Fascinating thread, here.
Of the three fears in the OP, fear of the dark is the only truly persistent one in my life. I have always been afraid of the dark, especially in large, open places (a big house, big woods, big yard, etc). I can overcome my fear of darkness in a contained place (a small apartment; I love my studio) or if someone else is in the vicinity (also why I like my apartment). Keep in mind that my parents let me watch tons of horror movies with them when I was pretty young... so I don't know how "instinctual" that one is, either.
As for falling, nope. Never really been afraid of that, as you can see from my sports interests: rock climbing, snow skiing, water skiing, and roller-blading. I've fallen hard in each activity, sometimes from a great height or speed, and usually with pain/bloodshed as a result, but that pain hasn't really conditioned me against doing those activities. I mean, I'm not an extreme-sport person, either... but basic falling doesn't scare me at all. I see it as a temporary setback to what is an otherwise VERY thrilling and fun activity.
I love the adrenaline rush... I think the only biological part of this fear may be if you were born with a more risk-seeking personality, in general.
And reptiles? Meh, they got nuthin' on creepy-crawlies. I detest spiders and other small, leggy and/or winged insects. Reptiles are fine with me, though... I love the feel of a living snake's body as it moves (if I'm holding one, for example).
I do have a very immediate and strong reaction whenever I see a cop on the road, though,
because I have a lead foot. Man, I feel the cortisols rush DIRECTLY into my bloodstream when that happens!!
I do think it all comes down to fear of the unknown, and, for many, many fears...
FEAR OF (unexpected) PAIN.