The development of feathers, which could not have conceivably "grown" from the scales of dinosaurs.
|From NatGeo.com: A modern bird and archaeopteryx|
Second, we have discovered a lot about the evolution of feathers which Carl Zimmer outlines in an article for National Geographic (read it here). Bird feathers are marvels of the biological world which have perplexed many scientists. Shortly after Darwin published On the Origin of Species, paleontologists unearthed archaeopteryx with a mixture of avian and reptilian traits. Most importantly, this bird/reptile had feathers. Later on, scientists discovered more similarities between our modern birds and the extinct dinosaurs. Theropod dinosaurs (T. rex and Velociraptors) shared many anatomical and behavioral similarities with birds, but most importantly they had feathers even though they were far to big to fly. It seems the fight evolved from reptiles with feathers, rather than feathers evolving in flying reptiles.
This enormous collection of fossil evidence linking birds and dinosaurs still does not answer the original puzzle: how do avian feathers evolve from reptilian scales? The answer begins like most evolutionary problems during development. Feathers erupt from the skin called a placode, which is the same way scale develops. While the reptilian placode expands horizontally (gets wider), the avian placode elongates into the bristle shape which modifies through evolutionary history into the feathers we see today. You can follow this pattern by observing the development of chicks.
To add an intriguing twist, the development of feathers is controlled by gene which researchers discovered in modern alligators who definitely don't have any feathers!