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Some non-protein coding DNA produces RNA which serves a purpose. We also know that there are large areas of non-coding DNA which are very important for transcri

• ilija139 2y ago
  Exactly! You make all the points. Nothing more left to say.
• bpodgursky 2y ago
  > But it remains true that there are large amounts of non-coding junk DNA which is under no selection pressure For people who may not understand how we know this -- there are "conserved" sections of DNA which don't change much over time. Very similar in mice and humans for example, because it performs important regulatory work, and if it doesn't, the animal dies. There are other large sections where it can disappear and nothing of consequence seems to happen. And we know that, because some people have micro-deletions or other variants in the region and they are completely benign. We will eventually identify a better classification than "intron" and "exon" to sort through the "junk" from "critical junk" but we are really only starting to untangle the situation.
  • causal 2y ago
    > There are other large sections where it can disappear and nothing of consequence seems to happen. So then we don't know for sure? I thought surely we must have some more rigorous means of identifying junk for OP's comment to be true, but trial and error removal seems really weak.
  • imoldfella 2y ago
    It's benign in the tested environment. You can't really test every possible environment (diet, climate, etc), so it seems roughly comparable to the halting problem; Does there exist a micro-deletion that in some environment causes this life to halt? It's unsolvable at DNA scale.
    • causal 2y ago
      Yeah I feel pretty incredulous about this too. Surely you would want to see a few hundred generations reproducing with the change before you could begin to say with any confidence that it might not have an effect.
    • bpodgursky 2y ago
      "Benign" in a clinical genetics context means "the variant is not linked to observed phenotype in patients". Patient lives their life without disability, reproduces without issue. Not really productive to imagine scenarios to unlock some hidden use. Sometimes junk is junk. Evolution is not hyper-efficient in the short term, stuff happens.
  • ackfoobar 2y ago
    >> non-coding junk DNA which is under no selection pressure > "conserved" sections of DNA which don't change much over time I'm not a biologist. I imagine DNA that does nothing and is under no selection pressure should have a bunch of random mutation accumulated - the opposite of what you described.
    • bpodgursky 2y ago
      The two quoted statements aren't talking about the same thing.
• exe34 2y ago
  there's even the endogenous retroviruses that make up 5-8% of our DNA - including bits that just repeat over and over without every doing anything.
  • causal 2y ago
    Viral origin says nothing of how important its function is.
    • exe34 2y ago
      https://sandwalk.blogspot.com/2018/03/whats-in-your-genome-pie-chart.html https://sandwalk.blogspot.com/2018/03/whats-in-your-genome-p... We don't need 1M copies of Alu: https://en.wikipedia.org/wiki/Alu_element https://en.wikipedia.org/wiki/Alu_element A lot of the sequences are defective copies. These are often how new genes arise, but they are not useful to the individual.
      • neom 2y ago
        I don't know what I'm talking about, but I kinda thought there was some ideas maybe it's used in anti-virus or something? https://pmc.ncbi.nlm.nih.gov/articles/PMC9963469/ https://pmc.ncbi.nlm.nih.gov/articles/PMC9963469/
• moralestapia 2y ago
  >But it remains true that there are large amounts of non-coding junk DNA which is under no selection pressure. Nope, you cannot ever assert that. Did you understand the article? What was once thought to be junk turned out not to be. Extrapolate from that.
  • schmidtleonard 2y ago
    Selection pressure can be measured. If a big chunk of DNA is missing from a third of a population with no apparent ill effects, the onus is on you to show that it was somehow important. Of course there is plenty of non-coding DNA which is under selection pressure and therefore does something important, but everyone has known this for decades. The single most common sin in all of science is to misrepresent the null hypothesis because it makes getting positive results easy. In article form, this translates to when you see a title "Everyone thought X but actually Y," 99% of the time nobody thought X and Y is otherwise unremarkable. They wanted to remark on Y, though, so they cooked up "Everyone Thought X" to facilitate the presentation.
    • moralestapia 2y ago
      >the onus is on you to show that it was somehow important What? Like ... not at all? Onus does not get assigned "by default" due the nature of things, lol. The onus falls on whoever comes up to propose an hypothesis. In this case that hypothesis is "all other DNA/RNA is junk", well, then "prove that thing is true", which is unfeasible and hence why one could not assert such thing.
      • searine 2y ago
        >In this case that hypothesis is "all other DNA/RNA is junk", Strawman. It is not as black and white as you think it is. Some non-coding DNA/RNA is functional. Some is not. Selection/conservation is often used as quick way to tell whether something is functional or not. Nobody actually in the field of genetics would say "all other DNA/RNA is junk". You'd get laughed out of the room, kind of in the same way if you said "all non-coding DNA is functional because 'epigenetics' ".
• PaulHoule 2y ago
  My understanding of it is that in eukaryotes the genome is folded up like the pages of a book and that one function of non-coding DNA is control of the opening up of these "pages" which in turn plays a major role. You are not just looking at RNAs being expressed but also sections of DNA that those RNAs bind to, pieces that bind to each other to keep pages shut, probably things like the hinges and springs in a pop-up book. Genetic engineering always had the problem that you just don't want to express a gene that makes a protein but you want to express that gene a lot. For instance the first version of Golden Rice produced detectable but not nutritionally significant amounts of Vitamin A. It took them quite a few more years to get Golden Rice 2 which produces enough to matter. It's been known a long time that a lot of genes associated with diseases are non-coding, but looking at what my RSS reader shows me it seems that very rapid progress is being made right now on understanding these hidden regulatory networks.
  • joshuahedlund 2y ago
    Could you share some of the feeds in your RSS or where to learn more about this very rapid progress?
    • PaulHoule 2y ago
      My RSS reader finds a lot of papers here https://phys.org/biology-news/ https://phys.org/biology-news/ for example https://phys.org/news/2024-12-microrna-evolutionary-mystery-butterfly-moth.html https://phys.org/news/2024-12-microrna-evolutionary-mystery-...
      • prox 2y ago
        Happy to hear about RSS alive and kicking! What is a good reader these days?
  • hinkley 2y ago
    The extremaphiles that survive radiation are both tetraploid and keep their dna packed tight when not coding proteins or whatnot. Packed DNA can spontaneously re-fuse broken chemical bonds to the original site rather than tearing or picking up new fragments.
• graypegg 2y ago
  This is just pure assumption from my part, I know nothing about this. But extrapolating from your point: > It may be important for spacing out sections of DNA Is it possible that there IS selection pressure for unread DNA? I could imagine that cells with comparatively huge chromosomes last a bit longer, since you'd hope that some percentage of those pairs are just cannon fodder for the usual mutagenic sources. (energy, viruses, being a European king, etc) Like you can either make the bullseye on the target smaller, or spread out the points across the whole face of the target. Again, no idea what I'm talking about, but maybe the researchers here are seeing a breakdown in the "control characters" around these parts? Maybe there's a sort of null start/null terminate at both ends in the "real" DNA, and when it breaks down, these unintended sacrificial spacers get parsed.
  • thaumasiotes 2y ago
    > you'd hope that some percentage of those pairs are just cannon fodder for the usual mutagenic sources. (energy, viruses, being a European king, etc) Inbreeding is a problem of not enough mutation, not a problem of too much.
    • robwwilliams 2y ago
      Not enough variation.
    • graypegg 2y ago
      Honestly, I just wanted to say something funny haha. But yes I see how those are different though, thanks!
• deleted 2y ago
  [deleted]
• altruios 2y ago
  That seems like a fallacy to claim to know that there is in fact junk dna. To know that: you need to iterate over every possible function for a section of dna could have and test against that. How is it known that there truly is junk dna?
  • searine 2y ago
    Most of the genome is non protein coding. Some is functional, most simply is not functional in any way. It is just empty space. Rates of mutation in these regions, and lack of conservation are hallmark clues which show that there isn't function in these regions. That doesn't mean totally useless, these non-functional regions provide the raw material for the creation of genes and functional elements. Its just that, right now, those regions aren't doing anything. No biologist calls it "junk DNA". That is just a simplified layman's term for media press releases.
  • _qua 2y ago
    I get the skepticism. There have been a lot of surprising revelations in biology and I don't think anyone would argue we have every angle nailed down. However, the idea that some DNA is genuinely “junk” is based on more than a hunch. It’s from looking at patterns across species. If a sequence really mattered, then changing it should cause a problem. That would put pressure on the sequence to stay the same, generation after generation. Yet we see big stretches of DNA mutating freely, at rates that exactly match what would be expected from accumulation of random copying errors. That suggests these sequences aren’t under selection for any important function. This isn’t just “we don’t know what it does, so it must be junk.” It’s more like, “We can’t find any sign that it matters, and everything we know about evolution says if it mattered, we’d see fewer random changes there.” Down the road we might uncover small roles for some of these regions, but at this point, calling them junk is just an honest read of the evidence we have.
    • patrickhogan1 2y ago
      The absence of clear selection pressure on certain RNA pairs doesn’t prove they lack function; many biological roles are subtle, context-dependent, or involve redundancy, making them difficult to detect with current methods. Freely mutating sequences could still influence genome architecture, gene regulation, or adaptation in ways not yet understood, as seen with elements like noncoding RNAs and transposable elements previously dismissed as “junk.” Additionally, these sequences may serve functions over long evolutionary or environmental time horizons, becoming critical under future conditions we cannot yet predict, underscoring the importance of not prematurely dismissing them.
• pinkmuffinere 2y ago
  I understand that you say “junk” dna in the context of the individual, but I’m curious if there could still be some selection pressure on this “junk”? For instance, I can imagine that “junk” which has more variety in it may generally result in more useful mutations, and this could put pressure on our “junk” to have high entropy, almost providing a source of randomness. I know very little about the field though — am i totally off base?
• w10-1 2y ago
  I don't think you have to argue for junk DNA to state that the article in question fails utterly to explain the findings except by way of not being the straw-man "junk". Yes, we find the significance of DNA by knocking it out and seeing what happens. Yes, crispr/cas-9 or /cas13 can be used for knocking out. Yes, it's interesting to compare across models to find relatively conserved behaviors. That's all known and done. What could be interesting about these results is exactly how they achieved scale and variety at reasonable time and cost. Labs typically build expertise in a particular model organism, and it's very hard to get things right in many cell types, no less to run essentially thousands of experiments. Developers have a vague sense of 3nm semiconductor process and the potential for on-chip memory (both yield/quality and potential), but we (I) have no sense how good the process is underlying findings like this.
  • _qua 2y ago
    I don't have an qualms with the research. I think it was shared on HN because of the never-ending articles about "it's not junk after all" which is what I was reacting to. The linked press release uses this term, but the original study does not. I agree with your points.
• codr7 2y ago
  Are we completely sure about that? In my mind it could just be that we don't understand it well enough yet. I mean, junk to us maybe. Nature tends to produce pretty optimal designs from my experience.
  • jostmey 2y ago
    Nature tends to select things that are just good enough. If nature was optimal, we wouldn't have appendices that need removal, a backward retina, or spines optimized for horizontal placement. Junk DNA can be vestigial. It had a purpose. It no longer does. If there's no selective pressure to get ride of it, it will remain, adrift. The belief that because it exists it must have a purpose could be a human bias
    • nickpsecurity 2y ago
      “ we wouldn't have appendices that need removal” That they weren’t needed was another myth. They turned out to be helpful at stopping one of the main killers of early humanity: diarrhea. Still kills lots of people in the third world. Appendix helps prevent stomach problems, too. Quite a few people whose were removed figured that out on their own.
    • haneul 2y ago
      Any reading on the topic you could point me to? Whenever I head about vestigial DNA, I’m reminded of the preserved wetlands which forced the roads to arc the long way around it. And in so doing, structurally affected traffic despite no cars ever going inside its bounds. I guess what I’m wondering how we can be sure that structure is function but non-coding structure has no function and exerts no selective pressure - isn’t the Golgi apparatus analogously “non-coding”?
    • inglor_cz 2y ago
      Could, but it also could be an indicator of "we don't really understand biology yet". Biology is more complicated than maths/physics. Multiple extinction crises that shaped the world are still written into our genome and there can be very subtle adaptations at play. People with certain patterns in their non-coding DNA are at much higher risk of ALS, a terrible disease [0] - it certainly looks that at least this part of DNA plays some role in our organisms. [0] https://pubmed.ncbi.nlm.nih.gov/38802183/ https://pubmed.ncbi.nlm.nih.gov/38802183/