We know there is conservation of mass and energy in nature. Any chemical engineer can write mass and energy balance equations that represent this conservation.
Calories in = Calories out is an simplified form of a more complex energy balance equation that looks something like this:
(Enthalpy in) - (Enthalpy out) + (Heat/Energy crossing boundary) - (Work) = (Change in Internal Energy/Accumulation)
... plus a few more equations that represent component energy balances.
Calories in = Calories out makes some naive assumptions and neglects all the internal biochemical reactions, and hence presents a skewed picture of the thermodynamics.
(Enthalpy in) - (Enthalpy out) + (Heat/Energy crossing boundary) - (Work) - (Change in Internal Energy/Accumulation) = 0
But when you state it like you did, there's an implication that the left hand side are the causal factors and that(Change in internal energy/accumulation) is the effect coming out of those causal factors. The problem is that there are many people with deranged metabolisms where their bodies are hormonally imbalanced to increased internal energy accumulation, which then by necessity disrupt the rest of the equation by either raising food intake or reducing energy expenditure.
http://www.bmj.com/content/349/bmj.g7257
>> Most people believed that fat is converted to energy or heat, which violates the law of conservation of mass. We suspect this misconception is caused by the “energy in/energy out” mantra and the focus on energy production in university biochemistry courses.
The energy balance equation is a fundamental thermodynamic equation. It is inherently coupled with mass balance equations. If we didn't get this right, we wouldn't have been able to design chemical reactors all these years.
Unfortunately because enthalpy is a more abstract concept, it isn't very appealing to folks who like simplifications like calories in = calories out. It is, however, the correct concept.
Basically it says that the metabolic mechanism of fructose is different from other forms of nutrition. Our bodies have no good ways to break it down without harming ourselves. The long term effects of eating fructose are comparable to long term alcohol drinking. I assume nobody would say that calories from alcohol are the same as other food sources?
That's an extreme statement you definitely need to provide source for. I read a lot of scientific journals on the subject and have never heard anything like that.