This post is just some of my current thoughts on chronic disease and is quite speculative at times
Underlying Pathologies Cause Disease
Why is the topic of chronic disease important? Chronic diseases are widespread and cause a lot of suffering: most people (7/10) will die from a chronic disease, nearly a half of adults have from at least one chronic disease and about a quarter of those with chronic disease experience significant limitations in daily activities (US figures from the CDC) 
Following from a previous post, despite chronic diseases being so common, it seems the default human condition is to be healthy*, seeing as hunter-gatherers, traditional cultures and wild animals have near population wide freedom from chronic diseases, such as obesity, type 2 diabetes, autoimmune diseases, cardiovascular diseases and cancer.
Chronic disease doesn’t ‘just happen’. Everything in science has an explanation. Unfortunately, overwhelmingly the explanations generally given for chronic disease are genetics (you got X due to family history), other non-modifiable risk factors (age, sex, ethnicity, etc), environmental factors that are obvious (drinking, smoking, no exercise) or vague (poor diet) or related to triggers (proximal causes), like a stressful period or an injury. While some triggers are quite relevant, they will generally not cause the disease or its symptoms without what some underlying problem/s (the ultimate cause/s) (which I refer to as the underlying pathology)
As a result of these limited explanations, someone who is health conscious, yet has a chronic disease feels powerless. They tried, but they still ended up fat and/or sick. At this point some people, including observers, give up, while others keep trying, but with limited information. The way the medical system treats chronic disease doesn’t help either. Despite a perception of drugs solving a problem, the drugs used for chronic disease often have limited efficacy and some adverse side effects.
What aren’t discussed are the ultimate causes, the underlying pathologies behind the disease in question. I got into blogging about chronic disease because I saw that in the literature there was a lot of information that fairly consistently pointed to various underlying pathologies causing diseases (like mitochondrial dysfunction in type 2 diabetes), information that you don’t generally hear about. This should make a lot sense since the body has many homeostatic processes to regulate things and function. Therefore underlying pathologies are required to disrupt homeostasis and diseases are a condition where function is impaired and has signs and symptoms.
Understanding the underlying pathologies is important for understanding how lifestyle and drugs have their effects, and also to make educated guesses on what to research in the future. However, there was much less information on how lifestyle can lead to underlying pathologies, which is fair enough because that step is much harder. Seeing as chronic disease is almost always caused by an underlying pathology I think we should be more interested in getting rid of the stuff that promotes pathology rather than adding in dietary/health gimmicks and obsessing over things like some obscure compound in a vegetable that reduces the risk of cancer (or whatever) by 10%.
The Jaminets propose that malnutrition, toxins and infections are the main causes of chronic disease, which I agree with. You might be able to add a few things to that list such as chronic stress (is that a toxin though**?), but otherwise it’s pretty complete. Seeing as malnutrition, toxins and infections often cause chronic disease through underlying pathologies a basic flowchart of chronic disease may look like this.
So far I’ve written about obesity, osteoporosis, autoimmune disease, depression, cancer, cardiovascular disease hypertension and acne (remember to check out the links in the summary posts, which direct you to the more in depth posts); and to some extent on insulin resistance, type 2 diabetes, Parkinson’s disease and Alzheimer’s disease
* Angelo Coppola also broadcasts this message, and like me believes it to be a major piece of the evolutionary/Paleo approach:“To me, Paleo is and always has been about “Human beings are not broken, by default.”" - Angelo Coppola
** Glucocorticoids have some very important functions, but they have many undesirable effects if chronically elevated
See Part 2