The article seems to indicate that, counterintuitively, your Total Energy Expenditure (TEE) wouldn't have changed much after you stopped the regular cycling (see the section about how hunter gatherers walking 8-14 km a day had the same TEE as average US), so your weight gain may have been from second-order effects of coming back to your diet.

Do you remember whether your diet changed at this time as well?

Some other anecdotes shared here seem to share a similar theme, that exercise helps in losing weight on a more meta-level by shifting yourself into a generally healthier mindset which, in turn, seems to help you eat "healthier" foods, which is probably a proxy for "low-calorie foods" like fruit and vegetables. Maybe when you're sedentary it's easier to reach for the bag of potato chips?

I'm starting to think that these kind of scientific studies, that focus on a single factor and rule every other variable aside, are not the best way to analyze weight loss.

Because following that logic, exercise supposedly does not work if you want to lose weight. But if every study around aerobic exercise arrives at that conclusion, why aren't the majority of athletes overweight? Where are the fat runners?

Is this a survivor bias? (Fat people even with great aerobic capacity end up hurting their joints so they stop running)

Is it because the addition of exercise generates other kind of changes in the body, like less insulin resistance, and overall more signals in the body to burn fat rather than store it?

Do runners spontaneously change their diets once they get used to their new lifestyle? Maybe the food they used to eat, both in amount and in composition, makes them uncomfortable so they start making lasting changes?

Yes, it does look like running a static amount every time has diminishing results. But, overall, people who run tend to be less overweight. And a lot of overweight people who start doing exercise and stick to it, tend to lose the weight, or at least they lose fat and gain muscle.

I am pretty sure my diet stayed pretty tight, as I monitor my caloric intake using my smartphone and it remained pretty consistent. Obviously this could be skewed for other reasons so it's not gospel.

The "much" is carrying a lot of weight, so to speak, in your comment. As a reference I went from running ~25 miles a week to just walking a fraction of that as I've recovered. I did keep up my other non-cardio calisthenics throughout, though.

Some napkin math suggests I was over my calorie target by just shy of 300 calories per day over the course of this time period.

That's very interesting because with some more napkin math...

If we assume 3500 additional calories is 1 lb of fat stored on your body, then 3500/300 = 11.6 days you gained 1lb

Assuming 6 months is 180 days, then 180/11.6 = 15.5 lbs over 6 months

Also the article did say specifically that the hunter-gatherers were within 10% TEE of the average US person. That's order-of-magnitude in line with the 300 calories/day, given that the NHS recommended calories/day for men is 2500 and 10% of that is 250 calories.

There’s an idea in the fitness industry called “skinny fat”. Thin people who “look” and eat healthy but when you actually look at their body composition have no muscle and relatively high fat percentage.

I’m my experience people severely underestimate the effects of having more muscles mass and the changes it can cause when you lose some from lack of training.

It also bleeds into peoples thinking. People view exercise as a way to lose weight. And eating less is, rightly, a more efficient way of losing weight. But body composition really matters not just for losing weight, but just life in general.

My own anecdote - when I started cycling about 6 miles to work each, I was ravenous by lunchtime and had much larger lunches than previously - put on a lot of weight.