This is not true. The laws of thermodynamics apply to open systems as well as long as you take into account the energy that enters and leaves the system, which is exactly what calories in, calories out mean. The brain influencing how many calories are spent is just part of calories out. What doesn't work is equating calories out with imprecise estimates from websites, watches etc, or equating calories in with imprecise calorie counts from food labels that people often miscount anyway. But when calories are carefully measured by scientists (i.e. in a metabolic chamber) and everything is accounted for, it's calories in, calories out all the way.