In my view, the principle limitations in human thought concern panlogism;  stemming of course from distinct ratiocinations of the mammalian species, clearly demonstrated by higher primate intellectual development, all of which is promulgated by the style of teaching at the college level, and in general the pedagogical nature of academia itself, particularly that of European root.  In short, the ends are affected by the mean, the mean being that educators, both religious and scientific feel and suggest that "all must make sense", in which case, panlogism in religion turns to pantheism, either deism or theism, with corresponding doctrine, and in science, into the scientific method with the presumed corresponding doctrine of the Standard Model.
    Indeed, it is a harsh criticism, though however valid.
    In the effort to explain Natural Science and the Cosmos, everyone resorts to of course, "explanation", for how else might we explain?  The spin-off of course is that those things inexplicable fall to the wayside.
    This is understandable, since "All reasoning ends in an appeal to self-evidence."
(Patmore)
    In other words, if the teacher can't somehow provide systemic logic concerning a particular issue, then there is nothing to learn;  directly and dangerously reinforcing the concept of panlogism.
    I say dangerously, because there are already two well taught and well worn notions derived from panlogism afflicting the sensibility of man's reason, notably the Big-Bang and genesis, and despite not only being completely wrong, but big lies, they are continually being taught to the world's youth, leading to an unstable, disharmonious, confrontational and hostile global society.
    One solution to this problem is the recognition that human conceptualization is usually wrong, whereas human constructs are more likely right, and as well, an exhaustive study of such concepts and their competing alternative views.  In the realm of religion, this was not done concerning creationism and in the realm of science, this was not done concerning evolutionary cosmological models.
    Once scholars begin to recognize these limitations, there is a far better chance in both  the adaptation and adoption of other views in all areas of theology and science.
    For more on this, as well as really profound hypothesii, go to 3dnsg.org. or Overview.htm