Calories are a measure chemical energy, not mass. Our digestive systems don't get anywhere near e=mc^2 in their efficiency. The conservation law is MIMO; calories are way more complicated. For example, people who extol CICO rarely take into account the fact that poop has a variable amount of chemical energy, which depends on a huge variety of factors including gut flora, hydration and fiber intake, or that most of our mass output is actually exhaled CO2.
Trying to be super precise about calories may be complicated, but nobody has to do that to reach a caloric deficit anyway so who cares. Eat less than you need by any reasonable ball park metric and you will lose weight, it's that simple.
The hard part is that for some reason a large percentage of the population can't regulate their intake naturally because what they require for calories to be a healthy weight is misaligned with what they are compelled to consume.
[0] http://www.cnn.com/2010/HEALTH/11/08/twinkie.diet.professor/...
> The laws of thermodynamics define a group of physical quantities, such as temperature, energy, and entropy, that characterize thermodynamic systems in thermodynamic equilibrium.
If you eat 2000 calories of food and burn 2000 calories (taking into account inefficiencies in the metabolic processes our bodies undertake to convert molecules to other molecules), there is no source of energy for you to accumulate fat, regardless of anything else.
Your metabolic rate and the chemical energy of your excrement and the amount of co2 you exhale can be affected by a myriad of factors, hormonal included. But they just change the CO part of the equation, not the fact that CICO is law.
CICO was never law.
The closest practical approximation of this is the calorie measurement we assign to foods. Sure our metabolic processes are not equivalent to a calorimeter - but its easier to measure calories than to account for the specific metabolic process each gram of macronutrient you consume goes through.
So for all practical purposes, and in the context of hormonal effects, energy in vs energy out ie CICO is still law.