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It used to be common for creationists to talk about “the missing link” between humans and earlier primates – to say that if humans really did evolve from apes, then there should be fossil evidence of species that were halfway between them, and that no such fossil evidence existed. For a while, this was a fair point; but then scientists actually did start discovering those missing fossils – the most famous of them being an Australopithecus afarensis nicknamed “Lucy” in 1974 – and they kept discovering even more in the ensuing decades. As it stands today, scientists have pieced together such a smooth progression of transitional species that the biggest problem is trying to differentiate exactly where one species ends and the next one begins – the fossil record is that comprehensive. You can go all the way back to the point about 7 million years ago when humans and chimpanzees first diverged, and from there you can trace the hominin family tree up through species like Sahelanthropus tchadensis, Ardipithecus kadabba, Ardipithecus ramidus, Australopithecus anamensis, Australopithecus afarensis, Australopithecus africanus, Kenyanthropus platyops, Homo habilis, Homo erectus, Homo heidelbergensis, and more, all the way up to the branch that would ultimately become Homo sapiens.

(Just as a side note, by the way, Neanderthals aren’t directly included in this ancestral chain – they’re more like our distant cousins than our direct predecessors – but Neanderthals did do a bit of interbreeding with early human populations, so all their modern descendants (i.e. anyone who’s not African) now have genomes that are about 1-4% Neanderthal.)

If we were detectives, trying to solve “the case of the missing link” as if it were a classic missing persons case, our job would be insultingly easy; we have the victims’ remains right here in front of us. And not only that – like any open-and-shut detective case, we have DNA confirmation as well. This is yet another line of evidence through which we can trace the evolutionary histories of different species; in the same way that we can use DNA analysis in criminal investigations, paternity tests, and family ancestry, we can use it to discover our deeper evolutionary ancestry too. The Cassiopeia Project explains:

Like fingerprints, the patterns recognizable in [certain sections of DNA] are unique to individuals. They are similar in relatives, and less similar in distant relatives. This is the basis of DNA fingerprinting. And since these sequences are passed down from parent to child, finding the same sequence in the same place in two different organisms is direct evidence that the two organisms have a common ancestor. Biologists have used this idea to demonstrate exactly how different species are genetically related.

And Underlings elaborates:

If all life is genetically related, then species that are closer to humans on the evolutionary tree (based on physical characteristics) should also share a higher percentage of DNA compared with species that are less similar. Sure enough, we now know that humans share approximately 99.5% of genes with other humans, 98% of genes with chimpanzees, 93% with monkeys, 92% with mice, 90% with cats, 84% with dogs, 80% with cows, 60% with chickens, 44% with fruit flies, 26% with yeast, 18% with plants, and 7% with bacteria. Creationism couldn’t have predicted that we would share any genes with other species, much less that the percentage of shared genes would align with the evolutionary tree.

[…]

Not only that, but in recent decades, we have discovered that DNA mutates at a predictable rate, and we can use the differences in DNA between any two species to determine how long ago those two species diverged from a common ancestor. The results of this molecular clock closely match the evolutionary tree and the radiometric dating of the fossil record. Again, there is no way creationism could ever predict this, but it is exactly what you would expect to see if evolution is true.

[…]

Another piece of evidence from DNA is the existence of pseudogenes, otherwise known as dead genes. These are genes that have become deactivated, usually because the species no longer needs them in order to survive, and so they are no longer selected for. For example, all primates lack the ability to produce vitamin C. This likely occurred because there was plenty of vitamin C in our ancestral diet, and thus the gene to construct it offered no survival advantage, which allowed it to accumulate damaging mutations. All primates still have the DNA sequence to make vitamin C, but it is missing a vital enzyme which has caused the gene to become inactive. Similarly, dolphins have genes for detecting odors in both water and air; however, since they are no longer land animals, they have little use for detecting odors in air, and now 80% of those genes have become deactivated. Also, only the most primitive mammals – the platypus and spiny anteater – lay eggs, but all other mammals contain dead genes for producing a yolk sack. Human embryos, for example, have a vestigial yolk sack that detaches in the second month of pregnancy and is reabsorbed by the body. If all species were original, perfect creations, the existence of these dead genes from ancient ancestors would make no sense. Their existence is thus evidence against a perfect creator. Pseudogenes only make sense in the light of evolution, where nature carries ancestral genetic baggage.

Yet another piece of evidence from DNA comes from another type of dead gene called endogenous retroviruses, or ERVs. Retroviruses reproduce by inserting their DNA into the DNA of a host’s cells. On rare occasions, they can leave dead genes in the host’s sex cells, which are then passed on to all future descendants of that host. Those dead genes act like an identifying bar code, so if two different species possess the same ERVs in the same locations in their genome, it indicates that the two species share a common ancestor that was infected prior to becoming two separate species. For example, the human genome contains more than half a dozen ERVs that are also shared by chimpanzees, which only makes sense if we once shared a common ancestor. This is another example of nature carrying ancestral baggage that we would expect to see if evolution is true. Creationism, on the other hand, would predict that such connections should not exist, and it has no credible explanation for ERVs.

There are two clips in particular that I highly recommend for understanding just how compelling the genetic evidence is. The first is from the Cassiopeia Project, and briefly discusses pseudogenes before presenting an especially insightful illustration of how ERVs confirm evolution:

The second one, from Ken Miller, demonstrates one last piece of genetic evidence for evolution – chromosomal fusion. This one, for me, was the final nail in the coffin when I first learned about it:

What this clip really drives home is the way in which evolutionary science doesn’t just explain the facts that are already there. It can actually make testable, falsifiable predictions about what else would have to be factual if evolution were true; and in every single case, those predictions have proven to be right. There’s no way that a creationist theory of biology would have been able to predict chromosomal fusion, or the exact location of the Tiktaalik fossil, or any of the countless other things evolutionary theory has successfully predicted. But time and time again, evolution points the way to new discoveries like these, not just in one narrow subspecialty of biology, but in every area of the field.

And that’s the other crucial point here: The scientific consensus around evolution isn’t just a product of a single line of evidence – it’s a convergence of evidence from multiple different fields (also known as consilience). If even just one of these lines of evidence pointed to evolution, then that alone would be enough to conclude with extremely high confidence that evolution was true. But in theory, there’s no reason why the evidence from genetics should necessarily match the evidence from the fossil record; they’re two completely different domains, and the age of a fossil in the ground is totally independent of the ordering of nucleotides in a genome. Yet these separate lines of evidence all agree with each other perfectly, down to the last detail; the distribution of vestigial organs and other such anatomical traits perfectly matches the distribution of mutations in the genetic code, which perfectly coincides with the chronology of the rock layers in which the fossils are found, which perfectly corresponds with the different species’ modern geographical distribution, and so on. Genetics, molecular biology, paleontology, geology, biogeography, comparative anatomy, comparative physiology – all of these fields are independent of each other, but they all point to the same evolutionary story: not just a tree of common ancestry, but the exact same tree of common ancestry. To suggest that all these different lines of inquiry could, by sheer coincidence, somehow produce the exact same answers to millions of different questions, completely independently of each another, beggars belief. If you were a detective trying to solve a crime, you might not trust the testimony of one eyewitness alone – but if there were multiple eyewitnesses, and phone records, and DNA testing, and video surveillance, and a hundred other things that all pointed to the same conclusion, you’d have no choice in the matter. And the same is true of the evidence for evolution; there’s just no word for the staggering confluence of evidence here other than “conclusive.”

Now of course, creationism insists that evolution is “just a theory.” But as QualiaSoup mentioned in his video earlier, this is based on a misunderstanding of how the scientific use of the word “theory” differs from the colloquial use of the word. Commenter DirtySketel reiterates the point:

In normal everyday language, we usually use ‘theory’ to mean ‘guess’ or ‘hypothesis’. In scientific terms, the theory is an explanation of the observable facts. A body of knowledge, if you will. For instance, ‘music theory’ is the body of knowledge surrounding musical composition. ‘Germ theory’ is the body of knowledge that explains illness and disease. ‘Cell theory’ is the theory that explains that all life is made of cells. ‘The theory of gravity’ is the study of gravity, and the explanations for the facts (or even laws) of gravity that we see in nature. The theory of evolution is no different. Evolution is a scientific, observable, fact, just like cells, germs, and gravity. The ‘theory of evolution’ is the study and explanation of these facts. If you’ve ever heard a creationist say ‘evolution is still only a theory’ or ‘evolution is not yet a law’ or ‘they’re still trying to prove the theory of evolution’, then they are simply wrong, and misunderstanding the scientific meaning of the word ‘theory.’

In other words, scientific theories don’t become facts when they’re proven true; they contain facts that have already been proven true, and explain why they’re true. The fact that evolution does occur is an inescapable reality of the world we live in. Evolutionary theory helps us understand how and why it occurs. At this point, there’s just no way to properly comprehend the living world without it. As the (Christian) evolutionary biologist Theodosius Dobzhansky famously put it, “Nothing in biology makes sense except in light of evolution.”

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