an increase in the effectiveness of absorbing calories, or something in the food affecting their metabolic rate.

you aren't a blast calorimeter, the food you eat obviously is not reduced to actual ash, so it's certainly possible that there are changes in either the inflow of calories that your body is able to actually absorb or that something in the food is changing the rate at which you burn it. There are also various diseases and syndromes that could affect either of those processes.

"calories in, calories out" is the only useful advice you can really give to people trying to lose weight, but that is not a scientifically rigorous position as far as the sum total of hormonal and microbiome processes involved in digestion and metabolism. Again, the food you eat is not reduced to ash, and there can definitely be changes in the processes involved.

And indeed that is what the facts show - lab animals being fed controlled diets are now getting fat, as are feral animal colonies, so it doesn't make sense to make reductive and antagonistic remarks like "thermodynamics suddenly not a thing!?". The scientific process has showed you that your hypothesis is wrong, and it's now your duty to re-examine your hypothesis and account for the discrepancy. Maybe it's the study, maybe not.

https://royalsocietypublishing.org/doi/full/10.1098/rspb.201...

But to be similarly reductive - "what, do you think feral cats are suddenly spending too much time at their desk job?"

Feral cats aren't getting sugar in their diets, they haven't reduced their activity levels, and any increase in food supply should result in an increase in feral cats until the population can no longer be sustained, the predator-prey population cycle is as immutable as thermodynamics. Why are they getting fat, if calories in = calories out? Thermodynamics still works, right? So what's your alternative explanation? Maybe it's... not quite that simple?

The most worrying potential answer is that we've created a variety of endocrine disruptors and those have permeated our environments. They get picked up by scavengers like mice and birds from our food and its packaging, they get picked up by cats who eat the mice and birds, etc. Potentially, they could end up even in things like fertilizer or pesticides that get turned into animal feed and fed to lab animals.

This is also potentially backed by other effects, such as the continuing decrease in the age of menarche. Nobody really knows whether it's tied to changing patterns of exercise/weight, or whether those are comorbid effects from exposure to endocrine disruptors/pseudo-hormones. It is definitely decreasing in societies where not everybody is working a desk job and eating 3000 calories a day but people would be exposed to the chemicals endemic to modern society.

Things like bisphenol compounds in receipts that we handle daily worry me greatly. 100 years ago people still had desk jobs, but they weren't handling thermopaper receipts and then throwing them in the trash where rats get them in the dumpster/etc. They weren't getting all their food in plastics and BPA-lined cans (or whatever the new compound they've moved onto since then). Food wasn't packaged in wrappers lined with BPA, they used wax paper. Etc etc.