I found these quotes in a popular MA Magazine (Black Belt...March's '05 issue), I think probably relates to this discussion.
The author of the article quoted Master Po (the Blind one played by Keye Luke) from the TV series "Kung Fu" it goes something like this...
"Disicpline your body, Grasshopper, that you may find a greater power. Those who surrender themselves find inner strength. When the heart knows no danger, no danger exists. When the soul becomes the warrior, all fear felts as the snowflake upon your hand."
.........
Quai-chang Kane: "How does one find the strength within himself?"
Master Po: "By being one with all that is without himself. "
.........
Master Po: (continuing) "That prevails which refuses to know the power of the other. Where fear is, does not danger also live? And where fear is not, does not danger also die? Where the tiger and the man are two, he may die. Yet, where the tiger and the man are one, there is no fear. There is no danger. For what creature, one with nature, will attack itself?"
This can be taken in context with the topic at hand and it can relate to several other MA-related themes.
The way I see this in realtion to the topic: Being one with all things one must be "at one" with themselves. Doing this one becomes aware of all things which would alert them to danger. Expanding outward their chi/ki they would know/sense what direction the danger (a club from behind, etc.) is coming from. Relying on gut feelings can only get you so far, but if you're attuned to them on a regular basis (i.e. driving quickly in rush-hour traffic, running in a crowded airport to catch a plane without knocking into anyone, etc.) it becomes instinct.
Yes, we are all born with some form of survivial instinct, we'd have to be but we also must train it, train ourselves to be attuned to it, to listen to it. We'll call it gut feelings, intutition, hunches, best guess but if it is not honed like a blade it can be dull and thus like a dull blade can cause us great damage.
I believe that Miyamoto Mushashi wrote about this somewhere in the book of Five Rings.
To me "gut feelings" and "(human) instincts" are the same thing just one is more finely honed to a razor's edge than the other. This I feel should be ONE of the essences' of a Martial Artist, of
any style. We talk about reading an opponent's telegraphing a kick or a punch. We should strive to be at the point where we already know what they would be doing before they do it. This is the fine line that seperates gut feelings and instinct. To be somewhere else before the blow is even struck, to strike before the opponent/attacker can move a muscle.
I recall reading that Bruce Lee was working on this,during the last few years of his life, honing his own instinct. Being able to read a person well enough to know they're going to strike so he strikes them first and finishes the fight before it even begins. Instead of reading the body set and the telegraphing signals and responding quicker than they would. This is still very servicable but I believe Lee was trying to go above and beyond that (in priviate study/practice) before he died. Read about it somewhere...

My own personal experience with the two (that are actually one) has saved me several times in combative and non-combative situations. Combative example: To turn my head left instead of right and avoiding a blow to that side of my head from behind. Non-combative example: Rappelling down a 710 foot deep mine-shaft (because it was there

) and stopping to rest and getting an overwhelming feeling to stop and head back up, turning around mid-rope and start climbing up, instead of continuing down and crossing another knot (several ropes were tied together), then hauling the rope up (end of the day/event) and finding one of the lower knots was tied improperly and thus wouldn't held. All because a little voice in my head said "not today ... not today." Was that instinct? A gut feeling? Or a higher power giving me a subtle hint? I'll call it a little of all three.

I
try to keep myself honed to this day, but I find myself still caught by surprise, turning around and someone is there that I didn't realize before. It says I still have a long long way to go. But I'm happy with what I got now and work continually to expand it.