[00:00:04] Speaker A: Id the future, a podcast about evolution and intelligent design.
[00:00:12] Speaker B: Welcome to id the future. I'm your host, Andrew McDermott. Well, today I'm sitting down with Casey Luskin to get an update on the myth of junk DNA, non protein coding sequences of DNA that some scientists claim don't do anything and amount to evolutionary junk. Dr. Luskin is a scientist and attorney with graduate degrees in science and law, giving him expertise in both the scientific and legal dimensions of the debate over evolution. He holds a PhD in geology from the University of Johannesburg, where he specialized in paleo magnetism and the early plate tectonic history of South Africa. Casey serves as associate director of the center for Science and Culture at the Discovery Institute. Welcome back, Casey.
[00:00:55] Speaker A: Great to be here with you, Andrew.
[00:00:57] Speaker B: Yeah, well, good to have you. Now, intelligent design theorists have long held that far from consisting mainly of junk, the genome is increasingly revealing itself to be a multidimensional, integrated system in which nonprotein coding DNA performs a wide variety of essential biological functions. Dr. Jonathan Wells's 2011 book, the myth of junk DNA, made this argument decisively. And since then, more and more revelations of function have been discovered for these nonprotein coding regions of DNA. Now, Casey, you've actually reported recently at Evolution News on yet another function for what was previously considered junk DNA. What have scientists discovered about the function of strs? Short tandem repeats.
[00:01:45] Speaker A: Yeah, well, there are papers coming out all the time, Andrew, discovering function for non protein coding DNA, or what has often been called junk DNA. So this is just one of the latest examples of a paper that discovered functions for, quote unquote junk DNA. And this time around, it's what we call short tandem repeats, or strs. These are short, repetitive sequences of DNA that make up about 5% of the human genome. And over time, they've been widely disregarded as junk because people think that these repetitive sequences just represent sort of mutations that accumulated and copied and duplicated segments over and over again. Maybe they were inserted by transposable elements over and over again, and they were just basically parasitic junk in our genome. But a recent paper published in Science in September of 2023 found that actually the length of these strs, or the number of repeats or copies of this repetitive sequence, can help to fine tune the expression of genes by modulating the ability of transcription factors to bind to those genes that they regulate. So because of this tuning ability, these strs were actually compared to Rio stats, which are engineering components that precisely control some function, like setting the temperature of your oven or controlling the exact amount of light that's coming out of the dimmer lights in your living room or something like that. So this is really striking because it shows that this type of repetitive DNA, which was dismissed as evolutionary junk, turns out to actually have very important functions and abilities to fine tune gene expression and finally control various genomic functions. So this is very interesting discovery. It's another example of junk DNA turning out to have function.
[00:03:24] Speaker B: Sure. Yeah. So interesting. Well, in your recent articles, you discuss a coonian paradigm shift against junk DNA. Can we start by explaining what a coonian paradigm shift is?
[00:03:36] Speaker A: Yeah, it certainly sounds like a weird phrase if you're not familiar with the history of science, but the phrase comes from the work of a famous Harvard historian of science and philosopher of science named Thomas Coon. And he wrote a very influential book in the 1970s titled the structure of Scientific Revolutions, where he documented how new ideas in science typically take hold through what are called paradigm shifts, where the leading framework in a field, which is called the paradigm, starts to accrue evidential problems. Essentially, the evidence will contradict that paradigm until the paradigm goes into, quote unquote crisis. And eventually, when enough of these evidential problems accrue and the paradigm is in sort of full blown crisis mode, then that paradigm finally gives way to some new idea that challenges that status quo paradigm. And so when the view of a fuel changes, that is called a paradigm shift. So that's what a coonian paradigm shift is. Probably familiar to folks who've heard the term paradigm shift. That's all it means is, in science, basically, the consensus or the standard view within a field is shifting.
[00:04:38] Speaker B: Yeah. Okay, well, tell us about the recent article in bio essays written by australian molecular biologist John Maddok.
[00:04:47] Speaker A: Yeah. John Maddok is a professor of rna biology at the University of New South Wales in Sydney, Australia. And I have no evidence that Maddok himself supports intelligent design. I don't think he does. As far as I know, he's just a standard evolutionary scientist. But he's a prime example of a bold scientist who's just willing to follow the evidence where it leads, without sort of letting the paradigm, quote unquote, so to speak, get in the way of his ideas, and he's willing to embrace new ideas that sometimes challenge these reigning paradigms. For years, Maddok has been indefatigable in following the evidence where it leads regarding evidence of function for junk DNA. And this is in part because of his work that biology today has experienced a paradigm shift away from the concept of junk DNA. In fact, Maddox's new article, which he published in a very prominent journal, Bioassays, is titled, quote, a kunian revolution in molecular biology. Most genes and complex organisms express regulatory rnas, in which he frames this revolution in thinking over junk DNA precisely in coonian paradigm shift terms. So I think that this is a very important article. It sort of, I think, is signaling that this paradigm shift in biology away from the concept of junk DNA really has finally taken place and has been completed.
[00:06:06] Speaker B: Okay, well, paradigms are usually held in sway by scientists with strong commitments to accepted dogma. And Maddox says that the reigning junk DNA paradigm in biology has come from, quote, prevailing assumptions, unquote. What are some of those assumptions? Casey?
[00:06:23] Speaker A: Yeah. Well, I would classify the assumptions that matic identifies into two general categories, those which derive from molecular biology and those which derive from evolutionary biology. So the molecular biology assumption is essentially this. The purpose of genes is to produce proteins, and proteins are by far the most important biomolecules in the cell. And this comes out, of course, what is known as the central dogma of biology, which is that DNA makes RNA and RNA makes protein. And this is true, of course. I mean, the central dogma is not completely wrong. DNA does make rna, and RNA does make protein, and proteins are very important in biology, and genes encode proteins. But what this paradigm misses is that DNA can also make rna, and those rnas themselves can perform all kinds of vital functions in the cell, especially regulatory functions. So basically, it's not just proteins that are important in the cell, and it's not just protein coding DNA that's important in the cell. This rna coding DNA is extremely important for regulating what the cell is doing. So those are the molecular biology assumptions that I think we're finding out are not quite right. But then there are also evolutionary assumptions. Now, again, as far as I know, matic is an evolutionist, but he certainly identifies certain evolutionary ideas which led to the misguided junk DNA paradigm. In particular, he notes that higher organisms will accumulate mutations in their genomes over time. And to avoid these mutations from being overly deleterious, evolutionary models require that the genomes of organisms, essentially, over time, will balloon up with junk. And so this evolutionary view that our genomes are the result of millions of years of random and unguided mutations, this has led to the idea that our genomes should be full of junk. And this is certainly an assumption that I think Maddok is willing to challenge.
[00:08:17] Speaker B: Okay, well, in his bioassays paper, matic cites ten anomalies that have challenged the current junk DNA paradigm. I thought maybe we could briefly walk through some of these lines of evidence against junk DNA. Well, first, there's the c value paradox. What's that?
[00:08:33] Speaker A: So the c value paradox is an observation that some types of organisms have unexpectedly large amounts of DNA in their genomes. And some folks have interpreted this to show that much of their genomes are junk. But others suspected that what it really showed is that these genomes are really more than just protein coding DNA, and that the non protein coding DNA actually has important functions. And so the onion is the classic example of an organism that has a lot more DNA than you would expect. And people will often cite the onion to sort of promote this C value paradox and this idea that most of our dna is junk. In fact, I love the way that one biologist I know has framed the argument. I won't name the person, but I don't want to take credit for it. But they sort of parody this argument as false. They say, oh, the onion has a huge amount of DNA, therefore, there is no deity. Okay, so this is sort of, I think, a mockery of the way this argument goes. But in seriousness, some folks actually do almost argue like this. But the C value paradox, and the idea that because some organisms have a lot more dna than you would expect, therefore it's all junk, really fails for a number of reasons. First of all, we've known for a long time that there is a positive correlation between genome size and cell volume, or the size of a cell's nucleus. And this could hint at structural reasons for why all that DNA is there. And we know in particular, onions can have very large cells. If you think back to your high school biology class, you probably looked at onion cells under the microscope because they're so big. So onions have very large cells. So there might be functional reasons for having all that extra dna. Another reason in particular for onions having a lot of DNA is that they're a plant. And plants often undergo what is called polyploidy, where their genomes will balloon in size through duplication type events. So it's not unusual for plants to have very large genomes. Again, there's also, in higher organisms, like vertebrates, there is a negative correlation between genome size and metabolic rates in various vertebrates. And this might hint at functional reasons for why we have a lower C value in vertebrates. But I think that the biggest problem here is that when we say that, oh, there's all this dna, therefore, it must be junk that we are making. We are repeating mistakes of the past where we are substituting our ignorance for the lack of function, for something, for therefore concluding that therefore it must not have function. We're sort of letting our ignorance dictate our conclusions. And the reality is we are far from fully understanding even the simplest bacterial genomes, much less our own. So when there are certain single celled protozoans or certain plants that supposedly are civil organisms that have large amounts of dna, I don't think it's fair to assume that that dna is just there for junk. And I think the c value paradox is really no paradox at all, once you realize that lots of different types of DNA that may not code for protein can have important functions.
[00:11:22] Speaker B: Okay, well, that makes sense. Well, then there's the repetitive sequences in animal and plant genomes that are called transposable elements, or tes. Tell us about those.
[00:11:33] Speaker A: Okay, so for this one, I think we need to go back and tell a little bit of biological history. In the late 1960s, the Nobel Prize winning biologist Barbara McClintock discovered, as matic puts it, that, quote, animal and plant genomes harbor large and variable numbers of repetitive sequences. And McClintock and others called these transposable elements, or tes. And these were also viewed as just another type of genetic garbage that is not benefiting the host organism, because it's thought that these tes are just basically types of genetic elements that can make copies of themselves and insert themselves into the genomes, into repetitive sequences over and over again, kind of like those short, repetitive elements that we talked about earlier. So Maddok mentions in his bioassay's paper that these repetitive elements were, quote, interpreted as the non functional remnants of parasitic, selfish transposons and retroviruses, despite McClintock's demonstrations and protestations that they are, quote, controlling elements. So matic essentially notes that it's been known for a long time that these transposable elements are vital parts of gene regulatory circuits, although he notes that they are quotes still commonly and erroneously invoked as indices of neutral evolution. So I think what we're seeing here with tes is that they have been viewed by most biologists as sort of junk or parasitic DNA. But even from the very beginning, there was an alternative view put out that they actually had important regulatory functions. In fact, there was an article in Scientific American years ago which noted that this view that repetitive DNA is junk has actually held back our knowledge of their functions. And I think this is a quote worth reading because this actually shows that even some mainstream evolutionary journals, like Scientific American, have recognized that the idea of junk DNA has held back science. It said. Although very catchy, the term junk DNA repelled mainstream researchers from studying non coding genetic material for many years. After all, who would like to dig through genomic garbage? Thankfully, though, there are some clotchards who, at the risk of being ridiculed, explored unpopular territories. And it is because of them that in the early 1990s, the view of junk DNA, especially repetitive elements, began to change. In fact, more and more biologists now regard repetitive elements as genomic treasures. So we can go on with this quote, but basically what it says is that we now know that these repetitive elements should not be viewed as just functionless junk parasitic DNA that is just sort of making copies of itself in your genome, providing no benefit to you.
[00:14:03] Speaker B: A reason for the repetition. That's interesting. And it does match up with us humans. When we repeat something, it's typically something we want to emphasize, therefore showing importance. Well, what about introns?
[00:14:16] Speaker A: Yeah, so another discovery was that the protein coding sections of genes, which are called exons, are often broken up by non coding sections in the genes called introns. And many biologists assumed that these introns were useless. They were not actually encoding the amino acid sequence of the protein, therefore they were genetic junk. And so Maddok in his bioass's paper actually says that, quote, introns were dismissed as the leftovers of early evolution, colonized by transposable elements, and preferred another manifestation of and further evidence for junk DNA. So this was the view for many years. And in fact, this bioassays paper is not the first time that matic has sounded the alarm about dismissing introns. A 2004 article in Scientific American, I remember this, came out and it quoted Maddox heavily. It was titled the unseen genome gems among the junk. And he was quoted in that paper as warning that, quote, the failure to recognize the importance of introns might go down as, quote, one of the biggest mistakes in the history of molecular biology. That was almost two decades ago. But as Maddox new paper recounts, it's now widely known that rnas produced by introns are vital for splicing exons together to form different variants of proteins. So they actually have a very large impact upon what mrnas exactly are translated at the ribosome into protein. And there's sort of this splicing code where rmrnas can be spliced together in different ways to be mixed and match and create different variants of proteins. And this is largely controlled through the introns. So introns are hugely important for producing different types of proteins.
[00:15:57] Speaker B: And what about the discovery of enhancers? What can you tell us about that?
[00:16:01] Speaker A: So enhancers serve as transcription factor binding sites, which are necessary for transcribing protein coding sections of DNA and mRNA. But they don't actually encode the protein. They're a non protein coding sequence, yet they're very important for regulating the production of proteins, and they also can express what are called long non coding rnas, or link rnas. So Maddok notes in his bioassay's paper that, quote, there are hundreds and thousands of enhancers in the human genome, and we now know that these enhancers are important for regulating the production of proteins, yet they are a type of non protein coding DNA.
[00:16:39] Speaker B: Okay, how do rnas produced by non protein coding DNA influence epigenetic processes?
[00:16:46] Speaker A: Well, epigenetics is a huge area where junk DNA is now being discovered to have important functions. And epigenetic processes are often controlled by rnas that are produced by non protein coding DNA elements. So matic notes in his paper that, quote, transcriptional and post transcriptional gene silencing involves the production of small rnas, which can influence epigenetic tagging of genes via what is called methylation to turn genes off or on. In fact, Maddok also refers in his paper to the quote unquote epigenetic code, which is found in DNA methylation and histone modification. And this is relevant because the long non coding rnas, or link rnas that are produced by non protein coding DNA also play a major role in this code. So there's a huge number of epigenetic functions that non protein coding DNA is performing.
[00:17:38] Speaker B: Okay, now, another anomaly matic sites is the g value enigma. Tell us about that.
[00:17:44] Speaker A: So the g value enigma refers to the discovery that the number of protein coding genes in an organism does not always correlate with its developmental complexity. So you might have very complex organisms that have fewer genes, fewer, fewer protein coding genes than maybe something that you would consider to be less complex than that organism. So what this suggests is that molecules other than the proteins, it's not just the proteins that matter. There must be other biomolecules in the organism, such as rnas produced by non protein coding DNA, that are very important to organismal development.
[00:18:19] Speaker B: And finally, what about pervasive transcription of plant and animal genomes as discovered by the encode project? What does this tell us about so called junk DNA?
[00:18:29] Speaker A: So, I'm glad that we put this one last, because I think that this line of evidence, perhaps more than any others, has been more instrumental in causing this paradigm shift away from junk DNA. So the EncodE project, which was a huge consortium of hundreds of international biologists working together to look at the non protein coding DNA, trying to understand what it is doing. And what they found is that there is pervasive transcription of the human genome. And we now know that pervasive transcription of plant and animal genomes is another important line of evidence that much DNA, beyond just the protein coding DNA, is important. And Maddok, in his paper, cites the, quote, unexpected finding that animal and plant genomes are pervasively transcribed to produce not only premrnas, but also large number of long non coding rnas, or link rnas, that are derived in tronically introgenically overlapping and antisense with respect to the protein coding genes. So there's all types of ways to produce these long non coding rnas produced by many different parts of the genome. And this is part of the fact that large percentages, huge proportions of our genome is being transcribed into rna. And he notes that many of these link rnas are cell type specific and they can play major roles in cell biology, developmental biology, brain function, diseases and cancer. So this pervasive transcription of our genomes into RNA has all kinds of myriads of different types of functions.
[00:19:58] Speaker B: Well, when you put all those anomalies together, it definitely seems like we have a paradigm and crisis here. So tell me, has the myth of junk DNA disappeared or is it still hanging around?
[00:20:08] Speaker A: Well, I would say that among most rank and file biologists, that the idea of junk DNA is certainly on the downswing. That's why matic is noting that there's been this paradigm shift. I mean, this article doesn't come out of nowhere. I think that people, again, were highly convinced by the data from encode that showed that over 80% of human DNA, in particular is biochemically functional and is being transcribed into RNA. But there have been other papers, I think, that have sort of reflected the fact that most biologists are now rejecting this idea of junk DNA. There was a 2021 paper in Nature which found that over 130,000 specific nonprotein coding DNA elements, what it calls, quote, genomic elements, previously called junk DNA, unquote, have been discovered now to have functions. And that discovery of these functions seems to be going up at a near exponential rate. Another paper published in 2021 in the journal Genome Biology and Evolution reported that, quote, the days of junk DNA are over. So I would say that the consensus of biology today really is reflected in the fact that there has been a paradigm shift away from junk DNA. In fact, even John Madok wrote in a 2023 book published by Taylor and Francis very prominent science publisher, he co wrote this with another biologist named Paulo Amaral. And they say that, quote, while the story is still unfolding, we conclude that 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 rnas. These rnas drive the trajectories and differentiation and development, underpin brain function, convey transgenerational memory of experience, much of it contrary to long held conceptions of genetic programming and the dogmas of evolutionary theory. Unquote. This is what they're saying, that basically this function mass functionality for junk DNA is contradictionary theory. And this is from their 2023 book with Taylor and Francis titled rna the epicenter of genetic information. So when you see mainstream academic biology publishers, publishing books that are saying things like this, I think it's fair to say that this is an idea that is taking hold, that the quote unquote junk DNA is actually, huh.
[00:22:27] Speaker B: And I do like the sound of that. Highly compact informational suites just full of information that the cell will use. And it's pretty awesome. Well, matic envisions a new paradigm for molecular biology, junk DNA and epigenetics. Tell us about the rna gene paradigm.
[00:22:46] Speaker A: Yeah, the paradigm, in short, is that we need to have a new understanding of what a gene is. And I'll quote from the video abstract that Maddok posted for his biosays paper. He says, quote, genes don't just encode proteins, they encode both proteins and regulatory rnas, often both, with the latter expanding with developmental complexity and eventually dominating the genetic programming of complex organisms, unquote. So his idea is that rna genes are extremely important for many functions in biology, from gene regulation to development to cell differentiation, determining what type of a cell it becomes, to epigenetics and many other functions in biology. And this comes back to the idea that we need to recognize rna genes. Genes are not just there to produce proteins, of course, many genes do produce proteins. But many genes are rna genes, and they are producing rnas. And those rnas, as an endpoint unto themselves, have very important functions in our cells.
[00:23:47] Speaker B: Okay, well, in your articles, which we're going to link to in our show notes for this podcast, you cite eleven recent papers detailing specific functions for non coding junk DNA. Can you tell us about just a few of those?
[00:24:01] Speaker A: Sure. I mean, I've kind of just been collecting these papers over the last couple of years, and I thought I'd just dump them in here because they're really interesting. I mean, there's so many papers coming out all the time finding function for non coding DNA that most of the time doesn't even make the news. But these were noteworthy because of what they were finding, the importance of what junk DNA is doing. One paper in biosystems in 2022 by James Shapiro found that the non coding, or junk DNA, is involved in forming new body plans. A paper in Nature Genetics in 2022 found that it's involved in regulating the cell cycle, including controlling apoptosis, when cells basically commit suicide and die. An article in Cell reports in 2022 found that junk DNA is involved in forming fear related memories and phobias. An article in nucleic acid research in 2022 found that actually, quote unquote nonprotein DNA or junk DNA sometimes actually does in fact encode proteins. In fact, pseudogenes can sometimes be translated into proteins. A 2021 paper in virus evolution found that ervs, what we think are these endogenous retroviral DNA, are actually involved in fighting viral infections, and they can be functional. Nature Review Genetics 2021 found that a repetitive DNA helps to control development in mammals. An article in 2022 in stem cell found that junk DNA regulates gene expression in human and chimp brains, and may even help explain the differences between human and chimp brains. Nature methods 2022 found that non coding rnas are involved in cell differentiation and development, essentially determining what kind of a cell a cell will turn into. The journal Nature 2021 found that rnas are involved in limb formation. An article in Nature to communications found that transposable elements are involved in controlling aging. And finally, an article in Nature found that retro transposons are involved in regulating immune responses. That's from 2023. So, again, we could go on and on. These are just a few examples of interesting papers that I've come across, but it's safe to say that junk DNA is producing rnas that are involved in just about everything you can think of inside the cell.
[00:26:15] Speaker B: Well, let me see if I can sum this up then, as we wrap up today's chat. Far from being junk, non protein coding DNA in animal and plant genomes may actually be part of the genetic workshop, a storage area with special DNA tools that assist in the development and differentiation of organisms and species.
[00:26:35] Speaker A: I think that's very fair, but it's not just that. It's so much more. I mean, even just very basic things like regulating the expression of protein coding genes and determining how much of a protein you're going to produce in a cell, when you're going to produce it, when you're going to stop producing it. So many different things are controlled by the non protein coding DNA. I would almost go so far as to say that it may even hold the blueprint of the organism, the non protein coding DNA.
[00:27:01] Speaker B: So in a word, this junk is essential.
[00:27:04] Speaker A: It's extremely important. And I'm thankful for biologists like John Maddok. Again, he's an evolutionary scientist, but there's no secret that intelligent design has been predicting function for junk DNA. So I think that if biologists had been listening to what intelligent design was saying, then other biologists like John Maddok would have gained a hearing much, much sooner, and we would have actually had this paradigm shift a long time ago.
[00:27:27] Speaker B: Science move slowly, right? What can we say? Well, Casey, thanks for joining us to share this important update about the myth of junk DNA. Where can listeners go if they want to dive deeper into this topic so.
[00:27:38] Speaker A: They can go to evolutionnews.org, where we published a few articles recently about this paper and bioassays. If you want to learn more about my own work, you can go to caseyluskin.com. But another fantastic resource on junk DNA is the book the myth of Junk DNA by Jonathan Wells. I highly recommend it. It was very prescient in predicting where this debate was going to go. And I think that an article like John Maddox and Bioassays really shows that Jonathan Wells has been vindicated that the idea of junk DNA is turning out to be a myth. So kudos to you, Dr. Wells, for getting it right.
[00:28:10] Speaker B: Absolutely. You called it. Well, that's it for now, listeners. Thanks again. Listen to more
[email protected] and for now, I'm andrew Mc pyramid with casey Luskin. Thanks for listening.
[00:28:26] Speaker A: Visit
[email protected] and intelligentdesign.org. This program is copyright Discovery institute and recorded by its center for Science and Culture.
