Powerful Evidence for Evolution: Non-Homologous End Joining (NHEJ)

There are so, so many independent lines of evidence that support evolution. If I had to pick one, though, that is really compelling and easy and quick to explain, it may be non-homologous end joining.

Sometimes DNA breaks. I mean both strands snap, a complete break. This injury could be the result of a stray proton, or a gamma ray, or something else. It is often due to radiation.

In many cases, the cell can repair the DNA effectively, using a nearby chromosome as a template. When a template is not available, the cell panics. Plan B is enacted. Plan B is called non-homologous end joining, or NHEJ for short. The process is quite complex. The end result is that the broken ends are often trimmed, and the two parts are joined back together.

Now, there are a few different versions of NHEJ. Especially with a couple of these in particular, such as theta-mediated end joining, the result is messy.[1] Parts of the DNA, like the part that got blown away by the proton particle, and some of the ends that got trimmed in the repair process, are missing. What’s more, the whole process is error prone, and we often see mutations at the repair site. And in some cases spare parts get pulled in as the cell grabs whatever is around to use in its fight to stay alive.

As Yuichiro Miyaoka and colleagues remark, “NHEJ is an error-prone mechanism in which broken ends of DNA are joined together, often resulting in a heterogeneous pool of insertions and deletions.”[2] Likewise, as Howard Chang and colleagues write, “This flexibility permits NHEJ to function on a wide range of DNA-end configurations, with the resulting repaired DNA junctions often containing mutations.”[3]

And again, as Graeme Finlay explains, “The stitched-up break might be held together by extraneous segments of DNA, usually copied from a site nearby on the same chromosome, but sometimes copied from anywhere else in the genome. The repair site may have lost some of the original base sequence, either when the injury happened or during the trimming of the loose ends by exonucleases. And a few bases may have been inserted that were not copied from any DNA template.”[4]

Finally, I’ll quote Michael Lieber, one of the foremost experts in this area. He comments, “NHEJ does not return the local DNA to its original sequence, thus accounting for the wide range of end results. Part of this heterogeneity arises from the diversity of the DNA ends, but much of it arises from the many alternative ways in which the nuclease, polymerases, and ligase can act during NHEJ.[5]

So, we can often tell there was a repair. There is a scar. And, the scars are not all alike. They are often recognizable from each other. As Graeme Finlay asserts,  “Any one double-stranded DNA break spliced together by NHEJ generates a unique mutational fingerprint that would provide a perfect marker of monoclonality in the descendants of the damaged cell.”[6]

And this is the key to how NHEJ proves evolution. We have found lots of these scars in the chimpanzee genome. “Scientists have scrolled through genome databases to search for segments of DNA that bear the fingerprints of DNA repair patches. The key indications are that a piece of DNA has been copied from one site into another, concomitantly with losses and gains of bases at the recipient site.”[7]

Then, when we look at the human genome, we see many cases of the same scar in the same place as in the chimp genome. We see this over and over again.[8]

How does this happen? The locations where stray photons break DNA strands should be random. Photons don’t aim at certain locations. And so it seems inconceivable that all these repairs would happen in chimps and humans in the exact same places, over and over and over again.

The explanation is quite clear: These breaks, and repairs, happened in the common ancestor of chimps and humans, and we inherited them, as did chimps. Chimps and humans share a common ancestor. Evolution is true. I haven’t seen an argument from direct creationists refuting this evidence. I don’t think there is any reasonable refutation.

Follow me at my YouTube channel:


[1] Kasey Rodgers and Mitch McVey, “Error-prone repair of DNA double strand breaks,” J Cell Physiol. 2016 January; 231(1): 15–24. doi:10.1002/jcp.25053.

[2] Yuichiro Miyaoka et al, “Systematic quantification of HDR and NHEJ reveals effects of locus, nuclease, and cell type on genome-editing,” Scientific Reports, Published: 31 March 2016

[3] Howard H.Y. Chang et al, “Non-homologous DNA end joining and alternative pathways to double-strand break repair,” Nature Reviews: Molecular Cell Biology, 2017 Aug;18(8):495-506. doi: 10.1038/nrm.2017.48. Epub 2017 May 17.

[4] Graeme Findlay, Human Evolution (Cambridge: Cambridge University Press, 2013), 139.

[5] Michael R Lieber, “The mechanism of human nonhomologous DNA end joining,” The Journal of Biological Chemistry January 4, 2008, 283(1).

[6] Graeme Findlay, Human Evolution (Cambridge: Cambridge University Press, 2013), 139.

[7] Graeme Findlay, Human Evolution (Cambridge: Cambridge University Press, 2013), 139.

[8] Graeme Findlay, Human Evolution (Cambridge: Cambridge University Press, 2013), 140.

Fossil Whales: A Conservative Evangelical Accepts Evolution (Evolution Series, Ep. 1)

Can a conservative evangelical accept evolution? Yes, absolutely. Like I did. The evidence would have to be strong, but guess what? It is Super strong. I believe God used evolution to create life on this planet. Today we’ll look at just a little piece of that evidence, the fossil record of whales.

Check out the video version of this essay at https://www.youtube.com/watch?v=hWihQ5KP1qs

First, some background. I used to be skeptical about evolution. I wasn’t at all convinced that it was true. Then I decided to look into it. I mean really look into it, like go to the primary sources. I’ve spent my life doing research, both professionally and academically, so I’m really good at this research thing. I was shocked by how extensive and sound the evidence is. I had been told that evolution was ‘just a theory.’ Well, yeah, it’s a theory, like gravity is a theory. It’s just as true—we can rely on it to the point where it’s treated as fact for all intents and purposes. The fossil record alone was enough to convince me. The genetics closed the deal, beyond any reasonable doubt. And then things like biogeography and vestigial structures and so on just poured icing on the cake. We may not yet understand all of the hows and whys of evolution, but we can see that it happens. This didn’t shake my Christian faith. It shouldn’t shake yours. And look, God creating life through a process as elegant as evolution gives him at least as much glory as would direct, “Poof” creation.

And this issue is really, really important. The church can’t afford to continue to be known as a body that rejects reality on this topic, as it has with other topics in the past like the heliocentric model of the solar system. And we can’t have potential believers thinking that they have to reject reality to affirm Christian beliefs.

Now if you are a direct creationist, an anti-evolutionist, you may say--- hey John, your PhD is not in Biology, or any earth science, its in Economics, a social science, so what makes you think you make this case for evolution? Well, the point is, you don’t have to be a biologist to come to the conclusion that evolution is true. You just need to follow the evidence and be willing to consider the possibility that you’re wrong. After all, if you’re not willing to consider the possibility that you’re wrong, how can you ever know that you’re right?. So, I may not be a biologist, but what I am is a fantastic researcher, so I can do the work that you don’t have time to do, and pull it all together and do essays like this to help you.

OK, let’s just look at just a tiny slice of the evidence: the fossil record of cetaceans— whales, dolphins, and porpoises. We’ll see that, based on this evidence, either God created by evolution, or he directly created many species in an order that makes it look exactly like he created by evolution.

Now, it is important to note that I am not saying that all the creatures in this video evolved directly from the one before it. Evolution is more like a bush than a ladder, and we have just an incomplete sketch of the fossil record. What we will see, though, is that there is a pattern over time of animals in the fossil record that look more and more like modern whales. We have transitional fossils galore.

It was long claimed that whales, being mammals, evolved from land mammals. From four-legged, furry land mammals. But for a long time, there were no transitional fossils to show this. Finally, transitional fossils were found. We now know of a series of creatures, from four-legged land mammals to modern whales, more or less following each other sequentially in time, each more whale-like than the last.

Before we get into a detailed trail, let me provide a good short summary, given by scholar Michael McGowen and colleagues: “Indohyus, a land mammal, had dense limb bones for walking underwater. Then Ambulocetus had shorter hind limbs and broad feet, better for swimming. Rodhocetus had nostrils toward the top of the head, good underwater hearing, and was a good paddler. Dorudon had forelimb flippers, even smaller hind legs, and a pelvis that was detached from the spine for better swimming. Basilosaurus (as well as Dorudon) had the ability to stay underwater for a long time and dive deep. Fast forwarding, Odontoceti had good echolocation, and Mysticeti had filter feeding with baleen. The trail is very detailed. And compelling.”[1] We’re going to go through those creatures, and more, right now.

OK, so let’s look at the transitional forms. For a long time, scientists thought that whales evolved from land creatures, but hadn’t found many transitional forms in the fossil record to show it. They thought that way because “Looking at a whale’s body and biology, there are plenty of clues that their ancestors lived on land. They breathe air and nurse their young with their own milk, they also have paddle-shaped flippers which encase hand bones with five ‘fingers’. As embryos, whales have tiny back limbs which disappear before birth.” [2]

One prime piece of evidence they were looking for is a bone in the inner ear. There is this bone, in the inner ear, called the involucrum. In whales, it is rounded and thick. It is found thick like this in modern cetaceans (whales, dolphins and porpoises), but in no living land animal. Scientists searched long and hard for involucrums in past land animals, and finally found some.

Indohyus appears to be very much like the land mammal that whales can count as their ancestor, or at least it is a great candidate. It looked like a “heavy set deer.”[3] The bones we have found are from 48 million years ago, but may have been around for a while before that.

The big clue that Indohyus is related to whales in that it had a thick involucrum. But there is other evidence as well. “Its bones were denser than those of fully terrestrial mammals, which kept the creature from bobbing about in the water, and...isotopes extracted from its teeth show that it absorbed a lot of oxygen from water.” [4] And that would be fresh water. Why did it go into water? We have to speculate, but it very likely lived near streams and marshes and likely hopped into water to avoid predators, and maybe to find food as well.

Next up is Pakicetus, which is a little more like a whale. Now, let me start with a detail that anti-evolutionists will likely jump on, and may appear to be the weakest link in my argument. The bones we have from Pakicetus are from 52 million years ago, which is 4 million years before the earliest known bones of Indohyus. Is this a problem? Not really. What likely happened is either that Indohyus lived back several million years before the specimen that we discovered lived, or both Indohyus and Pakicetus share a different, as yet undiscovered, common ancestor from which they both evolved. So let’s get to Pakicetus.

Instead of looking like a long-tailed deer [like Indohyus did], it had a longer jaw and looked more like a wolf, and was more adept at being in water, as anyone who owns a Labrador Retriever, a relative of wolves, knows. It had a long, powerful tail, good for swimming. [5] We think it spent the majority of its waking time in freshwater streams and ponds.

It did have an involucrum, of course, like every animal in this chain. It could not hear underwater. But, its skull exhibited changes in ways that set the stage for underwater hearing in later creatures. [6]

Now as we would expect from this initial foray into water, Pakicetus was awkward in the water. With long legs and the spine of a land animal, it would not be a good swimmer. It would have had to do the doggie paddle to get around. [7] So, Pakicetus was only partially suited for living in water.

Next up is ambulocetus. This appears a little later (closer to today) in the fossil record. As far as appearance, Ambulocetus was a fair bit larger than Pakicetus, and looked in some ways like a crocodile, with an elongated head (although no scales...instead it may have had hair, like a modern seal). A key change here is that Ambulocetus shifts toward a salt water lifestyle. It spent time in both fresh and salt water. It drank both! [8]

It was also a better swimmer. It’s hands and feet were in between land animal feet and flippers. [9] And it had a larger, stronger tail than Pakicetus. Indeed, “Its expanded hands and feet were almost certainly webbed, and it probably swam by undulating its spine to a limited degree and paddling with its feet.” [10]

Next up in time and development is a group of species known as Remingtonocetids. They looked a bit more like whales, with longer snouts and shorter limbs. They were better swimmers than Ambulocetus, as the lower back was more flexible, which made undulating in water easier. And their tails were thick and long. These limbs were still weight bearing, so they still could, and in all likelihood did, walk on land. They likely lived similar lifestyles to modern sea otters. Another advancement of Remingtonodetids is that they completely left freshwater behind. They spent their water time exclusively in salt water. We have evidence that they only ingested salt water. [11]

The next group of creatures in the chain, closer in time to today and more like today’s whales, is a group called the Protocetids. They hunted in the water (salt water, where they spent all their water time). Their prey lived in salt water. [12] They still had limbs, but the limbs were not weight bearing, so they couldn’t walk on land, but would flop around, much like modern seals, sea lions, and walruses. But still spent time on land, at least to give birth. They couldn’t give birth in water. [13] The eyes were on the side of the head, facing outward instead of straight ahead. This is like modern whales.

What about swimming? There were advancements here as well. The “pelvis was less strongly coupled to its spinal column, permitting the first kind of flexibility for tail-driven propulsion in whales.” [14] Whereas prior, the tail merely supplemented leg-powered propulsion, now the tail became the main driver of locomotion.

Next up is Basilosaurus, closer in time to us and much more like a modern whale. They were large! Up to 75 feet long, mostly tail. They looked sleek and eel like, but with a tail fluke and flippers. These guys left land behind for good. They took to the seas and swam all around the world, as we see their fossils in lots of places.

They still had small legs, with knees and toes, however. These were what is called vestigial structures, which means any trait in an organism that is reduced in function when compared to similar structures in other organisms. That topic is not for this video, but we need to pause on it a moment here. They still had feet, and legs with knees. Now, these were useless for walking or swimming. Indeed, the legs were very small, such that they “could not possibly have supported the body on land,” and could not have assisted in swimming either. [15] But they hadn’t gone away completely yet. Why didn’t they completely disappear? They found another use. They were likely used in the act of mating. Direct creationists say that because they had a use, in this case as “copulatory guides,” [16] that supports the view that God directly created them with legs for that purpose. But why would God create “copulatory guides” that looked exactly like miniature legs?! It is much more likely that the legs stuck around, in a much smaller form, because they were coopted for another purpose.

Moving on, there were lots of other changes evidenced in Basilosaurus. For example, the nostrils were halfway between the tip of the nose and the forehead. The elbows could lock, which helped with swimming, but inside the fins were still 5 fingers. And, it could hear underwater really well, unlike earlier forms. But, not yet a modern whale. For example, it still had a neck, it could not echolocate, and it had differentiated teeth and a relatively small brain.

It was a fierce predator. Ruled the ancient seas. A true sea monster. It is thought that it had a stronger bite force than and other living or extinct mammal! [17]

One of the creatures that Basilosaurus ate was Dorudon. Dorudon was quite a bit smaller than the giant Basilosaurus, but still a respectable size. It was different than Basilosaurus in one other important way, the way it swam. Whereas Basilosaurus swam by undulating its body, Dorudon, in contrast, propelled itself with its fluke, like a torpedo, and like modern whales.

It could do this because of a particular trait, first seen earlier than Durudon but really put to good use now: the “pelvis had detached from the spinal column, freeing up the lower spine to power greater tail movement.” [18]

After Basolisaurus and Dorudon, whales species proliferated, and evolution went off on two separate paths. One path was toward modern toothed whales and relatives, like Sperm Whales, porpoises, and dolphins. The other path led to the emergence of modern baleen whales, such as Blue whales, Gray whales, Right whales, and so forth.

So we get to modern day. One last question is worth pausing to consider is how toothless whales, which have baleen, got their baleen. It certainty seems like a big leap. Basilosaurus and Dorudon had teeth. Blue whales have baleen. How did that happen? Well, it appears to have happened gradually. First, there were older whales that had teeth but not baleen. Then, there were whales that had both teeth and baleen. Then, there were whales that just had baleen. [19] Also note that in today’s baleen whales, the embryos have, at an early stage, tooth buds! These tooth buds retract at a later embryonic stage of growth.

I think fossil whales present really good evidence for evolution. We see step by step changes in the record connecting Indohyus to today’s whales. Of course, there is genetic evidence as well, but we’re just exploring the fossil side of things here.

It seems that either God directly created all of these species, in an order that makes it look exactly like evolution took place, or else he created modern whales by an evolutionary process.

The latter choice seems much more likely to me.

[1] Micheal R. McGowen, John Gatesy, and Derek E. Wildman, “Molecular evolution tracks macroevolutionary transitions in Cetacea,” Trends in Ecology and Evolution, June 2014, Vol. 29, No. 6, pp. 336-346.

[2] https://us.whales.org/whales-dolphins/how-did-whales-evolve/

[3] J. G. M. Thewissen, The Walking Whales (Oakland, CA: University of California Press, 2014), 200.

[4] J. G. M. Thewissen, The Walking Whales (Oakland, CA: University of California Press, 2014), 200.

[5] J. G. M. “Hans” Thewissen, The Walking Whales (Oakland, CA: University of California Press, 2014), 144.

[6] Nummela, S., Thewissen, J., Bajpai, S. et al. Eocene evolution of whale hearing. Nature 430, 776–778 (2004). https://doi.org/10.1038/nature02720

[7] Brian Switek, Written in Stone (New York (NY): Bellevue Literary Press, 2010), 167.

[8] The evolution of whales, https://evolution.berkeley.edu/evolibrary/article/evograms_03, last accessed 9/1/19.

[9] The evolution of whales, https://evolution.berkeley.edu/evolibrary/article/evograms_03, last accessed 9/1/19

[10] Brian Switek, Written in Stone (New York: Bellevue Literary Press, 2010), 167.

[11] J. G. M. Thewissen and Sunil Bajpai, “Whale Origins as a Poster Child for Macroevolution: Fossils collected in the last decade document the ways in which Cetacea (whales, dolphins, and porpoises) became aquatic, a transition that is one of the best documented examples of macroevolution in mammals,” BioScience, Volume 51, Issue 12, December 2001, Pages 1037–1049.

[12] Mark T. Clementz et al, “Isotopic records from early whales and sea cows: contrasting patterns of ecological transition,” Journal of Vertebrate Paleontology 26, no. 2 (2006):355-370.

[13] Philip D. Gingerich et al, “New Protocetid Whale from the Middle Eocene of Pakistan: Birth on Land, Precocial Development, and Sexual Dimorphism,” PLoS One, 2009. 4(2).

[14] Nick Pyenson, Spying on Whales (Penguin Books, 2019), 35.

[15] Philip D. Gingerich et al., “Hind Limbs of Eocene Basilosaurus: Evidence of Feet in Whales,” Science 249 (1990): 154–157.

[16] Philip D. Gingerich et al., “Hind Limbs of Eocene Basilosaurus: Evidence of Feet in Whales,” Science 249 (1990): 154–157.

[17] Nick Pyenson, Spying on Whales (Penguin Books, 2019), 55.

[18] https://www.amnh.org/exhibitions/whales-giants-of-the-deep/whale-evolution

[19] Robert W. Merideth et al, “Pseudogenization of the tooth gene enamelysin (MMP20) in the common ancestor of extant baleen whales,” Proceedings of the Royal Society of Biological Sciences 278, issue 1708 (2010): 993-1002. doi: 10.1098/rspb.2010.1280