I found this article noting the problems, flawed approach, and time consuming method of counting calories.
I don't know who if anyone on his board subscribes to the "calories in vs. calories out" method, but this article sheds a lot of scientific light on why for many people, it just does not work.
As for myself, I generally focus only on macros (protein/fat/carb ratios).
Note that more and more emphasis is on the gut bacteria today. I expect to hear more research and article about it.
IT'S TIME TO BURN IT
The Calorie Is Broken
Cynthia Graber Nicola Twilley Jan 26 2016
Calories consumed minus calories burned: it’s the simple formula for weight loss or gain. But dieters often find that it doesn’t work. Cynthia Graber and Nicola Twilley of Gastropod investigate.
The Calorie Is Broken - Digg