You seem to be intentionally looking for confirmation bias, trying to find a way to place blame on 'modern'.

I have spent a lot of years reversing symptoms of my genetic disorder as well as reversing issues in my special needs sons. Altering my diet is a very big part of that. Humans have been around a long time. Some of the issues my sons and I have are relatively "new." I spend a lot of time wondering how much that is a product of "new" environments rather than "new" biological issues within humans themselves, if that makes any sense.

My dad was old enough to be my grandfather. He grew up on a farm, without the constant noise of modern life. When I lived with my parents during my divorce, I realized my oldest son had many things in common with my father. I had never before realized. The sensitivity to noise that is viewed as pathological and worthy of labeling as ASD or as having sensory issues is something both my parents had. They were just old, grew up in a different era, and expected the house to be kept quiet. No on acted like their preferences were a "special need" requiring a label...etc.

Sorry if that is not very clear. I wonder a lot at how much our modern "ills" are really a product of our modern lives -- of environments that did not exist until recently but which we view as something "normal" that "everyone" should be capable of coping with. It isn't looking for confirmation bias. It is wondering how much bias exists in some of the assumptions we make in how we frame certain kinds of problems.

This is why I caution you against confirmation bias. The modern life also allows plenty of people who weren't previously viable to achieve adulthood. I'm not talking about Spartan exposure of sick infants (which is an outlier), but that people with sensitive constitutions were more easily taken young by disease in the first place. The high infant mortality of the past is a significant example.

IBS (and Crohn's, which is really just a type of IBD), is an immune disorder characterized by chronic, uncontrolled inflammation. All the disease's symptoms stem from this state, so the specific germs involved may or may not be all that important, the body's reaction to them is. When you get down to it, many disease states are just a consequence of regulation of inflammation failing at a critical location.

But I think it's fair to say that the many benefits of modern diets are accompanied by some serious negative side effects, and that the human microbiome has not yet had enough time to evolve into an optimal state for coping with them. (It probably doesn't help that the "modern diet" isn't at all a stable target to optimize for, either.) Perhaps in another 20,000 years, evolution would naturally shape our microbiome to eliminate things like Crohn's disease and tooth decay.

Yeah, see, I didn't say that. You edited that to mean something completely different from what I said/meant. My sentence started with "perhaps", had no italics and I went on to ask how that could be tested. So I think this is a not great comment. It feels almost slanderous to me.

But I think it's fair to say that the many benefits of modern diets are accompanied by some serious negative side effects, and that the human microbiome has not yet had enough time to evolve into an optimal state for coping with them.

That's part of my assumption. But, also, it seems to me that the modern diet has chemical impacts that are pretty well-established as promoting disease. Not that we have to eat crap, but a lot of us do, in fact, live on rather crappy food -- microwave meals, food "products", etc. I think it's complicated and that the impact of food chemistry is not well studied or taken all that seriously. People who think relatively small changes may have big impacts tend to dismissed as quacks.

Perhaps my intent would have been clearer if I had said, "I don't think it WOULD BE fair to say...". I did not mean to suggest that you personally believed this to be true. That said, you were clearly suggesting that it is a possibility should be taken seriously, perhaps more seriously than biomedical experts have done to date.

And my addition of italics was entirely to emphasize which part of that suggestion I was responding to. In retrospect, a more careful post of mine ought to have said "[emphasis added]", though that still feels a bit like overkill to me. I think in the context of a threaded discussion I unthinkingly assumed that readers would have your original words and context freshly in mind when they saw my response.

It's disappointing to me that, given our evident agreement on much of the more substantive part of my comment, you took my initial words to be a hostile and deceptive attack.

I have been quite open about the fact that both on HN and elsewhere, I have had the shit kicked out of me for talking about my medical issues and what I have done to get healthier. What with being human, it's a little hard for me to not be "overly sensitive" about the topic. I do try to be as even-handed as possible but repeated vicious attacks do take their toll, no matter how much the victim wants to rise above it.

Have a great day.

1) The way to test a causal hypothesis is always, at bottom, to do a controlled experiment.[1] So we will tease out the effects of diet on different people by finding experimental volunteers, after institutional review boards approve the experiments, and subjecting the volunteers to controlled diets. This is very difficult to do, as almost all human beings eat when they feel like eating WHAT they feel like eating. Earlier human experiments on effects of diet have actually required the experiment subjects to live in the laboratory long-term, and to have every gram of everything they ate during the experiment measured exactly. Even at that, those experiments came up with few clear conclusions, perhaps because the experiments weren't lengthy enough or didn't include enough subjects for strong inferences.

2) Lots of different things cause lots of different diseases. Both poor diets and infections by microbes can cause some kinds of disease, each independently of the other. It is a fallacy of human thinking to think that there is only one true cause of disease.[2]

3) Yes, it would indeed be interesting to gather more data about biomarkers and tissues of people from more human groups, and especially so after experimental interventions as mentioned in my reply to your first question. It will take very detailed data-gathering to figure out what is going on at the causal level that makes the gut biomes different, and what the different gut biomes do.

4) Your "gut reaction" is correct that this study does not have what human geneticist Robert Plomin would call a "genetically sensitive design," such as what a study of twins[3] would have. The human behavior geneticists with whom I participate in a journal club during the school year have made me very sensitive to how much information is missed if studies of human subjects don't take into account genetic similarity and dissimilarity of the study subjects. Much more work needs to be done on this.

My comment to a friend on Facebook after I posted this same story and friends started talking about it was "One tricky thing for you and me doing 'research' on this is distinguishing short-term effects from long-term effects. My life expectancy here in the United States is already a lot longer than that of most people in the world." It may be that you and I, with the health problems we have today in the United States, are still much better off sticking with our current diets rather than emulating the diets of hunter-gatherers in Africa.

[1] http://escholarship.org/uc/item/6hb3k0nz

[2] http://www.sciencebasedmedicine.org/the-one-true-cause-of-al...

[3] http://www.hup.harvard.edu/catalog.php?isbn=9780674055469

You said: Lots of different things cause lots of different diseases.

Due to my genetic disorder, I am supposed to be overrun with disease and simply accept dying from it. I have been steadily getting well for the last thirteen years, which is very frequently met with incredibly dismissive feedback. (My favorite being: Thirteen years of steady forward progress is not evidence I know anything, it is mere wild coincidence. Stranger things have happened.)

My genetic disorder is known to cause the tissues to be too acid. There are multiple books about how the typical American diet is too acid. If you get certain kinds of sudden acidosis (this comes to mind: http://en.wikipedia.org/wiki/Diabetic_Ketoacidosis), they will promptly hospitalize you because it can be deadly within 72 hours. Yet, it is not standard practice to treat or even test for acidosis with my condition. Ant-acids are only prescribed for gut issues like GERD and acid reflux which can occur with my condition. Anecdotally, other people with CF report that they have fewer lung issues when on acid blockers and similar for their gut issues.

Altering my diet to make my body less acid has been one of the cornerstones of getting myself well. I have seen articles linking anti-biotic resistance and biofilms to high acidity and seen research that biofilms can be broken up and anti-biotic resistance reversed if acidity is addressed. Yet, again, this remains not a standard treatment for my condition, which kills you by fostering infections and, ultimately, antibiotic resistance in those infections.

My life expectancy is not supposed to be that high for a modern Westerner. It is supposed to be roughly mid-thirties (granted, my form of CF has an undetermined life expectancy, yet I did nearly die in my mid thirties).

Anyway, I just know of lots of different bits of information linking inflammation, acidity, infection and many of the issues typical of my disorder. So a) I would really like to see more biochemical data (like ph balance of sample tissues) in studies of this sort and b) I am ...flummoxed as to why people seem to think we do not have enough data to say, yea, verily, acidity is a primary issue we should treat for to control symptoms of various conditions. (Because there are a lot of conditions associated with my genetic disorder but not unique to it, such as early onset osteoporosis, diabetes, arthritis and on and on.)

For your first one: I didn't "test" anything. I followed progress symptomatically.

For your second one: I read up on alkaline foods and skewed my diet somewhat towards those (lettuce, white corn, and watermelon were a big part of my diet for a long time). I also took a lot of supplements ($300/month for years), some of which were alkaline minerals that people like me are typically deficient in (such as calcium and magnesium). I also found that excluding pro-inflammatory oils and certain other pro-inflammatory foods (like peanuts) made a big, big difference.

That's it in a nutshell, but, again, this is 13 years of work I am trying to summarize for you. So a nutshell doesn't really do it justice.

Edit: Sorry, I missed your third question: How it impacted my acidity. I no longer have acid reflux and similar. That's the best I can say about that specific question without being dismissed as a whack job. (I also have a lot less of other issues, but those issues are not things I can "prove" are related to reduced acidity.)