Show me the 'proof', is what we defenders of science hear constantly from creationist shills, usually followed up with a smug assertion that there is no 'proof' for evolution. Which kind of makes the initial question puzzling ...
Now of course, science does not deal in proof, what they mean is evidence. And yes, there's plenty of evidence for common descent.
Much of the evidence for common descent revolves around one of six main lines:
- Biostratification of the fossil record
- Transitional Fossils
- Molecular analysis and comparison of mitochondrial and nuclear DNA
- Vestigial Structures
- Observed speciation
- Comparative homology/anatomy/physiology
Most of us vaguely understand how a virus works. The little bastards sneak inside our cells by a variety of ingenious methods. They fool the active transport system in the cell wall, or they slowly burrow through nice and unobtrusive, or some of them just drill right in loud and ugly like some kind of squid from The Matrix, and go about their grisly work. Once inside, they head for the nucleus (Or in some cases they're specialized to attack organelle genetic material such as that in our mitochondrial DNA), where all our nuclear DNA is located. The virus can't reproduce by itself, it has to hijack the replicative machinery inside our own cells. And in doing so, the virus stops the DNA in a cells nucleus from doing it's job keeping our cell alive and healthy. Our DNA receives new instructions from Mr. Virus; churning out more viruses. Once the nuclear DNA has been taken over, a virus can replicate itself in this manner on the order of about six copies per second, and theoretically it won't stop until it eats through all three billion base pairs in a normal human genome.
Then the cell dies, the cell wall dissolves, and away the baby viruses go to infect another cell. This chain reaction can get out of hand real fast, as anyone who's gone from feeling fine, to flat on their back with a new strain of flu in a few hours can attest to.
Viruses are nasty buggers, causing everything from colds, to AIDS. When a virus interrupts a healthy gene it can even cause uncontrolled mitosis; cancer. Some are master puppeteers, such as the rabies virus, which takes control of both the infected hosts brain functions and salivary glands, producing uncontrolled aggression, and uncontrolled salivation, just brimming with more rabies viruses.
So it's nice to be able to say something nice about viruses in the context of evolution ...
Animals have defenses against viruses that shut them down in their tracks, usually anyway. Sometimes, the little bastards will insert in the genome, successfully replicate a few hundred times, the copies reinserting back into the genome, and then the antibody Calvary comes riding to the rescue and shuts those little suckers down before they kill every cell in our body. Once they're neutralized, those little scraps of viral remnants remain in the genome, like a signpost saying "I, Mr. Virus, was here". We can tell they're viral because they code for proteins not used in eukaryotic (Animal) cells such as viral enzymes. These preserved viral scraps are called Endogenous Retro-viruses or ERVs for short.
What's really interesting is occasionally, by chance, the cell thus partially infected with a virus will be a reproductive cell, which also happens to go on to produce progeny. And when that happens, every descendant of that individual will have that same dead viral base pair sequence, like a distinctive genetic 'scar', encoded in the same exact places in a genome that that one reproductive cell had. If you and I had the exact same, unique, viral fragments in the same hundreds of places in our genome, that would be proof-admissible in court-that you and I share a unique common ancestor.
Well, it so happens humans and chimpanzees, have seven, count'em, seven, of the exact same viral base pairs sequences, each roughly one-thousand or so pairs long, and each in several hundred respective locations in their respective genomes. We know how that can happen; chimps and humans shared a common ancestor. We can also estimate how long those viral fragments have been there because there are slight, random changes to the sequence over time. The molecular clock on the shared ERVs works out to about 5-8 million years. Which just happens, oddly enough, to be exactly what the fossil evidence would suggest for a split between the ancestors of chimps, and the ancestors of humans. What a flippin coinkidink, huh? Here's one such shown as a raw data schematic done by my friend, the sexy, hot, DR Lilith. (Lilith BTW, for you lonely science geeks, has a partial differential field equation tattooed on her back. [Hot heavy breathing])
There's more. In addition to ERVs, we also share broader genetic markers that have no function as far as we can tell called LINEs and SINEs. We share them with chimps, we share them with mice. But when a human-chimp ERV just happens to lie in the same region as a LINE or SINE we share with a mouse, why the mouse elements are overwritten by the human-chimp ERV! And that's exactly what you'd expect, if the ancestors of primates diverged from the ancestors of rodents before the chimps and humans split. And when you calculate those molecular clocks, why it works out to about 70-80 million years, which again just happens to line up with the fossil evidence for the primate-rodent split. Wow! Another coinkidink!
We can see how ERVs insert into genomes, we can see how those viral sequences get passed on to cells during mitosis. It's not controversial, we see it happening. We can make it happen on command in a lab. And the argument that it's 'common design' is going to be a particularly hard sale, given that these particular sequences aren't even native to the human and chimp genome, or any plant or animal, on earth. They're only used by viruses.
'Show me the proof' huh? Well, there it is. ERVs aren't just evidence folks, they're more than a smoking gun; ERVs are a high quality video surveillance tape of common descent pulling the trigger. The creationist response? Not much. Usually some vague assertion about 'common design', or that some ERV or other has been found to do something other than just lay there uselessly in the genome. Let's be clear about this; the critical fact here isn't that ERV's have no function, although as best we can tell the vast majority don't have any function at all. The critical fact is how they got to be in the same place on both the chimp and human genome in hundreds of places. Since the point of insertion is controlled by chance and local chemistry, the odds of seven distinct ERVs each inserting in the same exact respective places in both genomes, each genome being several billion base pairs long, and each of the seven inserting hundreds of times, is significantly greater than the chance of winning the lottery 25 consecutive times in a row ...
Creationists really don't have an answer for it, because the only plausible answer is common ancestry of humans and chimpanzees.
You could spend your entire scientific career studying human-chimp ERVs. And those ERVs are just one small piece of the genetic evidence for common descent between only two species, out of millions. And the genetic evidence in turn makes up only one small portion of the over all evidence for common descent. All of those lines of evidence converge on the same solution; we humans share ancestors with other creatures on earth, some more recently than others. This common ancestry interlocks consistently across all the lines of evidence; genetic, fossil, and comparative homology. And that kind of convergence is itself pretty damn powerful evidence.