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:
https://www.youtube.com/channel/UCqotSdoC6TXhJpsj7q6ybSg
[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.
The Dangers of Young Earth Creationism (and how to engage with our YEC brothers and sisters)
The Young Earth Creationist mis-reading of Genesis 1 causes some Christians to lose their faith. It also turns many open-minded unbelievers away from accepting Christianity in the first place. So how should we, who believe in an old earth, engage with the young earth subculture?
Quick programming note: you can view the video of this essay here:
https://www.youtube.com/watch?v=JeTnhbBO2UkF
Young earth creationists are Christians who believe that the earth was created in a span of six days, about 6,000 years ago, or at most 10,000 years ago. They believe that about 4,000 years ago there was a flood that covered the entire earth in water a mile deep and killed every human alive except for 8. In essence, they take early Genesis very literally, and are not convinced by the vast amount of evidence showing that the earth is old and there was no global flood in recent history.
A revival of this line of thought in the American church began with a vision experienced by Seventh Day Adventist prophetess Ellen White in the late 1800s, and accelerated after a book by John Whitcomb and Henry Morris in 1961. Today, a lot of Christians are Young Earth Creationists. Polls are a bit all over the place, but it seems clear that, for example, a sizable majority of conservative white protestants believe in a young earth.
From my own personal experience, the Young Earth Creationists I know generally have amazing faith, are intelligent, and really know their Scripture. They are passionate followers of Jesus. And it is this passion, and zeal for defending Scripture, I think, which leads many of them to hold fast to their belief in a young earth. This is admirable. However, Young Earth views…and especially the teaching that the only way to responsibly read the Bible is as affirming a young earth…is not responsible Christianity. It is problematic for the church. In three ways.
The first way is that it is not good for evangelism. YEC is a big turn off for many potential Christians, especially those who are scientifically minded. Many unbelievers feel they have certainty that the earth is old. And they don’t want to join a religion that teaches things they know are false. YEC really breaks trust and credibility. As Augustine said, when an unbeliever hears a Christian saying that the Bible teaches things the unbeliever knows to be false, the unbeliever will be less likely to believe the Christian on matters such as the resurrection and the kingdom of God.
And logically, who could blame them? You see, Young Earth advocates teach that the only way to understand Genesis 1 is as a literal, historical account. Then they assert—correctly—that the Bible tells a complete, internally consistent story, such that if one part is false then it calls into question the truth of the other parts. So if Genesis 1 is false, the foundation for the New Testament is weakened. Sometimes—and this is really dangerous—Young Earth advocates even teach that if you don’t believe in a young earth you shouldn’t believe in the resurrection.
To put it simply, if we tell unbelievers that in order to be Christians they have to deny almost the entirety of modern science, many are not going to come onboard. They’re gone.
The second reason that Young Earth Creationism is problematic is that it causes Christians, especially young Christians, to lose their faith. In the course of my research on this topic, I have come across many testimonials of people who were raised as Christians and had considered themselves to be Christian, but who left the church over conflicts with science. Typically, they had grown up in a YEC home, attended a YEC church, and internalized YEC teaching. Then, when they were inevitably prompted for one reason or another—perhaps a college geology course—to critically consider their Young Earth views, they realized that they had to give them up. Since young earth creationism was imbedded so deeply into their Christian worldview, they left the church altogether. Some later returned. Some did not. Look, young folks are leaving the church in droves. Science is one of the reasons. We should be doing all we can to address perceived science and faith conflicts.
The third reason that Young Earth Creationism teaching is problematic is that even among those who never leave the church, this issue has real import. Christians have legitimate struggles with science and faith issues. Some, perhaps many, Christians believe that their faith conflicts with science. For as long as that cognitive dissonance persists—even if it is suppressed or ignored—it may be hindering those believers’ spiritual growth. When Christians who cannot intellectually accept a young earth are persuaded that Genesis 1 may only be read literally, they may respond by doubting God’s Word. They may conclude that the first chapter of the Bible is not truth. Once the truth of Genesis 1 is discounted, it is tempting to discount the truth of other difficult parts of the Bible as well.
This happened to me, by the way. A few years ago I had a faith crisis over early Genesis, including Genesis 1. I was, and am, convinced that the earth is old, but I read the text as saying it was young. I was deeply bothered by this perceived contradiction. When I went to my church and saw what they were teaching, and went to my trusted Study Bible, and even, for good measure, went and saw what my kids’ school taught, it all came back the same—they all taught that the earth is young. I thought, well, if my entire faith community thinks this way, is that because the Bible actually teaches that! And if the Bible actually teaches that, how can I trust early Genesis? And if I can’t trust early Genesis, can I trust the New Testament? My church led me further into a faith crisis, which took a lot of time and work to emerge from. We should instead be assuring our Christian brethren that they may believe the earth is old without disbelieving the Bible.
So. All right. We have many brothers and sisters in Christ, whom we love, but with whom we disagree. And this is an important topic, and so we feel we need to engage with them on this issue. But how do we engage with the Young Earth subculture? There are four things to keep in mind.
Number 1. The first thing, and I think this is the most important thing, is to maintain unity. The age of the earth is not a salvation issue. Young Earth advocates and ourselves are both in the Christian family.
Maintaining a spirit of unity can be difficult at times. For me, I struggled with this for a while after my faith crisis. I had anger toward the churches and leaders who had taught me false things with regards to the Bible. I had to work through those issues and get my heart right.
And it was important that I did so. In John 17 Jesus prays that we may all be one, so that the world may see the love we have for one another and that will lead the world to believe in Jesus. Disunity would cause more harm to the church than faulty YEC theology.
So, practice Christian unity, and focus on all the really important things which we do agree on. Pray and worship with your Young Earth brothers and sisters. Also keep discourse respectful. Debate, do not argue. And despite frustration that they don’t accept an old earth, focus on how it is often coming from a place of deep reverence for Scripture. Also if you do get mistreated, called a heretic, or told you are not a Christian, or whatever, be quick to forgive. Living in Christian community provides plenty of great opportunities to practice forgiveness.
Number 2. Remember there are two issues we have to prevail on. We have the science, and we also have the interpretation of Scripture. The science proves an old earth. And the best way to interpret Genesis 1 is in a figurative sense, not a literal sense. Genesis 1 is in conversation with the creation myths of the surrounding cultures. It is about theology, not science.
Some of us are only able to speak to one of the two sides. That’s fine. But as a community, we need to engage on both sides. If we present a good case for the science, but not for interpretation, we won’t win many minds. Why will we not win many minds? On the science front, Young Earthers will keep coming up with new objections that they will say reveal a young earth. These can always be rebutted but the game can go on for a long time. It can become an endless game of whack-a-mole. In the end, even if we “win” on the science, by convincing them the science reveals an old earth, Young Earthers will just retreat to unfalsifiable positions, like that the earth was created to look old. And this could be true. After all, God could even have created the universe last Tuesday, and populated our minds with memories. I could have never actually created this video. But this turns God into a deceiver, and so it is not a healthy position for Christians to take. We don’t want Young Earthers retreating there, and many already do.
So we must also engage on interpretation. Making a good case for the genre of Genesis 1 not being literal history could go a long way toward getting Young Earthers to let their barricades down on the science front. Showing how the science used in the Bible is ancient science, not modern science, could help a lot too. There are many scholars, people like John Walton and Denis Lamoureux and many others, who have done great work here.
Number 3. We should have realistic goals. We can’t reach everyone. Many of our brothers and sisters are just not open to having their minds changed. Most people, of all stripes and persuasions, have difficulty changing their minds on important things. We just need to accept this. We may not be able to change their minds. The reasons for their stance are often psychological, not intellectual, and there may be nothing we can do.
But for some Young Earthers, while we can’t change their minds we can still convince them that a young earth is not the only biblically faithful interpretation of Genesis 1. That would go a long way to limiting the damage of YEC. That would be a victory. Also if we can just let Young Earthers who are already doubting their YEC conviction, but are stuck in the YEC bubble, know that there is a respite for them, an oasis, a safe harbor, a place they can go and give up their YEC beliefs but still be a faithful follower of Christ, that would be a victory too. We can save some who give up YEC from additionally giving up Christianity. That is an attainable and extremely worthwhile goal. This will involve going over the top of their pastors and faith leaders to speak directly to the church members in the pews. As well, if we can better educate the non-Christian community that they can become believers without accepting YEC views, that would be a great success.
Number 4. Lastly, we should be sensitive.
If we have friends who are firmly committed to Young Earth views, to the point that if they gave them up they may lose their faith, and if they are not going around preaching to people that if you are not YEC you are not a Christian, it may be best to let sleeping dogs lie. There is little to be gained by converting them and much to be potentially lost in the process. Basically, pick your battles wisely.
Jesus on the Cross (Psalm 22)
What was Jesus doing on the cross? What were his emotions? He was suffering, of course, but in the midst of his suffering he was also rejoicing! Grab a Bible and let's dig in.
OK, so, besides talking to the two criminals beside him, and talking to his mother and to John, and a few other bits, we don’t seem to know much about what Jesus was doing on the cross. In the Gospels there are 7 things listed that Jesus said. That’s not much. But I think we actually know more than this. His words, “My God, my God, why have you forsaken me?” and then his last words “it is finished” give us a marvelous clue as to what else he was doing on the cross.
I think that among other things Jesus was praying what we now call Psalm 22, in its entirety. And if he didn’t have the strength to sing or even speak, he would have prayed the words silently. That Psalm is a lament, but finishes with rejoicing and triumph.
OK. So first let me address why I think this. Then, we’ll walk though the Psalm and see what it says about Jesus.
Why do I think Jesus was praying Psalm 22? To start with, we know he said the first line of the Psalm. Matthew 27:46 says “And about the ninth hour Jesus cried out with a loud voice, saying, “Eli, Eli, lema sabachthani?” that is, “My God, my God, why have you forsaken me?”” And likewise Mark 15:34 indicates the exact same. Now, this is the first line of Psalm 22. It is not just coincidental that Jesus’ words match the Psalm. Jesus was clearly reciting Scripture. He was praying!
Further, the context of Mark and Matthew may suggest that he said the whole Psalm. Matthew and Mark had just a few verses to tell of the entire ordeal of the crucifixion. The narratives were condensed, with just the most important and representative pieces mentioned. So reporting Jesus saying the first line could have denoted that he said the whole thing. Keep in mind also that when these Gospels were written, the unofficial title of the psalm was likely the first line—that’s what everyone would have known it by. In this case then the text could well be giving the title of the Psalm, indicating that Jesus recited the whole Psalm.
Also The Gospel of John lends support to the view that Jesus said the whole Psalm. John 19:30 says that Jesus’ last words were “It is finished.” This matches a loose translation of the last line of Psalm 22!
So Jesus recites the first and last lines of the Psalm. What about all the stuff in the middle? The context of the situation strongly implies that Jesus was praying the entirety of Psalm 22 while he was on the cross. First of all we know who Jesus was, his person, his character, his personality. He would have been praying! (And we know he did pray for his executioners from Luke 23:34.) The only question is what would he have been praying? Well, there was a prayer written about the crucifixion. He would probably pray that! That prayer is…Psalm 22! Jesus, the Word, wrote Psalm 22 through the Spirit and through David. He wrote it to prophesy about his own death.
He wrote it also, I think, for this very moment in time, that of his crucifixion. For himself to pray in this moment! And think about it. As soldiers are casting lots for his clothing (Matthew 27:35), why wouldn’t he be praying the Psalm that tells of soldiers casting lots for his clothing? What else would he be praying at that moment? As onlookers are sneeringly saying, “He trusts in God; let God deliver him now, if he desires him” (Matthew 27:43), why wouldn’t he be praying the Psalm that describes the exact same thing?
Now, there is an additional reason I think the Psalm was written: To give us a window into what Jesus was thinking and feeling on the cross, so that we could get a clearer picture of who he is! Let’s walk through Psalm 22, to access this. The translation I am using is the ESV.
First, note that the Psalm may work on two levels. On one level it is written by David and may describe, in hyperbole, an unspecified personal odyssey of David. But we know of no experience in David’s life that fits this text. On the other level, underlaying the Psalm, in the prophetic, are lots of verses, and arguably every verse, that deal directly with Jesus’ ordeal. The prophetic meaning is shielded by the thin veil of David’s earthly experience or story.
The Psalm starts with that great cry of anguish: My God, my God, why have you forsaken me! This is a deeply personal cry. In the Psalms, the term “My God” is equivalent to “My Father.” In his humanity, Jesus is suffering mightily. Of course physically—Jesus has been beaten to within an inch of his life and then nailed to a cross and is painfully struggling to keep himself from suffocating to death. But also psychologically. He has been abandoned by his Father, for the first and only time, forsaken, ignored and left to die with no help given, suffering for our sins. The Father has withdrawn from Jesus. And yet Jesus reaches for his Father, who he knows loves him, even though he can’t feel it at all at the moment. In the rest of verse 1 and in verse 2 there are two more cries of anguish, making this a triplet for emphasis.
Next, verse 3. “Yet you are holy, enthroned on the praises of Israel.” In the midst of despair, Jesus praises his Father, and affirms the Fathers’ sovereign rule.
Verses 4 and 5. “In you our fathers trusted; they trusted, and you delivered them.” Just like the Father delivered Israel in the past, Jesus would be delivered from this abandonment, this forsakenness. Israel was not put to shame, and ultimately, Jesus would not be either.
And verses 6–8 show us what a shameful situation Jesus was in! “But I am a worm and not a man, scorned by mankind and despised by the people. All who see me mock me.” All his human dignity is lost. He is the lowest of the low, like a worm who lives in dirt. In the Jewish culture, to be hung on a tree was considered the most shameful way to die. And here he was, beaten, bloodied, broken, likely stripped naked, completely exposed in every way, hanging on a tree on a hill for all to see. And he is scorned, mocked, sneered at. The indignity of the King of the Universe mocked by men whom He created! No one has ever been brought lower.
Now, Verses 9–11. Jesus doesn’t have God with him, on the cross, but he comforts himself by remembering how his Father had been with him since even before birth. “On you was I cast from my birth, and from my mother’s womb you have been my God.”
Now skip ahead to verses 14–15. “I am poured out like water, and all of my bones are out of joint; my heart is like wax; it is melted away within my breast; my strength is dried up like a potsherd, and my tongue sticks to my jaws; you lay me in the dust of death.” Jesus’ focus shifts to his body, which is failing and on the point of death. These things he describes are things that happen, by the way, to a body when it suffers blood loss and dehydration and is crucified. He is in extreme distress. And, he acknowledges that he has been put there by his Father. He is literally being sacrificed by his Father.
In verses 16–18 things get even more intense. In these verses his persecution, rejection and shame are now mixed and jumbled with his physical torment, as his life is slipping away. Look at verse 17. Sandwiched in between telling of others persecuting him and gloating over him, he interjects a painful lament over being able to see all his bones. And he is probably struggling to lift his head at this point, so he is staring down at his body. His physical and emotional distress are merging together now, and mentally, he is likely struggling with disorientation. Indeed, I think he is struggling to maintain his mental sharpness at this point, as death is near and brain function may be failing—he has lost a lot of blood, his blood pressure is low, and his heart, weakened and stressed from the crucifixion, is having trouble pumping blood up to the brain. He is at his breaking point.
So in verse 19 he makes a final plea for help, which needs to come quickly to avert death. “O you my help, come quickly to me aid!”
And then in verse 21b we get the climax, the turning point. “You have rescued me from the horns of the wild oxen!” Jesus, in his abandonment, and now resigned to death, nonetheless knows with certainty that his Father will rescue him. But it will not be a rescue from earthly death! No, it will be taking Jesus from this lowest of low points, this worm, shamefully despised and scorned and mocked, and raising him to sit at the right hand of the Father, to rule in Glory! Jesus, at the lowest point imaginable, and while abandoned, he KNOWS, trusts fully, that his Father will turn his earthly defeat into great, cosmic Victory.
And so in verses 22–26, the focus shifts. Jesus, about to die, rejoices! He looks ahead to the great feast, the great and continual praise and worship of the kingdom of Heaven, where, see verse 26, where the saints, who share in his afflictions here on earth, “shall eat and be satisfied,” and their hearts live forever! What a wondrous vision.
So that’s a view of heaven. What will happen on earth? Look at verse 27. “All the ends of the earth shall remember and turn to the Lord, and all the families of the nations shall worship before you.” Jesus’ name will be proclaimed throughout all the earth, and there will be believers in all nations.
Finally, we get the final verse, 31. “they shall come and proclaim his righteousness to a people yet unborn.” “They” is us, it is you and me. Jesus, in his last moments of life, is rejoicing that we, his children, will be spreading the Gospel today, proclaiming his Glory today! As you sing praise and worship with your congregation, know that Jesus, on the cross, rejoiced that you are doing so. As you share Jesus with your neighbor, your friend, or on a mission trip, know that Jesus rejoiced with his final breath that you are doing so! You are part of his Victory! And we share a part in this way in his crucifixion.
And so finally, the last line, as the screen cuts to black: “that he has done it.” Well, if the person whom the Psalm is written about is telling it, which is what is happening here on the cross, it would be “that I have done it,” which is equivalent to…”it is finished!” Jesus’ last words were words of triumph, announcing that he had opened the gates of heaven to us, for the Glory of his Father. So now to Him, the victorious one, be all glory and honor and praise, forever!
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
Genesis 1: True but NOT literal history
What do you do when…you’re a Christian, and you trust your Bible, but one day you open it up, to the very first chapter of the very first book, and you start to read, and you think…”Wait, this just isn’t true!”
Check out the video version of this essay at https://www.youtube.com/watch?v=MYJ41yyijeg
So, to state the problem formally: A surface level reading of Genesis 1 depicts creation as having occurred in 6 days, 6,000 years ago. Well, I’m sure it didn’t happen that way. Instead, I believe the earth is billions of years old. Does this mean we can’t trust early Genesis? And if we can’t trust early Genesis, can we trust the New Testament?
This is a problem, and so properly understanding Genesis 1 is important to a wide range of people.
Perhaps you are a Christian who is curious about this really interesting and challenging portion of the Bible, and would like to learn more.
Or perhaps you are not a Christian, and are open minded toward the faith, but don’t want to believe in a religion that claims things you know are not true.
Or perhaps it is actually more serious. Perhaps you are a Christian who grew up being taught that the only way to read this part of the Bible was as literal history: That the earth was created 6,000 years ago, in the span of six days. Further, you may have been taught that in order to believe the Bible was truth, maybe even in order to believe in Jesus, you had to believe in a young earth. Jesus said so, you were told. And then one day you have to acknowledge to yourself that the earth is old. Really, really old. So if the truth value of the Bible depends upon the earth being young, and you learn that the earth is old, then maybe you don’t trust the Bible anymore. You may even walk away from Christianity. It happens a lot.
Or perhaps, like me, you didn’t grow up in a young earth creationist subculture, but just gravitated to a surface reading on your own because, well, you were never taught another way to read it. You just assumed that the author was intending to write literal history. But you know that the earth is old, and so you carry around some cognitive dissonance for a long time, hoping that some day you’ll understand the passage.
Quick backstory on my journey. My older son, who was 9 at the time, asked me if dinosaurs existed. I was about to say ‘well they sure did, 65 million years ago, when…I stopped. I instead told him I would get back to him. It struck me that in his Christian school—which was great for him, by the way—he was maybe learning that dinosaurs didn’t exist, or they died in the flood 4,000 years ago, or something. I wanted to prepare for how I was going to contradict his teacher, how I would break this to him. But then I thought, yeah, the Bible seems to teach that the earth is young. I figured there must be an explanation for the Bible teaching something that, on the surface, appears to be plainly false. I went to a trusted study bible and it said the Bible teaches that the earth is young. I went to my church’s archived sermons, and my church taught that the earth is young. My entire faith community was confirming that the Bible teaches something I knew was flat out false. That started a painful season of doubt for me.
OK, back to the main narrative here. So this is a problem. What are the responses to the problem? One response can be to stick your head in the sand, say you’re not a scientist, and just go on with your literal reading of the chapter. You can say, my personal reading of the Bible says the earth is young, so I believe the earth is young, and I’m going to ignore whatever the science says. That doesn’t work for me personally, and if you’re still watching this video it probably doesn’t apply to you either.
Another response is, rather than ignoring the science, is to reject the science. Like, most of the whole world of science. Geology, biology, chemistry, genetics, physics, and on and on. Many Christians do this. In my view this is not a credible or responsible response.
Another response is accept the science but to say that God made the world to look old, putting dinosaur bones in the ground even though there were no living dinosaurs, and so forth. This is possible, of course, but it makes God a deceiver. So I don’t buy it.
Another response is to try to find a way in which a literal reading of scripture is compatible with an old earth. That Genesis 1 literally explains the creation of the earth over billions of years. So, the word “day” in Genesis 1 could mean “a very long period of time.” I have a great deal of respect for people who take this approach, but I think it is wrong. For one thing, the data show it doesn’t work. In Genesis 1, even if the word day means a very long period of time, which I don’t think it does, the order of creation in the Bible doesn’t match what we see happened in the actual world.
At this point, it appears we are at a dead end in how to interpret the text.
But the Bible is true, so there is an answer. What is that answer? The answer is actually to learn to read Genesis 1 in the context of the time and place of the author and the original audience. This is, after all, the best way to approach Scripture anyway. This means, for one thing, not expecting modern day science in the pages of the Bible. It also means focusing intently on what kind of writing this is—what is the genre of Genesis 1? This was almost impossible until the 1800s, when archeologists started making a lot of very important discoveries in the Middle East.
We now know that Israel’s neighbors had their own creations stories. And, what is fascinating, is that there are conspicuous similarities and differences between Genesis 1 and these other creation stories. What seems clear, now, are two things: One. Accounts like that in Genesis 1 are the way that ancient, pre-literate, pre-scientific cultures told their creation stories. Two. Genesis 1 was in conversation with the stories of the surrounding cultures. Genesis 1 used the same format, but corrected the faulty pagan theology of the surrounding cultures. Genesis 1 was the Hebrews’ response to the surrounding cultures. It is about theology, not science. For example, Genesis 1 proclaims, in the midst of a polytheistic world, that there is only one God.
In fact, although the genre of Genesis 1 is really difficult to nail down, it may correctly be identified as “ancient mythology.” Now, when we moderns use the word myth we mean fairy tale, and devoid of truth content. But in ancient times that was not the case. Back then, myths were vehicles for transmitting truth content.
I encourage you to learn more about Genesis 1 in its proper historical and cultural context, like I did. I can help you in two ways. First, I aim to put out a series of blog posts on this topic, and YouTube videos. Second, I wrote a book about my journey through a faith crisis instigated by early Genesis, and it covers this whole topic in depth.
March 2021 Update
Hello Friends! Hope this letter finds you well.
Sorry for being out of touch for a couple of months. Lots has been going on.
First of all, my YouTube channel just launched. You can find me at https://www.youtube.com/channel/UCqotSdoC6TXhJpsj7q6ybSg
It’s quite exciting. I just have one video public right now, but I have 6 more ready to go, just waiting to release. I want to be able to keep to a consistent release schedule and not be rushing to produce stuff, so I’d like a buffer/inventory of about 5 videos. I figure I’ll release 3 videos a month, on the 1st, the 10th, and the 20th.
What will the videos be about? There are three buckets. The first is videos based upon the material in my books. For example I’ve started a series on Genesis 1. My first video, just released, is the first episode in that series, and I have Episodes 2 and 3 ready to go. The second bucket is evolution. I have a video on Whale Fossils in the hopper. The third bucket is miscellaneous interesting stuff. I have a video on what Jesus was doing on the cross ready to release in time for Good Friday, I have a bible study on the question of whether there are modern day apostles, and a video describing my evening at a healing service at a Charismatic conference. The videos range from 8 to 22 minutes in length. Eventually I’d like to do interviews, but for right now these are just talking head/blog videos.
If you think you’ll be interested in the content, consider subscribing.
This will be a marathon, not a sprint. I expect that I will get very little traction for like 2 years, as I build my library, improve my skills, and give the YouTube algorithm the confidence to recommend my videos. Eventually, I hope to catch fire a bit and gain momentum.
Talking about skills, there is a lot involved in this. Frankly, there are some important skills that I’m not good at right now. But I’ve already noticed tiny improvements from video to video, so I expect to get better over time.
Next up is my second book, Overcoming Doubt. That is moving forward, albeit slowly. My copyeditor has finished her work, and now I am going through the edits and making changes. This includes some rewriting, so it is a slow process.
Otherwise, things are good. I’m in an interesting place currently, theologically. I’ve got one foot in the conservative evangelical world and mindset, and the other foot in the Charismatic world and mindset. I’m figuring out which pieces of which I think are right. Is the office of Apostle for today? What about the doctrine of Once Saved Always Saved? And so forth. Faith and I are blessed to both be working and healthy in these COVID times. Pray that all of you are safe and managing well through this difficult period.
Another Pastor Falls
Just a quick note on a recent event in the church. This last week, a prominent pastor at Hillsong’s New York City branch was fired, for moral failings. Turns out he had an affair. It can be quite discouraging when our leaders fall. We can feel misled and even betrayed. The enemy can use these occasions to sow doubt in our minds about God and the power of his Spirit. We pray for the pastor and his family, for healing and reconciliation. We also pray for his congregation, for comfort and strength. Perhaps the lessons for us include: Let’s remember to not put pastors on a pedestal, and we should consider choosing pastors based more on their hearts and less on their raw outward talent.
What’s Up with the Deconversions?
In the last couple of years there have been a bunch of high-profile deconversions. It can seem like we have been slammed with announcements from well-known Christians, like pastors and worship leaders/musicians, disclosing that they had renounced their faith. Joshua Harris and Jon Steingard are two examples.
Quite possibly, Joshua and/or Jon may return to the faith, but for the sake of discussion, let’s assume they don’t. What does this say about salvation?
Nowadays, standard evangelical teaching is that you can’t lose your salvation. Once saved, always saved. Think of John 6:37, “All that the Father gives me will come to me, and whoever comes to me I will never cast out.” A common way to interpret this verse is that a Christian can never lose their salvation. But there are other verses too, such as Hebrews 3:14, which appear to warn us against abandoning our faith: “For we have come to share in Christ, if indeed we hold our original confidence firm to the end.” Notice the “if.”
So then what is going on here? Standard evangelical teaching is that folks like Harris and Steingard had had false conversions. They were never really saved. But does this make sense? I’m not sure. After all, many of us know someone who had been a self-proclaimed Christian for a long, long time before leaving the faith. In many of these cases, we had been convinced ourselves that they were Christians. Could we have been fooled in each case? Did all of the ex-believers fool themselves?
That seems hard to believe. But maybe it is true. I was watching an Alisa Childers YouTube video titled “What’s with all the deconstruction stories? With Sean McDowell.” Sean is a pastor, and went through a period of severe doubt in his faith walk, but returned to full faith. He has since talked with lots and lots of ex-Christians, former believers who left the faith. He says something very interesting. He says that in all those conversations, he has never had any of these ex-Christians report to him that they had ever in their lives had an experience of their sinfulness and crying out for God’s grace. Huh. Well, that’s the Gospel, right? Maybe it does indeed happen that many Christians, even pastors and worship leaders, join the church due to wanting to be part of the movement or having an experience at a youth conference, but never actually respond internally to the Gospel?
What’s Happening Now
Hey everyone. Pray you all are well. Lots going on here. My first book has been out for about 2 months. I am pleased with the initial sales, but now comes the hard part, getting people beyond my circle to buy it. Actually, to even get them to know about it! My first attempt at advertising, on Amazon, didn’t work well, but I’m learning and hopefully I’ll start to gain some traction. I’ve been encouraged, though, by readers in my target audience who have told me the book was very helpful to them.
Work on my second book is progressing nicely. I have a rough draft of three quarters of it done. I’m quite excited about it. Also, I gave a sermon on the Journey of Abraham a couple of weeks ago. It was a lot of fun.
I’m OK with things not getting out of the gates super-fast, as I’m content to play the long game here. This is a ministry and a hobby for me. In fact, I’m strongly considering starting a YouTube channel! That would be a lot of fun, and give me access to a much broader audience, potentially. Look out for announcements on that in the near future.
My Recent Sermon on Doubt
The Problem of Doubt
Sermon at Wonder Church International
September 13, 2020