Actually, DNA is being thrown out all the time. You only pass on 50% of it to your child, after all. Of course, since most people have more than one child, the other 50% isn't entirely lost. But it doesn't "taint" your descendents for ever. There's a 50% chance it may not "taint" them at all.
"Taint" is the wrong word in any case, but that's another discussion.
By the way, it's true only 1 % of the DNA is transcribed into protein, but that doesn't mean the remaining 99% is useless. It includes structural elements, binding sites, epigenetic regulators, and so on. In fact, new research suggests that most DNA is used. Just not as a template for protein.
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