[00:00:04] Speaker A: Id the future, a podcast about evolution and intelligent design.
[00:00:12] Speaker B: For decades, we've been told that only a tiny percentage of DNA is functional and that the vast majority is useless junk. Though this claim never made any sense from an engineering standpoint in the first place, it served as a powerful myth to push the narrative that were simply the result of unguided, undirected natural processes, a long string of mistakes and copying errors that left its imprint in the form of pervasive junk DNA. Welcome to id the future. I'm your host, Eric Anderson, and today, with Doctor Casey Luskin, we'll be unpacking the myth of junk DNA. Listeners will know. Doctor Luskin is our associate director at Discovery Institute center for Science and Culture. He holds a law degree from the University of San Diego, a bachelor's and a master's in earth sciences, and a PhD in geology from the University of Johannesburg. He has spoken and written extensively on evolution and intelligent design, and has contributed to or edited more books than I can mention. Welcome, Casey.
[00:01:07] Speaker A: Oh, thanks so much for having me, Eric.
[00:01:09] Speaker B: Yeah, really glad to have you here to talk about this wonderful topic. There was a video series that a lot of listeners will know called Long Story short. And I think the most recent or one of the most recent videos was a great video on the myth of Junk DNA. Tell me a little bit about. I'd encourage listeners to go check it out, but tell us a little bit about that video. Casey, what led to that video and why did you decide to focus on this particular concept?
[00:01:34] Speaker A: Yeah, so this latest myth of junk DNA video in our long story short series is part of a new sort of sub series we're doing within the long story short, larger YouTube playlist. And it's on basically information, and we're calling it the codes of Life series. So we came out with a video in sort of late 2023 that was all about how our cells are full of information, and information is sort of running the show in biology. And one of the messages that we wanted to put out with that first video in this codes of life series is that you are amazing and that you are full of. Your body is full of information and your cells are processing this information and using it to generate proteins and run these molecular machines that allow you to live and harness energy and allow your body to basically function. And so the way that our bodies use information is really quite extraordinary. So we talked a lot in that first video about how information in DNA is used to encode proteins. Well, we know that sort of the initial or the immediate rejoinder that you will get from many evolutionists. Is that okay? Well, yeah, there is, of course, protein coding DNA in our DNA, but there's a lot of DNA that we have that doesn't code for proteins. And some folks, in fact, many folks have said historically that that DNA doesn't do anything, and in fact, it is junk DNA. So in our second video in the codes of life series, we wanted to address this topic of junk DNA and ask, is our genome really actually, for the most part, largely useless junk DNA, where only maybe, say, a couple percent is encoding proteins? Or in fact, is the genome largely functional? Which is it? Because the answer to that question has huge implications for intelligent design.
[00:03:17] Speaker B: Yeah, yeah, that's great. So, again, I think most listeners will know, and we'll dive into the details here and the arguments, but just if you had to define junk DNA as it was defined typically in the literature, what would you say?
[00:03:31] Speaker A: Sure. So junk DNA is the idea that there are large parts of our genome that basically have no function that benefits the organism. Okay? They're there because of random mutations that have sort of filled up our genomes with bloatware, you might call it, over the eons. It's essentially just random mutation generating useless DNA, whether it's point mutations that are destroying vestiges of old genes, or maybe it is the result of duplications of parts of your genome, just randomly duplicating things for no reason, and then it just gets garbled and doesn't do anything. Or you have what are called transposable elements, which are actually make up a very large percentage of the genome, perhaps even 50% or more, which are supposed to be these segments of the genome, which can hop around your genome and sort of expand and copy number. And they are just there, kind of like Dawkins famous selfish gene concept, where you have DNA, it's just sort of a parasite that's copying itself within your body to make copies of itself. That's all it wants to do. These transposable elements are said by some folks, at least, to just make copies of themselves. They're sort of parasites that are hitching a ride on your DNA and trying to make as many copies of themselves as they can, but not to benefit you, just basically to proliferate themselves. And so when you look at our genome, according to this view, our genome is full of parasitic bloatware that isn't doing anything for you. That's the result of all these random mutations. And this reflects basically the evolutionary paradigm which says that, yeah, you are the result of unguided, blind and even random processes which generated your genome. Every once in a while, something happens that helps you, but for the most part, it's just random stuff that who knows what it's there for? It's just there because it happened, and it's just junk in your DNA. And of course, the argument is that no designer would create a genome that is full of so much useless genetic garbage that if the genome was really designed, you would not have all this unnecessary, useless DNA. And so this has been used for an argument since I've been involved in the debate. We could tell that story if you want, but it's an argument that goes way far back.
[00:05:41] Speaker B: Yeah, yeah. And just a couple of things to jump out at me from what you're saying there. So, first of all, this really fits nicely, if you will, within the evolutionary paradigm which says that everything came as a result of unguided, undirected processes, essentially mistakes, let's call it what it is, mistakes and copying errors. And so therefore, we should expect, on an evolutionary view, or it's unsurprising, let's put it that way, that our genome would be just a bunch of garbage. And occasionally something will work. Occasionally a copying error or a mistake will do something productive. And so that's why we have a small amount. You mentioned percentage case, a large portion. Just so listeners are clear, when you say large portion is junk DNA, according to this view, we're not talking ten or 15%, we're talking 80, 90, 95%. Some people claim, because it's the non coding regions for proteins that they were discussing primarily back in the day.
[00:06:39] Speaker A: That's right, Eric. The exact percentage depends upon who you ask. But I've seen it's not at all unusual to find numbers like 80% of our genome is junk or 90% of the genome is junk. Richard Dawkins even once said that 95% of the genome is junk. Or you can find very prominent folks saying that upwards of 50% of our genome is junk. In fact, Francis Collins, in his book the language of God, and obviously, Francis Collins is an evolutionary scientist, he's also a well known theistic evolutionist. But he said that 45% of our genome is what he called flotsam and jetsam. And of course, flotsam and jetsam is trash floating in the ocean. So even you know, that's a very large percentage of your genome to be essentially trash that's floating around. But you can get ranges from that all the way up to 95%, depending upon who you ask. And what argument they're making, right.
[00:07:32] Speaker B: And so you kind of picture, if you see it in your mindset, you kind of imagine this sea of junk, and within there, occasionally you'll have a useful sequence that does something helpful for the organism. Okay, so let me ask this. Is this just an innocent term, junk DNA, that was used by scientists, or did it have more theoretical baggage behind it? Why has this been an argument for evolution?
[00:07:55] Speaker A: Well, it's been an argument for evolution because, as we said, the idea that evolution is supposed to be a blind and random process. And so this very nicely reflects that things happen that have no benefit to the organism, that are random, that are blind, clearly, no designer would do this. But I think where this really becomes pernicious is that the concept of junk DNA has discouraged scientists from investigating and research what this non coding DNA is actually doing. And so it has actually hindered our ability to progress in our understanding of the genome and genomics. And this is not just me saying this. You can find leading scientists out there, papers in science and nature, who have said essentially that its folly to search for function for the junk DNA, or that this idea of junk DNA has discouraged or repressed scientists who wanted to maybe go out and study it. And so this has had real world implications for how quickly we have studied this non coding DNA and our ability to understand the genome. And so the irony here is that a lot of times folks will accuse intelligent design of being a science stopper. But in this case, we see that this evolution born concept of junk DNA, it has been a science stopper. Evolution has been a science stopper when it comes to our understanding of the genome, because it gave birth to the concept of junk DNA, and that whole concept was born and bred right out of the evolutionary paradigm.
[00:09:25] Speaker B: Yeah, well, I'm glad you brought that up. I wanted to press you a little bit on one point, which you've already mentioned here. So let me play devil's advocate a little bit, because I see now some evolutionists trying to rewrite history a little bit and say, no, no, no, we didn't really believe that.
Here's the devil's advocate argument, Casey. Aren't evolutionary critics just making a big noise about the common march of science? After all, science proposes ideas and eventually corrects them. And is it true that mainstream evolutionists were really making a big deal about junk DNA? Or maybe this was just a couple of rogue scientists out there and that this idea of junk DNA never really took hold within the scientific community?
[00:10:03] Speaker A: Well, like a good evolutionist, devil's advocate, there. Eric, you've thrown up a lot of objections all at once, and I'm going to have to deal with all of them one at a time. So let's take this one at a time. First of all, the idea that evolutionary biology did, in fact, anticipate function for junk DNA, well, on that count, we just have to look at history. And you can see over the years all these evolutionary scientists, and we've got the quotes to back this up. I'm not going to read them all right now. But, you know, we've talked about this on evolution news. I have a paper that I wrote titled the encode embroilement that actually documents many of these evolutionists over the years who said that this junk DNA is, in fact, function. And so this is not. If you want to claim that evolutionists anticipated function, you're basically going to have to rewrite history. So that's a problem right there. And in fact, some folks have tried to do that. In fact, one of my favorite examples of this is Richard Dawkins, who has a long history of saying that the junk DNA, that our genome, is largely junk. Dawkins in 2009 said that some 95% of our genome is junk. But then in 2012, we'll get to this in just a few minutes. But, you know, when the encode project came out in 2012 and they found evidence for biochemical functionality in over 80% of our genome, Dawkins has then said, oh, well, this is exactly what evolution would predict, evidence for function in the genome. And it's like, well, no, Dawkins, you yourself have had a major role to play in this idea of selfish genes and purposeless, parasitic DNA. You're one of the people who actually pushed the idea that our genome is largely junk. So you don't get to rewrite history and pretend that you never made those predictions. And Dawkins was very influential, but he was just part of a huge chorus of scientists in the evolutionary community who were saying that our genome was largely junk. So you cannot just rewrite history. Well, what about this idea that today people will say, well, some evolutionists were at least finding evidence or predicting that it was junk. And my argument there is that the scientists from the mainstream community, there were some who predicted that the junk would largely be functional, okay? There were some mainstream scientists who are evolutionists who did predict that we would find out that the junk DNA was not useless, but they were doing this all in spite of the evolutionary paradigm, not because of it, okay? And you need to understand that some of these folks have actually been very critical of the evolutionary paradigms, holding back of our progress of being able to study the junk DNA. A perfect example of this is an australian scientist named John Maddock. John Maddock is kind of a. I respect him a lot. He's like a rogue scientist. He's an evolutionist. But he has argued for decades that the non coding DNA is not largely junk, that it's highly functional. And last year, in 2023, he co authored a book with Taylor and Francis, which is a major, you know, science publishing house titled RNA the Epicenter of Genetic Information. And this book is, you know, hundreds of pages long. And it's just documenting what the rna in our body is doing. And this rna, of course, is produced by non protein coding DNA, which then produces rna, which has many functions in our bodies. And here's what he says. He says, while the story is still unfolding, we conclude that the genomes of humans and other complex organisms are not full of junk, but are rather 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 long held conceptions of genetic programming and the dogmas of evolutionary theory. Okay, so this is not me saying. This is him and another scientist named Paulo Amaral. They're saying that this discovery that our genome is producing huge amounts of regulatory rna that has very important functions, that this is, quote, contrary to the long held conceptions of genetic programming and the dogmas of evolutionary theory. Okay? And these guys are evolutionists. And they're saying that the dogmas of evolutionary theory that basically failed to predict these discoveries. And these are the guys that actually did predict it. All right? They were a couple of the few evolutionists who were bucking the trend and really sticking their necks out to say and for a long time, that we should not consider the junk DNA to be junk. I think what we see then is that, by and large, the evolutionary paradigm did not anticipate function for the junk DNA. And the few and far between folks who did, they actually have been critical of the evolutionary period. Time for getting it wrong on this point, even though they themselves are evolutionists.
You know, we have folks who kind of want to have it both ways these days, Eric, because now, you know, I think that folks are seeing that the trend line is in the direction of function for junk DNA. We have folks who want to say, oh, well, the genome is still full of junk, and yet evolution anticipated all of the function that we're discovering. Well, okay, well, which is it? Is the genome junkie or not? You know, are you claiming that the genome is full of junk or not? What are you. I mean, they want to have it both ways. And I think the truth is that we have all the quotes to back this up, that evolution did not anticipate this function. And the genome, in fact, is largely functional. It is not full of junk.
[00:15:29] Speaker B: Right, right. So take me back. You were mentioning this fellow from Australia. Do you remember when he started talking about this? Was this because the book was just last year? I mean, was this early on?
[00:15:40] Speaker A: Yes, absolutely. He was early on. In fact, I remember that there was an article that came out in scientific american back in the mid two thousands, I think it was around 2003, where he was quoted in, I believe it was against scientific american, basically saying that the failure to recognize the importance of introns will go down as one of the biggest failures of molecular biology. He said that? The exact quote is it was one of the biggest mistakes in the history of molecular biology to fail to understand the importance of introns, which, of course, are these stretches within the genes and also the long stretches of intergenic DNA between the genes.
He's looking at this DNA and saying that this is functional. This is back in 2003. So he's been around for a long time saying this.
[00:16:29] Speaker B: Well, go back even further than that, because I think there were some ID proponents who were even talking about pervasive functional DNA before that.
[00:16:38] Speaker A: That's right, Eric. And we talk about this in our long story short video. We document how intelligent design actually got these predictions right. I think that the earliest example of an ID proponent predicting function for junk DNA came in 1994, when Forrest Mims, who's a very well known popular science writer and also a very eminent and respected engineer, he wrote a letter to the Journal of Science warning against assuming that the junk DNA is useless.
Science, unfortunately, did not publish his letter, but the fact that he wrote this and made this prediction was very significant. We can now fast forward to around 1998, and Bill Demski wrote an article in sort of the christian faith journal, first things. And in this article, he says that we should, quote, consider the term junk DNA. Implicit in this term is the view that because the genome of the organism has been cobbled together through a long, undirected evolutionary process, the genome is a patchwork of which only limited portions are essential to the organism. Thus, on an evolutionary view, we would expect a lot of useless DNA. But then he says, if on the other hand organisms are designed, we expect DNA as much as possible to exhibit function. Here Bill Demski is in 1998, obviously a very leading id proponent, a leading id theorist at that time, articulating that intelligent design predicts function for junk DNA. And then, of course, we have Richard Sternberg, who in around the year 2002 published an article in Annals of the New York Academy of Sciences where he basically railed against the idea of junk DNA and said it's one of the neo darwinian icons of evolution that needs to be sort of thrown into the dustbin of scientific history. And then we have Jonathan Wells in 2004 writing an article in the old Id journal, Progress and complexity information design, again predicting function for junk DNA. And there's many other examples like this. So Id proponents have been predicting function for junk DNA. And these quotes that Im mentioning from the late nineties, mid nineties, early two thousands, all of this was being said at a time before the idea that our genome is largely functional was widely accepted. This was still very, very much a contrarian view that went against the consensus. The vast majority of scientists still believed that the junk DNA was junk at that time.
[00:19:08] Speaker B: Right, right. Okay, so just to summarize then, if we have sort of a correct view of the history, there was a very strong consensus. And by that I don't just mean a couple of people, I mean published articles in Nature textbooks, major proponents of evolutionary theory who proposed that the vast majority, or at least the majority of our DNA was junk. And not only that, but I would say used that as a club to beat over the head anybody who questioned evolution. This was propounded and put out there as great evidence for the truth of evolution and evidence against design. So that was the pervasive view.
[00:19:46] Speaker A: Can I speak to that really quick, Eric? Yeah. So as some folks may know, I got involved with the id conversation when I was an undergraduate at UC San Diego. And this was in the late nineties and early two thousands, I started a student club at UC San Diego called the intelligence, design and evolution awareness club, or the idea club for short. And so this was, we formed that club in 1999 and I was very involved with it until I graduated in 2001 and then still lived in San Diego until 2005. And the club was run by other students after I graduated and still stayed very involved with the club. And I can tell you that back in those days, we're talking like 1999 until 2003, four, five, whatever, we would go to the idea club and have conversations with people. And exactly as you said, Eric, they would use junk DNA as a club to beat us over the head saying, how can you say that the genome was designed when we so evidently can see that the vast majority of our genome is functional as junk? And this was around the time that the human genome project had been released and they made the surprising discovery that there are only about 20,000 genes in the genome. They were predicting maybe there were going to be upwards of 100,000 genes in our genome, but no, there's only 20,000 protein coding genes that they discovered, which represents only maybe one to 2% of our genome. So what's the other 98 99% of the genome doing? They would say it's junk, and that junk refutes intelligent design. We would hear these arguments and I would go to the club meetings and we would. We would have these conversations with evolutionists who would come to the club, including scientists who would come to the club, and what we would say was, you know what? We really. This is premature. You really don't know what that non coding DNA in the genome is doing. Maybe it will turn out to be junk. We didn't know at that time what was going to happen. We said, maybe it will turn out to be junk. Maybe you guys are going to turn out to be right, but we just don't know. So let's adopt a wait and see approach. Id is predicting that it's going to be functional, but, you know, or it's going to be at least largely functional, but if you guys turn out to be right, then we will concede that evolution has scored a major hit against intelligent design. But we just don't know the answer to that yet. And I don't want to concede an argument before the facts come in. And they were basically prematurely concluding that it was in fact, functionless junk. And we were the ones encouraging folks to take a wait and see approach, not discourage research. Let the research have the final say. Well, we can get into this, but, you know, the research came in within the next ten or 15 years and it came down decidedly on the side of the id prediction. I just want to affirm what you were saying. This argument has been used as a club against intelligent design. And at the idea club, we would have to deal with this. And we didn't have a good answer back then, other than to say that we didn't know, which was true. Nobody knew yet. So let's wait and see what the evidence said.
[00:22:34] Speaker B: Yeah, yeah, I would if I can. I would say it a little more strongly than that. I don't know what you were talking about at the club. There at the university. But, you know, when I was debating this kind of stuff back in those days, 20 years ago, there's a couple of things about this idea of pervasive junk DNA based on looking only at the coding regions that have been discovered at the time. First of all, the idea that the rest of the genome is largely junk is an argument from ignorance. Let's be very clear about that. You're looking at this vast majority of the genome and saying, we don't know what it does, therefore it must not do anything. So that's an argument from ignorance. Second, we knew at the time that there were hundreds of thousands, maybe millions, but I'll be conservative and say hundreds of thousands of biological functions that an organism, a large organism like ourselves, has to undergo. And you could just sit down and brainstorm about how a body is built and what things take place and what occurs. And yet only a tiny, tiny, minuscule number of those functions had been tied back to DNA and had been tied back even loosely to some sort of an explanation of how they occurred. And so the idea that we have this vast list of functions that we know exist, that we know occur in the real world, and yet we don't have function for them based on this small amount of DNA tells you that there is a vast amount of function remaining to be found, and it just has to be there. You can't have stuff just happening by accident. And so, you know, I was in conversations with folks back then who were making these kinds of arguments. You know, 95, 98% of the DNA is junk. And I said, I don't, again, like you say, we have to wait for the evidence to come in, but I was saying, no, I'm going to flip it the other way on you. I think it's going to be 95, 98% functional and kind of flipping that argument. Now, there's a technical point here, which is, can both evolution and id accommodate some amount of junk.
[00:24:36] Speaker A: Yeah. By the way, what you just said is a very articulate response, probably a better one than my rudimentary undergraduate arguments were making. But I think that you reasoned that out really well. But you made a great point, and I think we did make this point, too, that it's an argument for ignorance. We really didn't know what the evidence was going to say, so why prematurely conclude what the answer is?
[00:24:58] Speaker B: That's what you're saying. Exactly.
[00:24:59] Speaker A: Yeah. And that's how you actually end up discouraging scientific research when you make assumptions. But yes, can evolution accommodate some function? Absolutely. The answer to both of those questions is, yes, id does not say that 100% that absolutely every single nucleotide in the genome has a function. We recognize that there is such a thing as random mutations, that there is such a thing as genetic decay. I like to give this example. If you were to take my laptop and put it on the top of Mount Everest, come back in 30 years, it's not going to work anymore. And that is because you take something that was designed, that initially functioned very well, you subject it to the forces of nature, to entropy, to decay. You know, what is going to happen is it's going to lose functionality. Now, my laptop actually has problems even on a good day, so don't get me started on that. I kind of live in this crazy world of constant computer problems, but it's very normal for us to see that things that were designed can undergo some form of decay, break down and lose their function. So the idea that there is some junk in the genome is not incompatible with the idea that it may have been initially designed and lost its function. And I think that this is a good way of understanding many of the quote unquote pseudo genes that we see in our bodies. There are many pseudogenes that actually are not junk, that are functional, but there are some that may turn out to be legitimate examples of broken genes that were once functional that no longer do anything. Okay, fine. That's not evidence that the genome was never designed in the first place. It could be evidence that the genome was designed and yet has undergone degradation in some cases.
That is one way of looking at it. Now, there's also this idea. Can evolution accommodate some function for junk DNA? Well, sure, I don't have a problem. Even they will say that, you know, the way that they try to frame it is, oh, endogenous retroviruses. I don't think we have time to get into this too much today. But you know that the vast majority of endogenous retroviruses are junk DNA. They were ancient viral insertions that don't do anything. But every once in a while, maybe an endogenous retrovirus gets co opted by accident to do something useful for our bodies. Okay, yeah, and look, if you're an evolutionist, that's not, that doesn't sound like a totally unreasonable argument. Now, whether or not ervs are largely junk is a separate question that we can discuss some other time. But the reality is they don't get scared off by a little bit of function for the junk. But I think this is where we're not dealing in arguments that deal with precise and specific numbers, but we are dealing with arguments that deal with very clear and large generalities. Is the genome largely junk or is the genome largely functional? And evolutionists clearly predicted it was going to be largely junk. And what we have found is that the genome appears to be largely functional, and that is where things stand today. And that is where id got it right and evolution got it wrong.
[00:28:03] Speaker B: Yeah, I appreciate the way you described that. I just wanted to make sure our listeners understand that, yes, some amount of junk can be accommodated within the design framework, function can be accommodated within the evolutionary framework. But it's this larger picture, this larger expectation of the sense of what the majority would be. And as you say, evolution got it flatly wrong. And ID proponents even back decades ago were getting this right. So thats an important thing for us to keep in mind. All right, and we'll talk about, I do want to come back maybe in another conversation, another time, Casey, and talk about pseudogenesis and endogenous retroviruses and non coding DNA generally. Get into that a little bit.
[00:28:42] Speaker A: Yeah. And Eric, we have another long story short video coming out in the not too distant future that's going to address those topics. So when that one comes out, we'll have to continue this conversation.
[00:28:52] Speaker B: Yeah, yeah, absolutely. But let's fast forward to the encode project. Tell me a little bit about that, because we had this. When did it start? Like the seventies when Junk DNA started becoming really popular.
[00:29:03] Speaker A: Yeah, I mean, the idea of junk DNA was first articulated in the sixties and seventies, probably the late sixties, early seventies. But I don't think encode was around that early.
[00:29:12] Speaker B: No, no, no, I'm saying. So that's when the junk DNA idea kind of started. It started taking hold. It became really popular in the eighties and nineties and early two thousands. But then encode hit. Tell us about that.
[00:29:23] Speaker A: Yeah, so encode was a project that was started in probably the mid two thousands after the human genome project came out. And I think it was driven kind of by that intuition that you articulated earlier, Eric, that, look, there's a lot going on in our bodies that cannot be accounted for by just 20,000 genes. Right. So we've got to start looking for function elsewhere in the genome. In the genomes. And so a consortium of hundreds of international scientists started a project called EncoDE, which stands for the Encyclopedia of DNA elements. And this was a multi year project that was looking at the non coding DNA in the human genome. And they were trying to figure out, is it actually functional or what is it doing? They came up with an initial paper around 2007 that sort of said, yeah, from the little bit we've looked at so far, we're finding a lot of evidence of biochemical functionality. But then in 2012, there was sort of what I would call a game changing paper published in the journal Nature, as well as about 30 other papers that came alongside of that, which found that, quote, the vast majority of the human genome shows evidence of biochemical function. And they said, in the Nature paper, they said these data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well studied protein coding regions. And so some folks might say, well, okay, 80%. Does that mean that there's still 20% of the genome is junk? I mean, that seems like a lot. And the answer to that is no. Encode only studied a few, maybe, say, somewhere around 150 different types of cells in the human body. What they found in encode is that much of this non coding DNA is only activated in certain cell types at certain stages of the human life cycle. So catching every single nucleotide in action would actually be very difficult. You would have to study our genomes at a very, very precise, comprehensive, almost like every single moment of every day for a person's entire lifespan. Studying every cell to probably guarantee you're going to catch every single nucleotide in action. Even then, maybe not every nucleotide is going to be relevant. Maybe some are for certain contingencies that don't happen. Every single person.
[00:31:36] Speaker B: Or structural. And not transcribed.
[00:31:38] Speaker A: Or structural. Yeah. There was a lead encode researcher who predicted that if we were to study, you know, more and more cell types, that he said it's likely that 80% will go to 100%, and that actually he's predicting that every nucleotide essentially has a function. Now, of course, this reflects the fact that there is still a lot that we don't know about the genome. Okay, I'm not saying that we've discovered function for every single genetic element in our genome, but I do think that we have found that the genome is largely strong evidence that the genome is, in fact, largely functional. And that is where we are today.
[00:32:13] Speaker B: Yeah. So I remember when encode came out, that was indeed a huge game changer. So the response, Casey, just so we understand, the response from the evolutionary community was to say, oh, sorry, we got it wrong. You're right, it's mostly functional. Right? Was that the response?
[00:32:27] Speaker A: Well, no, actually, not at all. That was funny. Yeah, you kind of set me up there. Definitely not, Eric. Now, there were a lot of scientists who accepted the evidence for function that was discovered from encode. I want to make a little comment on that in just a moment. But the response from the evolution community, the evolution contingency of the biology community, was to actually deny encode's results and to say, okay, maybe this DNA is producing a lot of rna, but that is actually junk rna. So they move the goalpost. It's no longer junk DNA, it's now junk rna. And you'll even find some folks who will say, oh, well, even some of that rna that's being transcribed into protein isn't being used. So we also have junk protein. All right, so the evolutionists, as usual, are in love with this idea that our bodies are full of garbage, junky aspects that don't do anything, and they just can't get rid of this idea. They so much love the junk idea that they're just. They're going to find junk no matter what. So that is where we're at today. And they're going to claim that this transcription that's going on, you know, the fact that 80% of our genome is being transcribed into rna, that actually the vast majority of that is random, it's stochastic. It's not doing anything for you. It's actually your cells wasting resources. All this transcription, you know, it uses up a lot of ATP to run those rna polymerases along your DNA strands and generate all this rna. Okay? I mean, this is very. A lot of activity is being basically done for nothing, if you believe what the evolutionary scientists are studying.
[00:34:01] Speaker B: What a terrible design, right?
[00:34:02] Speaker A: What a terrible design. That's a really even worse than at least the junky day was just sitting there doing nothing. It wasn't wasting research.
[00:34:09] Speaker B: This is so ironic, because even under an evolutionary paradigm, you shouldn't have an organism that's spending 80% of its transcriptional resources on doing nothing helpful, gumming up the works, even making it worse.
[00:34:21] Speaker A: Yeah. Well, the good news here for us junk DNA skeptics is that the evidence does not suggest that the transcription is random. And you can go to some of the encode literature, which finds that the transcription that goes on in our bodies is not at all random. And in fact, it very much is non stochastic. It's happening in repeatable, predictable manners that allow scientists to actually predict what is going to be transcribed in certain stealth types or in certain cell states, et cetera, et cetera. And so clearly, this transcription that's going on, it has every evidence of being functional. It would be like, if you were to open up a circuit board, right. And find all these electrons flowing along predictable patterns, predictable wires and lineations in a circuit board. You're not going to say, oh, this is probably just random and happening for no reason. No, you're going to see that this switch opens up this circuit and turns on all these movements of electrons, and these electrons only move when this is happening in the circuit. You're finding patterns, you're finding evidence of function and logic going on. This has all the hallmarks of being highly, highly functional. I guess what I would say is that even though there's still a lot we don't know about the genome, all the evidence we found so far points to functionality.
[00:35:40] Speaker B: Yeah. And this is a good time to mention that book again, which just came out, I think you said last year it's an entire hundreds of pages devoted to helping us understand the function of these non protein coding RNA's, which are extensively utilized in the cell.
[00:35:57] Speaker A: Yeah, yeah, that's exactly right. There's a lot of scientists who are saying this, Eric, that the genome is producing huge amounts of regulatory rna's that do all kinds of important functions. One of the most important functions that they do is regulating the expression of the genes. So if you just had a bunch of genes being expressed, that's not going to help you unless you're expressing them in the right place and the right time and in the right manner and producing the right amount of each protein. Really, in many ways, it's a non coding DNA that contains the blueprint that tells your body when to produce proteins, how much to produce, when to stop producing them. And this is really the control mechanisms for the genome is found in the non coding rna. I want to also bring something really interesting out here, Eric. I was recently in conversation with a scientist who's a member of our community. I'm not going to mention their name, but you definitely know this person, and I'm not going to even allude to whether it's a he or a she. This person is a researcher at an Ivy leagues university in biology. That's all I'm going to say about this person. Okay. And we were talking about the idea of junk DNA, and I said to this person, and this person actually studies rna, okay? So they research in this specific field of RNA at an Ivy league school. And I said, you know, what is your take on that idea of junk RNA? Is that idea like, catching hold in your field? And you know what this person said to me? They said basically that in their field, nobody believes that if something is being transcribed, that it's probably being transcribed for no reason at all, that there is an assumption in their field that if transcription is happening, that it's happening for a reason. And this is from somebody who is basically swimming and living in just the normal scientific community that's full of scientists who are evolutionists but are looking at the data. They work in the bench lab world, where they're just looking at the data. What does the data tell us? And for these scientists, yes, they're evolutionists, but they're driven by the data. They don't even have a moment of interest for this idea of junk RNA. I mean, this is coming from the evolutionary biology community that is hold up on this idea that it must be largely junk. And so I think when you talk to normal biologists, the idea of junk drna is just not catching hold. This is something that's coming from folks who don't want to, you know, they're basically hiding out in caves and can't admit that the battle is over.
They don't want to believe that this has actually been settled in favor of functionality.
[00:38:28] Speaker B: Yeah, that's great. I appreciate you mentioning that. So it highlights two things for me. One, it's great to see that viewpoint sort of taking hold and being the norm within actual experimental biology. And second, it also highlights the great disconnect between experimental biology, systems biology, and evolutionary theory, which is not contributing to the understanding at this point. Instead, they're looking at this and saying, okay, we've seen a transcription factor here. We better. Or a transcription transcribed RNA. We better look for some function here.
[00:39:01] Speaker A: Yeah, I mean, that's the general view within the people who actually study how biology works.
That's how they see it. Now, this is the paradigm shift that's happened. In fact, there was an article in the journal Bioessays at the end of 2023. Eric, you probably read this paper by John Maddock, which said that there has been a quote unquote kunian paradigm shift away from the concept of junk DNA. And I think when you talk to Reagan phyobiologists, this is just accepted now.
[00:39:29] Speaker B: Yeah. People that are actually doing real work on the ground. Yeah. So, Casey, in the few minutes that we've got left, as we kind of step back and think about this whole episode, what can we learn from this lengthy episode about junk DNA in the history of science and as it relates to evolutionary theory?
[00:39:47] Speaker A: Sure. Well, there's a lot of things we can learn. Number one, we can learn that intelligent design makes predictions. And by the way, I think we never articulated this important point. Why does intelligent design predict function for junk DNA? Well, I've always thought it's very, very simple. Intelligent agents, when they act, they tend to do things for a purpose and for a function. And so if that is the case, then of course we're going to expect that our bodies are not going to be largely full of junk DNA, junk organs, vestigial, useless parts. There may be some things that have lost their function over time, but we're going to find out that our DNA is largely functional if, in fact, our bodies were designed because intelligent agents make things, that do things and do things for reasons and for purposes and for functions. Okay, so what we're finding, number one here, is that intelligent design is a useful scientific paradigm and that it makes predictions that we can test. And those predictions have in some cases turned out to be spectacularly correct in the face of the consensus from the biology community that went against those predictions. So we're finding out that id makes useful, testable predictions that turn out to be correct. We're also finding out that when someone makes an argument against intelligent design, and it seems like, okay, this sounds like a reasonable argument, but we really don't know for sure what the data says, don't give up too quickly on id. Right. Because back in the late nineties, early two thousands, when we were getting hit over the head with junk DNA like a club, those of us who were ID proponents, we decided to not give up on ID and take a wait and see approach and actually wait to see what the data said. And boy, aren't you glad we did that, Eric?
[00:41:27] Speaker B: I mean, yeah, yeah, absolutely. I think. Well said. And, you know, I'm going to maybe get on the soapbox here for a second because I have a little bit of a strong view maybe on this whole junk DNA thing, because my view, Casey, is that this was preposterous from the outset. You know, it's not as though. And we go back to the idea that you sometimes hear, you know, science is self correcting, and that's true in a lot of cases, and it's, you know, something that we appreciate. But this is not a case of scientists who came out with a well thought out, objective, reasonable claim that they were genuinely studying and genuinely trying to determine whether it was true, and then it turned out not to be true, and so they moved on and accepted the results. That's, that's not what we saw at all for the last 50 years, Casey. We saw an absolutely ridiculous claim based on ignorance that was not analyzed well, that was not thoughtful. That didn't take into account anything about sort of an engineering view of what it would actually take to build and maintain an organism in the real world. And that was based largely on ignorance. It was based on a worldview. It was based on an effort and a hope in some cases, you know, Dawkins and others, to be. To beat critics over the head with this club. And it's just turned out to be spectacularly wrong. And so I think one of the other takeaways for somebody, you know, anybody who believed that DNA was pervasively junk, anybody who bought into that, I mean, I think needs to take a strong look in the mirror and say, what was it about my viewpoint or my worldview or my lack of analysis that made me believe this? And how can I do better next time?
Why would I accept this idea that biological systems are some haphazard hodgepodge of accidental mistakes and copying errors? What made me believe that? And how can I change my view going forward and be a little more careful next time? Anyway, end of soapbox.
[00:43:26] Speaker A: No, very well said, Eric. And I think you talked about science being self correcting. This is a good example where science has been self correcting, and ultimately the data has won out over the idea of junk DNA. However, it's important to understand that we rejected the idea of junk DNA in spite of the evolutionary paradigm, not because of it. Okay? It's. The evolutionary paradigm is what drove the idea of junk DNA. And it was because of the data that overturned that paradigm, not evolutionists suddenly seeing the light of what their theory really predicted. And I want to maybe end with this quote. Well, you can end whenever you want to end. You're in charge here. I want to give this quote from a 2003 paper in the Journal of Science. Okay? Here's what it said. It said the term junk DNA for many years repelled mainstream researchers from studying non coding DNA. This is from the Journal of Science. Okay? And this article goes on to say that those who thought that there was going to be function in the junk did so at the risk of being ridiculed, unquote. Okay? So there was, like, pressure on scientists to not look at this. You're crazy. We all know evolution has shown that our genome is full of junk. Well, don't question that. Don't think outside the evolutionary box or you're going to be ridiculed. It's going to be death to your career. This is the way that evolution has stopped science from discovering the functions of this non coding junk DNA. And so there's a lot of lessons to learn here, and I hope that people will learn those lessons.
[00:44:57] Speaker B: Yeah. I appreciate you bringing up that quote and mentioning that, because we need to not let the history be rewritten here, both because it's fun to point out that folks were wrong and we were right, but more importantly, because we need to understand what happened and why this occurred. And it occurred because of some bad worldview and bad predictions based on a bad theory. Now, as you say. And in the end, the data won out, Casey. The data won out. But this is not a case of evolutionary theory, you know, self correcting. This is a case of people who went against the theory, who finally won out based on the data.
[00:45:32] Speaker A: Absolutely. And there are still evolutionists today who want us to believe that the genome is largely junk. It's producing junk RNA. So don't let anybody tell you that evolution is predicting this function when they're still arguing today that it's largely junk.
[00:45:45] Speaker B: Yeah. Yeah. All right, last question, just briefly. And again, we'll talk about specific portions of the genome later. But what is the general trend of the evidence, and what can we expect going forward, Casey, as we think about function in DNA?
[00:45:58] Speaker A: Yeah, so the general trend of the evidence is that functions for non coding, or junk DNA, are being discovered at what I would call an exponential rate. There was an article in the journal Nature a couple years ago that had a graph with two curves over time. And one of the curves showed the number of genes, protein coding genes, that we're aware of in our DNA. And this curve basically plateaued around the early two thousands, like 2001, 2003, whatever. And it's gone up a tiny bit since then, but not by much. And then it showed another curve, and that is our knowledge of the number of specific non protein coding DNA genetic elements for which we have discovered specific functions. And that curve in this paper was going up at an exponential rate, going up so quickly that it was like, you know, it looked like an exponential curve. And this paper said, we've now discovered over 130,000 specific examples of functional non coding junk DNA elements for which we know it has a function. Now, what this tells you is there's still a lot of the genome that we haven't studied yet in specific detail to figure out exactly what it's doing. All right, so there's still a lot we don't know, but the encode project gives us very, very powerful, prima facie evidence that it is, in fact, functional. Not only are we seeing transcription, but we're seeing transcription in non random patterns. That seems to be repeatable and predictable, all the evidence of functionality going on there. And so I think what we're going to find is that over time, this trend of just finding function after function after function for non coding DNA elements, it's going to continue. It shows no sign of slowing up. If anything, it's going to just get stronger and stronger and we're just going to continue to discover function for the non coding DNA. And this paradigm is just going to go further and further into the annals of the history of science, but not something that people actually believe anymore.
[00:47:55] Speaker B: Yeah. Wow. Over 130,000 already. That's great. I'd mentioned hundreds of thousands earlier, but we're going to surpass that, it sounds like.
That's great. Thanks for that. Gosh, that's really amazing. 130,000 functions for so called junk DNA. Unbelievable. And just getting started. Well, Casey, thanks so much for being with us today to help us understand more about the deep and pervasive function that we're starting to discover in DNA. Discoveries that point to an incredibly sophisticated and engineered system. And discoveries, I would say, that give the lie to the common evolutionary talking point, that our genome is a mishmash of accidental copying errors and useless junk. I really appreciate you helping us break down the issues and giving us the long and short of it, so to speak.
[00:48:36] Speaker A: Thank you so much, Eric. And I appreciate you being part of this conversation because you've been having these debates for so many years and you really appreciate the dynamics of what, what has really happened in the junk DNA debate. We've lived it. We lived through people beating us over the head with this. We saw ID make these predictions and then we saw ID's predictions come true. When you live to see those things happen, it really gives you confidence that there's something right in your paradigm.
[00:49:02] Speaker B: Well said. Well said.
Thank you for listening to this episode of ID the Future. To learn more about the incredible engineering and the growing evidence for extensive function in DNA, join us again soon at ID the future or our YouTube channel, Discovery Science, and help us spread these important messages by sharing a link with a friend. For id the future, Im Eric Anderson. Thanks for listening.
[00:49:25] Speaker A: Visit
[email protected] and intelligentdesign.org dot. This program is copyright Discovery Institute and recorded by its center for Science and Culture.
