Junk DNA has been getting redress for decades of ignominy. Now, retrotransposons and transposable elements may be next in line for a better reputation.
If lateral gene transfer is rampant throughout life, the universal tree of life becomes a matter of philosophical preference, not empirical demonstration.
Some evolutionists are becoming bolder in their assertions that information can arise from stochastic processes without intelligence.
Why not treat the whole genome as functional? This is a radical concept, but perhaps the focus on genes distorts our understanding.