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Just as bad, researchers have found that another danger of the Atkins (Low Carb) Diet is increased cortisol levels by allowing cortisol to stay in one's system longer.  High cortisol levels are bad for many reasons, including the fact that they attack neurons, cause weight gain and many other ills. (Read this link on the Brain for more details.)
It should also be pointed out that there was one very large study that found that a low carb diet did little nothing to reduce heart disease risk.  Now contrast all of that with our old friend, the Mediterranean Diet, which is a proven cancer, heart disease and erectile dysfunction fighter and which is low on saturated fat and meat. Study after study has shown the Mediterranean Diet. There is no equivalent body of research from the Paleolithic or Low Carb Diet crowd.
The same goes with the Low Carb (Ornish) Diet. It has actually decreased plaque in the arteries, drastically lowered blood pressure and cholesterol and has turned off hundred of Prostate Cancer genes. Again, the Atkins or Low Carb Diet has no equivalent body of research.
If all of that wasn't bad enough, there are several studies showing meat consumption is bad for the brain presenting yet another danger to males on such a diet. One recent large study with 15,000 participants found increased dementia associated with increased meat consumption.  Similarly, another recent large study of Latin American and Asian populations showed that the more meat consumption, the more the dementia.  In addition, a 2009 study on rats showed that a high fat diet (55%) impaired both cognition and exercise capacity. The animals essentially became "lazy and stupid". And many people eating fast food and/or an Atkins (Low Carb) Diet approach a diet with 55% fat levels. 
A Low Carb diet has also been shown to be much more worse for your mood and outlook. Australian scientists placed participants on a Low Fat Diet or Low Carb Diet and, not surprisingly, found that both groups lost an equal amount of weight. However, the low carb group "felt more angry, depressed and confused" than the Low Fat cohort. 
Finally, it has recently been found that rats fed a high fat diet developed cholecystokinin (CCK) resistance.  Cholecystokinin, or CCK, controls blood sugar production in the liver. A high fat diet limits CCK, leading to overly high CCK levels. Being CCK resistant will very likely prove to be just as bad as insulin resistant and a high fat diet appears to lead to this condition.
NOTE: Many of my readers are interested in enhancing their exercise performance, endurance, power and so on. The above 2009 study on rats found that animals on a high fat diet could run only about half as far as those on a low fat diet.  This is simple chemistry: fat is an inefficient energy source for your muscles. Just as bad is the fact that a recent study found that carbohydrates are just as essential as protein go muscle gains. 
All of this is the reason that you find researchers recommending either the Mediterranean Diet or Low Fat (Ornish) Diet which have a significant body of research showing improvements in heart, cancer and/or auto-immune outcomes.
Here are some related links for more information:
6) Clin Biochem,2004 Sep,37(9):830
7) J Nutr,Jun 2005,135:1339-1342
8) Nutr Metab (Lond),Nov 16 2005,2:31
9) Circulation, 2007, 116:II_819, "Abstract 3610: Comparative Effects of 3 Popular Diets on Lipids, Endothelial Function and Biomarkers of Atherothrombosis in the Absence of Weight Loss"
10) J Clin Endocrinology Metabolism, published online Sep 4, 2007
11) New England J of Med, Nov 9 2006, 355(19):1991-2002
12) Diabetes, 2005, 54:1926-1933
13) Diabetes Care, 2005, 28:1636-1642
14) Angiology, 2000, 51(10):817-826
15) Amer J Clin Nutr, Received for publication February 3, 2009. Accepted for publication May 21, 2009; Emiliano Albanese, et al; "Dietary fish and meat intake and dementia in Latin America, China, and India: a 10/66 Dementia Research Group population-based study"
16) Cell Metabolism, Aug 6 2009, 10(2):99-109, "Intestinal Cholecystokinin Controls Glucose Production through a Neuronal Network", Grace W.C. Cheung, et. al.
17) Amer J Clin Nutr, Received for publication February 3, 2009. Accepted for publication May 21, 2009; Emiliano Albanese, et al; "Dietary fish and meat intake and dementia in Latin America, China, and India: a 10/66 Dementia Research Group population-based study"
18) FASEB J, 2009 Aug 10. [Epub ahead of print], Murray, et. al., "Deterioration of physical performance and cognitive function in rats with short-term high-fat feeding"
19) "Vascular effects of a low-carbohydrate high-protein diet", Proceedings of the National Academy of Science, Published online 25 August 2009, Foo S, Heller ER, W20) Prevention, Apr 2010, p. 45.
20) European journal of applied physiology, 2010 Apr, 108:1125-1131, "Influence of dietary carbohydrate intake on the free testosterone: cortisol ratio responses to short-term intensive exercise training."
21) Journal of Exercise Physiology, 2009, 12(6): 33-39, "Dietary Carbohydrate and Protein Manipulation and Exercise Recovery in Novice Weight-Lifters"
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