Everyone that is born normal and healthy has the ability to have those qualities. Those qualities are enhanced by the parents when the baby is in its first few years. That is when the babies brain grows the most and all the neural pathways start forming. STUPID CAN BE FIXED... the person just has to want to fix it.
You are born with the capacity for all three, knowledge is gained with the employ of logic&intellect. With out the three you will not know God and with the use of the three you may loose sight of God. Yea, they are given with the capacity to know hence cerebral cortex so if God gave humans the capacity to know then all three are His work.
Intellect is something that you are born with. Logic I don't know. I have seen some booksmart people not be able to figure out something for themselves. They can quote facts, figures and laws, but not be able to reason out a complex problem. So I have to say that logic comes with birth as well. Knowledge is something learned. You can be can be a genius but without learning and experience your are the same as anyone else.
God doesn't like smart people - they tend to ask too many questions, demand evidence for fantastic claims before they'll believe anything supernatural, actually bother to study - in detail - exactly how the holy books were fabricated, think that the God of Love should intevene in preventing human suffering, think that those speaking to the flock on behalf of God are either charlatans or delusional or both, think supernatural beliefs are a direct outcome of superstition - which can't be validated in any credible way, constantly find errors in internal accuracies and the historicity in the holy books, have a repulsive reaction to childhood religious indoctrination and genital mutilation rituals, don't need a deity to be a moral human being, think religions should not escape taxation, are disgusted by so many otherwise intelligent people committing open intellectual dishonesty with themselves, and always claim that wherever you find a lack of knowledge - there you'll find religion, instead. Once science discovers that missing knowledge, after a battle with the zealots, religion scurries off to find some other gap where it can place God - until those demonic scientists again uncover new knowledge, filling in yet more gaps. Religion's only hope is to keep vigilant on indoctrination, frighten superstitious humans into submission, and imprint a version of Orwell's "doublethink" so that a challenged supplicant can always find comfort in magical thinking and endless scriptural quoting - thereby avoiding any reality based challenges to indoctrinated dogma.