The goal of part of the Atkins program, the induction phase, is actually to put you into ketosis. It's not a healthy place to be, as Clod says. You do lose weight but unless you eat quite a lot of healthy complex carbs your biochemistry really goes out of balance. Most people do eat too much saturated and animal fat on the diet (and Atkins never specified not to, just said to always eat full fat rather than reduced-fat foods) and that increases the risk of cardiovascular disease among other things.
It all depends on how it's done. The 'no refined sugar-no white flour' diet is a healthier version of Atkins, cutting out refined carbs but allowing any whole food (in reasonable portions). The big thing is to include a variety of plant-based whole foods, most of them with lots of color and fiber (i.e. cruciferous vegetables and greens in preference to white potatoes), leave out the refined carbs (those apple fritters!), and as Clod says, include nuts and legumes as protein sources. Although every food has protein - you don't have to go overboard on the legumes if they don't agree with you. Eating a variety of whole foods, it's almost impossible to get too little protein.
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The greatness of a nation and its moral progress can be judged by the way its animals are treated. - Ghandi
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