During times of war civilians are often healthier. Hunter gathers are often healthier. But it can be difficult to tell why. Is it calorie restriction, low fat, low carb, more physical exercise, a combination? Uncontrolled observational studies are good at generating hypotheses but not so good at proving anything because there are too many factors and they are open to different interpretations.
But we can test our hypotheses in animals and in human trials. It's well known that calorie restriction reduces disease. But un-calorie restricted 10% fat diets, (high in fiber and low glycemic index carbs) with and without an exercise program can reverse coronary artery disease in many people. They can also slow the growth of cancer and reduce the rate of diabetes. Insurance companies pay doctors to teach it to their patients because it saves them money on expensive heart surgery.
Based on uncontrolled observational studies, Gary Taubes hypothesized that the addition of refined carbohydrates was responsible for the increased rate of western diseases in hunter gatherers exposed to western food. If this is the only important change then an Atkins diet should work wonders. It is good for weight loss and controlling blood sugar. But when Americans try it, it increases heart disease, cancer and all cause mortality in the long run. The carbohydrate hypothesis has failed to explain western diseases.
What went wrong? Either Americans didn't have the right genes or there are additional differences between the hunter gathers and westerners that are more important that refined carbohydrates. It turns out that there are other differences that affect western diseases. Lack of calorie restriction, excess IGF1, vitamin D insufficiency, a sedentary lifestyle, a shortage of phytochemicals from fruit and vegetables, a shortage of omega-3, eating too much salt, excess alcohol and smoking all have large effects on Western diseases. And according to Weston Price free range meat and dairy (which contain more CLA and omega-3), organic produce, minimally processed food, calcium and fat soluble nutrients and whole grains were important reasons for the health of the people he studied. Since just eating a traditional Atkins diet by itself can't fix all these other problems it can't prevent western diseases other than obesity and diabetes.
There is evidence that glycemic load (mostly from sugar and white flour) is associated with risk factors for heart disease.
http://www.ncbi.nlm.nih.gov/pubmed/20700407
http://www.ncbi.nlm.nih.gov/pubmed/18326601
