Keep in mind as well that the percentage of calories in human feces is substantial and rises with higher caloric intake, and drops with lower caloric intake. I don’t see this as a violation of the calories in, calories out model, but we need to account for reduced calories IN, or increased calories OUT. I have seen estimates that extreme overeaters absorb less than half of ingested calories, and almost zero of the last marginal calories.
Also, some calories are derived from compounds more or less depending on the status of intestinal flora. Healthy gut bacteria turn each gram of fiber into approximately 1 calorie of short chain fatty acids.
Connelly argues for one thing that is puzzling though. He suggests that since a pound of fat releases approximately 3500 Kcal in a bomb calorimeter, that it should yield at least 3500 Kcal of work/heat since the body is inefficient, however that is the wrong application of efficiency. A bomb calorimeter should set an upward limit on the amount of work/heat that a pound of fat can do, and the body, being inefficient, should derive less, or no more than that. Personally, I always lose very close to 1 pound of measured fat per 3500 calorie deficit if my caloric deficit is not too great. The body though tends to become a lot more efficient as caloric reductions get greater, and as a result there is less heat, less calories lost in stool, less daily movement, and fewer metabolic end products released from the body that had energy left (urea etc.)
I will mention too, since he brought it up in his video that prednisone can dramatically raise appetite, increase water retention and blood volume, and increase the percentage of calories absorbed from food.
Back to 400 grams of protein, one concern is that it always raises protein oxidation and hormones that oxidize protein. Second is that it always increases ammonia levels. Third is that it could make it hard to achieve spikes in leucine levels since blood amino acid levels would likely be elevated all the time. That is why perhaps this is a strategy for people who are trying to retain muscle while losing fat, or who have other mechanisms of anabolism.
In the videos I posted, Connelly recommends to get to 200+ grams of protein and <200 grams of carbs. Frank Zane, by the way recommends approximately 200 grams of protein and cycling between three days of 100 grams of carbs with 1 day of 200 grams of carbs (on a deficit of 500-1000 total calories a day) cycling into ketosis. Ketosis itself may result in releasing energetic molecules without deriving the original calculated calories from the since ketones can be released from the body without being oxidized.