I'll upvote your set of questions and reply here rather than make my own top-level comment in this interesting thread.
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.
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.)
I'm curious, what tests do you use to check how acidic your tissues are? How have you changed your diet, and what impact did it have on your body's acidity?
I kind of hate answering questions like this because a) No, I don't have a one paragraph answer (I had a website at one time to try to catalog what I have done and I moved it twice, because of the very ugly attacks on me -- it still exists but not much of it is published online) and b) the answers generally just fuel more ugly attacks.
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.)
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