[00:00:00] Speaker A: Foreign the Future, a podcast about evolution and intelligent design.
[00:00:12] Speaker B: Welcome to ID the Future. I'm your host today, Emily Reeves. I'm excited to be joined by Dr. Casey Luskin, who holds a PhD in geology from the University of Johannesburg and a law degree from the University of San Diego.
Cayce is also knowledgeable about evolutionary biology, having studied it extensively during his bachelor's and master's degrees at the University of California at San Diego.
He has also written extensively on the topic of human origins and has continued to engage with the field for the past 20 years, making him a well informed voice on this subject. So welcome Casey, and maybe you can share just a few words about your personal interest in human origins and human chimp similarity before we dive into today's topic.
[00:01:01] Speaker A: Yeah. Thank you so much, Emily, for having this conversation. And yeah, I've been interested in the topic of human origins for a long time. My PhD research was not on human origins, but while I lived in South Africa doing my PhD, I had quite a few opportunities to go to some of the fossil sites that had some of these very famous hominid fossils. But increasingly I think that I've become interested in the genetic aspect of human origins. Right. Wrote a review of it in 2021 for Evolution News. In 2022, published a chapter in a South African academic book that sort of looked at attempts to compare the degree of genetic similarity between chimpanzees and humans. And what I discovered is that one of the issues that has hampered attempts to come up with an accurate measure of the degree of human chimp genetic similarity is the fact that many previous drafts of the chimp genome used to the human genome is like a scaffolding. When they constructed the drafts of the chimp genome, this made the chimp genomes appear more human like than they actually are.
This new Nature paper that I think we're going to talk about is really exciting because they now have a de novo or from scratch draft of the chimp genome, which allows us to make a more accurate comparison of the degree of genetic similarity between humans and chimps. I should note, Emily, that there was actually a 2018 paper in the journal Science that was authored by some of the same authors of this current study. And that 2018 study actually did do a de novo or from scratch sequencing of the chimp genome. However, that study did not report the complete chimp genome. So what makes this current study in nature so important is that not only is it a de novo or from scratch sequence of the chimp genome, but it's a Complete sequence of the chimp genome, as they put it. It's a telomere to telomere de novo sequence of the chimp genome and other ape genomes as well.
So this is really the first time that we can now hopefully get a much more accurate understanding of the true degree of genetic difference between humans and chimps. But I know, Emily, I mean, you have a PhD in biochemistry and also have done genome sequencing and you're familiar with the subject. So love to hear your thoughts on this and your perspective as well.
[00:03:07] Speaker B: Yeah, I think what you said about scaffolding is really an important thing for the public to understand because when you start off sequencing a new genome, you have lots of different fragments and you have to use some kind of reference to know where to put these different fragments. And so in the case of the early chimpanzee assemblies and stuff like that, they were using basically the human genome as a source of where to put the fragments of the chimpanzee genome. It's called human guided scaffolding. It was used to create the chimpanzee.
[00:03:44] Speaker A: Assemblies and so that makes the chimp genome look more human like than it really is.
So I think everybody has been waiting for a from scratch or de novo version of the chimp genome that was also a complete draft of the chimp genome. And that's what we have now.
[00:04:00] Speaker B: Yeah, yeah. So tell us, Casey, about this exciting study and why it's been generating so much buzz.
[00:04:06] Speaker A: Yeah. So on April 9, 2025, the journal Nature came out with a really huge, groundbreaking study that provided complete sequences of various ape genomes. Not just chimpanzee, but also orangutan, Simangs, gorilla. Major respect to the researchers who did this work. It was not easy. It took them many years to do it. And it was an international consortium of researchers from many different institutions working together to do this. So really appreciate the work that was done to bring out these chimp and other ape genomes. And as they said, this is going to shed lots of light on the origins of these various species and help us understand this better. So I think that's fantastic work that they've done. The big question is going to be what is the degree of similarity between the human and chimp genomes? We'll get to that in just a minute. But we can actually use this study to make a better analysis of that question than we've ever been able to do before.
[00:04:57] Speaker B: Yeah. So maybe you can tell our listeners what has the public been told so far about genetic similarity between humans and Chimps?
[00:05:06] Speaker A: Yeah, that is a really great question. I think a lot of folks are going to already know the answer to that question. Right, because we've heard this so many times. People have said that there is only a 1% genetic difference between humans and chimps, or that we're about 99, 98.8% similar genetically speaking to chimpanzees. So actually, a couple years ago, I was at the Smithsonian Museum of Natural History in, in Washington, D.C. and right there it says, UN chimps, 98.8% genetically similar. And this statistic has been quoted many other places. Bill Nye, the Science Guy, a very popular science spokesperson, he wrote in his 2014 book Undeniable, he said that as our understanding of DNA has increased, we have come to understand that we share around 98.8% of our gene sequence with chimpanzees. And then he goes on to say this is striking evidence for chimps and chumps to have a common ancestor. So very explicitly using the percent genetic similarity between humans and chimps as an argument for common ancestry. And you can see similar numbers quoted in just about every major scientific journal. National Geographic, the Journal of Science, the American Museum of Natural History, Scientific American, even the journal Nature prior to this study coming out, said that we share more than 98% of our DNA and almost all of our genes with our closest living relative, the chimpanzee. And so, you know, the implication of this from the evolutionist perspective is that this is showing that we have a common ancestor with apes and chimpanzees in particular, because we have such a high degree of genetic similarity.
[00:06:42] Speaker B: That's absolutely my experience as well. And we've all seen those statistics, 98.8% genetically similar between humans and chimps. So, Casey, would you say that this 1.2% difference or the 98.8% similarity has become an icon of evolution?
[00:07:01] Speaker A: Yeah, absolutely. I mean, Jonathan Wells, our friend Jonathan Wells, who passed away in 2024, he coined this term icons of evolution to refer to arguments that are very commonly made for evolution. They're just out there in the public's mind. Everybody knows about these. And Jonathan did not, I believe, actually use the percent similarity between humans and chimps as an icon of evolution. But he certainly could have. I mean, we've heard this all over the place. You hear it on tv, you see it in museums, like we said, at the Smithsonian Museum, the American Museum of Natural History as well. And one of the things about the icons of evolution is that they are often sort of assumed to be true regardless of what the evidence actually says. And that when you find evidence that goes against it, those icons don't die easily. So. So as we're gonna talk about here in this podcast, it turns out that actually this statistic is completely wrong. In fact, it's been known to have been wrong for a long time. This is not new information. I think the new information here is just how genetically different we are from chimpanzees. But for a long time, it's been known that this statistic was wrong. In fact, I remember back in 2007, after the chimp genome was initially sequenced, again, this was one of those drafts that was based on upon the human genome. But even back then, there was an article that came out in the journal Science that was called the myth of 1%. And so even back then, they were calling out this statistic as not being accurate. Despite that, it still is being quoted by Bill Nye by the Smithsonian Museum as if it is accurate. It's one of those arguments that just won't die. And so that's why in Jonathan Wells book Zombie Science, he said these icons of evolution are like zombies. No matter how often they've been proven wrong, they just won't die. They won't go away. And I think we're, we've seen that with this statistic in the past. And we're gonna continue to see this 1% statistic being cited in the future, despite the evidence that's come out in this paper.
[00:08:55] Speaker B: Yeah, but as you know, we're gonna talk about now, it might be a little bit harder. So tell us a little bit about what the journal Nature just published regarding the percent genetic similarity between humans and chimps. And yeah, tell us what that does to this 1.2% stat.
[00:09:13] Speaker A: Yeah, so what this Nature paper has shown is that the true degree of genetic difference between humans and chimps is at least an order of magnitude greater than the 1.2% difference statistic that we've always been told. And this paper has identified at least two different types of genetic differences between humans and chimps and also between humans and other apes. And what it found is that between 12.5 and 13.3% of the chimp and human genomes are, are so different that they cannot even be aligned with the genome of the other species. And they call this the gap divergence or the gap difference, because essentially when you look at these sections of the genome in one species, it's almost like there's a gap compared to the genome in the other species. Basically the problem is that genomes cannot be aligned in these sections. And I think that the higher value of 13.3% is probably the most relevant one here because that represents sections of the human genome that are not alignable with the chimp genome because they're just so different and, and there's a gap. And then on top of that, within the alignable sections of the genomes, which constitutes the bulk of the genomes, there are single nucleotide variations, also called short nucleotide variations, that represents a difference of about 1.5%. This is of course where you got that old original statistic of us being only 1% different from chimps. But we now know that that statistic is far from the whole story because now that they have completely sequenced the chimp genomes, we know that there are major sections in the human genome that simply don't align to the chimp genomes and major sections of the chimp genome that don't align to the human. So what you can do then is you can add these differences together, the differences stemming from the total gap divergence in these non alignable sections and the differences from the alignable sections in the short nucleotide variations and get a total genetic difference between humans and chimps that's about 14 to 14.9%.
And so again, I think that the higher value here, 14.9%, is arguably the most relevant one because that's basically the percent of the human genome that is different from the chimp genome. So I want to be clear here. What this data from this paper is saying is that the human genome is 14.9% different from the chimp genome. And it's interesting. I also want to note that if you look at the supplemental data, there's another place where they used a different method of comparing the genomes using a software package called Progressive Cactus. And they used this software tool to do an eight way genome alignment. And they did this analysis with both the haploid genomes and the diploid genomes for these species. This method gave very similar results to the other method that we just discussed where we added up the gap divergence and the single nucleotide variations. So to cut to the chase of what they found under this method, under the haploid autosomal chromosome alignment, that is the non sex chromosomes, only 91.47% of the chimp genome could be aligned with a human. And more importantly, only 84.95% of the nucleotides in the chimp genome had an identical one to one correspondence with the human genome. That's basically a haploid genomic difference between humans and chimps of 15.05% different.
Then when they did the diploid alignment analysis, looking at the full set of non sex autosomal chromosomes in the genomes, that percent difference grew to 16.11% because only 83.89% of the nucleotides in the diploid assembly of the autosomes in the chimp genome showed an identical one to one correspondence with the human genome. So there you go, that's pretty significant.
Now up to this point we've been talking about autosomes, that is the non sex chromosomes. So what about the X and Y sex chromosomes? How similar are those between the humans and chimps? Well, it's interesting. Under this progressive cactus alignment, the chimp X chromosome had only 79.88% of nucleotides that showed a one to one correspondence with a human X chromosome. So that's a difference of 20.12%. But the Y chromosome had by far the most differences. This is really incredible. Under this method, they reported that only 4.32% of the nucleotides in the chimp Y chromosome had a one to one correspondence with the human Y chromosome. And that's a difference of 95.68%. So the human and chimp Y chromosomes are extremely, extremely different. But the bottom line here is that regardless of exactly which method that you look at that they used, the human and chimp genomic differences come out to about 15%. Of course that's only looking at the non sex chromosomes, but when you look at the sex chromosomes, the differences seem to be even greater. So this is a huge, interesting finding. Whatever its implications are for evolution, whatever those implications may or may not be, this is a huge story because that old statistic that we're only 1% genetically different from chimps is not just wrong, it's wrong by more than an order of magnitude. The true percent genetic difference between humans and chimps is more like 14 to 14.9% or even 15%. So that old 1% statistic that's been used to argue for for human chimp common ancestry is simply not true.
[00:14:18] Speaker B: Now there are these regions of the genome that are unaligned.
As I've read in the study, those regions are around like centromeres or acrocentric short arms. They're not necessarily in these gene rich regions of the chromosomes. And some of the regions are highly repetitive, which is why the regions weren't able to be sequenced before.
So it definitely is really interesting what this study has uncovered, that in these regions that we weren't able to sequence before, we've now been able to sequence them. And we're seeing really some striking differences between human and chimp genomes in these areas.
[00:15:03] Speaker A: Yeah, you're quite right, Emily, that a lot of the sections that don't align well between these two genomes are repetitive DNA and, and they're often near centromeres or telomeres. And in fact, that's precisely why it was so difficult to accurately sequence these sections in the past. And now that they've been able to do that, we can start to understand them. But it's important to understand that these sections of the genome definitely can't just be dismissed as genetic junk that is maybe unimportant for encoding real differences between humans and chimps. In fact, there was another recent study in the journal Nucleic Acids Research where, which is precisely about these newly sequenced segments of the ape genomes. And in fact, it's offered by some of the same researchers who sequenced these complete ape genomes. And this study suggests that precisely this newly sequenced repetitive DNA in these ape genomes can perform important functions as what they call non B DNA. According to that paper, non B DNA is known to be, quote, important regulators of cellular processes and, and has, quote, unequivocal importance for genome function. They go on to say that non B DNA is increasingly recognized as a major regulator of myriad processes in the mammalian cell.
So what can this mean? Well, these kinds of functions can include being involved with DNA replication initiation, being involved with the life cycle of transposable elements, protecting chromosome ends at telomeres, regulating transcription, regulating chromatin organization and methylation, and also being involved in forming structured rna, which regulates alternative splicing, translation of messenger RNA and the function of non coding rna. It's also involved with the function of centromeres. And in fact, this repetitive non B DNA forms DNA that may even define centromeres.
So what's really interesting about this non B DNA, Emily, is that it can often function as structural DNA, where it's the shape that matters. The, the number of repetitive elements here is presumably determining those shapes, basically loops, hairpin, turns, et cetera. And to all of our friends out there who love junk DNA and can't seem to be able to imagine why the human genome would have so much repetitive DNA, well, right here is a core function for repetitive DNA, because yes, in repetitive DNA, the sequence can matter, but also the number of repeat Copies can matter because the number of repeats can help determine the, the three dimensional shape that the DNA is taking in the nucleus. And this can have all kinds of important implications for how genomes function, how genes are expressed and many other functions. So yes, the sequences of the repeats can matter, but the number of repeats can also matter because these can help form structures which are probably determined by the number of copies of repeats. And those structures have all kinds of functions. And in fact this is noted in the press release about the paper which says that this repetitive non b DNA can actually take on structural roles that are relevant to many cellular processes, including DNA replication, replication initiation during cell division, gene expression regulation and the function of telomeres. Now a lot of what I just said is me sort of quoting here and there directly from the paper or the press release, but my point here is that the repetitive DNA which makes up large portions of the newly discovered genetic differences between humans and chimps in these non alignable sections of the genomes very likely has functional importance and cannot simply be dismissed as unimportant junk DNA that's repetitive and isn't doing anything. So this is devastating news for proponents of junk DNA. Again, keep in mind that what I just said was being reported by a study that was precisely looking at the repetitive DNA that represents much of this newly sequenced DNA that is different but between the human chimp genome. So it's directly relevant to what we're talking about here. Now of course a lot more work has to be done to tease out exactly what this repetitive DNA is doing and all these genetic elements they're looking at. But this paper in Nucleic Acid's research suggests that we have every reason to believe that this repetitive DNA could be functional. But beyond this, I don't want us to distract from the main point here. And the main point is that for years the public has been told that that the human and chimp genomes are only 1% genetically different. And we now know from these completely sequenced ape genomes that this statistic is wrong by more than an order of magnitude. That difference between the human and chimp genomes is more like 14 to 15%. And there are huge portions of the human and chimp genomes that are so different that they can't simply be aligned and even compared. So that old 1% human chimp genetic different statistic was an icon of evolution. And, and in biologist Jonathan Wells way of putting it, that icon has been refuted.
[00:19:41] Speaker B: So I know we've talked quite a bit about chimpanzees in humans. And this study looked at other species of apes like gorillas, orangutans, and seamongs. Were any of those apes to be more similar to humans or what. What did the paper say about them?
[00:19:58] Speaker A: Yeah, so as we've often heard, we're most similar to chimpanzees compared to other species. Compared to gorilla, there was a difference between 17.9% and 27.3%. When you look at the gap difference, and when you add it all up, that could be a difference of up to 29.3%. So that's a huge difference between human and gorilla genome. With the bonobo, which of course is very similar to the chimpanzee, it was a 12.5 to 14.4% gap difference. And when you add it all up, it's 14 to 16% total genetic differences. And with the orangutan, it is a 15.4% to 16.5% gap difference. And when you add it all up, it's somewhere around 19 to 20.1% total genetic differences. So, yeah, I mean, very, very large and significant genetic differences between humans and all these species. And again, this is just showing that those old statistics that were just barely different genetically speaking from chimpanzees and other apes, it simply is not right. So if you're gonna say that we are 1% genetically different, sure, that does apply to some parts of the genome with chimpanzees, but that's not the whole story. You've gotta tell the whole story that there are huge sections of the genome that are so different they don't even align. And that's a big part of the story.
[00:21:16] Speaker B: Now, now you've written about how the nature papers.
And just so our audience can understand, there were at least three nature papers, one with like, the major findings of the study, and then two other more pop papers explaining what the study found.
So those papers did not make these numbers clear. What do you think about this? Like, what, what are your. What's your opinion about why everything was really buried in the supplementary data and, I don't know, share some of that for our audience.
[00:21:49] Speaker A: Sure, sure. So this was a really interesting part of this whole story. And one of the reasons why it's taken us, you know, well over a month since these papers came out is we wanted to do our due diligence and make sure that we were accurately representing the data in these papers. And one of the challenges with doing that is that nowhere in the technical paper are these numbers clearly reported saying, oh, humans are between 14 and 14.9% total genetic difference from chimpanzees. In order to find just the charts, the diagrams where they were showing some of that data, you had to dig deep into the supplementary data and it was just totally buried in the supplementary data. It was just completely opaque language and unclear. Even the explainer article in Nature and explainer articles usually do a really good job of translating important technical findings for the average scientist or even for a non scientist. They did not mention at all that this study finally allows us to do a more accurate comparison between the human and chimp genomes. Much less did they actually quote any numbers we had to go through, dig into the supplementary data, find the charts, find the curves, figure out which applies, in which ways do the calculations to come up with these numbers. Nowhere were these numbers clearly stated. And so this data has huge implications for that long quoted statistic that we're only 1% genetically different from chimps. It's interesting for implications for regarding evolution, origins, human exceptionalism. I mean these are really important questions that everybody wants to know about.
And yet the papers almost seemed like they wanted to obscure the numbers, making them hard to find for the average scientific or non scientific reader. How hard would it have been for the original Nature paper or even better the explainer articles to say, oh, these new data show that the human and chimp genomes are more like 14 to 15% different or 12.5% gap difference between humans and chimps. Why couldn't they just come out and say that plainly? For some strange reason they didn't do that. Now Emily, you have published scientific papers, as have I. And so we both know that sometimes publishing scientific papers is kind of like sausage making. It can be a very messy process. And to be fair to the authors of the Nature paper, I mean I didn't count them up, but there are, there are a few dozen authors of the technical paper and so I'm sure that different authors had different opinions about how to report this, what to say, and then it went through the review process. They probably had debates and even maybe the journal Nature had some say over exactly how to report this data. I don't know exactly whose fault it was. Maybe there were some authors of the Nature paper who wanted to report these applications more clearly and they just were not able to, perhaps because of other co authors or perhaps because of the journal Nature itself or the reviewers. I have no idea, I'm just speculating right now. I'm not. What I'm trying to say is can't look at the Authors of the paper and say, oh, any in particular, any one of them was trying to obscure this really important information and make it hard for it to come out to the public. I don't know what happened behind the scenes. I really, truly don't know. However, something happened, somehow it got obscured. Something went wrong here. And I think that this is a gross failure of the scientific community to clearly communicate really important implications for the public to know about. And I think the public deserves to know about this. So, I mean, I'm very confident that we have not misrepresented this paper. We've gone over it over and over again. We poured over, we talked to other folks who are experts to make sure that we were getting it right.
I'm pretty confident that we are not misstating these numbers. However, another interesting question is why did we have to be the ones to do this? Why couldn't the journal Nature, which published this research, or the researchers who, you know, again, deserve huge credit for doing fantastic work reporting this data to the public. I mean, they really deserve all the credit here. We're just talking about the work that they did. But why couldn't this really important question of the true degree of genetic similarity between humans and chimps, why could not they clearly state this in this research paper? I don't know. Something went wrong here and there's been a lot of talk in recent years about, you know, the public losing trust in the scientific community. I don't want to see that happen. But, you know, when you don't clearly state the implications of your findings, it's people are wondering, like, why aren't you doing that? And rightly so. So again, the researchers did great work here. They're all great scientists, no question there. But I would like to have seen the implications and these numbers explored a little bit more clearly. It shouldn't be us having to be the ones to break this story.
[00:26:39] Speaker B: Well said.
So what are the implications of this research for evolution and intelligent design?
[00:26:45] Speaker A: Well, of course, that's a question that many people are going to be asking. And you know, the funny thing is, Emily, what these findings of this paper show really don't change anything that I've been saying about the relevance of the degree of genetic similarity or difference between humans and chimps for human chimp common ancestry. I've been saying for a long time that whatever the final number is, you know, the exact degree of human chimp genetic similarity and difference, I don't think that that really is very relevant to assessing questions about human chimp common ancestry. And the reason why is whatever the final answer is, there is no question that we're going to have a fairly high degree of similarity, genetically speaking, between humans and chimps. And that similarity could be the result of common design. Where we're built based upon a common blueprint. It could be the result of common design just as much as it could be the result of common descent. So I don't think that the true degree of genetic similarity between humans and chimps really is a good indicator of whether or not we share common ancestry. Common ancestry could explain this high degree of genetic similarity. And also common design can also explain this high degree of human chimp genetic similarity. That was true when people claim that we were only 1% different. It's also true when we now know the facts that we're more like 14 to 14.9% genetically different between humans and chimps. Again, it's not really changing anything that I've been arguing. Now it does have, I think, implications for unguided evolutionary mechanisms. Okay, because we know the mutation rate between humans and chimps and this entails hundreds of millions of base pair genetic differences. Obviously they're not all single nucleotide variations. We're not just talking about point mutations. So a molecular clock may not have to account for all of that. But you also have to understand there were other cornea evolution, large scale mutations, there's probably large scale insertions, deletions, duplications, all kinds of stuff that has gone on according to an evolutionary view. And so we can ask the question, you know, is there enough time for just an unguided evolutionary history to explain the degree of human chimp genetic difference? Maybe there is, maybe there isn't. That's a question for somebody else to do another day. But that question is certainly going to come up. But regardless, I think that it's important to understand that, that, you know, whatever the exact percent degree of genetic similarity and difference is between humans and chimps, it could be explained by common design. That's always been a point that we've raised and it's important to noted that this argument from common design, it's not intended to somehow prove that species were created specially or designed separately or something like that. Rather, it's a rejoinder that we, we've put forth to defeat this evolutionist assertion. We heard Bill nye saying, oh, 98.8% genetic similarity indicates common ancestry, but we're making this common design point to say, no, genetic similarity does not necessarily indicate common ancestry because intelligent agents can use similar parts in different designs independently, they can use common parts in different designs to fulfill common functional goals. So high genetic similarity can reflect common design. So I think that where there are going to be some very interesting implications here will come in the field of human exceptionalism because this 1% statistic, as often quoted to say, oh, we're just slightly modified chimpanzees, well actually we've got huge genetic differences. The degree of genetic difference between humans and chimps is an order of magnitude greater than that 1% statistic that you've been told your whole life. And so what does that mean for human exceptionalism? Or you know, differences between humans and gorillas are perhaps as great as 29.7%. What does that say for human exceptionalism? These are things for the philosophers to debate. But I'm sure that these implications will be talked about.
[00:30:37] Speaker B: Absolutely. Do you think this is, this research is going to be the final word on how similar human and chimps are genetically, or do you think we're going to learn more beyond this study?
[00:30:52] Speaker A: I'm sure it won't be the final word. I'm sure there's still areas that need to be better resolved. We still have to understand more about what these repetitive sections mean and what these different sections mean. So yeah, I mean there's still way more work to be done. Emily and I look forward to seeing what research has done, but we can close this out by just giving kudos to the researchers who did this research. It was a lot of work, really important to get complete telomere to telomere sequences of these ape genomes and this is going to give lots of fodder for further studies. So I look forward to seeing what comes out.
[00:31:25] Speaker B: Yeah, Casey, you've given us so much to think about today. Thank you really so much for sharing this groundbreaking research and as you said, congratulations to the amazing team that no doubt spent hours and hours on this project and really has brought a whole new level of understanding to human and chimps similarity. For our listeners, if there's one key takeaway from this podcast, I would say it's that science really is a process constantly being refined by new data.
So we see that old claim that human and chimp genomes are 98.8% similar. Well now that's outdated and we have new evidence from much more complete genome analysis that shows that humans and chimps differ by at least 14%, which is a significant shift. So thanks again for updating us Casey listeners. If you enjoyed this episode, share it with a friend and check out Casey's blogs on evolution news.
Thanks for listening to ID the Future. I'm Emily Reeves.
[00:32:33] Speaker A: Visit
[email protected] and intelligentdesign.org this program is copyright Discovery Institute and recorded by its center for Science and Culture.
