I wouldn't feel too out of line to say that humans are built with the natural predisposition to differentiate reason and emotion. They may not be concrete mental substances, but nearly everyone intuits that good thoughts, sound logic and true conclusions are based on reason, while man's various irrationalities are attributable to in different ways to his emotions or passions.
Cognitive psychology makes for a more nuanced explanation of human thinking. Reason and passion, which lack discrete identities, are imprecisely replaced by what are often called System 1 and System 2 processes. System 1 encompasses reflexive judgments and heuristics that activate and draw conclusions without much or any conscious thought, while System 2 is replete with higher-order processes that require forethought and constant conscious attention.
It might be tempting to associate System 1 with emotional thinking, but there's not necessarily any emotional involvement in using related processes; a person can assess the reliability of a stranger, reflexively parse grammar and understand basic causality without any emotional disturbance, although all of these would fall under the inuition of System 1. System 2 is closer to traditional ideas of reason in that it's constituted of formalized structures: we process long division in a highly deductive and conscious manner, the same with formal logic and statistical generalizations.
One should resist the temptation to say that one field of processes is superior to the other. Although System 2 is a more recent and presumably complex psychological mechanism, System 1 is in many ways far more impressive: its heuristics are not only generally instantaneous, but it takes highly arcane data and extrapolates it into useful outcomes. System 2 may be useful in second-guessing those outcomes, but in terms of economy it is comparatively impoverished.
Of course it is interesting to see some savants who apparently evoke System 2 processes, often the algorithms for determining large math problems, as easily as System 1 processes. It's not necessarily ridiculous to say that this could gradually become a trait of the general human population, and much of our mental evolution may consist in reflexivizing formerly formal processes, as I'd posit was likely to have occurred with language.
What's important to realize is that instead of having discrete senses of discernment, humans have a hodgepodge of decision-making heuristics, all of which have evolved in a highly ad hoc fashion. We have incredibly complex mental machinery for computing certain arrangements of light as faces or other objects without significant cogitation, as well as a the higher capacity to learn algorithms for deductive logic.
In essence, there are no processes that are natively "good" or "bad" for discerning reality; each one is valuable in the situation in which it evolved, and of course even our more convoluted yet consistent rational thought has to rest on potentially premature generalizations of System 1. Humans may naturally distinguish "rational" from "irrational" reasoning with too much elaboration, but in some sense the overlap is more difficult to justify in cognitive psychology.