1. Calorie counts on labels undercount by up to 18%
2. Other factors to weight than pure calories, including genetics
3. Certain foods have low calorie counts but are worse than others with higher counts
4. Eating whole foods is better than non-whole foods and helped the subject of this article lose weight better than calorie counting & exercise
Worshipping whole foods is not the answer, you need balance. Plus who wants to live life like a Buddhist monk? Having a burger or pizza every once in a while is fun, it's just about moderation.
I'm calorie counting right now via a food journal, trying to stay under 2K a day (I also exercise 5-6 days a week, often 2x a day), and I'm oddly enjoying the experience.
One, I can't cheat myself. Before I'd get frustrated trying to lose weight and failing, feeling like I tried really hard and "deserved" it. But with the calorie count you know if you did or didn't. It's very easy to forget or not realize how much you're eating exactly, that's why you write it down.
Also, I feel rewarded if I eat salads every day, like I'm getting points in a game or something. Not everyone's brain works that way but for me calorie counting makes dieting more scientific, at least somewhat.
Articles like these are somewhat unhelpful because yes it's great to eat whole foods but so is 1) watching what you eat 2) relying on moderation and 3) exercising.
P.S. Didn't like how the article implicitly denigrates running as a weight loss tool just because this one person didn't succeed doing it -- not exactly a rigorous analysis.