Where to begin? This article begs more questions than it answers! For starters I love herpetology and all things reptile and have as long as I can remember (I have a Corn snake myself actually), so anything to do with reptiles intrigues me.
To jump in, we know mammals and birds evolved AFTER reptiles, i.e. Dinosaurs. So according to this article, feathers, scales, and hair all arise from the same structure of proteins. But modern reptiles may have a completely different skin structure from Dinosaurs, thus why hair, feathers, and scales all share a protein and are grouped together rather than hair and feathers being derived FROM scales (or at least the scales of today). Could this be why the reptiles we have today survived and the dinosaurs went extinct?
Is it possible that the common ancestor is the Dinosaurs? Chronologically Dinosaurs emerged before birds and the modern snakes, but both animals though having evolved after, still lived during the Dino age. As the titan of the skies, Quetzalcoatlus flew he began to share his airspace with feathered birds before the great Meteorite pounded the Earth. The last T-Rex stomped on the same Earth that early Boas slithered on, whom within five million years following the Dino's demise (a blink in evolutionary time), evolved to the peak of power in the form of the 50 foot one ton Titanoboa. Even the crocodiles shared the same waters as the Dinosaurs.
The difference is that some evolutionary advantage allowed them to survive while the Dinosaurs died out. Perhaps it was this protein structure that feathers, hair, and scales share. As we learned in Bio two years ago a certain chain of codons makes a protein. that becomes a part of the gene. But if along the way a mistake in the assembly of these chains occurs the result is a mutation. If this mutation which alters the protein which controls our traits is advantageous, we die and along with us our mutated legacy. But if the mutation IS an advantage then we survive with greater success than those with the original chain, we become the 2.0 model, pass on our gene, the old becomes obsolete, and evolution in a nutshell. The birds and the snakes along with the early mammals (little rodents) lived under the shadow of the Terrible Lizard for millions of years but when the meteor rained on their parade, the evolutionary difference in their skin allowed the birds to quickly dominate the sky, the Boa to reach colossal proportions, and the mammals to rapidly grow and diversify. What if the gene within the Dinosaurs was the original, the papa gene, the common ancestor, and our new skin protein, the winning mutation?
Say this is so, this begs the question. What really were the Dinosaurs covered in? More studies are showing Velociraptors coated in feather like coverings, but there is of course still the old thought of reptile-like scales. But if they were covered in scales, clearly they would have to be a very different scale than what we are used to seeing because if this theory is correct snakes survived because of their different skin protein. To think we still don't even know if Dinosaurs were scaly lizards or feathery birds!
Something I can add from personal knowledge is that Birds and Crocodiles both share the same fibrous protein Keratin. Keratin is like a combination of horn and scale and is what makes up the Croc's scaly hide and a bird's scaly feet. It also makes up many antlers, and the scales of turtles. The difference between snake scales and Croc scales is that snakes form theirs on the epidermis while Croc's form theirs from the deeper dermis (the reason a snake sheds it's skin and why we don't see 20 ft long Crocodile sheddings in the water). A study actually found that crocodile beta-Keratin are closer related to birds than the Keratin of other reptiles! And well we know birds to be the closest living relative to the Dinosaur...could there be a connection there?
And what does it mean when Milinkovitch says of the skin bumps in reptiles, "they appear briefly"? Do they go away after the fetal stage is complete? If so what does this suggest if they appear in mammals and birds but only the embryonic stage of reptiles. Also the article said they found the bumps in scaly bearded dragons but did they mean fully grown or embryonic? This too would be highly intriguing, that during the breeding process the breeders voided the gene for scales (a common practice in the pet snake trade, but resulting in expensive snakes), and in doing so brought back the gene that cause the skin bumps. Could this mean the skin thickening is simply not needed with the presence of scales, hence why it appears on furry, feathered, and scaleless skin?
As I said, this discovery begs more questions than it answers. In the words of Einstein, "As our circle of knowledge expands, so does the circumference of darkness surrounding it."