This write up in the NYTimes simply was poorly done. With a title like "Counting Calories?" -- implying counting calories doesn't work, they don't actually dispell it at all.
Where's the data like, "People who eat fruits, veggies, and whole grains actually ate more calories, yet lost weight". And "among those who ate lots of french fries and potato chips, but yet fewer calories than others, gained the most weight."
Of course I believe those who eat a lot french fries gain a lot of weight. It's a calorie dense food. As are chips.
I'm not saying the title is inaccurate, but rather the article doesn't really substantiate it.