Episode Transcript
[00:00:04] Speaker A: ID the Future, a podcast about evolution and intelligent design.
[00:00:10] Speaker B: A Nobel Prize for junk DNA function. What happened to the myth of junk DNA?
Well, my guest today is Dr. Casey Luskin. He's going to tell us more about these issues and he is associate director of Discovery Institute's center for Science and Culture.
Casey 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 and earned a law degree from the University of San Diego, where he focused on First Amendment law, education law and environmental law. His BS And Ms. Degrees in Earth sciences are from the University of California, San Diego, where he studied evolution extensively at the graduate and undergraduate levels. Casey, welcome back.
[00:00:58] Speaker A: Great to be back with you, Andrew.
[00:01:01] Speaker B: Well, so what was the 2024 Nobel Prize in Physiology or Medicine given for? Let's start there.
[00:01:08] Speaker A: Yeah, it was given for a really fascinating discovery about what are called micrornas, very short strands of RNA that play a major and important role in gene regulation. And so the official Nobel Prize press release gave this to Victor Ambrose and Gary Ruvkin, who are both American biologists, for, quote, the discovery of microrna and its role in post transcriptional gene regulation.
And so this is a very, very interesting mechanism that is used to control the way that genes are expressed and proteins are produced in the cell.
[00:01:44] Speaker B: Okay, so micrornas, is this something we didn't know about before?
Is it a completely new discovery?
[00:01:51] Speaker A: Well, we've known about these for a long time. They made the discovery back in, I think, the early 1990s that these very short strands of RNA exist and are very common. At least they found them in C. Elegans. But what they found is that they're involved in regulating the expression of genes. And basically what these micrornas can do is, is they can bind to the MRNA transcripts that would encode, you know, the protein and be translated into the protein at the ribosome. But when these micrornas can bind to these MRNA transcripts, they can basically kind of bind them up and not allow translation to occur.
And so it's a mechanism that cells use to regulate gene expression.
And, you know, at the time when, when this was first discovered, it was thought this was just sort of a peculiar thing that was only going on in C. Elegans. But now we know that microrna gene regulation is extremely common throughout numerous types of organisms. And it's actually sort of a normal way that cells can regulate gene expression.
[00:02:56] Speaker B: Okay, now if this Podcast were just about these two fortunate scientists who have received a Nobel Prize, they then it would be pretty short. But the main idea here is that the, what they've discovered, this function they've discovered was previously something that was dismissed as part of junk DNA. How do we know that these micrornas were previously considered junk DNA by scientists?
[00:03:22] Speaker A: Yeah, I mean there have been many, many examples of people noting that micro RNAs represent a type of basically they're encoded by the DNA of course, but they're coming from a type of DNA that was once thought to be junk DNA. So micrornas do not come from the protein coding sections of the DNA, they come from the non coding DNA.
And you know, it's been known for a long time that non coding DNA can have function, but certainly the type of non coding DNA that was producing these micrornas was thought to just be another type of genetic junk. And by and large the evolutionary community has viewed the non coding DNA in our genomes as, or in other animal genomes as for the most part being junk DNA. Okay. And so when they found these short RNAs, you know, initially these would have just been dismissed as oh, it's interesting, but it's just sort of random transcription, transcriptional noise, it's not actually doing anything. There was an article in Current Science that came out about this year's Nobel Prize that kind of told the story. And it said by the early 1990s some non coding genes, including some weird name gene in Drosophila, et cetera, in mammals, were known to be essential for organisms lives. They remained exceptions without making any dent in the widespread textbook level. Strong belief in selfish or junk DNA. In this backdrop, Ambrose and Rufkin's groups discovered that the LIN4 gene of C. Elegans produces a small non coding RNA that inhibits the activity of the LIN14 gene through RNA interference, decisively catalyzed a widespread interest in non coding RNAs that had thereto had been ostracized, had remained rather ostracized. And they go on to say that RNA interference also explained the mystery of the earlier known phenomena like post transcriptional gene silencing and quelling. So what they're saying is that previously these short RNAs, these MICRORNAs, they'd been ostracized, is that important?
But when they made this discovery, they realized this is actually part of the way that at least this one organism, C. Elegans, which is a worm, that it regulates gene expression. Okay, so the question then became, you know, how common is this.
And it's now known of course, that it's extremely common. But I think one of my favorite examples of a scientist talking about how the these micrornas were dismissed as junk comes from an Indian scientist named Subhash Lakota. And forgive me, I may very likely have mispronounced that name. But he's a distinguished professor of cytogenetics and zoology in India. He wrote an article titled Celebrating Tiny RNA that unraveled humongous complexity of biological regulation.
And in this he discusses what he calls selfish and junk DNA. And he asked the question why does the 1993 discovery of novel post transcriptional regulation of LIN14 gene by small non coding RNA in C. Elegans by Ambrose Ruvkin Labs did not make an immediate global impact? He wants to know why was this discovery not immediately accepted globally? And he points to skepticism arising from the belief in widespread junk DNA. And there are two answers he gives to the question of why their discovery that these micrornas regulate gene expression was not immediately accepted. He says, number one, the textbook level strong belief that anything but coding for protein is selfish or junk DNA. Okay, so anything that's not coding for protein is basically junk. That was what he says is a textbook level strong belief. This is his words. And, and he goes on to say the LIN4 and LIN14 genes were seen only in species related to C. Elegans, but not in other organisms. So he goes on to decry what he calls this reductionist belief in junk DNA and that he never believed that some part of the genome is useless or selfish or junk, unquote. So this is very, very interesting to see that this, basically what this means, Andrew, is that last year the Nobel Prize in Physiology and Medicine was awarded for the discovery of function for a type of junk DNA. And of course, you know, this gets into idea, evolution, conversations, but literally last year's Nobel Prize was awarded for the discovery of function for a type of junk DNA.
[00:07:49] Speaker B: And the obvious idea that you're suggesting is, you know, that the, that prize would not have been awarded if scientists had just dismissed that non coding, those non coding regions and just moved on. And so that's really the big story we're unpacking here and that you have highlighted now in your reporting of the myth of junk DNA and the paradigm shift that has been occurring.
You say that a lot of scientists are now willing to move past this, this myth of junk DNA having no function, just being evolutionary detritus. Is that true? Are we, are we now reaching that paradigm shift? Where we can move past that.
[00:08:32] Speaker A: Yeah, there has been legitimately, I think, a paradigm shift over the last 10 or 15 years over this question of junk DNA. In fact, in 2023 there was an article in the journal Bioassays that said we'd have a Kunian revolution.
And they were referring to the now understood belief that junk DNA is not junk, it actually has important functions. Kuhnian Revolution, of course refers to the famous historian of science, Thomas Kuhn, who said that we see paradigm shifts in biology when there are scientific revolutions. And so by saying by calling this a Kuhning revolution, that basically most genes and complex organisms are expressing these regulatory RNAs that are basically non coding DNA, that's encoding RNAs that perform all kinds of, of important functions, they are explicitly saying there's been a cunian paradigm shift against the idea of junk DNA. 2021, there was an article in the journal Genome Biology and Evolution which said the days of junk DNA are over. But where did this really start? It started in 2012 when the Encode project published a series of papers, including a major paper in the journal Nature, which which found that over 80% of the human genome shows evidence of biochemical functionality.
And the ENCODE project, of course, was a consortium of hundreds of biologists around the world who are trying to understand these non coding DNA elements and what they're actually doing.
And when that paper was published in Nature, you saw a lot of people saying, look, this really shows that we have to stop taking this idea of junk DNA seriously. Um, the journal Science wrote an article that said that the ENCODE project writes the eulogy for junk DNA. And they went on to say that it sounded the quote, the death knell for the idea that our DNA is mostly littered with useless bases. Francis Collins, head of the Human Genome project, in his 2006 book the Language of God, he said that about 45% of the human genome is Flotsman Jetsam. Okay, Flotsman Jetsam, of course, is trash floating in the ocean. But then in 2015, after this, this ENCODE paper came out, he said the following. This is really a very striking quote. He said, I would say in terms of junk DNA, we don't use that term anymore because I think it was pretty much a case of hubris to imagine that we could dispense with any part of the genome as if we knew enough to say it wasn't functional. He then goes on to say, so right there, what is he saying? He's saying that he doesn't use the term junk DNA anymore. So this was in 2015, about two and a half years after this major ENCODE papers came out that showed that the vast majority of our genome is biochemically functional.
Now of course, Collins then went on to say that there are some things like repeats or alus that he thinks is not doing anything. So he's still sort of into the junk DNA idea, but he says he doesn't use that term anymore. So we really have seen a paradigm shift away from the idea of junk DNA. And I think this was probably reflected in the Nobel Prize committee's recognition of, you know, the importance of discovering function for non coding or junk DNA. And this, this Nobel Prize I think is, is in some ways it's a recognition that the idea of junk DNA is really not an important thing in the scientific community today and that the scientific revolution against junk DNA has taken place.
[00:11:53] Speaker B: Now. Casey, you know this. The scientists in the intelligent design research community have been predicting function in non coding regions of DNA for decades. Is that not correct?
[00:12:06] Speaker A: That is absolutely true. In fact, the early example that I'm aware of was in 1994 when Pro ID engineer Forrest Mims, he wrote a letter to the journal Science warning them to not assume that quote unquote junction A was quote unquote useless. And so this would have been in the mid-90s, in a time when certainly at that point the vast majority of evolutionary scientists and biologists believed that the vast majority of our genome was junk. Another good example was in 1998, William Dembsky, well known ID theorist, wrote an article in the journal First Things where he basically said that design encourages scientists to look for function for junk DNA, whereas evolution discourages it. And then there are other examples. Rick Sternberg, an ID friendly biologist, wrote an article in Annals of the New York Academy of Sciences in 2002 where he critiqued the idea of junk DNA. And again, at this point, the idea that junk DNA was largely functional was still very radical in the scientific community.
And other examples could be given. Jonathan Wells wrote a paper in an ID journal in 2004 talking about how ID again encourages you to look for function for junk DNA. And by the way, why does ID encourage you to look for function for junk DNA? Why does ID predict function for junk DNA? Well, it's very simple. We know from experience that when intelligent agents make things, they tend to make things for a purpose or for a reason or a function. Okay? So if the genome really was designed, we would expect that as much as possible it will be functionally important.
And this stands in direct contrast to the standard evolutionary view, which has seen the vast majority of the genome as being basically just non functional junk. I mean, this is true even today. In 2023, a book from Larry Moran at the University of Toronto came out, published by University of Toronto Press, and the subtitle was that 90% of your genome is junk. Okay? Richard Dawkins, in his very well known book, the Greatest show on Earth about evolution, says that some 95% of our genome is genetic junk. I've even seen examples of evolutionary scientists saying that 98, 99% of our genome is genetic junk. So it depends on who you ask, but certainly for years they were predicting that the vast majority of our genome is junk. But I really think this idea has gone out the window. One last example, in 2021, there was an article in the journal Nature which said it talked about, over time, how, you know, our knowledge of the number of genes and our knowledge of the number of functional non coding genetic elements has grown. And basically, if you look at this chart in this paper, it said that around the year early 2000s, our knowledge of the number of protein coding genes in the human genome basically peaked out, okay, around 19 or 20,000.
However, if you look at this curve that they have, it shows that in the early 2000s, we began to have a, quote, explosion of interest in non coding regions of the genome. They call these other genomic elements previously called junk DNA. Those are their words, okay? And if you look at this curve of our knowledge of function for non coding, quote, unquote junk DNA elements, this curve goes up at almost an exponential rate. And it just takes off around the late 2000s, early 2010s. And in the 2010s, our knowledge of the number of functional non coding genetic elements has just exploded.
And so again, and now it says we have over 103,000 genetic elements, which in their own words, they say, previously called junk DNA that we now know to be functional. Okay? And this evidence of function for junk DNA, according to this chart, shows no sign of slowing down. In fact, the discovery of function for non coding, or what they call junk DNA, is just going up at almost like an exponential rate. So the bottom line is that this junk DNA evolutionary paradigm, I think has been very much rejected by many, many prominent folks in the mainstream scientific community today, to the point that today, you know, you can no longer just assume the default that if you don't know what it's doing, that therefore it's junk.
[00:16:27] Speaker B: Yeah, and this is why the myth of junk DNA story is Such a great one from our perspective. I mean, materialists, you know, will constantly come back saying, well, all right, you know, we'll amend our model and new evidence has come to light and we'll just adjust. But really, you know, now we can look back at this junk DNA, you know, paradigm and see how this Darwinian approach to it slowed down science. I think that is the big story here.
You know, again, you're just going to defend it, but you're showing that this is actually retarding or slowing down the process of science.
[00:17:07] Speaker A: Yeah, exactly. I didn't mean to cut you off. Yeah, no, exactly. And one of the most interesting things, as I was researching the story of this last year's Nobel Prize awarding function for micrornas, which are a form of, used to be thought of as junk DNA, was I found the Nobel committee press release and here's what they said. They said the published results were initially met with almost deafening silence. Deafening silence from the scientific community. Although the results were interesting, the unusual mechanism of gene regulation was considered a peculiarity of C. Elegans, likely irrelevant to humans and other more complex animals. Okay, so, so what happened? When they first discovered that these short micrornas are involved in regulating genes, it was basically dismissed by the mainstream scientific community. And they thought this was an anomaly. It was not actually a real, a real thing. It was just kind of a random thing that was not a normal biological process. We now know that microrna gene regulation is, is, is very widespread, very normal. But it was because of the junk DNA mindset that, that they dismissed it and it was met with such initial skepticism. Another example comes from that Indian scientist I mentioned, Subhash Lakotia, who asked the question why the 1993 discovery of novel post transcriptional regulation of LIN14 gene by small non coding RNA by Ambrose and Ruvkin Lab did not make an immediate global impact. And he answers that question in his article. He says it's because of the textbook level strong belief that anything not coding for protein is selfish or junk DNA. Those are his words. Okay, or we've got this article in, in the Current Science which says that it was against the backdrop of basically belief in this, quote unquote, textbook level strong belief in selfish or junk DNA that they made this discovery. And that article in Current Science even notes that belief in function for these non coding micro RNAs had been ostracized. Okay, So I think what we can see is there is good evidence from even the mainstream scientific community's discourse that not only is this microrna function, function for junk DNA. But that the scientific community accepting the evidence for function for this type of junk DNA was hindered by this belief in junk DNA. And so basically the evolutionary junk DNA paradigm hindered acceptance of a discovery that eventually won the Nobel Prize. Isn't that interesting, Andrew, that actually the evolutionary junk DNA viewpoint is now hindering acceptance of Nobel Prize winning research? I find that to be pretty striking.
[00:19:54] Speaker B: Yeah, yeah. And we've had people trying to call intelligent design the sign stopper the sign slower, but really we have a prime example here of how the Darwinian framework can, can slow down signs and retard progress in science.
[00:20:10] Speaker A: Absolutely. And you know, we're not the only ones who are making the case that the junk DNA mindset has slowed science. Listen to this quote that was published in the journal Science.
It says the term junk DNA for many years repelled mainstream researchers from studying non coding DNA.
There you have it right there. Okay, that's in the journal Science acknowledging that the term junk DNA, which was born and bred from the evolutionary paradigm, quote, repelled mainstream researchers from studying non coding DNA. And it went on to say who except a small number of genomic claw shards would like to dig through genomic garbage? However, in science as in normal life, there are some clash arts who had the risk of being ridiculed, explore unpopular territories. Now more and more biologists regard repetitive elements as a genomic treasure. So basically this is the journal Science acknowledging that the junk DNA mindset basically hindered our discovery of function for non coding DNA and also just how the genome operates. And of course this idea of junk DNA came from an evolutionary paradigm. So it does show, as you said, that the evolutionary perspective sometimes itself can actually hinder the progress of science.
[00:21:21] Speaker B: Gives new meaning to the.
The old saying, you know, one person's junk is another person's treasure.
[00:21:28] Speaker A: There you go. And it also is a cautionary tale to not assume that just because you don't know what some aspect of the genome or something in biology is doing, to not assume that it's just junk, that there's no reason for it. I, I think the more and more we discover biology, the more we're realizing that that assumption of junk or non functionality does not hold up.
[00:21:48] Speaker B: Yeah, yeah. Well, Casey, thanks for stopping by to unpack this. It's another exciting development and those listening and watching can follow this story and the whole paradigm shift with junk DNA and that myth on evolutionnews.org so check there for all the details and, and to follow this story. Well, Casey, thanks again for ID the Future. I'm Andrew McDermott. Thanks for joining us.
[00:22:12] Speaker A: ID the Future, a podcast about evolution and intelligent design.
