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Many riders who "ride by instinct" but don't understand what they are really doing end up doing the wrong thing in an emergency and crash when there was no reason to crash. Braking and steering are the two most commonly screwed up skills out there. I do think about countersteering when I'm out practicing on a twisty road. I sometimes practice avoiding things on the road with hard countersteering. By practicing it, countersteering is instinct when I need it. Many riders do run off the road in a curve when all they had to to was countersteer or they run into something in the road that could easily have been avoided.
I see discussions about braking on forums all the time and it's obvious a large percentage or riders are pretty clueless on that as well. They brake "by instinct." That may work in normal situations but not in an emergency. Now that there is ABS on most new bikes that is no longer as big of an issue. There is no mechanical device like ABS to save those who can't steer.
OH, and I forgot another important skill: Look where you want to go. Instinct is to look at what you want to avoid. This is a skill that must be understood and practiced or it won't happen in an emergency.
Although this does not have anything to do with countersteering, it follows the same thought process. I am one of those that did not have the experience to "follow my instinct". I took the MSF classes and was told the proper way to handle emergency situations. I did not practice what I was taught. Unfortunately for me, my instinct kicked in while turning into a driveway and a car blocked my entry. Instinct told me to STOP. I braked while in a turn and came off.
After they turned pointed my leg in the right direction, and months of healing, I now practice emergency braking, as well as counter steering on every ride.
I can think of a few things that I did wrong that day. I had a lot of couch time to reflect.