Introduction
The modern legless snake evolved on Day 6, as one of the creeping things listed in Genesis 1:24-25. It would seem that on Day 6, most ancestor species of today's animals were nearly wiped out around 33 million years ago, by what is known as the Grand Coupure.
Identifying the most likely time period of snake evolution is only part of the story, because most Christians interpret Genesis 3:14 as the time when snakes lost their legs, which was only 6,000 years ago. Given the symbolism of the word snake however, and its Hebrew usage to describe a whispering enchanter, combined with the symbolism of Genesis 3:15, it seems that removing the legs from the "serpent" was symbolic as well.
So, what do we know about snake evolution, and the snakes' loss of their legs? On the surface, not much. On the other hand, we know more than we realize.
Did Snakes Ever Have Legs?
At Answers in Genesis, the article "To Make a Snake" attempts to argue that there is no way snakes could have evolved. There are just too many steps between here and there. He believes that God must have done the changes Himself and done it 6,000 years ago. The author writes...
"Have you ever noticed that snakes move rather differently from other reptiles? Those who claim snakes are simply the legless descendants of other reptiles, really don’t appreciate just how unique snakes are. No matter how carefully you removed the legs from a lizard, it would never move like a snake. Snakes move the way they do, because they have a distinctive backbone. To make a lizard or alligator into a snake, you would need to add special backbones, (vertebrae) in special places. "
If done through surgery, the author is exactly right about how impossible this would be. Obviously, creating a snake this way can only be done by God. However, no one actually believes that snakes were created the way this author describes. However, they have identified some genetic differences that developed in snakes over time. Lenny Flank, a common critic of Young Earth Creationism describes it this way...
"As an aside, we now know, from genetic analysis, why snakes don't have vestigial FRONT limbs. During the evolutionary appearance of snakes, there was a change in one of the HOX genes that shifted the body plan forward a bit. As a result, snakes now have no neck vertebrae --- they are all thoracic and abdominal. Since, genetically, front limbs appear right where the cervical vertebrae begin, snakes can't have front limbs. The vestigial rear limbs appear where the abdominal vertebrae meet the tail. As photos show, the tail of a snake is extremely short. So, even though a snake LOOKS like it is all neck or all tail, in reality, it is all body." - Ed Babinski's Blog
In other words, God did not change the snake through reassembly as so much as He did through genetics. Did He do it all at once or over time? Scientists see evidence that it was done over time. But if that is the case, then one might expect to see transitional fossils. Of course, transitional fossils are rare for a reason... disasters are the primary source of them, and there can be very long time periods in between such disasters. Still, the AiG author believes this lack to be a problem...
"Not only is there no trace of transitional forms in the fossil record, but no one has ever seen a mutated lizard or snake which would give a clue as to how it could have evolved to become so legless, and yet so perfectly adapted to being a snake. In fact, snakes look so deliberately designed that scientists who say otherwise, haven’t really got a leg to stand on!"
Even if evolution were only through extreme random mutations, the lack of such today should not be troubling. Why not? Because according to Genesis 1:24-25, God clearly "let" the land produce the modern species we have today. That was evolution. On Day 7, God rested, meaning we do not see evolution today... or at least not macro-evolution.
As for transitional fossils, the scientific understanding of snakes has increased trememdously over the years, as scientists have discovered remains of legs in modern species. More than that, they have even found the fossil remains of an actual legged snake, dating to 90 million years ago. As Lenny Flank writes in his article "Evolution of Snakes"...
"The living boas and pythons all have tiny clawlike toes protruding from either side of their cloaca--these are the remnants of the that their ancestors once had, and are thus an evolutionary relic tying the snakes directly to their lizard ancestors."
National Geographic goes into even more detail in the article "Snakes Evolved on Land, New Fossil Find Suggests"...
"Many living snakes, such as pythons, have the vestiges of legs that are not attached to the backbone and simply hang from the body... By contrast, Apesteguía said, 'In Najash the hip was connected to the vertebrae, so it has a sacrum. No other known fossil or extant snake is so primitive as to retain this feature.' The sacrum is the bony structure that connects the spine to the hips in vertebrates, including humans. The animal's sacral region would have made its legs well suited to digging or crawling, the researchers say, giving weight to a land-based origin for snakes."
The Najash fossil dates back to 90 million years ago, a descendent of the reptile preceding it, an ancestor of the modern snakes that followed.
Conclusion
It should be no suprise that God would create leg-less snakes from legged one, and then symbolically take Satan's legs out from under him as punishment for his temptation of Adam and Eve. The evidence tells of extreme of changes in snake DNA, and in turn their anatomy. These are changes that were allowed to happen per God's command, and changes He mirrored symbolically as Satan's punishement in Genesis 3.
Bottom line: Snakes evolved. Jesus crafted them (Proverbs 8:30, John 1:1-3). God allowed them (Genesis 1:24-25). Satan acted like one (Genesis 3:1), and was cursed accordingly (Genesis 3:14-15).