1)     Apples as we know them today were first domesticated in Central Asia.  These, and other apple cultivars, started as small crabapples, and had to be selectively bred via grafting rootstocks.  Apples were spread out of Central Asia to Europe no less than 5500 years ago, but apple breeding didn't become popular until only a few hundred years ago.

2)     Modern apple breeding/domestication starts with a set of cultivars and then selectively breeds for favorable traits, such as flavor, disease resistance, drought tolerance, etc.

3)     Uncertainty in the scientific method forces large sample sizes, many attempts, countless mistakes, and much more upon us.  Without it, we'd only have to do stuff once, ever, to know if and how it worked.