we who have a chronic infection of the digestive tract become increasingly impaired in digesting carbohydrates. What’s more, complex carbs are one of the favorite foods of bacteria – harmful bacteria included – so what happens to all the free-floating complex carbohydrates that we crohnies eat but can’t digest? The bacteria that caused the initial infection puts it to good use: the infection becomes stronger; we get sicker. This is what Gottschall calls “the vicious cycle,” and it’s broken simply by not eating the complex carbs we can’t effectively digest and thus starving our gut flora and with them, the infection.

Perhaps because I had already gone a ways in cleansing my system of fungus, my results from adopting this book’s suggested diet, called the Specific Carbohydrate Diet, or SCD, were sudden and dramatic. Within forty-eight hours, my Crohn’s symptoms were gone. I don’t mean relieved; I mean gone. In fact, staying religiously within the parameters of this diet (though certainly not on the healthiest version of this diet I could have devised for myself) kept me totally without any digestive discomfort whatsoever for many months. Only when I picked up another chronic bug while in Ecuador (whoops) did I again start having some digestive problems. This last advent was partly just due to my own hubris in healthful glee (e.g. drinking Ecuadorian tap water and eating too much street food), but the fact that my infection persisted despite antibiotics before slowly subsiding over months (but probably didn’t go away entirely) points to a potential problem with the Specific Carbohydrate Diet and with my imperfect health.

Our bodies’ first, most massive line of defense against disease, along with one of its most crucial components for keeping toxins out of our body and bloodstream, is our gut flora. You have more bacterium in your colon than you have cells in the rest of your body. If you’re healthy, this little ecosystem of yeast and bacteria is composed of nearly a thousand species (mine’s probably composed of significantly less than that). “Good” bacteria and yeast are like good housekeepers. You got them initially through your mother’s milk, and by and large they can’t live outside you for long, so they want to keep everything functioning well. They eat what you eat, and some things you can’t digest (like vegetable fiber) they can, and they poo fatty acids, which are good, salubrious fare for us.

“Bad” bacteria and yeast just have a different life strategy. They don’t care so much for their host, at least not in the long-term. In their different life cycles they can be both more transient and more rooted than their “good” adversaries. When they literally put down roots in your intestines, this can open up fissures contributing to what’s called “leaky gut syndrome.” Then things like toxins, undigested proteins, viruses, and these goddamned bad bacteria can slip right into your blood stream, and that’s very bad.

It’s important to remember that the good bacteria which have come to unobtrusively protect us and assist us in digesting the indigestible have been evolving within us for hundreds of thousands of years, at a minimum. Like us, they’ve adapted to certain environmental conditions, which for them mostly consist of what we eat and drink – a diet which throughout most of our species’ history was probably pretty consistent (at least in terms of the basic types of foods we were eating, though the proportions of these probably varied considerably). However, about ten thousand years ago we added cereal grains and dairy to our diets; a couple hundred years ago we added sugar; and in the last hundred years or so we’ve added a slew of seed and legume oils, trans fats, chemicals, pesticides, and a whole lot more sugar. Today, by far the bulk of an average American’s calories come from foods our species never even ate previous to the Neolithic revolution 12,000 years ago, so recently our gut flora have been living through times of change, to say the least.

Recently studies have begun to show that different types of food support the growth of different species of gut flora…Duh. For example, one study showed that soluble vegetable fiber tended to promote the growth of beneficial gut flora, while insoluble fiber from cereal grains tended more to promote the growth of potentially harmful species. And when you consider that the “good” nature of beneficial bacteria is that they clean house well, fighting tooth and nail for us, while avoiding putting down roots, it seems plausible to me that if we flood our bodies chronically with toxins and toxic foods, this lack of roots could prove a liability for our little allies. They could be disproportionately swept away, while the nasty guys trying to set up colonies rooted in our intestinal walls are disproportionately left behind, to flourish. This is just my speculation, but it makes sense to me.

Anyway, I think this is what happened to me in my childhood and adolescent years, when I thought my sole preventable health risks were getting fat or having a heart-attack, and my chief guide to nutrition was a food pyramid on the back of a Rice Crispies box. I’m infinitely grateful to Elaine Gottschall and the SCD, but wiping out the majority of the bacteria that was causing my Crohn’s Disease was only the beginning of my road to complete health. The SCD is a wonderful first step for anyone who has Crohn’s (from what I’ve heard, it hasn’t proven as consistently effective for people with Colitis or other gastrointestinal diseases, but has had some amazing effects for some autistic children, to give you an idea of gut flora’s range of influence), but it does have potential weaknesses. Our bodies do need some glucose, especially to fuel certain aspects of our immune system. And the mucous forming polysaccharides which the SCD warns against may worsen one’s already heightened, mucous forming inflammatory response in the case of a chronic intestinal infection, thus further impairing digestion, but they are also vital for a healthy person’s immune system in protecting against and purging infection, as anyone who’s ever had a runny nose can testify to. I think this is why, several months after starting the SCD, I got a sinus infection for the first time. And what’s worse, a year and a half and two rounds of antibiotics later, I still have it.

It’s for this reason that I now believe the SCD diet, while a wonderful long-term intervention, especially if one regularly eats the carbohydrate rich vegetables like squash permitted on it (sadly I did not), is probably best to transition away from eventually, to a diet that is designed to maintain exceptional health. The best such diet I’ve come across was in the book Perfect Health Diet by Jaminet and Jaminet. The Jaminets take the “Paleo” approach to interpreting nutrition, which I alluded to earlier in my Neolithic Revolution comments, and find very compelling. But they do so in a way that isn’t overly speculative, as some Paleo literature I’ve read, but rather rely chiefly on a wealth of cutting-edge, nutritional research.

But what about those of us who feel our digestive immune systems have been greatly depleted and thrown out of balance by years of abuse from eating the wrong foods followed by handing the stewardship of our health over to the pharmaceutical industry? Is regaining truly excellent health in the cards for us? Maybe. There are a host of fermented foods which can be very helpful, and there are probiotics in supplement form. And with a great diet including these, in foods like kim chee, kambucha, and kefir, who knows how far we’ll get. But studies have shown that people with chronic digestive diseases usually have significantly fewer species of gut flora, and it’s not likely that a little of several species here and there will bring these people back to full recovery. There is one treatment though that’s consistently had amazing, curative results, but I’m not sure if you can stomach it – or colon it, I should say. It’s a fecal transplant, and it’s just what it sounds like.

You may think it sounds gross, but a fecal transplant is hardly invasive compared to a colonoscopy or getting part of your intestine cut out (standard practice for Crohn’s today). And rather than a relatively small amount of a handful of bacterial species, you take a sample from a donor with a healthy digestive system, and basically get an enema (a significantly larger dose than from probiotic pills or fermented food; crap is 60% gut flora by volume) of nearly a thousand species of bacteria and yeast –an entire eco-system – which then takes to its new environment, killing pathogens and setting up shop unbelievably well.

Right now fecal transplants are only used to treat one especially anti-biotic resistant and potentially deadly bacteria, called Clostridium difficile (which the treatment generally cures almost immediately!), but to my knowledge this is the only application it has been tried in (probably as a last resort due to this bacterium’s antibiotic resistant nature), and there’s no reason this treatment shouldn’t be tried more broadly. Of course, such a potential cure is anathema to the pharmaceutical industry’s paradigm of ‘treatment unto death,’ and maybe that’s why it’s not being used more broadly, but we sufferers of chronic digestive problems and immune dysfunction of all kinds should really be pressing our physicians and specialists for this. It could truly be a revolutionary treatment, and a way to significantly strengthen a large segment of the population’s immune systems cheaply!

You may think I’m being too optimistic about it, but consider what cow herders and dairy farmers have been doing with this technique pretty much since they’ve had means to do so, and to amazing effect. When a cow is sick, farmers often don’t even bother trying to diagnose the problem. Instead, they simply extract some gut flora from the rumen (where a cow’s gut flora live) of a healthy cow, and inject it into the rumen of the sick cow, and voila – much of the time this does the trick. Our good gut flora are like the first and strongest gatekeepers protecting our health, and the proper function of numerous physiological processes, from nutrient absorption to neurological function, depend upon their health. Restore that, and it’s like setting in place a solid cornerstone to build your health upon. I know I’m still presently without this cornerstone, so I’m trying to slowly build one, and am confident I can. And even if it proves a lengthy process, and the medical community never comes around to help, at least I’m pretty sure I’ve cured my Crohn’s disease.

Epigenetics and the Future of Food

It seems inescapable to me that sometime soon – probably during my lifetime or soon after it – human beings will enter a great evolutionary bottleneck that will take one of two forms. Either scientists will discover new sources of energy powerful enough to considerably forestall the imminent threat of resource depletion, and the economic model the world has adopted to fuel the development of technology (a model which posits economic growth on one side and on the other, deflation and collapse) will persevere long enough for scientists to understand genetics sufficiently to begin the continual process of engineering human beings into their historical moment’s image of perfection.  That will happen, or such discoveries won’t come to light, and the drying up of fossil fuels will coincide with a very different evolutionary bottleneck – a massive die-off of human beings that will nonetheless likely usher in a new age of cultural diversity.

There is a third scenario I’ve not much entertained which could indeed happen – that somewhere down the line new machines for harnessing energy are not only invented (if they haven’t been already and subsequently disappeared by current energy producers), but also constructed in a decentralized, open source fashion. But let’s assume these machines could be fully replicable, from their nuts and bolts on up to their integrated form, by small, decentralized communities. This would free such communities from the fate and exploitation of the larger techno-industrial system to some extent (still, there will always be the army), but would this make such machines some kind of technological panacea? To this latter question, I suspect the answer is ‘no.’ – The spreading technology of little, decentralized, perpetual power plants would lead to overpopulation and the scarcity of land and food as fast if not faster than the present system which manufactures artificial scarcity to ensure and increase profits.

The first and third of these scenarios would both likely result in an ever-expanding population which would lead to its own, unending chain of resource problems after (if not before) the hurdle of waning fossil fuels has been cleared. Both a centralized and decentralized system where electrical power is, say, infinitely abundant will still come to bump its head upon different kinds of resource ceilings eventually, and indeed, the more abundant electricity is, the more quickly humanity will come up against these other ceilings. That being said, a centralized techno-industrial system keeps in its repository of prospects the central one: the refashioning of human beings in the historical moment’s image of perfection. And wouldn’t that be wonderful? … That’s a rhetorical question. You’re not meant to answer it for yourself.

Leaving aside for now the question of whether our mastery in this genetic stage of Manifest Destiny would be a good thing or not, let’s consider what I meant the topic of this post to be – whether such mastery is even possible. It was certainly the faith of most medical scientists until recently that genetic diseases, and even deformities, environmental intolerances, etc., would soon be a thing of the past. Then it happened though: A field of science began to emerge at the turn of this century which in its own way could be just as significant as the dissemination of petroleum technology at the beginning of the last. Perhaps I’m overstating things, but properly understood, this new field of genetics is something that must help to shape our public discourse and behavior in this century if we’re to remain the vibrant, miraculous beings we’ve become over the countless generations of our species.

It was thought until somewhat recently that the parts of our DNA not directly involved in making proteins were junk – unusable residue from earlier stages of our evolution. This could indeed be plausible, except that over 98% of our DNA is this “junk,” and that seemed to geneticists altogether wasteful and unnecessarily complicated for evolution, a process which is not usually kind to wastefulness and unnecessarily complicated physiology.  Then, as I said, at around the turn of the century scientists discovered that these junk genes were not junk at all (go figure), but executive genes which, in a mind-bogglingly complex symphony of turning on and off, orchestrate the production of proteins that make up our bodies. But why is this discovery so important for everything from what you do in your free time, to the kind of society you live in, to geopolitics in general?  Here’s why:

Prior to the discovery of this new field of genetics, now called epigenetics, your genetic material was thought to be a relatively immutable blueprint for the construction of your body as it is and as it works. But now, in light of discoveries of epigenetics, it’s understood that the switching on and off of protein building genes – this executive gene symphony that’s responsible for orchestrating you in the womb and initiating the incredibly complex system of physiological processes that keep you alive and well, is much more responsive to your environment than your “hardwired” code of genetic material is (This code only changes through genetic mutation which is relatively rare, and recombination in an egg’s fertilization). And it is not the case that this switching on and off of genes, which often occurs in response to environmental factors, can only affect you. Many epigenetic changes, running the gamut from neuropathology, increased or decreased anxiety, asthmatic response, semi or total loss of eyesight (and even loss of eyeballs!), and many more, have been shown to become manifest not in the phenotype (that just means body) of the person or animal subjected to the epigenetic alteration, but in the phenotype of its offspring or even it’s offspring’s offspring! What’s more, epigenetic changes have often been shown to respond to environmental advents cumulatively, generation after generation.

There are of course many kinds of environmental factors which can bring about epigenetic changes, but of course, chief among them is the food we eat (or don’t eat). Perhaps the best illustration of this point was achieved by Francis Pottenger, MD in a series of experiments he carried out long before the discovery of DNA and seventy years before the rise of the field of epigenetics. I won’t go into the details of his studies, but if you haven’t already acquainted yourself with them I urge you to take a few minutes to do so. And the greatest ever scientific study of nutrition ever composed, Nutrition and Physical Degeneration, written by Weston A. Price over seventy years ago, is also indispensable in this context.

The reality is we are physically (and this also means mentally) degenerating from the poor quality of foods we eat, and that we have been for a long time. The first widespread assault on our epigenome, well documented in the fossil remains of our ancestors, actually occurred over ten thousand years ago as we began cultivating cereal grains for consumption and progressively moved away from our former fare of wild plants and animals. But in my eyes, that watershed change in diet is not nearly as ominous as those that have taken place since the industrial revolution. For it’s not only that more people are now more exclusively dependent on the insufficient (and often toxic) nutrition of cereal grains. It’s not only the extension of shelf life necessitated by longer supply chains which leave the micronutrients of meats and vegetables largely eroded by the time they reach our mouths. And it’s not only the hundreds of new foods and chemicals we’ve introduced to our diets in the past two centuries, some of them, like sugar and vegetable oils in staggering quantities. More troubling for me than all these realities is the fact that the sheer number of us and the mercilessly profit-driven practices of industrial agriculture which feed us are sucking the nutrients out of our soil at an alarming rate. These nutrients are vital for maintaining our epigenetic health, and the image of humanity vastly degenerated in its epigenetic health is quite frankly appalling to me: more stupid, anxious, prone to personality disturbances, sickly, ugly, and pained – and all these from causes that are only reversible through sustained dietary improvements over multiple generations! I read things about the urgent need for action on peak oil, peak coal, global warming, etc., and none of them seem as profound as the downward slope we’re already on, and have been on, with respect to nutrition.

Unlike these other global crises we face, whose consequences still lie largely in the future, we’re already in the grips of this nutritional crisis. We just don’t recognize it’s magnitude in the U.S. because we can palliate disease with a thousand and one pharmaceuticals. Autoimmune disease is overwhelmingly caused by poor and/or toxic nutrition, as is heart disease, metabolic syndrome, endocrine dysfunction, and many cancers, I’m sure. And there are other, subtler forms of degeneration which are almost universally rendered upon us by our deficient diets – so much so we accept them as normal, but they aren’t normal outside the context of the “diet of civilization” (see the prophetic work that is Nutrition and Physical Degeneration).

In light of all this, should one of the ultimate ends of our modern technological project still be to engineer a better genetic code? I don’t know what else our ultimate end in this project could be. Are we even in control of it anymore, at all? Let’s assume we are, and we do get to the point where we can deftly modify our genetic makeup. Even at that point, such know-how alone is not enough to engineer better human beings, because however good we hardwire ourselves, that hardwiring will quickly begin epigenetically expressing itself in unpredictable and corrupt ways given a deficient or toxic environment. Therefore, given that a society technologically advanced enough to intricately understand the human genome will almost certainly be heir to an overpopulated and toxic environment, should we at that point take it upon ourselves to start engineering from elemental materials all the vitamins and minerals necessary for activating our bodies’ thousands of physiological processes? Are we anywhere near being able to achieve that kind of chemical engineering on a massive scale? … Or might we engineer ourselves genetically to need less of these micronutrients to carry out our physiological reactions? …

I invite you to look at the information about our nutritional trajectory that’s already out there  (about the total disappearance of certain micronutrients from certain animals and vegetables in the industrial food supply, or about how approximately one-third the world’s population is nutritionally dependent on the haber process (of converting nitrogen to ammonia for fertilizer using heat generated from fossil fuels) because by the time the depth of this crisis becomes obvious to everybody who hasn’t engaged in any self-education, the window for radical, communal change may have closed. And at that point, I don’t think the genetics industry will be able to offer an escape hatch. And the medical industry will certainly be on hand, but with what? – oxycodone, perhaps?