[00:00:04] Speaker A: Id the Future, a podcast about evolution and intelligent design.
[00:00:12] Speaker B: Hello and welcome to id the future. I am Jonathan McClatchy, and I'm on the other side of the interview today. Today I'm going to be in conversation with Casey Luskin about a debate he recently did with an evolutionary biology professor from Rutgers University, doctor Daniel Stern Cardinali, who online goes by the name Doctor Dan. Doctor Dan hosts a YouTube channel called Creation Myths where he interviews various proponents of intelligent design and offers criticism of design arguments. So, Casey, it's great to have you on the program today. Welcome along.
[00:00:41] Speaker A: Yeah, thank you so much, Jonathan. It's great to do this sort of retrospective on the debate and talk about what happened.
[00:00:48] Speaker B: Yeah, absolutely. So maybe you could tell our listeners who Doctor Dan is and how this debate came about.
[00:00:54] Speaker A: Yeah. So Doctor Daniel Stern Cardinale is an evolutionary biologist at Rutgers University. As you said, he has a YouTube channel called Creation Myths, where he has a following. I think he does lots of critiques of intelligent design people and creationists and that sort of thing. And the debate came about because we put up a long story short video about a month ago on the topic of junk DNA. And Doctor Dan, as he goes by on his YouTube channel, put up a video critiquing our Junk DNA video with long story short. And of course we then responded, actually, he put up a comment on our YouTube video and I responded to his comment and then he wrote a response. And eventually we got in a dialogue with the host of a skeptic podcast on YouTube called the Non Sequitur show with Steve McRae. And Steve offered to invite Doctor Dan and I to do a debate on his YouTube channel on the topic of Junk DNA. And we sort of were able to recap what we've been discussing already through our back and forth on his YouTube channel and our blog and our YouTube channel regarding this topic.
[00:01:57] Speaker B: Great. And what were some of the main points that you put forward in your opening statement in the debate with Doctor Dan?
[00:02:03] Speaker A: Sure, sway. I basically made four main points in my opening statement. And the first one is that the best evidence shows that our genomes are largely functional and that junk DNA is the exception to the rule of mass functionality in our genome. And I talked about how when I was an undergraduate student at UC San Diego, I was part of this student club, the intelligent design and evolution awareness club. And this is in the late 1990s, early two thousands and people would come to this club and say, intelligent design is refuted because, you know, 90 95% plus of our genome isn't doing anything. It's genetic junk, and no designer would do that. And I said, well, if that's true, that probably is a reasonable argument against intelligent design. But this was before the human genome project had even come out. And I said that, you know, at that time, we really knew so little about the genome that it was premature to conclude that just because we didn't know what something was doing, that therefore we would assume that it was junk, nonfunctional DNA that was the result of random evolutionary mutations, basically evolutionary debris in our genome that refuted intelligent design. I said it was too early for us to conclude that and we should wait and see what the evidence shows. But I also noted in my opening statement that even in those days, back in the late nineties, early two thousands, intelligent design as a scientific theory was predicting that this non coding or junk DNA was going to turn out to have function. And so there's actually good documentation of id theorists from those time periods, Boris Mims, Bill Demski, Jonathan Wells, Richard Sternberg and others, predicting that the junk DNA would turn out to have function. Then my third point was that evolutionary biology did not predict that we would find function for junk DNA, and they did not predict this paradigm shift that we've seen over the last ten to 15 years away from the idea of junk DNA. And I also noted that I actually predicted what we would see in the conversation with Doctor Dan, that we would actually see that in his arguments that evolutionary scientists today are still strongly pushing the idea that our genome is largely junk. And I think, as we'll talk about, Jonathan, that that prediction came out to be true. Doctor Dan certainly did argue that the vast majority of our genome is, in fact, still junk DNA. And so this is a prediction they made in the past and a prediction or an assertion that they're making even today. And so what I then argued that is that this means that evolution has served and still serves as a science stopper, holding back science from discovering the functions for junk DNA by claiming that the vast majority, or a large proportion of our genome is junk. While I said that ID has led to fruitful predictions, that actually this paradigm shift that we've seen over the last ten to 15 years shows that the idea of junk DNA is no longer valid. And I actually mentioned examples of this, I talked about an Ivy League biologist that I'm friends with who is ID friendly, who studies rna, and I asked this person, you know, what is the vibe in your field? Is it still basically believed that the vast majority or the large proportion of our genome is junk, and this person said to me, no, actually, it is largely thought in their field that if it's being transcribed, that there probably is a function. And this goes to the evidence I cited during my opening statement from the Encode project. The Encode project. As you know, Jonathan found that over 80% of our genome is being transcribed from DNA into rna. And I argued during the debate and during my opening statement that that evidence of mass transcription of the genome is prima facie evidence of function. And as this Ivy League biologist told me, you know, basically they believe that if it is being transcribed, that's happening for a purpose, for a reason, and it's evidence of function. So we have basically prima facie evidence of function for the vast majority of the genome. Now, you might say, why only 80% of the genome? Does that mean that, you know, 20% is junk? Well, it's important to understand, and this will come into play in some of the points we'll discuss later, that the encode project only studied 147 different cell types in the human body. Of course we have many different cell types, you think of blood cells, bone cells, nerve cells, skin cells, et cetera. There are many different types of cells. In fact, there's probably hundreds, if not thousands, of different cell types in the human body. Encode results only come from 147 of those cell types. And some lead encode researchers have said that and actually predicted that as we study more and more cell types, that number of 80% of the genome being transcribed is gonna go up to 100%. The reason they said this is because for many elements of our DNA, many of our genetic segments in our DNA, they are only actively being transcribed and used in certain cell types, in certain stages of the human life cycle and certain stages of those cell types cycles. And so what we see is that it's kind of difficult time sometimes to catch certain DNA elements in action. You have to find them in just the right place and just the right time to figure out what they're doing. But we have this prima facie evidence that the vast majority of our genome is being transcribed into RNA, and that is evidence of function. A couple last points to show just, you know, the overwhelming evidence of mass functionality in our genome, you and Richard Sternberg and myself compiled a blog post with over 800 peer reviewed scientific papers that have found evidence of function for non protein coding DNA. And we posted this on evolution news about a day before the debate. This is powerful evidence that. And this, by the way, that is just the tip of the iceberg, right? There's far more papers than just those 800 that have found evidence of function for junk DNA. But we just did a quick literature review. This is what we came up with in just a day and a half of looking through our, our materials. But that's showing that there is a huge amount of evidence that has come out in the last ten to 15 years of function for junk DNA. And it's really important to understand that this kind of evidence really was not understood to exist. 1015 even 20 years ago, most people thought that the vast majority of our genome was junk. And this has all just come out in the last 10, 15, 20 years. And that's why you're getting papers right now. And I cited this also in my opening statement, like a paper in bio essays last year which said that there has been a paradigm shift away from the idea of junk DNA. Or there was a paper in the journal Genome Biology and Evolution which said that the days of junk DNA are over. I also quoted a quote from a book published by Taylor and Francis last year by John Maddock and Paulo Amaral. And I want to read this quote because it really, I think, tells the story of where we're at with our understanding the genome and what has happened to junk DNA. It says, quote, the genomes of humans and other complex organisms are not full of junk, but rather are highly compact information suites that are largely devoted to the specification of regulatory rna's. These rna's drive the trajectories of differentiation and development, underpin brain function, and convey transgenerational memory of experience, much of it contrary to the long held conceptions of genetic programming and the dogmas of evolutionary theory, unquote. So again, listen to that quote. They're saying that our genomes are not full of junk, but are rather highly complex information suites that are largely devoted to the specification of regulatory rna's. And they go on to say that this is, contrary to the, quote, dogmas of evolutionary theory. So we definitely have this historical dynamic going on in biology. Over the last ten or 15 years, that evolutionary theory has told us that the vast majority of our genome is junk. And now all this evidence has come out showing that it isn't junk. Now, I want to make one last point. I made it very clear in my opening statement that there is still a lot we don't understand about the genome. I mean, have we discovered the specific functions for many of the genetic elements in our genome? No, that's not true. There's a huge amount of work left to be done to understand specifically what every little genetic element in our genome is doing. But we have prima facie evidence that it is functional from encode. And the trend line of the data shows that we are discovering evidence of function at an ever increasing pace. And I'll give one last example of this. There was a paper in 2021 in nature called Gates et al that showed our knowledge of the number of functions, specific functions for specific genetic elements. And it is basically, it is an exponential curve. Okay? You can see that back in like the early 2000, late nineties, there was very few knowledge of specific functions for non coding junk DNA. And that number now is going up, up, up, and it's now over 130,000 different specific genetic elements that we've discovered functions for in the non coding parts of our genome. And it's going up. If you look at this curve, it looks like an exponential curve. It's going up at an exponential pace. Our knowledge of function for non coding junk DNA elements of the genome. So this is my argument that we've seen a paradigm shift in the realm of biology away from the idea of junk DNA. Id predicted it, evolution didn't that. That was my opening statement.
[00:11:07] Speaker B: Okay. And what, what did doctor Dan have to say about all this? What was his response when he gave his opening statement?
[00:11:12] Speaker A: Well, first of all, let me say Doctor Dan is a very smart guy, and I was very impressed with his cordiality and civility during the debate. I really appreciated him willing to have the conversation and he's clearly very knowledgeable about this subject. But Doctor Dan's basically, his main argument in his opening statement is that, yes, the vast majority of the genome is being transcribed, but he said that it's being transcribed at a very, very low level. And he quoted a paper from 2014 by Kellis et al. Which said that, quote, while rna transcripts of some kind can be detected from 75% of the genome, that nonetheless, quote, a significant portion of these are of low abundance. And he, and it goes on to say, quote, for polydenylated rna, where it is possible to estimate abundance levels, 70% of the documented coverage is below approximately one transcript per cell. And so what Doctor Dan argued, I believe these were about his exact words. He said, it is absolutely impossible that if you have rna, basically segments of our genome that are being transcribed at a level of less than one transcript per cell, that it is absolutely impossible that that could be functional, that it is basically what he would call transcriptional noise, or what I would say he's gone from junk DNA to junk RNA saying that, you know, all this rna that's being produced is just useless junk RNA that's not being transcribed for any reason, and that such a low degree of transcription is, he would say, is impossible for it to have function.
[00:12:44] Speaker B: And what did you say in response to the citation of that paper by kale saddle?
[00:12:48] Speaker A: Sure. So, thankfully, Jonathan, we were prepared for this argument. We dug into the literature quite a bit and we found what the literature actually says. First of all, you have to understand, it's a very strange statistic for this paper to be saying that there is below one transcript per cell. How could you have below one transcript per cell? That's kind of like when people say that if you want to keep the population at current levels, you have to have at least 2.1 children per couple, right? So you can't have 2.1 children. How can you have below one transcript per cell on average? Well, that's because it is. It's an average, right. So if you think about this as an average, it makes perfect sense what's going on. You could have, for example, a situation where in 145 of the 147 cell types that encode is studying, maybe that particular genetic element is not being used. So there's zero transcripts being produced. But then, say, in two of the cell types, maybe it is highly active and it's being used for some important function. Maybe in each of those two cell types, it produces, say, 50 transcripts per copy. Well, now I've got a situation where there are 100 transcripts being produced that have been detected by encode and 147 cell types. Well, guess what? That is an average of below one transcript per cell. And that's because, as we said earlier, the vast majority of our genome may only be active in certain cell types, in certain parts of the human life cycle. And so it's not actually being used most of the time. That doesn't mean it's not important. That doesn't mean it doesn't have an important function in those rare situations where it is activated and being used. So that is why, on average, you might get a very low copy number. But that doesn't mean that in certain cell types, that particular genetic element is not highly active and is not being used. And of course, as we mentioned earlier, encode hasn't even studied many of the cell types yet, so there's still a lot more to be discovered. But there's another important point, and this is also, I think, a very, very crucial point, and that is that even in situations where you have low copy numbers of transcripts, those transcripts can still be functional. And I quoted a paper, actually, that was in nature methods. And it was talking about the field of studying these non coding RNA's. And here's what the paper said it was for Marx 2022, it said. One criticism long leveled at the non coding rna field is that given their low abundance and low expression, non coding RNA's can't be that important. But then the paper goes on to quote a scientist who says that long non coding RNA's, quote, can punch above their weight and act in non stoichiometric ways to amplify their effects. And I quoted a paper by Mercer et al. 2012 in Nature Biotechnology, which said that there have been lawn non coding rna transcripts that are active, that are actually functional, but are present in an average of 0.006 transcripts per cell, quote indicating expression in only a small subpopulation of the cell sampled. By comparison, they said they found that there was a Hawks gene transcript that was present an average of 0.013 transcripts per cell. Well, of course, a Hox gene transcript is a very important transcript as a regulatory gene transcript. So what we're seeing here is that these long known coding RNA's, which we know are functional, can be present at very low copy levels on average, of course, and yet still have function. And even these Hox genes, which are regulatory rna's, they might be present at very low transcript levels, but that's because when you get these Hox genes, these regulatory genes that are often sort of initiating these gene regulatory networks, you only want them to be present at very low levels because they're sort of like initiating this cascade of a gene regulatory network, which is very important in development. And you start them off by very low levels of transcription. And so in many of these cases, these long non coding RNA's have important developmental properties and functions, and they don't need to be expressed at very, very high levels for them to have important transcripts. We also looked at that book I mentioned by John Maddock and Paulo Amaral, titled rna the epicenter of genetic information. And this book talked about how many regulatory rna's, quote, require relatively low average expression levels, um, and that you have these, quote, cryptic, unstable transcripts, which are important for regulatory, regulating gene expression and many other functions. So, basically, the evidence shows, and we found evidence from quite a few papers and authorities, you can have functional rna's even when they are expressed at very, very low levels. In fact, you only want them to be expressed at low levels so that they are able to initiate various regulatory processes in the cell.
[00:17:30] Speaker B: And did Doctor Dan ever come back to that or respond to that point.
[00:17:33] Speaker A: Well, that's a really interesting question, Jonathan, because this was basically Doctor Dan's a argument that these low levels of transcription of these rna's coming from non coding DNA make it impossible, absolutely impossible. He said that it could have function. And after I responded to that, he never raised that argument again. After we showed that this was an average, you could have some cell types where it's expressed at low levels, but others at high levels. But even if it is expressed at low levels, that in no way precludes it having functions. He never raised this argument again. So I felt like we kind of did a good job of, I would say, you know, basically refuting his a argument. And then the rest of the debate, he kind of fell back to another argument.
[00:18:13] Speaker B: And what was the other argument?
[00:18:15] Speaker A: So that other argument was that there are certain repetitive elements in our genome called transposable elements. And he focused specifically on line elements, which stands for long interspersed nuclear elements. And these line elements, under certain situations, they are able to produce basically proteins and transcripts, which are then translated into proteins which allow them to then retro transpose into new locations in the genome. And this allows them, according to what some biologists think, to basically hop around the genome and insert themselves. And some people would say that's why we have many copies of these in our genome. Well, Doctor Dan said that in some cases, or in fact, in many cases, you look at these line elements and they are so quote unquote degraded. That's what he called them, degraded, that they can no longer produce transcripts so that they can then produce the proteins that are needed for them to be able to retrotranspose into new locations in the genome. Okay, now, I was also prepared for this thanks to my great team of friends, you and Doctor Richard Sternberg, who are just, you know, have encyclopedic knowledge of the literature. And I cited to Doctor Dan, well, actually there are examples of what you are calling, quote unquote, degraded repetitive DNA where in fact it can still have function. They can have other functions besides just hopping around the genome. They could serve as enhancers or promoter sequences. They don't have to just b, you know, producing these enzymes that allow them to retrotranspose. There's other functions that they can have. But at that time, during the debate, I only had a couple examples of these. You know, I was ready for it, but we hadn't done like a deep literature dive. So after the debate, Jonathan, as you know, we did another sort of literature dive into the debate. And again, thanks to, I would say, the encyclopedic knowledge of Richard Sternberg. We were able to show that Doctor Dan's sort of fallback argument that, you know, some of these line elements look too degraded to have a function, that that argument also doesn't hold up. We. We actually posted on evolution news a bibliography of over 50 peer reviewed scientific papers finding function for what doctor Dan would call, quote unquote, degraded line elements.
[00:20:20] Speaker B: Okay, could you give a few examples of some of the functions that have been documented for line elements?
[00:20:26] Speaker A: Yeah. And I wanna make it clear these are for the quote unquote degraded line elements, which doctor Dan said during the debate could not possibly have a function. And according to the research and the literature review that we did, they can have many functions. These quote unquote degraded line elements, including DNA methylation and demethylation, transcriptional interference, and serving as molecular rheostats. They can be cis regulatory elements regulating gene expression. They can be heterochromatin inducers. They can be anti sense promoters. They can function as enhancers in embryonic stem cells. They can function as cis regulatory determinants and embryogenesis. They can be involved in rna processing, helping to form structural regions for the nuclear matrix and scaffolding. They can be involved in cell differentiation. They can be involved in inactivating x chromosomes and also helped to control the three dimensional organization of chromosomes and nuclear organizations. And there are other functions as well, but they can have many functions. And what this really showed, Jonathan, is that, look, this is exactly what evolutionary thinking does to our understanding of the genome. It assumes that if you don't know what something is doing or if you're, you know, if it's kind of like something you wouldn't expect, then it must have no function, because all this, our genomes are just full of evolutionary debris and random molecular junk that we don't need anymore. And an ID perspective would say, you know what? That's premature. Let's not assume that if we don't understand it, that it doesn't have a function. Let's go out and look for the function. And guess what? The ID prediction, in my experience, has always turned out to be right. The more we look for function, the more we're finding it. So I feel like even this debate itself is a good example of the rhetorical dynamics of this debate and why ID is a far superior approach to studying the genome than an evolutionary approach.
[00:22:08] Speaker B: Could you give a brief recap, for the sake of our listeners, of the rhetorical structure of the debate?
[00:22:13] Speaker A: All right, let's summarize the rhetorical structure of the debate. All right. I first argued that, that back in the day, evolutionary thinking made people think that the vast majority of our genome was junk. ID, on the other hand, predicted, let's wait and see. Let's actually study the non coding parts of the genome before we assume it's junk. Then, you know, 10, 15, 20 years later, all these rank and file biologists who were not trying to think about ID or evolution, they're just trying to understand what the genome is doing. They found evidence of mass functionality in the genome. We see that both from encode, which found that over 80% of the genome is being transcribed from DNA into rna, and also from just, you know, this huge tidal wave of papers finding functions for specific genetic elements. All right? And so I basically said that ID has predicted this paradigm shift that is being talked about in like the journal bioassays, away from the concept of junk DNA. Id predicted this shift. Evolution did not. Id is a better paradigm for studying the genome. Doctor Dan then replied, saying, well, actually the vast majority of the transcription that's going on is at such a low level it can't be functional. It's not. Essentially what he was arguing is that it's not junk DNA, it's actually junk RNA. Ivan replied saying that actually when we talk about low transcription levels, it's usually an average, and you could have high transcription levels in certain cell types where certain genetic elements are active. And I showed evidence that even at low transcription levels, you can still have functions. So his argument that low transcription precludes function simply isn't true. Then Doctor Dan spent, I would say, the rest of the debate, kind of hiding out in the unknowns. He was trying to argue that because we don't know what these, you know, quote unquote degraded line elements are doing, that, therefore they must be junk. And I am not allowed to argue that it's function. I said, no, actually, we know that the degraded repetitive DNA can in some cases have function, and we shouldn't be assuming that just because we don't know what it's doing or it's not doing what we think it should be doing, that therefore it is junk. And then after the debate, of course, Jonathan, we did another literature review, which again, I'm very grateful to you and Rick Sternberg for all the great research you guys did to help put this debate together. And we found that in fact, these line elements, when they are in a, quote unquote degraded state, can have a number of different very important functions in the cell. And so at the end of the day, I believe that this debate is just another object lesson of how evolutionary thinking is predicting that our bodies and our genomes are full of junk, and that prediction has turned out to be false. Time and time again, evolution does not give us a good paradigm for understanding how the genome operates, whereas intelligent design does. And so I think that, you know, the way this debate is sort of shaped up really confirmed our arguments and, and the id perspective on how to approach genomics.
[00:25:06] Speaker B: And of course, Doctor Dan published a video after the debates essentially celebrating that. In your concluding statement, you conceded that we don't know what more than half of the human genome is doing. Was this a damning concession on your part, Casey?
[00:25:17] Speaker A: Well, I never conceded that over half the genome is junk. First of all, I never said anything like that. But I said even in my opening statement, that, yeah, there's huge portions of the genome that we don't know exactly what it's doing, but not knowing the specific function doesn't mean we don't have evidence of function. And as I said, you know, during the debate, that this fact, the fact that we have this evidence of mass transcription of the genome from encode, that is prima facie evidence of function. And I talked about, you know, this Ivy League biologist I know who studies RNA, who's in the field, and basically in that field, their vibe is, if it's being transcribed, there's a reason for it, because that is how they, they see the genome is operating. Transcription happens for a reason. And so I don't think that, you know, just because we don't know the specific functions for many parts of the genome, that that means that therefore we should assume it's junk or that it's going to turn out to be junk. All the evidence, all the trendline of the data we've seen so far points in the opposite direction. That's that it's functional, and we're going to discover the specific function as time goes on.
[00:26:19] Speaker B: And finally, as we wrap up here, are there any resources you'd refer listeners to where they can learn more about this topic?
[00:26:24] Speaker A: Sure, I would definitely refer our listeners to our long story short video on Junk DNA. We're going to have another one coming out in the coming months. They can also read some of the blog posts that you, Richard Sternberg and myself have been putting up on evolution news about junk DNA. And then, of course, Jonathan Wells has an excellent book titled the myth of Junk DNA. It's a fantastic summary of the literature that was written in 2011. If you wanted a more up to date treatment, I think of the function for junk DNA, check out this book by John Maddock and Paulo Amaral titled rna the epicenter of Genetic Information. It's a bit technical, but if you want to really dive deep, it's a fantastic resource.
[00:27:03] Speaker B: Well, thank you, Casey, so much. It's been great having you on the program today.
[00:27:05] Speaker A: Thank you, Jonathan.
[00:27:06] Speaker B: I'm Jonathan McClatchy for id the future, and we'll see you next time.
[00:27:12] Speaker A: Visit
[email protected] and intelligentdesign.org dot. This program is copyright Discovery Installation Institute and recorded by its center for science and culture.
