I encounter many intelligent people (not usually LWers, though) who say that despite our recent scientific advances, human consciousness remains a mystery and currently intractable to science. This is wrong. Empirically distinguishable theories of consciousness have been around for at least 15 years, and the data are beginning to favor some theories over others. For a recent example, see this August 2011 article from Lau & Rosenthal in Trends in Cognitive Sciences, one of my favorite journals. (Review articles, yay!)
Abstract:
Higher-order theories of consciousness argue that conscious awareness crucially depends on higher-order mental representations that represent oneself as being in particular mental states. These theories have featured prominently in recent debates on conscious awareness. We provide new leverage on these debates by reviewing the empirical evidence in support of the higher-order view. We focus on evidence that distinguishes the higher-order view from its alternatives, such as the first-order, global workspace and recurrent visual processing theories. We defend the higher-order view against several major criticisms, such as prefrontal activity reflects attention but not awareness, and prefrontal lesion does not abolish awareness. Although the higher-order approach originated in philosophical discussions, we show that it is testable and has received substantial empirical support.
What we know is that reason is extremely useful when applied to mechanical/material subjects. We should continue to use it in that way.
We know that it has extreme difficulty in explaining and analyzing some key issues, including consciousness and all of its manifestations; pain/pleasure, emotions, imagination, and meaning in general as well as others. Once again, this seems to be the case because consciousness itself is extremely difficult to put into mechanical/material terms. Therefore reason has a problem with it.
If a tool is proficient in explaining some things but not other things, is it 'rational' to consider it a universal tool? In this way I am using reason itself to conclude that it is not a universal tool.
So your question is what then should we use to understand consciousness if not reason?
Just as reason seems to do well in understanding things of a certain nature (mechanical/physical), we can look at consciousness and conclude from its mysteries what kind of tool is needed to give us insight into it.
(Notice that I am still using reason throughout this process, it never really leaves our endeavors. We are just being honest in that we recognize something more is there that is beyond its limits.)
Consciousness does not seem to be mechanical or physical in nature because we are not able to even model in theory an explanation for it. Therefore the tool to be used to understand it should have a much more mysterious/abstract nature. Once we make that conclusion it is a whole other topic as to what that other 'tool' might be. Whatever it is, it will probably be more elusive and less universally apparent throughout the human population than reason is.