Our brains construct an internal, cross-correlated internal representation of external reality through experience. By cross-correlated I mean that if we see a wall within our reach, it is quite reasonable to expect that we could also touch the wall, hear it if we struck it, even smell it if we cared to get up close.
We are perceptually unaware, though, of the neural processes that are involved in constructing perception, let alone consciousness. Equally, we are unaware of the mechanism that leads to release of adrenaline from the adrenal gland upon sensing of danger–though we are certainly aware of the physiological effect of circulating adrenaline.
Similarly, we are unaware of emotional mechanisms, or the neural basis for memory formation. We are unaware of actin-myosin sliding although aware of muscle contraction–or of cellular secretion of hormones, or of mitosis. The examples of disconnection between cellular mechanisms and perception of those mechanisms are as numerous as our cellular activites. The apprehension problem lies partly because of matters of scale–we have evolved to be aware only of the large scale effects of cellular actions and it could not be otherwise.
Out of this divorce between mechanism and experience came mind-body dualism and the conceptualization of a motivating 'soul' beneath physiological mechanisms. Dualism is the 'common sense' idea that some kind of supernatural mechanism is intimately connect to and drives the physical. Dualism is a soul-of-the-perceptual-gap pseudoexplanation.
By extension, out of mind-body dualism came the equally ridiculous notion that some kind of transcendental 'intelligence' can operate in the universe independent of a neural substrate. Regardless of what overly argument-driven philosophers might believe, the evidence indicates that intelligence is an evolved, neural-based phenomenon. Period. End of story. Or, it should be.
(By argument-driven, I refer to the phenomenon of looking only at whether or not the construction of an argument follows the rules of logic, and whether or not the premises conform to Newtonian-level intuition.)
"The philosopher Isaiah Berlin once said that the trouble with academics and commentators is that they care more about whether ideas are interesting than whether they are true." Michael Ignatieff
I think that Berlin's comment also applies to some philosophers and definitely to theologians and apologists.
The potential for mistaken conceptualizations based on 'common sense' or intuitive reasoning ultimately led from philosophy, which sought to answer questions purely by 'thinking' about them, to experimental science that acknowledged, and compensated for, the limitation of pure rationalism. Science evolved philosophically to discard, by expert consensus, old outmoded metaphysical explanations for the physical. Philosophy, divorced as it can be from empirical testing of premises, has not necessarily discarded unsupported theories.
Theists, who must ignore the lack of evidence or counterevidence, have monopolized on this deficiency in philosophy. They call it theology or apologetics. Some of these arguments appear quite logical, but there is an inherent problem with arguments constructed purely on definition or analogy. Any philosophy that seeks to explain the physical, regardless of whether it defines itself as supernatural or ineffable, must cede the field to scientific explanations, where available, because only science can test, confirm, or falsify the physical.
Stephen Jay Gould was, I believe, quite incorrect about his appeasement position termed "non-overlapping magisteria".
apologetics, biological evolution, cell biology, cognition, intelligence, intelligent design, logic, molecular biology, neuroscience, philosophy, science, theology, Gould